+
+
+
+◆ get_path_base_name()
+
+
+
+
+
Returns the base path name for this path (i.e. the path's name without any subrange).
+
diff --git a/path_8cpp.html b/path_8cpp.html
index 61b788ea65..c5f65cbc5d 100644
--- a/path_8cpp.html
+++ b/path_8cpp.html
@@ -224,6 +224,11 @@
|
Alignment | vg::alignment_from_path (const HandleGraph &graph, const Path &path) |
|
+bool | vg::for_each_subpath_of (const PathPositionHandleGraph &graph, const string &path_name, const std::function< bool(const path_handle_t &path)> &iteratee) |
+ |
+std::string | vg::get_path_base_name (const PathPositionHandleGraph &graph, const path_handle_t &path) |
+ | Returns the base path name for this path (i.e. the path's name without any subrange). More...
|
+ |
void | vg::from_proto_edit (const Edit &proto_edit, edit_t &edit) |
|
void | vg::to_proto_edit (const edit_t &edit, Edit &proto_edit) |
diff --git a/path_8hpp.html b/path_8hpp.html
index 8f61904d8e..572810b359 100644
--- a/path_8hpp.html
+++ b/path_8hpp.html
@@ -245,6 +245,11 @@
|
Alignment | vg::alignment_from_path (const HandleGraph &graph, const Path &path) |
|
+bool | vg::for_each_subpath_of (const PathPositionHandleGraph &graph, const string &path_name, const std::function< bool(const path_handle_t &path)> &iteratee) |
+ |
+std::string | vg::get_path_base_name (const PathPositionHandleGraph &graph, const path_handle_t &path) |
+ | Returns the base path name for this path (i.e. the path's name without any subrange). More...
|
+ |
void | vg::from_proto_edit (const Edit &proto_edit, edit_t &edit) |
|
void | vg::to_proto_edit (const edit_t &edit, Edit &proto_edit) |
diff --git a/search/all_10.js b/search/all_10.js
index 952b35e6d3..2e0424fa26 100644
--- a/search/all_10.js
+++ b/search/all_10.js
@@ -1,496 +1,496 @@
var searchData=
[
- ['p_5fvalue_4317',['p_value',['../structvg_1_1SeqComplexity.html#a20dfb4fbec20a18a5decaccc046c10e8',1,'vg::SeqComplexity']]],
- ['p_5fvalue_5fmemo_4318',['p_value_memo',['../classvg_1_1MultipathMapper.html#a076b5202ca84c7836e93d3e8b71775bf',1,'vg::MultipathMapper']]],
- ['pack_4319',['pack',['../structhandlegraph_1_1number__bool__packing.html#af5082dc39a2f308585402bd19de0caa8',1,'handlegraph::number_bool_packing']]],
- ['pack_5fmain_2ecpp_4320',['pack_main.cpp',['../pack__main_8cpp.html',1,'']]],
- ['pack_5fnames_4321',['pack_names',['../classvg_1_1Viz.html#abb3fd61d416351930f2e7399e6f6001b',1,'vg::Viz']]],
- ['pack_5fquery_5fforward_4322',['pack_query_forward',['../classvg_1_1DozeuInterface.html#acd17348d5d2dd0ec4c10af98748fe67a',1,'vg::DozeuInterface::pack_query_forward()'],['../classvg_1_1XdropAligner.html#a9179d91b00ed33fbc3e9e6a4bd6b9321',1,'vg::XdropAligner::pack_query_forward()'],['../classvg_1_1QualAdjXdropAligner.html#a0e1140ad3ee66b2583869ccd2267841b',1,'vg::QualAdjXdropAligner::pack_query_forward()']]],
- ['pack_5fquery_5freverse_4323',['pack_query_reverse',['../classvg_1_1DozeuInterface.html#aa15876efde0e6d8f963d37ae245c8ead',1,'vg::DozeuInterface::pack_query_reverse()'],['../classvg_1_1XdropAligner.html#a3c3832ae9935773f0dd0b97ed031c70e',1,'vg::XdropAligner::pack_query_reverse()'],['../classvg_1_1QualAdjXdropAligner.html#a0d6b25927dccfe18f03eab6457486ac7',1,'vg::QualAdjXdropAligner::pack_query_reverse()']]],
- ['packed_5fdepth_5fof_5fbin_4324',['packed_depth_of_bin',['../namespacevg_1_1algorithms.html#a62ebbcbfe1250940eb8ebf0a2dcbc19a',1,'vg::algorithms']]],
- ['packed_5fdepths_4325',['packed_depths',['../namespacevg_1_1algorithms.html#abd431ebd9786d796f708a7046e643e2e',1,'vg::algorithms']]],
- ['packedgraph_4326',['PackedGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a3355e9401e49629ee5dcd20b107f3f67',1,'vg::IndexingParameters']]],
- ['packedtraversalsupportfinder_4327',['PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html',1,'vg::PackedTraversalSupportFinder'],['../classvg_1_1PackedTraversalSupportFinder.html#a5bb7b3f0b3fd9c72597403ce75f8791c',1,'vg::PackedTraversalSupportFinder::PackedTraversalSupportFinder()']]],
- ['packer_4328',['Packer',['../classvg_1_1Packer.html',1,'vg::Packer'],['../classvg_1_1PackedTraversalSupportFinder.html#ac48b605c781739b3920b8c36fdb6fcf8',1,'vg::PackedTraversalSupportFinder::packer()'],['../classvg_1_1Packer.html#a965acab0b6c7d973a67e449785955739',1,'vg::Packer::Packer(const HandleGraph *graph=nullptr)'],['../classvg_1_1Packer.html#ad52836b610249ada7cf0ad13c329b52c',1,'vg::Packer::Packer(const HandleGraph *graph, bool record_bases, bool record_edges, bool record_edits, bool record_qualities, size_t bin_size=0, size_t coverage_bins=1, size_t data_width=8)']]],
- ['packer_2ecpp_4329',['packer.cpp',['../packer_8cpp.html',1,'']]],
- ['packer_2ehpp_4330',['packer.hpp',['../packer_8hpp.html',1,'']]],
- ['packers_4331',['Packers',['../classvg_1_1Packers.html',1,'vg']]],
- ['packs_4332',['packs',['../classvg_1_1Viz.html#a350ea478ececb5f19170b16cf1539726',1,'vg::Viz']]],
- ['pad_5fband_2ecpp_4333',['pad_band.cpp',['../pad__band_8cpp.html',1,'']]],
- ['pad_5fband_2ehpp_4334',['pad_band.hpp',['../pad__band_8hpp.html',1,'']]],
- ['pad_5fband_5fconstant_4335',['pad_band_constant',['../namespacevg_1_1algorithms.html#ab48342aedc7d81e2334c52bb320223c2',1,'vg::algorithms::pad_band_constant()'],['../namespacevg_1_1algorithms.html#aaab5b2261edb66897af9d1158e7758d8',1,'vg::algorithms::pad_band_constant(size_t band_padding)']]],
- ['pad_5fband_5fmin_5frandom_5fwalk_4336',['pad_band_min_random_walk',['../namespacevg_1_1algorithms.html#a3363cc23e6c71e1bb5faac975af7920d',1,'vg::algorithms::pad_band_min_random_walk()'],['../namespacevg_1_1algorithms.html#a25a37b51facd101b8a29b1a57661f74f',1,'vg::algorithms::pad_band_min_random_walk(double band_padding_multiplier, size_t band_padding_memo_size, size_t max_padding)']]],
- ['pad_5fband_5frandom_5fwalk_4337',['pad_band_random_walk',['../namespacevg_1_1algorithms.html#a6a606c26b5751d935c71d7971a92d99b',1,'vg::algorithms::pad_band_random_walk()'],['../namespacevg_1_1algorithms.html#a1294ed71274673b7e4cc1d40e9472666',1,'vg::algorithms::pad_band_random_walk(double band_padding_multiplier, size_t band_padding_memo_size, size_t max_padding)']]],
- ['pad_5fband_5frandom_5fwalk_5finternal_4338',['pad_band_random_walk_internal',['../namespacevg_1_1algorithms.html#a9957e925ee25c57698383d4e1df21f0d',1,'vg::algorithms']]],
- ['pad_5fcluster_5fscore_5fthreshold_4339',['pad_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a70b206dc58a148a69657303ff292199f',1,'vg::MinimizerMapper']]],
- ['pad_5fsuspicious_5fanchors_5fto_5flength_4340',['pad_suspicious_anchors_to_length',['../classvg_1_1Surjector.html#a7231e0ecf35ed767417fc37184b0a806',1,'vg::Surjector']]],
- ['pad_5ftraversal_4341',['pad_traversal',['../classvg_1_1GAFOutputCaller.html#a697f4f2c00fa8317ba8143bbe99931fb',1,'vg::GAFOutputCaller']]],
- ['pad_5fzipcode_5ftree_5fscore_5fthreshold_4342',['pad_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#aafbc5c792144ae26630c312d2475b19a',1,'vg::MinimizerMapper']]],
- ['paint_4343',['paint',['../structvg_1_1Funnel_1_1PaintableSpace.html#a88c1043f7b0cae737da989f0abc44b0a',1,'vg::Funnel::PaintableSpace']]],
- ['paintablespace_4344',['PaintableSpace',['../structvg_1_1Funnel_1_1PaintableSpace.html',1,'vg::Funnel']]],
- ['pair_5fall_4345',['pair_all',['../classvg_1_1MinimizerMapper.html#a4493ab0315512da6b10a7cde3754afe2',1,'vg::MinimizerMapper']]],
- ['pair_5fcluster_5fmultiplicity_4346',['pair_cluster_multiplicity',['../classvg_1_1MultipathMapper.html#ae534f0c248a4b44bdf389ead66d105e3',1,'vg::MultipathMapper']]],
- ['pair_5fclusters_4347',['pair_clusters',['../classvg_1_1MEMClusterer.html#a4e84dd599bb8dc4341cbed2fd1de1ed0',1,'vg::MEMClusterer::pair_clusters()'],['../classvg_1_1NullClusterer.html#a1794ac271ce6d785e67b488a98ec87d6',1,'vg::NullClusterer::pair_clusters()'],['../classvg_1_1OrientedDistanceClusterer.html#a41e57b46abd69532d53855499d5042eb',1,'vg::OrientedDistanceClusterer::pair_clusters()'],['../classvg_1_1TVSClusterer.html#a1477ce3367e036c0ecc101e1518b49b9',1,'vg::TVSClusterer::pair_clusters()'],['../classvg_1_1MinDistanceClusterer.html#af561001a20cc91adc6238f74edca6480',1,'vg::MinDistanceClusterer::pair_clusters()']]],
- ['pair_5fconsistent_4348',['pair_consistent',['../classvg_1_1Mapper.html#ad3a62e0a91818c4e20508ab2a0f47fa5',1,'vg::Mapper']]],
- ['pair_5ffrom_5fedge_4349',['pair_from_edge',['../classvg_1_1NodeSide.html#ad48cc3d977ad0f6ffc5ce1034cbbae65',1,'vg::NodeSide::pair_from_edge(Edge *e)'],['../classvg_1_1NodeSide.html#a97eed27ab7b77be54b68062b780a9f36',1,'vg::NodeSide::pair_from_edge(const Edge &e)']]],
- ['pair_5ffrom_5fend_5fedge_4350',['pair_from_end_edge',['../classvg_1_1NodeSide.html#a23f18cf5f9ae9c7fc8475800d967275c',1,'vg::NodeSide']]],
- ['pair_5ffrom_5fstart_5fedge_4351',['pair_from_start_edge',['../classvg_1_1NodeSide.html#a3193e35c9e8349c427cc834335e25405',1,'vg::NodeSide']]],
- ['pair_5fhash_5fmap_4352',['pair_hash_map',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vector_3c_20vg_3a_3aalignment_20_2a_20_3e_20_3e_4353',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vector< vg::Alignment * > >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vg_3a_3aedge_20_2a_20_3e_4354',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vg::Edge * >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fmap_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_2c_20gbwt_3a_3anode_5ftype_20_3e_4355',['pair_hash_map< std::pair< gbwt::node_type, gbwt::node_type >, gbwt::node_type >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fset_4356',['pair_hash_set',['../classvg_1_1pair__hash__set.html',1,'vg']]],
- ['pair_5fhash_5fset_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_20_3e_4357',['pair_hash_set< std::pair< gbwt::node_type, gbwt::node_type > >',['../classvg_1_1pair__hash__set.html',1,'vg']]],
- ['pair_5fmapping_5flikelihoods_4358',['pair_mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a05dd8b61205954b988bb996479883989',1,'vg::MultipathMapper']]],
- ['pair_5forientation_5ffilter_4359',['pair_orientation_filter',['../classvg_1_1Filter.html#a16451e95cd6c7642df9f013d5b73c0c7',1,'vg::Filter']]],
- ['pair_5frescue_4360',['pair_rescue',['../classvg_1_1Mapper.html#a36248b0eb439694bfbd493fce0ce2b02',1,'vg::Mapper']]],
- ['pair_5frescue_5fhang_5fthreshold_4361',['pair_rescue_hang_threshold',['../classvg_1_1Mapper.html#a92e1f4de4e6ce576e09005713d1c1cd1',1,'vg::Mapper']]],
- ['pair_5frescue_5fretry_5fthreshold_4362',['pair_rescue_retry_threshold',['../classvg_1_1Mapper.html#a36ed72fe5d33907a75992011ff9ae244',1,'vg::Mapper']]],
- ['pair_5fto_5fstring_4363',['pair_to_string',['../haplotypes__main_8cpp.html#a7d4977594e9d93b802b94c95752f34a2',1,'haplotypes_main.cpp']]],
- ['paired_5fdistance_5fstdevs_4364',['paired_distance_stdevs',['../classvg_1_1MinimizerMapper.html#a94bd867270265d26c4f2abfbd730f316',1,'vg::MinimizerMapper']]],
- ['paired_5ffor_5feach_5fparallel_5fafter_5fwait_4365',['paired_for_each_parallel_after_wait',['../namespacevg_1_1io.html#af3c3dd4ad5c9b887fd3ee389e0b67ef6',1,'vg::io']]],
- ['paired_5fread_5fname_4366',['paired_read_name',['../structvg_1_1MultipathAlignment.html#a0664790bf6bd37af413697cddff370fb',1,'vg::MultipathAlignment']]],
- ['paired_5frescue_5fscore_5flimit_4367',['paired_rescue_score_limit',['../classvg_1_1MinimizerMapper.html#a923b2f2f9aa86e445add3be0d1c4abae',1,'vg::MinimizerMapper']]],
- ['pairedendmapper_4368',['PairedEndMapper',['../classvg_1_1PairedEndMapper.html',1,'vg']]],
- ['parallelkffreader_4369',['ParallelKFFReader',['../classvg_1_1ParallelKFFReader.html',1,'vg::ParallelKFFReader'],['../classvg_1_1ParallelKFFReader.html#a4b84d319b814d4b2a5f099d19d0426d5',1,'vg::ParallelKFFReader::ParallelKFFReader(const std::string &filename)'],['../classvg_1_1ParallelKFFReader.html#adcdc292236ba8b178c38666702b4e5c1',1,'vg::ParallelKFFReader::ParallelKFFReader(const ParallelKFFReader &)=delete']]],
- ['param_5ftype_4370',['param_type',['../classvg_1_1discrete__distribution.html#a923a04239b0ceb7026d193aa671100e4',1,'vg::discrete_distribution']]],
- ['parameters_4371',['Parameters',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html',1,'vg::HaplotypePartitioner::Parameters'],['../structvg_1_1Recombinator_1_1Parameters.html',1,'vg::Recombinator::Parameters'],['../structvg_1_1Recombinator_1_1Parameters.html#a3112d2a46538ce1575d53b6706f25756',1,'vg::Recombinator::Parameters::Parameters()']]],
- ['parent_4372',['parent',['../structvg_1_1WFANode.html#a78adf1a04bc5f5907cc3a46445061e62',1,'vg::WFANode::parent()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ae00d40d340f5114917a9f6ca1cec0460',1,'vg::SnarlManager::SnarlRecord::parent()'],['../structvg_1_1TreeNode.html#a4eb11d266cabbae3e6728d2918c80996',1,'vg::TreeNode::parent()'],['../structvg_1_1VectorView_1_1const__iterator.html#a41fafc961da593dbc8591c6288a33fd6',1,'vg::VectorView::const_iterator::parent()'],['../structvg_1_1Snarl.html#a054af14a2fccdda2209ef9a8f19aa032',1,'vg::Snarl::parent()'],['../classvg_1_1WFATree.html#ab6c9c25e1906e3a95bc6c853a2c5db3f',1,'vg::WFATree::parent()']]],
- ['parent_5fallele_4373',['parent_allele',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2f21b56cc895482f0f8a4829ccfa3463',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5fchain_4374',['parent_chain',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a37d7d2aa3460ba15b3a51ac4eedefd76',1,'vg::SnarlManager::SnarlRecord']]],
- ['parent_5fchain_5findex_4375',['parent_chain_index',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a7f98f1f84ba0d39301f1adc3333e6dfb',1,'vg::SnarlManager::SnarlRecord']]],
- ['parent_5fchains_4376',['parent_chains',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a3f1ca708ff05e4f649b0d9b22dc539fd',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['parent_5fdepth_4377',['parent_depth',['../structvg_1_1MIPayload.html#af3214bd006207b1d4c417c331b905290',1,'vg::MIPayload']]],
- ['parent_5fdirectory_4378',['parent_directory',['../structvg_1_1temp__file_1_1Handler.html#a1a791a5a813c3d0702594f5ad6915eaf',1,'vg::temp_file::Handler::parent_directory()'],['../structxg_1_1temp__file_1_1Handler.html#a16640b9f416a23bd671f56437bd09aa6',1,'xg::temp_file::Handler::parent_directory()']]],
- ['parent_5fgraph_4379',['parent_graph',['../classvg_1_1JoinedSpliceGraph.html#a274429d072e5be5687ac704393b903a4',1,'vg::JoinedSpliceGraph']]],
- ['parent_5fhandle_4380',['parent_handle',['../structvg_1_1MIPayload.html#a92ead268cf5b206f54e4cf0e95937dfc',1,'vg::MIPayload']]],
- ['parent_5fis_5fchain_4381',['parent_is_chain',['../structvg_1_1MIPayload.html#aa5abaa3ea722cf685fe73fe9502e00c1',1,'vg::MIPayload']]],
- ['parent_5fis_5froot_4382',['parent_is_root',['../structvg_1_1MIPayload.html#a36e03b459c31f012a17a78a1ec6f5391',1,'vg::MIPayload']]],
- ['parent_5flen_4383',['parent_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#abe519281b723c59979299b2657439f6e',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5fnet_5fhandle_4384',['parent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af940526569cd8d070de39e8446390e6f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['parent_5fof_4385',['parent_of',['../classvg_1_1SnarlManager.html#ad4c8dd034c160f2908164c1ebc2a0394',1,'vg::SnarlManager']]],
- ['parent_5fpath_5finterval_4386',['parent_path_interval',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a4aa790baef1ec47d6546e30f60851e9b',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5frecord_5foffset_4387',['parent_record_offset',['../structvg_1_1MIPayload.html#af185811088055cdd4c371f18883087b2',1,'vg::MIPayload']]],
- ['parent_5fref_5flen_4388',['parent_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ac311ca43aecb9c37302835adadce85af',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5fsnarls_4389',['parent_snarls',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a03f3e53e97f93f2d2b4daf66f99cd763',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['parent_5ftype_4390',['parent_type',['../structvg_1_1MIPayload.html#aa14d5e8cecee30a8e796832d5ead8578',1,'vg::MIPayload']]],
- ['parentgenotypeinfo_4391',['ParentGenotypeInfo',['../structvg_1_1ParentGenotypeInfo.html',1,'vg']]],
- ['pareto_5fpoint_4392',['pareto_point',['../namespacevg.html#a1aa2d026eb3edc0c692e19e5a493feef',1,'vg']]],
- ['parse_4393',['parse',['../classvg_1_1OptionInterface.html#aa658456e011e28d8e6d3073c8ccfc740',1,'vg::OptionInterface::parse()=0'],['../classvg_1_1OptionInterface.html#a5679dbc64e1f490d7caa35730de6d09b',1,'vg::OptionInterface::parse(const string &arg)=0'],['../classvg_1_1ConfigurableParser.html#a9c28ad9040822d975a38c982677065bd',1,'vg::ConfigurableParser::parse()'],['../classvg_1_1OptionValueParser.html#a4b43a211a8dca7c43a1fe3fc4fde1de5',1,'vg::OptionValueParser::parse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a27e910ec23c80fc2c829dcdb98da0ddc',1,'vg::OptionValueParser< vector< Item > >::parse()'],['../classvg_1_1BaseOption.html#a6682e454cf748d2a29623849d72f8d1d',1,'vg::BaseOption::parse()'],['../classvg_1_1BaseOption.html#ab17b0a67fe5bdb8de8ffb39f98a804e7',1,'vg::BaseOption::parse(const string &arg)'],['../classvg_1_1algorithms_1_1GFAParser.html#a575aa78bfa6a567735133c8cffa6da77',1,'vg::algorithms::GFAParser::parse()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a040fd55d950392ade69dad277adfb848',1,'vg::subcommand::BaseArgSpec::parse()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a8ddbad123ba28ff099c263d24b751889',1,'vg::subcommand::ValueArgSpec::parse()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a96a1df206d4ef889c7f3f6cf08dc1426',1,'vg::subcommand::FlagArgSpec::parse()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a6fa17a5e6d8fbc293d69063c947cb0aa',1,'vg::subcommand::BaseOptionGroup::parse()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aa4b885a991453bbc8cde726e35dd115f',1,'vg::subcommand::OptionGroup::parse()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aada2ded9febbec1c9bab141da4bfc0ce',1,'vg::subcommand::GroupedOptionGroup::parse()'],['../classvg_1_1OptionValueParser.html#a5a34866bb0ac6c4feae8b5a20aba93c7',1,'vg::OptionValueParser::parse()'],['../namespacevg.html#a1dd328fd8abb43338a3ae9e0a3b0be1f',1,'vg::parse(const string &arg, double &dest)'],['../namespacevg.html#a2d3193c0a90ba95bd11b8b3201de52c0',1,'vg::parse(const string &arg, float &dest)'],['../namespacevg.html#aa1de4a1752e875116c767ec49a8e2961',1,'vg::parse(const string &arg, std::regex &dest)'],['../namespacevg.html#aa4a3393960dd54c941e9d7c317923c2e',1,'vg::parse(const string &arg, pos_t &dest)'],['../namespacevg.html#a8873caafc22d22b52e0f6f3f164f6dc8',1,'vg::parse(const string &arg)'],['../namespacevg.html#a8c5c364797f623025b67b9aff0657112',1,'vg::parse(const char *arg)'],['../namespacevg.html#a627f5ad6fe6f1e6b4cc23ac97dfca4b8',1,'vg::parse(const string &arg, Result &dest)'],['../namespacevg.html#a2cd6368e7395f1d90c4e3be1a7293d0a',1,'vg::parse(const string &arg, typename enable_if< sizeof(Result)<=sizeof(long long) &&is_integral< Result >::value &&is_signed< Result >::value, Result >::type &dest)'],['../namespacevg.html#a1384531a1c8d8387bdd04961590bdf93',1,'vg::parse(const string &arg, typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &dest)']]],
- ['parse_5fattribute_5fvalue_4394',['parse_attribute_value',['../classvg_1_1Transcriptome.html#a401bd93346ea5e02f586823d8f3b458e',1,'vg::Transcriptome']]],
- ['parse_5fattributes_4395',['parse_attributes',['../structvg_1_1GFFRecord.html#ade5c97a34abe718fbb607977f11fb8f1',1,'vg::GFFRecord']]],
- ['parse_5fbed_4396',['parse_bed',['../mask__main_8cpp.html#a210b34f1b7dfefc99804b335b0cf6e19',1,'mask_main.cpp']]],
- ['parse_5fbed_5fregions_4397',['parse_bed_regions',['../namespacevg.html#a736f4c7b5d03a7efe78315b4c5490f15',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#ad88fe24ca988562008c8b734c22cb403',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)'],['../namespacevg.html#a8fd1e3436d98304996aaecece048cb45',1,'vg::parse_bed_regions(const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)']]],
- ['parse_5fdefault_4398',['parse_default',['../classvg_1_1OptionValueParser.html#ad2b7db7247de0c8cb7fe4e9501314b6b',1,'vg::OptionValueParser::parse_default()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#aa9624ebfad0e2421af39a86e7327edaf',1,'vg::OptionValueParser< vector< Item > >::parse_default()'],['../classvg_1_1OptionValueParser.html#acddd63568b5e1a7ece023abeccccd15b',1,'vg::OptionValueParser::parse_default()']]],
- ['parse_5ffrom_5fstring_4399',['parse_from_string',['../classvg_1_1io_1_1ProtobufIterator.html#ab37e50d3f1375c13a223a79938d5094d',1,'vg::io::ProtobufIterator']]],
- ['parse_5fgaf_5frecord_4400',['parse_gaf_record',['../namespacegafkluge.html#ab8a6f72dddac182a6d8d74a52a6fc92d',1,'gafkluge']]],
- ['parse_5fgbwt_5fconfig_4401',['parse_gbwt_config',['../gbwt__main_8cpp.html#a8153bcd09dec28c64e4a9bfad67cee40',1,'gbwt_main.cpp']]],
- ['parse_5fgff_5fregions_4402',['parse_gff_regions',['../namespacevg.html#a55cc20d96f38b54c590af4f3f3ac2498',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#a629c9fee8a51c4ca363511ae01ad4a09',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)']]],
- ['parse_5fh_4403',['parse_h',['../classvg_1_1algorithms_1_1GFAParser.html#a122490db3d620bc310b106e2231a9140',1,'vg::algorithms::GFAParser']]],
- ['parse_5fhaplotype_4404',['parse_haplotype',['../classhandlegraph_1_1PathMetadata.html#a69e57ea70c57b01b309cdf39da4eeeb5',1,'handlegraph::PathMetadata']]],
- ['parse_5fhaplotype_5ftranscript_5ffile_4405',['parse_haplotype_transcript_file',['../sim__main_8cpp.html#ae98175893da0d162097014dd65ba8ce2',1,'sim_main.cpp']]],
- ['parse_5fintron_5fdistr_5ffile_4406',['parse_intron_distr_file',['../mpmap__main_8cpp.html#a48bc366d5c5d1acbc0c60556944bcfe9',1,'mpmap_main.cpp']]],
- ['parse_5fintrons_4407',['parse_introns',['../classvg_1_1Transcriptome.html#ad040b82553e6b03ccd926c0fe622e84c',1,'vg::Transcriptome']]],
- ['parse_5fl_4408',['parse_l',['../classvg_1_1algorithms_1_1GFAParser.html#a6033f9ec4740e70dc79fbaae78f91773',1,'vg::algorithms::GFAParser']]],
- ['parse_5flocus_5fname_4409',['parse_locus_name',['../classhandlegraph_1_1PathMetadata.html#a978b48ca96f8817f7099587dae77b8b4',1,'handlegraph::PathMetadata']]],
- ['parse_5fmatrix_4410',['parse_matrix',['../classvg_1_1AlignerClient.html#a4a56c0bf099b670763c0f5ce3653811b',1,'vg::AlignerClient']]],
- ['parse_5fmemory_5fusage_4411',['parse_memory_usage',['../autoindex__main_8cpp.html#ad25ab5b852b7a1bc223505f7a2e23853',1,'autoindex_main.cpp']]],
- ['parse_5fonly_4412',['parse_only',['../structGBWTConfig.html#af8fc6affa1925b48a3af6fff48511340',1,'GBWTConfig']]],
- ['parse_5fp_4413',['parse_p',['../classvg_1_1algorithms_1_1GFAParser.html#a3f28df872d86abde347b3bbcc7f42948',1,'vg::algorithms::GFAParser']]],
- ['parse_5fpath_5fname_4414',['parse_path_name',['../classhandlegraph_1_1PathMetadata.html#ab6bcceaaedfbb03a4ea3f70499b06ade',1,'handlegraph::PathMetadata']]],
- ['parse_5fphase_5fblock_4415',['parse_phase_block',['../classhandlegraph_1_1PathMetadata.html#a3d9a3a974ab62d008104fa7dab849465',1,'handlegraph::PathMetadata']]],
- ['parse_5fprovide_5fstring_4416',['parse_provide_string',['../autoindex__main_8cpp.html#a8f62d94c211a4113595cbdf100129fc3',1,'autoindex_main.cpp']]],
- ['parse_5fregion_4417',['parse_region',['../namespacevg.html#a253257615743a1cfb948b749be7700e2',1,'vg::parse_region(const string &target, string &name, int64_t &start, int64_t &end)'],['../namespacevg.html#af0a3beb8908adf7a6e4d641243937830',1,'vg::parse_region(string ®ion, Region &out_region)']]],
- ['parse_5frg_5fsample_5fmap_4418',['parse_rg_sample_map',['../namespacevg.html#a637c855dffc0296c6575ae8a4cac6b43',1,'vg']]],
- ['parse_5frsem_5fexpression_5ffile_4419',['parse_rsem_expression_file',['../sim__main_8cpp.html#aa1964053fdd12fb9dde544ce6d18ab70',1,'sim_main.cpp']]],
- ['parse_5fs_4420',['parse_s',['../classvg_1_1algorithms_1_1GFAParser.html#af4ce322cdb902c01881afcbb4fea85f5',1,'vg::algorithms::GFAParser']]],
- ['parse_5fsam_5ftags_4421',['parse_sam_tags',['../namespacevg.html#a175da49ded2be9251e68ae642108248a',1,'vg']]],
- ['parse_5fsample_5fname_4422',['parse_sample_name',['../classhandlegraph_1_1PathMetadata.html#acbc675d9d41c36eebb174b4871c42435',1,'handlegraph::PathMetadata']]],
- ['parse_5fsense_4423',['parse_sense',['../classhandlegraph_1_1PathMetadata.html#aae6aa5f2738ce962e4e74d46a9c5e3e0',1,'handlegraph::PathMetadata']]],
- ['parse_5fsubrange_4424',['parse_subrange',['../classhandlegraph_1_1PathMetadata.html#a010d050ee3bf526da9ae45fde6dd1dc6',1,'handlegraph::PathMetadata']]],
- ['parse_5ftags_4425',['parse_tags',['../classvg_1_1algorithms_1_1GFAParser.html#a4fecb9e4836c67853d300ffd29b046e7',1,'vg::algorithms::GFAParser']]],
- ['parse_5ftid_5fpath_5fhandle_5fmap_4426',['parse_tid_path_handle_map',['../namespacevg.html#abc66619671bdc564023a9b3259558785',1,'vg']]],
- ['parse_5ftranscripts_4427',['parse_transcripts',['../classvg_1_1Transcriptome.html#ae7b6c679e3d635342029bbc7cc39d75d',1,'vg::Transcriptome']]],
- ['parse_5ftranslation_4428',['parse_translation',['../structvg_1_1PathIndex.html#aa5272234ddb7686f1ae88881ebf99a61',1,'vg::PathIndex']]],
- ['parse_5fvcf_4429',['parse_vcf',['../classvg_1_1HaplotypeIndexer.html#ad3eda4acd04b8bae303b4604410ece41',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::string &job_name="GBWT") const'],['../classvg_1_1HaplotypeIndexer.html#ad81dbd24bba40aaa14536d79754d387b',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::vector< path_handle_t > &paths, const std::string &job_name="GBWT") const']]],
- ['parse_5fw_4430',['parse_w',['../classvg_1_1algorithms_1_1GFAParser.html#ae03c9247eb49aed8f868039365f89cdd',1,'vg::algorithms::GFAParser']]],
- ['parsegenotypes_4431',['parseGenotypes',['../namespacevg.html#a8bcecf9fe02b7f50dd5e72e40dcd98e1',1,'vg']]],
- ['partition_5fgbwt_5fsequences_4432',['partition_gbwt_sequences',['../namespacevg.html#a802baeeacfe4ee75781afabac562588b',1,'vg']]],
- ['partition_5fhaplotypes_4433',['partition_haplotypes',['../classvg_1_1HaplotypePartitioner.html#a1c0a32c7f0ca0f86fd5abb9b746895c8',1,'vg::HaplotypePartitioner']]],
- ['partitioner_5fparameters_4434',['partitioner_parameters',['../structHaplotypesConfig.html#a6080d6a6e4ada9573d11d678b6de79d0',1,'HaplotypesConfig']]],
- ['pass_4435',['pass',['../classvg_1_1Funnel.html#aec19daea826d5951ecf1477769722d9a',1,'vg::Funnel']]],
- ['pass_5fnumber_4436',['pass_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#a9354b35a8f08891654da020502248f2e',1,'vg::algorithms::GFAFormatError']]],
- ['passed_5ffilters_4437',['passed_filters',['../structvg_1_1Funnel_1_1Item.html#a566978051c820d69d63e72763dc38b17',1,'vg::Funnel::Item']]],
- ['passed_5fstatistics_4438',['passed_statistics',['../structvg_1_1Funnel_1_1Item.html#a5ae29ab2e549daa3fa20626fd5d4fb59',1,'vg::Funnel::Item']]],
- ['passing_4439',['passing',['../structvg_1_1Funnel_1_1FilterPerformance.html#a9382a4983a52c3849412717c26205bde',1,'vg::Funnel::FilterPerformance']]],
- ['passing_5fcorrect_4440',['passing_correct',['../structvg_1_1Funnel_1_1FilterPerformance.html#a7622d6acfd5d4075e26ad60b911e72c4',1,'vg::Funnel::FilterPerformance']]],
- ['past_5fend_4441',['past_end',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a06f803fd96e9e94610bc8fa8f9db95f3',1,'vg::GraphSynchronizer::Lock']]],
- ['patch_5falignment_4442',['patch_alignment',['../classvg_1_1Mapper.html#ad8f03f4ff100a15ea885a5404222a0ad',1,'vg::Mapper']]],
- ['patch_5falignments_4443',['patch_alignments',['../classvg_1_1Mapper.html#a6c33dd8ad7af82e21f0ee6463e9456fc',1,'vg::Mapper']]],
- ['path_4444',['Path',['../structvg_1_1Path.html',1,'vg::Path'],['../structvg_1_1MatchPos.html#a6a24cd3b3befa706a8f4f934034843cf',1,'vg::MatchPos::path()'],['../structvg_1_1WFANode.html#ad947775b8a38d6d03e6c40b5a8ee06c2',1,'vg::WFANode::path()'],['../structvg_1_1GaplessExtension.html#a6d46f3e3d3525ea159b11f6e832a37e0',1,'vg::GaplessExtension::path()'],['../structvg_1_1WFAAlignment.html#afd65b83419307e4f56481adef5c96f71',1,'vg::WFAAlignment::path()'],['../classvg_1_1PathNode.html#aa955184b7b22179c0efd1febdfc55b92',1,'vg::PathNode::path()'],['../structvg_1_1RecombinatorHaplotype.html#ae37ea81b1f65f9c24f05620ecc3f2a80',1,'vg::RecombinatorHaplotype::path()'],['../structvg_1_1EditedTranscriptPath.html#a8945ac17c2039bc54e3697553c1563a2',1,'vg::EditedTranscriptPath::path()'],['../structvg_1_1CompletedTranscriptPath.html#ae6ea83076c2772ac2670e0e06587dc04',1,'vg::CompletedTranscriptPath::path()'],['../structvg_1_1algorithms_1_1walk__t.html#aee19ea04353c3d23bef5d5fd3689965c',1,'vg::algorithms::walk_t::path()'],['../classhandlegraph_1_1PathForEachSocket.html#a5bd264139b15b7e56ad5a2f6f691202b',1,'handlegraph::PathForEachSocket::path()'],['../structgafkluge_1_1GafRecord.html#ae9734ca0963cfb21cb966ee915c9224b',1,'gafkluge::GafRecord::path()'],['../structvg_1_1Graph.html#a850007eb60ce0d25a6bd9799050ec790',1,'vg::Graph::path()'],['../structvg_1_1Alignment.html#a4736db5fe121ef57784c18c3c27aea79',1,'vg::Alignment::path()'],['../structvg_1_1Subpath.html#a69056b48fb59ee83a8b0307838987e19',1,'vg::Subpath::path()'],['../classvg_1_1subpath__t.html#ad9d97e89f59cf75b1d00f0e54d979048',1,'vg::subpath_t::path()'],['../classvg_1_1Paths.html#a218a01d5d53bf945ef4f0acafd18d6bc',1,'vg::Paths::path()']]],
- ['path_2ecpp_4445',['path.cpp',['../path_8cpp.html',1,'']]],
- ['path_2ehpp_4446',['path.hpp',['../path_8hpp.html',1,'']]],
- ['path_5fback_4447',['path_back',['../classvg_1_1MemoizingGraph.html#a90d25a87afe426eb79582739848734c4',1,'vg::MemoizingGraph::path_back()'],['../classvg_1_1PathSubgraphOverlay.html#a7e9706b6c571a62a93c7dafb3be62f29',1,'vg::PathSubgraphOverlay::path_back()'],['../classvg_1_1VG.html#a1af5ef2df0289b964cab09d9400344c5',1,'vg::VG::path_back()'],['../classxg_1_1XG.html#aceaf4782f2fb6cbd169b6121fea8e4e8',1,'xg::XG::path_back()'],['../classhandlegraph_1_1PathHandleGraph.html#a31bb33a87ad8efd68876fc5ae1deeb09',1,'handlegraph::PathHandleGraph::path_back()']]],
- ['path_5fbegin_4448',['path_begin',['../classvg_1_1MemoizingGraph.html#ac40575d724c1d7053b9765e622cc3713',1,'vg::MemoizingGraph::path_begin()'],['../classvg_1_1PathSubgraphOverlay.html#a492b11a38ba4d31ee75341fc8777f19c',1,'vg::PathSubgraphOverlay::path_begin()'],['../classvg_1_1VG.html#af0fc3a05ce45e0100fb82812c5b1e35d',1,'vg::VG::path_begin()'],['../classxg_1_1XG.html#ad4894f85d76ca8101a5dd164a29379c5',1,'xg::XG::path_begin()'],['../classhandlegraph_1_1PathHandleGraph.html#a815759484087ed92214c2c1c6b9d1a11',1,'handlegraph::PathHandleGraph::path_begin()']]],
- ['path_5fchunk_5ft_4449',['path_chunk_t',['../classvg_1_1Surjector.html#a3ce06e344f93607bd066fd58d33fc7e0',1,'vg::Surjector']]],
- ['path_5fcollapse_5ftype_4450',['path_collapse_type',['../classvg_1_1Transcriptome.html#a539e8602c6f984142ae866af8730fd34',1,'vg::Transcriptome']]],
- ['path_5fcomponent_5findex_4451',['path_component_index',['../classvg_1_1PathOrientedDistanceMeasurer.html#aec1793ac0e2bf87292b90a5a2c8f14d8',1,'vg::PathOrientedDistanceMeasurer::path_component_index()'],['../classvg_1_1MultipathMapper.html#a0c64ee67ef473d5d5336ae6adf0b66e8',1,'vg::MultipathMapper::path_component_index()']]],
- ['path_5fcomponent_5findex_2ecpp_4452',['path_component_index.cpp',['../path__component__index_8cpp.html',1,'']]],
- ['path_5fcomponent_5findex_2ehpp_4453',['path_component_index.hpp',['../path__component__index_8hpp.html',1,'']]],
- ['path_5fcontains_5fhandle_4454',['path_contains_handle',['../classxg_1_1XG.html#ad55f3e5461c20199ccdb3a6fb4dacdf6',1,'xg::XG']]],
- ['path_5fcontains_5fnode_4455',['path_contains_node',['../structvg_1_1PathIndex.html#ab1bb8b7aec345a4b59242287ae1693c7',1,'vg::PathIndex']]],
- ['path_5fcontains_5fnode_5fin_5forientation_4456',['path_contains_node_in_orientation',['../structvg_1_1PathIndex.html#a0dbda80790b6d81aa0f9d83ac21f85a3',1,'vg::PathIndex']]],
- ['path_5fcount_4457',['path_count',['../classxg_1_1XG.html#a1859cb996668f8d86107d4e0117cf97f',1,'xg::XG']]],
- ['path_5fcover_4458',['path_cover',['../structGBWTConfig.html#a857449dfcac12577f54afbd7d8957336',1,'GBWTConfig']]],
- ['path_5fcover_5faugment_4459',['path_cover_augment',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a074342f434050b0213b77e7267c3d65a',1,'GBWTConfig']]],
- ['path_5fcover_5fdepth_4460',['path_cover_depth',['../structvg_1_1IndexingParameters.html#a1075d3f3c10502dc02deb564d85ff897',1,'vg::IndexingParameters']]],
- ['path_5fcover_5fgreedy_4461',['path_cover_greedy',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a0984604f4f41a7c9813edce20845b146',1,'GBWTConfig']]],
- ['path_5fcover_5flocal_4462',['path_cover_local',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a6f385ad96dac65846244dfafee7f4775',1,'GBWTConfig']]],
- ['path_5fcover_5fmode_4463',['path_cover_mode',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1',1,'GBWTConfig']]],
- ['path_5fcover_5fnone_4464',['path_cover_none',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1afd10e18b78dd3425247224d94f7e3dfc',1,'GBWTConfig']]],
- ['path_5fcover_5fparameters_4465',['path_cover_parameters',['../structGBWTConfig.html#a27d5429660a51913c09fa1b33477d27a',1,'GBWTConfig']]],
- ['path_5fdepth_5fof_5fbin_4466',['path_depth_of_bin',['../namespacevg_1_1algorithms.html#a8c66507d55ed6e10e9d77e1281d4bcfc',1,'vg::algorithms']]],
- ['path_5fdepths_4467',['path_depths',['../namespacevg_1_1algorithms.html#a85250c33b7d32346be371ab7e4404471',1,'vg::algorithms']]],
- ['path_5fdivergence_5ffilter_4468',['path_divergence_filter',['../classvg_1_1Filter.html#a961710b28527b3f9961948a068c3b860',1,'vg::Filter']]],
- ['path_5fedge_5fcount_4469',['path_edge_count',['../classvg_1_1VG.html#a5f1df72d85d8a72524b76abca972f33d',1,'vg::VG']]],
- ['path_5fend_4470',['path_end',['../structgafkluge_1_1GafRecord.html#ac1a2b5a9c4152dfb188a72571ecf746a',1,'gafkluge::GafRecord::path_end()'],['../classvg_1_1MemoizingGraph.html#a2e4006fc68d2db22228dcef6bed02666',1,'vg::MemoizingGraph::path_end()'],['../classvg_1_1PathSubgraphOverlay.html#a5d74d2d221394980ff65e2e9adc1818f',1,'vg::PathSubgraphOverlay::path_end()'],['../classvg_1_1VG.html#a2f532a7aeb7765b99c6c4e43ba961fdb',1,'vg::VG::path_end()'],['../classxg_1_1XG.html#a32e53f5b1a5cd650b5d731f0354c5c2d',1,'xg::XG::path_end()'],['../classhandlegraph_1_1PathHandleGraph.html#a5c3a5e04838d9e4a0a0ddf574c4de827',1,'handlegraph::PathHandleGraph::path_end()']]],
- ['path_5fend_5fnode_5foffset_4471',['path_end_node_offset',['../classvg_1_1VG.html#a8f45b42614f4ac36c8060634ec0d9805',1,'vg::VG']]],
- ['path_5fend_5fposition_4472',['path_end_position',['../namespacevg.html#af505a96db454fbd06e026f11cb6fbfba',1,'vg']]],
- ['path_5ffinder_4473',['path_finder',['../classvg_1_1VCFTraversalFinder.html#a7f529cb408098ee45d3e4868ed9fe2b8',1,'vg::VCFTraversalFinder']]],
- ['path_5ffor_5fcontig_4474',['path_for_contig',['../haplotypes__main_8cpp.html#a38d910b58a339b55e1135bad308a2aab',1,'haplotypes_main.cpp']]],
- ['path_5ffor_5fsample_5fcontig_4475',['path_for_sample_contig',['../haplotypes__main_8cpp.html#a3336c94d43159885886cca6dfef27b87',1,'haplotypes_main.cpp']]],
- ['path_5ffrom_5flength_4476',['path_from_length',['../namespacevg.html#a1524b7b1b7e67c048c0c5e88b204de08',1,'vg::path_from_length(const Path &path)'],['../namespacevg.html#ae87f325eb11aaf966e6d77d99be40c54',1,'vg::path_from_length(const path_t &path)']]],
- ['path_5ffrom_5fnode_5ftraversals_4477',['path_from_node_traversals',['../namespacevg.html#a3aef5ee16ad883f8defeaa0f52fc342c',1,'vg']]],
- ['path_5ffrom_5fpath_5fhandle_4478',['path_from_path_handle',['../namespacevg.html#a864fe6e3e163b18e84db0783f9a2e17d',1,'vg']]],
- ['path_5ffrom_5fthread_5ft_4479',['path_from_thread_t',['../namespacevg.html#ab0f225fb74f28ea09c6c8917ec14db73',1,'vg']]],
- ['path_5ffront_5fend_4480',['path_front_end',['../classvg_1_1MemoizingGraph.html#ac3db812ecb9ba33c323ed21f2fb30de2',1,'vg::MemoizingGraph::path_front_end()'],['../classvg_1_1PathSubgraphOverlay.html#a4e25154f03620214b41b52efe030ef2a',1,'vg::PathSubgraphOverlay::path_front_end()'],['../classvg_1_1VG.html#a5e1a4d7c14f1aaf601e9a6e231b6b7d3',1,'vg::VG::path_front_end()'],['../classxg_1_1XG.html#a7c14874c12caf4b94eb87af8d2daa686',1,'xg::XG::path_front_end()'],['../classhandlegraph_1_1PathHandleGraph.html#ad7412bf19084f2b38ffec42517a6a9e9',1,'handlegraph::PathHandleGraph::path_front_end()']]],
- ['path_5fgraph_4481',['path_graph',['../classvg_1_1MinimizerMapper.html#aa75ca7504db85f1ba5d340b8213036de',1,'vg::MinimizerMapper::path_graph()'],['../classvg_1_1PhaseUnfolder.html#a974791c770e3999168899eb36cbd2f48',1,'vg::PhaseUnfolder::path_graph()'],['../structGraphHandler.html#aeb4deb32f56c35702b331c0f506d3844',1,'GraphHandler::path_graph()']]],
- ['path_5fhandle_5fgraph_2ecpp_4482',['path_handle_graph.cpp',['../path__handle__graph_8cpp.html',1,'']]],
- ['path_5fhandle_5fgraph_2ehpp_4483',['path_handle_graph.hpp',['../path__handle__graph_8hpp.html',1,'']]],
- ['path_5fhandle_5ft_4484',['path_handle_t',['../structhandlegraph_1_1path__handle__t.html',1,'handlegraph::path_handle_t'],['../namespacevg.html#aaf7aeec04909c1aac0ad991764d48e24',1,'vg::path_handle_t()'],['../namespacevg_1_1io.html#a5cab7a1a96fc203865d8ca67a372b24f',1,'vg::io::path_handle_t()']]],
- ['path_5fidentity_4485',['path_identity',['../classvg_1_1VG.html#ad9bd4133841d1d781fb0df4171773139',1,'vg::VG']]],
- ['path_5findex_2ecpp_4486',['path_index.cpp',['../path__index_8cpp.html',1,'']]],
- ['path_5findex_2ehpp_4487',['path_index.hpp',['../path__index_8hpp.html',1,'']]],
- ['path_5findexes_4488',['path_indexes',['../classvg_1_1LegacyCaller.html#a5de5c60b4da9b71566fc10a76ed0e211',1,'vg::LegacyCaller']]],
- ['path_5fis_5fsimple_5fmatch_4489',['path_is_simple_match',['../namespacevg.html#a43c4a438edc31c7b0d2aa0731c522e8a',1,'vg']]],
- ['path_5fjaccard_5fwindow_4490',['path_jaccard_window',['../classvg_1_1Deconstructor.html#a0cf545ea26ebb9bbebafefe47524f87b',1,'vg::Deconstructor']]],
- ['path_5flength_4491',['path_length',['../structgafkluge_1_1GafRecord.html#ac9b7a4a556d78f32913392b0706e93e0',1,'gafkluge::GafRecord']]],
- ['path_5flength_5ffilter_4492',['path_length_filter',['../classvg_1_1Filter.html#a4b9e7a11ee8f1d58a4ae99d6a0a7aabf',1,'vg::Filter']]],
- ['path_5flengths_5fto_5fsinks_4493',['path_lengths_to_sinks',['../classvg_1_1BandedGlobalAligner.html#a52406c8606e4aa4c817251289651b4cc',1,'vg::BandedGlobalAligner']]],
- ['path_5flisteners_4494',['path_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aa856090842dafbe0dbaf22bed66fd411',1,'vg::algorithms::GFAParser']]],
- ['path_5fmapping_5fnode_5fid_4495',['path_mapping_node_id',['../structhaplo_1_1linear__haplo__structure.html#ae72d0e22919bc536e6ebc765f56b6271',1,'haplo::linear_haplo_structure']]],
- ['path_5fmapping_5foffset_4496',['path_mapping_offset',['../structhaplo_1_1linear__haplo__structure.html#a2d1b328d1268ef04ac035550eda05ebf',1,'haplo::linear_haplo_structure']]],
- ['path_5fmapping_5ft_4497',['path_mapping_t',['../classvg_1_1path__mapping__t.html',1,'vg::path_mapping_t'],['../classvg_1_1path__mapping__t.html#af53a6e6f24b6bc9fbd611bcf826845bd',1,'vg::path_mapping_t::path_mapping_t()=default'],['../classvg_1_1path__mapping__t.html#ab2a0922f085a4f2838437613525ff25c',1,'vg::path_mapping_t::path_mapping_t(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a64f8b90a2817811dd06ae831094c5fa5',1,'vg::path_mapping_t::path_mapping_t(path_mapping_t &&other)=default']]],
- ['path_5fmetadata_2ecpp_4498',['path_metadata.cpp',['../path__metadata_8cpp.html',1,'']]],
- ['path_5fmetadata_2ehpp_4499',['path_metadata.hpp',['../path__metadata_8hpp.html',1,'']]],
- ['path_5fmode_4500',['path_mode',['../structGBWTConfig.html#a218c5f96dd7101b89bdf8e64de3b9949',1,'GBWTConfig']]],
- ['path_5fname_4501',['path_name',['../structvg_1_1FeatureSet_1_1Feature.html#a645900ed3044cc3359c18e109f7460a7',1,'vg::FeatureSet::Feature::path_name()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad19c5f9cbb68abb1bcfe6e3a9fd65382',1,'vg::GraphSynchronizer::Lock::path_name()'],['../classxg_1_1XG.html#adf5cee0fdfb7bac641cf0e7e10371f8a',1,'xg::XG::path_name()']]],
- ['path_5fname_5fcsa_5fdelim_4502',['path_name_csa_delim',['../classxg_1_1XG.html#a5b2791b586efb23a131c2d5c00d85593',1,'xg::XG']]],
- ['path_5fnames_4503',['path_names',['../classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138',1,'vg::VariantAdder::path_names()'],['../structGBWTConfig.html#a96ccf4e2605d4dad1a32511169f51969',1,'GBWTConfig::path_names()']]],
- ['path_5fnames_5fby_5fprefix_4504',['path_names_by_prefix',['../classxg_1_1XG.html#a70a2bac209d84ee2b9165a7dfca5969e',1,'xg::XG']]],
- ['path_5fnode_4505',['path_node',['../namespacevg.html#a3bd8aa63fec8b9f6c3ed5808689975e6',1,'vg::path_node(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#ac6bdd8e00dd9f63a0d9049ffe3461d47',1,'vg::path_node(const gbwt::vector_type &path, size_t i)']]],
- ['path_5fnodes_4506',['path_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a76f9356cd0afea7dea3003caea2526eb',1,'vg::MultipathAlignmentGraph']]],
- ['path_5foffset_4507',['path_offset',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a58b1c09d2f45e4942afd52d975c85b9a',1,'vg::GraphSynchronizer::Lock']]],
- ['path_5foffset_5fcollection_5ft_4508',['path_offset_collection_t',['../namespacevg_1_1algorithms.html#a6474017f8ab54b0c6e20095206a880a8',1,'vg::algorithms']]],
- ['path_5forder_5fand_5flength_4509',['path_order_and_length',['../classvg_1_1HTSWriter.html#a2b0a5d9268a4b4901a699f82d857d6e2',1,'vg::HTSWriter']]],
- ['path_5foutput_4510',['path_output',['../structGBWTConfig.html#a91e5194d120c0dbae060bdfe5c60667a',1,'GBWTConfig']]],
- ['path_5fposition_5fhandle_5fgraph_4511',['path_position_handle_graph',['../classvg_1_1MCMCCaller.html#a240741cadefa13b2b4d472f0b6e3b8d3',1,'vg::MCMCCaller']]],
- ['path_5fposition_5fhandle_5fgraph_2ecpp_4512',['path_position_handle_graph.cpp',['../path__position__handle__graph_8cpp.html',1,'']]],
- ['path_5fposition_5fhandle_5fgraph_2ehpp_4513',['path_position_handle_graph.hpp',['../path__position__handle__graph_8hpp.html',1,'']]],
- ['path_5fpredecessors_4514',['path_predecessors',['../namespacevg.html#a72aa312e964fab8a03b93ec897f355ec',1,'vg']]],
- ['path_5franks_5fby_5fprefix_4515',['path_ranks_by_prefix',['../classxg_1_1XG.html#a93b333ee3c02b8309a139401f1dc661f',1,'xg::XG']]],
- ['path_5freverse_4516',['path_reverse',['../namespacevg.html#ae8fcec2fbe4151075a0b33bc6a0dd145',1,'vg::path_reverse(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#aa0439b7fcf30da565152d9800ff4473d',1,'vg::path_reverse(const gbwt::vector_type &path, size_t i)']]],
- ['path_5fsampler_4517',['path_sampler',['../classvg_1_1Sampler.html#a8125a49b29eecf4d5037067c813b2cd7',1,'vg::Sampler::path_sampler()'],['../classvg_1_1NGSSimulator.html#a6101d443a8c314416fbc23dbfd3d5bde',1,'vg::NGSSimulator::path_sampler()']]],
- ['path_5fscore_5fannotations_4518',['path_score_annotations',['../classvg_1_1Surjector.html#a9a83875480f04c8dad0207ead58003b8',1,'vg::Surjector']]],
- ['path_5fsequence_4519',['path_sequence',['../classvg_1_1VG.html#a4ce6fe02b243b4f0f82bbf801fd507fa',1,'vg::VG::path_sequence()'],['../namespacevg.html#aad7dc3b95a62cfd99b5fa6377c1a9545',1,'vg::path_sequence()']]],
- ['path_5fsize_4520',['path_size',['../namespacevg.html#aae876005c9e34df70bdc9e2e97776121',1,'vg::path_size(const vector< pair< vg::id_t, bool >> &path)'],['../namespacevg.html#a0c911ba34849a4afd407812fe6373579',1,'vg::path_size(const gbwt::vector_type &path)']]],
- ['path_5fstart_4521',['path_start',['../structgafkluge_1_1GafRecord.html#a14ce42efee5a241bebe4debf852afbae',1,'gafkluge::GafRecord']]],
- ['path_5fstart_5fposition_4522',['path_start_position',['../namespacevg.html#a2c3b1708b878655d0f6a50a2ba589bf9',1,'vg']]],
- ['path_5fstring_4523',['path_string',['../namespacevg_1_1algorithms.html#a7acc0acf3d99939a0943ca9e0b86e48a',1,'vg::algorithms']]],
- ['path_5fstring_2ecpp_4524',['path_string.cpp',['../path__string_8cpp.html',1,'']]],
- ['path_5fstring_2ehpp_4525',['path_string.hpp',['../path__string_8hpp.html',1,'']]],
- ['path_5fsubgraph_2ecpp_4526',['path_subgraph.cpp',['../path__subgraph_8cpp.html',1,'']]],
- ['path_5fsubgraph_2ehpp_4527',['path_subgraph.hpp',['../path__subgraph_8hpp.html',1,'']]],
- ['path_5fsubset_4528',['path_subset',['../classvg_1_1PathSubgraphOverlay.html#aef82f75c24c686645b0255685bc4c6f2',1,'vg::PathSubgraphOverlay']]],
- ['path_5ft_4529',['path_t',['../classvg_1_1path__t.html',1,'vg::path_t'],['../classvg_1_1path__t.html#ac49a26cfbfc0dc2d3bc16ec5b38fceda',1,'vg::path_t::path_t()=default'],['../classvg_1_1path__t.html#a75929a646a781440f67c3b374a6c9166',1,'vg::path_t::path_t(const path_t &other)=default'],['../classvg_1_1path__t.html#ad9d1b8c169d9819e70dda68bca1af668',1,'vg::path_t::path_t(path_t &&other)=default']]],
- ['path_5fto_5fgbwt_4530',['path_to_gbwt',['../namespacevg.html#a529e3aef69e8c01934184726b7937c37',1,'vg']]],
- ['path_5fto_5fgbwt_5fthread_5ft_4531',['path_to_gbwt_thread_t',['../namespacehaplo.html#a86bbe3de0c810d215fd574fe4dfadfee',1,'haplo']]],
- ['path_5fto_5finput_5fhaplotype_4532',['path_to_input_haplotype',['../structhaplo_1_1linear__haplo__structure.html#acf88c54b278bcacae66383f2668970b2',1,'haplo::linear_haplo_structure']]],
- ['path_5fto_5flength_4533',['path_to_length',['../namespacevg.html#a48108a0abc0fdfc187437d174f88e590',1,'vg::path_to_length(const Path &path)'],['../namespacevg.html#a16b3cfa2fc1c70ce96f7ebc695c8766d',1,'vg::path_to_length(const path_t &path)']]],
- ['path_5fto_5fploidy_4534',['path_to_ploidy',['../classvg_1_1VCFGenotyper.html#a248d8e2819ba7354c39b3d2077061fed',1,'vg::VCFGenotyper']]],
- ['path_5fto_5fsample_5fphase_4535',['path_to_sample_phase',['../classvg_1_1Deconstructor.html#a8a5562db89e9293a88b2f22e476d1d25',1,'vg::Deconstructor']]],
- ['path_5fto_5fstring_4536',['path_to_string',['../namespacevg.html#afbe0993e79f4ef7bb4b37456b0b08402',1,'vg']]],
- ['path_5fto_5fvcf_4537',['path_to_vcf',['../classvg_1_1HaplotypeIndexer.html#a5ff016a7fdf425ec4f3d5408d09b951f',1,'vg::HaplotypeIndexer']]],
- ['path_5ftrav_5ffinder_4538',['path_trav_finder',['../classvg_1_1Deconstructor.html#a73c6c008333acfbb0ffd6fde2360518c',1,'vg::Deconstructor']]],
- ['path_5ftype_4539',['path_type',['../classvg_1_1PhaseUnfolder.html#a402b0f84990279594bfbb1cd71ffd8e5',1,'vg::PhaseUnfolder::path_type()'],['../structjob__type.html#a8749aa5a745848ff8d5a6e72bdc002e6',1,'job_type::path_type()']]],
- ['pathbasedtraversalfinder_4540',['PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html',1,'vg::PathBasedTraversalFinder'],['../classvg_1_1PathBasedTraversalFinder.html#ae9824d8e0620854391925d43c7200da6',1,'vg::PathBasedTraversalFinder::PathBasedTraversalFinder()']]],
- ['pathbranch_4541',['PathBranch',['../structvg_1_1PathBranch.html',1,'vg']]],
- ['pathchunker_4542',['PathChunker',['../classvg_1_1PathChunker.html',1,'vg::PathChunker'],['../classvg_1_1PathChunker.html#a5b31a6a4f865a99818f69be54b7f9e40',1,'vg::PathChunker::PathChunker()']]],
- ['pathcomponentindex_4543',['PathComponentIndex',['../classvg_1_1PathComponentIndex.html',1,'vg::PathComponentIndex'],['../classvg_1_1PathComponentIndex.html#aa8aa8ec6a8bc50004db3e07d081d1942',1,'vg::PathComponentIndex::PathComponentIndex(const PathHandleGraph *graph)'],['../classvg_1_1PathComponentIndex.html#a9b093ea34524c9e95cd10375dd000c87',1,'vg::PathComponentIndex::PathComponentIndex()']]],
- ['pathforeachsocket_4544',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html',1,'handlegraph::PathForEachSocket'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ad5b94c4a72e3d6d48be27cb00bc41ca2',1,'handlegraph::PathForEachSocket::iterator::PathForEachSocket()'],['../classhandlegraph_1_1PathForEachSocket.html#a1ae98a885a8b37c66d522c3a282c5fd5',1,'handlegraph::PathForEachSocket::PathForEachSocket()=delete'],['../classhandlegraph_1_1PathForEachSocket.html#adea5ed0aea8a5167d7c09a731b9ab65e',1,'handlegraph::PathForEachSocket::PathForEachSocket(const PathHandleGraph *graph, const path_handle_t &path)']]],
- ['pathhandlegraph_4545',['PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html',1,'handlegraph::PathHandleGraph'],['../classhandlegraph_1_1PathForEachSocket.html#a4260787fbe094766e75485f7d7d9d0ca',1,'handlegraph::PathForEachSocket::PathHandleGraph()'],['../namespacevg.html#abeb2636bd0db3101259ef6803cb4e591',1,'vg::PathHandleGraph()']]],
- ['pathindex_4546',['PathIndex',['../structvg_1_1PathIndex.html',1,'vg::PathIndex'],['../structvg_1_1PathIndex.html#ac9bdc9df55bcad668ab35b713c366994',1,'vg::PathIndex::PathIndex(const Path &path)'],['../structvg_1_1PathIndex.html#a99878fd10f43e040987e334a70d22d87',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings)'],['../structvg_1_1PathIndex.html#a91e9971a2ddb597ea1c229659b9c9b93',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings, VG &vg)'],['../structvg_1_1PathIndex.html#a72ba06ae7c3fed7abba0cbe2dd6cac88',1,'vg::PathIndex::PathIndex(const Path &path, const HandleGraph &graph)'],['../structvg_1_1PathIndex.html#a9b82679a8d5040f0160edc008d8b348d',1,'vg::PathIndex::PathIndex(VG &vg, const string &path_name, bool extract_sequence=false)'],['../structvg_1_1PathIndex.html#a88a67933e88510cd99800348eb40aa57',1,'vg::PathIndex::PathIndex(const PathHandleGraph &graph, const string &path_name, bool extract_sequence=false)']]],
- ['pathinterval_4547',['PathInterval',['../namespacevg.html#ae8f438fe1484a4bcc51d06ad13058c9c',1,'vg']]],
- ['pathlist_4548',['PathList',['../structvg_1_1MatchPos_1_1PathList.html',1,'vg::MatchPos']]],
- ['pathmetadata_4549',['PathMetadata',['../classhandlegraph_1_1PathMetadata.html',1,'handlegraph::PathMetadata'],['../namespacevg.html#ab5f7f6692a7600f1fa62428255c5bb61',1,'vg::PathMetadata()']]],
- ['pathnode_4550',['PathNode',['../classvg_1_1PathNode.html',1,'vg']]],
- ['pathorienteddistancemeasurer_4551',['PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html',1,'vg::PathOrientedDistanceMeasurer'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a483512f5650b15d5f56935ce2d7ce1bf',1,'vg::PathOrientedDistanceMeasurer::PathOrientedDistanceMeasurer()']]],
- ['pathpositionhandlegraph_4552',['PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html',1,'handlegraph::PathPositionHandleGraph'],['../namespacevg.html#a2481be7fa8c46933b9b99108e4c797b3',1,'vg::PathPositionHandleGraph()']]],
- ['pathrestrictedtraversalfinder_4553',['PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html',1,'vg::PathRestrictedTraversalFinder'],['../classvg_1_1PathRestrictedTraversalFinder.html#aba5b15255fc6b93f745649eed9d0c535',1,'vg::PathRestrictedTraversalFinder::PathRestrictedTraversalFinder()']]],
- ['paths_4554',['Paths',['../classvg_1_1Paths.html',1,'vg::Paths'],['../classvg_1_1SurjectingAlignmentEmitter.html#a3193ef16804780255b9d0bbcef8dc6ca',1,'vg::SurjectingAlignmentEmitter::paths()'],['../classvg_1_1PathTraversalFinder.html#a5a931da9269d7834dcc04e5fb578ff45',1,'vg::PathTraversalFinder::paths()'],['../classvg_1_1VG.html#a7c5150aba84e7ed2bde7986462a79989',1,'vg::VG::paths()'],['../structjob__type.html#a1c12e7fbad645aa2081f00b1a49b296f',1,'job_type::paths()'],['../classxg_1_1XG.html#a1b5defef10208838d0d3a48ddeb91f85',1,'xg::XG::paths()'],['../classvg_1_1Paths.html#af048f547f9c4976c17aaa34f1cbec312',1,'vg::Paths::Paths(void)'],['../classvg_1_1Paths.html#a92fa1ad35d1cf495d96e8fbd468f2700',1,'vg::Paths::Paths(const Paths &other)'],['../classvg_1_1Paths.html#a7b932a39b910d477cd7f3e65a0af3c93',1,'vg::Paths::Paths(Paths &&other) noexcept']]],
- ['paths_5fas_5falignments_4555',['paths_as_alignments',['../classvg_1_1VG.html#a871d05e0a2d0b76092e20fe86bd12e2b',1,'vg::VG']]],
- ['paths_5fbetween_4556',['paths_between',['../classvg_1_1VG.html#a8dc8d762d07088089247b632c835a19d',1,'vg::VG::paths_between(Node *from, Node *to, vector< Path > &paths)'],['../classvg_1_1VG.html#a0a5a5cb1bac139c5a3a947a0d5a3313d',1,'vg::VG::paths_between(nid_t from, nid_t to, vector< Path > &paths)']]],
- ['paths_5ffrom_5fgraph_4557',['paths_from_graph',['../namespacevg.html#a1b5ffc03255d72f1901a7b1ce34c058a',1,'vg']]],
- ['paths_5fmain_2ecpp_4558',['paths_main.cpp',['../paths__main_8cpp.html',1,'']]],
- ['paths_5fof_5fhandle_4559',['paths_of_handle',['../classxg_1_1XG.html#a519fa3151a3b49f5939277a14dced503',1,'xg::XG']]],
- ['paths_5fon_5fsame_5fcomponent_4560',['paths_on_same_component',['../classvg_1_1PathComponentIndex.html#a77de0e355ad6b0893cc506ce18adb050',1,'vg::PathComponentIndex']]],
- ['pathsense_4561',['PathSense',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271c',1,'handlegraph::PathSense()'],['../namespacevg.html#a15c1e75e93ab89aacd0eb7e1f0299724',1,'vg::PathSense()']]],
- ['pathsubgraph_4562',['PathSubgraph',['../classvg_1_1PathSubgraph.html',1,'vg::PathSubgraph'],['../classvg_1_1PathSubgraph.html#a861b07c24488c1454b6c04b1f7f01b68',1,'vg::PathSubgraph::PathSubgraph()']]],
- ['pathsubgraphoverlay_4563',['PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html',1,'vg::PathSubgraphOverlay'],['../classvg_1_1PathSubgraphOverlay.html#a71b48d68fc02b88cf0b1c15ca26aa2c6',1,'vg::PathSubgraphOverlay::PathSubgraphOverlay()']]],
- ['pathtraversalfinder_4564',['PathTraversalFinder',['../classvg_1_1PathTraversalFinder.html',1,'vg::PathTraversalFinder'],['../classvg_1_1PathTraversalFinder.html#a49d66e050feec7374fb0d2ed3483b897',1,'vg::PathTraversalFinder::PathTraversalFinder()']]],
- ['payload_4565',['payload',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a9b29761900b87e78b6c17dbe8e38d4fe',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
- ['payload_5fnode_5flength_4566',['payload_node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ac80389e7a2ddaae480e60b286186e3aa',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
- ['payload_5fprefix_5fsum_4567',['payload_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ab809433b78a00f00ae46e7061972c9a9',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
- ['pb2json_4568',['pb2json',['../json2pb_8cpp.html#af6bb66946ffaf36b1fe45881291fee0d',1,'pb2json(const Message &msg): json2pb.cpp'],['../json2pb_8h.html#a7cc576c6ed1e52ba82cf5f264f8ba21d',1,'pb2json(const google::protobuf::Message &msg): json2pb.h']]],
- ['pbsize_4569',['pbSize',['../classvg_1_1io_1_1fdinbuf.html#a1756a5735e7daf8ea042bc81343f7a0f',1,'vg::io::fdinbuf::pbSize()'],['../classvg_1_1io_1_1streaminbuf.html#a4cdee06174136df70efd572abfced2c8',1,'vg::io::streaminbuf::pbSize()']]],
- ['peek_4570',['peek',['../classvg_1_1BitString.html#a2b6d10b59df3727c8f07c3fbe646d03c',1,'vg::BitString']]],
- ['penalties_4571',['penalties',['../structhaplo_1_1linear__haplo__structure.html#af55d7f33177180d033e8e925cf20e5fd',1,'haplo::linear_haplo_structure']]],
- ['per_5fbase_4572',['per_base',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a8a85161fa2d79301a9ca6489006a4c62',1,'vg::WFAExtender::ErrorModel::Event']]],
- ['percent_5fidentity_5ffilter_4573',['percent_identity_filter',['../classvg_1_1Filter.html#aba2f93a1c4087075ccf4924fd0e44392',1,'vg::Filter']]],
- ['percent_5furl_5fencode_4574',['percent_url_encode',['../namespacevg.html#a2ba15a613567689d941f30a5a17c6ead',1,'vg']]],
- ['perfect_5ffilter_4575',['perfect_filter',['../classvg_1_1Filter.html#af33b08ad08247167fbe7d90ac86047a3',1,'vg::Filter']]],
- ['perfect_5fpair_5fidentity_5fthreshold_4576',['perfect_pair_identity_threshold',['../classvg_1_1FragmentLengthStatistics.html#a4e65bc3de5657555df556429284f5251',1,'vg::FragmentLengthStatistics']]],
- ['perform_5fdp_4577',['perform_dp',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6a5314b3408ca05c265648b8b6053e1d',1,'vg::MEMClusterer::HitGraph']]],
- ['performed_5fduplications_4578',['performed_duplications',['../classvg_1_1DozeuPinningOverlay.html#af98692ca5587716febd938e4e216cf99',1,'vg::DozeuPinningOverlay']]],
- ['peripheral_5fattachments_4579',['peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa2e7c9a960855fa8758d9dd6da6454ea',1,'vg::GraphSynchronizer::Lock']]],
- ['periphery_4580',['periphery',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad9bebede56cef5ab20d80828e34d8b6a',1,'vg::GraphSynchronizer::Lock']]],
- ['permutation_5fidx_4581',['permutation_idx',['../classvg_1_1ShuffledPairs_1_1iterator.html#a52dd908e59ff6dac90191a40c63537e0',1,'vg::ShuffledPairs::iterator']]],
- ['permuted_4582',['permuted',['../classvg_1_1ShuffledPairs_1_1iterator.html#a19642461808615472b7b544e04c47243',1,'vg::ShuffledPairs::iterator']]],
- ['pessimistic_5fgap_4583',['pessimistic_gap',['../classvg_1_1MultipathMapper.html#ac4311460002c8df22a29b3e55cc4e1ff',1,'vg::MultipathMapper']]],
- ['pessimistic_5fgap_5fmemo_4584',['pessimistic_gap_memo',['../classvg_1_1MultipathMapper.html#a828e72945f3e24243d5802604e027b47',1,'vg::MultipathMapper']]],
- ['pessimistic_5fgap_5fmultiplier_4585',['pessimistic_gap_multiplier',['../classvg_1_1MultipathMapper.html#aef97cb46d48a242a68c6ed590039e832',1,'vg::MultipathMapper']]],
- ['pessimistic_5ftail_5fgap_4586',['pessimistic_tail_gap',['../classvg_1_1MultipathAlignmentGraph.html#a4c591d080bc48994fcdb2c9dc08d34a1',1,'vg::MultipathAlignmentGraph']]],
- ['pessimistic_5ftail_5fgap_5fmemo_4587',['pessimistic_tail_gap_memo',['../classvg_1_1MultipathAlignmentGraph.html#af46ba9972db437bf66f787a9bbe6c3cd',1,'vg::MultipathAlignmentGraph']]],
- ['phase_4588',['phase',['../structvg_1_1GFFRecord.html#adf3d82a77a4837edba29935e08cb2a53',1,'vg::GFFRecord']]],
- ['phase_5fblock_5fmatch_4589',['PHASE_BLOCK_MATCH',['../classhandlegraph_1_1PathMetadata.html#a08fb019956ae31b8ea31920c904ea5fc',1,'handlegraph::PathMetadata']]],
- ['phase_5fhomozygous_4590',['phase_homozygous',['../classvg_1_1HaplotypeIndexer.html#a881e755025092748b18f037fb1078e65',1,'vg::HaplotypeIndexer']]],
- ['phase_5funfolder_2ecpp_4591',['phase_unfolder.cpp',['../phase__unfolder_8cpp.html',1,'']]],
- ['phase_5funfolder_2ehpp_4592',['phase_unfolder.hpp',['../phase__unfolder_8hpp.html',1,'']]],
- ['phase_5fvisits_4593',['phase_visits',['../structvg_1_1VG_1_1Plan.html#ad18d84799bb31227175746bee50f6940',1,'vg::VG::Plan']]],
- ['phased_5fgenome_2ecpp_4594',['phased_genome.cpp',['../phased__genome_8cpp.html',1,'']]],
- ['phased_5fgenome_2ehpp_4595',['phased_genome.hpp',['../phased__genome_8hpp.html',1,'']]],
- ['phasedgenome_4596',['PhasedGenome',['../classvg_1_1PhasedGenome.html',1,'vg::PhasedGenome'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::Haplotype::PhasedGenome()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::iterator::PhasedGenome()'],['../classvg_1_1PhasedGenome.html#aa7a7cce5f88f52d20c659e64966ece28',1,'vg::PhasedGenome::PhasedGenome(const SnarlManager &snarl_manager)'],['../classvg_1_1PhasedGenome.html#a0e96410c065eb722e527be06b710c5d7',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome.html#ace57a61caa7e82942f94ea1e128bc3e3',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &&other)=delete']]],
- ['phaseunfolder_4597',['PhaseUnfolder',['../classvg_1_1PhaseUnfolder.html',1,'vg::PhaseUnfolder'],['../classvg_1_1PhaseUnfolder.html#a7d6868ce2e12eeae8a8df8b00c6b5003',1,'vg::PhaseUnfolder::PhaseUnfolder()']]],
- ['phi_4598',['Phi',['../namespacevg.html#afea3e6d4a8ac9b486d1a2b9b89eadd2f',1,'vg']]],
- ['phi_5finv_4599',['Phi_inv',['../namespacevg.html#a4ae7976a3a19fe08c4b2bce4b3f3c00f',1,'vg']]],
- ['phred_5fadd_4600',['phred_add',['../namespacevg.html#a211ba38329cdc76a7ad0b64bbb227bfd',1,'vg']]],
- ['phred_5ffor_5fat_5fleast_5fone_4601',['phred_for_at_least_one',['../namespacevg.html#a9a6ab3a0f45f6ab7b38320db7cc14583',1,'vg']]],
- ['phred_5fgeometric_5fmean_4602',['phred_geometric_mean',['../namespacevg.html#a04edc3daae77e9d3813a97da0f473def',1,'vg']]],
- ['phred_5fprob_4603',['phred_prob',['../classvg_1_1NGSSimulator.html#ab8ace60ed77440820944dbdaee5bb123',1,'vg::NGSSimulator']]],
- ['phred_5fsum_4604',['phred_sum',['../namespacevg.html#aaeddefa307b95defd68c8a2022db732c',1,'vg::phred_sum(const Iterator &begin_it, const Iterator &end_it)'],['../namespacevg.html#ad78072e330ae86c9ef80aeeb84f89e8f',1,'vg::phred_sum(const Collection &collection)']]],
- ['phred_5fto_5flogprob_4605',['phred_to_logprob',['../namespacevg.html#a35b531c82b765cd54702665668a98448',1,'vg']]],
- ['phred_5fto_5fprob_4606',['phred_to_prob',['../namespacevg.html#ab713ebc6e2988cc2c959be14bfa01200',1,'vg::phred_to_prob(uint8_t phred)'],['../namespacevg.html#afba77c5a550d5dd72f8cf7438f600676',1,'vg::phred_to_prob(double phred)']]],
- ['pi_5fiv_4607',['pi_iv',['../classxg_1_1XG.html#a31024f79e1a2564e990e1e4445fed0ce',1,'xg::XG']]],
- ['pick_5fmappings_5ffrom_5falignments_4608',['pick_mappings_from_alignments',['../classvg_1_1MinimizerMapper.html#a967245a85231b63dd7606b5cd4b4c672',1,'vg::MinimizerMapper']]],
- ['pictographs_4609',['Pictographs',['../classvg_1_1Pictographs.html',1,'vg::Pictographs'],['../classvg_1_1Pictographs.html#a9784714a3a94bd173fecdd31655a770b',1,'vg::Pictographs::Pictographs(void)'],['../classvg_1_1Pictographs.html#a997d5ba6f6e9c5cbdb039ed9c51625e9',1,'vg::Pictographs::Pictographs(int seed_val)']]],
- ['pictographs_2ehpp_4610',['pictographs.hpp',['../pictographs_8hpp.html',1,'']]],
- ['pileup_4611',['Pileup',['../structvg_1_1Pileup.html',1,'vg']]],
- ['pin_5foffset_4612',['pin_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aff4877147fc6b731179a8e89dfb99757',1,'vg::MinimizerMapper::Minimizer']]],
- ['pinned_5ftail_5fsize_4613',['pinned_tail_size',['../classvg_1_1VariantAdder.html#ab5dea4bb3c4143e8fb4e28205a4d2cd6',1,'vg::VariantAdder']]],
- ['pipeline_4614',['PIPELINE',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838a797a289a67a7dd20502b2436f0c9d305',1,'vg::subcommand']]],
- ['placed_4615',['PLACED',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85a0a4373ca716769f93112e16e251bb8a1',1,'vg::Funnel']]],
- ['plan_4616',['Plan',['../structvg_1_1VG_1_1Plan.html',1,'vg::VG::Plan'],['../structvg_1_1VG_1_1Plan.html#aa757327a3bf40e1828d8aacc5cf5dec5',1,'vg::VG::Plan::Plan()']]],
- ['plausible_5frescue_5fcluster_5fcoverage_5fdiff_4617',['plausible_rescue_cluster_coverage_diff',['../classvg_1_1MultipathMapper.html#aea5ee453023a73c3d7c02b929d9ef073',1,'vg::MultipathMapper']]],
- ['pmax_4618',['pmax',['../namespacevg.html#ac7f5da8e25414026729f0c4d09243f6d',1,'vg']]],
- ['pn_5fbv_4619',['pn_bv',['../classxg_1_1XG.html#a50b600c6e29135f595459d447fb1e6bb',1,'xg::XG']]],
- ['pn_5fbv_5frank_4620',['pn_bv_rank',['../classxg_1_1XG.html#a9e24932d14efdf5ab53dce331d424093',1,'xg::XG']]],
- ['pn_5fbv_5fselect_4621',['pn_bv_select',['../classxg_1_1XG.html#a541462516fe4a54499c0b42e4cc95a28',1,'xg::XG']]],
- ['pn_5fcsa_4622',['pn_csa',['../classxg_1_1XG.html#a638068e773deaf37cb68bd39eb4599fc',1,'xg::XG']]],
- ['pn_5fiv_4623',['pn_iv',['../classxg_1_1XG.html#aa9d0f9dc89210720c781d43b54f10e4b',1,'xg::XG']]],
- ['pointer_4624',['pointer',['../classvg_1_1count__back__inserter.html#ab120548e9cd73fcc1ed1f8680b4b5baa',1,'vg::count_back_inserter::pointer()'],['../structvg_1_1VectorView_1_1const__iterator.html#a8b8e23d22e4b85f617c466337d5f0ea2',1,'vg::VectorView::const_iterator::pointer()'],['../classvg_1_1SmallBitset.html#a7c4623fa954362f27858d7714acf38cf',1,'vg::SmallBitset::pointer()']]],
- ['pointerfy_4625',['pointerfy',['../namespacevg.html#ae6a210206858f806b345f8eb5c2c292a',1,'vg']]],
- ['points_4626',['points',['../classvg_1_1algorithms_1_1Anchor.html#a92c0db96b472fce0a3f130cdf281999d',1,'vg::algorithms::Anchor']]],
- ['points_5fper_5fpossible_5fmatch_4627',['points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a4cb0f074432b4ab94eecd529bc18a6c2',1,'vg::MinimizerMapper']]],
- ['poisson_5fprob_5fln_4628',['poisson_prob_ln',['../namespacevg.html#a9238b15cc78a87f27c335fc1e3627a62',1,'vg']]],
- ['poissoncallinfo_4629',['PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html',1,'vg::PoissonSupportSnarlCaller']]],
- ['poissonsupportsnarlcaller_4630',['PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html',1,'vg::PoissonSupportSnarlCaller'],['../classvg_1_1PoissonSupportSnarlCaller.html#aebde111c1431bf4af46929d8e56c7031',1,'vg::PoissonSupportSnarlCaller::PoissonSupportSnarlCaller()']]],
- ['polyploid_5fprior_5fsuccess_5flogprob_4631',['polyploid_prior_success_logprob',['../classvg_1_1Genotyper.html#a97aef0fe84f0514e17e2ec8e00162225',1,'vg::Genotyper']]],
- ['pop_4632',['pop',['../structvg_1_1MatchPos_1_1PathList.html#a6fa2799b0d2b17e437a6c7a92ef75a4d',1,'vg::MatchPos::PathList::pop()'],['../structvg_1_1MatchPos.html#a0bf4234ad56f10dd4d602102bfaf2297',1,'vg::MatchPos::pop()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3a64ce2b4dfae9f7712598d8d6b676a6',1,'vg::ZipCodeTree::reverse_iterator::pop()']]],
- ['pop_5fback_5fstep_4633',['pop_back_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a2db5e7a66ccee26fa257c50e0d084c59',1,'handlegraph::MutablePathHandleGraph']]],
- ['pop_5ffront_5fstep_4634',['pop_front_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a67c8bfd58c5ed8136c9324f427037a7a',1,'handlegraph::MutablePathHandleGraph']]],
- ['populate_5fpath_5ffrom_5ftraceback_4635',['populate_path_from_traceback',['../namespacevg.html#a191bf7b238ea717afbf8118df0afa999',1,'vg']]],
- ['populate_5fsnarl_5findex_4636',['populate_snarl_index',['../namespacevg.html#a7c9f1f64df265187309db52705a1bef7',1,'vg']]],
- ['population_5fmax_5fpaths_4637',['population_max_paths',['../classvg_1_1MultipathMapper.html#adfb100b024b23e3e94a31ea41d0b1ac8',1,'vg::MultipathMapper']]],
- ['population_5fpaths_5fhard_5fcap_4638',['population_paths_hard_cap',['../classvg_1_1MultipathMapper.html#aa9d339059fb2f60d192935126c82dbed',1,'vg::MultipathMapper']]],
- ['population_5fsize_4639',['population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#adbcb32fa9395d32959b7c0006f25855c',1,'haplo::haploMath::RRMemo']]],
- ['pos_4640',['pos',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#af6b3dfbfadf9eb6f64672bf7a2cfb9f6',1,'vg::SnarlDistanceIndexClusterer::Seed::pos()'],['../structvg_1_1ChainIterator.html#ae99bd64d13edc9f317cfd3bd9e9d3d2e',1,'vg::ChainIterator::pos()'],['../structvg_1_1KmerPosition.html#a31de02880d6006049d740e6216087961',1,'vg::KmerPosition::pos()'],['../structvg_1_1WFAPoint.html#a4ea055d164ce5425235ec19d65a7073f',1,'vg::WFAPoint::pos()']]],
- ['pos_5fat_4641',['pos_at',['../structMappingRun.html#ac8d70e01cbc733abc3612693b39a465c',1,'MappingRun']]],
- ['pos_5fchar_4642',['pos_char',['../classvg_1_1Sampler.html#a72d922b802775f51f2b02046398d3417',1,'vg::Sampler::pos_char()'],['../classxg_1_1XG.html#abf551ac03c1db6030da1cedb81efc779',1,'xg::XG::pos_char()']]],
- ['pos_5fkey_4643',['pos_key',['../classvg_1_1Packer.html#a128c9b21b9a784c6ea27501463b23862',1,'vg::Packer']]],
- ['pos_5fsubstr_4644',['pos_substr',['../classxg_1_1XG.html#aa61897c26d2cee1e8cc8c9fc7eec540b',1,'xg::XG']]],
- ['pos_5ft_4645',['pos_t',['../namespacevg.html#a8232142f432c4dd8e7cfe96e1f50e039',1,'vg::pos_t()'],['../namespacexg.html#aa22555920305243ff489dc6ed79db5d7',1,'xg::pos_t()'],['../namespacehandlegraph.html#a0abc3c64da852112ad2bc0fc9dd5afce',1,'handlegraph::pos_t()']]],
- ['pos_5fto_5fedit_5fto_5fdepth_4646',['pos_to_edit_to_depth',['../classvg_1_1Filter.html#a4de4cfcd2bafcc9405c0ffebe84b61dd',1,'vg::Filter']]],
- ['pos_5fto_5fgbwt_4647',['pos_to_gbwt',['../namespacevg.html#ae1296fd4e352a120122d4be0a0007819',1,'vg']]],
- ['pos_5fto_5fqual_4648',['pos_to_qual',['../classvg_1_1Filter.html#a619f209f11dd2e9b9ce72db535d402fe',1,'vg::Filter']]],
- ['pos_5fto_5ftrans_4649',['pos_to_trans',['../classvg_1_1Translator.html#ae41a08cff51e5f56aff61136b4c520f0',1,'vg::Translator']]],
- ['position_4650',['Position',['../structvg_1_1Position.html',1,'vg::Position'],['../structvg_1_1BREAKPOINT.html#a082deeca85819680dc38ceddf6ccbce7',1,'vg::BREAKPOINT::position()'],['../structvg_1_1RecombinatorHaplotype.html#abedb3835774104b4664b62acd3bea6b6',1,'vg::RecombinatorHaplotype::position()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#ae3a3d3091779285687ae5be43ee61652',1,'vg::algorithms::GFAFormatError::position()'],['../structvg_1_1Mapping.html#a2017c8c72a90df9044e14422a0799c86',1,'vg::Mapping::position()'],['../structvg_1_1KmerMatch.html#af0853c79fa538e1d94090514fd217feb',1,'vg::KmerMatch::position()'],['../classvg_1_1Funnel.html#adee7882f4f431a866847baec1fc77718',1,'vg::Funnel::position()'],['../classvg_1_1path__mapping__t.html#a64f6d0dd6e7ffd6bf6d538c5a25d39f3',1,'vg::path_mapping_t::position()'],['../classvg_1_1Sampler.html#a3d983fa5e24b8802ed2516bf0bb362bf',1,'vg::Sampler::position()']]],
- ['position_2ecpp_4651',['position.cpp',['../position_8cpp.html',1,'']]],
- ['position_2ehpp_4652',['position.hpp',['../position_8hpp.html',1,'']]],
- ['position_5fassuming_5facyclic_4653',['position_assuming_acyclic',['../structhaplo_1_1linear__haplo__structure.html#aa450a108f8b2bab6e98271fcef6b26aa',1,'haplo::linear_haplo_structure']]],
- ['position_5fat_4654',['position_at',['../namespacevg.html#a9a33db744c41ff651da5dacda9578712',1,'vg']]],
- ['position_5ffile_4655',['position_file',['../classvg_1_1NGSSimulator.html#a46a332d871425d98495b0b1215ad88e5',1,'vg::NGSSimulator']]],
- ['position_5fin_5fbasis_4656',['position_in_basis',['../classvg_1_1Packer.html#a6cb79c18881c68ac41b9f2ffa002ef02',1,'vg::Packer']]],
- ['position_5fin_5fpath_4657',['position_in_path',['../classxg_1_1XG.html#a870b3eae5f72331f2c498043b45b3d8d',1,'xg::XG']]],
- ['position_5fin_5fpaths_4658',['position_in_paths',['../classxg_1_1XG.html#a1bda47534cd275fdeca72b463303dc1e',1,'xg::XG']]],
- ['position_5ft_4659',['position_t',['../classvg_1_1position__t.html',1,'vg::position_t'],['../classvg_1_1position__t.html#a34def1328db6dda2482ccb6c64951704',1,'vg::position_t::position_t()'],['../classvg_1_1position__t.html#a47188716e3327201048ba032c10eb8fe',1,'vg::position_t::position_t(const position_t &other)=default'],['../classvg_1_1position__t.html#a1ad8e0a1fe655c7ebb31ff094e43f466',1,'vg::position_t::position_t(position_t &&other)=default']]],
- ['positionidscanner_4660',['PositionIDScanner',['../structvg_1_1PositionIDScanner.html',1,'vg']]],
- ['positions_4661',['positions',['../classvg_1_1MEMChainModel.html#ab273ba5c21fc25422f873dd5d4fd37c3',1,'vg::MEMChainModel::positions()'],['../classvg_1_1AlignmentChainModelVertex.html#a5b770fe52ded0e65dbfe6af4865a7d58',1,'vg::AlignmentChainModelVertex::positions()'],['../classvg_1_1AlignmentChainModel.html#ac37666966f063162a7bbcbb0b285ce6b',1,'vg::AlignmentChainModel::positions()'],['../classvg_1_1MaximalExactMatch.html#afd57ff44231f95d0ea6ef6d4ba24608e',1,'vg::MaximalExactMatch::positions()']]],
- ['possible_5fscores_4662',['possible_scores',['../classvg_1_1WFATree.html#a4646d73afa5c111f920ab006664c4e7b',1,'vg::WFATree']]],
- ['posterior_4663',['posterior',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#aae17dc073a03b6fc72eef3b281608b68',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['pow_5fln_4664',['pow_ln',['../namespacevg.html#a3a7a8c98d80a9daacbc72386bc6ad00c',1,'vg']]],
- ['precollapse_5forder_5flength_5fhits_4665',['precollapse_order_length_hits',['../classvg_1_1BaseMapper.html#aaf81156cb8c76c2e961b767a782dda59',1,'vg::BaseMapper']]],
- ['precollapse_5forder_5flength_5fruns_4666',['precollapse_order_length_runs',['../classvg_1_1BaseMapper.html#af4372862ebd4f21da3e9ed105249a5af',1,'vg::BaseMapper']]],
- ['predecessor_5foffset_4667',['predecessor_offset',['../classvg_1_1WFATree.html#a5caa4118319b9fa8e5cc87f257c31225',1,'vg::WFATree']]],
- ['prefilter_5fredundant_5fhits_4668',['prefilter_redundant_hits',['../classvg_1_1BaseMapper.html#afa408c8d202885a288f14ff6e2dc60e0',1,'vg::BaseMapper']]],
- ['prefilter_5fredundant_5fsub_5fmems_4669',['prefilter_redundant_sub_mems',['../classvg_1_1BaseMapper.html#ae3103b73da0ef6137ad1d1bd16e35d56',1,'vg::BaseMapper']]],
- ['prefix_4670',['prefix',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdead1db5c374c93da6cefc39869d1704f18',1,'vg::Haplotypes::Subchain::prefix()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#ae400b0d9c4fecf6b90fd0d708258df1e',1,'vg::BitStringTree::TreeNode::prefix()'],['../structvg_1_1GaplessExtension.html#af975b0dd4c3aab5d89093d9725372017',1,'vg::GaplessExtension::prefix()'],['../classvg_1_1WFAExtender.html#a5be8ff4d5922082dedf5e15665536be8',1,'vg::WFAExtender::prefix()'],['../structvg_1_1RecombinatorHaplotype.html#ad2a0e140251ae5dd203144bcbf49aab3',1,'vg::RecombinatorHaplotype::prefix()']]],
- ['prefix_5flength_4671',['prefix_length',['../structvg_1_1MultipathProblem.html#a5fdfec89c00fe647e234e84fa72879ed',1,'vg::MultipathProblem']]],
- ['prefix_5fscore_4672',['prefix_score',['../structvg_1_1MultipathProblem.html#a5e3610b3438d69baba7e3be6a6cfdcc0',1,'vg::MultipathProblem']]],
- ['prefix_5fsum_4673',['prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ac09ee425b8f2f95a4c8c4f45b39084b9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild::prefix_sum()'],['../structvg_1_1MIPayload.html#af0dcb83df9249928d947e23f368f41a0',1,'vg::MIPayload::prefix_sum()']]],
- ['prefix_5fsum_5for_5fidentifier_4674',['prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#aadf1912938760b4371b385865fa661f9',1,'vg::ZipCode::node_code_t::prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a736b6676259bc262d66d9814fbbb7142',1,'vg::ZipCode::snarl_code_t::prefix_sum_or_identifier()']]],
- ['prefix_5fsum_5fvalue_4675',['prefix_sum_value',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a09ed2f3574eb36ceccf98ded8c99e7f5',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['prefixes_4676',['prefixes',['../classvg_1_1PhaseUnfolder.html#a64f18b1c10e5d2104bd04df2013f5a0f',1,'vg::PhaseUnfolder']]],
- ['preflight_2ecpp_4677',['preflight.cpp',['../preflight_8cpp.html',1,'']]],
- ['preflight_2ehpp_4678',['preflight.hpp',['../preflight_8hpp.html',1,'']]],
- ['preflight_5fcheck_4679',['preflight_check',['../namespacevg.html#a65ac31e5878660a97207b6ade1418c81',1,'vg']]],
- ['preload_5fprogress_4680',['preload_progress',['../classvg_1_1Progressive.html#a4eb5050eb36ed519cbfa398748ef183b',1,'vg::Progressive']]],
- ['prepend_5fmapping_4681',['prepend_mapping',['../classvg_1_1Paths.html#acd1f02b9d6d41036a24a9aee1a261dc3',1,'vg::Paths::prepend_mapping(const string &name, const Mapping &m, bool warn_on_duplicates=false)'],['../classvg_1_1Paths.html#ab5679411e308c578583066e020dc4d4f',1,'vg::Paths::prepend_mapping(const string &name, id_t id, bool is_reverse, size_t length, size_t rank=0, bool warn_on_duplicates=false)']]],
- ['prepend_5fstep_4682',['prepend_step',['../classvg_1_1VG.html#a43c2858dc8e80ba160359ccf5e1508d2',1,'vg::VG::prepend_step()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#aed17038a0104017d37ff74e15f7f436a',1,'handlegraph::MutablePathHandleGraph::prepend_step()']]],
- ['preprocess_5fgraph_4683',['preprocess_graph',['../haplotypes__main_8cpp.html#abbe87c8ead89e4916934c55ee923b0c1',1,'haplotypes_main.cpp']]],
- ['present_4684',['present',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa24ced965e66bc34d849a25192e59fbdf',1,'vg::Recombinator::present()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a130ad1d08da8cb8ff5be5f254b904369',1,'vg::SnarlDistanceIndexClusterer::Cluster::present()']]],
- ['present_5fdiscount_4685',['PRESENT_DISCOUNT',['../classvg_1_1Recombinator.html#a5c415fe934bb25c07068a2ca0291ea00',1,'vg::Recombinator::PRESENT_DISCOUNT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a5f62e8ec5640f3d4d06bbda709b44bdc',1,'vg::Recombinator::Parameters::present_discount()']]],
- ['present_5fkmers_4686',['present_kmers',['../namespacevg.html#acc85734af557e4a1047554706a9b4580',1,'vg']]],
- ['present_5fsymbols_4687',['present_symbols',['../namespacevg.html#ace6690ca3c2bc1ce18c66801e500dce5',1,'vg']]],
- ['preserve_5fsinks_4688',['preserve_sinks',['../classvg_1_1DozeuPinningOverlay.html#a066fa04f3bf59c7302a0e57036154ab7',1,'vg::DozeuPinningOverlay']]],
- ['preset_4689',['Preset',['../structvg_1_1subcommand_1_1Preset.html',1,'vg::subcommand::Preset'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a7346ca8a4f692c5a10e0df88bc6c915d',1,'vg::subcommand::BaseArgSpec::preset()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a9e5bd3a2b4884185bc07417893cf476c',1,'vg::subcommand::ArgSpec::preset()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aac88ac0803a38344b6c87057bdfb9327',1,'vg::subcommand::BaseOptionGroup::preset()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a421492b900071c23ae1250b4882ffe52',1,'vg::subcommand::OptionGroup::preset()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a2ab60146762bd02d7ec5b1e870998021',1,'vg::subcommand::GroupedOptionGroup::preset()']]],
- ['preset_5fdefault_4690',['preset_default',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a7b22070ac7d633aa776868df9225baa9',1,'vg::Recombinator::Parameters']]],
- ['preset_5fdiploid_4691',['preset_diploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a645ffd73f63c0f007f249345c81d4f8a',1,'vg::Recombinator::Parameters']]],
- ['preset_5fhaploid_4692',['preset_haploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a115a5b3be57084265c380192cabde366',1,'vg::Recombinator::Parameters']]],
- ['preset_5ft_4693',['preset_t',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4',1,'vg::Recombinator::Parameters']]],
- ['prev_4694',['prev',['../classvg_1_1MEMChainModelVertex.html#a8b3867d0ba2a4797202be745d92d11de',1,'vg::MEMChainModelVertex::prev()'],['../classvg_1_1AlignmentChainModelVertex.html#a9979808dd8d6ddaf11d83643ab3e9db2',1,'vg::AlignmentChainModelVertex::prev()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#aea823a7f3329d308107c1de1cf20c1a6',1,'vg::PhasedGenome::HaplotypeNode::prev()']]],
- ['prev_5fchar_4695',['prev_char',['../structvg_1_1kmer__t.html#a006cf626b837e21d26b66925103a34c5',1,'vg::kmer_t']]],
- ['prev_5fchars_4696',['prev_chars',['../structvg_1_1KmerPosition.html#a6c6e2b384e3f9292342999e6f49684c3',1,'vg::KmerPosition']]],
- ['prev_5fcost_4697',['prev_cost',['../classvg_1_1MEMChainModelVertex.html#ad8ad4b22339e6ad06c893c78c63cda5a',1,'vg::MEMChainModelVertex::prev_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#a0dcdae4513868599a6bd50e719f9e4f5',1,'vg::AlignmentChainModelVertex::prev_cost()']]],
- ['prev_5fidx_4698',['prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#a6e44d4112d111f6b5796bfbd63b7e24d',1,'haplo::haplo_DP_rectangle']]],
- ['prev_5fpos_4699',['prev_pos',['../structvg_1_1kmer__t.html#acf511fd3c535a5d9e2109480ed1528e8',1,'vg::kmer_t']]],
- ['prev_5fsnarl_4700',['prev_snarl',['../classvg_1_1SnarlManager.html#af49cb83d06b303717c94da67974fb0d6',1,'vg::SnarlManager']]],
- ['prev_5fstage_5fitems_4701',['prev_stage_items',['../structvg_1_1Funnel_1_1Item.html#a9ee7530fac67298fbcdb27f8280b4a14',1,'vg::Funnel::Item']]],
- ['prev_5fsubpath_4702',['prev_subpath',['../structvg_1_1MultipathProblem.html#a51f2e682e6721f35d88cae8d1cf4a59d',1,'vg::MultipathProblem']]],
- ['previous_5findex_4703',['previous_index',['../structhaplo_1_1haplo__DP__rectangle.html#addd510174b8c5f83418aa6c23e278b36',1,'haplo::haplo_DP_rectangle']]],
- ['previous_5fr_4704',['previous_R',['../structhaplo_1_1haplo__DP__column.html#a0bcd7266aea2d97a6b234779739e7628',1,'haplo::haplo_DP_column']]],
- ['previous_5fsizes_4705',['previous_sizes',['../structhaplo_1_1haplo__DP__column.html#a2ece2d4c8c54fbd7fc8e898ced985e6a',1,'haplo::haplo_DP_column']]],
- ['previous_5fsum_4706',['previous_sum',['../structhaplo_1_1haplo__DP__column.html#a474364179d091eda8dd0684d4d86afa8',1,'haplo::haplo_DP_column']]],
- ['previous_5ftag_4707',['previous_tag',['../classvg_1_1io_1_1MessageIterator.html#affc663d4448fe1b213d1c2e9ec64b3bb',1,'vg::io::MessageIterator']]],
- ['previous_5fvalues_4708',['previous_values',['../structhaplo_1_1haplo__DP__column.html#a5e1664796c443719bd4e775f503ab8ad',1,'haplo::haplo_DP_column']]],
- ['primary_4709',['primary',['../classvg_1_1MaximalExactMatch.html#a2e34dcded590361daf8ca3a9ed3fb62f',1,'vg::MaximalExactMatch']]],
- ['primitive_5froot_4710',['primitive_root',['../classvg_1_1ShuffledPairs.html#a78c948366b8eec98b8393ae2ac75f86a',1,'vg::ShuffledPairs']]],
- ['print_4711',['print',['../structvg_1_1WFAAlignment.html#a455ada9f59d934bd167217583b2fbd92',1,'vg::WFAAlignment::print(const HandleGraph &graph, std::ostream &out) const'],['../structvg_1_1WFAAlignment.html#a37156be6786114a37da73499f8fe49da',1,'vg::WFAAlignment::print(std::ostream &out) const'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae35f9e4427c8c9da2dbef05000158990',1,'haplo::hDP_gbwt_graph_accessor::print()'],['../structhaplo_1_1haplo__DP__column.html#a8bdb3ddfa07590bf2d50f96bd43c096b',1,'haplo::haplo_DP_column::print()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a3f04e2d77070771ba779ebaf06f0d3ff',1,'vg::HaplotypePartitioner::Parameters::print()'],['../structvg_1_1Recombinator_1_1Statistics.html#a8cc215e629110af71f6d35da557eb0e8',1,'vg::Recombinator::Statistics::print()'],['../structvg_1_1Recombinator_1_1Parameters.html#aa00e847f40210d77acbd1432f6b485ea',1,'vg::Recombinator::Parameters::print()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a5b19dc7b348fc8a8b9b9120ae032559f',1,'vg::subcommand::BaseArgSpec::print()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#aecec3a3bb1a3d2e0e3d75a080d0206eb',1,'vg::subcommand::FlagArgSpec::print()']]],
- ['print_5fband_4712',['print_band',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac248371cbaae3b95340035f88de09e0a',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5fdefault_4713',['print_default',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a489497d47ddf82df3339a4e487274144',1,'vg::subcommand::BaseArgSpec::print_default()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a06e81f25a63218e0cba32ecd6320f9b2',1,'vg::subcommand::ValueArgSpec::print_default()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a85b5c5993e124831c65dd9e31b74aec7',1,'vg::subcommand::FlagArgSpec::print_default()']]],
- ['print_5fdefaults_4714',['print_defaults',['../prune__main_8cpp.html#a01acca05639635d047176302793da18d',1,'prune_main.cpp']]],
- ['print_5fedges_4715',['print_edges',['../classvg_1_1VG.html#a2b659686076f3d6b7b63ec9678d76a93',1,'vg::VG']]],
- ['print_5ffull_5fmatrices_4716',['print_full_matrices',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a521dac0777a22cd632a45ad72f320810',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5fgraph_4717',['print_graph',['../classxg_1_1XG.html#acb2f541cd3f91783d07532d75da80b0a',1,'xg::XG']]],
- ['print_5fhelp_4718',['print_help',['../classvg_1_1ConfigurableParser.html#a29abcf4fbb780c4e586130b095aa0098',1,'vg::ConfigurableParser']]],
- ['print_5fmatrix_4719',['print_matrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#aee399b25f2ed671ad8a17e6c55757671',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5fmetadata_4720',['print_metadata',['../gbwt__main_8cpp.html#af705c69cda26007b3ea9bb76849e21b1',1,'gbwt_main.cpp']]],
- ['print_5fmetavar_4721',['print_metavar',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a8f418067cef90e2290b3a67b8fd17b74',1,'vg::subcommand::BaseArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a4bf9aeb97acee678dfbd3d5c997e28c3',1,'vg::subcommand::ValueArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a9fcf875d6e0a843cb90af9cfe7e9e3a3',1,'vg::subcommand::FlagArgSpec::print_metavar()']]],
- ['print_5foptions_4722',['print_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad3063622c78d2a03519fcbc077c4cdcc',1,'vg::subcommand::BaseOptionGroup::print_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a99c032d391c4dd8f2936f4280e6dde77',1,'vg::subcommand::OptionGroup::print_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aaf906b5e74e2a072cd1f6a90ca685381',1,'vg::subcommand::GroupedOptionGroup::print_options()']]],
- ['print_5fphased_5fgenome_4723',['print_phased_genome',['../classvg_1_1PhasedGenome.html#a4727557def28b369312b2f4a56d86a7d',1,'vg::PhasedGenome']]],
- ['print_5frectangularized_5fbands_4724',['print_rectangularized_bands',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a6c94c4cb68bf76d3b8531f004c17b26d',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5freport_4725',['print_report',['../classvg_1_1IndexedVG.html#a08b7d5f9e8ad7c9b42d58ce8d2629000',1,'vg::IndexedVG']]],
- ['print_5fself_4726',['print_self',['../structvg_1_1varint__vector__t.html#a93a071296fab5dc6fabb363bf3cb66e5',1,'vg::varint_vector_t::print_self()'],['../classvg_1_1ZipCodeTree.html#afe8400e287661b3a9525d99da5329770',1,'vg::ZipCodeTree::print_self()'],['../classvg_1_1ZipCodeForest.html#a4cabd6faae5283f02bfe5397a17908fa',1,'vg::ZipCodeForest::print_self()']]],
- ['print_5fsnarl_4727',['print_snarl',['../classvg_1_1VCFOutputCaller.html#acd9942cb6cd9427e38c868efb23d8bda',1,'vg::VCFOutputCaller::print_snarl(const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) const'],['../classvg_1_1VCFOutputCaller.html#a3b9cfe228287ac605825ed4b0c8ea990',1,'vg::VCFOutputCaller::print_snarl(const Snarl &snarl, bool in_brackets=false) const']]],
- ['print_5fstatistics_4728',['print_statistics',['../classvg_1_1Genotyper.html#aadb967b3ab9daa067f8451c29fda0a5e',1,'vg::Genotyper']]],
- ['print_5ftable_4729',['print_table',['../namespacevg_1_1subcommand.html#a44e82d81de605a19980ffc9045984b3c',1,'vg::subcommand']]],
- ['print_5fupdates_4730',['print_updates',['../classvg_1_1VariantAdder.html#af52ce72b2446132042df93857eb12b63',1,'vg::VariantAdder']]],
- ['print_5fvalue_4731',['print_value',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a9a3e4636afe2471cc64ef92c35038733',1,'vg::subcommand::BaseArgSpec::print_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#ab47272ea8d46fdb7c1cf5ff206ff91b1',1,'vg::subcommand::ValueArgSpec::print_value()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ae81ab9ea31e2e812037c732c5e3961cc',1,'vg::subcommand::FlagArgSpec::print_value()']]],
- ['printalignment_4732',['PrintAlignment',['../classvg_1_1SSWAligner.html#ac52ca46f4e194c324fdd67093c54db01',1,'vg::SSWAligner']]],
- ['printid_4733',['printId',['../namespacevg.html#a8bf8f408b11966feb9695d4bb723dfac',1,'vg']]],
- ['priority_4734',['priority',['../classvg_1_1subcommand_1_1Subcommand.html#a3f995aec9b4e2367530e1a6bcccb2e53',1,'vg::subcommand::Subcommand']]],
- ['prng_4735',['prng',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ac95b66a8f2e2cda6bc2d45691d496f5e',1,'vg::NGSSimulator::MarkovDistribution::prng()'],['../classvg_1_1NGSSimulator.html#a8550502fd97de9b154d3df837c036859',1,'vg::NGSSimulator::prng()']]],
- ['prngs_4736',['prngs',['../classvg_1_1NGSSimulator.html#ab5d12a331a39e82fc07202152f254d70',1,'vg::NGSSimulator']]],
- ['prob_5ffor_5fat_5fleast_5fone_4737',['prob_for_at_least_one',['../namespacevg.html#ae46397f9d9aa9ac06a48b4ff30da7087',1,'vg']]],
- ['prob_5fsampler_4738',['prob_sampler',['../classvg_1_1NGSSimulator.html#a36ca291ed15a9a3942809d21d0574bc1',1,'vg::NGSSimulator']]],
- ['prob_5fto_5flogprob_4739',['prob_to_logprob',['../namespacevg.html#a476a2102f4f5aa82c06be87780ae6d42',1,'vg']]],
- ['prob_5fto_5fphred_4740',['prob_to_phred',['../namespacevg.html#acb81881c0a3b7cf276097d8142ddb312',1,'vg']]],
- ['problem_4741',['Problem',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9',1,'vg::AlignmentValidity::Problem()'],['../structvg_1_1AlignmentValidity.html#a1ca7f243aa52fe313bdfac808f4eba92',1,'vg::AlignmentValidity::problem()']]],
- ['problemdumpexplainer_4742',['ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html',1,'vg::ProblemDumpExplainer'],['../classvg_1_1ProblemDumpExplainer.html#adf8775736c7646ce19bd69c995bf7238',1,'vg::ProblemDumpExplainer::ProblemDumpExplainer()']]],
- ['process_5fin_5fout_5fgrowth_4743',['process_in_out_growth',['../classvg_1_1FlowSort.html#a31800555477d90ab371c08852c9cd05b',1,'vg::FlowSort']]],
- ['process_5funtil_5fthreshold_5fa_4744',['process_until_threshold_a',['../classvg_1_1MinimizerMapper.html#ae74362b0c750fb802b8c7a38c57c8823',1,'vg::MinimizerMapper']]],
- ['process_5funtil_5fthreshold_5fb_4745',['process_until_threshold_b',['../classvg_1_1MinimizerMapper.html#a121f1d7ca1b0cd5721b7c341d227fec8',1,'vg::MinimizerMapper']]],
- ['process_5funtil_5fthreshold_5fc_4746',['process_until_threshold_c',['../classvg_1_1MinimizerMapper.html#af1a420ad7240014c67269a6d7437bef6',1,'vg::MinimizerMapper']]],
- ['processed_5finput_4747',['processed_input',['../classvg_1_1Funnel.html#a94e07fb24eee3bb9284a1ba8945b010a',1,'vg::Funnel']]],
- ['processing_5finput_4748',['processing_input',['../classvg_1_1Funnel.html#a3c21502db704cde878d989f3cc75e91c',1,'vg::Funnel']]],
- ['produced_5foutput_4749',['produced_output',['../classvg_1_1Funnel.html#ae9dec7f539cf37d822328a71e376783a',1,'vg::Funnel']]],
- ['produces_5fone_5fgbwt_4750',['produces_one_gbwt',['../structGBWTConfig.html#ad752e9efebcc424e596e1c328a9eb583',1,'GBWTConfig']]],
- ['producing_5foutput_4751',['producing_output',['../classvg_1_1Funnel.html#a919aae2ef8cf780bcaba00b1ea1603b8',1,'vg::Funnel']]],
- ['progress_4752',['progress',['../classvg_1_1Progressive.html#af78e64e28b252828a0ba86439125fea4',1,'vg::Progressive']]],
- ['progress_5fbars_4753',['progress_bars',['../classvg_1_1VGset.html#acc491d0a5c0a54c6bbd0636fa44431b7',1,'vg::VGset']]],
- ['progress_5fcount_4754',['progress_count',['../classvg_1_1Progressive.html#a71e61fe99d71d23542d2d7387c23fd4d',1,'vg::Progressive']]],
- ['progress_5fmessage_4755',['progress_message',['../classvg_1_1Progressive.html#a4bb04fe23ceb41467dd14cdf8cc01a71',1,'vg::Progressive']]],
- ['progress_5fseen_4756',['progress_seen',['../classvg_1_1Progressive.html#ac6745d7e07b4b271f9510cd40f06d18e',1,'vg::Progressive']]],
- ['progressive_4757',['Progressive',['../classvg_1_1Progressive.html',1,'vg']]],
- ['progressive_2ecpp_4758',['progressive.cpp',['../progressive_8cpp.html',1,'']]],
- ['progressive_2ehpp_4759',['progressive.hpp',['../progressive_8hpp.html',1,'']]],
- ['project_4760',['project',['../classvg_1_1Funnel.html#a2b9e7695a998b23314c25f7fe3de4701',1,'vg::Funnel']]],
- ['project_5fgroup_4761',['project_group',['../classvg_1_1Funnel.html#a321b1e593102927ff8677214abce5592',1,'vg::Funnel']]],
- ['project_5fhaplotype_5ftranscripts_4762',['project_haplotype_transcripts',['../classvg_1_1Transcriptome.html#acaa534fdaa3f3926d7959255ab2f6feb',1,'vg::Transcriptome']]],
- ['project_5fhaplotype_5ftranscripts_5fcallback_4763',['project_haplotype_transcripts_callback',['../classvg_1_1Transcriptome.html#ae9f0bd481ee467f32d88be2b20c110c7',1,'vg::Transcriptome']]],
- ['project_5ftranscript_5fembedded_4764',['project_transcript_embedded',['../classvg_1_1Transcriptome.html#a8e9f42b9d9f57b675856c7f766d3c710',1,'vg::Transcriptome']]],
- ['project_5ftranscript_5fgbwt_4765',['project_transcript_gbwt',['../classvg_1_1Transcriptome.html#a4edf6085f024b736bef4be82c6fd854a',1,'vg::Transcriptome']]],
- ['projected_5fcount_4766',['projected_count',['../structvg_1_1Funnel_1_1Stage.html#a74c290d50af94a82c196350d3ee7223d',1,'vg::Funnel::Stage']]],
- ['proper_5fpair_4767',['proper_pair',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a92eba6d5ad7d830d3824261542991875',1,'vg::Counts']]],
- ['proposal_5fsample_4768',['proposal_sample',['../classvg_1_1MCMCGenotyper.html#a0e007a331bc2854ec8734557bd80962d',1,'vg::MCMCGenotyper']]],
- ['propose_5fdeflection_4769',['propose_deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a662b5ce1fa402a6c8e7a5f20f92773b3',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['proto_4770',['proto',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a05cf3104e11f544431c6ed6e709d2361',1,'vg::io::VGAlignmentEmitter::proto()'],['../vg_8proto.html#ace9afe7f815b63b3d93844da5eb8fbbc',1,'proto(): vg.proto']]],
- ['protobuf_5femitter_2ehpp_4771',['protobuf_emitter.hpp',['../protobuf__emitter_8hpp.html',1,'']]],
- ['protobuf_5fiterator_2ehpp_4772',['protobuf_iterator.hpp',['../protobuf__iterator_8hpp.html',1,'']]],
- ['protobuf_5fto_5ftag_4773',['protobuf_to_tag',['../structvg_1_1io_1_1Registry_1_1Tables.html#a9959a1192210db895c2d127dc6a197fc',1,'vg::io::Registry::Tables']]],
- ['protobufemitter_4774',['ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html',1,'vg::io::ProtobufEmitter< T >'],['../classvg_1_1io_1_1ProtobufEmitter.html#ab9d133fa3604ba677c12337ccf609ba7',1,'vg::io::ProtobufEmitter::ProtobufEmitter(std::ostream &out, bool compress=true, size_t max_group_size=1000)'],['../classvg_1_1io_1_1ProtobufEmitter.html#a1adf66f9c9242369dcdd38746f925855',1,'vg::io::ProtobufEmitter::ProtobufEmitter(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#accd8d7c57bffcfdc48ba7085f7a53561',1,'vg::io::ProtobufEmitter::ProtobufEmitter(ProtobufEmitter &&other)=default']]],
- ['protobufiterator_4775',['ProtobufIterator',['../classvg_1_1io_1_1ProtobufIterator.html',1,'vg::io::ProtobufIterator< T >'],['../classvg_1_1io_1_1ProtobufIterator.html#a0f2996a9653a98470e7c944879a69d70',1,'vg::io::ProtobufIterator::ProtobufIterator(istream &in)'],['../classvg_1_1io_1_1ProtobufIterator.html#a50ad0e8d7ee212617dbf9e456ea43e07',1,'vg::io::ProtobufIterator::ProtobufIterator()=default']]],
- ['provide_4776',['provide',['../classvg_1_1IndexRegistry.html#a72c4f8ea143cd9a982366234a8eed71e',1,'vg::IndexRegistry::provide(const IndexName &identifier, const string &filename)'],['../classvg_1_1IndexRegistry.html#a430536c995544af29060b78d04e3f5c1',1,'vg::IndexRegistry::provide(const IndexName &identifier, const vector< string > &filenames)'],['../classvg_1_1IndexFile.html#a116a29bacf28f3889ea318ac25a11dc7',1,'vg::IndexFile::provide()']]],
- ['provided_5fdirectly_4777',['provided_directly',['../classvg_1_1IndexFile.html#a32bf1b5189843cdcc3ba7eb6068dd46f',1,'vg::IndexFile']]],
- ['prune_2ecpp_4778',['prune.cpp',['../prune_8cpp.html',1,'']]],
- ['prune_2ehpp_4779',['prune.hpp',['../prune_8hpp.html',1,'']]],
- ['prune_5fand_5ftrim_5fanchors_4780',['prune_and_trim_anchors',['../classvg_1_1Surjector.html#ae34c7f96fff02c5490477fc8ad643908',1,'vg::Surjector']]],
- ['prune_5fcomplex_4781',['prune_complex',['../namespacevg_1_1algorithms.html#a09b6e838b2991d13e272ddcb41aacfbc',1,'vg::algorithms']]],
- ['prune_5fcomplex_5fwith_5fhead_5ftail_4782',['prune_complex_with_head_tail',['../namespacevg_1_1algorithms.html#a784ee29876a24431a865541426f42dee',1,'vg::algorithms']]],
- ['prune_5fhigh_5fshift_5fedges_4783',['prune_high_shift_edges',['../classvg_1_1MultipathAlignmentGraph.html#aa42ef4313d4d24ab4c19532e2bd30652',1,'vg::MultipathAlignmentGraph']]],
- ['prune_5flow_5fscoring_5fedges_4784',['prune_low_scoring_edges',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab2949f31f3e43410189eafa260544baf',1,'vg::MEMClusterer::HitGraph']]],
- ['prune_5fmain_2ecpp_4785',['prune_main.cpp',['../prune__main_8cpp.html',1,'']]],
- ['prune_5fshort_5fsubgraphs_4786',['prune_short_subgraphs',['../namespacevg_1_1algorithms.html#a83e87cf3f8a5ca4362776cf1a3050242',1,'vg::algorithms']]],
- ['prune_5fsubpaths_5fmultiplier_4787',['prune_subpaths_multiplier',['../classvg_1_1MultipathMapper.html#aa8409bc363c70b9df0c3590767d25e92',1,'vg::MultipathMapper']]],
- ['prune_5fsuspicious_5fanchors_4788',['prune_suspicious_anchors',['../classvg_1_1Surjector.html#af01db9677cefc7952fee698f8ee2b672',1,'vg::Surjector']]],
- ['prune_5fthread_5fbuffer_5fsize_4789',['PRUNE_THREAD_BUFFER_SIZE',['../namespacevg_1_1algorithms.html#a64f4abe5d8279f14a52b56ffb47fff34',1,'vg::algorithms']]],
- ['prune_5fto_5fconnecting_5fgraph_4790',['prune_to_connecting_graph',['../namespacevg_1_1algorithms.html#a3d74c519ccaa204e7735d5bd26c5095a',1,'vg::algorithms']]],
- ['prune_5fto_5fconnecting_5fgraph_2ecpp_4791',['prune_to_connecting_graph.cpp',['../prune__to__connecting__graph_8cpp.html',1,'']]],
- ['prune_5fto_5fconnecting_5fgraph_2ehpp_4792',['prune_to_connecting_graph.hpp',['../prune__to__connecting__graph_8hpp.html',1,'']]],
- ['prune_5fto_5fhigh_5fscoring_5fpaths_4793',['prune_to_high_scoring_paths',['../classvg_1_1MultipathAlignmentGraph.html#a8164834df4fc94907fb96b06062c9514',1,'vg::MultipathAlignmentGraph']]],
- ['prune_5funconnectable_4794',['prune_unconnectable',['../classvg_1_1Surjector.html#ab65da876e448d86bc64985c0b14d3e78',1,'vg::Surjector']]],
- ['pruning_5fmax_5fedge_5fcount_4795',['pruning_max_edge_count',['../structvg_1_1IndexingParameters.html#ad673cb8b7687d3a60aef1036d1b1dae3',1,'vg::IndexingParameters']]],
- ['pruning_5fmax_5fnode_5fdegree_4796',['pruning_max_node_degree',['../structvg_1_1IndexingParameters.html#a8041e911ac757df80b37fbdbc4943f74',1,'vg::IndexingParameters']]],
- ['pruning_5fmax_5fnode_5fdegree_5fdecrease_5ffactor_4797',['pruning_max_node_degree_decrease_factor',['../structvg_1_1IndexingParameters.html#ac3de2fff42441077c37ff61421b6415d',1,'vg::IndexingParameters']]],
- ['pruning_5fmin_5fcomponent_5fsize_4798',['pruning_min_component_size',['../structvg_1_1IndexingParameters.html#a1f955fc9bdfedd418b900163f36a2e15',1,'vg::IndexingParameters']]],
- ['pruning_5fwalk_5flength_4799',['pruning_walk_length',['../structvg_1_1IndexingParameters.html#ac9f7127d0df7aa1c90ced42a01755763',1,'vg::IndexingParameters']]],
- ['pruning_5fwalk_5flength_5fincrease_5ffactor_4800',['pruning_walk_length_increase_factor',['../structvg_1_1IndexingParameters.html#a7c483115dc36e1e7e8b25684f427442c',1,'vg::IndexingParameters']]],
- ['pruningmode_4801',['PruningMode',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248',1,'prune_main.cpp']]],
- ['pruningparameters_4802',['PruningParameters',['../structPruningParameters.html',1,'']]],
- ['pseudo_5flength_4803',['pseudo_length',['../classvg_1_1MultipathMapper.html#aa5ee46fa484ee95e45da33b47bcc4eb8',1,'vg::MultipathMapper']]],
- ['pseudo_5frandom_5fsequence_4804',['pseudo_random_sequence',['../namespacevg.html#a1924855da445b625609837c0920af7b2',1,'vg']]],
- ['ptr_4805',['ptr',['../structjson__autoptr.html#a8eeb7c64d99d1378d9524ede91d6faa4',1,'json_autoptr']]],
- ['purge_5funmapped_5falignments_4806',['purge_unmapped_alignments',['../classvg_1_1MultipathMapper.html#a009000ee2da67a965a4f627be468d976',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< multipath_alignment_t > &multipath_alns_out)'],['../classvg_1_1MultipathMapper.html#ab1c9f02cbadcd8df05b691e4ff5294f2',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, bool proper_paired)']]],
- ['push_4807',['push',['../structvg_1_1MatchPos_1_1PathList.html#a2979222c63cb87e2f530fceda30e56a5',1,'vg::MatchPos::PathList::push()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ade3a2a60c495a494d27fb6f8a72ef2db',1,'vg::ZipCodeTree::reverse_iterator::push()']]],
- ['push_5fback_4808',['push_back',['../structhaplo_1_1gbwt__thread__t.html#a726f2772b4725564569e4889f89db7c6',1,'haplo::gbwt_thread_t::push_back()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#ade3cdc2fdb2dc88b735bee5be2c04cee',1,'haplo::linear_haplo_structure::SNVvector::push_back()']]],
- ['push_5fedit_4809',['push_edit',['../classvg_1_1DozeuInterface.html#acc84e0c73002c23f8249ea17efff6848',1,'vg::DozeuInterface']]]
+ ['p_5fvalue_4319',['p_value',['../structvg_1_1SeqComplexity.html#a20dfb4fbec20a18a5decaccc046c10e8',1,'vg::SeqComplexity']]],
+ ['p_5fvalue_5fmemo_4320',['p_value_memo',['../classvg_1_1MultipathMapper.html#a076b5202ca84c7836e93d3e8b71775bf',1,'vg::MultipathMapper']]],
+ ['pack_4321',['pack',['../structhandlegraph_1_1number__bool__packing.html#af5082dc39a2f308585402bd19de0caa8',1,'handlegraph::number_bool_packing']]],
+ ['pack_5fmain_2ecpp_4322',['pack_main.cpp',['../pack__main_8cpp.html',1,'']]],
+ ['pack_5fnames_4323',['pack_names',['../classvg_1_1Viz.html#abb3fd61d416351930f2e7399e6f6001b',1,'vg::Viz']]],
+ ['pack_5fquery_5fforward_4324',['pack_query_forward',['../classvg_1_1DozeuInterface.html#acd17348d5d2dd0ec4c10af98748fe67a',1,'vg::DozeuInterface::pack_query_forward()'],['../classvg_1_1XdropAligner.html#a9179d91b00ed33fbc3e9e6a4bd6b9321',1,'vg::XdropAligner::pack_query_forward()'],['../classvg_1_1QualAdjXdropAligner.html#a0e1140ad3ee66b2583869ccd2267841b',1,'vg::QualAdjXdropAligner::pack_query_forward()']]],
+ ['pack_5fquery_5freverse_4325',['pack_query_reverse',['../classvg_1_1DozeuInterface.html#aa15876efde0e6d8f963d37ae245c8ead',1,'vg::DozeuInterface::pack_query_reverse()'],['../classvg_1_1XdropAligner.html#a3c3832ae9935773f0dd0b97ed031c70e',1,'vg::XdropAligner::pack_query_reverse()'],['../classvg_1_1QualAdjXdropAligner.html#a0d6b25927dccfe18f03eab6457486ac7',1,'vg::QualAdjXdropAligner::pack_query_reverse()']]],
+ ['packed_5fdepth_5fof_5fbin_4326',['packed_depth_of_bin',['../namespacevg_1_1algorithms.html#a62ebbcbfe1250940eb8ebf0a2dcbc19a',1,'vg::algorithms']]],
+ ['packed_5fdepths_4327',['packed_depths',['../namespacevg_1_1algorithms.html#abd431ebd9786d796f708a7046e643e2e',1,'vg::algorithms']]],
+ ['packedgraph_4328',['PackedGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a3355e9401e49629ee5dcd20b107f3f67',1,'vg::IndexingParameters']]],
+ ['packedtraversalsupportfinder_4329',['PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html',1,'vg::PackedTraversalSupportFinder'],['../classvg_1_1PackedTraversalSupportFinder.html#a5bb7b3f0b3fd9c72597403ce75f8791c',1,'vg::PackedTraversalSupportFinder::PackedTraversalSupportFinder()']]],
+ ['packer_4330',['Packer',['../classvg_1_1Packer.html',1,'vg::Packer'],['../classvg_1_1PackedTraversalSupportFinder.html#ac48b605c781739b3920b8c36fdb6fcf8',1,'vg::PackedTraversalSupportFinder::packer()'],['../classvg_1_1Packer.html#a965acab0b6c7d973a67e449785955739',1,'vg::Packer::Packer(const HandleGraph *graph=nullptr)'],['../classvg_1_1Packer.html#ad52836b610249ada7cf0ad13c329b52c',1,'vg::Packer::Packer(const HandleGraph *graph, bool record_bases, bool record_edges, bool record_edits, bool record_qualities, size_t bin_size=0, size_t coverage_bins=1, size_t data_width=8)']]],
+ ['packer_2ecpp_4331',['packer.cpp',['../packer_8cpp.html',1,'']]],
+ ['packer_2ehpp_4332',['packer.hpp',['../packer_8hpp.html',1,'']]],
+ ['packers_4333',['Packers',['../classvg_1_1Packers.html',1,'vg']]],
+ ['packs_4334',['packs',['../classvg_1_1Viz.html#a350ea478ececb5f19170b16cf1539726',1,'vg::Viz']]],
+ ['pad_5fband_2ecpp_4335',['pad_band.cpp',['../pad__band_8cpp.html',1,'']]],
+ ['pad_5fband_2ehpp_4336',['pad_band.hpp',['../pad__band_8hpp.html',1,'']]],
+ ['pad_5fband_5fconstant_4337',['pad_band_constant',['../namespacevg_1_1algorithms.html#ab48342aedc7d81e2334c52bb320223c2',1,'vg::algorithms::pad_band_constant()'],['../namespacevg_1_1algorithms.html#aaab5b2261edb66897af9d1158e7758d8',1,'vg::algorithms::pad_band_constant(size_t band_padding)']]],
+ ['pad_5fband_5fmin_5frandom_5fwalk_4338',['pad_band_min_random_walk',['../namespacevg_1_1algorithms.html#a3363cc23e6c71e1bb5faac975af7920d',1,'vg::algorithms::pad_band_min_random_walk()'],['../namespacevg_1_1algorithms.html#a25a37b51facd101b8a29b1a57661f74f',1,'vg::algorithms::pad_band_min_random_walk(double band_padding_multiplier, size_t band_padding_memo_size, size_t max_padding)']]],
+ ['pad_5fband_5frandom_5fwalk_4339',['pad_band_random_walk',['../namespacevg_1_1algorithms.html#a6a606c26b5751d935c71d7971a92d99b',1,'vg::algorithms::pad_band_random_walk()'],['../namespacevg_1_1algorithms.html#a1294ed71274673b7e4cc1d40e9472666',1,'vg::algorithms::pad_band_random_walk(double band_padding_multiplier, size_t band_padding_memo_size, size_t max_padding)']]],
+ ['pad_5fband_5frandom_5fwalk_5finternal_4340',['pad_band_random_walk_internal',['../namespacevg_1_1algorithms.html#a9957e925ee25c57698383d4e1df21f0d',1,'vg::algorithms']]],
+ ['pad_5fcluster_5fscore_5fthreshold_4341',['pad_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a70b206dc58a148a69657303ff292199f',1,'vg::MinimizerMapper']]],
+ ['pad_5fsuspicious_5fanchors_5fto_5flength_4342',['pad_suspicious_anchors_to_length',['../classvg_1_1Surjector.html#a7231e0ecf35ed767417fc37184b0a806',1,'vg::Surjector']]],
+ ['pad_5ftraversal_4343',['pad_traversal',['../classvg_1_1GAFOutputCaller.html#a697f4f2c00fa8317ba8143bbe99931fb',1,'vg::GAFOutputCaller']]],
+ ['pad_5fzipcode_5ftree_5fscore_5fthreshold_4344',['pad_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#aafbc5c792144ae26630c312d2475b19a',1,'vg::MinimizerMapper']]],
+ ['paint_4345',['paint',['../structvg_1_1Funnel_1_1PaintableSpace.html#a88c1043f7b0cae737da989f0abc44b0a',1,'vg::Funnel::PaintableSpace']]],
+ ['paintablespace_4346',['PaintableSpace',['../structvg_1_1Funnel_1_1PaintableSpace.html',1,'vg::Funnel']]],
+ ['pair_5fall_4347',['pair_all',['../classvg_1_1MinimizerMapper.html#a4493ab0315512da6b10a7cde3754afe2',1,'vg::MinimizerMapper']]],
+ ['pair_5fcluster_5fmultiplicity_4348',['pair_cluster_multiplicity',['../classvg_1_1MultipathMapper.html#ae534f0c248a4b44bdf389ead66d105e3',1,'vg::MultipathMapper']]],
+ ['pair_5fclusters_4349',['pair_clusters',['../classvg_1_1MEMClusterer.html#a4e84dd599bb8dc4341cbed2fd1de1ed0',1,'vg::MEMClusterer::pair_clusters()'],['../classvg_1_1NullClusterer.html#a1794ac271ce6d785e67b488a98ec87d6',1,'vg::NullClusterer::pair_clusters()'],['../classvg_1_1OrientedDistanceClusterer.html#a41e57b46abd69532d53855499d5042eb',1,'vg::OrientedDistanceClusterer::pair_clusters()'],['../classvg_1_1TVSClusterer.html#a1477ce3367e036c0ecc101e1518b49b9',1,'vg::TVSClusterer::pair_clusters()'],['../classvg_1_1MinDistanceClusterer.html#af561001a20cc91adc6238f74edca6480',1,'vg::MinDistanceClusterer::pair_clusters()']]],
+ ['pair_5fconsistent_4350',['pair_consistent',['../classvg_1_1Mapper.html#ad3a62e0a91818c4e20508ab2a0f47fa5',1,'vg::Mapper']]],
+ ['pair_5ffrom_5fedge_4351',['pair_from_edge',['../classvg_1_1NodeSide.html#ad48cc3d977ad0f6ffc5ce1034cbbae65',1,'vg::NodeSide::pair_from_edge(Edge *e)'],['../classvg_1_1NodeSide.html#a97eed27ab7b77be54b68062b780a9f36',1,'vg::NodeSide::pair_from_edge(const Edge &e)']]],
+ ['pair_5ffrom_5fend_5fedge_4352',['pair_from_end_edge',['../classvg_1_1NodeSide.html#a23f18cf5f9ae9c7fc8475800d967275c',1,'vg::NodeSide']]],
+ ['pair_5ffrom_5fstart_5fedge_4353',['pair_from_start_edge',['../classvg_1_1NodeSide.html#a3193e35c9e8349c427cc834335e25405',1,'vg::NodeSide']]],
+ ['pair_5fhash_5fmap_4354',['pair_hash_map',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vector_3c_20vg_3a_3aalignment_20_2a_20_3e_20_3e_4355',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vector< vg::Alignment * > >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vg_3a_3aedge_20_2a_20_3e_4356',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vg::Edge * >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fmap_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_2c_20gbwt_3a_3anode_5ftype_20_3e_4357',['pair_hash_map< std::pair< gbwt::node_type, gbwt::node_type >, gbwt::node_type >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fset_4358',['pair_hash_set',['../classvg_1_1pair__hash__set.html',1,'vg']]],
+ ['pair_5fhash_5fset_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_20_3e_4359',['pair_hash_set< std::pair< gbwt::node_type, gbwt::node_type > >',['../classvg_1_1pair__hash__set.html',1,'vg']]],
+ ['pair_5fmapping_5flikelihoods_4360',['pair_mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a05dd8b61205954b988bb996479883989',1,'vg::MultipathMapper']]],
+ ['pair_5forientation_5ffilter_4361',['pair_orientation_filter',['../classvg_1_1Filter.html#a16451e95cd6c7642df9f013d5b73c0c7',1,'vg::Filter']]],
+ ['pair_5frescue_4362',['pair_rescue',['../classvg_1_1Mapper.html#a36248b0eb439694bfbd493fce0ce2b02',1,'vg::Mapper']]],
+ ['pair_5frescue_5fhang_5fthreshold_4363',['pair_rescue_hang_threshold',['../classvg_1_1Mapper.html#a92e1f4de4e6ce576e09005713d1c1cd1',1,'vg::Mapper']]],
+ ['pair_5frescue_5fretry_5fthreshold_4364',['pair_rescue_retry_threshold',['../classvg_1_1Mapper.html#a36ed72fe5d33907a75992011ff9ae244',1,'vg::Mapper']]],
+ ['pair_5fto_5fstring_4365',['pair_to_string',['../haplotypes__main_8cpp.html#a7d4977594e9d93b802b94c95752f34a2',1,'haplotypes_main.cpp']]],
+ ['paired_5fdistance_5fstdevs_4366',['paired_distance_stdevs',['../classvg_1_1MinimizerMapper.html#a94bd867270265d26c4f2abfbd730f316',1,'vg::MinimizerMapper']]],
+ ['paired_5ffor_5feach_5fparallel_5fafter_5fwait_4367',['paired_for_each_parallel_after_wait',['../namespacevg_1_1io.html#af3c3dd4ad5c9b887fd3ee389e0b67ef6',1,'vg::io']]],
+ ['paired_5fread_5fname_4368',['paired_read_name',['../structvg_1_1MultipathAlignment.html#a0664790bf6bd37af413697cddff370fb',1,'vg::MultipathAlignment']]],
+ ['paired_5frescue_5fscore_5flimit_4369',['paired_rescue_score_limit',['../classvg_1_1MinimizerMapper.html#a923b2f2f9aa86e445add3be0d1c4abae',1,'vg::MinimizerMapper']]],
+ ['pairedendmapper_4370',['PairedEndMapper',['../classvg_1_1PairedEndMapper.html',1,'vg']]],
+ ['parallelkffreader_4371',['ParallelKFFReader',['../classvg_1_1ParallelKFFReader.html',1,'vg::ParallelKFFReader'],['../classvg_1_1ParallelKFFReader.html#a4b84d319b814d4b2a5f099d19d0426d5',1,'vg::ParallelKFFReader::ParallelKFFReader(const std::string &filename)'],['../classvg_1_1ParallelKFFReader.html#adcdc292236ba8b178c38666702b4e5c1',1,'vg::ParallelKFFReader::ParallelKFFReader(const ParallelKFFReader &)=delete']]],
+ ['param_5ftype_4372',['param_type',['../classvg_1_1discrete__distribution.html#a923a04239b0ceb7026d193aa671100e4',1,'vg::discrete_distribution']]],
+ ['parameters_4373',['Parameters',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html',1,'vg::HaplotypePartitioner::Parameters'],['../structvg_1_1Recombinator_1_1Parameters.html',1,'vg::Recombinator::Parameters'],['../structvg_1_1Recombinator_1_1Parameters.html#a3112d2a46538ce1575d53b6706f25756',1,'vg::Recombinator::Parameters::Parameters()']]],
+ ['parent_4374',['parent',['../structvg_1_1WFANode.html#a78adf1a04bc5f5907cc3a46445061e62',1,'vg::WFANode::parent()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ae00d40d340f5114917a9f6ca1cec0460',1,'vg::SnarlManager::SnarlRecord::parent()'],['../structvg_1_1TreeNode.html#a4eb11d266cabbae3e6728d2918c80996',1,'vg::TreeNode::parent()'],['../structvg_1_1VectorView_1_1const__iterator.html#a41fafc961da593dbc8591c6288a33fd6',1,'vg::VectorView::const_iterator::parent()'],['../structvg_1_1Snarl.html#a054af14a2fccdda2209ef9a8f19aa032',1,'vg::Snarl::parent()'],['../classvg_1_1WFATree.html#ab6c9c25e1906e3a95bc6c853a2c5db3f',1,'vg::WFATree::parent()']]],
+ ['parent_5fallele_4375',['parent_allele',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2f21b56cc895482f0f8a4829ccfa3463',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5fchain_4376',['parent_chain',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a37d7d2aa3460ba15b3a51ac4eedefd76',1,'vg::SnarlManager::SnarlRecord']]],
+ ['parent_5fchain_5findex_4377',['parent_chain_index',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a7f98f1f84ba0d39301f1adc3333e6dfb',1,'vg::SnarlManager::SnarlRecord']]],
+ ['parent_5fchains_4378',['parent_chains',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a3f1ca708ff05e4f649b0d9b22dc539fd',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['parent_5fdepth_4379',['parent_depth',['../structvg_1_1MIPayload.html#af3214bd006207b1d4c417c331b905290',1,'vg::MIPayload']]],
+ ['parent_5fdirectory_4380',['parent_directory',['../structvg_1_1temp__file_1_1Handler.html#a1a791a5a813c3d0702594f5ad6915eaf',1,'vg::temp_file::Handler::parent_directory()'],['../structxg_1_1temp__file_1_1Handler.html#a16640b9f416a23bd671f56437bd09aa6',1,'xg::temp_file::Handler::parent_directory()']]],
+ ['parent_5fgraph_4381',['parent_graph',['../classvg_1_1JoinedSpliceGraph.html#a274429d072e5be5687ac704393b903a4',1,'vg::JoinedSpliceGraph']]],
+ ['parent_5fhandle_4382',['parent_handle',['../structvg_1_1MIPayload.html#a92ead268cf5b206f54e4cf0e95937dfc',1,'vg::MIPayload']]],
+ ['parent_5fis_5fchain_4383',['parent_is_chain',['../structvg_1_1MIPayload.html#aa5abaa3ea722cf685fe73fe9502e00c1',1,'vg::MIPayload']]],
+ ['parent_5fis_5froot_4384',['parent_is_root',['../structvg_1_1MIPayload.html#a36e03b459c31f012a17a78a1ec6f5391',1,'vg::MIPayload']]],
+ ['parent_5flen_4385',['parent_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#abe519281b723c59979299b2657439f6e',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5fnet_5fhandle_4386',['parent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af940526569cd8d070de39e8446390e6f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['parent_5fof_4387',['parent_of',['../classvg_1_1SnarlManager.html#ad4c8dd034c160f2908164c1ebc2a0394',1,'vg::SnarlManager']]],
+ ['parent_5fpath_5finterval_4388',['parent_path_interval',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a4aa790baef1ec47d6546e30f60851e9b',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5frecord_5foffset_4389',['parent_record_offset',['../structvg_1_1MIPayload.html#af185811088055cdd4c371f18883087b2',1,'vg::MIPayload']]],
+ ['parent_5fref_5flen_4390',['parent_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ac311ca43aecb9c37302835adadce85af',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5fsnarls_4391',['parent_snarls',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a03f3e53e97f93f2d2b4daf66f99cd763',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['parent_5ftype_4392',['parent_type',['../structvg_1_1MIPayload.html#aa14d5e8cecee30a8e796832d5ead8578',1,'vg::MIPayload']]],
+ ['parentgenotypeinfo_4393',['ParentGenotypeInfo',['../structvg_1_1ParentGenotypeInfo.html',1,'vg']]],
+ ['pareto_5fpoint_4394',['pareto_point',['../namespacevg.html#a1aa2d026eb3edc0c692e19e5a493feef',1,'vg']]],
+ ['parse_4395',['parse',['../classvg_1_1OptionInterface.html#aa658456e011e28d8e6d3073c8ccfc740',1,'vg::OptionInterface::parse()=0'],['../classvg_1_1OptionInterface.html#a5679dbc64e1f490d7caa35730de6d09b',1,'vg::OptionInterface::parse(const string &arg)=0'],['../classvg_1_1ConfigurableParser.html#a9c28ad9040822d975a38c982677065bd',1,'vg::ConfigurableParser::parse()'],['../classvg_1_1OptionValueParser.html#a4b43a211a8dca7c43a1fe3fc4fde1de5',1,'vg::OptionValueParser::parse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a27e910ec23c80fc2c829dcdb98da0ddc',1,'vg::OptionValueParser< vector< Item > >::parse()'],['../classvg_1_1BaseOption.html#a6682e454cf748d2a29623849d72f8d1d',1,'vg::BaseOption::parse()'],['../classvg_1_1BaseOption.html#ab17b0a67fe5bdb8de8ffb39f98a804e7',1,'vg::BaseOption::parse(const string &arg)'],['../classvg_1_1algorithms_1_1GFAParser.html#a575aa78bfa6a567735133c8cffa6da77',1,'vg::algorithms::GFAParser::parse()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a040fd55d950392ade69dad277adfb848',1,'vg::subcommand::BaseArgSpec::parse()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a8ddbad123ba28ff099c263d24b751889',1,'vg::subcommand::ValueArgSpec::parse()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a96a1df206d4ef889c7f3f6cf08dc1426',1,'vg::subcommand::FlagArgSpec::parse()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a6fa17a5e6d8fbc293d69063c947cb0aa',1,'vg::subcommand::BaseOptionGroup::parse()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aa4b885a991453bbc8cde726e35dd115f',1,'vg::subcommand::OptionGroup::parse()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aada2ded9febbec1c9bab141da4bfc0ce',1,'vg::subcommand::GroupedOptionGroup::parse()'],['../classvg_1_1OptionValueParser.html#a5a34866bb0ac6c4feae8b5a20aba93c7',1,'vg::OptionValueParser::parse()'],['../namespacevg.html#a1dd328fd8abb43338a3ae9e0a3b0be1f',1,'vg::parse(const string &arg, double &dest)'],['../namespacevg.html#a2d3193c0a90ba95bd11b8b3201de52c0',1,'vg::parse(const string &arg, float &dest)'],['../namespacevg.html#aa1de4a1752e875116c767ec49a8e2961',1,'vg::parse(const string &arg, std::regex &dest)'],['../namespacevg.html#aa4a3393960dd54c941e9d7c317923c2e',1,'vg::parse(const string &arg, pos_t &dest)'],['../namespacevg.html#a8873caafc22d22b52e0f6f3f164f6dc8',1,'vg::parse(const string &arg)'],['../namespacevg.html#a8c5c364797f623025b67b9aff0657112',1,'vg::parse(const char *arg)'],['../namespacevg.html#a627f5ad6fe6f1e6b4cc23ac97dfca4b8',1,'vg::parse(const string &arg, Result &dest)'],['../namespacevg.html#a2cd6368e7395f1d90c4e3be1a7293d0a',1,'vg::parse(const string &arg, typename enable_if< sizeof(Result)<=sizeof(long long) &&is_integral< Result >::value &&is_signed< Result >::value, Result >::type &dest)'],['../namespacevg.html#a1384531a1c8d8387bdd04961590bdf93',1,'vg::parse(const string &arg, typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &dest)']]],
+ ['parse_5fattribute_5fvalue_4396',['parse_attribute_value',['../classvg_1_1Transcriptome.html#a401bd93346ea5e02f586823d8f3b458e',1,'vg::Transcriptome']]],
+ ['parse_5fattributes_4397',['parse_attributes',['../structvg_1_1GFFRecord.html#ade5c97a34abe718fbb607977f11fb8f1',1,'vg::GFFRecord']]],
+ ['parse_5fbed_4398',['parse_bed',['../mask__main_8cpp.html#a210b34f1b7dfefc99804b335b0cf6e19',1,'mask_main.cpp']]],
+ ['parse_5fbed_5fregions_4399',['parse_bed_regions',['../namespacevg.html#a736f4c7b5d03a7efe78315b4c5490f15',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#ad88fe24ca988562008c8b734c22cb403',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)'],['../namespacevg.html#a8fd1e3436d98304996aaecece048cb45',1,'vg::parse_bed_regions(const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)']]],
+ ['parse_5fdefault_4400',['parse_default',['../classvg_1_1OptionValueParser.html#ad2b7db7247de0c8cb7fe4e9501314b6b',1,'vg::OptionValueParser::parse_default()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#aa9624ebfad0e2421af39a86e7327edaf',1,'vg::OptionValueParser< vector< Item > >::parse_default()'],['../classvg_1_1OptionValueParser.html#acddd63568b5e1a7ece023abeccccd15b',1,'vg::OptionValueParser::parse_default()']]],
+ ['parse_5ffrom_5fstring_4401',['parse_from_string',['../classvg_1_1io_1_1ProtobufIterator.html#ab37e50d3f1375c13a223a79938d5094d',1,'vg::io::ProtobufIterator']]],
+ ['parse_5fgaf_5frecord_4402',['parse_gaf_record',['../namespacegafkluge.html#ab8a6f72dddac182a6d8d74a52a6fc92d',1,'gafkluge']]],
+ ['parse_5fgbwt_5fconfig_4403',['parse_gbwt_config',['../gbwt__main_8cpp.html#a8153bcd09dec28c64e4a9bfad67cee40',1,'gbwt_main.cpp']]],
+ ['parse_5fgff_5fregions_4404',['parse_gff_regions',['../namespacevg.html#a55cc20d96f38b54c590af4f3f3ac2498',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#a629c9fee8a51c4ca363511ae01ad4a09',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)']]],
+ ['parse_5fh_4405',['parse_h',['../classvg_1_1algorithms_1_1GFAParser.html#a122490db3d620bc310b106e2231a9140',1,'vg::algorithms::GFAParser']]],
+ ['parse_5fhaplotype_4406',['parse_haplotype',['../classhandlegraph_1_1PathMetadata.html#a69e57ea70c57b01b309cdf39da4eeeb5',1,'handlegraph::PathMetadata']]],
+ ['parse_5fhaplotype_5ftranscript_5ffile_4407',['parse_haplotype_transcript_file',['../sim__main_8cpp.html#ae98175893da0d162097014dd65ba8ce2',1,'sim_main.cpp']]],
+ ['parse_5fintron_5fdistr_5ffile_4408',['parse_intron_distr_file',['../mpmap__main_8cpp.html#a48bc366d5c5d1acbc0c60556944bcfe9',1,'mpmap_main.cpp']]],
+ ['parse_5fintrons_4409',['parse_introns',['../classvg_1_1Transcriptome.html#ad040b82553e6b03ccd926c0fe622e84c',1,'vg::Transcriptome']]],
+ ['parse_5fl_4410',['parse_l',['../classvg_1_1algorithms_1_1GFAParser.html#a6033f9ec4740e70dc79fbaae78f91773',1,'vg::algorithms::GFAParser']]],
+ ['parse_5flocus_5fname_4411',['parse_locus_name',['../classhandlegraph_1_1PathMetadata.html#a978b48ca96f8817f7099587dae77b8b4',1,'handlegraph::PathMetadata']]],
+ ['parse_5fmatrix_4412',['parse_matrix',['../classvg_1_1AlignerClient.html#a4a56c0bf099b670763c0f5ce3653811b',1,'vg::AlignerClient']]],
+ ['parse_5fmemory_5fusage_4413',['parse_memory_usage',['../autoindex__main_8cpp.html#ad25ab5b852b7a1bc223505f7a2e23853',1,'autoindex_main.cpp']]],
+ ['parse_5fonly_4414',['parse_only',['../structGBWTConfig.html#af8fc6affa1925b48a3af6fff48511340',1,'GBWTConfig']]],
+ ['parse_5fp_4415',['parse_p',['../classvg_1_1algorithms_1_1GFAParser.html#a3f28df872d86abde347b3bbcc7f42948',1,'vg::algorithms::GFAParser']]],
+ ['parse_5fpath_5fname_4416',['parse_path_name',['../classhandlegraph_1_1PathMetadata.html#ab6bcceaaedfbb03a4ea3f70499b06ade',1,'handlegraph::PathMetadata']]],
+ ['parse_5fphase_5fblock_4417',['parse_phase_block',['../classhandlegraph_1_1PathMetadata.html#a3d9a3a974ab62d008104fa7dab849465',1,'handlegraph::PathMetadata']]],
+ ['parse_5fprovide_5fstring_4418',['parse_provide_string',['../autoindex__main_8cpp.html#a8f62d94c211a4113595cbdf100129fc3',1,'autoindex_main.cpp']]],
+ ['parse_5fregion_4419',['parse_region',['../namespacevg.html#a253257615743a1cfb948b749be7700e2',1,'vg::parse_region(const string &target, string &name, int64_t &start, int64_t &end)'],['../namespacevg.html#af0a3beb8908adf7a6e4d641243937830',1,'vg::parse_region(string ®ion, Region &out_region)']]],
+ ['parse_5frg_5fsample_5fmap_4420',['parse_rg_sample_map',['../namespacevg.html#a637c855dffc0296c6575ae8a4cac6b43',1,'vg']]],
+ ['parse_5frsem_5fexpression_5ffile_4421',['parse_rsem_expression_file',['../sim__main_8cpp.html#aa1964053fdd12fb9dde544ce6d18ab70',1,'sim_main.cpp']]],
+ ['parse_5fs_4422',['parse_s',['../classvg_1_1algorithms_1_1GFAParser.html#af4ce322cdb902c01881afcbb4fea85f5',1,'vg::algorithms::GFAParser']]],
+ ['parse_5fsam_5ftags_4423',['parse_sam_tags',['../namespacevg.html#a175da49ded2be9251e68ae642108248a',1,'vg']]],
+ ['parse_5fsample_5fname_4424',['parse_sample_name',['../classhandlegraph_1_1PathMetadata.html#acbc675d9d41c36eebb174b4871c42435',1,'handlegraph::PathMetadata']]],
+ ['parse_5fsense_4425',['parse_sense',['../classhandlegraph_1_1PathMetadata.html#aae6aa5f2738ce962e4e74d46a9c5e3e0',1,'handlegraph::PathMetadata']]],
+ ['parse_5fsubrange_4426',['parse_subrange',['../classhandlegraph_1_1PathMetadata.html#a010d050ee3bf526da9ae45fde6dd1dc6',1,'handlegraph::PathMetadata']]],
+ ['parse_5ftags_4427',['parse_tags',['../classvg_1_1algorithms_1_1GFAParser.html#a4fecb9e4836c67853d300ffd29b046e7',1,'vg::algorithms::GFAParser']]],
+ ['parse_5ftid_5fpath_5fhandle_5fmap_4428',['parse_tid_path_handle_map',['../namespacevg.html#abc66619671bdc564023a9b3259558785',1,'vg']]],
+ ['parse_5ftranscripts_4429',['parse_transcripts',['../classvg_1_1Transcriptome.html#ae7b6c679e3d635342029bbc7cc39d75d',1,'vg::Transcriptome']]],
+ ['parse_5ftranslation_4430',['parse_translation',['../structvg_1_1PathIndex.html#aa5272234ddb7686f1ae88881ebf99a61',1,'vg::PathIndex']]],
+ ['parse_5fvcf_4431',['parse_vcf',['../classvg_1_1HaplotypeIndexer.html#ad3eda4acd04b8bae303b4604410ece41',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::string &job_name="GBWT") const'],['../classvg_1_1HaplotypeIndexer.html#ad81dbd24bba40aaa14536d79754d387b',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::vector< path_handle_t > &paths, const std::string &job_name="GBWT") const']]],
+ ['parse_5fw_4432',['parse_w',['../classvg_1_1algorithms_1_1GFAParser.html#ae03c9247eb49aed8f868039365f89cdd',1,'vg::algorithms::GFAParser']]],
+ ['parsegenotypes_4433',['parseGenotypes',['../namespacevg.html#a8bcecf9fe02b7f50dd5e72e40dcd98e1',1,'vg']]],
+ ['partition_5fgbwt_5fsequences_4434',['partition_gbwt_sequences',['../namespacevg.html#a802baeeacfe4ee75781afabac562588b',1,'vg']]],
+ ['partition_5fhaplotypes_4435',['partition_haplotypes',['../classvg_1_1HaplotypePartitioner.html#a1c0a32c7f0ca0f86fd5abb9b746895c8',1,'vg::HaplotypePartitioner']]],
+ ['partitioner_5fparameters_4436',['partitioner_parameters',['../structHaplotypesConfig.html#a6080d6a6e4ada9573d11d678b6de79d0',1,'HaplotypesConfig']]],
+ ['pass_4437',['pass',['../classvg_1_1Funnel.html#aec19daea826d5951ecf1477769722d9a',1,'vg::Funnel']]],
+ ['pass_5fnumber_4438',['pass_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#a9354b35a8f08891654da020502248f2e',1,'vg::algorithms::GFAFormatError']]],
+ ['passed_5ffilters_4439',['passed_filters',['../structvg_1_1Funnel_1_1Item.html#a566978051c820d69d63e72763dc38b17',1,'vg::Funnel::Item']]],
+ ['passed_5fstatistics_4440',['passed_statistics',['../structvg_1_1Funnel_1_1Item.html#a5ae29ab2e549daa3fa20626fd5d4fb59',1,'vg::Funnel::Item']]],
+ ['passing_4441',['passing',['../structvg_1_1Funnel_1_1FilterPerformance.html#a9382a4983a52c3849412717c26205bde',1,'vg::Funnel::FilterPerformance']]],
+ ['passing_5fcorrect_4442',['passing_correct',['../structvg_1_1Funnel_1_1FilterPerformance.html#a7622d6acfd5d4075e26ad60b911e72c4',1,'vg::Funnel::FilterPerformance']]],
+ ['past_5fend_4443',['past_end',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a06f803fd96e9e94610bc8fa8f9db95f3',1,'vg::GraphSynchronizer::Lock']]],
+ ['patch_5falignment_4444',['patch_alignment',['../classvg_1_1Mapper.html#ad8f03f4ff100a15ea885a5404222a0ad',1,'vg::Mapper']]],
+ ['patch_5falignments_4445',['patch_alignments',['../classvg_1_1Mapper.html#a6c33dd8ad7af82e21f0ee6463e9456fc',1,'vg::Mapper']]],
+ ['path_4446',['Path',['../structvg_1_1Path.html',1,'vg::Path'],['../structvg_1_1MatchPos.html#a6a24cd3b3befa706a8f4f934034843cf',1,'vg::MatchPos::path()'],['../structvg_1_1WFANode.html#ad947775b8a38d6d03e6c40b5a8ee06c2',1,'vg::WFANode::path()'],['../structvg_1_1GaplessExtension.html#a6d46f3e3d3525ea159b11f6e832a37e0',1,'vg::GaplessExtension::path()'],['../structvg_1_1WFAAlignment.html#afd65b83419307e4f56481adef5c96f71',1,'vg::WFAAlignment::path()'],['../classvg_1_1PathNode.html#aa955184b7b22179c0efd1febdfc55b92',1,'vg::PathNode::path()'],['../structvg_1_1RecombinatorHaplotype.html#ae37ea81b1f65f9c24f05620ecc3f2a80',1,'vg::RecombinatorHaplotype::path()'],['../structvg_1_1EditedTranscriptPath.html#a8945ac17c2039bc54e3697553c1563a2',1,'vg::EditedTranscriptPath::path()'],['../structvg_1_1CompletedTranscriptPath.html#ae6ea83076c2772ac2670e0e06587dc04',1,'vg::CompletedTranscriptPath::path()'],['../structvg_1_1algorithms_1_1walk__t.html#aee19ea04353c3d23bef5d5fd3689965c',1,'vg::algorithms::walk_t::path()'],['../classhandlegraph_1_1PathForEachSocket.html#a5bd264139b15b7e56ad5a2f6f691202b',1,'handlegraph::PathForEachSocket::path()'],['../structgafkluge_1_1GafRecord.html#ae9734ca0963cfb21cb966ee915c9224b',1,'gafkluge::GafRecord::path()'],['../structvg_1_1Graph.html#a850007eb60ce0d25a6bd9799050ec790',1,'vg::Graph::path()'],['../structvg_1_1Alignment.html#a4736db5fe121ef57784c18c3c27aea79',1,'vg::Alignment::path()'],['../structvg_1_1Subpath.html#a69056b48fb59ee83a8b0307838987e19',1,'vg::Subpath::path()'],['../classvg_1_1subpath__t.html#ad9d97e89f59cf75b1d00f0e54d979048',1,'vg::subpath_t::path()'],['../classvg_1_1Paths.html#a218a01d5d53bf945ef4f0acafd18d6bc',1,'vg::Paths::path()']]],
+ ['path_2ecpp_4447',['path.cpp',['../path_8cpp.html',1,'']]],
+ ['path_2ehpp_4448',['path.hpp',['../path_8hpp.html',1,'']]],
+ ['path_5fback_4449',['path_back',['../classvg_1_1MemoizingGraph.html#a90d25a87afe426eb79582739848734c4',1,'vg::MemoizingGraph::path_back()'],['../classvg_1_1PathSubgraphOverlay.html#a7e9706b6c571a62a93c7dafb3be62f29',1,'vg::PathSubgraphOverlay::path_back()'],['../classvg_1_1VG.html#a1af5ef2df0289b964cab09d9400344c5',1,'vg::VG::path_back()'],['../classxg_1_1XG.html#aceaf4782f2fb6cbd169b6121fea8e4e8',1,'xg::XG::path_back()'],['../classhandlegraph_1_1PathHandleGraph.html#a31bb33a87ad8efd68876fc5ae1deeb09',1,'handlegraph::PathHandleGraph::path_back()']]],
+ ['path_5fbegin_4450',['path_begin',['../classvg_1_1MemoizingGraph.html#ac40575d724c1d7053b9765e622cc3713',1,'vg::MemoizingGraph::path_begin()'],['../classvg_1_1PathSubgraphOverlay.html#a492b11a38ba4d31ee75341fc8777f19c',1,'vg::PathSubgraphOverlay::path_begin()'],['../classvg_1_1VG.html#af0fc3a05ce45e0100fb82812c5b1e35d',1,'vg::VG::path_begin()'],['../classxg_1_1XG.html#ad4894f85d76ca8101a5dd164a29379c5',1,'xg::XG::path_begin()'],['../classhandlegraph_1_1PathHandleGraph.html#a815759484087ed92214c2c1c6b9d1a11',1,'handlegraph::PathHandleGraph::path_begin()']]],
+ ['path_5fchunk_5ft_4451',['path_chunk_t',['../classvg_1_1Surjector.html#a3ce06e344f93607bd066fd58d33fc7e0',1,'vg::Surjector']]],
+ ['path_5fcollapse_5ftype_4452',['path_collapse_type',['../classvg_1_1Transcriptome.html#a539e8602c6f984142ae866af8730fd34',1,'vg::Transcriptome']]],
+ ['path_5fcomponent_5findex_4453',['path_component_index',['../classvg_1_1PathOrientedDistanceMeasurer.html#aec1793ac0e2bf87292b90a5a2c8f14d8',1,'vg::PathOrientedDistanceMeasurer::path_component_index()'],['../classvg_1_1MultipathMapper.html#a0c64ee67ef473d5d5336ae6adf0b66e8',1,'vg::MultipathMapper::path_component_index()']]],
+ ['path_5fcomponent_5findex_2ecpp_4454',['path_component_index.cpp',['../path__component__index_8cpp.html',1,'']]],
+ ['path_5fcomponent_5findex_2ehpp_4455',['path_component_index.hpp',['../path__component__index_8hpp.html',1,'']]],
+ ['path_5fcontains_5fhandle_4456',['path_contains_handle',['../classxg_1_1XG.html#ad55f3e5461c20199ccdb3a6fb4dacdf6',1,'xg::XG']]],
+ ['path_5fcontains_5fnode_4457',['path_contains_node',['../structvg_1_1PathIndex.html#ab1bb8b7aec345a4b59242287ae1693c7',1,'vg::PathIndex']]],
+ ['path_5fcontains_5fnode_5fin_5forientation_4458',['path_contains_node_in_orientation',['../structvg_1_1PathIndex.html#a0dbda80790b6d81aa0f9d83ac21f85a3',1,'vg::PathIndex']]],
+ ['path_5fcount_4459',['path_count',['../classxg_1_1XG.html#a1859cb996668f8d86107d4e0117cf97f',1,'xg::XG']]],
+ ['path_5fcover_4460',['path_cover',['../structGBWTConfig.html#a857449dfcac12577f54afbd7d8957336',1,'GBWTConfig']]],
+ ['path_5fcover_5faugment_4461',['path_cover_augment',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a074342f434050b0213b77e7267c3d65a',1,'GBWTConfig']]],
+ ['path_5fcover_5fdepth_4462',['path_cover_depth',['../structvg_1_1IndexingParameters.html#a1075d3f3c10502dc02deb564d85ff897',1,'vg::IndexingParameters']]],
+ ['path_5fcover_5fgreedy_4463',['path_cover_greedy',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a0984604f4f41a7c9813edce20845b146',1,'GBWTConfig']]],
+ ['path_5fcover_5flocal_4464',['path_cover_local',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a6f385ad96dac65846244dfafee7f4775',1,'GBWTConfig']]],
+ ['path_5fcover_5fmode_4465',['path_cover_mode',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1',1,'GBWTConfig']]],
+ ['path_5fcover_5fnone_4466',['path_cover_none',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1afd10e18b78dd3425247224d94f7e3dfc',1,'GBWTConfig']]],
+ ['path_5fcover_5fparameters_4467',['path_cover_parameters',['../structGBWTConfig.html#a27d5429660a51913c09fa1b33477d27a',1,'GBWTConfig']]],
+ ['path_5fdepth_5fof_5fbin_4468',['path_depth_of_bin',['../namespacevg_1_1algorithms.html#a8c66507d55ed6e10e9d77e1281d4bcfc',1,'vg::algorithms']]],
+ ['path_5fdepths_4469',['path_depths',['../namespacevg_1_1algorithms.html#a85250c33b7d32346be371ab7e4404471',1,'vg::algorithms']]],
+ ['path_5fdivergence_5ffilter_4470',['path_divergence_filter',['../classvg_1_1Filter.html#a961710b28527b3f9961948a068c3b860',1,'vg::Filter']]],
+ ['path_5fedge_5fcount_4471',['path_edge_count',['../classvg_1_1VG.html#a5f1df72d85d8a72524b76abca972f33d',1,'vg::VG']]],
+ ['path_5fend_4472',['path_end',['../structgafkluge_1_1GafRecord.html#ac1a2b5a9c4152dfb188a72571ecf746a',1,'gafkluge::GafRecord::path_end()'],['../classvg_1_1MemoizingGraph.html#a2e4006fc68d2db22228dcef6bed02666',1,'vg::MemoizingGraph::path_end()'],['../classvg_1_1PathSubgraphOverlay.html#a5d74d2d221394980ff65e2e9adc1818f',1,'vg::PathSubgraphOverlay::path_end()'],['../classvg_1_1VG.html#a2f532a7aeb7765b99c6c4e43ba961fdb',1,'vg::VG::path_end()'],['../classxg_1_1XG.html#a32e53f5b1a5cd650b5d731f0354c5c2d',1,'xg::XG::path_end()'],['../classhandlegraph_1_1PathHandleGraph.html#a5c3a5e04838d9e4a0a0ddf574c4de827',1,'handlegraph::PathHandleGraph::path_end()']]],
+ ['path_5fend_5fnode_5foffset_4473',['path_end_node_offset',['../classvg_1_1VG.html#a8f45b42614f4ac36c8060634ec0d9805',1,'vg::VG']]],
+ ['path_5fend_5fposition_4474',['path_end_position',['../namespacevg.html#af505a96db454fbd06e026f11cb6fbfba',1,'vg']]],
+ ['path_5ffinder_4475',['path_finder',['../classvg_1_1VCFTraversalFinder.html#a7f529cb408098ee45d3e4868ed9fe2b8',1,'vg::VCFTraversalFinder']]],
+ ['path_5ffor_5fcontig_4476',['path_for_contig',['../haplotypes__main_8cpp.html#a38d910b58a339b55e1135bad308a2aab',1,'haplotypes_main.cpp']]],
+ ['path_5ffor_5fsample_5fcontig_4477',['path_for_sample_contig',['../haplotypes__main_8cpp.html#a3336c94d43159885886cca6dfef27b87',1,'haplotypes_main.cpp']]],
+ ['path_5ffrom_5flength_4478',['path_from_length',['../namespacevg.html#a1524b7b1b7e67c048c0c5e88b204de08',1,'vg::path_from_length(const Path &path)'],['../namespacevg.html#ae87f325eb11aaf966e6d77d99be40c54',1,'vg::path_from_length(const path_t &path)']]],
+ ['path_5ffrom_5fnode_5ftraversals_4479',['path_from_node_traversals',['../namespacevg.html#a3aef5ee16ad883f8defeaa0f52fc342c',1,'vg']]],
+ ['path_5ffrom_5fpath_5fhandle_4480',['path_from_path_handle',['../namespacevg.html#a864fe6e3e163b18e84db0783f9a2e17d',1,'vg']]],
+ ['path_5ffrom_5fthread_5ft_4481',['path_from_thread_t',['../namespacevg.html#ab0f225fb74f28ea09c6c8917ec14db73',1,'vg']]],
+ ['path_5ffront_5fend_4482',['path_front_end',['../classvg_1_1MemoizingGraph.html#ac3db812ecb9ba33c323ed21f2fb30de2',1,'vg::MemoizingGraph::path_front_end()'],['../classvg_1_1PathSubgraphOverlay.html#a4e25154f03620214b41b52efe030ef2a',1,'vg::PathSubgraphOverlay::path_front_end()'],['../classvg_1_1VG.html#a5e1a4d7c14f1aaf601e9a6e231b6b7d3',1,'vg::VG::path_front_end()'],['../classxg_1_1XG.html#a7c14874c12caf4b94eb87af8d2daa686',1,'xg::XG::path_front_end()'],['../classhandlegraph_1_1PathHandleGraph.html#ad7412bf19084f2b38ffec42517a6a9e9',1,'handlegraph::PathHandleGraph::path_front_end()']]],
+ ['path_5fgraph_4483',['path_graph',['../classvg_1_1MinimizerMapper.html#aa75ca7504db85f1ba5d340b8213036de',1,'vg::MinimizerMapper::path_graph()'],['../classvg_1_1PhaseUnfolder.html#a974791c770e3999168899eb36cbd2f48',1,'vg::PhaseUnfolder::path_graph()'],['../structGraphHandler.html#aeb4deb32f56c35702b331c0f506d3844',1,'GraphHandler::path_graph()']]],
+ ['path_5fhandle_5fgraph_2ecpp_4484',['path_handle_graph.cpp',['../path__handle__graph_8cpp.html',1,'']]],
+ ['path_5fhandle_5fgraph_2ehpp_4485',['path_handle_graph.hpp',['../path__handle__graph_8hpp.html',1,'']]],
+ ['path_5fhandle_5ft_4486',['path_handle_t',['../structhandlegraph_1_1path__handle__t.html',1,'handlegraph::path_handle_t'],['../namespacevg.html#aaf7aeec04909c1aac0ad991764d48e24',1,'vg::path_handle_t()'],['../namespacevg_1_1io.html#a5cab7a1a96fc203865d8ca67a372b24f',1,'vg::io::path_handle_t()']]],
+ ['path_5fidentity_4487',['path_identity',['../classvg_1_1VG.html#ad9bd4133841d1d781fb0df4171773139',1,'vg::VG']]],
+ ['path_5findex_2ecpp_4488',['path_index.cpp',['../path__index_8cpp.html',1,'']]],
+ ['path_5findex_2ehpp_4489',['path_index.hpp',['../path__index_8hpp.html',1,'']]],
+ ['path_5findexes_4490',['path_indexes',['../classvg_1_1LegacyCaller.html#a5de5c60b4da9b71566fc10a76ed0e211',1,'vg::LegacyCaller']]],
+ ['path_5fis_5fsimple_5fmatch_4491',['path_is_simple_match',['../namespacevg.html#a43c4a438edc31c7b0d2aa0731c522e8a',1,'vg']]],
+ ['path_5fjaccard_5fwindow_4492',['path_jaccard_window',['../classvg_1_1Deconstructor.html#a0cf545ea26ebb9bbebafefe47524f87b',1,'vg::Deconstructor']]],
+ ['path_5flength_4493',['path_length',['../structgafkluge_1_1GafRecord.html#ac9b7a4a556d78f32913392b0706e93e0',1,'gafkluge::GafRecord']]],
+ ['path_5flength_5ffilter_4494',['path_length_filter',['../classvg_1_1Filter.html#a4b9e7a11ee8f1d58a4ae99d6a0a7aabf',1,'vg::Filter']]],
+ ['path_5flengths_5fto_5fsinks_4495',['path_lengths_to_sinks',['../classvg_1_1BandedGlobalAligner.html#a52406c8606e4aa4c817251289651b4cc',1,'vg::BandedGlobalAligner']]],
+ ['path_5flisteners_4496',['path_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aa856090842dafbe0dbaf22bed66fd411',1,'vg::algorithms::GFAParser']]],
+ ['path_5fmapping_5fnode_5fid_4497',['path_mapping_node_id',['../structhaplo_1_1linear__haplo__structure.html#ae72d0e22919bc536e6ebc765f56b6271',1,'haplo::linear_haplo_structure']]],
+ ['path_5fmapping_5foffset_4498',['path_mapping_offset',['../structhaplo_1_1linear__haplo__structure.html#a2d1b328d1268ef04ac035550eda05ebf',1,'haplo::linear_haplo_structure']]],
+ ['path_5fmapping_5ft_4499',['path_mapping_t',['../classvg_1_1path__mapping__t.html',1,'vg::path_mapping_t'],['../classvg_1_1path__mapping__t.html#af53a6e6f24b6bc9fbd611bcf826845bd',1,'vg::path_mapping_t::path_mapping_t()=default'],['../classvg_1_1path__mapping__t.html#ab2a0922f085a4f2838437613525ff25c',1,'vg::path_mapping_t::path_mapping_t(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a64f8b90a2817811dd06ae831094c5fa5',1,'vg::path_mapping_t::path_mapping_t(path_mapping_t &&other)=default']]],
+ ['path_5fmetadata_2ecpp_4500',['path_metadata.cpp',['../path__metadata_8cpp.html',1,'']]],
+ ['path_5fmetadata_2ehpp_4501',['path_metadata.hpp',['../path__metadata_8hpp.html',1,'']]],
+ ['path_5fmode_4502',['path_mode',['../structGBWTConfig.html#a218c5f96dd7101b89bdf8e64de3b9949',1,'GBWTConfig']]],
+ ['path_5fname_4503',['path_name',['../structvg_1_1FeatureSet_1_1Feature.html#a645900ed3044cc3359c18e109f7460a7',1,'vg::FeatureSet::Feature::path_name()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad19c5f9cbb68abb1bcfe6e3a9fd65382',1,'vg::GraphSynchronizer::Lock::path_name()'],['../classxg_1_1XG.html#adf5cee0fdfb7bac641cf0e7e10371f8a',1,'xg::XG::path_name()']]],
+ ['path_5fname_5fcsa_5fdelim_4504',['path_name_csa_delim',['../classxg_1_1XG.html#a5b2791b586efb23a131c2d5c00d85593',1,'xg::XG']]],
+ ['path_5fnames_4505',['path_names',['../classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138',1,'vg::VariantAdder::path_names()'],['../structGBWTConfig.html#a96ccf4e2605d4dad1a32511169f51969',1,'GBWTConfig::path_names()']]],
+ ['path_5fnames_5fby_5fprefix_4506',['path_names_by_prefix',['../classxg_1_1XG.html#a70a2bac209d84ee2b9165a7dfca5969e',1,'xg::XG']]],
+ ['path_5fnode_4507',['path_node',['../namespacevg.html#a3bd8aa63fec8b9f6c3ed5808689975e6',1,'vg::path_node(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#ac6bdd8e00dd9f63a0d9049ffe3461d47',1,'vg::path_node(const gbwt::vector_type &path, size_t i)']]],
+ ['path_5fnodes_4508',['path_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a76f9356cd0afea7dea3003caea2526eb',1,'vg::MultipathAlignmentGraph']]],
+ ['path_5foffset_4509',['path_offset',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a58b1c09d2f45e4942afd52d975c85b9a',1,'vg::GraphSynchronizer::Lock']]],
+ ['path_5foffset_5fcollection_5ft_4510',['path_offset_collection_t',['../namespacevg_1_1algorithms.html#a6474017f8ab54b0c6e20095206a880a8',1,'vg::algorithms']]],
+ ['path_5forder_5fand_5flength_4511',['path_order_and_length',['../classvg_1_1HTSWriter.html#a2b0a5d9268a4b4901a699f82d857d6e2',1,'vg::HTSWriter']]],
+ ['path_5foutput_4512',['path_output',['../structGBWTConfig.html#a91e5194d120c0dbae060bdfe5c60667a',1,'GBWTConfig']]],
+ ['path_5fposition_5fhandle_5fgraph_4513',['path_position_handle_graph',['../classvg_1_1MCMCCaller.html#a240741cadefa13b2b4d472f0b6e3b8d3',1,'vg::MCMCCaller']]],
+ ['path_5fposition_5fhandle_5fgraph_2ecpp_4514',['path_position_handle_graph.cpp',['../path__position__handle__graph_8cpp.html',1,'']]],
+ ['path_5fposition_5fhandle_5fgraph_2ehpp_4515',['path_position_handle_graph.hpp',['../path__position__handle__graph_8hpp.html',1,'']]],
+ ['path_5fpredecessors_4516',['path_predecessors',['../namespacevg.html#a72aa312e964fab8a03b93ec897f355ec',1,'vg']]],
+ ['path_5franks_5fby_5fprefix_4517',['path_ranks_by_prefix',['../classxg_1_1XG.html#a93b333ee3c02b8309a139401f1dc661f',1,'xg::XG']]],
+ ['path_5freverse_4518',['path_reverse',['../namespacevg.html#ae8fcec2fbe4151075a0b33bc6a0dd145',1,'vg::path_reverse(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#aa0439b7fcf30da565152d9800ff4473d',1,'vg::path_reverse(const gbwt::vector_type &path, size_t i)']]],
+ ['path_5fsampler_4519',['path_sampler',['../classvg_1_1Sampler.html#a8125a49b29eecf4d5037067c813b2cd7',1,'vg::Sampler::path_sampler()'],['../classvg_1_1NGSSimulator.html#a6101d443a8c314416fbc23dbfd3d5bde',1,'vg::NGSSimulator::path_sampler()']]],
+ ['path_5fscore_5fannotations_4520',['path_score_annotations',['../classvg_1_1Surjector.html#a9a83875480f04c8dad0207ead58003b8',1,'vg::Surjector']]],
+ ['path_5fsequence_4521',['path_sequence',['../classvg_1_1VG.html#a4ce6fe02b243b4f0f82bbf801fd507fa',1,'vg::VG::path_sequence()'],['../namespacevg.html#aad7dc3b95a62cfd99b5fa6377c1a9545',1,'vg::path_sequence()']]],
+ ['path_5fsize_4522',['path_size',['../namespacevg.html#aae876005c9e34df70bdc9e2e97776121',1,'vg::path_size(const vector< pair< vg::id_t, bool >> &path)'],['../namespacevg.html#a0c911ba34849a4afd407812fe6373579',1,'vg::path_size(const gbwt::vector_type &path)']]],
+ ['path_5fstart_4523',['path_start',['../structgafkluge_1_1GafRecord.html#a14ce42efee5a241bebe4debf852afbae',1,'gafkluge::GafRecord']]],
+ ['path_5fstart_5fposition_4524',['path_start_position',['../namespacevg.html#a2c3b1708b878655d0f6a50a2ba589bf9',1,'vg']]],
+ ['path_5fstring_4525',['path_string',['../namespacevg_1_1algorithms.html#a7acc0acf3d99939a0943ca9e0b86e48a',1,'vg::algorithms']]],
+ ['path_5fstring_2ecpp_4526',['path_string.cpp',['../path__string_8cpp.html',1,'']]],
+ ['path_5fstring_2ehpp_4527',['path_string.hpp',['../path__string_8hpp.html',1,'']]],
+ ['path_5fsubgraph_2ecpp_4528',['path_subgraph.cpp',['../path__subgraph_8cpp.html',1,'']]],
+ ['path_5fsubgraph_2ehpp_4529',['path_subgraph.hpp',['../path__subgraph_8hpp.html',1,'']]],
+ ['path_5fsubset_4530',['path_subset',['../classvg_1_1PathSubgraphOverlay.html#aef82f75c24c686645b0255685bc4c6f2',1,'vg::PathSubgraphOverlay']]],
+ ['path_5ft_4531',['path_t',['../classvg_1_1path__t.html',1,'vg::path_t'],['../classvg_1_1path__t.html#ac49a26cfbfc0dc2d3bc16ec5b38fceda',1,'vg::path_t::path_t()=default'],['../classvg_1_1path__t.html#a75929a646a781440f67c3b374a6c9166',1,'vg::path_t::path_t(const path_t &other)=default'],['../classvg_1_1path__t.html#ad9d1b8c169d9819e70dda68bca1af668',1,'vg::path_t::path_t(path_t &&other)=default']]],
+ ['path_5fto_5fgbwt_4532',['path_to_gbwt',['../namespacevg.html#a529e3aef69e8c01934184726b7937c37',1,'vg']]],
+ ['path_5fto_5fgbwt_5fthread_5ft_4533',['path_to_gbwt_thread_t',['../namespacehaplo.html#a86bbe3de0c810d215fd574fe4dfadfee',1,'haplo']]],
+ ['path_5fto_5finput_5fhaplotype_4534',['path_to_input_haplotype',['../structhaplo_1_1linear__haplo__structure.html#acf88c54b278bcacae66383f2668970b2',1,'haplo::linear_haplo_structure']]],
+ ['path_5fto_5flength_4535',['path_to_length',['../namespacevg.html#a48108a0abc0fdfc187437d174f88e590',1,'vg::path_to_length(const Path &path)'],['../namespacevg.html#a16b3cfa2fc1c70ce96f7ebc695c8766d',1,'vg::path_to_length(const path_t &path)']]],
+ ['path_5fto_5fploidy_4536',['path_to_ploidy',['../classvg_1_1VCFGenotyper.html#a248d8e2819ba7354c39b3d2077061fed',1,'vg::VCFGenotyper']]],
+ ['path_5fto_5fsample_5fphase_4537',['path_to_sample_phase',['../classvg_1_1Deconstructor.html#a8a5562db89e9293a88b2f22e476d1d25',1,'vg::Deconstructor']]],
+ ['path_5fto_5fstring_4538',['path_to_string',['../namespacevg.html#afbe0993e79f4ef7bb4b37456b0b08402',1,'vg']]],
+ ['path_5fto_5fvcf_4539',['path_to_vcf',['../classvg_1_1HaplotypeIndexer.html#a5ff016a7fdf425ec4f3d5408d09b951f',1,'vg::HaplotypeIndexer']]],
+ ['path_5ftrav_5ffinder_4540',['path_trav_finder',['../classvg_1_1Deconstructor.html#a73c6c008333acfbb0ffd6fde2360518c',1,'vg::Deconstructor']]],
+ ['path_5ftype_4541',['path_type',['../classvg_1_1PhaseUnfolder.html#a402b0f84990279594bfbb1cd71ffd8e5',1,'vg::PhaseUnfolder::path_type()'],['../structjob__type.html#a8749aa5a745848ff8d5a6e72bdc002e6',1,'job_type::path_type()']]],
+ ['pathbasedtraversalfinder_4542',['PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html',1,'vg::PathBasedTraversalFinder'],['../classvg_1_1PathBasedTraversalFinder.html#ae9824d8e0620854391925d43c7200da6',1,'vg::PathBasedTraversalFinder::PathBasedTraversalFinder()']]],
+ ['pathbranch_4543',['PathBranch',['../structvg_1_1PathBranch.html',1,'vg']]],
+ ['pathchunker_4544',['PathChunker',['../classvg_1_1PathChunker.html',1,'vg::PathChunker'],['../classvg_1_1PathChunker.html#a5b31a6a4f865a99818f69be54b7f9e40',1,'vg::PathChunker::PathChunker()']]],
+ ['pathcomponentindex_4545',['PathComponentIndex',['../classvg_1_1PathComponentIndex.html',1,'vg::PathComponentIndex'],['../classvg_1_1PathComponentIndex.html#aa8aa8ec6a8bc50004db3e07d081d1942',1,'vg::PathComponentIndex::PathComponentIndex(const PathHandleGraph *graph)'],['../classvg_1_1PathComponentIndex.html#a9b093ea34524c9e95cd10375dd000c87',1,'vg::PathComponentIndex::PathComponentIndex()']]],
+ ['pathforeachsocket_4546',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html',1,'handlegraph::PathForEachSocket'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ad5b94c4a72e3d6d48be27cb00bc41ca2',1,'handlegraph::PathForEachSocket::iterator::PathForEachSocket()'],['../classhandlegraph_1_1PathForEachSocket.html#a1ae98a885a8b37c66d522c3a282c5fd5',1,'handlegraph::PathForEachSocket::PathForEachSocket()=delete'],['../classhandlegraph_1_1PathForEachSocket.html#adea5ed0aea8a5167d7c09a731b9ab65e',1,'handlegraph::PathForEachSocket::PathForEachSocket(const PathHandleGraph *graph, const path_handle_t &path)']]],
+ ['pathhandlegraph_4547',['PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html',1,'handlegraph::PathHandleGraph'],['../classhandlegraph_1_1PathForEachSocket.html#a4260787fbe094766e75485f7d7d9d0ca',1,'handlegraph::PathForEachSocket::PathHandleGraph()'],['../namespacevg.html#abeb2636bd0db3101259ef6803cb4e591',1,'vg::PathHandleGraph()']]],
+ ['pathindex_4548',['PathIndex',['../structvg_1_1PathIndex.html',1,'vg::PathIndex'],['../structvg_1_1PathIndex.html#ac9bdc9df55bcad668ab35b713c366994',1,'vg::PathIndex::PathIndex(const Path &path)'],['../structvg_1_1PathIndex.html#a99878fd10f43e040987e334a70d22d87',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings)'],['../structvg_1_1PathIndex.html#a91e9971a2ddb597ea1c229659b9c9b93',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings, VG &vg)'],['../structvg_1_1PathIndex.html#a72ba06ae7c3fed7abba0cbe2dd6cac88',1,'vg::PathIndex::PathIndex(const Path &path, const HandleGraph &graph)'],['../structvg_1_1PathIndex.html#a9b82679a8d5040f0160edc008d8b348d',1,'vg::PathIndex::PathIndex(VG &vg, const string &path_name, bool extract_sequence=false)'],['../structvg_1_1PathIndex.html#a88a67933e88510cd99800348eb40aa57',1,'vg::PathIndex::PathIndex(const PathHandleGraph &graph, const string &path_name, bool extract_sequence=false)']]],
+ ['pathinterval_4549',['PathInterval',['../namespacevg.html#ae8f438fe1484a4bcc51d06ad13058c9c',1,'vg']]],
+ ['pathlist_4550',['PathList',['../structvg_1_1MatchPos_1_1PathList.html',1,'vg::MatchPos']]],
+ ['pathmetadata_4551',['PathMetadata',['../classhandlegraph_1_1PathMetadata.html',1,'handlegraph::PathMetadata'],['../namespacevg.html#ab5f7f6692a7600f1fa62428255c5bb61',1,'vg::PathMetadata()']]],
+ ['pathnode_4552',['PathNode',['../classvg_1_1PathNode.html',1,'vg']]],
+ ['pathorienteddistancemeasurer_4553',['PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html',1,'vg::PathOrientedDistanceMeasurer'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a483512f5650b15d5f56935ce2d7ce1bf',1,'vg::PathOrientedDistanceMeasurer::PathOrientedDistanceMeasurer()']]],
+ ['pathpositionhandlegraph_4554',['PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html',1,'handlegraph::PathPositionHandleGraph'],['../namespacevg.html#a2481be7fa8c46933b9b99108e4c797b3',1,'vg::PathPositionHandleGraph()']]],
+ ['pathrestrictedtraversalfinder_4555',['PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html',1,'vg::PathRestrictedTraversalFinder'],['../classvg_1_1PathRestrictedTraversalFinder.html#aba5b15255fc6b93f745649eed9d0c535',1,'vg::PathRestrictedTraversalFinder::PathRestrictedTraversalFinder()']]],
+ ['paths_4556',['Paths',['../classvg_1_1Paths.html',1,'vg::Paths'],['../classvg_1_1SurjectingAlignmentEmitter.html#a3193ef16804780255b9d0bbcef8dc6ca',1,'vg::SurjectingAlignmentEmitter::paths()'],['../classvg_1_1PathTraversalFinder.html#a5a931da9269d7834dcc04e5fb578ff45',1,'vg::PathTraversalFinder::paths()'],['../classvg_1_1VG.html#a7c5150aba84e7ed2bde7986462a79989',1,'vg::VG::paths()'],['../structjob__type.html#a1c12e7fbad645aa2081f00b1a49b296f',1,'job_type::paths()'],['../classxg_1_1XG.html#a1b5defef10208838d0d3a48ddeb91f85',1,'xg::XG::paths()'],['../classvg_1_1Paths.html#af048f547f9c4976c17aaa34f1cbec312',1,'vg::Paths::Paths(void)'],['../classvg_1_1Paths.html#a92fa1ad35d1cf495d96e8fbd468f2700',1,'vg::Paths::Paths(const Paths &other)'],['../classvg_1_1Paths.html#a7b932a39b910d477cd7f3e65a0af3c93',1,'vg::Paths::Paths(Paths &&other) noexcept']]],
+ ['paths_5fas_5falignments_4557',['paths_as_alignments',['../classvg_1_1VG.html#a871d05e0a2d0b76092e20fe86bd12e2b',1,'vg::VG']]],
+ ['paths_5fbetween_4558',['paths_between',['../classvg_1_1VG.html#a8dc8d762d07088089247b632c835a19d',1,'vg::VG::paths_between(Node *from, Node *to, vector< Path > &paths)'],['../classvg_1_1VG.html#a0a5a5cb1bac139c5a3a947a0d5a3313d',1,'vg::VG::paths_between(nid_t from, nid_t to, vector< Path > &paths)']]],
+ ['paths_5ffrom_5fgraph_4559',['paths_from_graph',['../namespacevg.html#a1b5ffc03255d72f1901a7b1ce34c058a',1,'vg']]],
+ ['paths_5fmain_2ecpp_4560',['paths_main.cpp',['../paths__main_8cpp.html',1,'']]],
+ ['paths_5fof_5fhandle_4561',['paths_of_handle',['../classxg_1_1XG.html#a519fa3151a3b49f5939277a14dced503',1,'xg::XG']]],
+ ['paths_5fon_5fsame_5fcomponent_4562',['paths_on_same_component',['../classvg_1_1PathComponentIndex.html#a77de0e355ad6b0893cc506ce18adb050',1,'vg::PathComponentIndex']]],
+ ['pathsense_4563',['PathSense',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271c',1,'handlegraph::PathSense()'],['../namespacevg.html#a15c1e75e93ab89aacd0eb7e1f0299724',1,'vg::PathSense()']]],
+ ['pathsubgraph_4564',['PathSubgraph',['../classvg_1_1PathSubgraph.html',1,'vg::PathSubgraph'],['../classvg_1_1PathSubgraph.html#a861b07c24488c1454b6c04b1f7f01b68',1,'vg::PathSubgraph::PathSubgraph()']]],
+ ['pathsubgraphoverlay_4565',['PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html',1,'vg::PathSubgraphOverlay'],['../classvg_1_1PathSubgraphOverlay.html#a71b48d68fc02b88cf0b1c15ca26aa2c6',1,'vg::PathSubgraphOverlay::PathSubgraphOverlay()']]],
+ ['pathtraversalfinder_4566',['PathTraversalFinder',['../classvg_1_1PathTraversalFinder.html',1,'vg::PathTraversalFinder'],['../classvg_1_1PathTraversalFinder.html#a49d66e050feec7374fb0d2ed3483b897',1,'vg::PathTraversalFinder::PathTraversalFinder()']]],
+ ['payload_4567',['payload',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a9b29761900b87e78b6c17dbe8e38d4fe',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
+ ['payload_5fnode_5flength_4568',['payload_node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ac80389e7a2ddaae480e60b286186e3aa',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
+ ['payload_5fprefix_5fsum_4569',['payload_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ab809433b78a00f00ae46e7061972c9a9',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
+ ['pb2json_4570',['pb2json',['../json2pb_8cpp.html#af6bb66946ffaf36b1fe45881291fee0d',1,'pb2json(const Message &msg): json2pb.cpp'],['../json2pb_8h.html#a7cc576c6ed1e52ba82cf5f264f8ba21d',1,'pb2json(const google::protobuf::Message &msg): json2pb.h']]],
+ ['pbsize_4571',['pbSize',['../classvg_1_1io_1_1fdinbuf.html#a1756a5735e7daf8ea042bc81343f7a0f',1,'vg::io::fdinbuf::pbSize()'],['../classvg_1_1io_1_1streaminbuf.html#a4cdee06174136df70efd572abfced2c8',1,'vg::io::streaminbuf::pbSize()']]],
+ ['peek_4572',['peek',['../classvg_1_1BitString.html#a2b6d10b59df3727c8f07c3fbe646d03c',1,'vg::BitString']]],
+ ['penalties_4573',['penalties',['../structhaplo_1_1linear__haplo__structure.html#af55d7f33177180d033e8e925cf20e5fd',1,'haplo::linear_haplo_structure']]],
+ ['per_5fbase_4574',['per_base',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a8a85161fa2d79301a9ca6489006a4c62',1,'vg::WFAExtender::ErrorModel::Event']]],
+ ['percent_5fidentity_5ffilter_4575',['percent_identity_filter',['../classvg_1_1Filter.html#aba2f93a1c4087075ccf4924fd0e44392',1,'vg::Filter']]],
+ ['percent_5furl_5fencode_4576',['percent_url_encode',['../namespacevg.html#a2ba15a613567689d941f30a5a17c6ead',1,'vg']]],
+ ['perfect_5ffilter_4577',['perfect_filter',['../classvg_1_1Filter.html#af33b08ad08247167fbe7d90ac86047a3',1,'vg::Filter']]],
+ ['perfect_5fpair_5fidentity_5fthreshold_4578',['perfect_pair_identity_threshold',['../classvg_1_1FragmentLengthStatistics.html#a4e65bc3de5657555df556429284f5251',1,'vg::FragmentLengthStatistics']]],
+ ['perform_5fdp_4579',['perform_dp',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6a5314b3408ca05c265648b8b6053e1d',1,'vg::MEMClusterer::HitGraph']]],
+ ['performed_5fduplications_4580',['performed_duplications',['../classvg_1_1DozeuPinningOverlay.html#af98692ca5587716febd938e4e216cf99',1,'vg::DozeuPinningOverlay']]],
+ ['peripheral_5fattachments_4581',['peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa2e7c9a960855fa8758d9dd6da6454ea',1,'vg::GraphSynchronizer::Lock']]],
+ ['periphery_4582',['periphery',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad9bebede56cef5ab20d80828e34d8b6a',1,'vg::GraphSynchronizer::Lock']]],
+ ['permutation_5fidx_4583',['permutation_idx',['../classvg_1_1ShuffledPairs_1_1iterator.html#a52dd908e59ff6dac90191a40c63537e0',1,'vg::ShuffledPairs::iterator']]],
+ ['permuted_4584',['permuted',['../classvg_1_1ShuffledPairs_1_1iterator.html#a19642461808615472b7b544e04c47243',1,'vg::ShuffledPairs::iterator']]],
+ ['pessimistic_5fgap_4585',['pessimistic_gap',['../classvg_1_1MultipathMapper.html#ac4311460002c8df22a29b3e55cc4e1ff',1,'vg::MultipathMapper']]],
+ ['pessimistic_5fgap_5fmemo_4586',['pessimistic_gap_memo',['../classvg_1_1MultipathMapper.html#a828e72945f3e24243d5802604e027b47',1,'vg::MultipathMapper']]],
+ ['pessimistic_5fgap_5fmultiplier_4587',['pessimistic_gap_multiplier',['../classvg_1_1MultipathMapper.html#aef97cb46d48a242a68c6ed590039e832',1,'vg::MultipathMapper']]],
+ ['pessimistic_5ftail_5fgap_4588',['pessimistic_tail_gap',['../classvg_1_1MultipathAlignmentGraph.html#a4c591d080bc48994fcdb2c9dc08d34a1',1,'vg::MultipathAlignmentGraph']]],
+ ['pessimistic_5ftail_5fgap_5fmemo_4589',['pessimistic_tail_gap_memo',['../classvg_1_1MultipathAlignmentGraph.html#af46ba9972db437bf66f787a9bbe6c3cd',1,'vg::MultipathAlignmentGraph']]],
+ ['phase_4590',['phase',['../structvg_1_1GFFRecord.html#adf3d82a77a4837edba29935e08cb2a53',1,'vg::GFFRecord']]],
+ ['phase_5fblock_5fmatch_4591',['PHASE_BLOCK_MATCH',['../classhandlegraph_1_1PathMetadata.html#a08fb019956ae31b8ea31920c904ea5fc',1,'handlegraph::PathMetadata']]],
+ ['phase_5fhomozygous_4592',['phase_homozygous',['../classvg_1_1HaplotypeIndexer.html#a881e755025092748b18f037fb1078e65',1,'vg::HaplotypeIndexer']]],
+ ['phase_5funfolder_2ecpp_4593',['phase_unfolder.cpp',['../phase__unfolder_8cpp.html',1,'']]],
+ ['phase_5funfolder_2ehpp_4594',['phase_unfolder.hpp',['../phase__unfolder_8hpp.html',1,'']]],
+ ['phase_5fvisits_4595',['phase_visits',['../structvg_1_1VG_1_1Plan.html#ad18d84799bb31227175746bee50f6940',1,'vg::VG::Plan']]],
+ ['phased_5fgenome_2ecpp_4596',['phased_genome.cpp',['../phased__genome_8cpp.html',1,'']]],
+ ['phased_5fgenome_2ehpp_4597',['phased_genome.hpp',['../phased__genome_8hpp.html',1,'']]],
+ ['phasedgenome_4598',['PhasedGenome',['../classvg_1_1PhasedGenome.html',1,'vg::PhasedGenome'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::Haplotype::PhasedGenome()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::iterator::PhasedGenome()'],['../classvg_1_1PhasedGenome.html#aa7a7cce5f88f52d20c659e64966ece28',1,'vg::PhasedGenome::PhasedGenome(const SnarlManager &snarl_manager)'],['../classvg_1_1PhasedGenome.html#a0e96410c065eb722e527be06b710c5d7',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome.html#ace57a61caa7e82942f94ea1e128bc3e3',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &&other)=delete']]],
+ ['phaseunfolder_4599',['PhaseUnfolder',['../classvg_1_1PhaseUnfolder.html',1,'vg::PhaseUnfolder'],['../classvg_1_1PhaseUnfolder.html#a7d6868ce2e12eeae8a8df8b00c6b5003',1,'vg::PhaseUnfolder::PhaseUnfolder()']]],
+ ['phi_4600',['Phi',['../namespacevg.html#afea3e6d4a8ac9b486d1a2b9b89eadd2f',1,'vg']]],
+ ['phi_5finv_4601',['Phi_inv',['../namespacevg.html#a4ae7976a3a19fe08c4b2bce4b3f3c00f',1,'vg']]],
+ ['phred_5fadd_4602',['phred_add',['../namespacevg.html#a211ba38329cdc76a7ad0b64bbb227bfd',1,'vg']]],
+ ['phred_5ffor_5fat_5fleast_5fone_4603',['phred_for_at_least_one',['../namespacevg.html#a9a6ab3a0f45f6ab7b38320db7cc14583',1,'vg']]],
+ ['phred_5fgeometric_5fmean_4604',['phred_geometric_mean',['../namespacevg.html#a04edc3daae77e9d3813a97da0f473def',1,'vg']]],
+ ['phred_5fprob_4605',['phred_prob',['../classvg_1_1NGSSimulator.html#ab8ace60ed77440820944dbdaee5bb123',1,'vg::NGSSimulator']]],
+ ['phred_5fsum_4606',['phred_sum',['../namespacevg.html#aaeddefa307b95defd68c8a2022db732c',1,'vg::phred_sum(const Iterator &begin_it, const Iterator &end_it)'],['../namespacevg.html#ad78072e330ae86c9ef80aeeb84f89e8f',1,'vg::phred_sum(const Collection &collection)']]],
+ ['phred_5fto_5flogprob_4607',['phred_to_logprob',['../namespacevg.html#a35b531c82b765cd54702665668a98448',1,'vg']]],
+ ['phred_5fto_5fprob_4608',['phred_to_prob',['../namespacevg.html#ab713ebc6e2988cc2c959be14bfa01200',1,'vg::phred_to_prob(uint8_t phred)'],['../namespacevg.html#afba77c5a550d5dd72f8cf7438f600676',1,'vg::phred_to_prob(double phred)']]],
+ ['pi_5fiv_4609',['pi_iv',['../classxg_1_1XG.html#a31024f79e1a2564e990e1e4445fed0ce',1,'xg::XG']]],
+ ['pick_5fmappings_5ffrom_5falignments_4610',['pick_mappings_from_alignments',['../classvg_1_1MinimizerMapper.html#a967245a85231b63dd7606b5cd4b4c672',1,'vg::MinimizerMapper']]],
+ ['pictographs_4611',['Pictographs',['../classvg_1_1Pictographs.html',1,'vg::Pictographs'],['../classvg_1_1Pictographs.html#a9784714a3a94bd173fecdd31655a770b',1,'vg::Pictographs::Pictographs(void)'],['../classvg_1_1Pictographs.html#a997d5ba6f6e9c5cbdb039ed9c51625e9',1,'vg::Pictographs::Pictographs(int seed_val)']]],
+ ['pictographs_2ehpp_4612',['pictographs.hpp',['../pictographs_8hpp.html',1,'']]],
+ ['pileup_4613',['Pileup',['../structvg_1_1Pileup.html',1,'vg']]],
+ ['pin_5foffset_4614',['pin_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aff4877147fc6b731179a8e89dfb99757',1,'vg::MinimizerMapper::Minimizer']]],
+ ['pinned_5ftail_5fsize_4615',['pinned_tail_size',['../classvg_1_1VariantAdder.html#ab5dea4bb3c4143e8fb4e28205a4d2cd6',1,'vg::VariantAdder']]],
+ ['pipeline_4616',['PIPELINE',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838a797a289a67a7dd20502b2436f0c9d305',1,'vg::subcommand']]],
+ ['placed_4617',['PLACED',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85a0a4373ca716769f93112e16e251bb8a1',1,'vg::Funnel']]],
+ ['plan_4618',['Plan',['../structvg_1_1VG_1_1Plan.html',1,'vg::VG::Plan'],['../structvg_1_1VG_1_1Plan.html#aa757327a3bf40e1828d8aacc5cf5dec5',1,'vg::VG::Plan::Plan()']]],
+ ['plausible_5frescue_5fcluster_5fcoverage_5fdiff_4619',['plausible_rescue_cluster_coverage_diff',['../classvg_1_1MultipathMapper.html#aea5ee453023a73c3d7c02b929d9ef073',1,'vg::MultipathMapper']]],
+ ['pmax_4620',['pmax',['../namespacevg.html#ac7f5da8e25414026729f0c4d09243f6d',1,'vg']]],
+ ['pn_5fbv_4621',['pn_bv',['../classxg_1_1XG.html#a50b600c6e29135f595459d447fb1e6bb',1,'xg::XG']]],
+ ['pn_5fbv_5frank_4622',['pn_bv_rank',['../classxg_1_1XG.html#a9e24932d14efdf5ab53dce331d424093',1,'xg::XG']]],
+ ['pn_5fbv_5fselect_4623',['pn_bv_select',['../classxg_1_1XG.html#a541462516fe4a54499c0b42e4cc95a28',1,'xg::XG']]],
+ ['pn_5fcsa_4624',['pn_csa',['../classxg_1_1XG.html#a638068e773deaf37cb68bd39eb4599fc',1,'xg::XG']]],
+ ['pn_5fiv_4625',['pn_iv',['../classxg_1_1XG.html#aa9d0f9dc89210720c781d43b54f10e4b',1,'xg::XG']]],
+ ['pointer_4626',['pointer',['../classvg_1_1count__back__inserter.html#ab120548e9cd73fcc1ed1f8680b4b5baa',1,'vg::count_back_inserter::pointer()'],['../structvg_1_1VectorView_1_1const__iterator.html#a8b8e23d22e4b85f617c466337d5f0ea2',1,'vg::VectorView::const_iterator::pointer()'],['../classvg_1_1SmallBitset.html#a7c4623fa954362f27858d7714acf38cf',1,'vg::SmallBitset::pointer()']]],
+ ['pointerfy_4627',['pointerfy',['../namespacevg.html#ae6a210206858f806b345f8eb5c2c292a',1,'vg']]],
+ ['points_4628',['points',['../classvg_1_1algorithms_1_1Anchor.html#a92c0db96b472fce0a3f130cdf281999d',1,'vg::algorithms::Anchor']]],
+ ['points_5fper_5fpossible_5fmatch_4629',['points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a4cb0f074432b4ab94eecd529bc18a6c2',1,'vg::MinimizerMapper']]],
+ ['poisson_5fprob_5fln_4630',['poisson_prob_ln',['../namespacevg.html#a9238b15cc78a87f27c335fc1e3627a62',1,'vg']]],
+ ['poissoncallinfo_4631',['PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html',1,'vg::PoissonSupportSnarlCaller']]],
+ ['poissonsupportsnarlcaller_4632',['PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html',1,'vg::PoissonSupportSnarlCaller'],['../classvg_1_1PoissonSupportSnarlCaller.html#aebde111c1431bf4af46929d8e56c7031',1,'vg::PoissonSupportSnarlCaller::PoissonSupportSnarlCaller()']]],
+ ['polyploid_5fprior_5fsuccess_5flogprob_4633',['polyploid_prior_success_logprob',['../classvg_1_1Genotyper.html#a97aef0fe84f0514e17e2ec8e00162225',1,'vg::Genotyper']]],
+ ['pop_4634',['pop',['../structvg_1_1MatchPos_1_1PathList.html#a6fa2799b0d2b17e437a6c7a92ef75a4d',1,'vg::MatchPos::PathList::pop()'],['../structvg_1_1MatchPos.html#a0bf4234ad56f10dd4d602102bfaf2297',1,'vg::MatchPos::pop()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3a64ce2b4dfae9f7712598d8d6b676a6',1,'vg::ZipCodeTree::reverse_iterator::pop()']]],
+ ['pop_5fback_5fstep_4635',['pop_back_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a2db5e7a66ccee26fa257c50e0d084c59',1,'handlegraph::MutablePathHandleGraph']]],
+ ['pop_5ffront_5fstep_4636',['pop_front_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a67c8bfd58c5ed8136c9324f427037a7a',1,'handlegraph::MutablePathHandleGraph']]],
+ ['populate_5fpath_5ffrom_5ftraceback_4637',['populate_path_from_traceback',['../namespacevg.html#a191bf7b238ea717afbf8118df0afa999',1,'vg']]],
+ ['populate_5fsnarl_5findex_4638',['populate_snarl_index',['../namespacevg.html#a7c9f1f64df265187309db52705a1bef7',1,'vg']]],
+ ['population_5fmax_5fpaths_4639',['population_max_paths',['../classvg_1_1MultipathMapper.html#adfb100b024b23e3e94a31ea41d0b1ac8',1,'vg::MultipathMapper']]],
+ ['population_5fpaths_5fhard_5fcap_4640',['population_paths_hard_cap',['../classvg_1_1MultipathMapper.html#aa9d339059fb2f60d192935126c82dbed',1,'vg::MultipathMapper']]],
+ ['population_5fsize_4641',['population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#adbcb32fa9395d32959b7c0006f25855c',1,'haplo::haploMath::RRMemo']]],
+ ['pos_4642',['pos',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#af6b3dfbfadf9eb6f64672bf7a2cfb9f6',1,'vg::SnarlDistanceIndexClusterer::Seed::pos()'],['../structvg_1_1ChainIterator.html#ae99bd64d13edc9f317cfd3bd9e9d3d2e',1,'vg::ChainIterator::pos()'],['../structvg_1_1KmerPosition.html#a31de02880d6006049d740e6216087961',1,'vg::KmerPosition::pos()'],['../structvg_1_1WFAPoint.html#a4ea055d164ce5425235ec19d65a7073f',1,'vg::WFAPoint::pos()']]],
+ ['pos_5fat_4643',['pos_at',['../structMappingRun.html#ac8d70e01cbc733abc3612693b39a465c',1,'MappingRun']]],
+ ['pos_5fchar_4644',['pos_char',['../classvg_1_1Sampler.html#a72d922b802775f51f2b02046398d3417',1,'vg::Sampler::pos_char()'],['../classxg_1_1XG.html#abf551ac03c1db6030da1cedb81efc779',1,'xg::XG::pos_char()']]],
+ ['pos_5fkey_4645',['pos_key',['../classvg_1_1Packer.html#a128c9b21b9a784c6ea27501463b23862',1,'vg::Packer']]],
+ ['pos_5fsubstr_4646',['pos_substr',['../classxg_1_1XG.html#aa61897c26d2cee1e8cc8c9fc7eec540b',1,'xg::XG']]],
+ ['pos_5ft_4647',['pos_t',['../namespacevg.html#a8232142f432c4dd8e7cfe96e1f50e039',1,'vg::pos_t()'],['../namespacexg.html#aa22555920305243ff489dc6ed79db5d7',1,'xg::pos_t()'],['../namespacehandlegraph.html#a0abc3c64da852112ad2bc0fc9dd5afce',1,'handlegraph::pos_t()']]],
+ ['pos_5fto_5fedit_5fto_5fdepth_4648',['pos_to_edit_to_depth',['../classvg_1_1Filter.html#a4de4cfcd2bafcc9405c0ffebe84b61dd',1,'vg::Filter']]],
+ ['pos_5fto_5fgbwt_4649',['pos_to_gbwt',['../namespacevg.html#ae1296fd4e352a120122d4be0a0007819',1,'vg']]],
+ ['pos_5fto_5fqual_4650',['pos_to_qual',['../classvg_1_1Filter.html#a619f209f11dd2e9b9ce72db535d402fe',1,'vg::Filter']]],
+ ['pos_5fto_5ftrans_4651',['pos_to_trans',['../classvg_1_1Translator.html#ae41a08cff51e5f56aff61136b4c520f0',1,'vg::Translator']]],
+ ['position_4652',['Position',['../structvg_1_1Position.html',1,'vg::Position'],['../structvg_1_1BREAKPOINT.html#a082deeca85819680dc38ceddf6ccbce7',1,'vg::BREAKPOINT::position()'],['../structvg_1_1RecombinatorHaplotype.html#abedb3835774104b4664b62acd3bea6b6',1,'vg::RecombinatorHaplotype::position()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#ae3a3d3091779285687ae5be43ee61652',1,'vg::algorithms::GFAFormatError::position()'],['../structvg_1_1Mapping.html#a2017c8c72a90df9044e14422a0799c86',1,'vg::Mapping::position()'],['../structvg_1_1KmerMatch.html#af0853c79fa538e1d94090514fd217feb',1,'vg::KmerMatch::position()'],['../classvg_1_1Funnel.html#adee7882f4f431a866847baec1fc77718',1,'vg::Funnel::position()'],['../classvg_1_1path__mapping__t.html#a64f6d0dd6e7ffd6bf6d538c5a25d39f3',1,'vg::path_mapping_t::position()'],['../classvg_1_1Sampler.html#a3d983fa5e24b8802ed2516bf0bb362bf',1,'vg::Sampler::position()']]],
+ ['position_2ecpp_4653',['position.cpp',['../position_8cpp.html',1,'']]],
+ ['position_2ehpp_4654',['position.hpp',['../position_8hpp.html',1,'']]],
+ ['position_5fassuming_5facyclic_4655',['position_assuming_acyclic',['../structhaplo_1_1linear__haplo__structure.html#aa450a108f8b2bab6e98271fcef6b26aa',1,'haplo::linear_haplo_structure']]],
+ ['position_5fat_4656',['position_at',['../namespacevg.html#a9a33db744c41ff651da5dacda9578712',1,'vg']]],
+ ['position_5ffile_4657',['position_file',['../classvg_1_1NGSSimulator.html#a46a332d871425d98495b0b1215ad88e5',1,'vg::NGSSimulator']]],
+ ['position_5fin_5fbasis_4658',['position_in_basis',['../classvg_1_1Packer.html#a6cb79c18881c68ac41b9f2ffa002ef02',1,'vg::Packer']]],
+ ['position_5fin_5fpath_4659',['position_in_path',['../classxg_1_1XG.html#a870b3eae5f72331f2c498043b45b3d8d',1,'xg::XG']]],
+ ['position_5fin_5fpaths_4660',['position_in_paths',['../classxg_1_1XG.html#a1bda47534cd275fdeca72b463303dc1e',1,'xg::XG']]],
+ ['position_5ft_4661',['position_t',['../classvg_1_1position__t.html',1,'vg::position_t'],['../classvg_1_1position__t.html#a34def1328db6dda2482ccb6c64951704',1,'vg::position_t::position_t()'],['../classvg_1_1position__t.html#a47188716e3327201048ba032c10eb8fe',1,'vg::position_t::position_t(const position_t &other)=default'],['../classvg_1_1position__t.html#a1ad8e0a1fe655c7ebb31ff094e43f466',1,'vg::position_t::position_t(position_t &&other)=default']]],
+ ['positionidscanner_4662',['PositionIDScanner',['../structvg_1_1PositionIDScanner.html',1,'vg']]],
+ ['positions_4663',['positions',['../classvg_1_1MEMChainModel.html#ab273ba5c21fc25422f873dd5d4fd37c3',1,'vg::MEMChainModel::positions()'],['../classvg_1_1AlignmentChainModelVertex.html#a5b770fe52ded0e65dbfe6af4865a7d58',1,'vg::AlignmentChainModelVertex::positions()'],['../classvg_1_1AlignmentChainModel.html#ac37666966f063162a7bbcbb0b285ce6b',1,'vg::AlignmentChainModel::positions()'],['../classvg_1_1MaximalExactMatch.html#afd57ff44231f95d0ea6ef6d4ba24608e',1,'vg::MaximalExactMatch::positions()']]],
+ ['possible_5fscores_4664',['possible_scores',['../classvg_1_1WFATree.html#a4646d73afa5c111f920ab006664c4e7b',1,'vg::WFATree']]],
+ ['posterior_4665',['posterior',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#aae17dc073a03b6fc72eef3b281608b68',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['pow_5fln_4666',['pow_ln',['../namespacevg.html#a3a7a8c98d80a9daacbc72386bc6ad00c',1,'vg']]],
+ ['precollapse_5forder_5flength_5fhits_4667',['precollapse_order_length_hits',['../classvg_1_1BaseMapper.html#aaf81156cb8c76c2e961b767a782dda59',1,'vg::BaseMapper']]],
+ ['precollapse_5forder_5flength_5fruns_4668',['precollapse_order_length_runs',['../classvg_1_1BaseMapper.html#af4372862ebd4f21da3e9ed105249a5af',1,'vg::BaseMapper']]],
+ ['predecessor_5foffset_4669',['predecessor_offset',['../classvg_1_1WFATree.html#a5caa4118319b9fa8e5cc87f257c31225',1,'vg::WFATree']]],
+ ['prefilter_5fredundant_5fhits_4670',['prefilter_redundant_hits',['../classvg_1_1BaseMapper.html#afa408c8d202885a288f14ff6e2dc60e0',1,'vg::BaseMapper']]],
+ ['prefilter_5fredundant_5fsub_5fmems_4671',['prefilter_redundant_sub_mems',['../classvg_1_1BaseMapper.html#ae3103b73da0ef6137ad1d1bd16e35d56',1,'vg::BaseMapper']]],
+ ['prefix_4672',['prefix',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdead1db5c374c93da6cefc39869d1704f18',1,'vg::Haplotypes::Subchain::prefix()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#ae400b0d9c4fecf6b90fd0d708258df1e',1,'vg::BitStringTree::TreeNode::prefix()'],['../structvg_1_1GaplessExtension.html#af975b0dd4c3aab5d89093d9725372017',1,'vg::GaplessExtension::prefix()'],['../classvg_1_1WFAExtender.html#a5be8ff4d5922082dedf5e15665536be8',1,'vg::WFAExtender::prefix()'],['../structvg_1_1RecombinatorHaplotype.html#ad2a0e140251ae5dd203144bcbf49aab3',1,'vg::RecombinatorHaplotype::prefix()']]],
+ ['prefix_5flength_4673',['prefix_length',['../structvg_1_1MultipathProblem.html#a5fdfec89c00fe647e234e84fa72879ed',1,'vg::MultipathProblem']]],
+ ['prefix_5fscore_4674',['prefix_score',['../structvg_1_1MultipathProblem.html#a5e3610b3438d69baba7e3be6a6cfdcc0',1,'vg::MultipathProblem']]],
+ ['prefix_5fsum_4675',['prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ac09ee425b8f2f95a4c8c4f45b39084b9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild::prefix_sum()'],['../structvg_1_1MIPayload.html#af0dcb83df9249928d947e23f368f41a0',1,'vg::MIPayload::prefix_sum()']]],
+ ['prefix_5fsum_5for_5fidentifier_4676',['prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#aadf1912938760b4371b385865fa661f9',1,'vg::ZipCode::node_code_t::prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a736b6676259bc262d66d9814fbbb7142',1,'vg::ZipCode::snarl_code_t::prefix_sum_or_identifier()']]],
+ ['prefix_5fsum_5fvalue_4677',['prefix_sum_value',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a09ed2f3574eb36ceccf98ded8c99e7f5',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['prefixes_4678',['prefixes',['../classvg_1_1PhaseUnfolder.html#a64f18b1c10e5d2104bd04df2013f5a0f',1,'vg::PhaseUnfolder']]],
+ ['preflight_2ecpp_4679',['preflight.cpp',['../preflight_8cpp.html',1,'']]],
+ ['preflight_2ehpp_4680',['preflight.hpp',['../preflight_8hpp.html',1,'']]],
+ ['preflight_5fcheck_4681',['preflight_check',['../namespacevg.html#a65ac31e5878660a97207b6ade1418c81',1,'vg']]],
+ ['preload_5fprogress_4682',['preload_progress',['../classvg_1_1Progressive.html#a4eb5050eb36ed519cbfa398748ef183b',1,'vg::Progressive']]],
+ ['prepend_5fmapping_4683',['prepend_mapping',['../classvg_1_1Paths.html#acd1f02b9d6d41036a24a9aee1a261dc3',1,'vg::Paths::prepend_mapping(const string &name, const Mapping &m, bool warn_on_duplicates=false)'],['../classvg_1_1Paths.html#ab5679411e308c578583066e020dc4d4f',1,'vg::Paths::prepend_mapping(const string &name, id_t id, bool is_reverse, size_t length, size_t rank=0, bool warn_on_duplicates=false)']]],
+ ['prepend_5fstep_4684',['prepend_step',['../classvg_1_1VG.html#a43c2858dc8e80ba160359ccf5e1508d2',1,'vg::VG::prepend_step()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#aed17038a0104017d37ff74e15f7f436a',1,'handlegraph::MutablePathHandleGraph::prepend_step()']]],
+ ['preprocess_5fgraph_4685',['preprocess_graph',['../haplotypes__main_8cpp.html#abbe87c8ead89e4916934c55ee923b0c1',1,'haplotypes_main.cpp']]],
+ ['present_4686',['present',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa24ced965e66bc34d849a25192e59fbdf',1,'vg::Recombinator::present()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a130ad1d08da8cb8ff5be5f254b904369',1,'vg::SnarlDistanceIndexClusterer::Cluster::present()']]],
+ ['present_5fdiscount_4687',['PRESENT_DISCOUNT',['../classvg_1_1Recombinator.html#a5c415fe934bb25c07068a2ca0291ea00',1,'vg::Recombinator::PRESENT_DISCOUNT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a5f62e8ec5640f3d4d06bbda709b44bdc',1,'vg::Recombinator::Parameters::present_discount()']]],
+ ['present_5fkmers_4688',['present_kmers',['../namespacevg.html#acc85734af557e4a1047554706a9b4580',1,'vg']]],
+ ['present_5fsymbols_4689',['present_symbols',['../namespacevg.html#ace6690ca3c2bc1ce18c66801e500dce5',1,'vg']]],
+ ['preserve_5fsinks_4690',['preserve_sinks',['../classvg_1_1DozeuPinningOverlay.html#a066fa04f3bf59c7302a0e57036154ab7',1,'vg::DozeuPinningOverlay']]],
+ ['preset_4691',['Preset',['../structvg_1_1subcommand_1_1Preset.html',1,'vg::subcommand::Preset'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a7346ca8a4f692c5a10e0df88bc6c915d',1,'vg::subcommand::BaseArgSpec::preset()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a9e5bd3a2b4884185bc07417893cf476c',1,'vg::subcommand::ArgSpec::preset()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aac88ac0803a38344b6c87057bdfb9327',1,'vg::subcommand::BaseOptionGroup::preset()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a421492b900071c23ae1250b4882ffe52',1,'vg::subcommand::OptionGroup::preset()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a2ab60146762bd02d7ec5b1e870998021',1,'vg::subcommand::GroupedOptionGroup::preset()']]],
+ ['preset_5fdefault_4692',['preset_default',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a7b22070ac7d633aa776868df9225baa9',1,'vg::Recombinator::Parameters']]],
+ ['preset_5fdiploid_4693',['preset_diploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a645ffd73f63c0f007f249345c81d4f8a',1,'vg::Recombinator::Parameters']]],
+ ['preset_5fhaploid_4694',['preset_haploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a115a5b3be57084265c380192cabde366',1,'vg::Recombinator::Parameters']]],
+ ['preset_5ft_4695',['preset_t',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4',1,'vg::Recombinator::Parameters']]],
+ ['prev_4696',['prev',['../classvg_1_1MEMChainModelVertex.html#a8b3867d0ba2a4797202be745d92d11de',1,'vg::MEMChainModelVertex::prev()'],['../classvg_1_1AlignmentChainModelVertex.html#a9979808dd8d6ddaf11d83643ab3e9db2',1,'vg::AlignmentChainModelVertex::prev()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#aea823a7f3329d308107c1de1cf20c1a6',1,'vg::PhasedGenome::HaplotypeNode::prev()']]],
+ ['prev_5fchar_4697',['prev_char',['../structvg_1_1kmer__t.html#a006cf626b837e21d26b66925103a34c5',1,'vg::kmer_t']]],
+ ['prev_5fchars_4698',['prev_chars',['../structvg_1_1KmerPosition.html#a6c6e2b384e3f9292342999e6f49684c3',1,'vg::KmerPosition']]],
+ ['prev_5fcost_4699',['prev_cost',['../classvg_1_1MEMChainModelVertex.html#ad8ad4b22339e6ad06c893c78c63cda5a',1,'vg::MEMChainModelVertex::prev_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#a0dcdae4513868599a6bd50e719f9e4f5',1,'vg::AlignmentChainModelVertex::prev_cost()']]],
+ ['prev_5fidx_4700',['prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#a6e44d4112d111f6b5796bfbd63b7e24d',1,'haplo::haplo_DP_rectangle']]],
+ ['prev_5fpos_4701',['prev_pos',['../structvg_1_1kmer__t.html#acf511fd3c535a5d9e2109480ed1528e8',1,'vg::kmer_t']]],
+ ['prev_5fsnarl_4702',['prev_snarl',['../classvg_1_1SnarlManager.html#af49cb83d06b303717c94da67974fb0d6',1,'vg::SnarlManager']]],
+ ['prev_5fstage_5fitems_4703',['prev_stage_items',['../structvg_1_1Funnel_1_1Item.html#a9ee7530fac67298fbcdb27f8280b4a14',1,'vg::Funnel::Item']]],
+ ['prev_5fsubpath_4704',['prev_subpath',['../structvg_1_1MultipathProblem.html#a51f2e682e6721f35d88cae8d1cf4a59d',1,'vg::MultipathProblem']]],
+ ['previous_5findex_4705',['previous_index',['../structhaplo_1_1haplo__DP__rectangle.html#addd510174b8c5f83418aa6c23e278b36',1,'haplo::haplo_DP_rectangle']]],
+ ['previous_5fr_4706',['previous_R',['../structhaplo_1_1haplo__DP__column.html#a0bcd7266aea2d97a6b234779739e7628',1,'haplo::haplo_DP_column']]],
+ ['previous_5fsizes_4707',['previous_sizes',['../structhaplo_1_1haplo__DP__column.html#a2ece2d4c8c54fbd7fc8e898ced985e6a',1,'haplo::haplo_DP_column']]],
+ ['previous_5fsum_4708',['previous_sum',['../structhaplo_1_1haplo__DP__column.html#a474364179d091eda8dd0684d4d86afa8',1,'haplo::haplo_DP_column']]],
+ ['previous_5ftag_4709',['previous_tag',['../classvg_1_1io_1_1MessageIterator.html#affc663d4448fe1b213d1c2e9ec64b3bb',1,'vg::io::MessageIterator']]],
+ ['previous_5fvalues_4710',['previous_values',['../structhaplo_1_1haplo__DP__column.html#a5e1664796c443719bd4e775f503ab8ad',1,'haplo::haplo_DP_column']]],
+ ['primary_4711',['primary',['../classvg_1_1MaximalExactMatch.html#a2e34dcded590361daf8ca3a9ed3fb62f',1,'vg::MaximalExactMatch']]],
+ ['primitive_5froot_4712',['primitive_root',['../classvg_1_1ShuffledPairs.html#a78c948366b8eec98b8393ae2ac75f86a',1,'vg::ShuffledPairs']]],
+ ['print_4713',['print',['../structvg_1_1WFAAlignment.html#a455ada9f59d934bd167217583b2fbd92',1,'vg::WFAAlignment::print(const HandleGraph &graph, std::ostream &out) const'],['../structvg_1_1WFAAlignment.html#a37156be6786114a37da73499f8fe49da',1,'vg::WFAAlignment::print(std::ostream &out) const'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae35f9e4427c8c9da2dbef05000158990',1,'haplo::hDP_gbwt_graph_accessor::print()'],['../structhaplo_1_1haplo__DP__column.html#a8bdb3ddfa07590bf2d50f96bd43c096b',1,'haplo::haplo_DP_column::print()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a3f04e2d77070771ba779ebaf06f0d3ff',1,'vg::HaplotypePartitioner::Parameters::print()'],['../structvg_1_1Recombinator_1_1Statistics.html#a8cc215e629110af71f6d35da557eb0e8',1,'vg::Recombinator::Statistics::print()'],['../structvg_1_1Recombinator_1_1Parameters.html#aa00e847f40210d77acbd1432f6b485ea',1,'vg::Recombinator::Parameters::print()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a5b19dc7b348fc8a8b9b9120ae032559f',1,'vg::subcommand::BaseArgSpec::print()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#aecec3a3bb1a3d2e0e3d75a080d0206eb',1,'vg::subcommand::FlagArgSpec::print()']]],
+ ['print_5fband_4714',['print_band',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac248371cbaae3b95340035f88de09e0a',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5fdefault_4715',['print_default',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a489497d47ddf82df3339a4e487274144',1,'vg::subcommand::BaseArgSpec::print_default()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a06e81f25a63218e0cba32ecd6320f9b2',1,'vg::subcommand::ValueArgSpec::print_default()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a85b5c5993e124831c65dd9e31b74aec7',1,'vg::subcommand::FlagArgSpec::print_default()']]],
+ ['print_5fdefaults_4716',['print_defaults',['../prune__main_8cpp.html#a01acca05639635d047176302793da18d',1,'prune_main.cpp']]],
+ ['print_5fedges_4717',['print_edges',['../classvg_1_1VG.html#a2b659686076f3d6b7b63ec9678d76a93',1,'vg::VG']]],
+ ['print_5ffull_5fmatrices_4718',['print_full_matrices',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a521dac0777a22cd632a45ad72f320810',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5fgraph_4719',['print_graph',['../classxg_1_1XG.html#acb2f541cd3f91783d07532d75da80b0a',1,'xg::XG']]],
+ ['print_5fhelp_4720',['print_help',['../classvg_1_1ConfigurableParser.html#a29abcf4fbb780c4e586130b095aa0098',1,'vg::ConfigurableParser']]],
+ ['print_5fmatrix_4721',['print_matrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#aee399b25f2ed671ad8a17e6c55757671',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5fmetadata_4722',['print_metadata',['../gbwt__main_8cpp.html#af705c69cda26007b3ea9bb76849e21b1',1,'gbwt_main.cpp']]],
+ ['print_5fmetavar_4723',['print_metavar',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a8f418067cef90e2290b3a67b8fd17b74',1,'vg::subcommand::BaseArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a4bf9aeb97acee678dfbd3d5c997e28c3',1,'vg::subcommand::ValueArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a9fcf875d6e0a843cb90af9cfe7e9e3a3',1,'vg::subcommand::FlagArgSpec::print_metavar()']]],
+ ['print_5foptions_4724',['print_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad3063622c78d2a03519fcbc077c4cdcc',1,'vg::subcommand::BaseOptionGroup::print_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a99c032d391c4dd8f2936f4280e6dde77',1,'vg::subcommand::OptionGroup::print_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aaf906b5e74e2a072cd1f6a90ca685381',1,'vg::subcommand::GroupedOptionGroup::print_options()']]],
+ ['print_5fphased_5fgenome_4725',['print_phased_genome',['../classvg_1_1PhasedGenome.html#a4727557def28b369312b2f4a56d86a7d',1,'vg::PhasedGenome']]],
+ ['print_5frectangularized_5fbands_4726',['print_rectangularized_bands',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a6c94c4cb68bf76d3b8531f004c17b26d',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5freport_4727',['print_report',['../classvg_1_1IndexedVG.html#a08b7d5f9e8ad7c9b42d58ce8d2629000',1,'vg::IndexedVG']]],
+ ['print_5fself_4728',['print_self',['../structvg_1_1varint__vector__t.html#a93a071296fab5dc6fabb363bf3cb66e5',1,'vg::varint_vector_t::print_self()'],['../classvg_1_1ZipCodeTree.html#afe8400e287661b3a9525d99da5329770',1,'vg::ZipCodeTree::print_self()'],['../classvg_1_1ZipCodeForest.html#a4cabd6faae5283f02bfe5397a17908fa',1,'vg::ZipCodeForest::print_self()']]],
+ ['print_5fsnarl_4729',['print_snarl',['../classvg_1_1VCFOutputCaller.html#acd9942cb6cd9427e38c868efb23d8bda',1,'vg::VCFOutputCaller::print_snarl(const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) const'],['../classvg_1_1VCFOutputCaller.html#a3b9cfe228287ac605825ed4b0c8ea990',1,'vg::VCFOutputCaller::print_snarl(const Snarl &snarl, bool in_brackets=false) const']]],
+ ['print_5fstatistics_4730',['print_statistics',['../classvg_1_1Genotyper.html#aadb967b3ab9daa067f8451c29fda0a5e',1,'vg::Genotyper']]],
+ ['print_5ftable_4731',['print_table',['../namespacevg_1_1subcommand.html#a44e82d81de605a19980ffc9045984b3c',1,'vg::subcommand']]],
+ ['print_5fupdates_4732',['print_updates',['../classvg_1_1VariantAdder.html#af52ce72b2446132042df93857eb12b63',1,'vg::VariantAdder']]],
+ ['print_5fvalue_4733',['print_value',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a9a3e4636afe2471cc64ef92c35038733',1,'vg::subcommand::BaseArgSpec::print_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#ab47272ea8d46fdb7c1cf5ff206ff91b1',1,'vg::subcommand::ValueArgSpec::print_value()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ae81ab9ea31e2e812037c732c5e3961cc',1,'vg::subcommand::FlagArgSpec::print_value()']]],
+ ['printalignment_4734',['PrintAlignment',['../classvg_1_1SSWAligner.html#ac52ca46f4e194c324fdd67093c54db01',1,'vg::SSWAligner']]],
+ ['printid_4735',['printId',['../namespacevg.html#a8bf8f408b11966feb9695d4bb723dfac',1,'vg']]],
+ ['priority_4736',['priority',['../classvg_1_1subcommand_1_1Subcommand.html#a3f995aec9b4e2367530e1a6bcccb2e53',1,'vg::subcommand::Subcommand']]],
+ ['prng_4737',['prng',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ac95b66a8f2e2cda6bc2d45691d496f5e',1,'vg::NGSSimulator::MarkovDistribution::prng()'],['../classvg_1_1NGSSimulator.html#a8550502fd97de9b154d3df837c036859',1,'vg::NGSSimulator::prng()']]],
+ ['prngs_4738',['prngs',['../classvg_1_1NGSSimulator.html#ab5d12a331a39e82fc07202152f254d70',1,'vg::NGSSimulator']]],
+ ['prob_5ffor_5fat_5fleast_5fone_4739',['prob_for_at_least_one',['../namespacevg.html#ae46397f9d9aa9ac06a48b4ff30da7087',1,'vg']]],
+ ['prob_5fsampler_4740',['prob_sampler',['../classvg_1_1NGSSimulator.html#a36ca291ed15a9a3942809d21d0574bc1',1,'vg::NGSSimulator']]],
+ ['prob_5fto_5flogprob_4741',['prob_to_logprob',['../namespacevg.html#a476a2102f4f5aa82c06be87780ae6d42',1,'vg']]],
+ ['prob_5fto_5fphred_4742',['prob_to_phred',['../namespacevg.html#acb81881c0a3b7cf276097d8142ddb312',1,'vg']]],
+ ['problem_4743',['Problem',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9',1,'vg::AlignmentValidity::Problem()'],['../structvg_1_1AlignmentValidity.html#a1ca7f243aa52fe313bdfac808f4eba92',1,'vg::AlignmentValidity::problem()']]],
+ ['problemdumpexplainer_4744',['ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html',1,'vg::ProblemDumpExplainer'],['../classvg_1_1ProblemDumpExplainer.html#adf8775736c7646ce19bd69c995bf7238',1,'vg::ProblemDumpExplainer::ProblemDumpExplainer()']]],
+ ['process_5fin_5fout_5fgrowth_4745',['process_in_out_growth',['../classvg_1_1FlowSort.html#a31800555477d90ab371c08852c9cd05b',1,'vg::FlowSort']]],
+ ['process_5funtil_5fthreshold_5fa_4746',['process_until_threshold_a',['../classvg_1_1MinimizerMapper.html#ae74362b0c750fb802b8c7a38c57c8823',1,'vg::MinimizerMapper']]],
+ ['process_5funtil_5fthreshold_5fb_4747',['process_until_threshold_b',['../classvg_1_1MinimizerMapper.html#a121f1d7ca1b0cd5721b7c341d227fec8',1,'vg::MinimizerMapper']]],
+ ['process_5funtil_5fthreshold_5fc_4748',['process_until_threshold_c',['../classvg_1_1MinimizerMapper.html#af1a420ad7240014c67269a6d7437bef6',1,'vg::MinimizerMapper']]],
+ ['processed_5finput_4749',['processed_input',['../classvg_1_1Funnel.html#a94e07fb24eee3bb9284a1ba8945b010a',1,'vg::Funnel']]],
+ ['processing_5finput_4750',['processing_input',['../classvg_1_1Funnel.html#a3c21502db704cde878d989f3cc75e91c',1,'vg::Funnel']]],
+ ['produced_5foutput_4751',['produced_output',['../classvg_1_1Funnel.html#ae9dec7f539cf37d822328a71e376783a',1,'vg::Funnel']]],
+ ['produces_5fone_5fgbwt_4752',['produces_one_gbwt',['../structGBWTConfig.html#ad752e9efebcc424e596e1c328a9eb583',1,'GBWTConfig']]],
+ ['producing_5foutput_4753',['producing_output',['../classvg_1_1Funnel.html#a919aae2ef8cf780bcaba00b1ea1603b8',1,'vg::Funnel']]],
+ ['progress_4754',['progress',['../classvg_1_1Progressive.html#af78e64e28b252828a0ba86439125fea4',1,'vg::Progressive']]],
+ ['progress_5fbars_4755',['progress_bars',['../classvg_1_1VGset.html#acc491d0a5c0a54c6bbd0636fa44431b7',1,'vg::VGset']]],
+ ['progress_5fcount_4756',['progress_count',['../classvg_1_1Progressive.html#a71e61fe99d71d23542d2d7387c23fd4d',1,'vg::Progressive']]],
+ ['progress_5fmessage_4757',['progress_message',['../classvg_1_1Progressive.html#a4bb04fe23ceb41467dd14cdf8cc01a71',1,'vg::Progressive']]],
+ ['progress_5fseen_4758',['progress_seen',['../classvg_1_1Progressive.html#ac6745d7e07b4b271f9510cd40f06d18e',1,'vg::Progressive']]],
+ ['progressive_4759',['Progressive',['../classvg_1_1Progressive.html',1,'vg']]],
+ ['progressive_2ecpp_4760',['progressive.cpp',['../progressive_8cpp.html',1,'']]],
+ ['progressive_2ehpp_4761',['progressive.hpp',['../progressive_8hpp.html',1,'']]],
+ ['project_4762',['project',['../classvg_1_1Funnel.html#a2b9e7695a998b23314c25f7fe3de4701',1,'vg::Funnel']]],
+ ['project_5fgroup_4763',['project_group',['../classvg_1_1Funnel.html#a321b1e593102927ff8677214abce5592',1,'vg::Funnel']]],
+ ['project_5fhaplotype_5ftranscripts_4764',['project_haplotype_transcripts',['../classvg_1_1Transcriptome.html#acaa534fdaa3f3926d7959255ab2f6feb',1,'vg::Transcriptome']]],
+ ['project_5fhaplotype_5ftranscripts_5fcallback_4765',['project_haplotype_transcripts_callback',['../classvg_1_1Transcriptome.html#ae9f0bd481ee467f32d88be2b20c110c7',1,'vg::Transcriptome']]],
+ ['project_5ftranscript_5fembedded_4766',['project_transcript_embedded',['../classvg_1_1Transcriptome.html#a8e9f42b9d9f57b675856c7f766d3c710',1,'vg::Transcriptome']]],
+ ['project_5ftranscript_5fgbwt_4767',['project_transcript_gbwt',['../classvg_1_1Transcriptome.html#a4edf6085f024b736bef4be82c6fd854a',1,'vg::Transcriptome']]],
+ ['projected_5fcount_4768',['projected_count',['../structvg_1_1Funnel_1_1Stage.html#a74c290d50af94a82c196350d3ee7223d',1,'vg::Funnel::Stage']]],
+ ['proper_5fpair_4769',['proper_pair',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a92eba6d5ad7d830d3824261542991875',1,'vg::Counts']]],
+ ['proposal_5fsample_4770',['proposal_sample',['../classvg_1_1MCMCGenotyper.html#a0e007a331bc2854ec8734557bd80962d',1,'vg::MCMCGenotyper']]],
+ ['propose_5fdeflection_4771',['propose_deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a662b5ce1fa402a6c8e7a5f20f92773b3',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['proto_4772',['proto',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a05cf3104e11f544431c6ed6e709d2361',1,'vg::io::VGAlignmentEmitter::proto()'],['../vg_8proto.html#ace9afe7f815b63b3d93844da5eb8fbbc',1,'proto(): vg.proto']]],
+ ['protobuf_5femitter_2ehpp_4773',['protobuf_emitter.hpp',['../protobuf__emitter_8hpp.html',1,'']]],
+ ['protobuf_5fiterator_2ehpp_4774',['protobuf_iterator.hpp',['../protobuf__iterator_8hpp.html',1,'']]],
+ ['protobuf_5fto_5ftag_4775',['protobuf_to_tag',['../structvg_1_1io_1_1Registry_1_1Tables.html#a9959a1192210db895c2d127dc6a197fc',1,'vg::io::Registry::Tables']]],
+ ['protobufemitter_4776',['ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html',1,'vg::io::ProtobufEmitter< T >'],['../classvg_1_1io_1_1ProtobufEmitter.html#ab9d133fa3604ba677c12337ccf609ba7',1,'vg::io::ProtobufEmitter::ProtobufEmitter(std::ostream &out, bool compress=true, size_t max_group_size=1000)'],['../classvg_1_1io_1_1ProtobufEmitter.html#a1adf66f9c9242369dcdd38746f925855',1,'vg::io::ProtobufEmitter::ProtobufEmitter(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#accd8d7c57bffcfdc48ba7085f7a53561',1,'vg::io::ProtobufEmitter::ProtobufEmitter(ProtobufEmitter &&other)=default']]],
+ ['protobufiterator_4777',['ProtobufIterator',['../classvg_1_1io_1_1ProtobufIterator.html',1,'vg::io::ProtobufIterator< T >'],['../classvg_1_1io_1_1ProtobufIterator.html#a0f2996a9653a98470e7c944879a69d70',1,'vg::io::ProtobufIterator::ProtobufIterator(istream &in)'],['../classvg_1_1io_1_1ProtobufIterator.html#a50ad0e8d7ee212617dbf9e456ea43e07',1,'vg::io::ProtobufIterator::ProtobufIterator()=default']]],
+ ['provide_4778',['provide',['../classvg_1_1IndexRegistry.html#a72c4f8ea143cd9a982366234a8eed71e',1,'vg::IndexRegistry::provide(const IndexName &identifier, const string &filename)'],['../classvg_1_1IndexRegistry.html#a430536c995544af29060b78d04e3f5c1',1,'vg::IndexRegistry::provide(const IndexName &identifier, const vector< string > &filenames)'],['../classvg_1_1IndexFile.html#a116a29bacf28f3889ea318ac25a11dc7',1,'vg::IndexFile::provide()']]],
+ ['provided_5fdirectly_4779',['provided_directly',['../classvg_1_1IndexFile.html#a32bf1b5189843cdcc3ba7eb6068dd46f',1,'vg::IndexFile']]],
+ ['prune_2ecpp_4780',['prune.cpp',['../prune_8cpp.html',1,'']]],
+ ['prune_2ehpp_4781',['prune.hpp',['../prune_8hpp.html',1,'']]],
+ ['prune_5fand_5ftrim_5fanchors_4782',['prune_and_trim_anchors',['../classvg_1_1Surjector.html#ae34c7f96fff02c5490477fc8ad643908',1,'vg::Surjector']]],
+ ['prune_5fcomplex_4783',['prune_complex',['../namespacevg_1_1algorithms.html#a09b6e838b2991d13e272ddcb41aacfbc',1,'vg::algorithms']]],
+ ['prune_5fcomplex_5fwith_5fhead_5ftail_4784',['prune_complex_with_head_tail',['../namespacevg_1_1algorithms.html#a784ee29876a24431a865541426f42dee',1,'vg::algorithms']]],
+ ['prune_5fhigh_5fshift_5fedges_4785',['prune_high_shift_edges',['../classvg_1_1MultipathAlignmentGraph.html#aa42ef4313d4d24ab4c19532e2bd30652',1,'vg::MultipathAlignmentGraph']]],
+ ['prune_5flow_5fscoring_5fedges_4786',['prune_low_scoring_edges',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab2949f31f3e43410189eafa260544baf',1,'vg::MEMClusterer::HitGraph']]],
+ ['prune_5fmain_2ecpp_4787',['prune_main.cpp',['../prune__main_8cpp.html',1,'']]],
+ ['prune_5fshort_5fsubgraphs_4788',['prune_short_subgraphs',['../namespacevg_1_1algorithms.html#a83e87cf3f8a5ca4362776cf1a3050242',1,'vg::algorithms']]],
+ ['prune_5fsubpaths_5fmultiplier_4789',['prune_subpaths_multiplier',['../classvg_1_1MultipathMapper.html#aa8409bc363c70b9df0c3590767d25e92',1,'vg::MultipathMapper']]],
+ ['prune_5fsuspicious_5fanchors_4790',['prune_suspicious_anchors',['../classvg_1_1Surjector.html#af01db9677cefc7952fee698f8ee2b672',1,'vg::Surjector']]],
+ ['prune_5fthread_5fbuffer_5fsize_4791',['PRUNE_THREAD_BUFFER_SIZE',['../namespacevg_1_1algorithms.html#a64f4abe5d8279f14a52b56ffb47fff34',1,'vg::algorithms']]],
+ ['prune_5fto_5fconnecting_5fgraph_4792',['prune_to_connecting_graph',['../namespacevg_1_1algorithms.html#a3d74c519ccaa204e7735d5bd26c5095a',1,'vg::algorithms']]],
+ ['prune_5fto_5fconnecting_5fgraph_2ecpp_4793',['prune_to_connecting_graph.cpp',['../prune__to__connecting__graph_8cpp.html',1,'']]],
+ ['prune_5fto_5fconnecting_5fgraph_2ehpp_4794',['prune_to_connecting_graph.hpp',['../prune__to__connecting__graph_8hpp.html',1,'']]],
+ ['prune_5fto_5fhigh_5fscoring_5fpaths_4795',['prune_to_high_scoring_paths',['../classvg_1_1MultipathAlignmentGraph.html#a8164834df4fc94907fb96b06062c9514',1,'vg::MultipathAlignmentGraph']]],
+ ['prune_5funconnectable_4796',['prune_unconnectable',['../classvg_1_1Surjector.html#ab65da876e448d86bc64985c0b14d3e78',1,'vg::Surjector']]],
+ ['pruning_5fmax_5fedge_5fcount_4797',['pruning_max_edge_count',['../structvg_1_1IndexingParameters.html#ad673cb8b7687d3a60aef1036d1b1dae3',1,'vg::IndexingParameters']]],
+ ['pruning_5fmax_5fnode_5fdegree_4798',['pruning_max_node_degree',['../structvg_1_1IndexingParameters.html#a8041e911ac757df80b37fbdbc4943f74',1,'vg::IndexingParameters']]],
+ ['pruning_5fmax_5fnode_5fdegree_5fdecrease_5ffactor_4799',['pruning_max_node_degree_decrease_factor',['../structvg_1_1IndexingParameters.html#ac3de2fff42441077c37ff61421b6415d',1,'vg::IndexingParameters']]],
+ ['pruning_5fmin_5fcomponent_5fsize_4800',['pruning_min_component_size',['../structvg_1_1IndexingParameters.html#a1f955fc9bdfedd418b900163f36a2e15',1,'vg::IndexingParameters']]],
+ ['pruning_5fwalk_5flength_4801',['pruning_walk_length',['../structvg_1_1IndexingParameters.html#ac9f7127d0df7aa1c90ced42a01755763',1,'vg::IndexingParameters']]],
+ ['pruning_5fwalk_5flength_5fincrease_5ffactor_4802',['pruning_walk_length_increase_factor',['../structvg_1_1IndexingParameters.html#a7c483115dc36e1e7e8b25684f427442c',1,'vg::IndexingParameters']]],
+ ['pruningmode_4803',['PruningMode',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248',1,'prune_main.cpp']]],
+ ['pruningparameters_4804',['PruningParameters',['../structPruningParameters.html',1,'']]],
+ ['pseudo_5flength_4805',['pseudo_length',['../classvg_1_1MultipathMapper.html#aa5ee46fa484ee95e45da33b47bcc4eb8',1,'vg::MultipathMapper']]],
+ ['pseudo_5frandom_5fsequence_4806',['pseudo_random_sequence',['../namespacevg.html#a1924855da445b625609837c0920af7b2',1,'vg']]],
+ ['ptr_4807',['ptr',['../structjson__autoptr.html#a8eeb7c64d99d1378d9524ede91d6faa4',1,'json_autoptr']]],
+ ['purge_5funmapped_5falignments_4808',['purge_unmapped_alignments',['../classvg_1_1MultipathMapper.html#a009000ee2da67a965a4f627be468d976',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< multipath_alignment_t > &multipath_alns_out)'],['../classvg_1_1MultipathMapper.html#ab1c9f02cbadcd8df05b691e4ff5294f2',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, bool proper_paired)']]],
+ ['push_4809',['push',['../structvg_1_1MatchPos_1_1PathList.html#a2979222c63cb87e2f530fceda30e56a5',1,'vg::MatchPos::PathList::push()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ade3a2a60c495a494d27fb6f8a72ef2db',1,'vg::ZipCodeTree::reverse_iterator::push()']]],
+ ['push_5fback_4810',['push_back',['../structhaplo_1_1gbwt__thread__t.html#a726f2772b4725564569e4889f89db7c6',1,'haplo::gbwt_thread_t::push_back()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#ade3cdc2fdb2dc88b735bee5be2c04cee',1,'haplo::linear_haplo_structure::SNVvector::push_back()']]],
+ ['push_5fedit_4811',['push_edit',['../classvg_1_1DozeuInterface.html#acc84e0c73002c23f8249ea17efff6848',1,'vg::DozeuInterface']]]
];
diff --git a/search/all_11.js b/search/all_11.js
index 5598ffa7b0..6f562309dc 100644
--- a/search/all_11.js
+++ b/search/all_11.js
@@ -1,30 +1,30 @@
var searchData=
[
- ['qual_5fadj_5faligner_4810',['qual_adj_aligner',['../classvg_1_1AlignerClient.html#ad808371671d657c01a8c0a57b34a2046',1,'vg::AlignerClient']]],
- ['qual_5fadj_5ffull_5flength_5fbonuses_4811',['qual_adj_full_length_bonuses',['../classvg_1_1QualAdjAligner.html#a1ada9d3482ad01904b72041f7051647f',1,'vg::QualAdjAligner']]],
- ['qual_5fadj_5fxdrop_5faligner_2ecpp_4812',['qual_adj_xdrop_aligner.cpp',['../qual__adj__xdrop__aligner_8cpp.html',1,'']]],
- ['qual_5fadjusted_5fbonuses_4813',['qual_adjusted_bonuses',['../classvg_1_1QualAdjAligner.html#a8e36e10804dcd53c0ac30f351311f2cc',1,'vg::QualAdjAligner']]],
- ['qual_5fadjusted_5fmatrix_4814',['qual_adjusted_matrix',['../classvg_1_1QualAdjAligner.html#a44f320fb6e114e25c9ff8856954b10aa',1,'vg::QualAdjAligner']]],
- ['qual_5ffilter_4815',['qual_filter',['../classvg_1_1Filter.html#ac0b864f9350cb8d9be52e2c13e69c30c',1,'vg::Filter']]],
- ['qual_5foffset_4816',['qual_offset',['../classvg_1_1Filter.html#ac989d47373aa80519790159a8a67cfc8',1,'vg::Filter']]],
- ['qualadjaligner_4817',['QualAdjAligner',['../classvg_1_1QualAdjAligner.html',1,'vg::QualAdjAligner'],['../classvg_1_1QualAdjAligner.html#a1eb97ac4416d8ae7e23351c2c03e0314',1,'vg::QualAdjAligner::QualAdjAligner()']]],
- ['qualadjxdropaligner_4818',['QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html',1,'vg::QualAdjXdropAligner'],['../classvg_1_1QualAdjXdropAligner.html#a72ca9e0f8a6b3f73bba3299b7fd2698b',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const int8_t *_score_matrix, const int8_t *_qual_adj_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1QualAdjXdropAligner.html#aa7bfa5bd489eda65d0c4060532d0f556',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner()=default'],['../classvg_1_1QualAdjXdropAligner.html#aa9244a0f908625e90a714acfd92e49db',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a9c73cbd3ad52ec62d102ec4958311dd2',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(QualAdjXdropAligner &&other)']]],
- ['qualities_4819',['qualities',['../structvg_1_1BasePileup.html#aad9e72ab33cea5e54f6f3b37724699d9',1,'vg::BasePileup::qualities()'],['../structvg_1_1EdgePileup.html#a0102dbbfce9153e00bae0520dd15d1ec',1,'vg::EdgePileup::qualities()']]],
- ['quality_4820',['quality',['../structvg_1_1Alignment.html#afe4dfd54e11b8139c3ccbb493faf98dc',1,'vg::Alignment::quality()'],['../structvg_1_1MultipathAlignment.html#aa507c2c93acbbcc309d7808ebae603b6',1,'vg::MultipathAlignment::quality()'],['../structvg_1_1Support.html#aef1cd52697f504165b42fb74ab55bfa9',1,'vg::Support::quality()'],['../classvg_1_1multipath__alignment__t.html#aebdfc9e1f214a2b934e42cda1810932b',1,'vg::multipath_alignment_t::quality()']]],
- ['quality_5faligners_4821',['quality_aligners',['../classvg_1_1Genotyper.html#a2705913bdfb5f6679afb5475a22ecf61',1,'vg::Genotyper']]],
- ['quality_5fcache_4822',['quality_cache',['../classvg_1_1Packer.html#a36c50d1d60cff7036fd853b3c02b450d',1,'vg::Packer']]],
- ['quality_5fchar_5fto_5fshort_4823',['quality_char_to_short',['../namespacevg_1_1io.html#a64f819396b817978940de263c04713f9',1,'vg::io']]],
- ['quality_5fshort_5fto_5fchar_4824',['quality_short_to_char',['../namespacevg_1_1io.html#a62d15de4c2614e383b6bc00e34eefe15',1,'vg::io']]],
- ['queried_5fcount_4825',['queried_count',['../classvg_1_1MaximalExactMatch.html#a538bd4e79e6c025d41031bcc46b3a516',1,'vg::MaximalExactMatch']]],
- ['query_4826',['query',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75221ee25fded8f4d4afcf7a11357413',1,'vg::IndexedVG::CacheEntry::query()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ac21892177de65eac5e2fc9237292c7dc',1,'vg::subcommand::BaseArgSpec::query()'],['../structvg_1_1subcommand_1_1ArgSpec.html#aa3a10b563ddbdd0f555f2ef46d8e9b97',1,'vg::subcommand::ArgSpec::query()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abc7e6b6b7265d1bd3224768712748f65',1,'vg::subcommand::BaseOptionGroup::query()'],['../structvg_1_1subcommand_1_1OptionGroup.html#ae9fc4713f74d5ae9f8d94b8ee29c9775',1,'vg::subcommand::OptionGroup::query()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a8b15018e5e8f03ef99d63ab382e484f5',1,'vg::subcommand::GroupedOptionGroup::query()']]],
- ['query_5fcluster_5fgraphs_4827',['query_cluster_graphs',['../classvg_1_1MultipathMapper.html#aa07b31689dd15a1f85752cbebbb42994',1,'vg::MultipathMapper']]],
- ['query_5fend_4828',['query_end',['../structgafkluge_1_1GafRecord.html#a44e865cbd6ee8693c0ecda102e7271b9',1,'gafkluge::GafRecord']]],
- ['query_5flength_4829',['query_length',['../structgafkluge_1_1GafRecord.html#a63f1b67e656da360cc9260005e8c0ecd',1,'gafkluge::GafRecord']]],
- ['query_5fname_4830',['query_name',['../structgafkluge_1_1GafRecord.html#adb0c145a0585ca84e235acb160506811',1,'gafkluge::GafRecord']]],
- ['query_5foffset_4831',['query_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a97a6361d1ab730d37f88d27b92218d83',1,'vg::DozeuInterface::graph_pos_s']]],
- ['query_5foverlap_4832',['query_overlap',['../namespacevg.html#acffe466a3ca83097eceac30a09b9a010',1,'vg']]],
- ['query_5fposition_4833',['query_position',['../structvg_1_1Alignment.html#a17a81788105d3cb6a777ed6a202cd36f',1,'vg::Alignment']]],
- ['query_5fstart_4834',['query_start',['../structgafkluge_1_1GafRecord.html#a7a92ff5f2dcd4035bfcc661f64d863cd',1,'gafkluge::GafRecord']]],
- ['queue_4835',['queue',['../classvg_1_1JobSchedule.html#ad9c195bda4329dcf7f90e1135388a2bd',1,'vg::JobSchedule']]],
- ['quote_4836',['QUOTE',['../version_8cpp.html#a1e7841038b1293b9a250d8999f6c8ac8',1,'version.cpp']]]
+ ['qual_5fadj_5faligner_4812',['qual_adj_aligner',['../classvg_1_1AlignerClient.html#ad808371671d657c01a8c0a57b34a2046',1,'vg::AlignerClient']]],
+ ['qual_5fadj_5ffull_5flength_5fbonuses_4813',['qual_adj_full_length_bonuses',['../classvg_1_1QualAdjAligner.html#a1ada9d3482ad01904b72041f7051647f',1,'vg::QualAdjAligner']]],
+ ['qual_5fadj_5fxdrop_5faligner_2ecpp_4814',['qual_adj_xdrop_aligner.cpp',['../qual__adj__xdrop__aligner_8cpp.html',1,'']]],
+ ['qual_5fadjusted_5fbonuses_4815',['qual_adjusted_bonuses',['../classvg_1_1QualAdjAligner.html#a8e36e10804dcd53c0ac30f351311f2cc',1,'vg::QualAdjAligner']]],
+ ['qual_5fadjusted_5fmatrix_4816',['qual_adjusted_matrix',['../classvg_1_1QualAdjAligner.html#a44f320fb6e114e25c9ff8856954b10aa',1,'vg::QualAdjAligner']]],
+ ['qual_5ffilter_4817',['qual_filter',['../classvg_1_1Filter.html#ac0b864f9350cb8d9be52e2c13e69c30c',1,'vg::Filter']]],
+ ['qual_5foffset_4818',['qual_offset',['../classvg_1_1Filter.html#ac989d47373aa80519790159a8a67cfc8',1,'vg::Filter']]],
+ ['qualadjaligner_4819',['QualAdjAligner',['../classvg_1_1QualAdjAligner.html',1,'vg::QualAdjAligner'],['../classvg_1_1QualAdjAligner.html#a1eb97ac4416d8ae7e23351c2c03e0314',1,'vg::QualAdjAligner::QualAdjAligner()']]],
+ ['qualadjxdropaligner_4820',['QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html',1,'vg::QualAdjXdropAligner'],['../classvg_1_1QualAdjXdropAligner.html#a72ca9e0f8a6b3f73bba3299b7fd2698b',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const int8_t *_score_matrix, const int8_t *_qual_adj_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1QualAdjXdropAligner.html#aa7bfa5bd489eda65d0c4060532d0f556',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner()=default'],['../classvg_1_1QualAdjXdropAligner.html#aa9244a0f908625e90a714acfd92e49db',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a9c73cbd3ad52ec62d102ec4958311dd2',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(QualAdjXdropAligner &&other)']]],
+ ['qualities_4821',['qualities',['../structvg_1_1BasePileup.html#aad9e72ab33cea5e54f6f3b37724699d9',1,'vg::BasePileup::qualities()'],['../structvg_1_1EdgePileup.html#a0102dbbfce9153e00bae0520dd15d1ec',1,'vg::EdgePileup::qualities()']]],
+ ['quality_4822',['quality',['../structvg_1_1Alignment.html#afe4dfd54e11b8139c3ccbb493faf98dc',1,'vg::Alignment::quality()'],['../structvg_1_1MultipathAlignment.html#aa507c2c93acbbcc309d7808ebae603b6',1,'vg::MultipathAlignment::quality()'],['../structvg_1_1Support.html#aef1cd52697f504165b42fb74ab55bfa9',1,'vg::Support::quality()'],['../classvg_1_1multipath__alignment__t.html#aebdfc9e1f214a2b934e42cda1810932b',1,'vg::multipath_alignment_t::quality()']]],
+ ['quality_5faligners_4823',['quality_aligners',['../classvg_1_1Genotyper.html#a2705913bdfb5f6679afb5475a22ecf61',1,'vg::Genotyper']]],
+ ['quality_5fcache_4824',['quality_cache',['../classvg_1_1Packer.html#a36c50d1d60cff7036fd853b3c02b450d',1,'vg::Packer']]],
+ ['quality_5fchar_5fto_5fshort_4825',['quality_char_to_short',['../namespacevg_1_1io.html#a64f819396b817978940de263c04713f9',1,'vg::io']]],
+ ['quality_5fshort_5fto_5fchar_4826',['quality_short_to_char',['../namespacevg_1_1io.html#a62d15de4c2614e383b6bc00e34eefe15',1,'vg::io']]],
+ ['queried_5fcount_4827',['queried_count',['../classvg_1_1MaximalExactMatch.html#a538bd4e79e6c025d41031bcc46b3a516',1,'vg::MaximalExactMatch']]],
+ ['query_4828',['query',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75221ee25fded8f4d4afcf7a11357413',1,'vg::IndexedVG::CacheEntry::query()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ac21892177de65eac5e2fc9237292c7dc',1,'vg::subcommand::BaseArgSpec::query()'],['../structvg_1_1subcommand_1_1ArgSpec.html#aa3a10b563ddbdd0f555f2ef46d8e9b97',1,'vg::subcommand::ArgSpec::query()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abc7e6b6b7265d1bd3224768712748f65',1,'vg::subcommand::BaseOptionGroup::query()'],['../structvg_1_1subcommand_1_1OptionGroup.html#ae9fc4713f74d5ae9f8d94b8ee29c9775',1,'vg::subcommand::OptionGroup::query()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a8b15018e5e8f03ef99d63ab382e484f5',1,'vg::subcommand::GroupedOptionGroup::query()']]],
+ ['query_5fcluster_5fgraphs_4829',['query_cluster_graphs',['../classvg_1_1MultipathMapper.html#aa07b31689dd15a1f85752cbebbb42994',1,'vg::MultipathMapper']]],
+ ['query_5fend_4830',['query_end',['../structgafkluge_1_1GafRecord.html#a44e865cbd6ee8693c0ecda102e7271b9',1,'gafkluge::GafRecord']]],
+ ['query_5flength_4831',['query_length',['../structgafkluge_1_1GafRecord.html#a63f1b67e656da360cc9260005e8c0ecd',1,'gafkluge::GafRecord']]],
+ ['query_5fname_4832',['query_name',['../structgafkluge_1_1GafRecord.html#adb0c145a0585ca84e235acb160506811',1,'gafkluge::GafRecord']]],
+ ['query_5foffset_4833',['query_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a97a6361d1ab730d37f88d27b92218d83',1,'vg::DozeuInterface::graph_pos_s']]],
+ ['query_5foverlap_4834',['query_overlap',['../namespacevg.html#acffe466a3ca83097eceac30a09b9a010',1,'vg']]],
+ ['query_5fposition_4835',['query_position',['../structvg_1_1Alignment.html#a17a81788105d3cb6a777ed6a202cd36f',1,'vg::Alignment']]],
+ ['query_5fstart_4836',['query_start',['../structgafkluge_1_1GafRecord.html#a7a92ff5f2dcd4035bfcc661f64d863cd',1,'gafkluge::GafRecord']]],
+ ['queue_4837',['queue',['../classvg_1_1JobSchedule.html#ad9c195bda4329dcf7f90e1135388a2bd',1,'vg::JobSchedule']]],
+ ['quote_4838',['QUOTE',['../version_8cpp.html#a1e7841038b1293b9a250d8999f6c8ac8',1,'version.cpp']]]
];
diff --git a/search/all_12.js b/search/all_12.js
index 38952e101e..cf3dfd1d12 100644
--- a/search/all_12.js
+++ b/search/all_12.js
@@ -1,410 +1,410 @@
var searchData=
[
- ['r_4837',['R',['../structhaplo_1_1haplo__DP__rectangle.html#a93bec5529e8477c30fca8118e3e44f5f',1,'haplo::haplo_DP_rectangle']]],
- ['r_5findex_4838',['r_index',['../classvg_1_1HaplotypePartitioner.html#a1eac0315eb7daaca955438f4c69f0fcb',1,'vg::HaplotypePartitioner']]],
- ['r_5findex_5fname_4839',['r_index_name',['../structGBWTConfig.html#a230387b96ed4b3bee6cfa11c27cccc63',1,'GBWTConfig::r_index_name()'],['../structHaplotypesConfig.html#ac184346f750f8486f7e68f1e20e95d32',1,'HaplotypesConfig::r_index_name()']]],
- ['r_5fiv_4840',['r_iv',['../classxg_1_1XG.html#aa5b5890158459739ca5e986555bcf74e',1,'xg::XG']]],
- ['radix_5fsort_5fzipcodes_4841',['radix_sort_zipcodes',['../classvg_1_1ZipCodeForest.html#aade4c028524fd9e0c4a6267335584171',1,'vg::ZipCodeForest']]],
- ['random_4842',['RANDOM',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046ba170e02e86972c2be8559884cc3c12254',1,'vg::StreamSorter::RANDOM()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a7fbab14a93d170a9ab8395e8bad9b15d',1,'vg::Counts::random()'],['../classvg_1_1Colors.html#aa655272ae2bc4944fe7096d3e9e072b8',1,'vg::Colors::random()'],['../classvg_1_1Pictographs.html#ac61d6a97566ac6cc8c21158688fcfdf3',1,'vg::Pictographs::random()']]],
- ['random_5fengine_4843',['random_engine',['../classvg_1_1MCMCGenotyper.html#a742e3fb0ca54f531f23d1a8f18cb4da5',1,'vg::MCMCGenotyper']]],
- ['random_5fmatch_5flength_4844',['random_match_length',['../classvg_1_1BaseMapper.html#a2884c6722e6bd9c9aab6671a85a6c3c0',1,'vg::BaseMapper']]],
- ['random_5fmatch_5fp_5fvalue_4845',['random_match_p_value',['../classvg_1_1MultipathMapper.html#afbf8bce27b441ba87f83c72d5c65c592',1,'vg::MultipathMapper']]],
- ['random_5fread_4846',['random_read',['../classvg_1_1VG.html#a8452af466a3e1ad4b0b463ea0d5da933',1,'vg::VG']]],
- ['random_5fsequence_4847',['random_sequence',['../namespacevg.html#ab80fc8c8920c7ec53cfee81dc2fce852',1,'vg']]],
- ['random_5fsequence_5fgen_4848',['random_sequence_gen',['../namespacevg.html#a4012afd56ccb35387121c71c2119e244',1,'vg']]],
- ['range_4849',['Range',['../structvg_1_1Range.html',1,'vg::Range< Number >'],['../structvg_1_1Range.html#a08e1ef06cddbc0efcb0660d34cf3bc5d',1,'vg::Range::Range()'],['../structvg_1_1Range.html#a4becc4a909e9ff23a62318da327af7ff',1,'vg::Range::Range(const Number &val)'],['../structvg_1_1Range.html#a10c624eaeb6a83b450c9d24fdbaa8555',1,'vg::Range::Range(const Range &other)'],['../structvg_1_1Range.html#a7bf784228c365aa72150fec926de77ae',1,'vg::Range::Range(Range &&other)'],['../classvg_1_1MaximalExactMatch.html#a8652369dde83e159dd8c5638745a749c',1,'vg::MaximalExactMatch::range()'],['../classvg_1_1io_1_1MessageIterator.html#af88ac04ab7cbb8245a86d21a71a5dd76',1,'vg::io::MessageIterator::range()'],['../classvg_1_1io_1_1ProtobufIterator.html#acf75c4c7a16e406f9bb860e3f0c7dae9',1,'vg::io::ProtobufIterator::range()']]],
- ['range_3c_20t_20_3e_4850',['Range< T >',['../structvg_1_1Range.html',1,'vg']]],
- ['range_5fend_5fmatch_4851',['RANGE_END_MATCH',['../classhandlegraph_1_1PathMetadata.html#a938d44c0ba47de41907a6987c6487878',1,'handlegraph::PathMetadata']]],
- ['range_5fend_5fseparator_4852',['RANGE_END_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#acf3518dc192f0f1cc87bdfa85665dc91',1,'handlegraph::PathMetadata']]],
- ['range_5fstart_5fmatch_4853',['RANGE_START_MATCH',['../classhandlegraph_1_1PathMetadata.html#a15ce180ff76a984e3408a70ccf13fd62',1,'handlegraph::PathMetadata']]],
- ['range_5fstart_5fseparator_4854',['RANGE_START_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#a3c20334a1732192586b48a7ac51860ee',1,'handlegraph::PathMetadata']]],
- ['range_5ftable_4855',['range_table',['../classvg_1_1MEMAccelerator.html#a950e1c4779d5f0e8c0088f7b16f36770',1,'vg::MEMAccelerator']]],
- ['range_5fterminator_4856',['RANGE_TERMINATOR',['../classhandlegraph_1_1PathMetadata.html#a1b41a72cbd2850c02a01aa7c8a2b516a',1,'handlegraph::PathMetadata']]],
- ['range_5fvector_4857',['range_vector',['../namespacevg.html#a931d9271de88fc786030fdd0ab4bf534',1,'vg::range_vector(size_t begin, size_t end)'],['../namespacevg.html#a39adca1737de5d28d007d95b809deb7f',1,'vg::range_vector(size_t end)']]],
- ['rangeargspec_4858',['RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html',1,'vg::subcommand']]],
- ['rank_4859',['rank',['../classvg_1_1mapping__t.html#a8f97d898f658a36c3046b8fcc2c846ff',1,'vg::mapping_t::rank()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ab8b58edefb4cb58e014344c6010eec62',1,'vg::PhasedGenome::iterator::rank()'],['../structvg_1_1Mapping.html#a9ad71eb17b88b2cdd00cee8476e6c7b3',1,'vg::Mapping::rank()']]],
- ['rank_5fby_5fsupport_4860',['rank_by_support',['../classvg_1_1PoissonSupportSnarlCaller.html#a300ca3bbff527fb43fbc12e65177d053',1,'vg::PoissonSupportSnarlCaller']]],
- ['rank_5fto_5fhandle_4861',['rank_to_handle',['../classhandlegraph_1_1RankedHandleGraph.html#aacf6651545adbd407082a539222f8a69',1,'handlegraph::RankedHandleGraph']]],
- ['rank_5fto_5fid_4862',['rank_to_id',['../classxg_1_1XG.html#aee052f301d8cae7b30c50c115c6b950b',1,'xg::XG::rank_to_id()'],['../classhandlegraph_1_1RankedHandleGraph.html#a5bf563241454b21539effcad11406ec9',1,'handlegraph::RankedHandleGraph::rank_to_id()']]],
- ['ranked_5fhandle_5fgraph_2ecpp_4863',['ranked_handle_graph.cpp',['../ranked__handle__graph_8cpp.html',1,'']]],
- ['rankedhandlegraph_4864',['RankedHandleGraph',['../classhandlegraph_1_1RankedHandleGraph.html',1,'handlegraph::RankedHandleGraph'],['../namespacevg.html#a215e44b59d26cf0745f02218dfd902a2',1,'vg::RankedHandleGraph()']]],
- ['rare_5fvariant_5fsimplifier_2ecpp_4865',['rare_variant_simplifier.cpp',['../rare__variant__simplifier_8cpp.html',1,'']]],
- ['rare_5fvariant_5fsimplifier_2ehpp_4866',['rare_variant_simplifier.hpp',['../rare__variant__simplifier_8hpp.html',1,'']]],
- ['rarevariantsimplifier_4867',['RareVariantSimplifier',['../classvg_1_1RareVariantSimplifier.html',1,'vg::RareVariantSimplifier'],['../classvg_1_1RareVariantSimplifier.html#a08cf82d7c40db195176b9bf177a50e32',1,'vg::RareVariantSimplifier::RareVariantSimplifier()']]],
- ['ratiosupportsnarlcaller_4868',['RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html',1,'vg::RatioSupportSnarlCaller'],['../classvg_1_1RatioSupportSnarlCaller.html#ad6905b3e30632f2a0a3e304cdfd15faa',1,'vg::RatioSupportSnarlCaller::RatioSupportSnarlCaller()']]],
- ['re_5fgenotype_4869',['re_genotype',['../classvg_1_1LegacyCaller.html#a6c23ee5b732d26d4f55bd3b5b4830fca',1,'vg::LegacyCaller']]],
- ['reachable_5fwith_5fgap_4870',['reachable_with_gap',['../structvg_1_1WFATree_1_1ScoreProperties.html#aeef86ffa6d221e25dfc15d97436c408c',1,'vg::WFATree::ScoreProperties']]],
- ['read_4871',['read',['../structvg_1_1alignment__index__t.html#aedfedbedee05ac92a82889330b7a7159',1,'vg::alignment_index_t::read()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9afdd907960f4e4f4792f9986a37c69b3c',1,'vg::Counts::read()'],['../structhFILE__backend.html#ad710f254730683318f2d62b9c1ef3d60',1,'hFILE_backend::read()'],['../classvg_1_1ParallelKFFReader.html#ae34ae06b01651343a3e07b87ce019aa7',1,'vg::ParallelKFFReader::read()']]],
- ['read_5f1_5fadapter_4872',['read_1_adapter',['../classvg_1_1MultipathMapper.html#ac11fe37f1e47b1f3697e1eeeb703a467',1,'vg::MultipathMapper']]],
- ['read_5f1_5fadapter_5flps_4873',['read_1_adapter_lps',['../classvg_1_1MultipathMapper.html#a72cfecb533ba72974ca4fe736f5e4616',1,'vg::MultipathMapper']]],
- ['read_5f2_5fadapter_4874',['read_2_adapter',['../classvg_1_1MultipathMapper.html#a9dda8a58ca0a9a3b5f8cf6bb6b72b907',1,'vg::MultipathMapper']]],
- ['read_5f2_5fadapter_5flps_4875',['read_2_adapter_lps',['../classvg_1_1MultipathMapper.html#ab14d5973d561097ca08d9e989b04265b',1,'vg::MultipathMapper']]],
- ['read_5falignment_5findex_5ft_4876',['read_alignment_index_t',['../structvg_1_1read__alignment__index__t.html',1,'vg']]],
- ['read_5fbest_5fleft_4877',['read_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6573a9b29b9df17f33cc6ce50889f408',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['read_5fbest_5fright_4878',['read_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a9509065fa738b008fa7e75325a34b9fe',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['read_5fcluster_5fheads_4879',['read_cluster_heads',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3d23f2d455846fcb6d5ea634926f7dce',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['read_5fdistance_5flimit_4880',['read_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a96bda025a3c371cef79b565d66b31a2a',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['read_5fend_4881',['read_end',['../classvg_1_1algorithms_1_1Anchor.html#a335ebe332424cb49cae4da84c91a5367',1,'vg::algorithms::Anchor']]],
- ['read_5fexclusion_5fend_4882',['read_exclusion_end',['../classvg_1_1algorithms_1_1Anchor.html#a12554fafcdf8309d3119b349e3bf6e59',1,'vg::algorithms::Anchor']]],
- ['read_5fexclusion_5fstart_4883',['read_exclusion_start',['../classvg_1_1algorithms_1_1Anchor.html#a1de27e657461d6de450a84aab34becb4',1,'vg::algorithms::Anchor']]],
- ['read_5fgroup_4884',['read_group',['../classvg_1_1MinimizerMapper.html#aee3e4b7c4e777da6c09f70218481e3d6',1,'vg::MinimizerMapper::read_group()'],['../classvg_1_1MultipathAlignmentEmitter.html#a931f4785a73cfd9069d7447ba63b71ef',1,'vg::MultipathAlignmentEmitter::read_group()'],['../structvg_1_1Alignment.html#a95102c70d75046f86a2f0a829ba1efe0',1,'vg::Alignment::read_group()'],['../structvg_1_1MultipathAlignment.html#abdc748afaea04b662f170156d8c88343',1,'vg::MultipathAlignment::read_group()']]],
- ['read_5finterval_4885',['read_interval',['../structvg_1_1GaplessExtension.html#a32b115618388c2254ef91c06ac0c9840',1,'vg::GaplessExtension']]],
- ['read_5flog_5flikelihood_4886',['read_log_likelihood',['../classvg_1_1PhasedGenome.html#af754f8a4e9793ebd5f4aa3b673b7e442',1,'vg::PhasedGenome']]],
- ['read_5fmapped_4887',['read_mapped',['../structvg_1_1Alignment.html#af2fc72c769b77c355632e6aab7573046',1,'vg::Alignment']]],
- ['read_5fmapping_4888',['read_mapping',['../classvg_1_1PhaseUnfolder.html#adbf93e421183b64f73276639c3c23dfb',1,'vg::PhaseUnfolder']]],
- ['read_5fnum_4889',['read_num',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#aeb827f9966141503abe98ebcce7b2db2',1,'vg::SnarlDistanceIndexClusterer::ClusterHead']]],
- ['read_5foffset_4890',['read_offset',['../structMappingRun.html#a730efdfaef634a4173efe0bd9e4e3da1',1,'MappingRun']]],
- ['read_5fon_5freverse_5fstrand_4891',['read_on_reverse_strand',['../structvg_1_1Alignment.html#a10b4d599e1812ee007e348f8ce8bfe49',1,'vg::Alignment']]],
- ['read_5fpaired_4892',['read_paired',['../structvg_1_1Alignment.html#a2bfa3fffb5f4ea6ab3e98a6340ad16bb',1,'vg::Alignment']]],
- ['read_5fstart_4893',['read_start',['../classvg_1_1algorithms_1_1Anchor.html#a21c07ed7e05dfd2194d580022f2005c4',1,'vg::algorithms::Anchor']]],
- ['read_5ftoo_5fshort_4894',['READ_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a997b7fe4b82277b56702572e730d3eb7',1,'vg::AlignmentValidity']]],
- ['read_5funion_5ffind_4895',['read_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#afbf1772f189edd4c5f4a8e74914a4d6c',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['reader_4896',['reader',['../classvg_1_1ParallelKFFReader.html#a88e22492b07cf27f746ca0086d48c6dd',1,'vg::ParallelKFFReader::reader()'],['../classvg_1_1WindowedVcfBuffer.html#a064a56b55dbb562f1b52034a54ed3583',1,'vg::WindowedVcfBuffer::reader()']]],
- ['readfilter_4897',['ReadFilter',['../classvg_1_1ReadFilter.html',1,'vg']]],
- ['readfilter_2ecpp_4898',['readfilter.cpp',['../readfilter_8cpp.html',1,'']]],
- ['readfilter_2ehpp_4899',['readfilter.hpp',['../readfilter_8hpp.html',1,'']]],
- ['readmasker_4900',['ReadMasker',['../classvg_1_1ReadMasker.html',1,'vg::ReadMasker'],['../classvg_1_1ReadMasker.html#a99656ed3430d86e7a34b908914991945',1,'vg::ReadMasker::ReadMasker()']]],
- ['readrestrictedtraversalfinder_4901',['ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html',1,'vg::ReadRestrictedTraversalFinder'],['../classvg_1_1ReadRestrictedTraversalFinder.html#a8cf6a940b0fce108e8af39d8a50a380f',1,'vg::ReadRestrictedTraversalFinder::ReadRestrictedTraversalFinder()']]],
- ['reads_4902',['Reads',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4a9989ae14c6b6c27998126ab745488926',1,'vg::Genotyper']]],
- ['reads_5fby_5fname_4903',['reads_by_name',['../classvg_1_1PathRestrictedTraversalFinder.html#ac08d8f72efc63adb1bf169d9ed7c107e',1,'vg::PathRestrictedTraversalFinder']]],
- ['real_5ft_4904',['real_t',['../namespacevg.html#a7392de2ef03532b2ec3461ebb178c75a',1,'vg']]],
- ['realign_5findels_4905',['realign_indels',['../classvg_1_1Genotyper.html#a79ac39be882405a426afaeeef65c9660',1,'vg::Genotyper']]],
- ['realigning_5fsurject_4906',['realigning_surject',['../classvg_1_1Surjector.html#a2629f80135104fb8486ef823f525b843',1,'vg::Surjector']]],
- ['reallocate_5fatomic_5fint_5fvector_4907',['reallocate_atomic_int_vector',['../namespacevg_1_1algorithms.html#acd891e00c4846e53f760d504434ead12',1,'vg::algorithms']]],
- ['reassign_5fnode_4908',['reassign_node',['../classvg_1_1Paths.html#aed5ea00a6a8dab5b54eeedd9e8f91a7b',1,'vg::Paths']]],
- ['reassign_5fnode_5fids_4909',['reassign_node_ids',['../classvg_1_1VG.html#aca4a358ff4c7f387c1c6d5d239499a07',1,'vg::VG::reassign_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a4805d276a83a1dad2462e6b8dd2443dc',1,'handlegraph::MutableHandleGraph::reassign_node_ids()']]],
- ['reassign_5fsplit_5fclusters_4910',['reassign_split_clusters',['../classvg_1_1MultipathMapper.html#a5d8b62d4d55e83f80da09173e8520874',1,'vg::MultipathMapper']]],
- ['rebuild_5fedge_5findexes_4911',['rebuild_edge_indexes',['../classvg_1_1VG.html#a6541146b6410cec4be3e2a7379ea3bcf',1,'vg::VG']]],
- ['rebuild_5fgbwt_4912',['rebuild_gbwt',['../namespacevg.html#a95d54bf0a30125f9ded043bb099cb25f',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob > &jobs, const std::unordered_map< nid_t, size_t > &node_to_job, const RebuildParameters ¶meters)'],['../namespacevg.html#ade5b1e6daa5da7101533d444d3d8ff41',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob::mapping_type > &mappings)']]],
- ['rebuild_5fgbwt_5fjob_4913',['rebuild_gbwt_job',['../namespacevg.html#a16b175479dee254341d60fc037dae233',1,'vg']]],
- ['rebuild_5findexes_4914',['rebuild_indexes',['../classvg_1_1VG.html#a63d4e45a9a410c451b1cad44ef7068ad',1,'vg::VG']]],
- ['rebuild_5fmapping_5faux_4915',['rebuild_mapping_aux',['../classvg_1_1Paths.html#a5f80df5846bdac0b502a70af97dc65de',1,'vg::Paths']]],
- ['rebuild_5fnode_5fmapping_4916',['rebuild_node_mapping',['../classvg_1_1Paths.html#a7e9d9388475dcd8f23af072430e7383c',1,'vg::Paths']]],
- ['rebuildjob_4917',['RebuildJob',['../structvg_1_1RebuildJob.html',1,'vg']]],
- ['rebuildparameters_4918',['RebuildParameters',['../structvg_1_1RebuildParameters.html',1,'vg']]],
- ['recipe_5fregistry_4919',['recipe_registry',['../classvg_1_1IndexRegistry.html#a963c33ba471ce5e0c4e5403d4a86e753',1,'vg::IndexRegistry']]],
- ['recipefunc_4920',['RecipeFunc',['../namespacevg.html#a1ff09b399af11722aeee121ae6f4fd9b',1,'vg']]],
- ['recipename_4921',['RecipeName',['../namespacevg.html#a6119d0b9707c042b0c2cde5d77b670cb',1,'vg']]],
- ['recoding_4922',['recoding',['../classvg_1_1ParallelKFFReader.html#aaf7eee70fc5bfbb863fc68ee8840a812',1,'vg::ParallelKFFReader']]],
- ['recombination_5fpenalty_4923',['recombination_penalty',['../classvg_1_1BaseMapper.html#af0e6c250a81dc74df57136242174aa54',1,'vg::BaseMapper::recombination_penalty()'],['../classvg_1_1MultipathMapper.html#a26993f76e9bbe5c48e0b436cc9c3fda8',1,'vg::MultipathMapper::recombination_penalty()']]],
- ['recombinator_4924',['Recombinator',['../classvg_1_1Recombinator.html',1,'vg::Recombinator'],['../classvg_1_1Recombinator.html#a9248c550bcc5aa267abde6eefec69e88',1,'vg::Recombinator::Recombinator()']]],
- ['recombinator_2ecpp_4925',['recombinator.cpp',['../recombinator_8cpp.html',1,'']]],
- ['recombinator_2ehpp_4926',['recombinator.hpp',['../recombinator_8hpp.html',1,'']]],
- ['recombinator_5fparameters_4927',['recombinator_parameters',['../structHaplotypesConfig.html#a10886974a276f98f45a26c7b2c51c350',1,'HaplotypesConfig']]],
- ['recombinator_5fsanity_5fchecks_4928',['recombinator_sanity_checks',['../namespacevg.html#aa81f31f29a47e669812c3ef57bd1aab6',1,'vg']]],
- ['recombinatorfragment_4929',['RecombinatorFragment',['../structvg_1_1RecombinatorFragment.html',1,'vg::RecombinatorFragment'],['../structvg_1_1RecombinatorFragment.html#aab79ba107e9e086b432dfa9fcf4a2807',1,'vg::RecombinatorFragment::RecombinatorFragment()']]],
- ['recombinatorhaplotype_4930',['RecombinatorHaplotype',['../structvg_1_1RecombinatorHaplotype.html',1,'vg']]],
- ['record_4931',['record',['../classvg_1_1SnarlManager.html#a45e3765bfd07b196b6e30b7a9b62aefd',1,'vg::SnarlManager::record(const Snarl *snarl) const'],['../classvg_1_1SnarlManager.html#a3ce002195299049e9925e94546d989b9',1,'vg::SnarlManager::record(Snarl *snarl)']]],
- ['record_5fbases_4932',['record_bases',['../classvg_1_1Packer.html#a7a3debd842c660a3fc4755fc887c74ec',1,'vg::Packer']]],
- ['record_5fedges_4933',['record_edges',['../classvg_1_1Packer.html#ab6fa0636229479a7368286e43f20ffa2',1,'vg::Packer']]],
- ['record_5fedits_4934',['record_edits',['../classvg_1_1Packer.html#a8200ea3c39e408f3394c4a65fe2e3786',1,'vg::Packer']]],
- ['record_5ffanouts_4935',['record_fanouts',['../classvg_1_1MultipathMapper.html#a0b4e3381a53cf532acdf7cbadc6d9985',1,'vg::MultipathMapper']]],
- ['record_5ffragment_5fconfiguration_4936',['record_fragment_configuration',['../classvg_1_1FragmentLengthStatistics.html#ae63195a980c56907de548ba00098c794',1,'vg::FragmentLengthStatistics']]],
- ['record_5foffset_4937',['record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa4c597fb92b3074c231b3b02f1dd58a4',1,'vg::ZipCode::snarl_code_t']]],
- ['record_5fqualities_4938',['record_qualities',['../classvg_1_1Packer.html#ab29c0bdd5ae1db4a89db3476ba70ef68',1,'vg::Packer']]],
- ['record_5fread_5fpair_5fquality_4939',['record_read_pair_quality',['../classvg_1_1NGSSimulator.html#aec434f0c212aec15e1760f4c4b1185e2',1,'vg::NGSSimulator']]],
- ['record_5fread_5fquality_4940',['record_read_quality',['../classvg_1_1NGSSimulator.html#a8f34614e3dc660e31d26d9c18970e736',1,'vg::NGSSimulator']]],
- ['record_5ftransition_4941',['record_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ab3609f759c7b20d77c1bc0ca7160c26a',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['recover_5flog_5fbase_4942',['recover_log_base',['../classvg_1_1GSSWAligner.html#ab5102e690e6e2e0e72aa35ea769179a2',1,'vg::GSSWAligner']]],
- ['recursealways_4943',['RecurseAlways',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ade8537831952f7d91199da0ded53a8d2',1,'vg::GraphCaller']]],
- ['recursenever_4944',['RecurseNever',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ad50ac99caa8bae55f8d5d8ed7a4aef04',1,'vg::GraphCaller']]],
- ['recurseonfail_4945',['RecurseOnFail',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ae25246a2b8e3ba65437d72bf513be31c',1,'vg::GraphCaller']]],
- ['recursetype_4946',['RecurseType',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5',1,'vg::GraphCaller']]],
- ['recursively_5femit_5fsnarls_4947',['recursively_emit_snarls',['../classvg_1_1CactusSnarlFinder.html#aad8a90f6cd0fddf6ab908f6287e3ddf3',1,'vg::CactusSnarlFinder']]],
- ['reduce_5fto_5fsingle_5fpath_4948',['reduce_to_single_path',['../classvg_1_1MultipathMapper.html#a0a3360fde5883dc2c0927b63be0a3bd5',1,'vg::MultipathMapper']]],
- ['redundant_5fvertexes_4949',['redundant_vertexes',['../classvg_1_1MEMChainModel.html#a6a4132f34b8c9636e02c186ffa75a333',1,'vg::MEMChainModel::redundant_vertexes()'],['../classvg_1_1AlignmentChainModel.html#a2fd794e91dfc7ee2db7fdc9f921c5134',1,'vg::AlignmentChainModel::redundant_vertexes()']]],
- ['reencode_5fold_5fg_5fvector_4950',['reencode_old_g_vector',['../classxg_1_1XG.html#a8a5068e08156a861e35e62cc3fa94204',1,'xg::XG']]],
- ['reestimation_5ffrequency_4951',['reestimation_frequency',['../classvg_1_1FragmentLengthDistribution.html#a648954fbcb1fd0295fb22a37d79ed3e7',1,'vg::FragmentLengthDistribution']]],
- ['ref_5fbase_4952',['ref_base',['../structvg_1_1BasePileup.html#a8d68d6e5d3ce5d2a9a448f90ed6dfc09',1,'vg::BasePileup']]],
- ['ref_5foffset_4953',['ref_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a0d0812a9f6be0ad3610fb860fb1bc2d2',1,'vg::DozeuInterface::graph_pos_s']]],
- ['ref_5foffsets_4954',['ref_offsets',['../classvg_1_1LegacyCaller.html#a9aa5ae8255c13d5c19a4cae14f998a8e',1,'vg::LegacyCaller::ref_offsets()'],['../classvg_1_1FlowCaller.html#a454f9cba510f7ebf9e8929c53092583a',1,'vg::FlowCaller::ref_offsets()'],['../classvg_1_1NestedFlowCaller.html#a389525ad359e73ad07da1bac80cb3595',1,'vg::NestedFlowCaller::ref_offsets()'],['../classvg_1_1MCMCCaller.html#acccde0cf44eb8781fc43830f0b3736b3',1,'vg::MCMCCaller::ref_offsets()']]],
- ['ref_5fpath_4955',['ref_path',['../structvg_1_1FlowSort_1_1Growth.html#a34ba660c358c1ec59cd7c70e62780a8c',1,'vg::FlowSort::Growth']]],
- ['ref_5fpath_5fdistance_4956',['ref_path_distance',['../namespacevg_1_1algorithms.html#aa5e4dc632e98b58b67a99af6749d9e05',1,'vg::algorithms']]],
- ['ref_5fpath_5fdistance_2ecpp_4957',['ref_path_distance.cpp',['../ref__path__distance_8cpp.html',1,'']]],
- ['ref_5fpath_5fdistance_2ehpp_4958',['ref_path_distance.hpp',['../ref__path__distance_8hpp.html',1,'']]],
- ['ref_5fpath_5fhandle_4959',['ref_path_handle',['../structhaplo_1_1linear__haplo__structure.html#a57eb7d1ebc0bc29e9ba3d1c3955650e9',1,'haplo::linear_haplo_structure']]],
- ['ref_5fpath_5fhandles_4960',['ref_path_handles',['../classvg_1_1MultipathMapper.html#a2ee3920a6e8758880172f6fd07c5f7f2',1,'vg::MultipathMapper']]],
- ['ref_5fpath_5finterval_4961',['ref_path_interval',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#afb6f9c3dbe7a55c17d953489de39e656',1,'vg::NestedFlowCaller::CallRecord']]],
- ['ref_5fpath_5flengths_4962',['ref_path_lengths',['../classvg_1_1MCMCCaller.html#a7638f220d989784503287ea538da21f4',1,'vg::MCMCCaller']]],
- ['ref_5fpath_5fname_4963',['ref_path_name',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a69d34c61dd53d99246bebffa0b68def0',1,'vg::NestedFlowCaller::CallRecord']]],
- ['ref_5fpath_5foffsets_4964',['ref_path_offsets',['../classvg_1_1MCMCCaller.html#a614597d6c55c252d2efb88cdd0048eff',1,'vg::MCMCCaller']]],
- ['ref_5fpath_5fset_4965',['ref_path_set',['../classvg_1_1FlowCaller.html#ac85f8948b4a0c6f9bcb66cccf498c372',1,'vg::FlowCaller::ref_path_set()'],['../classvg_1_1NestedFlowCaller.html#a934f25461550667e553a51ed2fee1fb2',1,'vg::NestedFlowCaller::ref_path_set()']]],
- ['ref_5fpaths_4966',['ref_paths',['../classvg_1_1Deconstructor.html#a8da74d6fff7d5af6caed96723d0bccd9',1,'vg::Deconstructor::ref_paths()'],['../classvg_1_1GAFOutputCaller.html#a2675564b819e50ac8a21ca51eb14c99c',1,'vg::GAFOutputCaller::ref_paths()'],['../classvg_1_1LegacyCaller.html#a73beb7401923d192f8542beb938ea33c',1,'vg::LegacyCaller::ref_paths()'],['../classvg_1_1FlowCaller.html#adb1bb384ccb36d214a22cef04919920c',1,'vg::FlowCaller::ref_paths()'],['../classvg_1_1NestedFlowCaller.html#a5206505cf92654951bef22b42d50381e',1,'vg::NestedFlowCaller::ref_paths()'],['../classvg_1_1MCMCCaller.html#a081ed012622de090f1aad2a82526a59e',1,'vg::MCMCCaller::ref_paths()'],['../structvg_1_1Recombinator_1_1Statistics.html#ac3404816da5f78c7712ad69eb8f9594f',1,'vg::Recombinator::Statistics::ref_paths()']]],
- ['ref_5fploidies_4967',['ref_ploidies',['../classvg_1_1LegacyCaller.html#ac82406147f3603e97d22418ee0e7bdc4',1,'vg::LegacyCaller::ref_ploidies()'],['../classvg_1_1FlowCaller.html#a2487ac1acadd5052a3a18204c426591d',1,'vg::FlowCaller::ref_ploidies()'],['../classvg_1_1NestedFlowCaller.html#a021b1013fe64a99b598ffa291a423e5b',1,'vg::NestedFlowCaller::ref_ploidies()']]],
- ['ref_5fposition_4968',['ref_position',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a442f4e740bc94b1671c9590f65bb65a4',1,'haplo::linear_haplo_structure::SNVvector']]],
- ['ref_5fpositions_4969',['ref_positions',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a6065969d77968cd3afc31ca7b8b1a9f0',1,'haplo::linear_haplo_structure::SNVvector']]],
- ['ref_5fsample_4970',['ref_sample',['../structHaplotypesConfig.html#a1575fa9f328d1d823e788f422b6bde43',1,'HaplotypesConfig']]],
- ['ref_5fsamples_4971',['ref_samples',['../classvg_1_1Deconstructor.html#a72834c9d1d667e3283e93f60a3f5057b',1,'vg::Deconstructor']]],
- ['ref_5fspan_4972',['ref_span',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8aabba00d1035f3425a2ff43984b99a3d4',1,'haplo::linear_haplo_structure']]],
- ['ref_5fsteps_4973',['ref_steps',['../structvg_1_1ParentGenotypeInfo.html#a45d8b5d863b3f74e9eb499acef7a2916',1,'vg::ParentGenotypeInfo']]],
- ['ref_5ftrav_5fidx_4974',['ref_trav_idx',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a7a265b17dc3bc9a34603de7e064230f8',1,'vg::NestedFlowCaller::CallRecord']]],
- ['ref_5ftraversal_4975',['ref_traversal',['../structvg_1_1ParentGenotypeInfo.html#a4e02433e8ac8eae0491d4290f5b78515',1,'vg::ParentGenotypeInfo']]],
- ['refactor_5fsplit_5falignment_4976',['refactor_split_alignment',['../classvg_1_1Filter.html#af5c53d7fa62dff67d24ff0daa4d5f925',1,'vg::Filter']]],
- ['reference_4977',['reference',['../classvg_1_1count__back__inserter.html#a84eca4db3ffead0102aa62bd53000631',1,'vg::count_back_inserter::reference()'],['../structvg_1_1VectorView_1_1const__iterator.html#a037cb8cbbd9c2be6c471ee6aa9bfbb1d',1,'vg::VectorView::const_iterator::reference()'],['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cadcd320d017d7f3c317bc8b234287bc9f',1,'handlegraph::REFERENCE()']]],
- ['reference_5fpaths_4978',['reference_paths',['../classvg_1_1PhaseUnfolder.html#a2bfa46441300e0817643b310aced989b',1,'vg::PhaseUnfolder']]],
- ['reference_5ftranscript_5fpaths_4979',['reference_transcript_paths',['../classvg_1_1Transcriptome.html#aacf1ad40a7a5d42985c4149b03fe936e',1,'vg::Transcriptome']]],
- ['referenceinterval_4980',['ReferenceInterval',['../structReferenceInterval.html',1,'']]],
- ['referencepathvectorizableoverlayhelper_4981',['ReferencePathVectorizableOverlayHelper',['../call__main_8cpp.html#adc0e01cf2a62b559e7c67d23dfbd757e',1,'call_main.cpp']]],
- ['reflect_4982',['reflect',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa5776efd133ed466cb82ef4f4b161dfd',1,'vg::GraphSynchronizer::Lock']]],
- ['refpos_4983',['refpos',['../structvg_1_1Alignment.html#a584c3aa15a5c1386d14a97c0ce85c0cf',1,'vg::Alignment']]],
- ['region_4984',['Region',['../structvg_1_1Region.html',1,'vg']]],
- ['region_2ecpp_4985',['region.cpp',['../region_8cpp.html',1,'']]],
- ['region_2ehpp_4986',['region.hpp',['../region_8hpp.html',1,'']]],
- ['region_5fexpander_2ecpp_4987',['region_expander.cpp',['../region__expander_8cpp.html',1,'']]],
- ['region_5fexpander_2ehpp_4988',['region_expander.hpp',['../region__expander_8hpp.html',1,'']]],
- ['regionexpander_4989',['RegionExpander',['../classvg_1_1RegionExpander.html',1,'vg::RegionExpander'],['../classvg_1_1RegionExpander.html#a42c0f501da7fabf0045f5c434b55f705',1,'vg::RegionExpander::RegionExpander()']]],
- ['regions_4990',['regions',['../structvg_1_1Funnel_1_1PaintableSpace.html#a001cb606b7e4f79f8be9550b17c6f1b4',1,'vg::Funnel::PaintableSpace::regions()'],['../classvg_1_1HaplotypeIndexer.html#a85285e19121d708649f61b5420ab0777',1,'vg::HaplotypeIndexer::regions()']]],
- ['register_5falias_4991',['register_alias',['../classvg_1_1AliasGraph.html#a4f21c7d2e0aa761fd5ff4ccd43bd72af',1,'vg::AliasGraph']]],
- ['register_5fbare_5floader_4992',['register_bare_loader',['../classvg_1_1io_1_1Registry.html#a025929701767e23673356cae9e7024a5',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_4993',['register_bare_loader_saver',['../classvg_1_1io_1_1Registry.html#aab501bb8db46d45e8b1946da37f0b382',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fheader_5fcheck_4994',['register_bare_loader_saver_with_header_check',['../classvg_1_1io_1_1Registry.html#a873d317a5ec04d5af5223008310043df',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_4995',['register_bare_loader_saver_with_magic',['../classvg_1_1io_1_1Registry.html#ad3f16de5d24cb503429d358e2af8c831',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_5fand_5ffilename_4996',['register_bare_loader_saver_with_magic_and_filename',['../classvg_1_1io_1_1Registry.html#acfda4299247a88075080004beba4a136',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fmagics_4997',['register_bare_loader_saver_with_magics',['../classvg_1_1io_1_1Registry.html#af4180fbb60edaa1cd1aec325945d2af5',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fwith_5ffilename_4998',['register_bare_loader_with_filename',['../classvg_1_1io_1_1Registry.html#abb7a1aefe860153a36614efa54bcde29',1,'vg::io::Registry']]],
- ['register_5fbarrier_4999',['register_barrier',['../classvg_1_1io_1_1StreamMultiplexer.html#acb05844bf345313fc1710db7f3610ac5',1,'vg::io::StreamMultiplexer']]],
- ['register_5fbreakpoint_5000',['register_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#a562910d0ca3b3fac6b95b0c3ee3c81dd',1,'vg::io::StreamMultiplexer']]],
- ['register_5fconfigurable_5001',['register_configurable',['../classvg_1_1ConfigurableParser.html#a3c42646beeac7fb48f57c44f1420ec7b',1,'vg::ConfigurableParser']]],
- ['register_5feverything_5002',['register_everything',['../classvg_1_1io_1_1Registry.html#ad1b4d2c277bdb07c2bf4cc4b60e35745',1,'vg::io::Registry']]],
- ['register_5ffragment_5flength_5003',['register_fragment_length',['../classvg_1_1FragmentLengthDistribution.html#a888c21e626cb2fd984f9e0ffd39adefc',1,'vg::FragmentLengthDistribution']]],
- ['register_5fgeneralization_5004',['register_generalization',['../classvg_1_1IndexRegistry.html#a2e1c0e83f49e8719459e644ce143302b',1,'vg::IndexRegistry']]],
- ['register_5findex_5005',['register_index',['../classvg_1_1IndexRegistry.html#ad8f48075fe06df92c65bc5fd0207f9bc',1,'vg::IndexRegistry']]],
- ['register_5flibvg_5fio_5006',['register_libvg_io',['../namespacevg_1_1io.html#ad93f27be4f07ab9c6a91a1501b992f70',1,'vg::io']]],
- ['register_5flibvg_5fio_2ecpp_5007',['register_libvg_io.cpp',['../register__libvg__io_8cpp.html',1,'']]],
- ['register_5flibvg_5fio_2ehpp_5008',['register_libvg_io.hpp',['../register__libvg__io_8hpp.html',1,'']]],
- ['register_5floader_5009',['register_loader',['../classvg_1_1io_1_1Registry.html#a82c329d405f2dc83880623561a10962f',1,'vg::io::Registry::register_loader(const string &tag, load_function_t loader)'],['../classvg_1_1io_1_1Registry.html#abdbc23294daf5a1f44b34da481929891',1,'vg::io::Registry::register_loader(const std::vector< std::string > &tags, load_function_t loader)']]],
- ['register_5floader_5fparams_5fjson_5010',['register_loader_params_json',['../namespacevg_1_1io.html#a113c8011c25b00d36f77f49062726bbb',1,'vg::io']]],
- ['register_5floader_5fparams_5fjson_2ecpp_5011',['register_loader_params_json.cpp',['../register__loader__params__json_8cpp.html',1,'']]],
- ['register_5floader_5fparams_5fjson_2ehpp_5012',['register_loader_params_json.hpp',['../register__loader__params__json_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5013',['register_loader_saver',['../classvg_1_1io_1_1Registry.html#a3dfd842b470ff701fb805838e2d7fe61',1,'vg::io::Registry::register_loader_saver(const string &tag, load_function_t loader, save_function_t saver)'],['../classvg_1_1io_1_1Registry.html#a56e76bb9dcab4c47f400d844430536b6',1,'vg::io::Registry::register_loader_saver(const std::vector< std::string > &tags, load_function_t loader, save_function_t saver)']]],
- ['register_5floader_5fsaver_5fdistance_5findex_5014',['register_loader_saver_distance_index',['../namespacevg_1_1io.html#a45372f8f761a3bce9e7ef6e1422db47b',1,'vg::io']]],
- ['register_5floader_5fsaver_5fdistance_5findex_2ecpp_5015',['register_loader_saver_distance_index.cpp',['../register__loader__saver__distance__index_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fdistance_5findex_2ehpp_5016',['register_loader_saver_distance_index.hpp',['../register__loader__saver__distance__index_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwt_5017',['register_loader_saver_gbwt',['../namespacevg_1_1io.html#a47fc4c5122bf0f0810993822d194eb20',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbwt_2ecpp_5018',['register_loader_saver_gbwt.cpp',['../register__loader__saver__gbwt_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwt_2ehpp_5019',['register_loader_saver_gbwt.hpp',['../register__loader__saver__gbwt_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwtgraph_5020',['register_loader_saver_gbwtgraph',['../namespacevg_1_1io.html#a6143362abf3060042589f1ffb22ff498',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbwtgraph_2ecpp_5021',['register_loader_saver_gbwtgraph.cpp',['../register__loader__saver__gbwtgraph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwtgraph_2ehpp_5022',['register_loader_saver_gbwtgraph.hpp',['../register__loader__saver__gbwtgraph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbz_5023',['register_loader_saver_gbz',['../namespacevg_1_1io.html#adb36b3bf6da822750c5c6c9cd2d987e0',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbz_2ecpp_5024',['register_loader_saver_gbz.cpp',['../register__loader__saver__gbz_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbz_2ehpp_5025',['register_loader_saver_gbz.hpp',['../register__loader__saver__gbz_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbzgraph_5026',['register_loader_saver_gbzgraph',['../namespacevg_1_1io.html#a81649e999e30d305e02187c16b257d07',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbzgraph_2ecpp_5027',['register_loader_saver_gbzgraph.cpp',['../register__loader__saver__gbzgraph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbzgraph_2ehpp_5028',['register_loader_saver_gbzgraph.hpp',['../register__loader__saver__gbzgraph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgcsa_5029',['register_loader_saver_gcsa',['../namespacevg_1_1io.html#affca170910f12393eb1381c4d72e4e73',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgcsa_2ecpp_5030',['register_loader_saver_gcsa.cpp',['../register__loader__saver__gcsa_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgcsa_2ehpp_5031',['register_loader_saver_gcsa.hpp',['../register__loader__saver__gcsa_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgfa_5032',['register_loader_saver_gfa',['../namespacevg_1_1io.html#a1fadf5a0f7d91d61c9d2c27d35987c6a',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgfa_2ecpp_5033',['register_loader_saver_gfa.cpp',['../register__loader__saver__gfa_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgfa_2ehpp_5034',['register_loader_saver_gfa.hpp',['../register__loader__saver__gfa_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fhash_5fgraph_5035',['register_loader_saver_hash_graph',['../namespacevg_1_1io.html#a49d41e6f52ad981f96d772396fd4eee5',1,'vg::io']]],
- ['register_5floader_5fsaver_5fhash_5fgraph_2ecpp_5036',['register_loader_saver_hash_graph.cpp',['../register__loader__saver__hash__graph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fhash_5fgraph_2ehpp_5037',['register_loader_saver_hash_graph.hpp',['../register__loader__saver__hash__graph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5flcp_5038',['register_loader_saver_lcp',['../namespacevg_1_1io.html#af7df97a78891ada683647c88c6393eb9',1,'vg::io']]],
- ['register_5floader_5fsaver_5flcp_2ecpp_5039',['register_loader_saver_lcp.cpp',['../register__loader__saver__lcp_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5flcp_2ehpp_5040',['register_loader_saver_lcp.hpp',['../register__loader__saver__lcp_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fminimizer_5041',['register_loader_saver_minimizer',['../namespacevg_1_1io.html#aa69bc026abe7a1db4530704dfc7e7b3f',1,'vg::io']]],
- ['register_5floader_5fsaver_5fminimizer_2ecpp_5042',['register_loader_saver_minimizer.cpp',['../register__loader__saver__minimizer_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fminimizer_2ehpp_5043',['register_loader_saver_minimizer.hpp',['../register__loader__saver__minimizer_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fpacked_5fgraph_5044',['register_loader_saver_packed_graph',['../namespacevg_1_1io.html#a776b6490958856d44dc2d962d629440d',1,'vg::io']]],
- ['register_5floader_5fsaver_5fpacked_5fgraph_2ecpp_5045',['register_loader_saver_packed_graph.cpp',['../register__loader__saver__packed__graph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fpacked_5fgraph_2ehpp_5046',['register_loader_saver_packed_graph.hpp',['../register__loader__saver__packed__graph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fr_5findex_5047',['register_loader_saver_r_index',['../namespacevg_1_1io.html#a6ce32e4ae1d4f5d244c0d80d3ac09beb',1,'vg::io']]],
- ['register_5floader_5fsaver_5fr_5findex_2ecpp_5048',['register_loader_saver_r_index.cpp',['../register__loader__saver__r__index_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fr_5findex_2ehpp_5049',['register_loader_saver_r_index.hpp',['../register__loader__saver__r__index_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fsnarl_5fmanager_5050',['register_loader_saver_snarl_manager',['../namespacevg_1_1io.html#a8072168ee8165f81afb2688ef0825ea8',1,'vg::io']]],
- ['register_5floader_5fsaver_5fsnarl_5fmanager_2ecpp_5051',['register_loader_saver_snarl_manager.cpp',['../register__loader__saver__snarl__manager_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fsnarl_5fmanager_2ehpp_5052',['register_loader_saver_snarl_manager.hpp',['../register__loader__saver__snarl__manager_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fvg_5053',['register_loader_saver_vg',['../namespacevg_1_1io.html#ac3485846033fd4accb221b0a866dfeb7',1,'vg::io']]],
- ['register_5floader_5fsaver_5fvg_2ecpp_5054',['register_loader_saver_vg.cpp',['../register__loader__saver__vg_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fvg_2ehpp_5055',['register_loader_saver_vg.hpp',['../register__loader__saver__vg_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fxg_5056',['register_loader_saver_xg',['../namespacevg_1_1io.html#a7a23bf45ec66db4b724b7f8a9f223c33',1,'vg::io']]],
- ['register_5floader_5fsaver_5fxg_2ecpp_5057',['register_loader_saver_xg.cpp',['../register__loader__saver__xg_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fxg_2ehpp_5058',['register_loader_saver_xg.hpp',['../register__loader__saver__xg_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fzip_5fcodes_5059',['register_loader_saver_zip_codes',['../namespacevg_1_1io.html#ac0521f6b9e5e9e78ab0837548bef8f0e',1,'vg::io']]],
- ['register_5floader_5fsaver_5fzip_5fcodes_2ecpp_5060',['register_loader_saver_zip_codes.cpp',['../register__loader__saver__zip__codes_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fzip_5fcodes_2ehpp_5061',['register_loader_saver_zip_codes.hpp',['../register__loader__saver__zip__codes_8hpp.html',1,'']]],
- ['register_5foption_5062',['register_option',['../classvg_1_1Configurable.html#afa7bba48c6289ea9b9095acd79a5658e',1,'vg::Configurable']]],
- ['register_5fprotobuf_5063',['register_protobuf',['../classvg_1_1io_1_1Registry.html#ae4880fe254039bfe44b73b9050ce0abc',1,'vg::io::Registry']]],
- ['register_5frecipe_5064',['register_recipe',['../classvg_1_1IndexRegistry.html#afdda05f4e7f1dfd93ecb33ad3b582aad',1,'vg::IndexRegistry']]],
- ['register_5fsampled_5fposition_5065',['register_sampled_position',['../classvg_1_1NGSSimulator.html#ab9adc2b15f1d2c31301e5801e773dcbd',1,'vg::NGSSimulator']]],
- ['register_5fsaver_5066',['register_saver',['../classvg_1_1io_1_1Registry.html#a1bba520da840207b627aface669b80c6',1,'vg::io::Registry']]],
- ['registered_5fsuffixes_5067',['registered_suffixes',['../classvg_1_1IndexRegistry.html#ad3422d12216130fa07d77dcc3e62ae34',1,'vg::IndexRegistry']]],
- ['registry_5068',['Registry',['../classvg_1_1io_1_1Registry.html',1,'vg::io::Registry'],['../classvg_1_1IndexingPlan.html#a7a8e639fb6e8225162a5ff532c4b963d',1,'vg::IndexingPlan::registry()']]],
- ['registry_2ecpp_5069',['registry.cpp',['../registry_8cpp.html',1,'']]],
- ['registry_2ehpp_5070',['registry.hpp',['../registry_8hpp.html',1,'']]],
- ['regress_5071',['regress',['../namespacevg.html#aab16fbb8659a66f16f2004fcc3e8f9db',1,'vg']]],
- ['regular_5faligner_5072',['regular_aligner',['../classvg_1_1AlignerClient.html#af164f37a5efb0c05b10fea3841b78e83',1,'vg::AlignerClient']]],
- ['regular_5fsnarl_5073',['REGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a857cb70dc6bd3383a768a8696e67689c',1,'vg::ZipCode']]],
- ['regular_5fsnarl_5fis_5freversed_5foffset_5074',['REGULAR_SNARL_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a40ebd5bef9b1916bbe944baaaff0b122',1,'vg::ZipCode']]],
- ['regular_5fsnarl_5fsize_5075',['REGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a14c19ec53976a951ef9a16f9202ac19e',1,'vg::ZipCode']]],
- ['regularize_5076',['regularize',['../classvg_1_1SnarlManager.html#ae5015eacc04d12d02ef5196fb23f3075',1,'vg::SnarlManager']]],
- ['release_5077',['release',['../structjson__autoptr.html#ad3ee76d343667fd42bdbe504f32e7042',1,'json_autoptr']]],
- ['remaining_5ftree_5078',['remaining_tree',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1f7d072e5054742f4c391b294fe5d839',1,'vg::ZipCodeTree::iterator']]],
- ['remap_5079',['remap',['../classvg_1_1Filter.html#a66768cd6584270f71d190d525c99a9c4',1,'vg::Filter::remap(Alignment &aln)'],['../classvg_1_1Filter.html#aea9d6813e578a5957131fa6c4c8eff52',1,'vg::Filter::remap(string seq)']]],
- ['remove_5080',['remove',['../classvg_1_1PhasedGenome.html#a3706e208421ac10d5695ed5d5ec45090',1,'vg::PhasedGenome::remove()'],['../namespacevg_1_1temp__file.html#a9885078330e16129fccc5fb6d8717ec5',1,'vg::temp_file::remove()'],['../namespacexg_1_1temp__file.html#aa4e7fb2251b2ba8f6d054d873eae4988',1,'xg::temp_file::remove()']]],
- ['remove_5fbonuses_5081',['remove_bonuses',['../classvg_1_1GSSWAligner.html#a35fe72b24fc734d75864275c8cc1257e',1,'vg::GSSWAligner']]],
- ['remove_5fclipped_5fportion_5082',['remove_clipped_portion',['../classvg_1_1Filter.html#ac246ae985a763a2d10edc92c81639913',1,'vg::Filter']]],
- ['remove_5fdirectory_5083',['remove_directory',['../structvg_1_1temp__file_1_1Handler.html#acb21b507190287960d50a614ccf611bf',1,'vg::temp_file::Handler']]],
- ['remove_5fdominated_5fchunks_5084',['remove_dominated_chunks',['../classvg_1_1Surjector.html#aafa4eb4d310ac530ed186170dc34dba9',1,'vg::Surjector']]],
- ['remove_5fduplicate_5fedges_5085',['remove_duplicate_edges',['../namespacevg.html#add4d3a3d1917566a8df138c80b38e548',1,'vg']]],
- ['remove_5fduplicate_5fnodes_5086',['remove_duplicate_nodes',['../namespacevg.html#a6dbe8468f2f2bcf8ceb859e6a0f8b4b1',1,'vg']]],
- ['remove_5fduplicated_5fin_5087',['remove_duplicated_in',['../classvg_1_1VG.html#a33424c3be8c3e088631dfb37c48773d3',1,'vg::VG']]],
- ['remove_5fduplicates_5088',['remove_duplicates',['../classvg_1_1VG.html#aba9fb73c326ecfab70e35e44dff6a937',1,'vg::VG::remove_duplicates()'],['../namespacevg.html#a5d00fa3c72ac473353496aab96965e60',1,'vg::remove_duplicates(std::vector< GaplessExtension > &result)'],['../namespacevg.html#aecd2e49750e94ed6f9de917dd9c72ac2',1,'vg::remove_duplicates(Graph &graph)']]],
- ['remove_5fedge_5089',['remove_edge',['../classvg_1_1FlowSort.html#ad5203a8e590cc8e2bdb7038057963aaf',1,'vg::FlowSort']]],
- ['remove_5fedit_5ftmpfiles_5090',['remove_edit_tmpfiles',['../classvg_1_1Packer.html#a2612eb978cfad2220946fab00cc3360f',1,'vg::Packer']]],
- ['remove_5fempty_5falignment_5fsections_5091',['remove_empty_alignment_sections',['../namespacevg.html#af3fb034fcd6d50c2b84f40026b40f284',1,'vg']]],
- ['remove_5ffailing_5fedits_5092',['remove_failing_edits',['../classvg_1_1Filter.html#aea2a2fc6de506793111639e609376bf0',1,'vg::Filter']]],
- ['remove_5ffull_5flength_5fbonuses_5093',['remove_full_length_bonuses',['../classvg_1_1Mapper.html#a2e8194d4eb73fe32467ab37ed9468e09',1,'vg::Mapper']]],
- ['remove_5fhigh_5fdegree_5fnodes_5094',['remove_high_degree_nodes',['../namespacevg_1_1algorithms.html#a96020f05a81255adfca3821f538c02b9',1,'vg::algorithms']]],
- ['remove_5finverting_5fedges_5095',['remove_inverting_edges',['../classvg_1_1VG.html#a76005ed499eea217c9f778028751137c',1,'vg::VG']]],
- ['remove_5flow_5fscoring_5fsections_5096',['remove_low_scoring_sections',['../namespacevg.html#a0ea49989e31a688e22265eb41291c0ae',1,'vg']]],
- ['remove_5fmapping_5097',['remove_mapping',['../classvg_1_1Paths.html#ad52958174f83ec940328d8610563dc1a',1,'vg::Paths']]],
- ['remove_5fnode_5098',['remove_node',['../classvg_1_1Paths.html#ab74cefb48d501d96b8dc81e3865770d1',1,'vg::Paths']]],
- ['remove_5fnode_5fforwarding_5fedges_5099',['remove_node_forwarding_edges',['../classvg_1_1VG.html#ab92694e7fd89275603c967739e60e0d2',1,'vg::VG']]],
- ['remove_5fnon_5fpath_5100',['remove_non_path',['../classvg_1_1VG.html#ad517da731d2bf9c81cc28e0a1367af33',1,'vg::VG']]],
- ['remove_5fnon_5ftranscribed_5fnodes_5101',['remove_non_transcribed_nodes',['../classvg_1_1Transcriptome.html#aed6ea709b303bcc0055ea41217b5e1be',1,'vg::Transcriptome']]],
- ['remove_5fnull_5fnodes_5102',['remove_null_nodes',['../classvg_1_1VG.html#a9b107027697644d771eb529037201f71',1,'vg::VG']]],
- ['remove_5fnull_5fnodes_5fforwarding_5fedges_5103',['remove_null_nodes_forwarding_edges',['../classvg_1_1VG.html#a0e887a7b2cfc666f2210889a2dec791b',1,'vg::VG']]],
- ['remove_5forphan_5fedges_5104',['remove_orphan_edges',['../classvg_1_1VG.html#a40dd9bc0458a4948afd676374ae8d1f0',1,'vg::VG::remove_orphan_edges()'],['../namespacevg.html#a0b38f4f0d7e63b1f7f20d2dc985f88c4',1,'vg::remove_orphan_edges()']]],
- ['remove_5fpath_5105',['remove_path',['../classvg_1_1Paths.html#ad3893e02f5e0429a13621ae333208f9e',1,'vg::Paths::remove_path()'],['../classvg_1_1VG.html#a30c369b4c1b0dfa4e9fbc0d3bce82648',1,'vg::VG::remove_path()']]],
- ['remove_5fpaths_5106',['remove_paths',['../classvg_1_1Paths.html#a975ff2ed8ee5718aae414cb0cb2fb39b',1,'vg::Paths::remove_paths()'],['../namespacevg.html#ad5e16e94675197650b9d6edb9e7a9081',1,'vg::remove_paths()']]],
- ['remove_5fredundant_5ftranscript_5fpaths_5107',['remove_redundant_transcript_paths',['../classvg_1_1Transcriptome.html#aa7bf08bef8301bcff774dff1bc92d484',1,'vg::Transcriptome']]],
- ['remove_5fsamples_5108',['remove_samples',['../gbwt__main_8cpp.html#a9750054dfc43368b363ed04acd832b15',1,'gbwt_main.cpp']]],
- ['remove_5ftransitive_5fedges_5109',['remove_transitive_edges',['../classvg_1_1MultipathAlignmentGraph.html#aeb9c58b7f20245a4c400dd14e8488069',1,'vg::MultipathAlignmentGraph']]],
- ['rename_5fpath_5110',['rename_path',['../classhandlegraph_1_1MutablePathHandleGraph.html#a95370bd388b2c113cf0556f266993418',1,'handlegraph::MutablePathHandleGraph']]],
- ['rename_5fvariants_5111',['rename_variants',['../classvg_1_1HaplotypeIndexer.html#a8061130697dc26811303c4b67b081245',1,'vg::HaplotypeIndexer']]],
- ['rend_5112',['rend',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a864f0d7f9c86b6f057e2b2889ef478a2',1,'vg::ZipCodeTree::reverse_iterator::rend()'],['../classvg_1_1ZipCodeTree.html#acb87f941c2eb8bcef3f6008c248f07c4',1,'vg::ZipCodeTree::rend()']]],
- ['reorder_5fadjacency_5flists_5113',['reorder_adjacency_lists',['../classvg_1_1MultipathAlignmentGraph.html#adba05a33bf075eb3eb7260e229245f06',1,'vg::MultipathAlignmentGraph']]],
- ['reorder_5fexons_5114',['reorder_exons',['../classvg_1_1Transcriptome.html#ae6f600db9b276fe332d4f14919bba983',1,'vg::Transcriptome']]],
- ['repeat_5115',['repeat',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9af8ac0bddf37c11c94f041c84a20a636b',1,'vg::Counts']]],
- ['repeat_5fsize_5116',['repeat_size',['../classvg_1_1ReadFilter.html#a95e0303086c9c6dc7a17d452b7d7f928',1,'vg::ReadFilter']]],
- ['repetitiveness_5117',['repetitiveness',['../structvg_1_1SeqComplexity.html#a192996fb41444e1ccddd6b6e334cf2d3',1,'vg::SeqComplexity']]],
- ['replace_5fin_5fstring_5118',['replace_in_string',['../namespacevg.html#ab169ac1e2fc6ba662eebc1ede1ffe157',1,'vg']]],
- ['replace_5flocal_5fhaplotype_5119',['replace_local_haplotype',['../classvg_1_1GenomeState.html#a8048b04c0d1d0b438ec76bdc1c0b5779',1,'vg::GenomeState']]],
- ['replace_5fmapping_5120',['replace_mapping',['../classvg_1_1Paths.html#a906246385a06c6825aaf9b3c58cbdeac',1,'vg::Paths']]],
- ['replace_5foccurrence_5121',['replace_occurrence',['../structvg_1_1PathIndex.html#ae8806eb31bcd8b8f9305180fea7b746f',1,'vg::PathIndex']]],
- ['replace_5fsnarl_5fhaplotype_5122',['replace_snarl_haplotype',['../classvg_1_1GenomeState.html#a83cd070b1d65189fbba77a5bda91d405',1,'vg::GenomeState']]],
- ['replacelocalhaplotypecommand_5123',['ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html',1,'vg']]],
- ['replacesnarlhaplotypecommand_5124',['ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html',1,'vg']]],
- ['report_5faffinities_5125',['report_affinities',['../classvg_1_1Genotyper.html#abe8c49eaf4799ae7202e19b6e09288a7',1,'vg::Genotyper']]],
- ['report_5fallelic_5fmapq_5126',['report_allelic_mapq',['../classvg_1_1MultipathMapper.html#a6cc2a29a0a539f37606482c57c78b015',1,'vg::MultipathMapper']]],
- ['report_5fexception_5127',['report_exception',['../namespacevg.html#a638a54aabac7956dae6fd882468a86fe',1,'vg']]],
- ['report_5fgroup_5fmapq_5128',['report_group_mapq',['../classvg_1_1MultipathMapper.html#a42577bd89395f56ea2045c378b745456',1,'vg::MultipathMapper']]],
- ['report_5flibrary_5129',['report_library',['../namespacevg.html#a040485dc93c5bf925dc58fe4eaa0bd02',1,'vg']]],
- ['report_5fsnarl_5130',['report_snarl',['../classvg_1_1Genotyper.html#a6c9c525615b0c453f0685ea2ed987cde',1,'vg::Genotyper']]],
- ['report_5fsnarl_5ftraversal_5131',['report_snarl_traversal',['../classvg_1_1Genotyper.html#a1a141641a0939e35dc6ee19281001628',1,'vg::Genotyper']]],
- ['report_5ftime_5fmemory_5132',['report_time_memory',['../gbwt__main_8cpp.html#aa6ba12498251a288731312b850bba212',1,'gbwt_main.cpp']]],
- ['representative_5133',['Representative',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4aca000fa2f53ba37764dedd204e1fd27e',1,'vg::Genotyper']]],
- ['representativetraversalfinder_5134',['RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html',1,'vg::RepresentativeTraversalFinder'],['../classvg_1_1RepresentativeTraversalFinder.html#a5dd3d9602c8056d016d42ba5cb760f11',1,'vg::RepresentativeTraversalFinder::RepresentativeTraversalFinder()']]],
- ['require_5135',['require',['../classvg_1_1IndexRegistry.html#ac52737ce471d6fb1ea968a2e57dc4b7f',1,'vg::IndexRegistry']]],
- ['rescore_5136',['rescore',['../classvg_1_1ReadFilter.html#a7373ef70ee64562dd779628a234c1080',1,'vg::ReadFilter']]],
- ['rescue_5falgorithm_5137',['rescue_algorithm',['../classvg_1_1MinimizerMapper.html#a17f800e4588567e473ea18a55bd186b9',1,'vg::MinimizerMapper']]],
- ['rescue_5fdozeu_5138',['rescue_dozeu',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a4120cab71587100aa2d1308010fec524',1,'vg::MinimizerMapper']]],
- ['rescue_5fgraph_5fstd_5fdevs_5139',['rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#aab3573cb5d2878a13b0a40d427e8c943',1,'vg::MultipathMapper']]],
- ['rescue_5fgssw_5140',['rescue_gssw',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4aa3089b08bc714c195447adf06eff27d9',1,'vg::MinimizerMapper']]],
- ['rescue_5fhigh_5fcount_5forder_5flength_5fmems_5141',['rescue_high_count_order_length_mems',['../classvg_1_1BaseMapper.html#aa7a71951ec7acdbf2c31ae9318ceb035',1,'vg::BaseMapper']]],
- ['rescue_5fnone_5142',['rescue_none',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a830c2c22efd3590551f37663c11f61e7',1,'vg::MinimizerMapper']]],
- ['rescue_5fonly_5fanchor_5fmax_5143',['rescue_only_anchor_max',['../classvg_1_1MultipathMapper.html#acd7c1016549d1f96af13b9c317f239f3',1,'vg::MultipathMapper']]],
- ['rescue_5fonly_5fmin_5144',['rescue_only_min',['../classvg_1_1MultipathMapper.html#a2ad423f9fc1a81bbe31e9c25992de378',1,'vg::MultipathMapper']]],
- ['rescue_5fseed_5flimit_5145',['rescue_seed_limit',['../classvg_1_1MinimizerMapper.html#a0a0c7111b38792069bb74af9b74b0978',1,'vg::MinimizerMapper']]],
- ['rescue_5fsubgraph_5fstdevs_5146',['rescue_subgraph_stdevs',['../classvg_1_1MinimizerMapper.html#a411fb85396b07aab41fabc8e34b92481',1,'vg::MinimizerMapper']]],
- ['rescuealgorithm_5147',['RescueAlgorithm',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4',1,'vg::MinimizerMapper']]],
- ['rescued_5148',['RESCUED',['../classvg_1_1MultipathMapper.html#ab559f7eb874ac770dbbda734c5bc395a',1,'vg::MultipathMapper']]],
- ['resect_5fsnarls_5ffrom_5fpaths_5149',['resect_snarls_from_paths',['../classvg_1_1MultipathAlignmentGraph.html#a9c49582fe16bcb4c87b95e8e3ee93319',1,'vg::MultipathAlignmentGraph']]],
- ['reserved_5150',['reserved',['../structvg_1_1Alignment.html#a8374111b6348509e8e9ecca0cd1ac046',1,'vg::Alignment']]],
- ['reset_5151',['reset',['../classvg_1_1IndexRegistry.html#abcba0a09cee5a43096a09d05556353c1',1,'vg::IndexRegistry::reset()'],['../classvg_1_1IndexFile.html#aa16d18589ef1a9944b8e2af8c8ea1232',1,'vg::IndexFile::reset()'],['../structvg_1_1Counts.html#a90e02c9fc99656e6325f5c8fbfccda86',1,'vg::Counts::reset()'],['../classvg_1_1uniform__real__distribution.html#ad9ba8ac53f8a0af213db9d4f8da12617',1,'vg::uniform_real_distribution::reset()'],['../classvg_1_1normal__distribution.html#a7bae578d38533043f42f09413c7c1e32',1,'vg::normal_distribution::reset()'],['../classvg_1_1truncated__normal__distribution.html#ae1ebb560eee14b873305a4b5bf97616e',1,'vg::truncated_normal_distribution::reset()'],['../classvg_1_1uniform__int__distribution.html#a38594c45008dfc36cfbb4f9b9e4193dd',1,'vg::uniform_int_distribution::reset()'],['../classvg_1_1discrete__distribution.html#a5a3ca0751a139bef583b819118188780',1,'vg::discrete_distribution::reset()'],['../structvg_1_1Range.html#a3bf0b390a74ca7ea5f806f6cd98aac2c',1,'vg::Range::reset()']]],
- ['reset_5falong_5fchain_5152',['reset_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#ade116b41b24892b20ac4fa95a9b5539e',1,'vg::subcommand::TickChainLink::reset_along_chain()'],['../structvg_1_1Range.html#a475da5fc747b64bfa869524e932077df',1,'vg::Range::reset_along_chain()']]],
- ['reset_5falong_5fchain_5fparent_5153',['reset_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#a8934c072a3cdbc8652e8f7fa9f9ef553',1,'vg::subcommand::TickChainLink']]],
- ['reset_5fchain_5154',['reset_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a5a3dd8ac3d8a86fec1d2062e6d864c73',1,'vg::subcommand::TickChainLink::reset_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a05855ac56b836299fc0fc12292555b37',1,'vg::subcommand::OptionGroup::reset_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a73c92bfa80186ac2d64f9b24233aacb8',1,'vg::subcommand::GroupedOptionGroup::reset_chain()']]],
- ['resize_5findexes_5155',['resize_indexes',['../classvg_1_1VG.html#af8879b1e6aab38b9a246deba0f05ccfe',1,'vg::VG']]],
- ['restore_5fpaths_5156',['restore_paths',['../classvg_1_1PhaseUnfolder.html#a3cdfb31928c3a4127d9888d543872e1c',1,'vg::PhaseUnfolder']]],
- ['restrained_5fgraph_5fextraction_5157',['restrained_graph_extraction',['../classvg_1_1MultipathMapper.html#a0ad5a21ab0cf3c77e3905e299b7d26c4',1,'vg::MultipathMapper']]],
- ['result_5ftype_5158',['result_type',['../classvg_1_1uniform__real__distribution.html#a45f57ac9dad3e93958eda6a596748faa',1,'vg::uniform_real_distribution::result_type()'],['../classvg_1_1normal__distribution.html#a3cf267467b3608710fc42fc70f5df9ab',1,'vg::normal_distribution::result_type()'],['../classvg_1_1truncated__normal__distribution.html#a4a25c23c8e6024d988a0ac8617415897',1,'vg::truncated_normal_distribution::result_type()'],['../classvg_1_1WideningPRNG.html#a167ab33bf96b19131d4d85738c37e5ce',1,'vg::WideningPRNG::result_type()'],['../classvg_1_1uniform__int__distribution.html#a06f14fe90ff4a3b995f9e2100b11487d',1,'vg::uniform_int_distribution::result_type()'],['../classvg_1_1discrete__distribution.html#a06c8d8862509e0b67c9ed940b7a6c204',1,'vg::discrete_distribution::result_type()']]],
- ['retry_5fon_5fns_5159',['retry_on_Ns',['../classvg_1_1NGSSimulator.html#a95f6ffd660c8c041e4d8b1d36a823bdd',1,'vg::NGSSimulator']]],
- ['retry_5fpairing_5fspliced_5falignments_5160',['retry_pairing_spliced_alignments',['../classvg_1_1MultipathMapper.html#ae388023023d7b1a862a77416d9ed1ede',1,'vg::MultipathMapper']]],
- ['return_5ftype_5fof_5161',['return_type_of',['../structhandlegraph_1_1return__type__of.html',1,'handlegraph']]],
- ['return_5ftype_5fof_3c_20returns_28_2a_29_28args_2e_2e_2e_29_3e_5162',['return_type_of< Returns(*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
- ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_20const_20_3e_5163',['return_type_of< Returns(Owner::*)(Args...) const >',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html',1,'handlegraph']]],
- ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_3e_5164',['return_type_of< Returns(Owner::*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
- ['rev_5fcomp_5fmultipath_5falignment_5165',['rev_comp_multipath_alignment',['../namespacevg.html#a785f128b2eeb9aa2a4ee5477e5b9942b',1,'vg']]],
- ['rev_5fcomp_5fmultipath_5falignment_5fin_5fplace_5166',['rev_comp_multipath_alignment_in_place',['../namespacevg.html#ab9aa92b68bb45684a3b751060508c709',1,'vg']]],
- ['rev_5fcomp_5fsubpath_5167',['rev_comp_subpath',['../namespacevg.html#a4d802144c81c58c86f814507e1f99e22',1,'vg']]],
- ['revdna3bit_5168',['revdna3bit',['../namespacexg.html#a09a061b73b78b2ba029940f09ccb6f5b',1,'xg']]],
- ['reverse_5169',['reverse',['../structvg_1_1Support.html#acc2aa2a4b0278503817664600938c8a2',1,'vg::Support::reverse()'],['../classvg_1_1NodeTraversal.html#a748acf3ae485ab57fe649e70cad17c5d',1,'vg::NodeTraversal::reverse()'],['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda3720d917b5b410fbff17c73d58c1eaf2',1,'vg::MultipathMapper::Reverse()'],['../namespacevg.html#a91adfc6327b5709dc73fcc7edbe5da57',1,'vg::reverse(const Position &pos, size_t node_length)'],['../namespacevg.html#a2e300d25fd8281f9453366f68b484196',1,'vg::reverse(const Visit &visit)'],['../namespacevg.html#ac52fd5878b0be1d53de644eea3458663',1,'vg::reverse(const pos_t &pos, size_t node_length)'],['../namespacexg.html#ad11c9145dd19a26ea95db548d7aaac79',1,'xg::reverse()']]],
- ['reverse_5fadjacencies_5170',['reverse_adjacencies',['../classvg_1_1Surjector.html#a98ca84936638bdcb054e3304b6f959f1',1,'vg::Surjector']]],
- ['reverse_5falignment_5171',['reverse_alignment',['../classvg_1_1MultipathAlignmentGraph.html#a91aa5268618d2f4c1d7b8665108d455c',1,'vg::MultipathAlignmentGraph']]],
- ['reverse_5fbase_5fpos_5172',['reverse_base_pos',['../namespacevg.html#ae2f3762e2a8a852c7608d71f030e0345',1,'vg::reverse_base_pos()'],['../namespacexg.html#af6d74fb0781bfeb012e78af79758ab9c',1,'xg::reverse_base_pos()']]],
- ['reverse_5fcomplement_5173',['reverse_complement',['../namespacevg.html#aa65de7dea52585f07bee6ae7f762eb95',1,'vg::reverse_complement(const char &c)'],['../namespacevg.html#a30732a1a1e8d20d6eaaaeafecc8a50a7',1,'vg::reverse_complement(const string &seq)'],['../namespacexg.html#ac667d522781e3c31d191e4c6db520eaa',1,'xg::reverse_complement(const char &c)'],['../namespacexg.html#ab4f0205fd0abe6aaa4077cd20abcd36f',1,'xg::reverse_complement(const std::string &seq)']]],
- ['reverse_5fcomplement_2ecpp_5174',['reverse_complement.cpp',['../reverse__complement_8cpp.html',1,'']]],
- ['reverse_5fcomplement_5falignment_5175',['reverse_complement_alignment',['../namespacevg.html#a98e512ed0fca2503ccc370435591a6c1',1,'vg']]],
- ['reverse_5fcomplement_5falignment_5fin_5fplace_5176',['reverse_complement_alignment_in_place',['../namespacevg.html#ab96610ffc81d6207e0b13f675296c234',1,'vg']]],
- ['reverse_5fcomplement_5falignments_5177',['reverse_complement_alignments',['../namespacevg.html#aed045b02277d7704e997cbede67c2662',1,'vg']]],
- ['reverse_5fcomplement_5fedit_5178',['reverse_complement_edit',['../namespacevg_1_1io.html#a52a77b52c33c165637fb00be3e9f54e0',1,'vg::io']]],
- ['reverse_5fcomplement_5fgraph_5179',['reverse_complement_graph',['../classvg_1_1VG.html#a82185028afbc17aaf60b294297507fd2',1,'vg::VG::reverse_complement_graph()'],['../namespacehandlegraph_1_1algorithms.html#a3cb6868def99085050dca0efdd3eb0c9',1,'handlegraph::algorithms::reverse_complement_graph()']]],
- ['reverse_5fcomplement_5fin_5fplace_5180',['reverse_complement_in_place',['../namespacevg.html#ae6353d47c867f1b4cc7053d82aef42f4',1,'vg::reverse_complement_in_place()'],['../namespacexg.html#a18e172174952ffa498b10715acdc031c',1,'xg::reverse_complement_in_place()']]],
- ['reverse_5fcomplement_5fmapping_5181',['reverse_complement_mapping',['../namespacevg.html#a3ce6fa1d8f3ba4f8f361fa77a6fd5261',1,'vg::reverse_complement_mapping(const Mapping &m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a798565f048dc7844739ea4913d950d31',1,'vg::reverse_complement_mapping(const path_mapping_t &m, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fcomplement_5fmapping_5fin_5fplace_5182',['reverse_complement_mapping_in_place',['../namespacevg.html#af2dc9d6ee4403027eb5965aa6a71eb4e',1,'vg::reverse_complement_mapping_in_place(Mapping *m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#abc9bd04ab1099c6d9bd655a2accbe52e',1,'vg::reverse_complement_mapping_in_place(path_mapping_t *m, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fcomplement_5fpath_5183',['reverse_complement_path',['../namespacevg.html#a463d9eaed29cd6d46a8e2afb645c8fda',1,'vg::reverse_complement_path(const Path &path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a3df9f25ec47163ccbfa328673bd28ab5',1,'vg::reverse_complement_path(const path_t &path, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fcomplement_5fpath_5fin_5fplace_5184',['reverse_complement_path_in_place',['../namespacevg.html#af2941a3c80481d02c65d9d72bd835807',1,'vg::reverse_complement_path_in_place(Path *path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a0df8f9c5838119e79ee1f671cd823740',1,'vg::reverse_complement_path_in_place(path_t *path, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fedge_5185',['reverse_edge',['../classvg_1_1FlowSort.html#a237e09746b80c67a96290eac62fbd2c8',1,'vg::FlowSort']]],
- ['reverse_5ffrom_5fstart_5fto_5fend_5fedge_5186',['reverse_from_start_to_end_edge',['../classvg_1_1FlowSort.html#a095e96bd8ef6f016a600bdbc6af730ee',1,'vg::FlowSort']]],
- ['reverse_5fgraph_2ecpp_5187',['reverse_graph.cpp',['../reverse__graph_8cpp.html',1,'']]],
- ['reverse_5fgraph_2ehpp_5188',['reverse_graph.hpp',['../reverse__graph_8hpp.html',1,'']]],
- ['reverse_5fiterator_5189',['reverse_iterator',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html',1,'vg::ZipCodeTree::reverse_iterator'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a58d6dc8114a797ef5fa8b3ef95d3e282',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(vector< tree_item_t >::const_reverse_iterator rbegin, vector< tree_item_t >::const_reverse_iterator rend, size_t distance_limit=std::numeric_limits< size_t >::max())'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa454b7553be8ff9226e7622476de7515',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ac2889d055d75873e7d1d834c758c17ea',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(reverse_iterator &&other)']]],
- ['reversegraph_5190',['ReverseGraph',['../classvg_1_1ReverseGraph.html',1,'vg::ReverseGraph'],['../classvg_1_1ReverseGraph.html#a9122b516caa1f30b202ef7ef4cd83d60',1,'vg::ReverseGraph::ReverseGraph(const HandleGraph *forward_graph, bool complement)'],['../classvg_1_1ReverseGraph.html#a4715727accf496a2b7f908688638d873',1,'vg::ReverseGraph::ReverseGraph()=default']]],
- ['reversing_5ffilter_5191',['reversing_filter',['../classvg_1_1Filter.html#a5ac9ddf9392d973aa726ad6ee4d53b9f',1,'vg::Filter']]],
- ['reversing_5fwalk_5flength_5192',['reversing_walk_length',['../classvg_1_1MultipathMapper.html#af87eaae1274e33230fffe9dca05dbbec',1,'vg::MultipathMapper']]],
- ['rewindplanexception_5193',['RewindPlanException',['../classvg_1_1RewindPlanException.html',1,'vg::RewindPlanException'],['../classvg_1_1RewindPlanException.html#ad1b916e8d35f9825b9352045b7e77146',1,'vg::RewindPlanException::RewindPlanException()=delete'],['../classvg_1_1RewindPlanException.html#a28ad0274056215792783b0b3bc8fd258',1,'vg::RewindPlanException::RewindPlanException(const string &msg, const IndexGroup &rewind_to) noexcept']]],
- ['rewrite_5fsegment_5194',['rewrite_segment',['../classvg_1_1VG.html#abb2dc75f200cfb7480e671fd55207410',1,'vg::VG::rewrite_segment()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#af28f1372aa6dad2654a22eb8463e2a07',1,'handlegraph::MutablePathHandleGraph::rewrite_segment()']]],
- ['rgfa_5flisteners_5195',['rgfa_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a3caa995d2ef8a311e87b1202da714b53',1,'vg::algorithms::GFAParser']]],
- ['rho_5196',['rho',['../structhaplo_1_1haploMath_1_1RRMemo.html#a7536987972e5d717ba43a951adcece82',1,'haplo::haploMath::RRMemo']]],
- ['right_5197',['right',['../structvg_1_1Support.html#ab2fd7cba17f56ce67501f47fda6ae153',1,'vg::Support']]],
- ['right_5fdegree_5198',['right_degree',['../classvg_1_1VG.html#a23622195177dff4c7c8416edffb7fc93',1,'vg::VG']]],
- ['right_5fends_5199',['right_ends',['../structvg_1_1ConstructedChunk.html#ac20dbdc398181350e73bee0429fe2842',1,'vg::ConstructedChunk']]],
- ['right_5ffull_5200',['right_full',['../structvg_1_1GaplessExtension.html#ae7ca191732330cb5a6db94ee5531f2ed',1,'vg::GaplessExtension']]],
- ['right_5fhandle_5ftrans_5201',['right_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#aceac5a4b442fbce2c7c422acbdbdd097',1,'vg::JoinedSpliceGraph']]],
- ['right_5fmaximal_5202',['right_maximal',['../structvg_1_1GaplessExtension.html#a8e4d53c78f3c355b5b17bf3e959bbd41',1,'vg::GaplessExtension']]],
- ['right_5fseed_5fnode_5203',['right_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a83d9a8edb6fb9fd1ac20ffa976355155',1,'vg::JoinedSpliceGraph']]],
- ['right_5fsplice_5fnode_5204',['right_splice_node',['../classvg_1_1JoinedSpliceGraph.html#adf8ca2fd45b0d024bf4b12ea04fbfc79',1,'vg::JoinedSpliceGraph']]],
- ['right_5fsplice_5foffset_5205',['right_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a152eb3987232cdba5fff9dd9a15ed952',1,'vg::JoinedSpliceGraph']]],
- ['right_5fsubgraph_5206',['right_subgraph',['../classvg_1_1JoinedSpliceGraph.html#a42ce6f52135018237e3e29d2a53c4291',1,'vg::JoinedSpliceGraph']]],
- ['right_5ftelomere_5fnode_5207',['right_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a3d771a24b8889ea668939eac31276ea3',1,'vg::PhasedGenome::Haplotype']]],
- ['ring_5fbuffer_5fempty_5208',['ring_buffer_empty',['../classvg_1_1io_1_1StreamMultiplexer.html#a92c3f4f2de80a840aef85574935758ac',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5ffull_5209',['ring_buffer_full',['../classvg_1_1io_1_1StreamMultiplexer.html#a0d671fb79357a83af6c5becfa890a6f2',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5fpeek_5210',['ring_buffer_peek',['../classvg_1_1io_1_1StreamMultiplexer.html#aa03a8b8e99c728355ade20923bcb4c2f',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5fpop_5211',['ring_buffer_pop',['../classvg_1_1io_1_1StreamMultiplexer.html#ac4f6095e2eb79970075f9b2279e990ce',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5fpush_5212',['ring_buffer_push',['../classvg_1_1io_1_1StreamMultiplexer.html#a925607e24a8c6e905fc45c4b77bbe62c',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5fsize_5213',['RING_BUFFER_SIZE',['../classvg_1_1io_1_1StreamMultiplexer.html#a6e4432baab9571a1783b2a793b29905a',1,'vg::io::StreamMultiplexer']]],
- ['rna_5fmain_2ecpp_5214',['rna_main.cpp',['../rna__main_8cpp.html',1,'']]],
- ['rng_5215',['rng',['../classvg_1_1Colors.html#a79a79da7cbc2bef7eea8c3ff1e229b7c',1,'vg::Colors::rng()'],['../classvg_1_1Pictographs.html#ac7600f845d01a084a15cff9aacc6bc3e',1,'vg::Pictographs::rng()'],['../classvg_1_1Sampler.html#ad26ea071330c6a4b580af84bec064453',1,'vg::Sampler::rng()'],['../classvg_1_1LazyRNG.html#a6aac64a985fa2fc60c2d32079bd26a63',1,'vg::LazyRNG::rng()']]],
- ['robust_5festimation_5ffraction_5216',['robust_estimation_fraction',['../classvg_1_1FragmentLengthDistribution.html#aa5a2f20742b369464d132a751f52aaf3',1,'vg::FragmentLengthDistribution']]],
- ['root_5217',['root',['../classvg_1_1BitStringTree.html#a69741fde7d47ad2f46dd952eb6bd2d66',1,'vg::BitStringTree::root()'],['../structvg_1_1Tree.html#a730cd8796e579d01c66bea46217047d7',1,'vg::Tree::root()']]],
- ['root_5fchain_5218',['ROOT_CHAIN',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3350f37a328be806a1a8bb7534d7fb8c',1,'vg::ZipCode']]],
- ['root_5fchain_5fcomponent_5fcount_5foffset_5219',['ROOT_CHAIN_COMPONENT_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a79816fb11ec20354e677a6b1acd17905',1,'vg::ZipCode']]],
- ['root_5fchain_5fsize_5220',['ROOT_CHAIN_SIZE',['../classvg_1_1ZipCode.html#af83f8e5c14d24fd45ad2318e229299d0',1,'vg::ZipCode']]],
- ['root_5fchains_5221',['root_chains',['../classvg_1_1SnarlManager.html#a2d9758d889f875b1260f49985cf3ef35',1,'vg::SnarlManager']]],
- ['root_5fchildren_5222',['root_children',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a8b902ff993db7c62075ce3371622e781',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['root_5fidentifier_5foffset_5223',['ROOT_IDENTIFIER_OFFSET',['../classvg_1_1ZipCode.html#a9320699634e827ab9c91ade7b39220a9',1,'vg::ZipCode']]],
- ['root_5fis_5fchain_5foffset_5224',['ROOT_IS_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a9fcb55636a3bd5e25d6592952880662b',1,'vg::ZipCode']]],
- ['root_5fnode_5225',['ROOT_NODE',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3c192049eca2f2b4aafe984ff4a965d3',1,'vg::ZipCode']]],
- ['root_5fnode_5flength_5foffset_5226',['ROOT_NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a97232d726929bf2ebb8fb7fdfbde94fd',1,'vg::ZipCode']]],
- ['root_5fnode_5for_5fchain_5fconnectivity_5for_5flength_5foffset_5227',['ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#afa760e19cc391b5de5adba6b4ca3cdb0',1,'vg::ZipCode']]],
- ['root_5fnode_5fsize_5228',['ROOT_NODE_SIZE',['../classvg_1_1ZipCode.html#afa378af1f64a51675d658d2c4ecb5d95',1,'vg::ZipCode']]],
- ['root_5fsnarl_5229',['ROOT_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a438bae58eb821bbbc90b1b4bc486d682',1,'vg::ZipCode']]],
- ['root_5fsnarl_5fsize_5230',['ROOT_SNARL_SIZE',['../classvg_1_1ZipCode.html#aa2cdcd63b1ac93b431e0e4d5d25df346',1,'vg::ZipCode']]],
- ['root_5ftrim_5231',['root_trim',['../classvg_1_1TreeSubgraph.html#a04044896f4bed03dc15a6c0a07df675d',1,'vg::TreeSubgraph']]],
- ['roots_5232',['roots',['../classvg_1_1SnarlManager.html#ab13a661f6abe1feaf2c4ca4471a85a90',1,'vg::SnarlManager']]],
- ['round_5foutward_5233',['round_outward',['../structvg_1_1PathIndex.html#ac02dd3e22c5b29670ef48b6f725a9797',1,'vg::PathIndex']]],
- ['row_5fidx_5234',['row_idx',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2345d3706d3d46b657e205865f4d4122',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['rr_5fmemos_5235',['rr_memos',['../classvg_1_1MultipathMapper.html#a5709f5cdf31de90145a1178fa166be44',1,'vg::MultipathMapper']]],
- ['rrmemo_5236',['RRMemo',['../structhaplo_1_1haploMath_1_1RRMemo.html',1,'haplo::haploMath::RRMemo'],['../structhaplo_1_1haploMath_1_1RRMemo.html#a3958ec23ff1fbaac901d909c5f134f27',1,'haplo::haploMath::RRMemo::RRMemo()']]],
- ['run_5237',['run',['../classvg_1_1Genotyper.html#af760be5c99e086b2c41510b3d3a47e5a',1,'vg::Genotyper']]],
- ['run_5fbenchmark_5238',['run_benchmark',['../namespacevg.html#ac101c453ab2076d74f0324f73d174695',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &under_test)'],['../namespacevg.html#added44ff3bb1c0ce606563a40923c513',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &setup, const function< void(void)> &under_test)']]],
- ['run_5fdp_5239',['run_dp',['../classvg_1_1DeletionAligner.html#a0eb6b38dc11173f5da75c5cafd3053fe',1,'vg::DeletionAligner']]],
- ['run_5fgenotype_5240',['run_genotype',['../classvg_1_1MCMCGenotyper.html#a3bae6f8b2947e030935d5e9cf46fb324',1,'vg::MCMCGenotyper']]],
- ['run_5fmultipath_5fdp_5241',['run_multipath_dp',['../namespacevg.html#ae57a78071537c87e2f0f57bfea18ba71',1,'vg']]],
- ['running_5242',['running',['../structvg_1_1Range.html#abbd18ac55fecb0e698fcabebc7ae48ad',1,'vg::Range']]],
- ['runs_5243',['runs',['../structvg_1_1BenchmarkResult.html#a564ed18fb2f561f09e74a254854e2d88',1,'vg::BenchmarkResult']]]
+ ['r_4839',['R',['../structhaplo_1_1haplo__DP__rectangle.html#a93bec5529e8477c30fca8118e3e44f5f',1,'haplo::haplo_DP_rectangle']]],
+ ['r_5findex_4840',['r_index',['../classvg_1_1HaplotypePartitioner.html#a1eac0315eb7daaca955438f4c69f0fcb',1,'vg::HaplotypePartitioner']]],
+ ['r_5findex_5fname_4841',['r_index_name',['../structGBWTConfig.html#a230387b96ed4b3bee6cfa11c27cccc63',1,'GBWTConfig::r_index_name()'],['../structHaplotypesConfig.html#ac184346f750f8486f7e68f1e20e95d32',1,'HaplotypesConfig::r_index_name()']]],
+ ['r_5fiv_4842',['r_iv',['../classxg_1_1XG.html#aa5b5890158459739ca5e986555bcf74e',1,'xg::XG']]],
+ ['radix_5fsort_5fzipcodes_4843',['radix_sort_zipcodes',['../classvg_1_1ZipCodeForest.html#aade4c028524fd9e0c4a6267335584171',1,'vg::ZipCodeForest']]],
+ ['random_4844',['RANDOM',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046ba170e02e86972c2be8559884cc3c12254',1,'vg::StreamSorter::RANDOM()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a7fbab14a93d170a9ab8395e8bad9b15d',1,'vg::Counts::random()'],['../classvg_1_1Colors.html#aa655272ae2bc4944fe7096d3e9e072b8',1,'vg::Colors::random()'],['../classvg_1_1Pictographs.html#ac61d6a97566ac6cc8c21158688fcfdf3',1,'vg::Pictographs::random()']]],
+ ['random_5fengine_4845',['random_engine',['../classvg_1_1MCMCGenotyper.html#a742e3fb0ca54f531f23d1a8f18cb4da5',1,'vg::MCMCGenotyper']]],
+ ['random_5fmatch_5flength_4846',['random_match_length',['../classvg_1_1BaseMapper.html#a2884c6722e6bd9c9aab6671a85a6c3c0',1,'vg::BaseMapper']]],
+ ['random_5fmatch_5fp_5fvalue_4847',['random_match_p_value',['../classvg_1_1MultipathMapper.html#afbf8bce27b441ba87f83c72d5c65c592',1,'vg::MultipathMapper']]],
+ ['random_5fread_4848',['random_read',['../classvg_1_1VG.html#a8452af466a3e1ad4b0b463ea0d5da933',1,'vg::VG']]],
+ ['random_5fsequence_4849',['random_sequence',['../namespacevg.html#ab80fc8c8920c7ec53cfee81dc2fce852',1,'vg']]],
+ ['random_5fsequence_5fgen_4850',['random_sequence_gen',['../namespacevg.html#a4012afd56ccb35387121c71c2119e244',1,'vg']]],
+ ['range_4851',['Range',['../structvg_1_1Range.html',1,'vg::Range< Number >'],['../structvg_1_1Range.html#a08e1ef06cddbc0efcb0660d34cf3bc5d',1,'vg::Range::Range()'],['../structvg_1_1Range.html#a4becc4a909e9ff23a62318da327af7ff',1,'vg::Range::Range(const Number &val)'],['../structvg_1_1Range.html#a10c624eaeb6a83b450c9d24fdbaa8555',1,'vg::Range::Range(const Range &other)'],['../structvg_1_1Range.html#a7bf784228c365aa72150fec926de77ae',1,'vg::Range::Range(Range &&other)'],['../classvg_1_1MaximalExactMatch.html#a8652369dde83e159dd8c5638745a749c',1,'vg::MaximalExactMatch::range()'],['../classvg_1_1io_1_1MessageIterator.html#af88ac04ab7cbb8245a86d21a71a5dd76',1,'vg::io::MessageIterator::range()'],['../classvg_1_1io_1_1ProtobufIterator.html#acf75c4c7a16e406f9bb860e3f0c7dae9',1,'vg::io::ProtobufIterator::range()']]],
+ ['range_3c_20t_20_3e_4852',['Range< T >',['../structvg_1_1Range.html',1,'vg']]],
+ ['range_5fend_5fmatch_4853',['RANGE_END_MATCH',['../classhandlegraph_1_1PathMetadata.html#a938d44c0ba47de41907a6987c6487878',1,'handlegraph::PathMetadata']]],
+ ['range_5fend_5fseparator_4854',['RANGE_END_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#acf3518dc192f0f1cc87bdfa85665dc91',1,'handlegraph::PathMetadata']]],
+ ['range_5fstart_5fmatch_4855',['RANGE_START_MATCH',['../classhandlegraph_1_1PathMetadata.html#a15ce180ff76a984e3408a70ccf13fd62',1,'handlegraph::PathMetadata']]],
+ ['range_5fstart_5fseparator_4856',['RANGE_START_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#a3c20334a1732192586b48a7ac51860ee',1,'handlegraph::PathMetadata']]],
+ ['range_5ftable_4857',['range_table',['../classvg_1_1MEMAccelerator.html#a950e1c4779d5f0e8c0088f7b16f36770',1,'vg::MEMAccelerator']]],
+ ['range_5fterminator_4858',['RANGE_TERMINATOR',['../classhandlegraph_1_1PathMetadata.html#a1b41a72cbd2850c02a01aa7c8a2b516a',1,'handlegraph::PathMetadata']]],
+ ['range_5fvector_4859',['range_vector',['../namespacevg.html#a931d9271de88fc786030fdd0ab4bf534',1,'vg::range_vector(size_t begin, size_t end)'],['../namespacevg.html#a39adca1737de5d28d007d95b809deb7f',1,'vg::range_vector(size_t end)']]],
+ ['rangeargspec_4860',['RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html',1,'vg::subcommand']]],
+ ['rank_4861',['rank',['../classvg_1_1mapping__t.html#a8f97d898f658a36c3046b8fcc2c846ff',1,'vg::mapping_t::rank()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ab8b58edefb4cb58e014344c6010eec62',1,'vg::PhasedGenome::iterator::rank()'],['../structvg_1_1Mapping.html#a9ad71eb17b88b2cdd00cee8476e6c7b3',1,'vg::Mapping::rank()']]],
+ ['rank_5fby_5fsupport_4862',['rank_by_support',['../classvg_1_1PoissonSupportSnarlCaller.html#a300ca3bbff527fb43fbc12e65177d053',1,'vg::PoissonSupportSnarlCaller']]],
+ ['rank_5fto_5fhandle_4863',['rank_to_handle',['../classhandlegraph_1_1RankedHandleGraph.html#aacf6651545adbd407082a539222f8a69',1,'handlegraph::RankedHandleGraph']]],
+ ['rank_5fto_5fid_4864',['rank_to_id',['../classxg_1_1XG.html#aee052f301d8cae7b30c50c115c6b950b',1,'xg::XG::rank_to_id()'],['../classhandlegraph_1_1RankedHandleGraph.html#a5bf563241454b21539effcad11406ec9',1,'handlegraph::RankedHandleGraph::rank_to_id()']]],
+ ['ranked_5fhandle_5fgraph_2ecpp_4865',['ranked_handle_graph.cpp',['../ranked__handle__graph_8cpp.html',1,'']]],
+ ['rankedhandlegraph_4866',['RankedHandleGraph',['../classhandlegraph_1_1RankedHandleGraph.html',1,'handlegraph::RankedHandleGraph'],['../namespacevg.html#a215e44b59d26cf0745f02218dfd902a2',1,'vg::RankedHandleGraph()']]],
+ ['rare_5fvariant_5fsimplifier_2ecpp_4867',['rare_variant_simplifier.cpp',['../rare__variant__simplifier_8cpp.html',1,'']]],
+ ['rare_5fvariant_5fsimplifier_2ehpp_4868',['rare_variant_simplifier.hpp',['../rare__variant__simplifier_8hpp.html',1,'']]],
+ ['rarevariantsimplifier_4869',['RareVariantSimplifier',['../classvg_1_1RareVariantSimplifier.html',1,'vg::RareVariantSimplifier'],['../classvg_1_1RareVariantSimplifier.html#a08cf82d7c40db195176b9bf177a50e32',1,'vg::RareVariantSimplifier::RareVariantSimplifier()']]],
+ ['ratiosupportsnarlcaller_4870',['RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html',1,'vg::RatioSupportSnarlCaller'],['../classvg_1_1RatioSupportSnarlCaller.html#ad6905b3e30632f2a0a3e304cdfd15faa',1,'vg::RatioSupportSnarlCaller::RatioSupportSnarlCaller()']]],
+ ['re_5fgenotype_4871',['re_genotype',['../classvg_1_1LegacyCaller.html#a6c23ee5b732d26d4f55bd3b5b4830fca',1,'vg::LegacyCaller']]],
+ ['reachable_5fwith_5fgap_4872',['reachable_with_gap',['../structvg_1_1WFATree_1_1ScoreProperties.html#aeef86ffa6d221e25dfc15d97436c408c',1,'vg::WFATree::ScoreProperties']]],
+ ['read_4873',['read',['../structvg_1_1alignment__index__t.html#aedfedbedee05ac92a82889330b7a7159',1,'vg::alignment_index_t::read()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9afdd907960f4e4f4792f9986a37c69b3c',1,'vg::Counts::read()'],['../structhFILE__backend.html#ad710f254730683318f2d62b9c1ef3d60',1,'hFILE_backend::read()'],['../classvg_1_1ParallelKFFReader.html#ae34ae06b01651343a3e07b87ce019aa7',1,'vg::ParallelKFFReader::read()']]],
+ ['read_5f1_5fadapter_4874',['read_1_adapter',['../classvg_1_1MultipathMapper.html#ac11fe37f1e47b1f3697e1eeeb703a467',1,'vg::MultipathMapper']]],
+ ['read_5f1_5fadapter_5flps_4875',['read_1_adapter_lps',['../classvg_1_1MultipathMapper.html#a72cfecb533ba72974ca4fe736f5e4616',1,'vg::MultipathMapper']]],
+ ['read_5f2_5fadapter_4876',['read_2_adapter',['../classvg_1_1MultipathMapper.html#a9dda8a58ca0a9a3b5f8cf6bb6b72b907',1,'vg::MultipathMapper']]],
+ ['read_5f2_5fadapter_5flps_4877',['read_2_adapter_lps',['../classvg_1_1MultipathMapper.html#ab14d5973d561097ca08d9e989b04265b',1,'vg::MultipathMapper']]],
+ ['read_5falignment_5findex_5ft_4878',['read_alignment_index_t',['../structvg_1_1read__alignment__index__t.html',1,'vg']]],
+ ['read_5fbest_5fleft_4879',['read_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6573a9b29b9df17f33cc6ce50889f408',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['read_5fbest_5fright_4880',['read_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a9509065fa738b008fa7e75325a34b9fe',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['read_5fcluster_5fheads_4881',['read_cluster_heads',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3d23f2d455846fcb6d5ea634926f7dce',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['read_5fdistance_5flimit_4882',['read_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a96bda025a3c371cef79b565d66b31a2a',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['read_5fend_4883',['read_end',['../classvg_1_1algorithms_1_1Anchor.html#a335ebe332424cb49cae4da84c91a5367',1,'vg::algorithms::Anchor']]],
+ ['read_5fexclusion_5fend_4884',['read_exclusion_end',['../classvg_1_1algorithms_1_1Anchor.html#a12554fafcdf8309d3119b349e3bf6e59',1,'vg::algorithms::Anchor']]],
+ ['read_5fexclusion_5fstart_4885',['read_exclusion_start',['../classvg_1_1algorithms_1_1Anchor.html#a1de27e657461d6de450a84aab34becb4',1,'vg::algorithms::Anchor']]],
+ ['read_5fgroup_4886',['read_group',['../classvg_1_1MinimizerMapper.html#aee3e4b7c4e777da6c09f70218481e3d6',1,'vg::MinimizerMapper::read_group()'],['../classvg_1_1MultipathAlignmentEmitter.html#a931f4785a73cfd9069d7447ba63b71ef',1,'vg::MultipathAlignmentEmitter::read_group()'],['../structvg_1_1Alignment.html#a95102c70d75046f86a2f0a829ba1efe0',1,'vg::Alignment::read_group()'],['../structvg_1_1MultipathAlignment.html#abdc748afaea04b662f170156d8c88343',1,'vg::MultipathAlignment::read_group()']]],
+ ['read_5finterval_4887',['read_interval',['../structvg_1_1GaplessExtension.html#a32b115618388c2254ef91c06ac0c9840',1,'vg::GaplessExtension']]],
+ ['read_5flog_5flikelihood_4888',['read_log_likelihood',['../classvg_1_1PhasedGenome.html#af754f8a4e9793ebd5f4aa3b673b7e442',1,'vg::PhasedGenome']]],
+ ['read_5fmapped_4889',['read_mapped',['../structvg_1_1Alignment.html#af2fc72c769b77c355632e6aab7573046',1,'vg::Alignment']]],
+ ['read_5fmapping_4890',['read_mapping',['../classvg_1_1PhaseUnfolder.html#adbf93e421183b64f73276639c3c23dfb',1,'vg::PhaseUnfolder']]],
+ ['read_5fnum_4891',['read_num',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#aeb827f9966141503abe98ebcce7b2db2',1,'vg::SnarlDistanceIndexClusterer::ClusterHead']]],
+ ['read_5foffset_4892',['read_offset',['../structMappingRun.html#a730efdfaef634a4173efe0bd9e4e3da1',1,'MappingRun']]],
+ ['read_5fon_5freverse_5fstrand_4893',['read_on_reverse_strand',['../structvg_1_1Alignment.html#a10b4d599e1812ee007e348f8ce8bfe49',1,'vg::Alignment']]],
+ ['read_5fpaired_4894',['read_paired',['../structvg_1_1Alignment.html#a2bfa3fffb5f4ea6ab3e98a6340ad16bb',1,'vg::Alignment']]],
+ ['read_5fstart_4895',['read_start',['../classvg_1_1algorithms_1_1Anchor.html#a21c07ed7e05dfd2194d580022f2005c4',1,'vg::algorithms::Anchor']]],
+ ['read_5ftoo_5fshort_4896',['READ_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a997b7fe4b82277b56702572e730d3eb7',1,'vg::AlignmentValidity']]],
+ ['read_5funion_5ffind_4897',['read_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#afbf1772f189edd4c5f4a8e74914a4d6c',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['reader_4898',['reader',['../classvg_1_1ParallelKFFReader.html#a88e22492b07cf27f746ca0086d48c6dd',1,'vg::ParallelKFFReader::reader()'],['../classvg_1_1WindowedVcfBuffer.html#a064a56b55dbb562f1b52034a54ed3583',1,'vg::WindowedVcfBuffer::reader()']]],
+ ['readfilter_4899',['ReadFilter',['../classvg_1_1ReadFilter.html',1,'vg']]],
+ ['readfilter_2ecpp_4900',['readfilter.cpp',['../readfilter_8cpp.html',1,'']]],
+ ['readfilter_2ehpp_4901',['readfilter.hpp',['../readfilter_8hpp.html',1,'']]],
+ ['readmasker_4902',['ReadMasker',['../classvg_1_1ReadMasker.html',1,'vg::ReadMasker'],['../classvg_1_1ReadMasker.html#a99656ed3430d86e7a34b908914991945',1,'vg::ReadMasker::ReadMasker()']]],
+ ['readrestrictedtraversalfinder_4903',['ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html',1,'vg::ReadRestrictedTraversalFinder'],['../classvg_1_1ReadRestrictedTraversalFinder.html#a8cf6a940b0fce108e8af39d8a50a380f',1,'vg::ReadRestrictedTraversalFinder::ReadRestrictedTraversalFinder()']]],
+ ['reads_4904',['Reads',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4a9989ae14c6b6c27998126ab745488926',1,'vg::Genotyper']]],
+ ['reads_5fby_5fname_4905',['reads_by_name',['../classvg_1_1PathRestrictedTraversalFinder.html#ac08d8f72efc63adb1bf169d9ed7c107e',1,'vg::PathRestrictedTraversalFinder']]],
+ ['real_5ft_4906',['real_t',['../namespacevg.html#a7392de2ef03532b2ec3461ebb178c75a',1,'vg']]],
+ ['realign_5findels_4907',['realign_indels',['../classvg_1_1Genotyper.html#a79ac39be882405a426afaeeef65c9660',1,'vg::Genotyper']]],
+ ['realigning_5fsurject_4908',['realigning_surject',['../classvg_1_1Surjector.html#a2629f80135104fb8486ef823f525b843',1,'vg::Surjector']]],
+ ['reallocate_5fatomic_5fint_5fvector_4909',['reallocate_atomic_int_vector',['../namespacevg_1_1algorithms.html#acd891e00c4846e53f760d504434ead12',1,'vg::algorithms']]],
+ ['reassign_5fnode_4910',['reassign_node',['../classvg_1_1Paths.html#aed5ea00a6a8dab5b54eeedd9e8f91a7b',1,'vg::Paths']]],
+ ['reassign_5fnode_5fids_4911',['reassign_node_ids',['../classvg_1_1VG.html#aca4a358ff4c7f387c1c6d5d239499a07',1,'vg::VG::reassign_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a4805d276a83a1dad2462e6b8dd2443dc',1,'handlegraph::MutableHandleGraph::reassign_node_ids()']]],
+ ['reassign_5fsplit_5fclusters_4912',['reassign_split_clusters',['../classvg_1_1MultipathMapper.html#a5d8b62d4d55e83f80da09173e8520874',1,'vg::MultipathMapper']]],
+ ['rebuild_5fedge_5findexes_4913',['rebuild_edge_indexes',['../classvg_1_1VG.html#a6541146b6410cec4be3e2a7379ea3bcf',1,'vg::VG']]],
+ ['rebuild_5fgbwt_4914',['rebuild_gbwt',['../namespacevg.html#a95d54bf0a30125f9ded043bb099cb25f',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob > &jobs, const std::unordered_map< nid_t, size_t > &node_to_job, const RebuildParameters ¶meters)'],['../namespacevg.html#ade5b1e6daa5da7101533d444d3d8ff41',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob::mapping_type > &mappings)']]],
+ ['rebuild_5fgbwt_5fjob_4915',['rebuild_gbwt_job',['../namespacevg.html#a16b175479dee254341d60fc037dae233',1,'vg']]],
+ ['rebuild_5findexes_4916',['rebuild_indexes',['../classvg_1_1VG.html#a63d4e45a9a410c451b1cad44ef7068ad',1,'vg::VG']]],
+ ['rebuild_5fmapping_5faux_4917',['rebuild_mapping_aux',['../classvg_1_1Paths.html#a5f80df5846bdac0b502a70af97dc65de',1,'vg::Paths']]],
+ ['rebuild_5fnode_5fmapping_4918',['rebuild_node_mapping',['../classvg_1_1Paths.html#a7e9d9388475dcd8f23af072430e7383c',1,'vg::Paths']]],
+ ['rebuildjob_4919',['RebuildJob',['../structvg_1_1RebuildJob.html',1,'vg']]],
+ ['rebuildparameters_4920',['RebuildParameters',['../structvg_1_1RebuildParameters.html',1,'vg']]],
+ ['recipe_5fregistry_4921',['recipe_registry',['../classvg_1_1IndexRegistry.html#a963c33ba471ce5e0c4e5403d4a86e753',1,'vg::IndexRegistry']]],
+ ['recipefunc_4922',['RecipeFunc',['../namespacevg.html#a1ff09b399af11722aeee121ae6f4fd9b',1,'vg']]],
+ ['recipename_4923',['RecipeName',['../namespacevg.html#a6119d0b9707c042b0c2cde5d77b670cb',1,'vg']]],
+ ['recoding_4924',['recoding',['../classvg_1_1ParallelKFFReader.html#aaf7eee70fc5bfbb863fc68ee8840a812',1,'vg::ParallelKFFReader']]],
+ ['recombination_5fpenalty_4925',['recombination_penalty',['../classvg_1_1BaseMapper.html#af0e6c250a81dc74df57136242174aa54',1,'vg::BaseMapper::recombination_penalty()'],['../classvg_1_1MultipathMapper.html#a26993f76e9bbe5c48e0b436cc9c3fda8',1,'vg::MultipathMapper::recombination_penalty()']]],
+ ['recombinator_4926',['Recombinator',['../classvg_1_1Recombinator.html',1,'vg::Recombinator'],['../classvg_1_1Recombinator.html#a9248c550bcc5aa267abde6eefec69e88',1,'vg::Recombinator::Recombinator()']]],
+ ['recombinator_2ecpp_4927',['recombinator.cpp',['../recombinator_8cpp.html',1,'']]],
+ ['recombinator_2ehpp_4928',['recombinator.hpp',['../recombinator_8hpp.html',1,'']]],
+ ['recombinator_5fparameters_4929',['recombinator_parameters',['../structHaplotypesConfig.html#a10886974a276f98f45a26c7b2c51c350',1,'HaplotypesConfig']]],
+ ['recombinator_5fsanity_5fchecks_4930',['recombinator_sanity_checks',['../namespacevg.html#aa81f31f29a47e669812c3ef57bd1aab6',1,'vg']]],
+ ['recombinatorfragment_4931',['RecombinatorFragment',['../structvg_1_1RecombinatorFragment.html',1,'vg::RecombinatorFragment'],['../structvg_1_1RecombinatorFragment.html#aab79ba107e9e086b432dfa9fcf4a2807',1,'vg::RecombinatorFragment::RecombinatorFragment()']]],
+ ['recombinatorhaplotype_4932',['RecombinatorHaplotype',['../structvg_1_1RecombinatorHaplotype.html',1,'vg']]],
+ ['record_4933',['record',['../classvg_1_1SnarlManager.html#a45e3765bfd07b196b6e30b7a9b62aefd',1,'vg::SnarlManager::record(const Snarl *snarl) const'],['../classvg_1_1SnarlManager.html#a3ce002195299049e9925e94546d989b9',1,'vg::SnarlManager::record(Snarl *snarl)']]],
+ ['record_5fbases_4934',['record_bases',['../classvg_1_1Packer.html#a7a3debd842c660a3fc4755fc887c74ec',1,'vg::Packer']]],
+ ['record_5fedges_4935',['record_edges',['../classvg_1_1Packer.html#ab6fa0636229479a7368286e43f20ffa2',1,'vg::Packer']]],
+ ['record_5fedits_4936',['record_edits',['../classvg_1_1Packer.html#a8200ea3c39e408f3394c4a65fe2e3786',1,'vg::Packer']]],
+ ['record_5ffanouts_4937',['record_fanouts',['../classvg_1_1MultipathMapper.html#a0b4e3381a53cf532acdf7cbadc6d9985',1,'vg::MultipathMapper']]],
+ ['record_5ffragment_5fconfiguration_4938',['record_fragment_configuration',['../classvg_1_1FragmentLengthStatistics.html#ae63195a980c56907de548ba00098c794',1,'vg::FragmentLengthStatistics']]],
+ ['record_5foffset_4939',['record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa4c597fb92b3074c231b3b02f1dd58a4',1,'vg::ZipCode::snarl_code_t']]],
+ ['record_5fqualities_4940',['record_qualities',['../classvg_1_1Packer.html#ab29c0bdd5ae1db4a89db3476ba70ef68',1,'vg::Packer']]],
+ ['record_5fread_5fpair_5fquality_4941',['record_read_pair_quality',['../classvg_1_1NGSSimulator.html#aec434f0c212aec15e1760f4c4b1185e2',1,'vg::NGSSimulator']]],
+ ['record_5fread_5fquality_4942',['record_read_quality',['../classvg_1_1NGSSimulator.html#a8f34614e3dc660e31d26d9c18970e736',1,'vg::NGSSimulator']]],
+ ['record_5ftransition_4943',['record_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ab3609f759c7b20d77c1bc0ca7160c26a',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['recover_5flog_5fbase_4944',['recover_log_base',['../classvg_1_1GSSWAligner.html#ab5102e690e6e2e0e72aa35ea769179a2',1,'vg::GSSWAligner']]],
+ ['recursealways_4945',['RecurseAlways',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ade8537831952f7d91199da0ded53a8d2',1,'vg::GraphCaller']]],
+ ['recursenever_4946',['RecurseNever',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ad50ac99caa8bae55f8d5d8ed7a4aef04',1,'vg::GraphCaller']]],
+ ['recurseonfail_4947',['RecurseOnFail',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ae25246a2b8e3ba65437d72bf513be31c',1,'vg::GraphCaller']]],
+ ['recursetype_4948',['RecurseType',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5',1,'vg::GraphCaller']]],
+ ['recursively_5femit_5fsnarls_4949',['recursively_emit_snarls',['../classvg_1_1CactusSnarlFinder.html#aad8a90f6cd0fddf6ab908f6287e3ddf3',1,'vg::CactusSnarlFinder']]],
+ ['reduce_5fto_5fsingle_5fpath_4950',['reduce_to_single_path',['../classvg_1_1MultipathMapper.html#a0a3360fde5883dc2c0927b63be0a3bd5',1,'vg::MultipathMapper']]],
+ ['redundant_5fvertexes_4951',['redundant_vertexes',['../classvg_1_1MEMChainModel.html#a6a4132f34b8c9636e02c186ffa75a333',1,'vg::MEMChainModel::redundant_vertexes()'],['../classvg_1_1AlignmentChainModel.html#a2fd794e91dfc7ee2db7fdc9f921c5134',1,'vg::AlignmentChainModel::redundant_vertexes()']]],
+ ['reencode_5fold_5fg_5fvector_4952',['reencode_old_g_vector',['../classxg_1_1XG.html#a8a5068e08156a861e35e62cc3fa94204',1,'xg::XG']]],
+ ['reestimation_5ffrequency_4953',['reestimation_frequency',['../classvg_1_1FragmentLengthDistribution.html#a648954fbcb1fd0295fb22a37d79ed3e7',1,'vg::FragmentLengthDistribution']]],
+ ['ref_5fbase_4954',['ref_base',['../structvg_1_1BasePileup.html#a8d68d6e5d3ce5d2a9a448f90ed6dfc09',1,'vg::BasePileup']]],
+ ['ref_5foffset_4955',['ref_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a0d0812a9f6be0ad3610fb860fb1bc2d2',1,'vg::DozeuInterface::graph_pos_s']]],
+ ['ref_5foffsets_4956',['ref_offsets',['../classvg_1_1LegacyCaller.html#a9aa5ae8255c13d5c19a4cae14f998a8e',1,'vg::LegacyCaller::ref_offsets()'],['../classvg_1_1FlowCaller.html#a454f9cba510f7ebf9e8929c53092583a',1,'vg::FlowCaller::ref_offsets()'],['../classvg_1_1NestedFlowCaller.html#a389525ad359e73ad07da1bac80cb3595',1,'vg::NestedFlowCaller::ref_offsets()'],['../classvg_1_1MCMCCaller.html#acccde0cf44eb8781fc43830f0b3736b3',1,'vg::MCMCCaller::ref_offsets()']]],
+ ['ref_5fpath_4957',['ref_path',['../structvg_1_1FlowSort_1_1Growth.html#a34ba660c358c1ec59cd7c70e62780a8c',1,'vg::FlowSort::Growth']]],
+ ['ref_5fpath_5fdistance_4958',['ref_path_distance',['../namespacevg_1_1algorithms.html#aa5e4dc632e98b58b67a99af6749d9e05',1,'vg::algorithms']]],
+ ['ref_5fpath_5fdistance_2ecpp_4959',['ref_path_distance.cpp',['../ref__path__distance_8cpp.html',1,'']]],
+ ['ref_5fpath_5fdistance_2ehpp_4960',['ref_path_distance.hpp',['../ref__path__distance_8hpp.html',1,'']]],
+ ['ref_5fpath_5fhandle_4961',['ref_path_handle',['../structhaplo_1_1linear__haplo__structure.html#a57eb7d1ebc0bc29e9ba3d1c3955650e9',1,'haplo::linear_haplo_structure']]],
+ ['ref_5fpath_5fhandles_4962',['ref_path_handles',['../classvg_1_1MultipathMapper.html#a2ee3920a6e8758880172f6fd07c5f7f2',1,'vg::MultipathMapper']]],
+ ['ref_5fpath_5finterval_4963',['ref_path_interval',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#afb6f9c3dbe7a55c17d953489de39e656',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['ref_5fpath_5flengths_4964',['ref_path_lengths',['../classvg_1_1MCMCCaller.html#a7638f220d989784503287ea538da21f4',1,'vg::MCMCCaller']]],
+ ['ref_5fpath_5fname_4965',['ref_path_name',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a69d34c61dd53d99246bebffa0b68def0',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['ref_5fpath_5foffsets_4966',['ref_path_offsets',['../classvg_1_1MCMCCaller.html#a614597d6c55c252d2efb88cdd0048eff',1,'vg::MCMCCaller']]],
+ ['ref_5fpath_5fset_4967',['ref_path_set',['../classvg_1_1FlowCaller.html#ac85f8948b4a0c6f9bcb66cccf498c372',1,'vg::FlowCaller::ref_path_set()'],['../classvg_1_1NestedFlowCaller.html#a934f25461550667e553a51ed2fee1fb2',1,'vg::NestedFlowCaller::ref_path_set()']]],
+ ['ref_5fpaths_4968',['ref_paths',['../classvg_1_1Deconstructor.html#a8da74d6fff7d5af6caed96723d0bccd9',1,'vg::Deconstructor::ref_paths()'],['../classvg_1_1GAFOutputCaller.html#a2675564b819e50ac8a21ca51eb14c99c',1,'vg::GAFOutputCaller::ref_paths()'],['../classvg_1_1LegacyCaller.html#a73beb7401923d192f8542beb938ea33c',1,'vg::LegacyCaller::ref_paths()'],['../classvg_1_1FlowCaller.html#adb1bb384ccb36d214a22cef04919920c',1,'vg::FlowCaller::ref_paths()'],['../classvg_1_1NestedFlowCaller.html#a5206505cf92654951bef22b42d50381e',1,'vg::NestedFlowCaller::ref_paths()'],['../classvg_1_1MCMCCaller.html#a081ed012622de090f1aad2a82526a59e',1,'vg::MCMCCaller::ref_paths()'],['../structvg_1_1Recombinator_1_1Statistics.html#ac3404816da5f78c7712ad69eb8f9594f',1,'vg::Recombinator::Statistics::ref_paths()']]],
+ ['ref_5fploidies_4969',['ref_ploidies',['../classvg_1_1LegacyCaller.html#ac82406147f3603e97d22418ee0e7bdc4',1,'vg::LegacyCaller::ref_ploidies()'],['../classvg_1_1FlowCaller.html#a2487ac1acadd5052a3a18204c426591d',1,'vg::FlowCaller::ref_ploidies()'],['../classvg_1_1NestedFlowCaller.html#a021b1013fe64a99b598ffa291a423e5b',1,'vg::NestedFlowCaller::ref_ploidies()']]],
+ ['ref_5fposition_4970',['ref_position',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a442f4e740bc94b1671c9590f65bb65a4',1,'haplo::linear_haplo_structure::SNVvector']]],
+ ['ref_5fpositions_4971',['ref_positions',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a6065969d77968cd3afc31ca7b8b1a9f0',1,'haplo::linear_haplo_structure::SNVvector']]],
+ ['ref_5fsample_4972',['ref_sample',['../structHaplotypesConfig.html#a1575fa9f328d1d823e788f422b6bde43',1,'HaplotypesConfig']]],
+ ['ref_5fsamples_4973',['ref_samples',['../classvg_1_1Deconstructor.html#a72834c9d1d667e3283e93f60a3f5057b',1,'vg::Deconstructor']]],
+ ['ref_5fspan_4974',['ref_span',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8aabba00d1035f3425a2ff43984b99a3d4',1,'haplo::linear_haplo_structure']]],
+ ['ref_5fsteps_4975',['ref_steps',['../structvg_1_1ParentGenotypeInfo.html#a45d8b5d863b3f74e9eb499acef7a2916',1,'vg::ParentGenotypeInfo']]],
+ ['ref_5ftrav_5fidx_4976',['ref_trav_idx',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a7a265b17dc3bc9a34603de7e064230f8',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['ref_5ftraversal_4977',['ref_traversal',['../structvg_1_1ParentGenotypeInfo.html#a4e02433e8ac8eae0491d4290f5b78515',1,'vg::ParentGenotypeInfo']]],
+ ['refactor_5fsplit_5falignment_4978',['refactor_split_alignment',['../classvg_1_1Filter.html#af5c53d7fa62dff67d24ff0daa4d5f925',1,'vg::Filter']]],
+ ['reference_4979',['reference',['../classvg_1_1count__back__inserter.html#a84eca4db3ffead0102aa62bd53000631',1,'vg::count_back_inserter::reference()'],['../structvg_1_1VectorView_1_1const__iterator.html#a037cb8cbbd9c2be6c471ee6aa9bfbb1d',1,'vg::VectorView::const_iterator::reference()'],['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cadcd320d017d7f3c317bc8b234287bc9f',1,'handlegraph::REFERENCE()']]],
+ ['reference_5fpaths_4980',['reference_paths',['../classvg_1_1PhaseUnfolder.html#a2bfa46441300e0817643b310aced989b',1,'vg::PhaseUnfolder']]],
+ ['reference_5ftranscript_5fpaths_4981',['reference_transcript_paths',['../classvg_1_1Transcriptome.html#aacf1ad40a7a5d42985c4149b03fe936e',1,'vg::Transcriptome']]],
+ ['referenceinterval_4982',['ReferenceInterval',['../structReferenceInterval.html',1,'']]],
+ ['referencepathvectorizableoverlayhelper_4983',['ReferencePathVectorizableOverlayHelper',['../call__main_8cpp.html#adc0e01cf2a62b559e7c67d23dfbd757e',1,'call_main.cpp']]],
+ ['reflect_4984',['reflect',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa5776efd133ed466cb82ef4f4b161dfd',1,'vg::GraphSynchronizer::Lock']]],
+ ['refpos_4985',['refpos',['../structvg_1_1Alignment.html#a584c3aa15a5c1386d14a97c0ce85c0cf',1,'vg::Alignment']]],
+ ['region_4986',['Region',['../structvg_1_1Region.html',1,'vg']]],
+ ['region_2ecpp_4987',['region.cpp',['../region_8cpp.html',1,'']]],
+ ['region_2ehpp_4988',['region.hpp',['../region_8hpp.html',1,'']]],
+ ['region_5fexpander_2ecpp_4989',['region_expander.cpp',['../region__expander_8cpp.html',1,'']]],
+ ['region_5fexpander_2ehpp_4990',['region_expander.hpp',['../region__expander_8hpp.html',1,'']]],
+ ['regionexpander_4991',['RegionExpander',['../classvg_1_1RegionExpander.html',1,'vg::RegionExpander'],['../classvg_1_1RegionExpander.html#a42c0f501da7fabf0045f5c434b55f705',1,'vg::RegionExpander::RegionExpander()']]],
+ ['regions_4992',['regions',['../structvg_1_1Funnel_1_1PaintableSpace.html#a001cb606b7e4f79f8be9550b17c6f1b4',1,'vg::Funnel::PaintableSpace::regions()'],['../classvg_1_1HaplotypeIndexer.html#a85285e19121d708649f61b5420ab0777',1,'vg::HaplotypeIndexer::regions()']]],
+ ['register_5falias_4993',['register_alias',['../classvg_1_1AliasGraph.html#a4f21c7d2e0aa761fd5ff4ccd43bd72af',1,'vg::AliasGraph']]],
+ ['register_5fbare_5floader_4994',['register_bare_loader',['../classvg_1_1io_1_1Registry.html#a025929701767e23673356cae9e7024a5',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_4995',['register_bare_loader_saver',['../classvg_1_1io_1_1Registry.html#aab501bb8db46d45e8b1946da37f0b382',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fheader_5fcheck_4996',['register_bare_loader_saver_with_header_check',['../classvg_1_1io_1_1Registry.html#a873d317a5ec04d5af5223008310043df',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_4997',['register_bare_loader_saver_with_magic',['../classvg_1_1io_1_1Registry.html#ad3f16de5d24cb503429d358e2af8c831',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_5fand_5ffilename_4998',['register_bare_loader_saver_with_magic_and_filename',['../classvg_1_1io_1_1Registry.html#acfda4299247a88075080004beba4a136',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fmagics_4999',['register_bare_loader_saver_with_magics',['../classvg_1_1io_1_1Registry.html#af4180fbb60edaa1cd1aec325945d2af5',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fwith_5ffilename_5000',['register_bare_loader_with_filename',['../classvg_1_1io_1_1Registry.html#abb7a1aefe860153a36614efa54bcde29',1,'vg::io::Registry']]],
+ ['register_5fbarrier_5001',['register_barrier',['../classvg_1_1io_1_1StreamMultiplexer.html#acb05844bf345313fc1710db7f3610ac5',1,'vg::io::StreamMultiplexer']]],
+ ['register_5fbreakpoint_5002',['register_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#a562910d0ca3b3fac6b95b0c3ee3c81dd',1,'vg::io::StreamMultiplexer']]],
+ ['register_5fconfigurable_5003',['register_configurable',['../classvg_1_1ConfigurableParser.html#a3c42646beeac7fb48f57c44f1420ec7b',1,'vg::ConfigurableParser']]],
+ ['register_5feverything_5004',['register_everything',['../classvg_1_1io_1_1Registry.html#ad1b4d2c277bdb07c2bf4cc4b60e35745',1,'vg::io::Registry']]],
+ ['register_5ffragment_5flength_5005',['register_fragment_length',['../classvg_1_1FragmentLengthDistribution.html#a888c21e626cb2fd984f9e0ffd39adefc',1,'vg::FragmentLengthDistribution']]],
+ ['register_5fgeneralization_5006',['register_generalization',['../classvg_1_1IndexRegistry.html#a2e1c0e83f49e8719459e644ce143302b',1,'vg::IndexRegistry']]],
+ ['register_5findex_5007',['register_index',['../classvg_1_1IndexRegistry.html#ad8f48075fe06df92c65bc5fd0207f9bc',1,'vg::IndexRegistry']]],
+ ['register_5flibvg_5fio_5008',['register_libvg_io',['../namespacevg_1_1io.html#ad93f27be4f07ab9c6a91a1501b992f70',1,'vg::io']]],
+ ['register_5flibvg_5fio_2ecpp_5009',['register_libvg_io.cpp',['../register__libvg__io_8cpp.html',1,'']]],
+ ['register_5flibvg_5fio_2ehpp_5010',['register_libvg_io.hpp',['../register__libvg__io_8hpp.html',1,'']]],
+ ['register_5floader_5011',['register_loader',['../classvg_1_1io_1_1Registry.html#a82c329d405f2dc83880623561a10962f',1,'vg::io::Registry::register_loader(const string &tag, load_function_t loader)'],['../classvg_1_1io_1_1Registry.html#abdbc23294daf5a1f44b34da481929891',1,'vg::io::Registry::register_loader(const std::vector< std::string > &tags, load_function_t loader)']]],
+ ['register_5floader_5fparams_5fjson_5012',['register_loader_params_json',['../namespacevg_1_1io.html#a113c8011c25b00d36f77f49062726bbb',1,'vg::io']]],
+ ['register_5floader_5fparams_5fjson_2ecpp_5013',['register_loader_params_json.cpp',['../register__loader__params__json_8cpp.html',1,'']]],
+ ['register_5floader_5fparams_5fjson_2ehpp_5014',['register_loader_params_json.hpp',['../register__loader__params__json_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5015',['register_loader_saver',['../classvg_1_1io_1_1Registry.html#a3dfd842b470ff701fb805838e2d7fe61',1,'vg::io::Registry::register_loader_saver(const string &tag, load_function_t loader, save_function_t saver)'],['../classvg_1_1io_1_1Registry.html#a56e76bb9dcab4c47f400d844430536b6',1,'vg::io::Registry::register_loader_saver(const std::vector< std::string > &tags, load_function_t loader, save_function_t saver)']]],
+ ['register_5floader_5fsaver_5fdistance_5findex_5016',['register_loader_saver_distance_index',['../namespacevg_1_1io.html#a45372f8f761a3bce9e7ef6e1422db47b',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fdistance_5findex_2ecpp_5017',['register_loader_saver_distance_index.cpp',['../register__loader__saver__distance__index_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fdistance_5findex_2ehpp_5018',['register_loader_saver_distance_index.hpp',['../register__loader__saver__distance__index_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwt_5019',['register_loader_saver_gbwt',['../namespacevg_1_1io.html#a47fc4c5122bf0f0810993822d194eb20',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbwt_2ecpp_5020',['register_loader_saver_gbwt.cpp',['../register__loader__saver__gbwt_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwt_2ehpp_5021',['register_loader_saver_gbwt.hpp',['../register__loader__saver__gbwt_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwtgraph_5022',['register_loader_saver_gbwtgraph',['../namespacevg_1_1io.html#a6143362abf3060042589f1ffb22ff498',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbwtgraph_2ecpp_5023',['register_loader_saver_gbwtgraph.cpp',['../register__loader__saver__gbwtgraph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwtgraph_2ehpp_5024',['register_loader_saver_gbwtgraph.hpp',['../register__loader__saver__gbwtgraph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbz_5025',['register_loader_saver_gbz',['../namespacevg_1_1io.html#adb36b3bf6da822750c5c6c9cd2d987e0',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbz_2ecpp_5026',['register_loader_saver_gbz.cpp',['../register__loader__saver__gbz_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbz_2ehpp_5027',['register_loader_saver_gbz.hpp',['../register__loader__saver__gbz_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbzgraph_5028',['register_loader_saver_gbzgraph',['../namespacevg_1_1io.html#a81649e999e30d305e02187c16b257d07',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbzgraph_2ecpp_5029',['register_loader_saver_gbzgraph.cpp',['../register__loader__saver__gbzgraph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbzgraph_2ehpp_5030',['register_loader_saver_gbzgraph.hpp',['../register__loader__saver__gbzgraph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgcsa_5031',['register_loader_saver_gcsa',['../namespacevg_1_1io.html#affca170910f12393eb1381c4d72e4e73',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgcsa_2ecpp_5032',['register_loader_saver_gcsa.cpp',['../register__loader__saver__gcsa_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgcsa_2ehpp_5033',['register_loader_saver_gcsa.hpp',['../register__loader__saver__gcsa_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgfa_5034',['register_loader_saver_gfa',['../namespacevg_1_1io.html#a1fadf5a0f7d91d61c9d2c27d35987c6a',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgfa_2ecpp_5035',['register_loader_saver_gfa.cpp',['../register__loader__saver__gfa_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgfa_2ehpp_5036',['register_loader_saver_gfa.hpp',['../register__loader__saver__gfa_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fhash_5fgraph_5037',['register_loader_saver_hash_graph',['../namespacevg_1_1io.html#a49d41e6f52ad981f96d772396fd4eee5',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fhash_5fgraph_2ecpp_5038',['register_loader_saver_hash_graph.cpp',['../register__loader__saver__hash__graph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fhash_5fgraph_2ehpp_5039',['register_loader_saver_hash_graph.hpp',['../register__loader__saver__hash__graph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5flcp_5040',['register_loader_saver_lcp',['../namespacevg_1_1io.html#af7df97a78891ada683647c88c6393eb9',1,'vg::io']]],
+ ['register_5floader_5fsaver_5flcp_2ecpp_5041',['register_loader_saver_lcp.cpp',['../register__loader__saver__lcp_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5flcp_2ehpp_5042',['register_loader_saver_lcp.hpp',['../register__loader__saver__lcp_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fminimizer_5043',['register_loader_saver_minimizer',['../namespacevg_1_1io.html#aa69bc026abe7a1db4530704dfc7e7b3f',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fminimizer_2ecpp_5044',['register_loader_saver_minimizer.cpp',['../register__loader__saver__minimizer_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fminimizer_2ehpp_5045',['register_loader_saver_minimizer.hpp',['../register__loader__saver__minimizer_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fpacked_5fgraph_5046',['register_loader_saver_packed_graph',['../namespacevg_1_1io.html#a776b6490958856d44dc2d962d629440d',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fpacked_5fgraph_2ecpp_5047',['register_loader_saver_packed_graph.cpp',['../register__loader__saver__packed__graph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fpacked_5fgraph_2ehpp_5048',['register_loader_saver_packed_graph.hpp',['../register__loader__saver__packed__graph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fr_5findex_5049',['register_loader_saver_r_index',['../namespacevg_1_1io.html#a6ce32e4ae1d4f5d244c0d80d3ac09beb',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fr_5findex_2ecpp_5050',['register_loader_saver_r_index.cpp',['../register__loader__saver__r__index_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fr_5findex_2ehpp_5051',['register_loader_saver_r_index.hpp',['../register__loader__saver__r__index_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fsnarl_5fmanager_5052',['register_loader_saver_snarl_manager',['../namespacevg_1_1io.html#a8072168ee8165f81afb2688ef0825ea8',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fsnarl_5fmanager_2ecpp_5053',['register_loader_saver_snarl_manager.cpp',['../register__loader__saver__snarl__manager_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fsnarl_5fmanager_2ehpp_5054',['register_loader_saver_snarl_manager.hpp',['../register__loader__saver__snarl__manager_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fvg_5055',['register_loader_saver_vg',['../namespacevg_1_1io.html#ac3485846033fd4accb221b0a866dfeb7',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fvg_2ecpp_5056',['register_loader_saver_vg.cpp',['../register__loader__saver__vg_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fvg_2ehpp_5057',['register_loader_saver_vg.hpp',['../register__loader__saver__vg_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fxg_5058',['register_loader_saver_xg',['../namespacevg_1_1io.html#a7a23bf45ec66db4b724b7f8a9f223c33',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fxg_2ecpp_5059',['register_loader_saver_xg.cpp',['../register__loader__saver__xg_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fxg_2ehpp_5060',['register_loader_saver_xg.hpp',['../register__loader__saver__xg_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fzip_5fcodes_5061',['register_loader_saver_zip_codes',['../namespacevg_1_1io.html#ac0521f6b9e5e9e78ab0837548bef8f0e',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fzip_5fcodes_2ecpp_5062',['register_loader_saver_zip_codes.cpp',['../register__loader__saver__zip__codes_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fzip_5fcodes_2ehpp_5063',['register_loader_saver_zip_codes.hpp',['../register__loader__saver__zip__codes_8hpp.html',1,'']]],
+ ['register_5foption_5064',['register_option',['../classvg_1_1Configurable.html#afa7bba48c6289ea9b9095acd79a5658e',1,'vg::Configurable']]],
+ ['register_5fprotobuf_5065',['register_protobuf',['../classvg_1_1io_1_1Registry.html#ae4880fe254039bfe44b73b9050ce0abc',1,'vg::io::Registry']]],
+ ['register_5frecipe_5066',['register_recipe',['../classvg_1_1IndexRegistry.html#afdda05f4e7f1dfd93ecb33ad3b582aad',1,'vg::IndexRegistry']]],
+ ['register_5fsampled_5fposition_5067',['register_sampled_position',['../classvg_1_1NGSSimulator.html#ab9adc2b15f1d2c31301e5801e773dcbd',1,'vg::NGSSimulator']]],
+ ['register_5fsaver_5068',['register_saver',['../classvg_1_1io_1_1Registry.html#a1bba520da840207b627aface669b80c6',1,'vg::io::Registry']]],
+ ['registered_5fsuffixes_5069',['registered_suffixes',['../classvg_1_1IndexRegistry.html#ad3422d12216130fa07d77dcc3e62ae34',1,'vg::IndexRegistry']]],
+ ['registry_5070',['Registry',['../classvg_1_1io_1_1Registry.html',1,'vg::io::Registry'],['../classvg_1_1IndexingPlan.html#a7a8e639fb6e8225162a5ff532c4b963d',1,'vg::IndexingPlan::registry()']]],
+ ['registry_2ecpp_5071',['registry.cpp',['../registry_8cpp.html',1,'']]],
+ ['registry_2ehpp_5072',['registry.hpp',['../registry_8hpp.html',1,'']]],
+ ['regress_5073',['regress',['../namespacevg.html#aab16fbb8659a66f16f2004fcc3e8f9db',1,'vg']]],
+ ['regular_5faligner_5074',['regular_aligner',['../classvg_1_1AlignerClient.html#af164f37a5efb0c05b10fea3841b78e83',1,'vg::AlignerClient']]],
+ ['regular_5fsnarl_5075',['REGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a857cb70dc6bd3383a768a8696e67689c',1,'vg::ZipCode']]],
+ ['regular_5fsnarl_5fis_5freversed_5foffset_5076',['REGULAR_SNARL_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a40ebd5bef9b1916bbe944baaaff0b122',1,'vg::ZipCode']]],
+ ['regular_5fsnarl_5fsize_5077',['REGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a14c19ec53976a951ef9a16f9202ac19e',1,'vg::ZipCode']]],
+ ['regularize_5078',['regularize',['../classvg_1_1SnarlManager.html#ae5015eacc04d12d02ef5196fb23f3075',1,'vg::SnarlManager']]],
+ ['release_5079',['release',['../structjson__autoptr.html#ad3ee76d343667fd42bdbe504f32e7042',1,'json_autoptr']]],
+ ['remaining_5ftree_5080',['remaining_tree',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1f7d072e5054742f4c391b294fe5d839',1,'vg::ZipCodeTree::iterator']]],
+ ['remap_5081',['remap',['../classvg_1_1Filter.html#a66768cd6584270f71d190d525c99a9c4',1,'vg::Filter::remap(Alignment &aln)'],['../classvg_1_1Filter.html#aea9d6813e578a5957131fa6c4c8eff52',1,'vg::Filter::remap(string seq)']]],
+ ['remove_5082',['remove',['../classvg_1_1PhasedGenome.html#a3706e208421ac10d5695ed5d5ec45090',1,'vg::PhasedGenome::remove()'],['../namespacevg_1_1temp__file.html#a9885078330e16129fccc5fb6d8717ec5',1,'vg::temp_file::remove()'],['../namespacexg_1_1temp__file.html#aa4e7fb2251b2ba8f6d054d873eae4988',1,'xg::temp_file::remove()']]],
+ ['remove_5fbonuses_5083',['remove_bonuses',['../classvg_1_1GSSWAligner.html#a35fe72b24fc734d75864275c8cc1257e',1,'vg::GSSWAligner']]],
+ ['remove_5fclipped_5fportion_5084',['remove_clipped_portion',['../classvg_1_1Filter.html#ac246ae985a763a2d10edc92c81639913',1,'vg::Filter']]],
+ ['remove_5fdirectory_5085',['remove_directory',['../structvg_1_1temp__file_1_1Handler.html#acb21b507190287960d50a614ccf611bf',1,'vg::temp_file::Handler']]],
+ ['remove_5fdominated_5fchunks_5086',['remove_dominated_chunks',['../classvg_1_1Surjector.html#aafa4eb4d310ac530ed186170dc34dba9',1,'vg::Surjector']]],
+ ['remove_5fduplicate_5fedges_5087',['remove_duplicate_edges',['../namespacevg.html#add4d3a3d1917566a8df138c80b38e548',1,'vg']]],
+ ['remove_5fduplicate_5fnodes_5088',['remove_duplicate_nodes',['../namespacevg.html#a6dbe8468f2f2bcf8ceb859e6a0f8b4b1',1,'vg']]],
+ ['remove_5fduplicated_5fin_5089',['remove_duplicated_in',['../classvg_1_1VG.html#a33424c3be8c3e088631dfb37c48773d3',1,'vg::VG']]],
+ ['remove_5fduplicates_5090',['remove_duplicates',['../classvg_1_1VG.html#aba9fb73c326ecfab70e35e44dff6a937',1,'vg::VG::remove_duplicates()'],['../namespacevg.html#a5d00fa3c72ac473353496aab96965e60',1,'vg::remove_duplicates(std::vector< GaplessExtension > &result)'],['../namespacevg.html#aecd2e49750e94ed6f9de917dd9c72ac2',1,'vg::remove_duplicates(Graph &graph)']]],
+ ['remove_5fedge_5091',['remove_edge',['../classvg_1_1FlowSort.html#ad5203a8e590cc8e2bdb7038057963aaf',1,'vg::FlowSort']]],
+ ['remove_5fedit_5ftmpfiles_5092',['remove_edit_tmpfiles',['../classvg_1_1Packer.html#a2612eb978cfad2220946fab00cc3360f',1,'vg::Packer']]],
+ ['remove_5fempty_5falignment_5fsections_5093',['remove_empty_alignment_sections',['../namespacevg.html#af3fb034fcd6d50c2b84f40026b40f284',1,'vg']]],
+ ['remove_5ffailing_5fedits_5094',['remove_failing_edits',['../classvg_1_1Filter.html#aea2a2fc6de506793111639e609376bf0',1,'vg::Filter']]],
+ ['remove_5ffull_5flength_5fbonuses_5095',['remove_full_length_bonuses',['../classvg_1_1Mapper.html#a2e8194d4eb73fe32467ab37ed9468e09',1,'vg::Mapper']]],
+ ['remove_5fhigh_5fdegree_5fnodes_5096',['remove_high_degree_nodes',['../namespacevg_1_1algorithms.html#a96020f05a81255adfca3821f538c02b9',1,'vg::algorithms']]],
+ ['remove_5finverting_5fedges_5097',['remove_inverting_edges',['../classvg_1_1VG.html#a76005ed499eea217c9f778028751137c',1,'vg::VG']]],
+ ['remove_5flow_5fscoring_5fsections_5098',['remove_low_scoring_sections',['../namespacevg.html#a0ea49989e31a688e22265eb41291c0ae',1,'vg']]],
+ ['remove_5fmapping_5099',['remove_mapping',['../classvg_1_1Paths.html#ad52958174f83ec940328d8610563dc1a',1,'vg::Paths']]],
+ ['remove_5fnode_5100',['remove_node',['../classvg_1_1Paths.html#ab74cefb48d501d96b8dc81e3865770d1',1,'vg::Paths']]],
+ ['remove_5fnode_5fforwarding_5fedges_5101',['remove_node_forwarding_edges',['../classvg_1_1VG.html#ab92694e7fd89275603c967739e60e0d2',1,'vg::VG']]],
+ ['remove_5fnon_5fpath_5102',['remove_non_path',['../classvg_1_1VG.html#ad517da731d2bf9c81cc28e0a1367af33',1,'vg::VG']]],
+ ['remove_5fnon_5ftranscribed_5fnodes_5103',['remove_non_transcribed_nodes',['../classvg_1_1Transcriptome.html#aed6ea709b303bcc0055ea41217b5e1be',1,'vg::Transcriptome']]],
+ ['remove_5fnull_5fnodes_5104',['remove_null_nodes',['../classvg_1_1VG.html#a9b107027697644d771eb529037201f71',1,'vg::VG']]],
+ ['remove_5fnull_5fnodes_5fforwarding_5fedges_5105',['remove_null_nodes_forwarding_edges',['../classvg_1_1VG.html#a0e887a7b2cfc666f2210889a2dec791b',1,'vg::VG']]],
+ ['remove_5forphan_5fedges_5106',['remove_orphan_edges',['../classvg_1_1VG.html#a40dd9bc0458a4948afd676374ae8d1f0',1,'vg::VG::remove_orphan_edges()'],['../namespacevg.html#a0b38f4f0d7e63b1f7f20d2dc985f88c4',1,'vg::remove_orphan_edges()']]],
+ ['remove_5fpath_5107',['remove_path',['../classvg_1_1Paths.html#ad3893e02f5e0429a13621ae333208f9e',1,'vg::Paths::remove_path()'],['../classvg_1_1VG.html#a30c369b4c1b0dfa4e9fbc0d3bce82648',1,'vg::VG::remove_path()']]],
+ ['remove_5fpaths_5108',['remove_paths',['../classvg_1_1Paths.html#a975ff2ed8ee5718aae414cb0cb2fb39b',1,'vg::Paths::remove_paths()'],['../namespacevg.html#ad5e16e94675197650b9d6edb9e7a9081',1,'vg::remove_paths()']]],
+ ['remove_5fredundant_5ftranscript_5fpaths_5109',['remove_redundant_transcript_paths',['../classvg_1_1Transcriptome.html#aa7bf08bef8301bcff774dff1bc92d484',1,'vg::Transcriptome']]],
+ ['remove_5fsamples_5110',['remove_samples',['../gbwt__main_8cpp.html#a9750054dfc43368b363ed04acd832b15',1,'gbwt_main.cpp']]],
+ ['remove_5ftransitive_5fedges_5111',['remove_transitive_edges',['../classvg_1_1MultipathAlignmentGraph.html#aeb9c58b7f20245a4c400dd14e8488069',1,'vg::MultipathAlignmentGraph']]],
+ ['rename_5fpath_5112',['rename_path',['../classhandlegraph_1_1MutablePathHandleGraph.html#a95370bd388b2c113cf0556f266993418',1,'handlegraph::MutablePathHandleGraph']]],
+ ['rename_5fvariants_5113',['rename_variants',['../classvg_1_1HaplotypeIndexer.html#a8061130697dc26811303c4b67b081245',1,'vg::HaplotypeIndexer']]],
+ ['rend_5114',['rend',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a864f0d7f9c86b6f057e2b2889ef478a2',1,'vg::ZipCodeTree::reverse_iterator::rend()'],['../classvg_1_1ZipCodeTree.html#acb87f941c2eb8bcef3f6008c248f07c4',1,'vg::ZipCodeTree::rend()']]],
+ ['reorder_5fadjacency_5flists_5115',['reorder_adjacency_lists',['../classvg_1_1MultipathAlignmentGraph.html#adba05a33bf075eb3eb7260e229245f06',1,'vg::MultipathAlignmentGraph']]],
+ ['reorder_5fexons_5116',['reorder_exons',['../classvg_1_1Transcriptome.html#ae6f600db9b276fe332d4f14919bba983',1,'vg::Transcriptome']]],
+ ['repeat_5117',['repeat',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9af8ac0bddf37c11c94f041c84a20a636b',1,'vg::Counts']]],
+ ['repeat_5fsize_5118',['repeat_size',['../classvg_1_1ReadFilter.html#a95e0303086c9c6dc7a17d452b7d7f928',1,'vg::ReadFilter']]],
+ ['repetitiveness_5119',['repetitiveness',['../structvg_1_1SeqComplexity.html#a192996fb41444e1ccddd6b6e334cf2d3',1,'vg::SeqComplexity']]],
+ ['replace_5fin_5fstring_5120',['replace_in_string',['../namespacevg.html#ab169ac1e2fc6ba662eebc1ede1ffe157',1,'vg']]],
+ ['replace_5flocal_5fhaplotype_5121',['replace_local_haplotype',['../classvg_1_1GenomeState.html#a8048b04c0d1d0b438ec76bdc1c0b5779',1,'vg::GenomeState']]],
+ ['replace_5fmapping_5122',['replace_mapping',['../classvg_1_1Paths.html#a906246385a06c6825aaf9b3c58cbdeac',1,'vg::Paths']]],
+ ['replace_5foccurrence_5123',['replace_occurrence',['../structvg_1_1PathIndex.html#ae8806eb31bcd8b8f9305180fea7b746f',1,'vg::PathIndex']]],
+ ['replace_5fsnarl_5fhaplotype_5124',['replace_snarl_haplotype',['../classvg_1_1GenomeState.html#a83cd070b1d65189fbba77a5bda91d405',1,'vg::GenomeState']]],
+ ['replacelocalhaplotypecommand_5125',['ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html',1,'vg']]],
+ ['replacesnarlhaplotypecommand_5126',['ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html',1,'vg']]],
+ ['report_5faffinities_5127',['report_affinities',['../classvg_1_1Genotyper.html#abe8c49eaf4799ae7202e19b6e09288a7',1,'vg::Genotyper']]],
+ ['report_5fallelic_5fmapq_5128',['report_allelic_mapq',['../classvg_1_1MultipathMapper.html#a6cc2a29a0a539f37606482c57c78b015',1,'vg::MultipathMapper']]],
+ ['report_5fexception_5129',['report_exception',['../namespacevg.html#a638a54aabac7956dae6fd882468a86fe',1,'vg']]],
+ ['report_5fgroup_5fmapq_5130',['report_group_mapq',['../classvg_1_1MultipathMapper.html#a42577bd89395f56ea2045c378b745456',1,'vg::MultipathMapper']]],
+ ['report_5flibrary_5131',['report_library',['../namespacevg.html#a040485dc93c5bf925dc58fe4eaa0bd02',1,'vg']]],
+ ['report_5fsnarl_5132',['report_snarl',['../classvg_1_1Genotyper.html#a6c9c525615b0c453f0685ea2ed987cde',1,'vg::Genotyper']]],
+ ['report_5fsnarl_5ftraversal_5133',['report_snarl_traversal',['../classvg_1_1Genotyper.html#a1a141641a0939e35dc6ee19281001628',1,'vg::Genotyper']]],
+ ['report_5ftime_5fmemory_5134',['report_time_memory',['../gbwt__main_8cpp.html#aa6ba12498251a288731312b850bba212',1,'gbwt_main.cpp']]],
+ ['representative_5135',['Representative',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4aca000fa2f53ba37764dedd204e1fd27e',1,'vg::Genotyper']]],
+ ['representativetraversalfinder_5136',['RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html',1,'vg::RepresentativeTraversalFinder'],['../classvg_1_1RepresentativeTraversalFinder.html#a5dd3d9602c8056d016d42ba5cb760f11',1,'vg::RepresentativeTraversalFinder::RepresentativeTraversalFinder()']]],
+ ['require_5137',['require',['../classvg_1_1IndexRegistry.html#ac52737ce471d6fb1ea968a2e57dc4b7f',1,'vg::IndexRegistry']]],
+ ['rescore_5138',['rescore',['../classvg_1_1ReadFilter.html#a7373ef70ee64562dd779628a234c1080',1,'vg::ReadFilter']]],
+ ['rescue_5falgorithm_5139',['rescue_algorithm',['../classvg_1_1MinimizerMapper.html#a17f800e4588567e473ea18a55bd186b9',1,'vg::MinimizerMapper']]],
+ ['rescue_5fdozeu_5140',['rescue_dozeu',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a4120cab71587100aa2d1308010fec524',1,'vg::MinimizerMapper']]],
+ ['rescue_5fgraph_5fstd_5fdevs_5141',['rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#aab3573cb5d2878a13b0a40d427e8c943',1,'vg::MultipathMapper']]],
+ ['rescue_5fgssw_5142',['rescue_gssw',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4aa3089b08bc714c195447adf06eff27d9',1,'vg::MinimizerMapper']]],
+ ['rescue_5fhigh_5fcount_5forder_5flength_5fmems_5143',['rescue_high_count_order_length_mems',['../classvg_1_1BaseMapper.html#aa7a71951ec7acdbf2c31ae9318ceb035',1,'vg::BaseMapper']]],
+ ['rescue_5fnone_5144',['rescue_none',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a830c2c22efd3590551f37663c11f61e7',1,'vg::MinimizerMapper']]],
+ ['rescue_5fonly_5fanchor_5fmax_5145',['rescue_only_anchor_max',['../classvg_1_1MultipathMapper.html#acd7c1016549d1f96af13b9c317f239f3',1,'vg::MultipathMapper']]],
+ ['rescue_5fonly_5fmin_5146',['rescue_only_min',['../classvg_1_1MultipathMapper.html#a2ad423f9fc1a81bbe31e9c25992de378',1,'vg::MultipathMapper']]],
+ ['rescue_5fseed_5flimit_5147',['rescue_seed_limit',['../classvg_1_1MinimizerMapper.html#a0a0c7111b38792069bb74af9b74b0978',1,'vg::MinimizerMapper']]],
+ ['rescue_5fsubgraph_5fstdevs_5148',['rescue_subgraph_stdevs',['../classvg_1_1MinimizerMapper.html#a411fb85396b07aab41fabc8e34b92481',1,'vg::MinimizerMapper']]],
+ ['rescuealgorithm_5149',['RescueAlgorithm',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4',1,'vg::MinimizerMapper']]],
+ ['rescued_5150',['RESCUED',['../classvg_1_1MultipathMapper.html#ab559f7eb874ac770dbbda734c5bc395a',1,'vg::MultipathMapper']]],
+ ['resect_5fsnarls_5ffrom_5fpaths_5151',['resect_snarls_from_paths',['../classvg_1_1MultipathAlignmentGraph.html#a9c49582fe16bcb4c87b95e8e3ee93319',1,'vg::MultipathAlignmentGraph']]],
+ ['reserved_5152',['reserved',['../structvg_1_1Alignment.html#a8374111b6348509e8e9ecca0cd1ac046',1,'vg::Alignment']]],
+ ['reset_5153',['reset',['../classvg_1_1IndexRegistry.html#abcba0a09cee5a43096a09d05556353c1',1,'vg::IndexRegistry::reset()'],['../classvg_1_1IndexFile.html#aa16d18589ef1a9944b8e2af8c8ea1232',1,'vg::IndexFile::reset()'],['../structvg_1_1Counts.html#a90e02c9fc99656e6325f5c8fbfccda86',1,'vg::Counts::reset()'],['../classvg_1_1uniform__real__distribution.html#ad9ba8ac53f8a0af213db9d4f8da12617',1,'vg::uniform_real_distribution::reset()'],['../classvg_1_1normal__distribution.html#a7bae578d38533043f42f09413c7c1e32',1,'vg::normal_distribution::reset()'],['../classvg_1_1truncated__normal__distribution.html#ae1ebb560eee14b873305a4b5bf97616e',1,'vg::truncated_normal_distribution::reset()'],['../classvg_1_1uniform__int__distribution.html#a38594c45008dfc36cfbb4f9b9e4193dd',1,'vg::uniform_int_distribution::reset()'],['../classvg_1_1discrete__distribution.html#a5a3ca0751a139bef583b819118188780',1,'vg::discrete_distribution::reset()'],['../structvg_1_1Range.html#a3bf0b390a74ca7ea5f806f6cd98aac2c',1,'vg::Range::reset()']]],
+ ['reset_5falong_5fchain_5154',['reset_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#ade116b41b24892b20ac4fa95a9b5539e',1,'vg::subcommand::TickChainLink::reset_along_chain()'],['../structvg_1_1Range.html#a475da5fc747b64bfa869524e932077df',1,'vg::Range::reset_along_chain()']]],
+ ['reset_5falong_5fchain_5fparent_5155',['reset_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#a8934c072a3cdbc8652e8f7fa9f9ef553',1,'vg::subcommand::TickChainLink']]],
+ ['reset_5fchain_5156',['reset_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a5a3dd8ac3d8a86fec1d2062e6d864c73',1,'vg::subcommand::TickChainLink::reset_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a05855ac56b836299fc0fc12292555b37',1,'vg::subcommand::OptionGroup::reset_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a73c92bfa80186ac2d64f9b24233aacb8',1,'vg::subcommand::GroupedOptionGroup::reset_chain()']]],
+ ['resize_5findexes_5157',['resize_indexes',['../classvg_1_1VG.html#af8879b1e6aab38b9a246deba0f05ccfe',1,'vg::VG']]],
+ ['restore_5fpaths_5158',['restore_paths',['../classvg_1_1PhaseUnfolder.html#a3cdfb31928c3a4127d9888d543872e1c',1,'vg::PhaseUnfolder']]],
+ ['restrained_5fgraph_5fextraction_5159',['restrained_graph_extraction',['../classvg_1_1MultipathMapper.html#a0ad5a21ab0cf3c77e3905e299b7d26c4',1,'vg::MultipathMapper']]],
+ ['result_5ftype_5160',['result_type',['../classvg_1_1uniform__real__distribution.html#a45f57ac9dad3e93958eda6a596748faa',1,'vg::uniform_real_distribution::result_type()'],['../classvg_1_1normal__distribution.html#a3cf267467b3608710fc42fc70f5df9ab',1,'vg::normal_distribution::result_type()'],['../classvg_1_1truncated__normal__distribution.html#a4a25c23c8e6024d988a0ac8617415897',1,'vg::truncated_normal_distribution::result_type()'],['../classvg_1_1WideningPRNG.html#a167ab33bf96b19131d4d85738c37e5ce',1,'vg::WideningPRNG::result_type()'],['../classvg_1_1uniform__int__distribution.html#a06f14fe90ff4a3b995f9e2100b11487d',1,'vg::uniform_int_distribution::result_type()'],['../classvg_1_1discrete__distribution.html#a06c8d8862509e0b67c9ed940b7a6c204',1,'vg::discrete_distribution::result_type()']]],
+ ['retry_5fon_5fns_5161',['retry_on_Ns',['../classvg_1_1NGSSimulator.html#a95f6ffd660c8c041e4d8b1d36a823bdd',1,'vg::NGSSimulator']]],
+ ['retry_5fpairing_5fspliced_5falignments_5162',['retry_pairing_spliced_alignments',['../classvg_1_1MultipathMapper.html#ae388023023d7b1a862a77416d9ed1ede',1,'vg::MultipathMapper']]],
+ ['return_5ftype_5fof_5163',['return_type_of',['../structhandlegraph_1_1return__type__of.html',1,'handlegraph']]],
+ ['return_5ftype_5fof_3c_20returns_28_2a_29_28args_2e_2e_2e_29_3e_5164',['return_type_of< Returns(*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
+ ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_20const_20_3e_5165',['return_type_of< Returns(Owner::*)(Args...) const >',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html',1,'handlegraph']]],
+ ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_3e_5166',['return_type_of< Returns(Owner::*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
+ ['rev_5fcomp_5fmultipath_5falignment_5167',['rev_comp_multipath_alignment',['../namespacevg.html#a785f128b2eeb9aa2a4ee5477e5b9942b',1,'vg']]],
+ ['rev_5fcomp_5fmultipath_5falignment_5fin_5fplace_5168',['rev_comp_multipath_alignment_in_place',['../namespacevg.html#ab9aa92b68bb45684a3b751060508c709',1,'vg']]],
+ ['rev_5fcomp_5fsubpath_5169',['rev_comp_subpath',['../namespacevg.html#a4d802144c81c58c86f814507e1f99e22',1,'vg']]],
+ ['revdna3bit_5170',['revdna3bit',['../namespacexg.html#a09a061b73b78b2ba029940f09ccb6f5b',1,'xg']]],
+ ['reverse_5171',['reverse',['../structvg_1_1Support.html#acc2aa2a4b0278503817664600938c8a2',1,'vg::Support::reverse()'],['../classvg_1_1NodeTraversal.html#a748acf3ae485ab57fe649e70cad17c5d',1,'vg::NodeTraversal::reverse()'],['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda3720d917b5b410fbff17c73d58c1eaf2',1,'vg::MultipathMapper::Reverse()'],['../namespacevg.html#a91adfc6327b5709dc73fcc7edbe5da57',1,'vg::reverse(const Position &pos, size_t node_length)'],['../namespacevg.html#a2e300d25fd8281f9453366f68b484196',1,'vg::reverse(const Visit &visit)'],['../namespacevg.html#ac52fd5878b0be1d53de644eea3458663',1,'vg::reverse(const pos_t &pos, size_t node_length)'],['../namespacexg.html#ad11c9145dd19a26ea95db548d7aaac79',1,'xg::reverse()']]],
+ ['reverse_5fadjacencies_5172',['reverse_adjacencies',['../classvg_1_1Surjector.html#a98ca84936638bdcb054e3304b6f959f1',1,'vg::Surjector']]],
+ ['reverse_5falignment_5173',['reverse_alignment',['../classvg_1_1MultipathAlignmentGraph.html#a91aa5268618d2f4c1d7b8665108d455c',1,'vg::MultipathAlignmentGraph']]],
+ ['reverse_5fbase_5fpos_5174',['reverse_base_pos',['../namespacevg.html#ae2f3762e2a8a852c7608d71f030e0345',1,'vg::reverse_base_pos()'],['../namespacexg.html#af6d74fb0781bfeb012e78af79758ab9c',1,'xg::reverse_base_pos()']]],
+ ['reverse_5fcomplement_5175',['reverse_complement',['../namespacevg.html#aa65de7dea52585f07bee6ae7f762eb95',1,'vg::reverse_complement(const char &c)'],['../namespacevg.html#a30732a1a1e8d20d6eaaaeafecc8a50a7',1,'vg::reverse_complement(const string &seq)'],['../namespacexg.html#ac667d522781e3c31d191e4c6db520eaa',1,'xg::reverse_complement(const char &c)'],['../namespacexg.html#ab4f0205fd0abe6aaa4077cd20abcd36f',1,'xg::reverse_complement(const std::string &seq)']]],
+ ['reverse_5fcomplement_2ecpp_5176',['reverse_complement.cpp',['../reverse__complement_8cpp.html',1,'']]],
+ ['reverse_5fcomplement_5falignment_5177',['reverse_complement_alignment',['../namespacevg.html#a98e512ed0fca2503ccc370435591a6c1',1,'vg']]],
+ ['reverse_5fcomplement_5falignment_5fin_5fplace_5178',['reverse_complement_alignment_in_place',['../namespacevg.html#ab96610ffc81d6207e0b13f675296c234',1,'vg']]],
+ ['reverse_5fcomplement_5falignments_5179',['reverse_complement_alignments',['../namespacevg.html#aed045b02277d7704e997cbede67c2662',1,'vg']]],
+ ['reverse_5fcomplement_5fedit_5180',['reverse_complement_edit',['../namespacevg_1_1io.html#a52a77b52c33c165637fb00be3e9f54e0',1,'vg::io']]],
+ ['reverse_5fcomplement_5fgraph_5181',['reverse_complement_graph',['../classvg_1_1VG.html#a82185028afbc17aaf60b294297507fd2',1,'vg::VG::reverse_complement_graph()'],['../namespacehandlegraph_1_1algorithms.html#a3cb6868def99085050dca0efdd3eb0c9',1,'handlegraph::algorithms::reverse_complement_graph()']]],
+ ['reverse_5fcomplement_5fin_5fplace_5182',['reverse_complement_in_place',['../namespacevg.html#ae6353d47c867f1b4cc7053d82aef42f4',1,'vg::reverse_complement_in_place()'],['../namespacexg.html#a18e172174952ffa498b10715acdc031c',1,'xg::reverse_complement_in_place()']]],
+ ['reverse_5fcomplement_5fmapping_5183',['reverse_complement_mapping',['../namespacevg.html#a3ce6fa1d8f3ba4f8f361fa77a6fd5261',1,'vg::reverse_complement_mapping(const Mapping &m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a798565f048dc7844739ea4913d950d31',1,'vg::reverse_complement_mapping(const path_mapping_t &m, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fcomplement_5fmapping_5fin_5fplace_5184',['reverse_complement_mapping_in_place',['../namespacevg.html#af2dc9d6ee4403027eb5965aa6a71eb4e',1,'vg::reverse_complement_mapping_in_place(Mapping *m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#abc9bd04ab1099c6d9bd655a2accbe52e',1,'vg::reverse_complement_mapping_in_place(path_mapping_t *m, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fcomplement_5fpath_5185',['reverse_complement_path',['../namespacevg.html#a463d9eaed29cd6d46a8e2afb645c8fda',1,'vg::reverse_complement_path(const Path &path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a3df9f25ec47163ccbfa328673bd28ab5',1,'vg::reverse_complement_path(const path_t &path, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fcomplement_5fpath_5fin_5fplace_5186',['reverse_complement_path_in_place',['../namespacevg.html#af2941a3c80481d02c65d9d72bd835807',1,'vg::reverse_complement_path_in_place(Path *path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a0df8f9c5838119e79ee1f671cd823740',1,'vg::reverse_complement_path_in_place(path_t *path, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fedge_5187',['reverse_edge',['../classvg_1_1FlowSort.html#a237e09746b80c67a96290eac62fbd2c8',1,'vg::FlowSort']]],
+ ['reverse_5ffrom_5fstart_5fto_5fend_5fedge_5188',['reverse_from_start_to_end_edge',['../classvg_1_1FlowSort.html#a095e96bd8ef6f016a600bdbc6af730ee',1,'vg::FlowSort']]],
+ ['reverse_5fgraph_2ecpp_5189',['reverse_graph.cpp',['../reverse__graph_8cpp.html',1,'']]],
+ ['reverse_5fgraph_2ehpp_5190',['reverse_graph.hpp',['../reverse__graph_8hpp.html',1,'']]],
+ ['reverse_5fiterator_5191',['reverse_iterator',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html',1,'vg::ZipCodeTree::reverse_iterator'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a58d6dc8114a797ef5fa8b3ef95d3e282',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(vector< tree_item_t >::const_reverse_iterator rbegin, vector< tree_item_t >::const_reverse_iterator rend, size_t distance_limit=std::numeric_limits< size_t >::max())'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa454b7553be8ff9226e7622476de7515',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ac2889d055d75873e7d1d834c758c17ea',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(reverse_iterator &&other)']]],
+ ['reversegraph_5192',['ReverseGraph',['../classvg_1_1ReverseGraph.html',1,'vg::ReverseGraph'],['../classvg_1_1ReverseGraph.html#a9122b516caa1f30b202ef7ef4cd83d60',1,'vg::ReverseGraph::ReverseGraph(const HandleGraph *forward_graph, bool complement)'],['../classvg_1_1ReverseGraph.html#a4715727accf496a2b7f908688638d873',1,'vg::ReverseGraph::ReverseGraph()=default']]],
+ ['reversing_5ffilter_5193',['reversing_filter',['../classvg_1_1Filter.html#a5ac9ddf9392d973aa726ad6ee4d53b9f',1,'vg::Filter']]],
+ ['reversing_5fwalk_5flength_5194',['reversing_walk_length',['../classvg_1_1MultipathMapper.html#af87eaae1274e33230fffe9dca05dbbec',1,'vg::MultipathMapper']]],
+ ['rewindplanexception_5195',['RewindPlanException',['../classvg_1_1RewindPlanException.html',1,'vg::RewindPlanException'],['../classvg_1_1RewindPlanException.html#ad1b916e8d35f9825b9352045b7e77146',1,'vg::RewindPlanException::RewindPlanException()=delete'],['../classvg_1_1RewindPlanException.html#a28ad0274056215792783b0b3bc8fd258',1,'vg::RewindPlanException::RewindPlanException(const string &msg, const IndexGroup &rewind_to) noexcept']]],
+ ['rewrite_5fsegment_5196',['rewrite_segment',['../classvg_1_1VG.html#abb2dc75f200cfb7480e671fd55207410',1,'vg::VG::rewrite_segment()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#af28f1372aa6dad2654a22eb8463e2a07',1,'handlegraph::MutablePathHandleGraph::rewrite_segment()']]],
+ ['rgfa_5flisteners_5197',['rgfa_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a3caa995d2ef8a311e87b1202da714b53',1,'vg::algorithms::GFAParser']]],
+ ['rho_5198',['rho',['../structhaplo_1_1haploMath_1_1RRMemo.html#a7536987972e5d717ba43a951adcece82',1,'haplo::haploMath::RRMemo']]],
+ ['right_5199',['right',['../structvg_1_1Support.html#ab2fd7cba17f56ce67501f47fda6ae153',1,'vg::Support']]],
+ ['right_5fdegree_5200',['right_degree',['../classvg_1_1VG.html#a23622195177dff4c7c8416edffb7fc93',1,'vg::VG']]],
+ ['right_5fends_5201',['right_ends',['../structvg_1_1ConstructedChunk.html#ac20dbdc398181350e73bee0429fe2842',1,'vg::ConstructedChunk']]],
+ ['right_5ffull_5202',['right_full',['../structvg_1_1GaplessExtension.html#ae7ca191732330cb5a6db94ee5531f2ed',1,'vg::GaplessExtension']]],
+ ['right_5fhandle_5ftrans_5203',['right_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#aceac5a4b442fbce2c7c422acbdbdd097',1,'vg::JoinedSpliceGraph']]],
+ ['right_5fmaximal_5204',['right_maximal',['../structvg_1_1GaplessExtension.html#a8e4d53c78f3c355b5b17bf3e959bbd41',1,'vg::GaplessExtension']]],
+ ['right_5fseed_5fnode_5205',['right_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a83d9a8edb6fb9fd1ac20ffa976355155',1,'vg::JoinedSpliceGraph']]],
+ ['right_5fsplice_5fnode_5206',['right_splice_node',['../classvg_1_1JoinedSpliceGraph.html#adf8ca2fd45b0d024bf4b12ea04fbfc79',1,'vg::JoinedSpliceGraph']]],
+ ['right_5fsplice_5foffset_5207',['right_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a152eb3987232cdba5fff9dd9a15ed952',1,'vg::JoinedSpliceGraph']]],
+ ['right_5fsubgraph_5208',['right_subgraph',['../classvg_1_1JoinedSpliceGraph.html#a42ce6f52135018237e3e29d2a53c4291',1,'vg::JoinedSpliceGraph']]],
+ ['right_5ftelomere_5fnode_5209',['right_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a3d771a24b8889ea668939eac31276ea3',1,'vg::PhasedGenome::Haplotype']]],
+ ['ring_5fbuffer_5fempty_5210',['ring_buffer_empty',['../classvg_1_1io_1_1StreamMultiplexer.html#a92c3f4f2de80a840aef85574935758ac',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5ffull_5211',['ring_buffer_full',['../classvg_1_1io_1_1StreamMultiplexer.html#a0d671fb79357a83af6c5becfa890a6f2',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5fpeek_5212',['ring_buffer_peek',['../classvg_1_1io_1_1StreamMultiplexer.html#aa03a8b8e99c728355ade20923bcb4c2f',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5fpop_5213',['ring_buffer_pop',['../classvg_1_1io_1_1StreamMultiplexer.html#ac4f6095e2eb79970075f9b2279e990ce',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5fpush_5214',['ring_buffer_push',['../classvg_1_1io_1_1StreamMultiplexer.html#a925607e24a8c6e905fc45c4b77bbe62c',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5fsize_5215',['RING_BUFFER_SIZE',['../classvg_1_1io_1_1StreamMultiplexer.html#a6e4432baab9571a1783b2a793b29905a',1,'vg::io::StreamMultiplexer']]],
+ ['rna_5fmain_2ecpp_5216',['rna_main.cpp',['../rna__main_8cpp.html',1,'']]],
+ ['rng_5217',['rng',['../classvg_1_1Colors.html#a79a79da7cbc2bef7eea8c3ff1e229b7c',1,'vg::Colors::rng()'],['../classvg_1_1Pictographs.html#ac7600f845d01a084a15cff9aacc6bc3e',1,'vg::Pictographs::rng()'],['../classvg_1_1Sampler.html#ad26ea071330c6a4b580af84bec064453',1,'vg::Sampler::rng()'],['../classvg_1_1LazyRNG.html#a6aac64a985fa2fc60c2d32079bd26a63',1,'vg::LazyRNG::rng()']]],
+ ['robust_5festimation_5ffraction_5218',['robust_estimation_fraction',['../classvg_1_1FragmentLengthDistribution.html#aa5a2f20742b369464d132a751f52aaf3',1,'vg::FragmentLengthDistribution']]],
+ ['root_5219',['root',['../classvg_1_1BitStringTree.html#a69741fde7d47ad2f46dd952eb6bd2d66',1,'vg::BitStringTree::root()'],['../structvg_1_1Tree.html#a730cd8796e579d01c66bea46217047d7',1,'vg::Tree::root()']]],
+ ['root_5fchain_5220',['ROOT_CHAIN',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3350f37a328be806a1a8bb7534d7fb8c',1,'vg::ZipCode']]],
+ ['root_5fchain_5fcomponent_5fcount_5foffset_5221',['ROOT_CHAIN_COMPONENT_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a79816fb11ec20354e677a6b1acd17905',1,'vg::ZipCode']]],
+ ['root_5fchain_5fsize_5222',['ROOT_CHAIN_SIZE',['../classvg_1_1ZipCode.html#af83f8e5c14d24fd45ad2318e229299d0',1,'vg::ZipCode']]],
+ ['root_5fchains_5223',['root_chains',['../classvg_1_1SnarlManager.html#a2d9758d889f875b1260f49985cf3ef35',1,'vg::SnarlManager']]],
+ ['root_5fchildren_5224',['root_children',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a8b902ff993db7c62075ce3371622e781',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['root_5fidentifier_5foffset_5225',['ROOT_IDENTIFIER_OFFSET',['../classvg_1_1ZipCode.html#a9320699634e827ab9c91ade7b39220a9',1,'vg::ZipCode']]],
+ ['root_5fis_5fchain_5foffset_5226',['ROOT_IS_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a9fcb55636a3bd5e25d6592952880662b',1,'vg::ZipCode']]],
+ ['root_5fnode_5227',['ROOT_NODE',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3c192049eca2f2b4aafe984ff4a965d3',1,'vg::ZipCode']]],
+ ['root_5fnode_5flength_5foffset_5228',['ROOT_NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a97232d726929bf2ebb8fb7fdfbde94fd',1,'vg::ZipCode']]],
+ ['root_5fnode_5for_5fchain_5fconnectivity_5for_5flength_5foffset_5229',['ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#afa760e19cc391b5de5adba6b4ca3cdb0',1,'vg::ZipCode']]],
+ ['root_5fnode_5fsize_5230',['ROOT_NODE_SIZE',['../classvg_1_1ZipCode.html#afa378af1f64a51675d658d2c4ecb5d95',1,'vg::ZipCode']]],
+ ['root_5fsnarl_5231',['ROOT_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a438bae58eb821bbbc90b1b4bc486d682',1,'vg::ZipCode']]],
+ ['root_5fsnarl_5fsize_5232',['ROOT_SNARL_SIZE',['../classvg_1_1ZipCode.html#aa2cdcd63b1ac93b431e0e4d5d25df346',1,'vg::ZipCode']]],
+ ['root_5ftrim_5233',['root_trim',['../classvg_1_1TreeSubgraph.html#a04044896f4bed03dc15a6c0a07df675d',1,'vg::TreeSubgraph']]],
+ ['roots_5234',['roots',['../classvg_1_1SnarlManager.html#ab13a661f6abe1feaf2c4ca4471a85a90',1,'vg::SnarlManager']]],
+ ['round_5foutward_5235',['round_outward',['../structvg_1_1PathIndex.html#ac02dd3e22c5b29670ef48b6f725a9797',1,'vg::PathIndex']]],
+ ['row_5fidx_5236',['row_idx',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2345d3706d3d46b657e205865f4d4122',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['rr_5fmemos_5237',['rr_memos',['../classvg_1_1MultipathMapper.html#a5709f5cdf31de90145a1178fa166be44',1,'vg::MultipathMapper']]],
+ ['rrmemo_5238',['RRMemo',['../structhaplo_1_1haploMath_1_1RRMemo.html',1,'haplo::haploMath::RRMemo'],['../structhaplo_1_1haploMath_1_1RRMemo.html#a3958ec23ff1fbaac901d909c5f134f27',1,'haplo::haploMath::RRMemo::RRMemo()']]],
+ ['run_5239',['run',['../classvg_1_1Genotyper.html#af760be5c99e086b2c41510b3d3a47e5a',1,'vg::Genotyper']]],
+ ['run_5fbenchmark_5240',['run_benchmark',['../namespacevg.html#ac101c453ab2076d74f0324f73d174695',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &under_test)'],['../namespacevg.html#added44ff3bb1c0ce606563a40923c513',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &setup, const function< void(void)> &under_test)']]],
+ ['run_5fdp_5241',['run_dp',['../classvg_1_1DeletionAligner.html#a0eb6b38dc11173f5da75c5cafd3053fe',1,'vg::DeletionAligner']]],
+ ['run_5fgenotype_5242',['run_genotype',['../classvg_1_1MCMCGenotyper.html#a3bae6f8b2947e030935d5e9cf46fb324',1,'vg::MCMCGenotyper']]],
+ ['run_5fmultipath_5fdp_5243',['run_multipath_dp',['../namespacevg.html#ae57a78071537c87e2f0f57bfea18ba71',1,'vg']]],
+ ['running_5244',['running',['../structvg_1_1Range.html#abbd18ac55fecb0e698fcabebc7ae48ad',1,'vg::Range']]],
+ ['runs_5245',['runs',['../structvg_1_1BenchmarkResult.html#a564ed18fb2f561f09e74a254854e2d88',1,'vg::BenchmarkResult']]]
];
diff --git a/search/all_13.js b/search/all_13.js
index 144d9039f5..a975ee157c 100644
--- a/search/all_13.js
+++ b/search/all_13.js
@@ -1,705 +1,705 @@
var searchData=
[
- ['s_5fbv_5244',['s_bv',['../classxg_1_1XG.html#ac8f0eaf8d0d58d489a6da321d8303c46',1,'xg::XG']]],
- ['s_5fbv_5frank_5245',['s_bv_rank',['../classxg_1_1XG.html#a14eb778ecdf51cca8ced32eb42112200',1,'xg::XG']]],
- ['s_5fbv_5fselect_5246',['s_bv_select',['../classxg_1_1XG.html#a45b6e0fcf1dd90f451df245f0ffc3e1c',1,'xg::XG']]],
- ['s_5fiv_5247',['s_iv',['../classxg_1_1XG.html#aa8e40fcbfa8174b689067d87acd818be',1,'xg::XG']]],
- ['s_5fscan_5fchain_5248',['S_SCAN_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a5a2a20c895df5cb7d5b27e3335827d84',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fscan_5fsnarl_5249',['S_SCAN_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a3eb7a4cb13ea66f6f4e7e44d06aa41bc',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fskip_5fchain_5250',['S_SKIP_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a98d325e41f9d476ccc2b82e79c873341',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fstack_5fsnarl_5251',['S_STACK_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a45d7d8cf2973c828ad7bd10774a879e4',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fstart_5252',['S_START',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a159863dec1d44845928b1b3df0d24a2a',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['sa_5fto_5fda_5253',['sa_to_da',['../namespacevg.html#aaac16668663556af1aea74159a73d4ed',1,'vg']]],
- ['safe_5fto_5fget_5254',['safe_to_get',['../classvg_1_1VcfBuffer.html#ac280837b05f233e4420c6e8a7bbef32b',1,'vg::VcfBuffer']]],
- ['sam_5255',['SAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baa4f1866efe56ebd234e7d5135ecca03e',1,'vg::MultipathAlignmentEmitter']]],
- ['sam_5ffiles_5256',['sam_files',['../classvg_1_1HTSWriter.html#a57a7f16757fc6ce944636d69c48903cb',1,'vg::HTSWriter']]],
- ['sam_5fflag_5257',['sam_flag',['../namespacevg.html#ae37c6d66a01cef6f92707d367ebf4cdb',1,'vg']]],
- ['sam_5fheader_5258',['sam_header',['../classvg_1_1HTSWriter.html#a95cd5874834de9191faf18d39fef9534',1,'vg::HTSWriter']]],
- ['same_5fcontext_5259',['same_context',['../classvg_1_1VG.html#a96f99984ada5a3a13332ddb2ab0a1c97',1,'vg::VG']]],
- ['sample_5fcounter_5260',['sample_counter',['../classvg_1_1NGSSimulator.html#ab162ca660d69f66c18c41516a1a69d24',1,'vg::NGSSimulator']]],
- ['sample_5fgam_5fdepth_5261',['sample_gam_depth',['../namespacevg_1_1algorithms.html#a80703607cfe21f1f593f7b2f03c08b40',1,'vg::algorithms']]],
- ['sample_5fhaplotypes_5262',['sample_haplotypes',['../giraffe__main_8cpp.html#a6343c45d56779ead6309ffefbf066fdc',1,'sample_haplotypes(const vector< pair< string, string >> &indexes, string &basename, string &sample_name, string &haplotype_file, string &kff_file, bool progress): giraffe_main.cpp'],['../haplotypes__main_8cpp.html#a13d462ac627c7beb00b431280ac9b0c6',1,'sample_haplotypes(const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, const HaplotypesConfig &config): haplotypes_main.cpp']]],
- ['sample_5finterval_5263',['sample_interval',['../structvg_1_1RebuildParameters.html#aa4adeffb1f91f55c6f1709e6d1c9cfcb',1,'vg::RebuildParameters']]],
- ['sample_5fmapping_5fdepth_5264',['sample_mapping_depth',['../namespacevg_1_1algorithms.html#a16bd0de261a829b2d81ec48eed9d6482',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const string &input_filename, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq, const string &format)'],['../namespacevg_1_1algorithms.html#a244822514c71473756cfd5ad87f79e08',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const vector< Alignment > &alignments, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq)']]],
- ['sample_5fminimal_5265',['sample_minimal',['../namespacevg_1_1algorithms.html#a175ee345e226732cb1c37da13a2f045e',1,'vg::algorithms']]],
- ['sample_5fminimal_2ecpp_5266',['sample_minimal.cpp',['../sample__minimal_8cpp.html',1,'']]],
- ['sample_5fminimal_2ehpp_5267',['sample_minimal.hpp',['../sample__minimal_8hpp.html',1,'']]],
- ['sample_5fname_5268',['sample_name',['../classvg_1_1VCFOutputCaller.html#a70e8288543e7facfb79f5211ce33fa7f',1,'vg::VCFOutputCaller::sample_name()'],['../classvg_1_1MCMCCaller.html#a59582bcf7ba0dc3ae52f3f9a7c8eb80c',1,'vg::MCMCCaller::sample_name()'],['../classvg_1_1MinimizerMapper.html#a2f47382b14baf0482c43034e6484d086',1,'vg::MinimizerMapper::sample_name()'],['../classvg_1_1MultipathAlignmentEmitter.html#a6fa324b9dee313b1fceab7bafa62db24',1,'vg::MultipathAlignmentEmitter::sample_name()'],['../structvg_1_1Alignment.html#ad823d9ed3f413faaf35700a41cfab6e7',1,'vg::Alignment::sample_name()'],['../structvg_1_1MultipathAlignment.html#a90d675553385456c66b572a88fa88650',1,'vg::MultipathAlignment::sample_name()']]],
- ['sample_5fnames_5269',['sample_names',['../classvg_1_1Deconstructor.html#a56f3119a427b1076d0d0d5ca7f478832',1,'vg::Deconstructor']]],
- ['sample_5fpath_5270',['sample_path',['../classvg_1_1NGSSimulator.html#a57ee602010b5295685556acc30e0355a',1,'vg::NGSSimulator']]],
- ['sample_5fploidys_5271',['sample_ploidys',['../classvg_1_1Deconstructor.html#a337113fedde38a57458c9329ffd86aac',1,'vg::Deconstructor']]],
- ['sample_5frange_5272',['sample_range',['../classvg_1_1HaplotypeIndexer.html#a53cb273305c8fb1c039581c1a1b3d76e',1,'vg::HaplotypeIndexer']]],
- ['sample_5fread_5273',['sample_read',['../classvg_1_1ReadFilter.html#aa592c88e758fc257fdf17418b0f189a8',1,'vg::ReadFilter::sample_read()'],['../classvg_1_1Sampler.html#ab48bd0062b357dfe0cf418beb1e18ad4',1,'vg::Sampler::sample_read()'],['../classvg_1_1NGSSimulator.html#a50a20af9dd3edd86233edf1de13a5cda',1,'vg::NGSSimulator::sample_read()']]],
- ['sample_5fread_5finternal_5274',['sample_read_internal',['../classvg_1_1NGSSimulator.html#a957be55e0adcf59449587ccb1f8db9de',1,'vg::NGSSimulator']]],
- ['sample_5fread_5fpair_5275',['sample_read_pair',['../classvg_1_1Sampler.html#a598b41433f5bb9a040749e7a2327b78d',1,'vg::Sampler::sample_read_pair()'],['../classvg_1_1NGSSimulator.html#a5b12189ad9dcf0a4656a321fcf5ff840',1,'vg::NGSSimulator::sample_read_pair()']]],
- ['sample_5fread_5fquality_5276',['sample_read_quality',['../classvg_1_1NGSSimulator.html#a49ad65d878edb1d76518f589aa0bf02c',1,'vg::NGSSimulator']]],
- ['sample_5fread_5fquality_5finternal_5277',['sample_read_quality_internal',['../classvg_1_1NGSSimulator.html#a03fb08f4267424aca8d8892a403b134a',1,'vg::NGSSimulator']]],
- ['sample_5fread_5fquality_5fpair_5278',['sample_read_quality_pair',['../classvg_1_1NGSSimulator.html#a71f6e4ba9442273d4cf1588f24578f55',1,'vg::NGSSimulator']]],
- ['sample_5fstart_5fgraph_5fpos_5279',['sample_start_graph_pos',['../classvg_1_1NGSSimulator.html#ada5f04218c531191b20a8c28cc57d94e',1,'vg::NGSSimulator']]],
- ['sample_5fstart_5fpath_5fpos_5280',['sample_start_path_pos',['../classvg_1_1NGSSimulator.html#ad2f821c685108e8ee6912713f0ced8d3',1,'vg::NGSSimulator']]],
- ['sample_5fstart_5fpos_5281',['sample_start_pos',['../classvg_1_1NGSSimulator.html#a889b49669939bfb7832bad23f02cd02c',1,'vg::NGSSimulator']]],
- ['sample_5fto_5fhaplotypes_5282',['sample_to_haplotypes',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a5e006ad54f202447a37975fa4919481c',1,'vg::Deconstructor::NestingInfo']]],
- ['sample_5fto_5fploidy_5283',['sample_to_ploidy',['../structvg_1_1ParentGenotypeInfo.html#a5ac680b0203fe3cccab8959c84f5d556',1,'vg::ParentGenotypeInfo']]],
- ['sample_5ftransition_5284',['sample_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a4434cebe872c32c384c1f916111fc2e1',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['sample_5funsheared_5fpaths_5285',['sample_unsheared_paths',['../classvg_1_1NGSSimulator.html#af7441bd12030f0e189aca5ba2e0b47ef',1,'vg::NGSSimulator']]],
- ['sampler_5286',['Sampler',['../classvg_1_1Sampler.html',1,'vg::Sampler'],['../classvg_1_1Sampler.html#ab1d1e96bcf702979dfc86a92dcd8d24b',1,'vg::Sampler::Sampler()']]],
- ['sampler_2ecpp_5287',['sampler.cpp',['../sampler_8cpp.html',1,'']]],
- ['sampler_2ehpp_5288',['sampler.hpp',['../sampler_8hpp.html',1,'']]],
- ['samplers_5289',['samplers',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a8d2808d7b690045d11af93fd6619fbf7',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['samples_5290',['samples',['../structGBWTConfig.html#ae5a3dac168e1ea3d38ddd13f5097fa40',1,'GBWTConfig']]],
- ['samples_5fin_5fbatch_5291',['samples_in_batch',['../classvg_1_1HaplotypeIndexer.html#a681bcf3fb6014ae885adb3dec25ff2fc',1,'vg::HaplotypeIndexer']]],
- ['sanitize_5fsequence_5fin_5fplace_5292',['sanitize_sequence_in_place',['../classvg_1_1Constructor.html#a1d90ed36989b851bb3c072f4d67b52dd',1,'vg::Constructor']]],
- ['save_5293',['save',['../classvg_1_1StreamIndexBase.html#a99761d4d917dc5ba1db1e08a36ceb312',1,'vg::StreamIndexBase::save()'],['../classvg_1_1io_1_1VPKG.html#a80551b46351f1e8d47e8b3ebaf028847',1,'vg::io::VPKG::save(const Have &have, ostream &out)'],['../classvg_1_1io_1_1VPKG.html#a0472c51ab91f4b8663a56a150e0e0f12',1,'vg::io::VPKG::save(const Have &have, const string &filename)']]],
- ['save_5fbed_5294',['save_bed',['../classvg_1_1FeatureSet.html#a2914a7c47c085b00a454df2bfc5eda67',1,'vg::FeatureSet']]],
- ['save_5fexplanations_5295',['save_explanations',['../classvg_1_1Explainer.html#a3510aece27ab20079a8a3e87fa702596',1,'vg::Explainer']]],
- ['save_5ffrag_5flens_5fto_5falns_5296',['save_frag_lens_to_alns',['../classvg_1_1FragmentLengthStatistics.html#ab9376051edd07e128f52f57ac2b5a410',1,'vg::FragmentLengthStatistics']]],
- ['save_5ffunction_5ft_5297',['save_function_t',['../namespacevg_1_1io.html#a161bd20a13c1fd9993bcddd7ea3cbe57',1,'vg::io']]],
- ['save_5fgbwt_5298',['save_gbwt',['../namespacevg.html#a790122d8b3f28068aaf09f1eb5b966a9',1,'vg::save_gbwt(const gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a8385d575383b7bae35726e90851a2795',1,'vg::save_gbwt(const gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
- ['save_5fgbwtgraph_5299',['save_gbwtgraph',['../namespacevg.html#aea7640260b1c70795335439f3d6c2eac',1,'vg']]],
- ['save_5fgbz_5300',['save_gbz',['../namespacevg.html#a017e7cda40a98b4b044507ab78a34da9',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a6beaace0e6d90b654dc9c382afb39ce0',1,'vg::save_gbz(const gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#af7669e457f62e6f197f3120086a091e2',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
- ['save_5fgcsa_5301',['save_gcsa',['../namespacevg.html#aa2840fc8dbdb12c000769a3baa39b808',1,'vg']]],
- ['save_5fhandle_5fgraph_5302',['save_handle_graph',['../namespacevg_1_1io.html#af3f5510bd6a0e5514d3083fcd2ffdd32',1,'vg::io::save_handle_graph(HandleGraph *graph, ostream &os)'],['../namespacevg_1_1io.html#a571f402ff74b738d9070a598a41b58da',1,'vg::io::save_handle_graph(HandleGraph *graph, const string &dest_path)']]],
- ['save_5fhandle_5fgraph_2ehpp_5303',['save_handle_graph.hpp',['../save__handle__graph_8hpp.html',1,'']]],
- ['save_5flcp_5304',['save_lcp',['../namespacevg.html#a604f783fb59cb6c3e7fcc783a8286822',1,'vg']]],
- ['save_5fminimizer_5305',['save_minimizer',['../namespacevg.html#af7885143ca20185816afadc669813f12',1,'vg']]],
- ['save_5fr_5findex_5306',['save_r_index',['../namespacevg.html#a50d4b5eef7efd656daeb423af1f6a3c6',1,'vg']]],
- ['save_5frecords_5307',['save_records',['../classvg_1_1HTSWriter.html#a4d3f2772a76d36733f1bb1ccf93f498b',1,'vg::HTSWriter']]],
- ['save_5fto_5ffile_5308',['save_to_file',['../classvg_1_1Packer.html#a936e5283142e2fb3ac089730b217d533',1,'vg::Packer']]],
- ['scan_5309',['scan',['../classvg_1_1DozeuInterface.html#a73d9afd8c6b52ff715ae0606bbae4b63',1,'vg::DozeuInterface::scan()'],['../classvg_1_1XdropAligner.html#a3bf50d433186476abc2f732525bf1377',1,'vg::XdropAligner::scan()'],['../classvg_1_1QualAdjXdropAligner.html#a2e8adea58e74731765b5c7d0eb54386f',1,'vg::QualAdjXdropAligner::scan()'],['../structvg_1_1PositionIDScanner.html#a32743fa0fd2721702fe8fc34d565c64a',1,'vg::PositionIDScanner::scan()'],['../structvg_1_1IDScanner.html#a36577d4a2c2ac0d7a12383ae6e9e999d',1,'vg::IDScanner::scan()'],['../structvg_1_1WrappingPositionScanner.html#ac9e28c724f1361a03b6a07e0f9e29ada',1,'vg::WrappingPositionScanner::scan()'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)']]],
- ['scan_5fbackward_5310',['scan_backward',['../classvg_1_1StreamIndexBase.html#addb451cabccc43915ae629925b3ed3ee',1,'vg::StreamIndexBase']]],
- ['scan_5fcontig_5flengths_5311',['scan_contig_lengths',['../classvg_1_1VCFGenotyper.html#a28f3c05eb4ffefef243a18dc27562b15',1,'vg::VCFGenotyper']]],
- ['scan_5ffor_5fdeletion_5312',['scan_for_deletion',['../classvg_1_1VCFTraversalFinder.html#a7842cce2da7786e41fbd110c78e45ef6',1,'vg::VCFTraversalFinder']]],
- ['scan_5fp_5fvisits_5313',['scan_p_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a04d2b3f11fa053b6d6cdbbcae94b4873',1,'vg::algorithms::GFAParser']]],
- ['scan_5fpath_5314',['scan_path',['../classhandlegraph_1_1PathHandleGraph.html#aa071f31a10a02d8231b029d0a7ddef0b',1,'handlegraph::PathHandleGraph']]],
- ['scan_5fseed_5fposition_5315',['scan_seed_position',['../classvg_1_1DozeuInterface.html#a472afdc993f32bfa38518a9cfbd14dcb',1,'vg::DozeuInterface']]],
- ['scan_5fsnarl_5316',['scan_snarl',['../classvg_1_1VCFOutputCaller.html#ad6cbf084906bc4676fae7715495888b3',1,'vg::VCFOutputCaller']]],
- ['scan_5fvisits_5317',['scan_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a58ceb0c0017e5ea50b35854e5c52f0f4',1,'vg::algorithms::GFAParser']]],
- ['scan_5fw_5fvisits_5318',['scan_w_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a7e83307cfe42aae91205fa7180b802b4',1,'vg::algorithms::GFAParser']]],
- ['scanner_2ecpp_5319',['scanner.cpp',['../scanner_8cpp.html',1,'']]],
- ['scanner_2ehpp_5320',['scanner.hpp',['../scanner_8hpp.html',1,'']]],
- ['scc_5fcopy_5fcount_5321',['scc_copy_count',['../classvg_1_1DagifiedGraph.html#a780a2eb98c2a1ad1b106283048f95cf0',1,'vg::DagifiedGraph']]],
- ['scc_5fcopy_5fof_5fhandle_5322',['scc_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a015efe5e782831e59aaa3c2d6f98cbfd',1,'vg::DagifiedGraph']]],
- ['scc_5fcopy_5fof_5fnode_5fid_5323',['scc_copy_of_node_id',['../classvg_1_1DagifiedGraph.html#a26161bf79e0a6385ff8f6fb67a1e907b',1,'vg::DagifiedGraph']]],
- ['scc_5fof_5fhandle_5324',['scc_of_handle',['../classvg_1_1DagifiedGraph.html#afc531153860777849e241cd95ac06b03',1,'vg::DagifiedGraph']]],
- ['score_5325',['score',['../classvg_1_1MEMChainModelVertex.html#a10cf4210b2f802b628111fe2cd1f309b',1,'vg::MEMChainModelVertex::score()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aa0f6834e2a0860792afc6a701d3396c3',1,'vg::MEMClusterer::HitNode::score()'],['../structvg_1_1Funnel_1_1Item.html#a91b9d511109c7c561be120d3346ea3df',1,'vg::Funnel::Item::score()'],['../structvg_1_1WFAPoint.html#a6358c051265bfcc41d857f6df091eebb',1,'vg::WFAPoint::score()'],['../structvg_1_1GaplessExtension.html#a0989b2a97d4403b381dbf68768757d32',1,'vg::GaplessExtension::score()'],['../structvg_1_1WFAAlignment.html#a066d6b546e0308e8df7fc74f42d5de67',1,'vg::WFAAlignment::score()'],['../structvg_1_1Genotyper_1_1Affinity.html#aa0fa1b63d720aa196205be34ee80ee07',1,'vg::Genotyper::Affinity::score()'],['../structvg_1_1GFFRecord.html#aabb70a3b691d378e87cb3fc3fef418ac',1,'vg::GFFRecord::score()'],['../classvg_1_1AlignmentChainModelVertex.html#a207cf7885f1eb8d129d9f599791b0dea',1,'vg::AlignmentChainModelVertex::score()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a002868b55e87a630c4e4f1e1ff213008',1,'vg::MinimizerMapper::Minimizer::score()'],['../structvg_1_1Recombinator_1_1Statistics.html#a348046df697bf6a89261ecfcb6ac6765',1,'vg::Recombinator::Statistics::score()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#abe1c7432c38de20678f5a74798d96bd4',1,'vg::SnarlDistanceIndexClusterer::Cluster::score()'],['../classvg_1_1algorithms_1_1TracedScore.html#a6c63f6d5199ec14c3e912e06f74d9974',1,'vg::algorithms::TracedScore::score()'],['../structvg_1_1Alignment.html#a5c57b95a7ea122139a092427b592ebeb',1,'vg::Alignment::score()'],['../structvg_1_1Subpath.html#acffb5adff6c20c194740186323f1f484',1,'vg::Subpath::score()'],['../structvg_1_1Connection.html#a5e880c9306bb072e08ab6315bdbb1c6f',1,'vg::Connection::score()'],['../structvg_1_1BenchmarkResult.html#a4baad39dafa27d171b65df225666c887',1,'vg::BenchmarkResult::score()'],['../classvg_1_1MEMChainModel.html#aca053d2a91e4ea7ac440edd670893a84',1,'vg::MEMChainModel::score()'],['../classvg_1_1Funnel.html#a9cdacae4561ece776ba90e293299f930',1,'vg::Funnel::score()'],['../structhaplo_1_1haplo__DP.html#aadc492bf7d73b8d551ed56bb62266baa',1,'haplo::haplo_DP::score(const vg::Path &path, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1haplo__DP.html#a3204316e386c183faa191b9ee6f0b34e',1,'haplo::haplo_DP::score(const gbwt_thread_t &thread, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1linear__haplo__structure.html#a100ae7bbb7fa336e7d273c066f251e29',1,'haplo::linear_haplo_structure::score()'],['../classhaplo_1_1ScoreProvider.html#a4dd1edd0db2c92780af0fce9e62e8a1f',1,'haplo::ScoreProvider::score()'],['../classhaplo_1_1GBWTScoreProvider.html#a9970037ed1e272daa0e0bfdf358c9bce',1,'haplo::GBWTScoreProvider::score()'],['../classhaplo_1_1LinearScoreProvider.html#a0d95fe4eff2760404bce49d3aa50e2f0',1,'haplo::LinearScoreProvider::score()'],['../classvg_1_1AlignmentChainModel.html#a562dbec7e2dc602c82b92ad202620429',1,'vg::AlignmentChainModel::score()'],['../classvg_1_1connection__t.html#a8f34943152ac67f59c15ff776da592e8',1,'vg::connection_t::score()'],['../classvg_1_1subpath__t.html#a9e59579440b9a90f5b0c606dc3cf400a',1,'vg::subpath_t::score()'],['../classvg_1_1algorithms_1_1Anchor.html#aff7b7e2c62b7b7154edd3a9f64b0e5a7',1,'vg::algorithms::Anchor::score()']]],
- ['score_5falignment_5326',['score_alignment',['../classvg_1_1Mapper.html#aa541cae3a3598e10a7baf7d5ed78f644',1,'vg::Mapper']]],
- ['score_5falignment_5fpair_5327',['score_alignment_pair',['../classvg_1_1MinimizerMapper.html#a99ce46a1525f7be9fa393163ca1eac40',1,'vg::MinimizerMapper']]],
- ['score_5fbest_5fchain_5328',['score_best_chain',['../namespacevg_1_1algorithms.html#ad91b7ceb67d3923a4c5cace56a5c4f6e',1,'vg::algorithms']]],
- ['score_5fbound_5329',['score_bound',['../classvg_1_1WFATree.html#afdb599de97d172e2afde161ea0f8efc9',1,'vg::WFATree']]],
- ['score_5fchain_5fgap_5330',['score_chain_gap',['../namespacevg_1_1algorithms.html#abdc2933db32d78a14a8e439f7e9643ab',1,'vg::algorithms']]],
- ['score_5fcluster_5331',['score_cluster',['../classvg_1_1MinimizerMapper.html#a12e67c2dfdb80db4080d3675ed6a18d4',1,'vg::MinimizerMapper']]],
- ['score_5fcontiguous_5falignment_5332',['score_contiguous_alignment',['../classvg_1_1GSSWAligner.html#a95753239b9d5fa388198ea04ac6c559b',1,'vg::GSSWAligner']]],
- ['score_5fdiscontiguous_5falignment_5333',['score_discontiguous_alignment',['../classvg_1_1GSSWAligner.html#a795072356e28310d80f95bb5f0bb61f3',1,'vg::GSSWAligner']]],
- ['score_5ferror_5334',['score_error',['../structvg_1_1BenchmarkResult.html#a880a443c67063f66623006cd82b5ec9d',1,'vg::BenchmarkResult']]],
- ['score_5fexact_5fmatch_5335',['score_exact_match',['../classvg_1_1GSSWAligner.html#ac33af43d7d8d4a3d94a5ef1582c50cc4',1,'vg::GSSWAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const =0'],['../classvg_1_1GSSWAligner.html#ac8e1b97332df85221c6a2be61cbd1b3d',1,'vg::GSSWAligner::score_exact_match(const string &sequence, const string &base_quality) const =0'],['../classvg_1_1GSSWAligner.html#ac2969d865d7cb4652a7476feabd9c9b5',1,'vg::GSSWAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1Aligner.html#a4e087eea3154fc52fff10cbe14d0cd32',1,'vg::Aligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1Aligner.html#ab18b86459ab4471de6361bce2d8e8459',1,'vg::Aligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1Aligner.html#a86b2a95cc4d4de88a78ab6ce8ccc4b79',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#ae88c5b0e7c75fec448d4ed245cebe9b9',1,'vg::Aligner::score_exact_match(const string &sequence) const'],['../classvg_1_1Aligner.html#a2acc9c763d0b7c16ad69472a148ce75b',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end) const'],['../classvg_1_1QualAdjAligner.html#adf03ac873ae9a9cfbc21e589775111be',1,'vg::QualAdjAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1QualAdjAligner.html#a51941e8914296630f63d303c548cee8d',1,'vg::QualAdjAligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1QualAdjAligner.html#a8348afe2de6738fd4cd26e3fd6358818',1,'vg::QualAdjAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const']]],
- ['score_5fextension_5fgroup_5336',['score_extension_group',['../classvg_1_1MinimizerMapper.html#a2c8ab02743227cb2550fcfd295043253',1,'vg::MinimizerMapper']]],
- ['score_5fextensions_5337',['score_extensions',['../classvg_1_1MinimizerMapper.html#af9ff5e0a1b8c7925ccdb8a23d29872ef',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::vector< GaplessExtension >> &extensions, const Alignment &aln, Funnel &funnel) const'],['../classvg_1_1MinimizerMapper.html#a421cdd65bac59fac39fd3b87cce0f3ae',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::pair< std::vector< GaplessExtension >, size_t >> &extensions, const Alignment &aln, Funnel &funnel) const']]],
- ['score_5ffrom_5338',['score_from',['../classvg_1_1algorithms_1_1TracedScore.html#a999c0829c8c11a2d7478630612b60b74',1,'vg::algorithms::TracedScore']]],
- ['score_5ffull_5flength_5fbonus_5339',['score_full_length_bonus',['../classvg_1_1GSSWAligner.html#ad6bac86acf59cc8edd4969bd671fcf5d',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1GSSWAligner.html#a952bb420992b5e5e4c81388b015caf97',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const =0'],['../classvg_1_1Aligner.html#aaf87ac123c806ef49c509c494b431c9c',1,'vg::Aligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a442d01bf1ed7d011d015d790f0595817',1,'vg::Aligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const'],['../classvg_1_1QualAdjAligner.html#ac4505d206516b2ad51bdc2387309ae9e',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1QualAdjAligner.html#a84b8bacfebeb426d367ec4441800a4e4',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const']]],
- ['score_5fgap_5340',['score_gap',['../classvg_1_1GSSWAligner.html#a4071f79659899761586807411d5ab767',1,'vg::GSSWAligner::score_gap()'],['../namespacevg.html#aea0e7a0965b967bed3ff54e6ff630f91',1,'vg::score_gap()']]],
- ['score_5fmatrix_5341',['score_matrix',['../classvg_1_1GSSWAligner.html#a9ad471080a267eb489e31523ef2b5f2b',1,'vg::GSSWAligner']]],
- ['score_5fmismatch_5342',['score_mismatch',['../classvg_1_1GSSWAligner.html#ab40663f27266555cd2718fca337ac348',1,'vg::GSSWAligner::score_mismatch()'],['../classvg_1_1Aligner.html#a7e359a8a6af31e1fba84a681c751ec23',1,'vg::Aligner::score_mismatch(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a6728bc34b9e4daa49c1045c8ded44553',1,'vg::Aligner::score_mismatch(size_t length) const'],['../classvg_1_1QualAdjAligner.html#ada69f388d291f6c3693812d91c84231a',1,'vg::QualAdjAligner::score_mismatch()']]],
- ['score_5foutput_5343',['score_output',['../structHaplotypesConfig.html#aea2a24fbc9fbe00f814c1b98d8607079',1,'HaplotypesConfig']]],
- ['score_5fpartial_5falignment_5344',['score_partial_alignment',['../classvg_1_1GSSWAligner.html#adc950708e8d5ff812a838116c6b50910',1,'vg::GSSWAligner::score_partial_alignment()'],['../classvg_1_1Aligner.html#a4537844a4aa7783f6a41c7cefd758602',1,'vg::Aligner::score_partial_alignment()'],['../classvg_1_1QualAdjAligner.html#aee20bae08e744224825723a878d57bef',1,'vg::QualAdjAligner::score_partial_alignment()']]],
- ['score_5fsort_5fand_5fdeduplicate_5falignments_5345',['score_sort_and_deduplicate_alignments',['../classvg_1_1Mapper.html#ae820fb3edeac9da2ef475cb6b0e0f0e9',1,'vg::Mapper']]],
- ['score_5fto_5funnormalized_5flikelihood_5fln_5346',['score_to_unnormalized_likelihood_ln',['../classvg_1_1GSSWAligner.html#a59623587d4dfb1e0310fb608e9def2f0',1,'vg::GSSWAligner']]],
- ['score_5ftree_5347',['score_tree',['../classvg_1_1MinimizerMapper.html#ad4b6267b5e93d0fb618de0584cf2b213',1,'vg::MinimizerMapper']]],
- ['scoreproperties_5348',['ScoreProperties',['../structvg_1_1WFATree_1_1ScoreProperties.html',1,'vg::WFATree']]],
- ['scoreprovider_5349',['ScoreProvider',['../classhaplo_1_1ScoreProvider.html',1,'haplo']]],
- ['scores_5350',['scores',['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ab466534da431354516132617d0f14e95',1,'vg::Recombinator::LocalHaplotype']]],
- ['scoringoptions_5351',['ScoringOptions',['../structScoringOptions.html',1,'']]],
- ['scratch_5352',['scratch',['../structvg_1_1ChainIterator.html#a277447dceb98d18d597a73f2c790e15c',1,'vg::ChainIterator']]],
- ['search_5fleft_5353',['search_left',['../classvg_1_1NestedTraversalFinder.html#a04465d6248557f427e5d35b657292e25',1,'vg::NestedTraversalFinder']]],
- ['search_5fmultipath_5falignment_5354',['search_multipath_alignment',['../namespacevg.html#aa9d71371be6972c8284b267d42fac754',1,'vg']]],
- ['search_5fright_5355',['search_right',['../classvg_1_1NestedTraversalFinder.html#a2b020fead8b7c40b06f9c0e1041b2cb5',1,'vg::NestedTraversalFinder']]],
- ['search_5fthreads_5356',['search_threads',['../structGBWTConfig.html#a1e999f204cdd3655aac4739f12b3265f',1,'GBWTConfig']]],
- ['search_5ftype_5357',['search_type',['../classvg_1_1PhaseUnfolder.html#a7484966dc448f4c3b894a53233f46d9f',1,'vg::PhaseUnfolder']]],
- ['secondary_5frescue_5fattempts_5358',['secondary_rescue_attempts',['../classvg_1_1MultipathMapper.html#a0203a68c7b346ec30bf2854c78bb3434',1,'vg::MultipathMapper']]],
- ['secondary_5frescue_5fscore_5fdiff_5359',['secondary_rescue_score_diff',['../classvg_1_1MultipathMapper.html#ac5ba763f99c22ff9feccb76333cf1039',1,'vg::MultipathMapper']]],
- ['secondary_5frescue_5fsubopt_5fdiff_5360',['secondary_rescue_subopt_diff',['../classvg_1_1MultipathMapper.html#aee081b4a0ee6adadb2dff205a24a2c7a',1,'vg::MultipathMapper']]],
- ['secondary_5fscore_5361',['secondary_score',['../structvg_1_1Alignment.html#a58502a21a2588a5ac8baaa6e31c81eb4',1,'vg::Alignment']]],
- ['seed_5362',['Seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html',1,'vg::SnarlDistanceIndexClusterer::Seed'],['../classvg_1_1MCMCGenotyper.html#aa2399e6a45d2595e08053cdb66207b37',1,'vg::MCMCGenotyper::seed()'],['../classvg_1_1NGSSimulator.html#a99ce1e3ba72956bbf9d1cbaa0fd89014',1,'vg::NGSSimulator::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a1430e1d0dccc75ffa1962408e6226a21',1,'vg::SnarlDistanceIndexClusterer::SeedCache::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#aae124944787f51e8d8fc23cb274f0350',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::seed()'],['../classvg_1_1SpliceRegion.html#a10732e3be85dbecaf6d046ba52f9f716',1,'vg::SpliceRegion::seed()'],['../classvg_1_1StreamSorter.html#a8875748639a885dfacf261956a9b3ee4',1,'vg::StreamSorter::seed()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a38ffc441fe03ec44c1c089eba2b76ae2',1,'vg::ZipCodeTree::oriented_seed_t::seed()'],['../classvg_1_1MinimizerMapper.html#ab964411462aea4fc777127a887a9a6f7',1,'vg::MinimizerMapper::Seed()'],['../classvg_1_1ZipCodeTree.html#a50817b343d4ad6368df659e16b9a7549',1,'vg::ZipCodeTree::Seed()'],['../classvg_1_1ZipCodeForest.html#a93f9eaa38dd8024a73a2aeca456e5156',1,'vg::ZipCodeForest::Seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#adf405ffb00189f3c469f3fc7e79fde01',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed()=default'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#ad6d85e239a68f94ff5dbf2b0362f3c52',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(pos_t pos, size_t source, ZipCode zipcode)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a7859f190024d96f7182de94f197df881',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(Seed &&other)'],['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adab044c319f32f470727c5c2ba078487f5',1,'vg::ZipCodeTree::SEED()']]],
- ['seed_5fcount_5fprefix_5fsum_5363',['seed_count_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af787cd3652afaa91cdebf97673456004',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['seed_5fend_5364',['seed_end',['../classvg_1_1algorithms_1_1Anchor.html#a2db67aba40631bb9e462e2ae744a2ddd',1,'vg::algorithms::Anchor']]],
- ['seed_5findices_5365',['seed_indices',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ad587cbee5a1b577adbc9548a99f857b4',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['seed_5fis_5freversed_5fat_5fdepth_5366',['seed_is_reversed_at_depth',['../classvg_1_1ZipCodeTree.html#a984f21c55ccaf7b053ce0e4fe77f91ff',1,'vg::ZipCodeTree']]],
- ['seed_5flength_5367',['seed_length',['../classvg_1_1algorithms_1_1Anchor.html#a739e4bcbda94fa20b8d99ad5340b5fc6',1,'vg::algorithms::Anchor']]],
- ['seed_5fresult_5ft_5368',['seed_result_t',['../structvg_1_1ZipCodeTree_1_1seed__result__t.html',1,'vg::ZipCodeTree']]],
- ['seed_5fsort_5forder_5369',['seed_sort_order',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ae40d481f31fd4ece290a206482ed5a13',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['seed_5fstart_5370',['seed_start',['../classvg_1_1algorithms_1_1Anchor.html#af68c4af649ee5dfbf4cfff0e0e4493c8',1,'vg::algorithms::Anchor']]],
- ['seed_5ftype_5371',['seed_type',['../structvg_1_1GaplessExtension.html#a8c8a3d415e13a943e87b4c1e33347081',1,'vg::GaplessExtension::seed_type()'],['../classvg_1_1GaplessExtender.html#a8891a422c7921863c589850636d9f252',1,'vg::GaplessExtender::seed_type()']]],
- ['seedcache_5372',['SeedCache',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html',1,'vg::SnarlDistanceIndexClusterer']]],
- ['seeds_5373',['seeds',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a7451a72162f19b00d1bd44fc62be0297',1,'vg::BandedGlobalAligner::BAMatrix::seeds()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a0531ebefe7a686d6624c7b5f60357aeb',1,'vg::SnarlDistanceIndexClusterer::Cluster::seeds()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ac8b2807cb1f656be384407ed36b1c926',1,'vg::ZipCodeForest::forest_growing_state_t::seeds()']]],
- ['seeds_5fin_5fsubgraph_5374',['seeds_in_subgraph',['../classvg_1_1MinimizerMapper.html#a98117858da937a277f445898bcc2d125',1,'vg::MinimizerMapper']]],
- ['seek_5375',['seek',['../structhFILE__backend.html#a93b5b1dcb35560b106e1cccb38476ddb',1,'hFILE_backend::seek()'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa221be19182d88b7caa36ead3e63c829',1,'vg::io::BlockedGzipInputStream::Seek()']]],
- ['seek_5fgroup_5376',['seek_group',['../classvg_1_1io_1_1MessageIterator.html#a97a1561c82f55827a208b2bea5e8da71',1,'vg::io::MessageIterator::seek_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#aad5921d9a10314f8060b0835225fc3cd',1,'vg::io::ProtobufIterator::seek_group()']]],
- ['seen_5fread_5fnames_5377',['seen_read_names',['../classvg_1_1ReadFilter.html#a613b00bb83a119d89911ed4315e4e24a',1,'vg::ReadFilter']]],
- ['segment_5fto_5fname_5378',['segment_to_name',['../classvg_1_1FlatFileBackTranslation.html#a09f2373723a0f9901698cf8315a3f813',1,'vg::FlatFileBackTranslation']]],
- ['segment_5ftranslation_5379',['segment_translation',['../structGBWTConfig.html#a8415ef08abc7ef4e9d854dc100d0df15',1,'GBWTConfig']]],
- ['select_5fdiploid_5380',['select_diploid',['../namespacevg.html#a5b634a10b029be9c22dccc3ef362f61c',1,'vg']]],
- ['select_5fhaplotypes_5381',['select_haplotypes',['../namespacevg.html#af2de3a2f2b77abef4336df983356fc23',1,'vg']]],
- ['sense_5fto_5fstring_5382',['SENSE_TO_STRING',['../paths__main_8cpp.html#a16ad253f4e8c46b88b363e1ffc613c51',1,'paths_main.cpp']]],
- ['separator_5383',['SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#ac50cb6403ceaabd3f878e2c4f2195f56',1,'handlegraph::PathMetadata']]],
- ['seq_5384',['seq',['../structvg_1_1kmer__t.html#a98b04ac70a36cf6feae80b03b3a32eb2',1,'vg::kmer_t::seq()'],['../structvg_1_1Region.html#a938cc852fd08f11656bdfbd204843017',1,'vg::Region::seq()'],['../structvg_1_1VG_1_1Plan.html#a4bb5a9fa8f5bb32c2e94d3c038f9cf95',1,'vg::VG::Plan::seq()'],['../structvg_1_1algorithms_1_1kmer__t.html#a5c235e7c7f3a819e291956d8e307821a',1,'vg::algorithms::kmer_t::seq()'],['../structvg_1_1algorithms_1_1walk__t.html#a65bec2a64da1b8f7c3820d49b5bef09f',1,'vg::algorithms::walk_t::seq()']]],
- ['seq_5fchain_5ffor_5fpath_5385',['seq_chain_for_path',['../haplotypes__main_8cpp.html#a462a39ecca4a3d1298196a6f23ef24a5',1,'haplotypes_main.cpp']]],
- ['seq_5fdoes_5fnot_5fmatch_5386',['SEQ_DOES_NOT_MATCH',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9acc8619639d089c16381dd05298fe3df8',1,'vg::AlignmentValidity']]],
- ['seq_5ffor_5fchain_5387',['seq_for_chain',['../haplotypes__main_8cpp.html#ace19d06b45cb66b44602157c3bc24916',1,'haplotypes_main.cpp']]],
- ['seq_5flength_5388',['seq_length',['../classvg_1_1Viz.html#a2f5862e76ca098060b503d03de76c024',1,'vg::Viz::seq_length()'],['../classxg_1_1XG.html#a7eadd7681a21479f7f31c240047cdffe',1,'xg::XG::seq_length()']]],
- ['seq_5foffset_5389',['seq_offset',['../structvg_1_1MatchPos.html#a85fc0d2a7af86db887d649d3c968755e',1,'vg::MatchPos::seq_offset()'],['../structvg_1_1WFAPoint.html#a14ceda5614586a0e3ef44b729ad179c0',1,'vg::WFAPoint::seq_offset()'],['../structvg_1_1WFAAlignment.html#a1fc0e09c8462c5aa10d4f0acbc2a8f2d',1,'vg::WFAAlignment::seq_offset()']]],
- ['seqcomplexity_5390',['SeqComplexity',['../structvg_1_1SeqComplexity.html',1,'vg::SeqComplexity< MaxOrder >'],['../structvg_1_1SeqComplexity.html#a18ab1a3d85623f42d1e8848fcf94846d',1,'vg::SeqComplexity::SeqComplexity(string::const_iterator begin, string::const_iterator end)'],['../structvg_1_1SeqComplexity.html#ac7a2e970b541883c812fafa7851d6278',1,'vg::SeqComplexity::SeqComplexity(const string &seq)']]],
- ['sequence_5391',['sequence',['../classvg_1_1ExtraNodeGraph.html#ad485e6609536566720fe5a48f7e2af84',1,'vg::ExtraNodeGraph::sequence()'],['../classvg_1_1WFATree.html#abbd67ff2f910ad5a4c0c1f49b10394a5',1,'vg::WFATree::sequence()'],['../structvg_1_1PathIndex.html#a0b807b5252299d9b0f1c9168079a591f',1,'vg::PathIndex::sequence()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#a2e6f784aa4bde512d84c0f1d3cedd01f',1,'vg::Recombinator::LocalHaplotype::sequence()'],['../structvg_1_1Node.html#a9a0e8995bc48aa5e24977d1bd20e91a3',1,'vg::Node::sequence()'],['../structvg_1_1Edit.html#a4a7726b24b28ed819d37b9c39ae839d1',1,'vg::Edit::sequence()'],['../structvg_1_1Alignment.html#a2ae1f06d48c37997cee72b7cd3210a83',1,'vg::Alignment::sequence()'],['../structvg_1_1MultipathAlignment.html#ae6c263b75effad9b08e514c5852f1221',1,'vg::MultipathAlignment::sequence()'],['../structvg_1_1KmerMatch.html#ab434e30bbaf0fbb10425d5bc35ac50b2',1,'vg::KmerMatch::sequence()'],['../classvg_1_1MaximalExactMatch.html#a9746bd3ef368dbeae05459381223cebc',1,'vg::MaximalExactMatch::sequence()'],['../classvg_1_1multipath__alignment__t.html#a5637161345c2b1a557a40188b564dd55',1,'vg::multipath_alignment_t::sequence()'],['../classvg_1_1edit__t.html#aca5aef83ea5f5195699732c61c44b86d',1,'vg::edit_t::sequence()'],['../classvg_1_1Sampler.html#a355de4870a71a88834406f3e7f297272',1,'vg::Sampler::sequence()']]],
- ['sequence_5fcomplexity_2ehpp_5392',['sequence_complexity.hpp',['../sequence__complexity_8hpp.html',1,'']]],
- ['sequence_5fid_5393',['sequence_id',['../structvg_1_1GFFRecord.html#a91b952a4d9d5c4f44e6def80e33073c8',1,'vg::GFFRecord::sequence_id()'],['../structvg_1_1RecombinatorHaplotype.html#a3b372fd165a3e707a50e2a0a1f61cef5',1,'vg::RecombinatorHaplotype::sequence_id()']]],
- ['sequence_5fpositions_5394',['sequence_positions',['../classvg_1_1BaseMapper.html#a1fc5077e5ea4a236ddf8edcf93288eb9',1,'vg::BaseMapper']]],
- ['sequence_5fsource_5395',['sequence_source',['../structGraphHandler.html#a1583ae5e2c88d3099b62255a28978316',1,'GraphHandler']]],
- ['sequence_5ftype_5396',['sequence_type',['../structvg_1_1RecombinatorHaplotype.html#a20c784c55500a6e02c9ad4762be12176',1,'vg::RecombinatorHaplotype::sequence_type()'],['../classvg_1_1Haplotypes.html#aebc70f387d48bd0e5c8f0c607c496535',1,'vg::Haplotypes::sequence_type()'],['../classvg_1_1HaplotypePartitioner.html#aa06fc618c54377342c05b7306b8dec72',1,'vg::HaplotypePartitioner::sequence_type()'],['../classvg_1_1Recombinator.html#a8a1ad77c3ad37fbcfa48dc5f89f591af',1,'vg::Recombinator::sequence_type()']]],
- ['sequences_5397',['sequences',['../structvg_1_1Haplotypes_1_1Subchain.html#aae0d847a9118ccb4ff178c3ac7c759eb',1,'vg::Haplotypes::Subchain']]],
- ['serializable_5398',['Serializable',['../classhandlegraph_1_1Serializable.html',1,'handlegraph']]],
- ['serializable_2ecpp_5399',['serializable.cpp',['../serializable_8cpp.html',1,'']]],
- ['serializable_2ehpp_5400',['serializable.hpp',['../serializable_8hpp.html',1,'']]],
- ['serializable_5fhandle_5fgraph_2ehpp_5401',['serializable_handle_graph.hpp',['../serializable__handle__graph_8hpp.html',1,'']]],
- ['serializablehandlegraph_5402',['SerializableHandleGraph',['../classhandlegraph_1_1SerializableHandleGraph.html',1,'handlegraph::SerializableHandleGraph'],['../namespacevg.html#a7378a177b4ed2e7be87e02a9bfcb7d4e',1,'vg::SerializableHandleGraph()']]],
- ['serialize_5403',['serialize',['../structvg_1_1GBWTHandler.html#aa855690c481cca126734e20f5d126d04',1,'vg::GBWTHandler::serialize()'],['../classvg_1_1Packer.html#a833e1fa21ac3f5f5f6a001c5c5ee0f4c',1,'vg::Packer::serialize()'],['../classvg_1_1SnarlManager.html#afdcb932a1a891671acbdaaf445aee0b2',1,'vg::SnarlManager::serialize()'],['../classvg_1_1VG.html#a0ee4603518e9cd5915a65e65c2d763b2',1,'vg::VG::serialize()'],['../classvg_1_1ZipCodeCollection.html#afb7d15490acd1b076664049072184914',1,'vg::ZipCodeCollection::serialize()'],['../classxg_1_1XGPath.html#a74e7b70ac4829545e7b48c137808d6e4',1,'xg::XGPath::serialize()'],['../classhandlegraph_1_1Serializable.html#adae323cce9552f03774ab71dd5fb07d0',1,'handlegraph::Serializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1Serializable.html#ac6e9dfc830acdf96fbfe53d83d33802e',1,'handlegraph::Serializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1Serializable.html#a050e6c2b6e2fccd85362e908da60d20b',1,'handlegraph::Serializable::serialize(std::ostream &out)'],['../classhandlegraph_1_1Serializable.html#aa97699c9b50235d5f2439eb57c5df653',1,'handlegraph::Serializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#acaec0b472d85de2ff98b8635b5fbf33c',1,'handlegraph::TriviallySerializable::serialize(const std::function< void(const void *, size_t)> &iteratee) const =0'],['../classhandlegraph_1_1TriviallySerializable.html#a2881d2d598bd35cc68008ad3dc4b82d5',1,'handlegraph::TriviallySerializable::serialize(int fd)=0'],['../classhandlegraph_1_1TriviallySerializable.html#ab04c99b94217a13ce598e8fd484b09c1',1,'handlegraph::TriviallySerializable::serialize(int fd) const'],['../classhandlegraph_1_1TriviallySerializable.html#aaeb37dbdd6e221e2c5ddfba9cb226c56',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1TriviallySerializable.html#a6c306e7cce2dfe6079b093aa2fae77a0',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#a674a89ff2072c5e57c7f5f07d915d049',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1TriviallySerializable.html#a89624195e0d24768774e98c61d17c779',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out)']]],
- ['serialize_5fand_5fmeasure_5404',['serialize_and_measure',['../classxg_1_1XG.html#aac0ec5744208c54abfc692bf7ff66536',1,'xg::XG']]],
- ['serialize_5fmembers_5405',['serialize_members',['../classxg_1_1XG.html#a99af109d31808040b7f1819c6a236b05',1,'xg::XG::serialize_members()'],['../classhandlegraph_1_1Serializable.html#a79235728e5f1e8fb1c0e19e275a33fff',1,'handlegraph::Serializable::serialize_members()']]],
- ['serialize_5fmembers_5fand_5fmeasure_5406',['serialize_members_and_measure',['../classxg_1_1XG.html#af7c089f5d1342620dd573b2aa4197ca8',1,'xg::XG']]],
- ['serialize_5fsegment_5ftranslation_5407',['serialize_segment_translation',['../structGraphHandler.html#ad8ffb0dac5a43b9c1dee33eba093d02e',1,'GraphHandler']]],
- ['serialize_5fto_5femitter_5408',['serialize_to_emitter',['../classvg_1_1VG.html#a59121c0226c3fd8c328641490bf2fac6',1,'vg::VG']]],
- ['serialize_5fto_5ffile_5409',['serialize_to_file',['../classvg_1_1VG.html#a3522042a3a00ac802d6738d0bec6269c',1,'vg::VG']]],
- ['serialize_5fto_5ffunction_5410',['serialize_to_function',['../classvg_1_1VG.html#ad3187dd6ce750583f6b1a7c32f278d2a',1,'vg::VG']]],
- ['serialize_5fto_5fostream_5411',['serialize_to_ostream',['../classvg_1_1VG.html#a70e67b525bca0f766d7f0170759ed1d0',1,'vg::VG']]],
- ['set_5412',['set',['../structvg_1_1subcommand_1_1BaseArgSpec.html#ae73224926db6d8d7730212d2714e1dcf',1,'vg::subcommand::BaseArgSpec::set()'],['../structvg_1_1subcommand_1_1ArgSpec.html#afd6266196b810cf1b11c88e5ad3fd2a2',1,'vg::subcommand::ArgSpec::set()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad81d797abdd9ece7dece847ad979f80c',1,'vg::subcommand::BaseOptionGroup::set()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a667b46c883efd1b60966679f31bb03fe',1,'vg::subcommand::OptionGroup::set()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a72309d1c25433c7e3a6e3e7dac0930fd',1,'vg::subcommand::GroupedOptionGroup::set()']]],
- ['set_5falignment_5fscores_5413',['set_alignment_scores',['../classvg_1_1AlignerClient.html#a1fde3e4537147030d153d403fd04ec77',1,'vg::AlignerClient::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#adbdd2fabd7a36353526663aede3cb555',1,'vg::AlignerClient::set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#a79424f53b6e4f588da23ea531a600b84',1,'vg::AlignerClient::set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1BaseMapper.html#addc9b0af15050357598c372e135d6a0e',1,'vg::BaseMapper::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1BaseMapper.html#aed94c577ba8f01eb8098d1be74b8d70a',1,'vg::BaseMapper::set_alignment_scores(istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1MinimizerMapper.html#a98a602ac6b9f20d9da825d8a542ceebd',1,'vg::MinimizerMapper::set_alignment_scores()'],['../classvg_1_1MultipathMapper.html#ad897513b9554b2dabebea47cc3f3da9f',1,'vg::MultipathMapper::set_alignment_scores()']]],
- ['set_5fallele_5414',['set_allele',['../classvg_1_1PhasedGenome.html#ad0fdafbc6cb6fbfb576be92f6f6bc17d',1,'vg::PhasedGenome']]],
- ['set_5fannotation_5415',['set_annotation',['../classvg_1_1multipath__alignment__t.html#aebfe1bbda50606c4feb85bb674698c4e',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name)'],['../classvg_1_1multipath__alignment__t.html#a1927cf1ca631a6efb5ed6c83072e2e2c',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, double value)'],['../classvg_1_1multipath__alignment__t.html#a37e9679383b80b3a5028017155d04296',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, bool value)'],['../classvg_1_1multipath__alignment__t.html#aca07d0a515d16b62eca1f1c9ad44ffc9',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, const string &value)'],['../namespacevg.html#adea29af7b94ac90b1db0eacd908511c0',1,'vg::set_annotation(Annotated *annotated, const string &name, const AnnotationType &annotation)'],['../namespacevg.html#a54bcd5d5fc5318bbdbe784f224b906bd',1,'vg::set_annotation(Annotated &annotated, const string &name, const AnnotationType &annotation)']]],
- ['set_5fautomatic_5fmin_5fclustering_5flength_5416',['set_automatic_min_clustering_length',['../classvg_1_1MultipathMapper.html#ac0a6f15f0273faa48ff52a59a08855e1',1,'vg::MultipathMapper']]],
- ['set_5favg_5417',['set_avg',['../classvg_1_1Filter.html#a3629b0035db72bc575a6f0d440b52288',1,'vg::Filter']]],
- ['set_5fbaseline_5ferror_5418',['set_baseline_error',['../classvg_1_1PoissonSupportSnarlCaller.html#a41964acba3d81c26b01f9b00cd49257a',1,'vg::PoissonSupportSnarlCaller']]],
- ['set_5fchain_5fcomponent_5419',['set_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a6d70e8ff87f9e2a2d47511b9aece4980',1,'vg::ZipCode::node_code_t::set_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a05fecca7e22cfd80595143e5b6fe1b74',1,'vg::ZipCode::snarl_code_t::set_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a969b901d95d609ce1a065278ef6bd7fb',1,'vg::ZipCodeForest::sort_value_t::set_chain_component()']]],
- ['set_5fchain_5forder_5420',['set_chain_order',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a33c2b7d50ccefb836fe376dec56c9c09',1,'vg::ZipCodeForest::sort_value_t']]],
- ['set_5fchain_5fvalues_5421',['set_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae0c994c6c86ccbc4b32689baa6183349',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['set_5fchild_5fcount_5422',['set_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04d8cd3924cd20476f71d21690530ee6',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fcircularity_5423',['set_circularity',['../classvg_1_1VG.html#a73c97ce0157b90f95b888e4b6983f5c8',1,'vg::VG::set_circularity()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a9172694447503e35d50093d55e845eb8',1,'handlegraph::MutablePathHandleGraph::set_circularity()']]],
- ['set_5fcode_5ftype_5424',['set_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aeac2169d6f24e91993e1b8c28b8d5a30',1,'vg::ZipCode::snarl_code_t::set_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ab80c26e62009341686000a010bb0d5c3',1,'vg::ZipCodeForest::sort_value_t::set_code_type()']]],
- ['set_5fcompressed_5fannotation_5425',['set_compressed_annotation',['../namespacevg.html#a3f6c363cc3cb03b7379635741d1b0837',1,'vg::set_compressed_annotation(Annotated *annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)'],['../namespacevg.html#a0efd9e2e5d1ab86647910ccd002109cd',1,'vg::set_compressed_annotation(Annotated &annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)']]],
- ['set_5fconnection_5426',['set_connection',['../classvg_1_1subpath__t.html#ae0073c7a92ebfc9ea0acfe7e17837bd1',1,'vg::subpath_t']]],
- ['set_5fconnectivity_5427',['set_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac59bb21ee878d8f2923ac7f8dc857641',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fcrash_5fcontext_5428',['set_crash_context',['../namespacevg.html#ac801de9444375b2f131d3c21d125e83b',1,'vg']]],
- ['set_5fdir_5429',['set_dir',['../namespacevg_1_1temp__file.html#a13270094cd53cedbd540c7fd4412f0d6',1,'vg::temp_file::set_dir()'],['../namespacexg_1_1temp__file.html#a43d250a4567f29ba269e8a3f4c39dbb6',1,'xg::temp_file::set_dir()']]],
- ['set_5fdistance_5fend_5fleft_5430',['set_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a9b8478c75baaf1a65691dd2d72f4c54d',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fdistance_5fend_5fright_5431',['set_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#acb835fdaed8979f3faa044171bfcbe8f',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fdistance_5fstart_5fleft_5432',['set_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2a611cd876f68bb23d5a62babde8bdf9',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fdistance_5fstart_5fright_5433',['set_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3a6fa5c7c47f14100596b3384d72d51f',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fedge_5434',['set_edge',['../classvg_1_1VG.html#ae1131c1ff0a94ed2ec9ef35cb678801b',1,'vg::VG']]],
- ['set_5ffilter_5fmatches_5435',['set_filter_matches',['../classvg_1_1Filter.html#ad45e46ca49dca65ee8e3d838d28d71b6',1,'vg::Filter']]],
- ['set_5ffragment_5flength_5fdistr_5fparams_5436',['set_fragment_length_distr_params',['../classvg_1_1PairedEndMapper.html#a09e89f6da87d25f0ad66fb9eb3139a98',1,'vg::PairedEndMapper']]],
- ['set_5ffrom_5flength_5437',['set_from_length',['../classvg_1_1edit__t.html#aba75c7882507dcced8ca80081b4b504b',1,'vg::edit_t']]],
- ['set_5fhash_5fcolor_5438',['set_hash_color',['../classvg_1_1Viz.html#ab5559043258bf1e1cd4e3a754342cdde',1,'vg::Viz']]],
- ['set_5fhet_5fbias_5439',['set_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a0cb5e2761e2c2feebc901d54a5891454',1,'vg::RatioSupportSnarlCaller']]],
- ['set_5fid_5fincrement_5440',['set_id_increment',['../classvg_1_1VG.html#aebe71b82645b85e73342366cea0a4549',1,'vg::VG::set_id_increment()'],['../classhandlegraph_1_1MutableHandleGraph.html#ab844ab426cd9f289414aca4d8b892ca9',1,'handlegraph::MutableHandleGraph::set_id_increment()']]],
- ['set_5finsertion_5fbias_5441',['set_insertion_bias',['../classvg_1_1PoissonSupportSnarlCaller.html#abeb1d41aaa26a91cb3319cc5fe6b0af0',1,'vg::PoissonSupportSnarlCaller']]],
- ['set_5fintermediate_5ffile_5fkeeping_5442',['set_intermediate_file_keeping',['../classvg_1_1IndexRegistry.html#a983cdafc1b28ea24def5349f90e415eb',1,'vg::IndexRegistry']]],
- ['set_5fintersection_5443',['set_intersection',['../namespacevg.html#a234b2ca417edb50a3c738991fcfc269a',1,'vg']]],
- ['set_5fintron_5flength_5fdistribution_5444',['set_intron_length_distribution',['../classvg_1_1MultipathMapper.html#a8c6768f5299e424b19d569dd077dbafe',1,'vg::MultipathMapper']]],
- ['set_5finverse_5445',['set_inverse',['../classvg_1_1Filter.html#afb65a7ed6bb059f22196415c631680e9',1,'vg::Filter']]],
- ['set_5fis_5freverse_5446',['set_is_reverse',['../classvg_1_1mapping__t.html#ad248204841f7ba0ce4c3604ec138556d',1,'vg::mapping_t::set_is_reverse()'],['../classvg_1_1position__t.html#a3d78fabe1cda0e0243071a36ccd73996',1,'vg::position_t::set_is_reverse()']]],
- ['set_5fis_5freversed_5447',['set_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#aaab7c0874ce7df9a462009840404e8fb',1,'vg::ZipCode::node_code_t::set_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8836324bf0af9142171328634fba592d',1,'vg::ZipCode::snarl_code_t::set_is_reversed()']]],
- ['set_5flast_5fcomponent_5448',['set_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a98cac9a41d2c53554c96084e35a591b5',1,'vg::ZipCode::chain_code_t']]],
- ['set_5flength_5449',['set_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a2ef78836b286d95e1ad7d0b88c55cbaf',1,'vg::ZipCode::node_code_t::set_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a138235f7ccb84dcc25134cf6f200aecb',1,'vg::ZipCode::chain_code_t::set_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a51cb4c8c5a89e591cede7c9a27d77c8b',1,'vg::ZipCode::snarl_code_t::set_length()']]],
- ['set_5flog_5fodds_5fagainst_5fsplice_5450',['set_log_odds_against_splice',['../classvg_1_1MultipathMapper.html#a8902c35e23b24555f94fd2f7d95ef806',1,'vg::MultipathMapper']]],
- ['set_5fmapping_5fquality_5451',['set_mapping_quality',['../classvg_1_1multipath__alignment__t.html#a492c704bcf2ec27123143b83d8218ad9',1,'vg::multipath_alignment_t']]],
- ['set_5fmax_5fmerge_5fsupression_5flength_5452',['set_max_merge_supression_length',['../classvg_1_1MultipathMapper.html#a3db9d73e2a4b296df8df495c028a615b',1,'vg::MultipathMapper']]],
- ['set_5fmin_5fbp_5fedge_5foverride_5453',['set_min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a920ba7030a3946b9b239b1a7f1abbe44',1,'vg::TraversalSupportFinder']]],
- ['set_5fmin_5fdepth_5454',['set_min_depth',['../classvg_1_1Filter.html#a94d0c4f93831a6faf70411dc6caf0ac3',1,'vg::Filter']]],
- ['set_5fmin_5fpercent_5fidentity_5455',['set_min_percent_identity',['../classvg_1_1Filter.html#ae1837a93c7c3575c52dcba37538070f8',1,'vg::Filter']]],
- ['set_5fmin_5fqual_5456',['set_min_qual',['../classvg_1_1Filter.html#a5c3851f5838da69576fd3e59443bb8d3',1,'vg::Filter']]],
- ['set_5fmin_5fsoftclip_5flength_5ffor_5fsplice_5457',['set_min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#ad3848a9b82e967ca119dd94add068597',1,'vg::MultipathMapper']]],
- ['set_5fmin_5fsplice_5flength_5458',['set_min_splice_length',['../classvg_1_1MultipathAlignmentEmitter.html#aa6e3289654a2ebe8ed2b934a1fcd6d40',1,'vg::MultipathAlignmentEmitter']]],
- ['set_5fmin_5fsupports_5459',['set_min_supports',['../classvg_1_1SupportBasedSnarlCaller.html#a3afbd8d1bc78b6716c587b93424db8cb',1,'vg::SupportBasedSnarlCaller']]],
- ['set_5fmy_5fpath_5fposition_5fgraph_5460',['set_my_path_position_graph',['../classvg_1_1Filter.html#a8986008ebcb92629e17da5ed45a23734',1,'vg::Filter']]],
- ['set_5fmy_5fvg_5461',['set_my_vg',['../classvg_1_1Filter.html#a8742f0354b0e40a55ba2dd7270bd197d',1,'vg::Filter']]],
- ['set_5fnested_5462',['set_nested',['../classvg_1_1VCFOutputCaller.html#a35f5b2f9d93ea764e0d8f5f957ba4c3a',1,'vg::VCFOutputCaller']]],
- ['set_5fnext_5463',['set_next',['../classvg_1_1connection__t.html#adc3fded850671e336763eaa0c6d87e78',1,'vg::connection_t::set_next()'],['../classvg_1_1subpath__t.html#a2f0c0e1b1e509de732a1318919af0177',1,'vg::subpath_t::set_next()']]],
- ['set_5fnode_5fid_5464',['set_node_id',['../classvg_1_1mapping__t.html#a3101ac21e398f36c0367a89b20360cd0',1,'vg::mapping_t::set_node_id()'],['../classvg_1_1position__t.html#a5e2f0de1d8da70bb8b233522597bd02b',1,'vg::position_t::set_node_id()']]],
- ['set_5foffset_5465',['set_offset',['../structhaplo_1_1haplo__DP__rectangle.html#a9ca4ea25d72d1a40b9a0e1a170e88274',1,'haplo::haplo_DP_rectangle::set_offset()'],['../classvg_1_1position__t.html#ad34d5af7aab58a425f33faa2358ef57e',1,'vg::position_t::set_offset()']]],
- ['set_5foption_5fvalue_5466',['set_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abdc58a9c90f9adbcac68d3e18f6c7d36',1,'vg::subcommand::BaseOptionGroup']]],
- ['set_5fpaired_5fall_5467',['set_paired_all',['../structvg_1_1Counts.html#a038f57bbb1cabd1f83b544c22562a0d9',1,'vg::Counts']]],
- ['set_5fpaired_5fany_5468',['set_paired_any',['../structvg_1_1Counts.html#ad4e3e7b118ed1ec1286d933a57bdbf23',1,'vg::Counts']]],
- ['set_5fpath_5fposition_5469',['set_path_position',['../classvg_1_1Surjector.html#ac4e7823cc2ce4b65bb8910ef2c1dcbee',1,'vg::Surjector']]],
- ['set_5fprefix_5470',['set_prefix',['../classvg_1_1IndexRegistry.html#aefc2da48af951d3b300ee0b5c70559c3',1,'vg::IndexRegistry']]],
- ['set_5fprefix_5fsum_5for_5fidentifier_5471',['set_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a0c99221572a9dce4051fa68a79bb540f',1,'vg::ZipCode::node_code_t::set_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8a66d4f3fba23bebe13618b0d45988a4',1,'vg::ZipCode::snarl_code_t::set_prefix_sum_or_identifier()']]],
- ['set_5fprev_5fidx_5472',['set_prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#ad1c78747473f9b8816c459949b8b8e8e',1,'haplo::haplo_DP_rectangle']]],
- ['set_5fquality_5473',['set_quality',['../classvg_1_1multipath__alignment__t.html#a2ff40ca9f44290aeb5406764ccbb5ebf',1,'vg::multipath_alignment_t']]],
- ['set_5fraw_5fchain_5fcomponent_5474',['set_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a32b61e2274b266a217cebace47e2907a',1,'vg::ZipCode::node_code_t::set_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab4c8a0b7d2e5b20bab6ff83558581a4d',1,'vg::ZipCode::snarl_code_t::set_raw_chain_component()']]],
- ['set_5fraw_5fchild_5fcount_5475',['set_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ace304ea5d619189a001274a3c117a97b',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fcode_5ftype_5476',['set_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a4b2441552754d8c09003a86ed412af6e',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fconnectivity_5477',['set_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a7e9fc82b6947464a05b05ad154a706dd',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fraw_5fdistance_5fend_5fleft_5478',['set_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6d9d20da8c7cee397bc621395ebb0595',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fdistance_5fend_5fright_5479',['set_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34782c4f89ca5b5ed549c086d782a49a',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fdistance_5fstart_5fleft_5480',['set_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6ef05afc876f9d157a4a22ece67ec14b',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fdistance_5fstart_5fright_5481',['set_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3c42e8e885b205135c84167f3d0c30f9',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fis_5freversed_5482',['set_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ce29ebd996f8894ed6942633fb387b9',1,'vg::ZipCode::node_code_t::set_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af7cdb5f02946631384bab58c2732c305',1,'vg::ZipCode::snarl_code_t::set_raw_is_reversed()']]],
- ['set_5fraw_5flast_5fcomponent_5483',['set_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a389422a0482e9a0fe88b77bacc88b2fa',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fraw_5flength_5484',['set_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a9eaa33f8ee594c5fe686c4e5e0bfbe30',1,'vg::ZipCode::node_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a373aeb1528f44cf694a7711ab827d088',1,'vg::ZipCode::chain_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6f15f89fa329bcd06088318bb17bbdb2',1,'vg::ZipCode::snarl_code_t::set_raw_length()']]],
- ['set_5fraw_5fprefix_5fsum_5for_5fidentifier_5485',['set_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a02b5011800febaebbef6c517fc08320e',1,'vg::ZipCode::node_code_t::set_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a38cb2f04ee15fc31ec69d5ef06f45ac1',1,'vg::ZipCode::snarl_code_t::set_raw_prefix_sum_or_identifier()']]],
- ['set_5fraw_5frecord_5foffset_5486',['set_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5a5034d3c583b9220450bcc2da59f31f',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fsnarl_5frank_5for_5fidentifier_5487',['set_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a214ccf14cf2a287d7756d10036ce9bff',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fread_5f1_5fadapter_5488',['set_read_1_adapter',['../classvg_1_1MultipathMapper.html#aaf7ee8334193018b945900b00cec8826',1,'vg::MultipathMapper']]],
- ['set_5fread_5f2_5fadapter_5489',['set_read_2_adapter',['../classvg_1_1MultipathMapper.html#a1c1674e89e4702168e75bca6fdb4d0bd',1,'vg::MultipathMapper']]],
- ['set_5fread_5fcoverage_5490',['set_read_coverage',['../classvg_1_1MultipathMapper.html#a2ce30f7fe70325b6101356f5eb67df3d',1,'vg::MultipathMapper']]],
- ['set_5fread_5fgroup_5491',['set_read_group',['../classvg_1_1MultipathAlignmentEmitter.html#ad772e7a7315be2a57899c234116de800',1,'vg::MultipathAlignmentEmitter']]],
- ['set_5frecord_5foffset_5492',['set_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a33b431da2b73e995db51480fd2e5385b',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5frefpos_5493',['set_refpos',['../classvg_1_1MinimizerMapper.html#a7fe47fe6075b79253609a04601d0995e',1,'vg::MinimizerMapper']]],
- ['set_5fregion_5494',['set_region',['../classvg_1_1VcfBuffer.html#a0a636a74fef67c3cfd59730db3ed427c',1,'vg::VcfBuffer::set_region()'],['../classvg_1_1WindowedVcfBuffer.html#ab6c81f821d5ddcace1e67e7081793142',1,'vg::WindowedVcfBuffer::set_region()']]],
- ['set_5fremove_5ffailing_5fedits_5495',['set_remove_failing_edits',['../classvg_1_1Filter.html#ab91fdad4a96917a43f1fed85e11a9645',1,'vg::Filter']]],
- ['set_5fsample_5fname_5496',['set_sample_name',['../classvg_1_1MultipathAlignmentEmitter.html#a398cd239c156944100299fc5babb6194',1,'vg::MultipathAlignmentEmitter']]],
- ['set_5fscore_5497',['set_score',['../classvg_1_1connection__t.html#ab7e71cc31834606883ce7fee437bdd7b',1,'vg::connection_t::set_score()'],['../classvg_1_1subpath__t.html#a7229edbbe9e72084b114bd03079cc105',1,'vg::subpath_t::set_score()'],['../namespacevg.html#a3b05a1318d7be5ecf3547a3eca837618',1,'vg::set_score()']]],
- ['set_5fsequence_5498',['set_sequence',['../classvg_1_1multipath__alignment__t.html#a5cabf8eec673f7aaf7d28add560a7e32',1,'vg::multipath_alignment_t::set_sequence()'],['../classvg_1_1edit__t.html#aa2a77df9db620c8500a3eb4802229f43',1,'vg::edit_t::set_sequence()']]],
- ['set_5fshow_5fprogress_5499',['set_show_progress',['../classvg_1_1GraphCaller.html#a1005b4de9fde3d23adcd1d35f8fece09',1,'vg::GraphCaller']]],
- ['set_5fsnarl_5frank_5for_5fidentifier_5500',['set_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a43ebf63adc3f81a82dd4b9bb77be2772',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fsnarl_5fvalues_5501',['set_snarl_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a858ed22ff1cba852000f4815bd03e20f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['set_5fsoft_5fclip_5flimit_5502',['set_soft_clip_limit',['../classvg_1_1Filter.html#a8e69a6bc40641a3377dd60f44ec52816',1,'vg::Filter']]],
- ['set_5fsort_5fvalue_5503',['set_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aa1ea92740944abf659a9080acc7fa0b3',1,'vg::ZipCodeForest::sort_value_t']]],
- ['set_5fsource_5fpaths_5504',['set_source_paths',['../classvg_1_1Sampler.html#ab217a74d97bc905480c236ab66d30232',1,'vg::Sampler']]],
- ['set_5fsplit_5fread_5flimit_5505',['set_split_read_limit',['../classvg_1_1Filter.html#a377d6661a880d4d3798e8780d61d6db0',1,'vg::Filter']]],
- ['set_5fstart_5506',['set_start',['../classvg_1_1multipath__alignment__t.html#a9230aa70e0c93066e0c8f9f4c4af28fa',1,'vg::multipath_alignment_t']]],
- ['set_5fsupport_5fswitch_5fthreshold_5507',['set_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a53940205edddd5d3bb379b82ede4f74f',1,'vg::TraversalSupportFinder']]],
- ['set_5fsystem_5fdir_5508',['set_system_dir',['../namespacevg_1_1temp__file.html#ac061a6d187921157d4e62930445996e8',1,'vg::temp_file']]],
- ['set_5ftags_5509',['set_tags',['../gbwt__main_8cpp.html#ab3856151a0825f396467961305716704',1,'gbwt_main.cpp']]],
- ['set_5ftarget_5fmemory_5fusage_5510',['set_target_memory_usage',['../classvg_1_1IndexRegistry.html#aee06106e4888a5a17d12fa10f1e87893',1,'vg::IndexRegistry']]],
- ['set_5fto_5flength_5511',['set_to_length',['../classvg_1_1edit__t.html#a9b38a79f561f60c377c35e186c5cfd96',1,'vg::edit_t']]],
- ['set_5ftranslation_5512',['set_translation',['../classvg_1_1VCFOutputCaller.html#a918bfde23f9f6afacec9b10319030414',1,'vg::VCFOutputCaller']]],
- ['set_5fvalue_5513',['set_value',['../structvg_1_1subcommand_1_1ArgSpec.html#a1e31767c05c4a085a3b8087067af70c4',1,'vg::subcommand::ArgSpec::set_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a25817ff171a0199cf4e21fee15261f14',1,'vg::subcommand::ValueArgSpec::set_value()']]],
- ['set_5fwindow_5flength_5514',['set_window_length',['../classvg_1_1Filter.html#adb96fca6a301e45c84b010f5461440a9',1,'vg::Filter']]],
- ['setk_5515',['setK',['../classvg_1_1FlowTraversalFinder.html#adf6216e25b6f61a09aa13816eafcd6e3',1,'vg::FlowTraversalFinder']]],
- ['settotalbyteslimit_5516',['SetTotalBytesLimit',['../message__iterator_8hpp.html#ad3271079865fad5b2725dab227556443',1,'message_iterator.hpp']]],
- ['sha1_5fvariant_5fname_5517',['sha1_variant_name',['../classvg_1_1Constructor.html#afafc25fc7021c48463894db9abce2f66',1,'vg::Constructor']]],
- ['sha1head_5518',['sha1head',['../namespacevg.html#a6821cd887e206752c50c1a7be764d1f5',1,'vg']]],
- ['sha1sum_5519',['sha1sum',['../namespacevg.html#a0cada7d579d914675f53490e0488ab53',1,'vg']]],
- ['shallow_5fcontents_5520',['shallow_contents',['../classvg_1_1SnarlManager.html#afb7f6b946d3ec05ed619e09491e0a92d',1,'vg::SnarlManager']]],
- ['share_5fterminal_5fpositions_5521',['share_terminal_positions',['../classvg_1_1MultipathMapper.html#aaff4140e7e711a25b1eb284d7c830c2c',1,'vg::MultipathMapper']]],
- ['shift_5fprune_5fdiff_5522',['shift_prune_diff',['../classvg_1_1Surjector.html#a3768ca4fe69ba4c58cdbfe81343c56bd',1,'vg::Surjector']]],
- ['short_5fmem_5ffilter_5ffactor_5523',['short_mem_filter_factor',['../classvg_1_1BaseMapper.html#ac92eb174ad81e8714bf43e4b08aecdb9',1,'vg::BaseMapper']]],
- ['short_5fmode_5fname_5524',['short_mode_name',['../prune__main_8cpp.html#adf85e917657920f23dce6cefc2ecd2b9',1,'prune_main.cpp']]],
- ['short_5foption_5525',['short_option',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a60f696e33fce1e021b3454176ce0885f',1,'vg::subcommand::BaseArgSpec']]],
- ['short_5foptions_5526',['short_options',['../classvg_1_1ConfigurableParser.html#adfde71f165bbcb110831c12e862aa891',1,'vg::ConfigurableParser']]],
- ['short_5fopts_5527',['short_opts',['../classvg_1_1BaseOption.html#a04134150cfd3143bf1f43f55af5fd3d6',1,'vg::BaseOption']]],
- ['short_5fread_5fminimizer_5fk_5528',['short_read_minimizer_k',['../structvg_1_1IndexingParameters.html#a74ed1f6b8e93329efc15654c9eac5749',1,'vg::IndexingParameters']]],
- ['short_5fread_5fminimizer_5fw_5529',['short_read_minimizer_W',['../structvg_1_1IndexingParameters.html#a882b758e0f629a9cd2e9297b193c42df',1,'vg::IndexingParameters::short_read_minimizer_W()'],['../structvg_1_1IndexingParameters.html#acf0c2287ca7ee00853bd27af02757650',1,'vg::IndexingParameters::short_read_minimizer_w()']]],
- ['shortest_5fcycle_2ecpp_5530',['shortest_cycle.cpp',['../shortest__cycle_8cpp.html',1,'']]],
- ['shortest_5fcycle_2ehpp_5531',['shortest_cycle.hpp',['../shortest__cycle_8hpp.html',1,'']]],
- ['shortest_5fcycle_5flength_5532',['shortest_cycle_length',['../namespacevg_1_1algorithms.html#acfe6f985e8bedbad1b33861c62379772',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph, const handle_t &source)'],['../namespacevg_1_1algorithms.html#a012fced2754c445ec404ff5420018982',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph)']]],
- ['shortest_5fcycle_5flength_5finternal_5533',['shortest_cycle_length_internal',['../namespacevg_1_1algorithms.html#aa87ca8c58307fdb47d448deb2ec43389',1,'vg::algorithms']]],
- ['shortest_5fseq_5fpaths_5534',['shortest_seq_paths',['../classvg_1_1BandedGlobalAligner.html#a7156058732c9d6f40226609f650944a2',1,'vg::BandedGlobalAligner']]],
- ['show_5fcnv_5535',['show_cnv',['../classvg_1_1Viz.html#ace366df624ca2b225d3c8d20d9cb15db',1,'vg::Viz']]],
- ['show_5fdna_5536',['show_dna',['../classvg_1_1Viz.html#a2b8e6f510bca9925fd39e37feddce251',1,'vg::Viz']]],
- ['show_5fpath_5finfo_5537',['show_path_info',['../classvg_1_1Deconstructor.html#a6d2894dc3b9ea0fea97e2a78e11e2a51',1,'vg::Deconstructor']]],
- ['show_5fpaths_5538',['show_paths',['../classvg_1_1Viz.html#a501ab25fb94a4d3abd508af7bc77aac3',1,'vg::Viz']]],
- ['show_5fprogress_5539',['show_progress',['../structvg_1_1GBWTHandler.html#a7513df04845c0145e6933236346ec8fc',1,'vg::GBWTHandler::show_progress()'],['../structvg_1_1RebuildParameters.html#a4a86fbc222841919a70452f4a6e8c463',1,'vg::RebuildParameters::show_progress()'],['../classvg_1_1Genotyper.html#a72599c00acaed553e0d235e5c73d4b82',1,'vg::Genotyper::show_progress()'],['../classvg_1_1GraphCaller.html#a1179324159b5518ebd0eb7d5fb71edd5',1,'vg::GraphCaller::show_progress()'],['../classvg_1_1Progressive.html#a6653625f496832c4cb8711185d5e04cb',1,'vg::Progressive::show_progress()'],['../classvg_1_1Transcriptome.html#af92e5c3f2b2216b98f30f5518fc3b785',1,'vg::Transcriptome::show_progress()'],['../classvg_1_1VGset.html#aa848e2230f2d5c016c0a816cfa14501e',1,'vg::VGset::show_progress()'],['../structGBWTConfig.html#a075b0013542a10eb0708e94f20cb18a6',1,'GBWTConfig::show_progress()']]],
- ['show_5fstructure_5540',['show_structure',['../classvg_1_1Packer.html#a4aacf109dc6290d39630e5b25020004e',1,'vg::Packer']]],
- ['show_5fwork_5541',['show_work',['../classvg_1_1MinimizerMapper.html#a089bb5c8a56a7614a2f494690f3b5acd',1,'vg::MinimizerMapper']]],
- ['shuffledpairs_5542',['ShuffledPairs',['../classvg_1_1ShuffledPairs.html',1,'vg::ShuffledPairs'],['../classvg_1_1ShuffledPairs_1_1iterator.html#a716354d123e5197d160a8d6c4da7817d',1,'vg::ShuffledPairs::iterator::ShuffledPairs()'],['../classvg_1_1ShuffledPairs.html#a7143ff811c0359854ac091749b1f5642',1,'vg::ShuffledPairs::ShuffledPairs()']]],
- ['sibling_5findices_5fat_5fdepth_5543',['sibling_indices_at_depth',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a0c95aeef3ec92915788ebf083154e265',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['sides_5fcontext_5544',['sides_context',['../classvg_1_1VG.html#ad363c6c82e88dcb1b88d05ff55074ed6',1,'vg::VG']]],
- ['sides_5ffrom_5545',['sides_from',['../classvg_1_1VG.html#ac670f3c729f93ebaa7c8bd5063225597',1,'vg::VG::sides_from(NodeSide side)'],['../classvg_1_1VG.html#a95c975ed419a0873c894cef7a2f2d3ba',1,'vg::VG::sides_from(nid_t id)']]],
- ['sides_5fof_5546',['sides_of',['../classvg_1_1VG.html#a030b75d2ad50905cc01fe4b7223cbb83',1,'vg::VG']]],
- ['sides_5fto_5547',['sides_to',['../classvg_1_1VG.html#a1a156ac1e1fde520bae82850105c6c66',1,'vg::VG::sides_to(NodeSide side)'],['../classvg_1_1VG.html#a68733706482bf7b2627be32438160af3',1,'vg::VG::sides_to(nid_t id)']]],
- ['sift_5fmain_2ecpp_5548',['sift_main.cpp',['../sift__main_8cpp.html',1,'']]],
- ['sigma_5549',['sigma',['../classvg_1_1FragmentLengthDistribution.html#a6462bb11645a893b5dc2de057714d8f6',1,'vg::FragmentLengthDistribution']]],
- ['signature_5550',['signature',['../namespacevg.html#a2616dde2763b947a15ac562fd631e688',1,'vg::signature(const Alignment &aln)'],['../namespacevg.html#a134fc6762c4b66dd4847078b0ddbfdd6',1,'vg::signature(const Alignment &aln1, const Alignment &aln2)']]],
- ['sim_5fmain_2ecpp_5551',['sim_main.cpp',['../sim__main_8cpp.html',1,'']]],
- ['simple_5fcomponents_5552',['simple_components',['../namespacehandlegraph_1_1algorithms.html#acc16afc14f0a9dd0a34a4c173b229a4b',1,'handlegraph::algorithms']]],
- ['simple_5foffsets_5fin_5fpaths_5553',['simple_offsets_in_paths',['../namespacevg_1_1algorithms.html#a9ddb73ef3cf5a8891aa82001f272c3c4',1,'vg::algorithms']]],
- ['simple_5fsds_5fload_5554',['simple_sds_load',['../structvg_1_1Haplotypes_1_1Subchain.html#a9dfc087f0bada7635e975b6c8e8479a8',1,'vg::Haplotypes::Subchain::simple_sds_load()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a34163c2bf756a469dd6bba7880836f82',1,'vg::Haplotypes::TopLevelChain::simple_sds_load()'],['../classvg_1_1Haplotypes.html#a908ed1a2f1147a2162051be87e5ba389',1,'vg::Haplotypes::simple_sds_load()']]],
- ['simple_5fsds_5fserialize_5555',['simple_sds_serialize',['../structvg_1_1Haplotypes_1_1Subchain.html#ab30088a7f754d1bfb579773000ac73e0',1,'vg::Haplotypes::Subchain::simple_sds_serialize()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ad5f88539013b3d1c0caed224550e3a06',1,'vg::Haplotypes::TopLevelChain::simple_sds_serialize()'],['../classvg_1_1Haplotypes.html#a3a5a36c107109c893cf382064ad9ea69',1,'vg::Haplotypes::simple_sds_serialize()']]],
- ['simple_5fsds_5fsize_5556',['simple_sds_size',['../structvg_1_1Haplotypes_1_1Subchain.html#a5f1258caf8b13bd3880f2db6e2967908',1,'vg::Haplotypes::Subchain::simple_sds_size()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#afb004505c7fcc83e89b15c229da33a03',1,'vg::Haplotypes::TopLevelChain::simple_sds_size()'],['../classvg_1_1Haplotypes.html#ac0ebaa605235ee2b6f62c084cfdc6126',1,'vg::Haplotypes::simple_sds_size()']]],
- ['simpleconsistencycalculator_5557',['SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html',1,'vg']]],
- ['simpletraversalsupportcalculator_5558',['SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html',1,'vg']]],
- ['simplify_5559',['simplify',['../classvg_1_1RareVariantSimplifier.html#af17e24fe2acb6700bb7b6d39514af7af',1,'vg::RareVariantSimplifier::simplify()'],['../classvg_1_1SmallSnarlSimplifier.html#a9abe74e35298d7e22f13039a4c6ea5ba',1,'vg::SmallSnarlSimplifier::simplify()'],['../namespacevg.html#a486054f13a4dc43e37c0f0131f6a51ad',1,'vg::simplify(const Alignment &a, bool trim_internal_deletions)'],['../namespacevg.html#a86653c665afe3c8932f60cc39163e202',1,'vg::simplify(const Path &p, bool trim_internal_deletions)'],['../namespacevg.html#a9514446da89671007ae40e420c1297d7',1,'vg::simplify(const Mapping &m, bool trim_internal_deletions)']]],
- ['simplify_5fcigar_5560',['simplify_cigar',['../namespacevg.html#a553c3fcfd7de2e51f41a6f174c313947',1,'vg']]],
- ['simplify_5fcomplicated_5fmultipath_5falignment_5561',['simplify_complicated_multipath_alignment',['../classvg_1_1MultipathMapper.html#a92de908372ba0730cfe40638218d815f',1,'vg::MultipathMapper']]],
- ['simplify_5ffiltered_5fedits_5562',['simplify_filtered_edits',['../namespacevg.html#ad6a42e8ba843cd728b9f84738756b30e',1,'vg']]],
- ['simplify_5fmain_2ecpp_5563',['simplify_main.cpp',['../simplify__main_8cpp.html',1,'']]],
- ['simplify_5fonce_5564',['simplify_once',['../classvg_1_1SmallSnarlSimplifier.html#afc5525b90ddf851ee7d43a6476acd99d',1,'vg::SmallSnarlSimplifier']]],
- ['simplify_5fsiblings_5565',['simplify_siblings',['../namespacevg_1_1algorithms.html#a9e4cebdfc1e901db4588c4612653df96',1,'vg::algorithms']]],
- ['simplify_5fsiblings_2ecpp_5566',['simplify_siblings.cpp',['../simplify__siblings_8cpp.html',1,'']]],
- ['simplify_5fsiblings_2ehpp_5567',['simplify_siblings.hpp',['../simplify__siblings_8hpp.html',1,'']]],
- ['simplify_5ftopologies_5568',['simplify_topologies',['../classvg_1_1MultipathMapper.html#a5f865a27bd34ffce2e2ea1d05fc02b43',1,'vg::MultipathMapper']]],
- ['simultaneous_5fpair_5falignment_5569',['simultaneous_pair_alignment',['../classvg_1_1Mapper.html#ae83170a63789f8984e82e225486ca5bd',1,'vg::Mapper']]],
- ['since_5flast_5ffragment_5flength_5festimate_5570',['since_last_fragment_length_estimate',['../classvg_1_1FragmentLengthStatistics.html#ae79e46e68a3b9aa6c87863a6354c01a2',1,'vg::FragmentLengthStatistics']]],
- ['single_5fstranded_5forientation_5571',['single_stranded_orientation',['../namespacehandlegraph_1_1algorithms.html#a61255fd1513da53219871ea01283e360',1,'handlegraph::algorithms']]],
- ['sink_5ffwd_5572',['sink_fwd',['../classvg_1_1SourceSinkOverlay.html#a2718021aade5e48683cdc07c5d5b16f7',1,'vg::SourceSinkOverlay']]],
- ['sink_5fid_5573',['sink_id',['../classvg_1_1SourceSinkOverlay.html#a02ca8620a0e90dbf0190fe285d11a687',1,'vg::SourceSinkOverlay']]],
- ['sink_5fnodes_5574',['sink_nodes',['../classvg_1_1BandedGlobalAligner.html#ad3ba4ffebb1e61d6ce59a995eac74f68',1,'vg::BandedGlobalAligner']]],
- ['sink_5frev_5575',['sink_rev',['../classvg_1_1SourceSinkOverlay.html#a4c00143bd29d3f3adbf571f6333ea761',1,'vg::SourceSinkOverlay']]],
- ['site_5fends_5576',['site_ends',['../classvg_1_1PhasedGenome.html#afc338c2bf1776ec1ccb29c8efee6aaa3',1,'vg::PhasedGenome']]],
- ['site_5fmanager_5577',['site_manager',['../classvg_1_1SmallSnarlSimplifier.html#a4991294aedb029a70d1d4f459e009bd3',1,'vg::SmallSnarlSimplifier']]],
- ['site_5fstarts_5578',['site_starts',['../classvg_1_1PhasedGenome.html#accfaae53e12f924b914623734a68102f',1,'vg::PhasedGenome']]],
- ['sites_5579',['sites',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a7fee7818b260154898be386649d3bfe7',1,'vg::PhasedGenome::Haplotype']]],
- ['size_5580',['size',['../classvg_1_1algorithms_1_1Anchor.html#a96921a8307e8e97ba77869b58d6d7292',1,'vg::algorithms::Anchor::size()'],['../structjob__type.html#adbc606f42800cfce3697b017578356b9',1,'job_type::size()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#acdf72785ba0579f5985b227ef1ccd48b',1,'vg::DozeuInterface::OrderedGraph::size()'],['../structvg_1_1MatchPos_1_1PathList.html#aee5bea8ee39007b6bf5be7ea72d3695b',1,'vg::MatchPos::PathList::size()'],['../classvg_1_1WFATree.html#ad5da24b01eb588c58e07419dbd5eaca4',1,'vg::WFATree::size()'],['../classvg_1_1SnarlState.html#a02f1d46e384b6617ad43f2390fe0ef98',1,'vg::SnarlState::size()'],['../structhaplo_1_1int__itvl__t.html#acee0f4db1fc8cdfd535e6d181093f01f',1,'haplo::int_itvl_t::size()'],['../structhaplo_1_1gbwt__thread__t.html#a5d4d9e80558ff8e4dbab247cc9782a0c',1,'haplo::gbwt_thread_t::size()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a979f8d5623d9040439803c13e7ebf9b6',1,'haplo::linear_haplo_structure::SNVvector::size()'],['../classvg_1_1HandleGraphNodeSet.html#ae66b372aeb3110162c4d9b5c85e3a28d',1,'vg::HandleGraphNodeSet::size()'],['../classvg_1_1MultipathAlignmentGraph.html#a4ec09c91391cfb06c1c9eea132ce4246',1,'vg::MultipathAlignmentGraph::size()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a028494e0f37785dc8a39de6c4f2876a4',1,'vg::Option< vector< Item >, Parser >::size()'],['../classvg_1_1Paths.html#ac2fb517ea95acdd1eb378bf104c16912',1,'vg::Paths::size()'],['../classvg_1_1SmallBitset.html#a1b3ff28863a53eae0c4b47ff854b4d2d',1,'vg::SmallBitset::size()'],['../classvg_1_1SparseUnionFind.html#a85bfb663efac82a593533bd58890c615',1,'vg::SparseUnionFind::size()'],['../structvg_1_1VectorView.html#a62ec6d3c6520fa2b6d70a23abc473e44',1,'vg::VectorView::size()'],['../classvg_1_1VG.html#a9e3720ce267c8167ce679a015063dab6',1,'vg::VG::size()'],['../classvg_1_1ZipCodeCollection.html#ae1aab3360a759d00d8c43e921dba92f6',1,'vg::ZipCodeCollection::size()']]],
- ['size_5ft_5fis_5fnonzero_5581',['size_t_is_nonzero',['../namespacevg_1_1subcommand.html#a62e7f4f685f1aabc28ff82aa02f00f7f',1,'vg::subcommand']]],
- ['size_5ft_5fis_5fpositive_5582',['size_t_is_positive',['../namespacevg_1_1subcommand.html#ae20ec7174b0b153b2657c4931dcca448',1,'vg::subcommand']]],
- ['sizelimitexceededexception_5583',['SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html',1,'vg::SizeLimitExceededException'],['../classvg_1_1SizeLimitExceededException.html#aeb5d2801f912937112f0e638717156a8',1,'vg::SizeLimitExceededException::SizeLimitExceededException()']]],
- ['skip_5584',['Skip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#af3849b5292df406dec93738920615987',1,'vg::io::BlockedGzipInputStream']]],
- ['skip_5falt_5585',['skip_alt',['../classvg_1_1VCFTraversalFinder.html#acc753182667fd49d9afe5eba697c92da',1,'vg::VCFTraversalFinder']]],
- ['skip_5fstructural_5fduplications_5586',['skip_structural_duplications',['../classvg_1_1VariantAdder.html#a0c90a9845a662358588f517e2cf91501',1,'vg::VariantAdder']]],
- ['skippable_5587',['skippable',['../classvg_1_1algorithms_1_1Anchor.html#ade34685bea83f218a9756478bcca25a0',1,'vg::algorithms::Anchor']]],
- ['slope_5588',['slope',['../namespacevg.html#ad477b45059373004136e69022e802e0b',1,'vg']]],
- ['slug_5589',['SLUG',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa9c42a12326ffdacf390a8b88c9fe1804',1,'vg::subcommand']]],
- ['small_5590',['small',['../classvg_1_1SmallBitset.html#a8e787b217e48311220e91f7fd191fe14',1,'vg::SmallBitset']]],
- ['small_5fbitset_2ehpp_5591',['small_bitset.hpp',['../small__bitset_8hpp.html',1,'']]],
- ['small_5fsnarl_5fsimplifier_2ecpp_5592',['small_snarl_simplifier.cpp',['../small__snarl__simplifier_8cpp.html',1,'']]],
- ['small_5fsnarl_5fsimplifier_2ehpp_5593',['small_snarl_simplifier.hpp',['../small__snarl__simplifier_8hpp.html',1,'']]],
- ['smallbitset_5594',['SmallBitset',['../classvg_1_1SmallBitset.html',1,'vg::SmallBitset'],['../classvg_1_1SmallBitset.html#afcefdbe6a3f708ded8d874537ba0616f',1,'vg::SmallBitset::SmallBitset()'],['../classvg_1_1SmallBitset.html#a5c0e06b1e0482ff98adde62fdf9476f2',1,'vg::SmallBitset::SmallBitset(size_t n)'],['../classvg_1_1SmallBitset.html#ae09de51997e95c9c7c85650748e6d9ab',1,'vg::SmallBitset::SmallBitset(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#a59da25f6a4ae99cc7ff12936930ad5e3',1,'vg::SmallBitset::SmallBitset(SmallBitset &&another)']]],
- ['smallsnarlsimplifier_5595',['SmallSnarlSimplifier',['../classvg_1_1SmallSnarlSimplifier.html',1,'vg::SmallSnarlSimplifier'],['../classvg_1_1SmallSnarlSimplifier.html#ae19c2fcf37820ed9112671fbc7e64033',1,'vg::SmallSnarlSimplifier::SmallSnarlSimplifier()']]],
- ['smart_5falign_5596',['smart_align',['../classvg_1_1VariantAdder.html#ad3c7e7030142e70f27bc9f0bc42c2cce',1,'vg::VariantAdder']]],
- ['smellslikegzip_5597',['SmellsLikeGzip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa45ae9d5a0c1689efa567d573ad5747c',1,'vg::io::BlockedGzipInputStream']]],
- ['sn_5fdeletion_5fbetween_5fref_5598',['sn_deletion_between_ref',['../structhaplo_1_1linear__haplo__structure.html#aa6e425ddac2acb985a1364dd91a2f948',1,'haplo::linear_haplo_structure']]],
- ['snarl_5599',['Snarl',['../structvg_1_1Snarl.html',1,'vg::Snarl'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#aee85ad3c21e883f05b67c62fbf05be72',1,'vg::ReplaceSnarlHaplotypeCommand::snarl()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#acad9926afa69d4de3d5424ac1f03582d',1,'vg::SnarlManager::SnarlRecord::snarl()'],['../structvg_1_1Visit.html#a7e671bbc7437a16dd3549a6fc49fd2a9',1,'vg::Visit::snarl()']]],
- ['snarl_5fboundary_5findex_5600',['snarl_boundary_index',['../classvg_1_1SnarlManager.html#a77a449f2f85f37760da1a7182cc1e08b',1,'vg::SnarlManager']]],
- ['snarl_5fcaller_5601',['snarl_caller',['../classvg_1_1GraphCaller.html#a4b8c6f32019db8528bb6835fdce12ddb',1,'vg::GraphCaller']]],
- ['snarl_5fcaller_2ecpp_5602',['snarl_caller.cpp',['../snarl__caller_8cpp.html',1,'']]],
- ['snarl_5fcaller_2ehpp_5603',['snarl_caller.hpp',['../snarl__caller_8hpp.html',1,'']]],
- ['snarl_5fchain_5fcomponent_5foffset_5604',['SNARL_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#a807c487a518301d1726f87f7eda443a4',1,'vg::ZipCode']]],
- ['snarl_5fchild_5fcount_5foffset_5605',['SNARL_CHILD_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a37503629f90af0de452b6bc534ad43f5',1,'vg::ZipCode']]],
- ['snarl_5fcode_5ft_5606',['snarl_code_t',['../structvg_1_1ZipCode_1_1snarl__code__t.html',1,'vg::ZipCode']]],
- ['snarl_5fdecomposition_2ecpp_5607',['snarl_decomposition.cpp',['../snarl__decomposition_8cpp.html',1,'']]],
- ['snarl_5fdecomposition_2ehpp_5608',['snarl_decomposition.hpp',['../snarl__decomposition_8hpp.html',1,'']]],
- ['snarl_5fdistance_5findex_2ecpp_5609',['snarl_distance_index.cpp',['../snarl__distance__index_8cpp.html',1,'']]],
- ['snarl_5fdistance_5findex_2ehpp_5610',['snarl_distance_index.hpp',['../snarl__distance__index_8hpp.html',1,'']]],
- ['snarl_5fend_5611',['SNARL_END',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adaaa317dff9d3024c633f537d3b8b08cc7',1,'vg::ZipCodeTree']]],
- ['snarl_5fend_5findex_5612',['snarl_end_index',['../classvg_1_1SnarlManager.html#a1fd57d0de5eec34fc037ad0afbdfcb77',1,'vg::SnarlManager']]],
- ['snarl_5finto_5613',['snarl_into',['../classvg_1_1SnarlManager.html#a0f1d327aa074d59976802999d0d179d1',1,'vg::SnarlManager']]],
- ['snarl_5fis_5fregular_5foffset_5614',['SNARL_IS_REGULAR_OFFSET',['../classvg_1_1ZipCode.html#ad56c1879d223a2151795d2532932d1c8',1,'vg::ZipCode']]],
- ['snarl_5flength_5foffset_5615',['SNARL_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#ade2f247378ce48537e06399e215013d5',1,'vg::ZipCode']]],
- ['snarl_5fless_5616',['snarl_less',['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
- ['snarl_5fmanager_5617',['snarl_manager',['../classvg_1_1GraphCaller.html#a55afa68762956066ccbea2e332342266',1,'vg::GraphCaller::snarl_manager()'],['../classvg_1_1SnarlGraph.html#a292ca2c610a5f06fd06325f193557823',1,'vg::SnarlGraph::snarl_manager()'],['../classvg_1_1Masker.html#a4554deca5d95bdb68843ca7a656170fa',1,'vg::Masker::snarl_manager()'],['../classvg_1_1MCMCCaller.html#a4dad48c8bc658476ff4a6b0ed22817de',1,'vg::MCMCCaller::snarl_manager()'],['../classvg_1_1MultipathMapper.html#a82e1a1af4b8ba0170cf7817cd44f1008',1,'vg::MultipathMapper::snarl_manager()'],['../classvg_1_1NestedTraversalFinder.html#a3b15745919bd3bd7427d487eea14884b',1,'vg::NestedTraversalFinder::snarl_manager()'],['../classvg_1_1PhasedGenome.html#a56494287a449d9b95f24ac7d0e505522',1,'vg::PhasedGenome::snarl_manager()'],['../classvg_1_1RegionExpander.html#ac7c7121e538614d43356e7318769db65',1,'vg::RegionExpander::snarl_manager()'],['../classvg_1_1SupportBasedSnarlCaller.html#a86c40f2d62950d1f484aa6dd84abf60d',1,'vg::SupportBasedSnarlCaller::snarl_manager()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a8e29fb04ba5a9516d74d1da133f06330',1,'vg::ExhaustiveTraversalFinder::snarl_manager()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#a0c4e67f35a6f1e8536a81a781c7cba22',1,'vg::ReadRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a015de241431375a1b43ac32b852246f6',1,'vg::PathRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1RepresentativeTraversalFinder.html#a48de8b31240c6ddda7ff40164ae7708b',1,'vg::RepresentativeTraversalFinder::snarl_manager()'],['../classvg_1_1VCFTraversalFinder.html#ae2fac6aac1b86163b495ef183e3340d9',1,'vg::VCFTraversalFinder::snarl_manager()'],['../classvg_1_1FlowTraversalFinder.html#ab0f619b27f1f2d911e6625ab61ecddeb',1,'vg::FlowTraversalFinder::snarl_manager()'],['../classvg_1_1TraversalSupportFinder.html#adc97ab06de5c4aa553db92bae3879ee5',1,'vg::TraversalSupportFinder::snarl_manager()']]],
- ['snarl_5fnumber_5618',['snarl_number',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#add50ce54457a4031ed0d8fd0b3b34e9f',1,'vg::SnarlManager::SnarlRecord::snarl_number()'],['../classvg_1_1SnarlManager.html#aa779c0eaea2403d9c36761243a7f9262',1,'vg::SnarlManager::snarl_number()']]],
- ['snarl_5foffset_5fin_5fchain_5foffset_5619',['SNARL_OFFSET_IN_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a65ff5123c5439118b1b390179cffd818',1,'vg::ZipCode']]],
- ['snarl_5frank_5for_5fidentifier_5620',['snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4859d74d9e82058d5e6066dd0e99470e',1,'vg::ZipCode::chain_code_t']]],
- ['snarl_5freference_5flength_5fhistogram_5621',['snarl_reference_length_histogram',['../classvg_1_1Genotyper.html#ac0d4917131823fc2dab43927347d4623',1,'vg::Genotyper']]],
- ['snarl_5fseed_5fclusterer_2ecpp_5622',['snarl_seed_clusterer.cpp',['../snarl__seed__clusterer_8cpp.html',1,'']]],
- ['snarl_5fseed_5fclusterer_2ehpp_5623',['snarl_seed_clusterer.hpp',['../snarl__seed__clusterer_8hpp.html',1,'']]],
- ['snarl_5fsharing_5fend_5624',['snarl_sharing_end',['../classvg_1_1SnarlManager.html#a2ca9eb75908bfcc4cfac8b241236295b',1,'vg::SnarlManager']]],
- ['snarl_5fsharing_5fstart_5625',['snarl_sharing_start',['../classvg_1_1SnarlManager.html#a43ecf19c495295c45ca828d499651481',1,'vg::SnarlManager']]],
- ['snarl_5fstart_5626',['SNARL_START',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adad9686e72ac57aa50bd713fce51da5666',1,'vg::ZipCodeTree']]],
- ['snarl_5fstart_5findex_5627',['snarl_start_index',['../classvg_1_1SnarlManager.html#a10a771b6ada139c76e1b435ee301fdb8',1,'vg::SnarlManager']]],
- ['snarl_5ftraversals_5628',['snarl_traversals',['../classvg_1_1Genotyper.html#a7ec1915674299d727c61377e91385974',1,'vg::Genotyper']]],
- ['snarlcaller_5629',['SnarlCaller',['../classvg_1_1SnarlCaller.html',1,'vg']]],
- ['snarldecomposition_5630',['SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html',1,'handlegraph']]],
- ['snarldistanceindexclusterer_5631',['SnarlDistanceIndexClusterer',['../classvg_1_1SnarlDistanceIndexClusterer.html',1,'vg::SnarlDistanceIndexClusterer'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a0333d80b03665df71c7d448b7cfb0b06',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a66a56a78a0500f79258057cd3d688966',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a2275f78a71459c60e56929b106d4ed46',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#ae2d9080f0e9ddf775de34ae3aaab7019',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index)']]],
- ['snarlfinder_5632',['SnarlFinder',['../classvg_1_1SnarlFinder.html',1,'vg']]],
- ['snarlgraph_5633',['SnarlGraph',['../classvg_1_1SnarlGraph.html',1,'vg::SnarlGraph'],['../classvg_1_1SnarlGraph.html#a0a6e447620c3a37ca37345854330ffd3',1,'vg::SnarlGraph::SnarlGraph()']]],
- ['snarlmanager_5634',['SnarlManager',['../classvg_1_1SnarlManager.html',1,'vg::SnarlManager'],['../classvg_1_1PathBasedTraversalFinder.html#a905239f50078de78279dd9f0ff82faf3',1,'vg::PathBasedTraversalFinder::snarlmanager()'],['../classvg_1_1SnarlManager.html#a1037a2341484dc7b54a68cd7207d34b8',1,'vg::SnarlManager::SnarlManager(SnarlIterator begin, SnarlIterator end)'],['../classvg_1_1SnarlManager.html#a61b2b80def0128deea2d2da4886b955e',1,'vg::SnarlManager::SnarlManager(istream &in)'],['../classvg_1_1SnarlManager.html#afe16f481e15e098c885d63f47eceb59c',1,'vg::SnarlManager::SnarlManager(const function< void(const function< void(Snarl &)> &)> &for_each_snarl)'],['../classvg_1_1SnarlManager.html#a43b0ecd9e372556380231f29788948d5',1,'vg::SnarlManager::SnarlManager()=default'],['../classvg_1_1SnarlManager.html#a8e61adc170e3d9241a723ca7593883da',1,'vg::SnarlManager::SnarlManager(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#a7549f1ed7e0e02ae36f172ab5f1d3dbd',1,'vg::SnarlManager::SnarlManager(SnarlManager &&other)=default']]],
- ['snarlmindistance_5635',['SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html',1,'vg::SnarlMinDistance'],['../classvg_1_1SnarlMinDistance.html#adc8c303e683b90d923c522790355abad',1,'vg::SnarlMinDistance::SnarlMinDistance()=delete'],['../classvg_1_1SnarlMinDistance.html#aa8efbd4c363589a72da76621b5b4330d',1,'vg::SnarlMinDistance::SnarlMinDistance(SnarlDistanceIndex &distance_index)']]],
- ['snarlorienteddistancemeasurer_5636',['SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html',1,'vg::SnarlOrientedDistanceMeasurer'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a81db285adff1ae830dcaf2511652e17a',1,'vg::SnarlOrientedDistanceMeasurer::SnarlOrientedDistanceMeasurer()']]],
- ['snarlrecord_5637',['SnarlRecord',['../structvg_1_1SnarlManager_1_1SnarlRecord.html',1,'vg::SnarlManager']]],
- ['snarls_5638',['snarls',['../classvg_1_1SnarlGraph.html#ac9db23e9d10f3c39f25a5397afb9d4fa',1,'vg::SnarlGraph::snarls()'],['../classvg_1_1MCMCGenotyper.html#a23913225e8b2d0d4dfbdb713ccf495c3',1,'vg::MCMCGenotyper::snarls()'],['../classvg_1_1SnarlManager.html#ab56cf756bc65189eeb1d4f1f3f6573b6',1,'vg::SnarlManager::snarls()']]],
- ['snarls_2ecpp_5639',['snarls.cpp',['../snarls_8cpp.html',1,'']]],
- ['snarls_2ehpp_5640',['snarls.hpp',['../snarls_8hpp.html',1,'']]],
- ['snarls_5fmain_2ecpp_5641',['snarls_main.cpp',['../snarls__main_8cpp.html',1,'']]],
- ['snarlstate_5642',['SnarlState',['../classvg_1_1SnarlState.html',1,'vg::SnarlState'],['../classvg_1_1SnarlState.html#a14db6ed9f20936f71de90d0d12f92468',1,'vg::SnarlState::SnarlState()']]],
- ['snarltraversal_5643',['SnarlTraversal',['../structvg_1_1SnarlTraversal.html',1,'vg']]],
- ['snarltreechild_5644',['SnarlTreeChild',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['snarltreenodeproblem_5645',['SnarlTreeNodeProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a119a5148780cd1bf7dd073e91974f255',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, const SnarlDistanceIndex &distance_index, const SeedCache *seed, size_t zipcode_depth)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a26ebc81ba9dff9a498a2d222ff72291c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, bool is_reversed_in_parent, size_t node_length, size_t prefix_sum, size_t component, const SeedCache *seed, size_t zipcode_depth)']]],
- ['snarltype_5646',['SnarlType',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97',1,'vg']]],
- ['sniff_5fmagic_5647',['sniff_magic',['../classvg_1_1io_1_1Registry.html#aea2d7b2c4852a48417eeac861974b9c1',1,'vg::io::Registry']]],
- ['sniff_5ftag_5648',['sniff_tag',['../classvg_1_1io_1_1MessageIterator.html#ac9b3fff8dbbff744fe1ff60805af1c20',1,'vg::io::MessageIterator::sniff_tag(istream &stream)'],['../classvg_1_1io_1_1MessageIterator.html#aabd024a7358bae988de897aebff39645',1,'vg::io::MessageIterator::sniff_tag(::google::protobuf::io::ZeroCopyInputStream &stream)']]],
- ['snv_5649',['snv',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a80993050ce71b03df8d926cbe0cde822',1,'haplo::linear_haplo_structure']]],
- ['snvs_5650',['SNVs',['../structhaplo_1_1linear__haplo__structure.html#acde3b4cb1fc9eae479ee626bb0916992',1,'haplo::linear_haplo_structure']]],
- ['snvvector_5651',['SNVvector',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html',1,'haplo::linear_haplo_structure']]],
- ['soft_5fclip_5ffilter_5652',['soft_clip_filter',['../classvg_1_1Filter.html#aff62aad43f70cd8de756bdbdf94b962d',1,'vg::Filter']]],
- ['soft_5fclip_5flimit_5653',['soft_clip_limit',['../classvg_1_1Filter.html#abe44432fa541eee27db7789cc9db066b',1,'vg::Filter']]],
- ['soft_5fclipped_5654',['soft_clipped',['../structvg_1_1Alignment.html#a6cb12eae3f4fa017bc98b59a91a5414f',1,'vg::Alignment']]],
- ['softclip_5fend_5655',['softclip_end',['../namespacevg.html#a05d6d0388148a996d9423524fa4bcc91',1,'vg::softclip_end(const Alignment &alignment)'],['../namespacevg.html#aa84e4c417206a9b3a910dfde0fec3857',1,'vg::softclip_end(const Mapping &mapping)']]],
- ['softclip_5fstart_5656',['softclip_start',['../namespacevg.html#a90f2af92a34fdf5fb4ddfee8f8880b48',1,'vg::softclip_start(const Alignment &alignment)'],['../namespacevg.html#a9fe66eebecbc5017b05c9044413b2b4e',1,'vg::softclip_start(const Mapping &mapping)']]],
- ['softclip_5fthreshold_5657',['softclip_threshold',['../classvg_1_1Mapper.html#a4320fc9bb3cda3bd7b25ebc5b8644d80',1,'vg::Mapper']]],
- ['softclip_5ftrim_5658',['softclip_trim',['../namespacevg.html#a947760b26fa8669d55f2f420174a578c',1,'vg']]],
- ['sort_5659',['sort',['../classvg_1_1StreamSorter.html#a8372ac35036ca7723bfc90a686115166',1,'vg::StreamSorter::sort()'],['../classvg_1_1VG.html#a902d516631c77d074aa2a11ae70a6957',1,'vg::VG::sort()']]],
- ['sort_5fanchor_5findexes_5660',['sort_anchor_indexes',['../namespacevg_1_1algorithms.html#aaeeaa766337fc50f0a9b4d3214271923',1,'vg::algorithms']]],
- ['sort_5fand_5fcompute_5fmapping_5fquality_5661',['sort_and_compute_mapping_quality',['../classvg_1_1MultipathMapper.html#a2994778198719e960d1a2875fa0815e8',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< multipath_alignment_t > &multipath_alns, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#afcc5ceaad2a3f21c4c38beb05c59f474',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< pair< size_t, size_t >> *duplicate_pairs_out=nullptr, vector< double > *pair_multiplicities=nullptr) const']]],
- ['sort_5fby_5fchain_5fscore_5662',['sort_by_chain_score',['../classvg_1_1MinimizerMapper.html#a1006ffeadb8f60e819d8cfbf24e33109',1,'vg::MinimizerMapper']]],
- ['sort_5fby_5fid_5663',['sort_by_id',['../namespacevg.html#af25c227066a422379ff06d81b5990865',1,'vg']]],
- ['sort_5fby_5fid_5fdedup_5fand_5fclean_5664',['sort_by_id_dedup_and_clean',['../namespacevg.html#a984c1d2199f90f58677096772b870390',1,'vg']]],
- ['sort_5fby_5fmapping_5frank_5665',['sort_by_mapping_rank',['../classvg_1_1Paths.html#a2970302cae3a54ef7f4296dbf49266fd',1,'vg::Paths']]],
- ['sort_5fcompact_5fnodes_5666',['sort_compact_nodes',['../classvg_1_1Transcriptome.html#af7de0784cde3273b344757b81d9bffd5',1,'vg::Transcriptome']]],
- ['sort_5fedges_5fby_5fid_5667',['sort_edges_by_id',['../namespacevg.html#a90cc117e3ac781c77cf8fdaa7802048b',1,'vg']]],
- ['sort_5fmain_2ecpp_5668',['sort_main.cpp',['../sort__main_8cpp.html',1,'']]],
- ['sort_5fminimizers_5fby_5fscore_5669',['sort_minimizers_by_score',['../classvg_1_1MinimizerMapper.html#ad72222c1d644b6f676c91511b4b36789',1,'vg::MinimizerMapper']]],
- ['sort_5fnodes_5fby_5fid_5670',['sort_nodes_by_id',['../namespacevg.html#afb37b16823e6e26cfd8571a1bb621651',1,'vg']]],
- ['sort_5fone_5finterval_5671',['sort_one_interval',['../classvg_1_1ZipCodeForest.html#a499f52fbb75374e2dc06ce7998ad8fd6',1,'vg::ZipCodeForest']]],
- ['sort_5fpair_5fby_5fsecond_5672',['sort_pair_by_second',['../namespacevg.html#a47c7102baf9a07b2c701e9937d53351f',1,'vg']]],
- ['sort_5fpath_5foffsets_5673',['sort_path_offsets',['../namespacevg_1_1algorithms.html#ad8e5913b682c7c14f119543eca7e7548',1,'vg::algorithms']]],
- ['sort_5fpermutation_5674',['sort_permutation',['../namespacevg.html#ae031408254f8c4031ba0b632f5456059',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end, const std::function< bool(const typename Iterator::value_type &, const typename Iterator::value_type &)> &comparator)'],['../namespacevg.html#ab03fad9d3c71a090606afbe1ef22ce71',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end)']]],
- ['sort_5fshuffling_5fties_5675',['sort_shuffling_ties',['../namespacevg.html#afe3de0ca79c815a4eaf63df34805f6d0',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp, LazyRNG &rng)'],['../namespacevg.html#aa071bccfee3a9078930f2c385e8dda20',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp)']]],
- ['sort_5ftranscript_5fpaths_5fby_5fname_5676',['sort_transcript_paths_by_name',['../namespacevg.html#aaddbcf35ad2ff899bf2ae0caf901f778',1,'vg']]],
- ['sort_5ftranscript_5fpaths_5fupdate_5fcopy_5fid_5677',['sort_transcript_paths_update_copy_id',['../classvg_1_1Transcriptome.html#af8caf627ac2480d7439231a2d26162eb',1,'vg::Transcriptome']]],
- ['sort_5fvalue_5678',['sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a0c2510fe5ebea3b2a8cc9105e5a9d9fc',1,'vg::ZipCodeForest::sort_value_t']]],
- ['sort_5fvalue_5ft_5679',['sort_value_t',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html',1,'vg::ZipCodeForest::sort_value_t'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ac93c5ff7c1b231cd78122b1e1f009aae',1,'vg::ZipCodeForest::sort_value_t::sort_value_t()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a42776d8b3810278dfb5830307fe8190c',1,'vg::ZipCodeForest::sort_value_t::sort_value_t(size_t sort_value, ZipCode::code_type_t code_type, size_t chain_order)']]],
- ['sort_5fvalues_5fby_5fseed_5680',['sort_values_by_seed',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a94161554748068a953a678af49bc31b7',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['sorted_5fid_5franges_5681',['sorted_id_ranges',['../namespacevg_1_1algorithms.html#a64bd6b3ff0d2e22bf752e29e3522a98d',1,'vg::algorithms']]],
- ['sorted_5fid_5franges_2ecpp_5682',['sorted_id_ranges.cpp',['../sorted__id__ranges_8cpp.html',1,'']]],
- ['sorted_5fid_5franges_2ehpp_5683',['sorted_id_ranges.hpp',['../sorted__id__ranges_8hpp.html',1,'']]],
- ['source_5684',['source',['../structvg_1_1GFFRecord.html#a5bc594d1d69edca2081740dcc5e27bbf',1,'vg::GFFRecord::source()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a440d7f98f38d52de226e584f88784381',1,'vg::SnarlDistanceIndexClusterer::Seed::source()'],['../classvg_1_1algorithms_1_1TracedScore.html#aefa6367efc91b8d4e0964cd66e4f51d7',1,'vg::algorithms::TracedScore::source()']]],
- ['source_5ffwd_5685',['source_fwd',['../classvg_1_1SourceSinkOverlay.html#ae2d7c52a07eeef273ad95972c158c940',1,'vg::SourceSinkOverlay']]],
- ['source_5fid_5686',['source_id',['../classvg_1_1SourceSinkOverlay.html#a3bc0ab05f0048a8a6b8a31055b3d35c0',1,'vg::SourceSinkOverlay']]],
- ['source_5fnodes_5687',['source_nodes',['../classvg_1_1BandedGlobalAligner.html#a15f4ae7556005bd51512b6be93112291',1,'vg::BandedGlobalAligner']]],
- ['source_5fpaths_5688',['source_paths',['../classvg_1_1Sampler.html#aea2c52dbdae36a6729621fe3279c2d61',1,'vg::Sampler::source_paths()'],['../classvg_1_1NGSSimulator.html#ac377f66a4c6d84f5cb660950d56022ff',1,'vg::NGSSimulator::source_paths()']]],
- ['source_5frev_5689',['source_rev',['../classvg_1_1SourceSinkOverlay.html#a4ad14a56e07ef3fdc3a0346f4f6e0e05',1,'vg::SourceSinkOverlay']]],
- ['source_5fsink_5foverlay_2ecpp_5690',['source_sink_overlay.cpp',['../source__sink__overlay_8cpp.html',1,'']]],
- ['source_5fsink_5foverlay_2ehpp_5691',['source_sink_overlay.hpp',['../source__sink__overlay_8hpp.html',1,'']]],
- ['sourcesinkoverlay_5692',['SourceSinkOverlay',['../classvg_1_1SourceSinkOverlay.html',1,'vg::SourceSinkOverlay'],['../classvg_1_1SourceSinkOverlay.html#a6eaf260d8530ba866753bb3bcb612e15',1,'vg::SourceSinkOverlay::SourceSinkOverlay()']]],
- ['space_5fefficient_5fcounting_5693',['space_efficient_counting',['../structvg_1_1IndexingParameters.html#ad22ab98cf3f06bb2c033578dc15ae49e',1,'vg::IndexingParameters']]],
- ['sparse_5fto_5fdense_5694',['sparse_to_dense',['../classvg_1_1SparseUnionFind.html#a4c161121ec4681cee764e1c261af865d',1,'vg::SparseUnionFind']]],
- ['sparse_5funion_5ffind_2ecpp_5695',['sparse_union_find.cpp',['../sparse__union__find_8cpp.html',1,'']]],
- ['sparse_5funion_5ffind_2ehpp_5696',['sparse_union_find.hpp',['../sparse__union__find_8hpp.html',1,'']]],
- ['sparseunionfind_5697',['SparseUnionFind',['../classvg_1_1SparseUnionFind.html',1,'vg::SparseUnionFind'],['../classvg_1_1SparseUnionFind.html#aabd42adac47a3df51b0dfb55d7cde0f4',1,'vg::SparseUnionFind::SparseUnionFind()']]],
- ['splice_5frescue_5fgraph_5fstd_5fdevs_5698',['splice_rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#a0fcadd278d752aba5c9bb143f5f3a0d6',1,'vg::MultipathMapper']]],
- ['splice_5fstats_5699',['splice_stats',['../classvg_1_1MultipathMapper.html#a64556e12bae6880e876d0d16fe44efb9',1,'vg::MultipathMapper']]],
- ['spliced_5fcigar_5fagainst_5fpath_5700',['spliced_cigar_against_path',['../classvg_1_1SplicedHTSAlignmentEmitter.html#ac447d6f996b11f12c3b8b2267ff4110e',1,'vg::SplicedHTSAlignmentEmitter']]],
- ['spliced_5fdefault_5fsubgraph_5flimit_5701',['SPLICED_DEFAULT_SUBGRAPH_LIMIT',['../classvg_1_1Surjector.html#a8af3e56b9463fbbf483e78477f4a7172',1,'vg::Surjector']]],
- ['spliced_5fsurject_5702',['spliced_surject',['../classvg_1_1Surjector.html#a8418e7a55b6b53456c80cbcf937406b5',1,'vg::Surjector']]],
- ['splicedhtsalignmentemitter_5703',['SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html',1,'vg::SplicedHTSAlignmentEmitter'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#a8e546a34b4f2155fe6fb916123a0135d',1,'vg::SplicedHTSAlignmentEmitter::SplicedHTSAlignmentEmitter()']]],
- ['spliceregion_5704',['SpliceRegion',['../classvg_1_1SpliceRegion.html',1,'vg::SpliceRegion'],['../classvg_1_1SpliceRegion.html#a3ca49fd7bedbe0b97117f87f7a5edba4',1,'vg::SpliceRegion::SpliceRegion(const pos_t &seed_pos, bool search_left, int64_t search_dist, const HandleGraph &graph, const DinucleotideMachine &dinuc_machine, const SpliceStats &splice_stats)'],['../classvg_1_1SpliceRegion.html#a5935bbc5e17cceae08ee9ef0b91b9abe',1,'vg::SpliceRegion::SpliceRegion()=default']]],
- ['splicestats_5705',['SpliceStats',['../classvg_1_1SpliceStats.html',1,'vg::SpliceStats'],['../classvg_1_1SpliceStats.html#ac508ff2143cf8296531945e7674702bc',1,'vg::SpliceStats::SpliceStats(const GSSWAligner &scorer)'],['../classvg_1_1SpliceStats.html#a1808c3a4e73d0be56de7caca04142b01',1,'vg::SpliceStats::SpliceStats(const vector< tuple< string, string, double >> &motifs, const vector< double > &lognormal_mixture_weights, const vector< pair< double, double >> &lognormal_component_params, const GSSWAligner &scorer)']]],
- ['splicestrand_5706',['SpliceStrand',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccd',1,'vg::MultipathMapper']]],
- ['splicing_2ecpp_5707',['splicing.cpp',['../splicing_8cpp.html',1,'']]],
- ['splicing_2ehpp_5708',['splicing.hpp',['../splicing_8hpp.html',1,'']]],
- ['split_5709',['split',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aaf22613489ec859693457e82fd026e3b',1,'vg::Counts::split()'],['../classvg_1_1BitString.html#af826e3c7bce1aeada3f989b1b7d1bcc5',1,'vg::BitString::split()']]],
- ['split_5fdelims_5710',['split_delims',['../namespacevg.html#acb2577b9163299f775898c17bcd3f72d',1,'vg::split_delims(const std::string &s, const std::string &delims, std::vector< std::string > &elems, size_t max_cuts)'],['../namespacevg.html#a335fce1edcad06f9840edcfad2c53e34',1,'vg::split_delims(const std::string &s, const std::string &delims, size_t max_cuts)']]],
- ['split_5fext_5711',['split_ext',['../namespacevg.html#a984d142cea24f43a1025bf7bb7b48a53',1,'vg']]],
- ['split_5fmulticomponent_5falignments_5712',['split_multicomponent_alignments',['../classvg_1_1MultipathMapper.html#af91f97b8331648b4df7587a461ca36b2',1,'vg::MultipathMapper::split_multicomponent_alignments(vector< multipath_alignment_t > &multipath_alns_out, const Alignment *alignment=nullptr, vector< clustergraph_t > *cluster_graphs=nullptr, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#a9257a7f9cc75ddd76a8daef803f2d031',1,'vg::MultipathMapper::split_multicomponent_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &multiplicities) const']]],
- ['split_5fread_5ffilter_5713',['split_read_filter',['../classvg_1_1Filter.html#a0bc2a72604a0cb134c1f5bad7889a1bf',1,'vg::Filter']]],
- ['split_5fread_5flimit_5714',['split_read_limit',['../classvg_1_1Filter.html#a0a0eca1fab7afdaec1d6311116dfe4a4',1,'vg::Filter']]],
- ['split_5fsplice_5fsegment_5715',['split_splice_segment',['../namespacevg.html#aee945465384e60bdda619684ffca2ece',1,'vg']]],
- ['split_5fstrand_5fgraph_2ecpp_5716',['split_strand_graph.cpp',['../split__strand__graph_8cpp.html',1,'']]],
- ['split_5fstrand_5fgraph_2ehpp_5717',['split_strand_graph.hpp',['../split__strand__graph_8hpp.html',1,'']]],
- ['split_5fstrands_5718',['split_strands',['../namespacehandlegraph_1_1algorithms.html#a1a7504e7155f6f9726c772a4b7c0f2c7',1,'handlegraph::algorithms']]],
- ['split_5fstrands_2ecpp_5719',['split_strands.cpp',['../split__strands_8cpp.html',1,'']]],
- ['split_5fsupports_5720',['split_supports',['../structvg_1_1BREAKPOINT.html#ad93eef0590346c5658ceb194c78204c5',1,'vg::BREAKPOINT']]],
- ['ssw_5faligner_2ecpp_5721',['ssw_aligner.cpp',['../ssw__aligner_8cpp.html',1,'']]],
- ['ssw_5faligner_2ehpp_5722',['ssw_aligner.hpp',['../ssw__aligner_8hpp.html',1,'']]],
- ['ssw_5fto_5fvg_5723',['ssw_to_vg',['../classvg_1_1SSWAligner.html#a8daaaa17b12f1283c006d633d4c9a8fa',1,'vg::SSWAligner']]],
- ['sswaligner_5724',['SSWAligner',['../classvg_1_1SSWAligner.html',1,'vg::SSWAligner'],['../classvg_1_1SSWAligner.html#ae91911b3a1357b0d3ae9bcecd51a592a',1,'vg::SSWAligner::SSWAligner()']]],
- ['stack_5725',['stack',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa26ad54b66a37b0f31fa846c48d59882',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['stack_5fdata_5726',['stack_data',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a8c90da41cf4a8c9beb5794ce8bb0bd1c',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['stack_5fpermutations_5727',['stack_permutations',['../namespacevg.html#a5e9c563a243faef4e5357eca9c7c8500',1,'vg']]],
- ['stack_5fup_5fvalid_5fwalks_5728',['stack_up_valid_walks',['../classvg_1_1ExhaustiveTraversalFinder.html#ab37a28d916291506bfe78a6818943585',1,'vg::ExhaustiveTraversalFinder']]],
- ['stacktrace_5fmanually_5729',['stacktrace_manually',['../namespacevg.html#a8d771862cc44504508267240462cb043',1,'vg']]],
- ['stage_5730',['Stage',['../structvg_1_1Funnel_1_1Stage.html',1,'vg::Funnel::Stage'],['../classvg_1_1Funnel.html#a21b5f8762aa446a64b5ddb3809e5c8e2',1,'vg::Funnel::stage(const string &name)']]],
- ['stage_5fname_5731',['stage_name',['../classvg_1_1Funnel.html#a832c7d0be58aa6fa1e8dd8e7780e6850',1,'vg::Funnel']]],
- ['stage_5fstart_5ftime_5732',['stage_start_time',['../classvg_1_1Funnel.html#a74a7f57094e7e1a8040ed9df34932aee',1,'vg::Funnel']]],
- ['stage_5fstop_5733',['stage_stop',['../classvg_1_1Funnel.html#a87e1b8deccb4438d7f71267ee5f12ced',1,'vg::Funnel']]],
- ['stages_5734',['stages',['../classvg_1_1Funnel.html#a48bdc3457d5f66a3f454bcde8d42883e',1,'vg::Funnel']]],
- ['standard_5fextend_5735',['standard_extend',['../structhaplo_1_1haplo__DP__column.html#a5364cc0f365e68434e346c2b48eea996',1,'haplo::haplo_DP_column']]],
- ['standard_5flibrary_5736',['STANDARD_LIBRARY',['../classvg_1_1Version.html#a679d78a021abc99f587596a38e2fbf84',1,'vg::Version']]],
- ['star_5fallele_5737',['star_allele',['../classvg_1_1Deconstructor.html#a11591e3c8e54882b5c695f691cec6a62',1,'vg::Deconstructor']]],
- ['start_5738',['START',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3ab5854c3018055ccefae586f717850711',1,'handlegraph::SnarlDecomposition::START()'],['../structvg_1_1BREAKPOINT.html#a624e7af692ef989d559a3e14e5075d4b',1,'vg::BREAKPOINT::start()'],['../structvg_1_1GFFRecord.html#a1515c4a06b600c34d84b012b0195423a',1,'vg::GFFRecord::start()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#af564269e9eaf8eb68f4c4c3ce1ba3932',1,'vg::GraphSynchronizer::Lock::start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af3baaf52c08ac684ac2571a9f4f56ec0',1,'vg::Haplotypes::Subchain::start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a16932e227f0ac0972fb63bc300a5374d',1,'vg::HaplotypePartitioner::Subchain::start()'],['../structvg_1_1Region.html#a3905a368a833ae5f090f3faafa1b55bc',1,'vg::Region::start()'],['../classvg_1_1NetGraph.html#a2d7b0b659aae1f47312bb76aae43dda0',1,'vg::NetGraph::start()'],['../classvg_1_1algorithms_1_1Anchor.html#a67c31c873448badab1dab33385f290bc',1,'vg::algorithms::Anchor::start()'],['../structMappingRun.html#ae556594581cecb906e1972405df7c460',1,'MappingRun::start()'],['../structReferenceInterval.html#aaeb76d7fd3436409b6bf5500350527dd',1,'ReferenceInterval::start()'],['../structvg_1_1Range.html#a372fbc9ba00e9eb4785fcd049b2451cf',1,'vg::Range::start()'],['../structgafkluge_1_1GafStep.html#abd90c68888f2f19e733a03597e520d2f',1,'gafkluge::GafStep::start()'],['../structvg_1_1MultipathAlignment.html#a8003b8991108e99465d8fd80fc74cc03',1,'vg::MultipathAlignment::start()'],['../structvg_1_1Snarl.html#a2a35b60b251ab2d8429b6afcd387448f',1,'vg::Snarl::start()'],['../classvg_1_1Funnel.html#a4ba2b8db1575820b05d069cd6c802e31',1,'vg::Funnel::start()'],['../classvg_1_1multipath__alignment__t.html#a4cd9b91704e89c799019d9c8962b16bb',1,'vg::multipath_alignment_t::start() const'],['../classvg_1_1multipath__alignment__t.html#ae79344b60aed1577a39391b4b42574f3',1,'vg::multipath_alignment_t::start(size_t i) const']]],
- ['start_5fbackward_5739',['start_backward',['../namespacevg.html#a43f061abac718e0386965aa537398e74',1,'vg']]],
- ['start_5fdegree_5740',['start_degree',['../classvg_1_1VG.html#a1ff00edd627e3445eee7f43927bb1518',1,'vg::VG']]],
- ['start_5fend_5freachable_5741',['start_end_reachable',['../structvg_1_1Snarl.html#acab3c449de2871769eb9a39ba5f9b8f8',1,'vg::Snarl']]],
- ['start_5fhandle_5742',['start_handle',['../structvg_1_1Haplotypes_1_1Subchain.html#a8b8950af5c76b20ab93ef40dc086da93',1,'vg::Haplotypes::Subchain']]],
- ['start_5fhint_5743',['start_hint',['../classvg_1_1algorithms_1_1Anchor.html#a1be30d40d8252c36c162bfbb568554a1',1,'vg::algorithms::Anchor']]],
- ['start_5fhint_5foffset_5744',['start_hint_offset',['../classvg_1_1algorithms_1_1Anchor.html#afe9a192ac276676633aab322189732b0',1,'vg::algorithms::Anchor']]],
- ['start_5foffset_5745',['start_offset',['../classvg_1_1algorithms_1_1Anchor.html#af25f1f44ad6e51d8f5d318a9b2d816f9',1,'vg::algorithms::Anchor']]],
- ['start_5fpos_5746',['start_pos',['../classvg_1_1MEMClusterer_1_1HitNode.html#ac1772330432b54080ac41ec1a4302d8d',1,'vg::MEMClusterer::HitNode::start_pos()'],['../classvg_1_1algorithms_1_1Anchor.html#a78487c55bbc790fc1f2a05396ded3530',1,'vg::algorithms::Anchor::start_pos()']]],
- ['start_5fpos_5fsamplers_5747',['start_pos_samplers',['../classvg_1_1NGSSimulator.html#abe06d132967858ffa36a6f5235a506f2',1,'vg::NGSSimulator']]],
- ['start_5fseed_5748',['start_seed',['../classvg_1_1algorithms_1_1Anchor.html#a3eb9aa25a9ead7787d829468c571bdd0',1,'vg::algorithms::Anchor']]],
- ['start_5fself_5freachable_5749',['start_self_reachable',['../structvg_1_1Snarl.html#a9a2de860018e3c8cfd512f6a1904f18c',1,'vg::Snarl']]],
- ['start_5fsize_5750',['start_size',['../classvg_1_1multipath__alignment__t.html#a8155e732811cdcc1e6fcee417b25bf10',1,'vg::multipath_alignment_t']]],
- ['start_5ftime_5751',['start_time',['../classvg_1_1Funnel.html#af72a0ecffb7bd38fcd89ee3c71dd638b',1,'vg::Funnel']]],
- ['start_5fvcf_5752',['start_vcf',['../classvg_1_1Genotyper.html#a8a5aed6de86a488fe78a223d5e4d6bd6',1,'vg::Genotyper']]],
- ['start_5fzip_5753',['start_zip',['../classvg_1_1algorithms_1_1Anchor.html#a7cd7ad6f5f36dfb5c760ac995a258d88',1,'vg::algorithms::Anchor']]],
- ['startfile_5754',['StartFile',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaf788a0a0553f9cc0c531fecb941f228',1,'vg::io::BlockedGzipOutputStream']]],
- ['starting_5fposition_5755',['starting_position',['../structvg_1_1GaplessExtension.html#a2dc9687b1ac33335f593028c981fe494',1,'vg::GaplessExtension']]],
- ['starts_5fat_5756',['starts_at',['../classhandlegraph_1_1SnarlDecomposition.html#ac6bb78bc95acfd353ff8d6c44915e524',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fat_5fend_5757',['starts_at_end',['../classhandlegraph_1_1SnarlDecomposition.html#aab710270e1997f22d1b09a4fd40a3eaf',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fat_5fstart_5758',['starts_at_start',['../classhandlegraph_1_1SnarlDecomposition.html#adb1c7cccea8188c8e24a4e53c34117bb',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fat_5ftip_5759',['starts_at_tip',['../classhandlegraph_1_1SnarlDecomposition.html#ac47bc288b1c0303d3356e953de4878e2',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fwith_5760',['starts_with',['../namespacevg.html#a7b58d5d004a85a09906301781567970a',1,'vg']]],
- ['stat_5fcollection_5ft_5761',['stat_collection_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['stat_5fset_5ft_5762',['stat_set_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['state_5763',['state',['../structvg_1_1WFANode.html#ac59b2dd030133cc65cc0bf47af486ef0',1,'vg::WFANode::state()'],['../structvg_1_1GaplessExtension.html#a1b799cab247ae9b2551e902a9f7f2b25',1,'vg::GaplessExtension::state()'],['../classvg_1_1GenomeState.html#ab0f68d58776dcd18a1ef85409a29e452',1,'vg::GenomeState::state()'],['../structhaplo_1_1haplo__DP__rectangle.html#aff798553a0dfd177413b1649e049e574',1,'haplo::haplo_DP_rectangle::state()'],['../classvg_1_1Watchdog.html#a0cecf66da11a5f71e837a9d1b6f6c291',1,'vg::Watchdog::state()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4a2a145b0221202c440cca81c0ba89c9',1,'vg::ZipCodeTree::reverse_iterator::state()'],['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85',1,'vg::Funnel::State()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19',1,'vg::ZipCodeTree::reverse_iterator::State()']]],
- ['state_5fhash_5764',['state_hash',['../structvg_1_1state__hash.html',1,'vg']]],
- ['state_5ftype_5765',['state_type',['../classvg_1_1PhaseUnfolder.html#a95529e399d5ef61f6a426e1b5cfe9237',1,'vg::PhaseUnfolder']]],
- ['states_5766',['states',['../classvg_1_1PhaseUnfolder.html#ac7d3333de41989b2ca10db84ddb1d5a8',1,'vg::PhaseUnfolder']]],
- ['statistics_5767',['Statistics',['../structvg_1_1Recombinator_1_1Statistics.html',1,'vg::Recombinator']]],
- ['statistics_2ecpp_5768',['statistics.cpp',['../statistics_8cpp.html',1,'']]],
- ['statistics_2ehpp_5769',['statistics.hpp',['../statistics_8hpp.html',1,'']]],
- ['stats_5fmain_2ecpp_5770',['stats_main.cpp',['../stats__main_8cpp.html',1,'']]],
- ['std_5771',['std',['../namespacestd.html',1,'']]],
- ['std_5fdev_5772',['std_dev',['../classvg_1_1FragmentLengthDistribution.html#a4da22f6209796ad178bd6ae88a995c03',1,'vg::FragmentLengthDistribution']]],
- ['stddev_5773',['stddev',['../classvg_1_1normal__distribution.html#aaf593ce22610d686f290face7b5db895',1,'vg::normal_distribution::stddev()'],['../classvg_1_1truncated__normal__distribution.html#a49f7b71f827df31a5590d120e04dcbcf',1,'vg::truncated_normal_distribution::stddev()']]],
- ['stdev_5774',['stdev',['../structvg_1_1SummaryStatistics.html#abea415bc0808b7714dee7cb6556dcf30',1,'vg::SummaryStatistics::stdev()'],['../namespacevg.html#a11df8bd14dab3c0cfb7ecfa377a362f5',1,'vg::stdev()']]],
- ['step_5775',['step',['../structvg_1_1Range.html#a05a0a35957e0a0e127b9ef55a305df76',1,'vg::Range::step()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a44f22277ea90f802ae502bdb5bf8e478',1,'handlegraph::PathForEachSocket::iterator::step()']]],
- ['step_5f1_5fbuild_5fgbwts_5776',['step_1_build_gbwts',['../gbwt__main_8cpp.html#a099d84c7e00d3a536ab0c89a42824a67',1,'gbwt_main.cpp']]],
- ['step_5f2_5fmerge_5fgbwts_5777',['step_2_merge_gbwts',['../gbwt__main_8cpp.html#a81911b71bc15131cf9f9cc9652cccf0a',1,'gbwt_main.cpp']]],
- ['step_5f3_5falter_5fgbwt_5778',['step_3_alter_gbwt',['../gbwt__main_8cpp.html#aa89c3d0220f759b0de6756841c3bbfae',1,'gbwt_main.cpp']]],
- ['step_5f4_5fpath_5fcover_5779',['step_4_path_cover',['../gbwt__main_8cpp.html#ac6ed5f1a6fdf7794797be7ab94278897',1,'gbwt_main.cpp']]],
- ['step_5f5_5fgbwtgraph_5780',['step_5_gbwtgraph',['../gbwt__main_8cpp.html#a61f18988124c373bf3aa037ad24719f2',1,'gbwt_main.cpp']]],
- ['step_5f6_5fr_5findex_5781',['step_6_r_index',['../gbwt__main_8cpp.html#a240e0e93804c406946adb930f58c87aa',1,'gbwt_main.cpp']]],
- ['step_5f7_5fmetadata_5782',['step_7_metadata',['../gbwt__main_8cpp.html#a7d810cefdbee01df4d4fe50406806e30',1,'gbwt_main.cpp']]],
- ['step_5f8_5fpaths_5783',['step_8_paths',['../gbwt__main_8cpp.html#a859c16083955e4f1ab36c130fe6cce27',1,'gbwt_main.cpp']]],
- ['step_5fhandle_5ft_5784',['step_handle_t',['../structhandlegraph_1_1step__handle__t.html',1,'handlegraph::step_handle_t'],['../namespacevg.html#a40b137bbd07d198ca2b77962eeeaf7c8',1,'vg::step_handle_t()'],['../namespacevg_1_1io.html#a5473f8a5ac351719453cfd62655beebb',1,'vg::io::step_handle_t()']]],
- ['step_5fin_5fpath_5785',['step_in_path',['../classvg_1_1VCFTraversalFinder.html#aefa5cf40bc0244f81e52ae2bdb4904d0',1,'vg::VCFTraversalFinder']]],
- ['step_5frank_5fat_5fposition_5786',['step_rank_at_position',['../classxg_1_1XGPath.html#a92b0745ad293f585d5fb20d1bf20f7cc',1,'xg::XGPath']]],
- ['steps_5787',['steps',['../classvg_1_1IndexingPlan.html#afe22bdcd727f981fb262b8d29819dee2',1,'vg::IndexingPlan']]],
- ['steps_5fof_5fhandle_5788',['steps_of_handle',['../classvg_1_1MemoizingGraph.html#ab96deef5a4149f287541058c256a1115',1,'vg::MemoizingGraph::steps_of_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a015b050f33861cbc8e2a0efaaf771a30',1,'handlegraph::PathHandleGraph::steps_of_handle()']]],
- ['steps_5fof_5fhandle_5fmemo_5789',['steps_of_handle_memo',['../classvg_1_1MemoizingGraph.html#ac2e7cde55ff928b866d7e26caccdd35e',1,'vg::MemoizingGraph']]],
- ['stop_5790',['stop',['../classvg_1_1Funnel.html#adbe0233346c63f1693fa865eca0083b2',1,'vg::Funnel']]],
- ['stop_5fon_5fduplicate_5fpaths_5791',['stop_on_duplicate_paths',['../classvg_1_1algorithms_1_1GFAParser.html#abe8f148f7941fc1fbc449687b9623c21',1,'vg::algorithms::GFAParser']]],
- ['stop_5ftime_5792',['stop_time',['../classvg_1_1Funnel.html#a59b3ea467d461a57b8801c8845b0bdb3',1,'vg::Funnel']]],
- ['stop_5fwatcher_5793',['stop_watcher',['../classvg_1_1Watchdog.html#a2fbb9a2b514a26515e508ee665295449',1,'vg::Watchdog']]],
- ['stored_5fcrash_5fcontext_5794',['stored_crash_context',['../namespacevg.html#aeb1b2d0c77858355b8bfbbe4406f0931',1,'vg']]],
- ['stored_5fedge_5ft_5795',['stored_edge_t',['../classvg_1_1DiagramExplainer.html#a6eca0d51970a6782f49171a354aaeb74',1,'vg::DiagramExplainer']]],
- ['str_5796',['STR',['../version_8cpp.html#a6a96991688ffe6ae2293f0a4b5f813d2',1,'version.cpp']]],
- ['strand_5797',['strand',['../structgafkluge_1_1GafRecord.html#a38f3845982a15cf080267890fe7e0b3b',1,'gafkluge::GafRecord']]],
- ['strand_5fis_5frev_5798',['strand_is_rev',['../structvg_1_1GFFRecord.html#a08edb7d13481c70c0cfbba949e4f81ce',1,'vg::GFFRecord']]],
- ['strand_5fsampler_5799',['strand_sampler',['../classvg_1_1NGSSimulator.html#a71a4b2c30a477a86d4b7c9f5d6ab3a28',1,'vg::NGSSimulator']]],
- ['strandsplitgraph_5800',['StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html',1,'vg::StrandSplitGraph'],['../classvg_1_1StrandSplitGraph.html#a0e170b8ad07ca370e31497b804932220',1,'vg::StrandSplitGraph::StrandSplitGraph(const HandleGraph *graph)'],['../classvg_1_1StrandSplitGraph.html#aede16e10fc0b17f2527a62861f155c6d',1,'vg::StrandSplitGraph::StrandSplitGraph()=default']]],
- ['stream_2ecpp_5801',['stream.cpp',['../stream_8cpp.html',1,'']]],
- ['stream_2ehpp_5802',['stream.hpp',['../stream_8hpp.html',1,'']]],
- ['stream_5findex_2ecpp_5803',['stream_index.cpp',['../stream__index_8cpp.html',1,'']]],
- ['stream_5findex_2ehpp_5804',['stream_index.hpp',['../stream__index_8hpp.html',1,'']]],
- ['stream_5fmultiplexer_2ecpp_5805',['stream_multiplexer.cpp',['../stream__multiplexer_8cpp.html',1,'']]],
- ['stream_5fmultiplexer_2ehpp_5806',['stream_multiplexer.hpp',['../stream__multiplexer_8hpp.html',1,'']]],
- ['stream_5fsort_5807',['stream_sort',['../classvg_1_1StreamSorter.html#a3ef7c0c822f58db91184e6b069c3ce59',1,'vg::StreamSorter']]],
- ['stream_5fsorter_2ecpp_5808',['stream_sorter.cpp',['../stream__sorter_8cpp.html',1,'']]],
- ['stream_5fsorter_2ehpp_5809',['stream_sorter.hpp',['../stream__sorter_8hpp.html',1,'']]],
- ['streamcompressstring_5810',['StreamCompressString',['../namespacezstdutil.html#a64155ae3ce93620ea7868913f4c49ab3',1,'zstdutil']]],
- ['streamdecompressstring_5811',['StreamDecompressString',['../namespacezstdutil.html#a2b6cfe0b4f483fea633845a8d912e8dd',1,'zstdutil']]],
- ['streaminbuf_5812',['streaminbuf',['../classvg_1_1io_1_1streaminbuf.html',1,'vg::io::streaminbuf'],['../classvg_1_1io_1_1streaminbuf.html#a611fcbbde05222173c867ea92cf20ed6',1,'vg::io::streaminbuf::streaminbuf()']]],
- ['streamindex_5813',['StreamIndex',['../classvg_1_1StreamIndex.html',1,'vg::StreamIndex< Message >'],['../classvg_1_1StreamIndex.html#a3508617dbf1b8e8d1df051f4a214fa5e',1,'vg::StreamIndex::StreamIndex()']]],
- ['streamindex_3c_20vg_3a_3aalgorithms_3a_3agraph_20_3e_5814',['StreamIndex< vg::algorithms::Graph >',['../classvg_1_1StreamIndex.html',1,'vg']]],
- ['streamindexbase_5815',['StreamIndexBase',['../classvg_1_1StreamIndexBase.html',1,'vg::StreamIndexBase'],['../classvg_1_1StreamIndexBase.html#a2df03d2ee53e9f171e4aa519a079901e',1,'vg::StreamIndexBase::StreamIndexBase()=default'],['../classvg_1_1StreamIndexBase.html#a85207efd00788e14df4df717d88233b7',1,'vg::StreamIndexBase::StreamIndexBase(const StreamIndexBase &other)=delete']]],
- ['streaming_5fmerge_5816',['streaming_merge',['../classvg_1_1StreamSorter.html#a1c19cdfb158ff9771e471fbbc2b4ac74',1,'vg::StreamSorter::streaming_merge(list< cursor_t > &cursors, emitter_t &emitter, size_t expected_messages=0)'],['../classvg_1_1StreamSorter.html#a77590f7da1d1418fc00e7bdaec2a76e5',1,'vg::StreamSorter::streaming_merge(const vector< string > &temp_names_in, unordered_map< string, size_t > *messages_per_file=nullptr)']]],
- ['streamistream_5817',['streamistream',['../classvg_1_1io_1_1streamistream.html',1,'vg::io::streamistream'],['../classvg_1_1io_1_1streamistream.html#a0b87c404670f610d20f49f1e2c166648',1,'vg::io::streamistream::streamistream()']]],
- ['streammultiplexer_5818',['StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html',1,'vg::io::StreamMultiplexer'],['../classvg_1_1io_1_1StreamMultiplexer.html#ae72f4179a6cb14beb1b6460603d88233',1,'vg::io::StreamMultiplexer::StreamMultiplexer(ostream &backing, size_t max_threads)'],['../classvg_1_1io_1_1StreamMultiplexer.html#ad8b06aab5797747b1ce3d544be0cc965',1,'vg::io::StreamMultiplexer::StreamMultiplexer(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#af8352f0fcbb63f162734d48d2ec573ce',1,'vg::io::StreamMultiplexer::StreamMultiplexer(StreamMultiplexer &&other)=delete']]],
- ['streamsorter_5819',['StreamSorter',['../classvg_1_1StreamSorter.html',1,'vg::StreamSorter< Message >'],['../classvg_1_1StreamSorter.html#a9ef0b8a33f5011eaf655b9420d86b0f5',1,'vg::StreamSorter::StreamSorter()']]],
- ['strict_5fconflict_5fchecking_5820',['strict_conflict_checking',['../classvg_1_1Deconstructor.html#a565e2bb8d83d007a630f8f3db37c8b43',1,'vg::Deconstructor']]],
- ['string_5821',['String',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eab41cf4db950b9da3d95a7c1400a5369e',1,'vg::multipath_alignment_t']]],
- ['string_5fhash_5fmap_5822',['string_hash_map',['../classvg_1_1string__hash__map.html',1,'vg']]],
- ['string_5fhash_5fset_5823',['string_hash_set',['../classvg_1_1string__hash__set.html',1,'vg']]],
- ['string_5fquality_5fchar_5fto_5fshort_5824',['string_quality_char_to_short',['../namespacevg_1_1io.html#a4450d95b60550d44cbfe712467e92947',1,'vg::io']]],
- ['string_5fquality_5fshort_5fto_5fchar_5825',['string_quality_short_to_char',['../namespacevg_1_1io.html#a33f3f10cba44d4ab370628c9579f9ca4',1,'vg::io']]],
- ['string_5fto_5fint_5826',['string_to_int',['../namespacegafkluge.html#a35bc1201781dd4bab3581189c777a8af',1,'gafkluge']]],
- ['strip_5fbonuses_5827',['strip_bonuses',['../classvg_1_1BaseMapper.html#a34ab4a12d44f5b17b5b6caa03ea4cd79',1,'vg::BaseMapper']]],
- ['strip_5ffrom_5fend_5828',['strip_from_end',['../namespacevg.html#adbe45b79675104ebc36691774d4124c4',1,'vg']]],
- ['strip_5ffrom_5fstart_5829',['strip_from_start',['../namespacevg.html#acd6786ea9551b426f95fba325beff138',1,'vg']]],
- ['strip_5ffull_5flength_5fbonuses_5830',['strip_full_length_bonuses',['../classvg_1_1MultipathMapper.html#a1147b64d4c4aeffa84403f5341de52bf',1,'vg::MultipathMapper']]],
- ['strip_5fsubrange_5831',['strip_subrange',['../classvg_1_1Paths.html#aaae6abfe6b12aecfe82457fe8b8b44a8',1,'vg::Paths']]],
- ['strip_5fsuffixes_5832',['strip_suffixes',['../giraffe__main_8cpp.html#ada042c5c5040b9b72848655d3dc5fcf8',1,'giraffe_main.cpp']]],
- ['stripped_5fmatch_5falg_5fmax_5flength_5833',['stripped_match_alg_max_length',['../classvg_1_1MultipathMapper.html#aee2a7d30863137faeb2b9925c195262d',1,'vg::MultipathMapper']]],
- ['stripped_5fmatch_5falg_5fstrip_5flength_5834',['stripped_match_alg_strip_length',['../classvg_1_1MultipathMapper.html#a892c094e2a5b4dcce87b47a0ee27bff8',1,'vg::MultipathMapper']]],
- ['stripped_5fmatch_5falg_5ftarget_5fcount_5835',['stripped_match_alg_target_count',['../classvg_1_1MultipathMapper.html#a3a8af36f7fbbe431ea804f83e75a684d',1,'vg::MultipathMapper']]],
- ['strongly_5fconnected_5fcomponents_5836',['strongly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a3c63833d51eac5a3141211367935e9e5',1,'handlegraph::algorithms']]],
- ['strongly_5fconnected_5fcomponents_2ecpp_5837',['strongly_connected_components.cpp',['../strongly__connected__components_8cpp.html',1,'']]],
- ['stubbify_5fref_5fpaths_5838',['stubbify_ref_paths',['../namespacevg.html#a9e14750889892e0d70b8bc18fcc9f905',1,'vg']]],
- ['sub_5fdurations_5839',['sub_durations',['../structvg_1_1Funnel_1_1Stage.html#af090e9aa3d82046a91766e05cdec814d',1,'vg::Funnel::Stage']]],
- ['sub_5fmem_5fcount_5fthinning_5840',['sub_mem_count_thinning',['../classvg_1_1BaseMapper.html#a8d9a00e1d809346bc62f6f2c1e4fbe32',1,'vg::BaseMapper']]],
- ['sub_5fmem_5fthinning_5fburn_5fin_5841',['sub_mem_thinning_burn_in',['../classvg_1_1BaseMapper.html#a4e17a40bafbd8832d551acb01298403d',1,'vg::BaseMapper']]],
- ['sub_5foverlaps_5fof_5ffirst_5faln_5842',['sub_overlaps_of_first_aln',['../namespacevg.html#ab63c41956b73af429507b469108d1759',1,'vg']]],
- ['sub_5fpoly_5frate_5843',['sub_poly_rate',['../classvg_1_1NGSSimulator.html#a2078f130a3782a67206ad9c2c20067ea',1,'vg::NGSSimulator']]],
- ['sub_5fscore_5844',['sub_score',['../classvg_1_1ReadFilter.html#a529c0b978b3855bab3dc1074fd18a711',1,'vg::ReadFilter']]],
- ['subchain_5845',['Subchain',['../structvg_1_1HaplotypePartitioner_1_1Subchain.html',1,'vg::HaplotypePartitioner::Subchain'],['../structvg_1_1Haplotypes_1_1Subchain.html',1,'vg::Haplotypes::Subchain']]],
- ['subchain_5fid_5846',['subchain_id',['../structHaplotypesConfig.html#ae5e75f47f0768d4e5da28a15baaa702e',1,'HaplotypesConfig']]],
- ['subchain_5fintervals_5847',['subchain_intervals',['../haplotypes__main_8cpp.html#aed90215616b71a8c576afeeb7a137596',1,'haplotypes_main.cpp']]],
- ['subchain_5flength_5848',['SUBCHAIN_LENGTH',['../classvg_1_1HaplotypePartitioner.html#a3343e960c394c9c092d08ff931f37081',1,'vg::HaplotypePartitioner::SUBCHAIN_LENGTH()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#ac912479fc22acc7c9078978e71597ad9',1,'vg::HaplotypePartitioner::Parameters::subchain_length()'],['../namespacehaplotypes__defaults.html#af6cc9d47b0c3862d9c0cdea27b55f477',1,'haplotypes_defaults::subchain_length()']]],
- ['subchain_5fstatistics_5849',['subchain_statistics',['../haplotypes__main_8cpp.html#a559cad6ab46d0a7dc260987e61ed1175',1,'haplotypes_main.cpp']]],
- ['subchain_5ft_5850',['subchain_t',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbde',1,'vg::Haplotypes::Subchain']]],
- ['subchain_5fto_5fstring_5851',['subchain_to_string',['../haplotypes__main_8cpp.html#ae88c7a2ca3744f1826af903b27b2df53',1,'haplotypes_main.cpp']]],
- ['subchains_5852',['subchains',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ae31e41720bb3a859e4762aa9e2c5318b',1,'vg::Haplotypes::TopLevelChain::subchains()'],['../structvg_1_1Recombinator_1_1Statistics.html#ab6d38eac9e036f7b2b0f19736529e3a9',1,'vg::Recombinator::Statistics::subchains()']]],
- ['subcommand_5853',['Subcommand',['../classvg_1_1subcommand_1_1Subcommand.html',1,'vg::subcommand::Subcommand'],['../classvg_1_1subcommand_1_1Subcommand.html#ad5faf589dd98c3ff0c0d1071fcf90090',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, int priority, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#a38458556194aa9d47b1a49fc8958f345',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#ad2cb9a00761644300914d9ed8439cbe1',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, std::function< int(int, char **)> main_function)']]],
- ['subcommand_2ecpp_5854',['subcommand.cpp',['../subcommand_8cpp.html',1,'']]],
- ['subcommand_2ehpp_5855',['subcommand.hpp',['../subcommand_8hpp.html',1,'']]],
- ['subgraph_5856',['subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aae76f24549ed2f49dc12176f46dfea8d',1,'vg::GraphSynchronizer::Lock::subgraph()'],['../classvg_1_1SpliceRegion.html#aa12379182f8abfc5239c38b433d1b4b8',1,'vg::SpliceRegion::subgraph()'],['../classvg_1_1SubgraphExplainer.html#a6a8bb147fa3f638f7bc0c2a098475999',1,'vg::SubgraphExplainer::subgraph()']]],
- ['subgraph_2ecpp_5857',['subgraph.cpp',['../subgraph_8cpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8cpp.html',1,'(Global Namespace)']]],
- ['subgraph_2ehpp_5858',['subgraph.hpp',['../subgraph_8hpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8hpp.html',1,'(Global Namespace)']]],
- ['subgraph_5fcontaining_5fpath_5fsnarls_5859',['subgraph_containing_path_snarls',['../namespacevg.html#acc960c295c1e3088dc8e71ab1af5c4d6',1,'vg']]],
- ['subgraph_5fin_5fdistance_5frange_5860',['subgraph_in_distance_range',['../namespacevg.html#aff8a7aca57dd525bc2def1369abae3fe',1,'vg']]],
- ['subgraph_5fin_5fdistance_5frange_5fwalk_5facross_5fchain_5861',['subgraph_in_distance_range_walk_across_chain',['../namespacevg.html#a30f08b56f8c117103357ed4b8ebc08b8',1,'vg']]],
- ['subgraph_5fin_5fdistance_5frange_5fwalk_5fgraph_5862',['subgraph_in_distance_range_walk_graph',['../namespacevg.html#a0312bffc43a4f4176aad1c37073b59df',1,'vg']]],
- ['subgraph_5fmin_5863',['subgraph_min',['../structPruningParameters.html#ada52c2750edf0333574238f15adb1c84',1,'PruningParameters']]],
- ['subgraph_5foverlay_2ecpp_5864',['subgraph_overlay.cpp',['../subgraph__overlay_8cpp.html',1,'']]],
- ['subgraph_5foverlay_2ehpp_5865',['subgraph_overlay.hpp',['../subgraph__overlay_8hpp.html',1,'']]],
- ['subgraph_5fprune_5866',['subgraph_prune',['../classvg_1_1VariantAdder.html#a39e87cff1b1cf12920a36b78bdcc2ddc',1,'vg::VariantAdder']]],
- ['subgraphexplainer_5867',['SubgraphExplainer',['../classvg_1_1SubgraphExplainer.html',1,'vg::SubgraphExplainer'],['../classvg_1_1SubgraphExplainer.html#adbcee01cfe7c72e36071da4ed5aa1aec',1,'vg::SubgraphExplainer::SubgraphExplainer()']]],
- ['subgraphoverlay_5868',['SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html',1,'vg::SubgraphOverlay'],['../classvg_1_1SubgraphOverlay.html#ac9ffa71f1e615eb30efc626006c11242',1,'vg::SubgraphOverlay::SubgraphOverlay()']]],
- ['subgroups_5869',['subgroups',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a17a3b23ed098272dfa4f3a9226ac5bef',1,'vg::subcommand::GroupedOptionGroup']]],
- ['subhandlegraph_5870',['SubHandleGraph',['../classvg_1_1SubHandleGraph.html',1,'vg::SubHandleGraph'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html',1,'handlegraph::algorithms::SubHandleGraph'],['../classvg_1_1SubHandleGraph.html#ae02101c50fc316637a11ed674637e6a4',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super, HandleIter begin, HandleIter end)'],['../classvg_1_1SubHandleGraph.html#a1426a494a5d412485f5c4959f3b853c8',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super)'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4455c7d0983b1fcce544022a60fa76ab',1,'handlegraph::algorithms::SubHandleGraph::SubHandleGraph()']]],
- ['subpath_5871',['Subpath',['../structvg_1_1Subpath.html',1,'vg::Subpath'],['../structvg_1_1MultipathAlignment.html#aa92c4cbfee9b5e076c41ca466b44617c',1,'vg::MultipathAlignment::subpath()'],['../classvg_1_1multipath__alignment__t.html#a87bb864c7cd6e424fe9487cc662cade6',1,'vg::multipath_alignment_t::subpath() const'],['../classvg_1_1multipath__alignment__t.html#a5544e1c157233fda1b528bdd3e426f90',1,'vg::multipath_alignment_t::subpath(size_t i) const']]],
- ['subpath_5fhandles_5872',['subpath_handles',['../classvg_1_1SubpathOverlay.html#ab1edd258ddd2cce726bfbc79b32b2476',1,'vg::SubpathOverlay']]],
- ['subpath_5foverlay_2ecpp_5873',['subpath_overlay.cpp',['../subpath__overlay_8cpp.html',1,'']]],
- ['subpath_5foverlay_2ehpp_5874',['subpath_overlay.hpp',['../subpath__overlay_8hpp.html',1,'']]],
- ['subpath_5fsize_5875',['subpath_size',['../classvg_1_1multipath__alignment__t.html#a3b6820ac77fa5438c55300ba1eb7a97d',1,'vg::multipath_alignment_t']]],
- ['subpath_5ft_5876',['subpath_t',['../classvg_1_1subpath__t.html',1,'vg::subpath_t'],['../classvg_1_1subpath__t.html#a17ac16fd98564bfa3ab34e9b9b20517e',1,'vg::subpath_t::subpath_t()=default'],['../classvg_1_1subpath__t.html#a31254046fc840d936d42012b2c7b23b5',1,'vg::subpath_t::subpath_t(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a096b12ec158dd2cf139dbe38f55ca2f3',1,'vg::subpath_t::subpath_t(subpath_t &&)=default']]],
- ['subpath_5fto_5flength_5877',['subpath_to_length',['../classvg_1_1HTSWriter.html#a24dca4e57dcfb498da8f18946194f600',1,'vg::HTSWriter']]],
- ['subpath_5ftopological_5forder_5878',['subpath_topological_order',['../namespacevg.html#ab1dcbe73351c8eaeea745f4b5191b8f0',1,'vg']]],
- ['subpathoverlay_5879',['SubpathOverlay',['../classvg_1_1SubpathOverlay.html',1,'vg::SubpathOverlay'],['../classvg_1_1SubpathOverlay.html#a63691d737697292e0a2fd4233024dfb8',1,'vg::SubpathOverlay::SubpathOverlay(const PathHandleGraph *backing, const step_handle_t &begin, const step_handle_t &end)'],['../classvg_1_1SubpathOverlay.html#aa3cc8559a68870f144d69eb44829c95a',1,'vg::SubpathOverlay::SubpathOverlay()=default']]],
- ['subrange_5ft_5880',['subrange_t',['../namespacevg.html#ae28b502adf2ce7302acbb3138280f06c',1,'vg::subrange_t()'],['../namespacehandlegraph.html#a097e656b1ffb02a80c0b530b1987984a',1,'handlegraph::subrange_t()']]],
- ['subsequence_5881',['subsequence',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9acf76097b099973339661134c01b30e59',1,'vg::Counts']]],
- ['subsequences_5882',['subsequences',['../classvg_1_1ReadFilter.html#a98cd220c402ec88c512121825ed690df',1,'vg::ReadFilter']]],
- ['substage_5883',['substage',['../classvg_1_1Funnel.html#a0520d00fd1dcd9fa4af18d715580c900',1,'vg::Funnel']]],
- ['substage_5fname_5884',['substage_name',['../classvg_1_1Funnel.html#a4cfa61145fcd97f5710c3d609e72a997',1,'vg::Funnel']]],
- ['substage_5fstart_5ftime_5885',['substage_start_time',['../classvg_1_1Funnel.html#ae8b9248bf65562b44ac8b65f50619c70',1,'vg::Funnel']]],
- ['substage_5fstop_5886',['substage_stop',['../classvg_1_1Funnel.html#ab5934891f37d57dc9309e5b0e9f80d9e',1,'vg::Funnel']]],
- ['subtract_5flog_5887',['subtract_log',['../namespacevg.html#a33c8f5153ad0766df2c72bbec623aa19',1,'vg']]],
- ['successor_5foffset_5888',['successor_offset',['../classvg_1_1WFATree.html#a33c5e80cc73d5367a95343deb20d8dac',1,'vg::WFATree']]],
- ['suffix_5889',['suffix',['../classvg_1_1IndexFile.html#acc1a7b94cb2a464d4941e7092aa83612',1,'vg::IndexFile::suffix()'],['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea831a2ebb5fe5a6b08270dfa5b9b6c7ac',1,'vg::Haplotypes::Subchain::suffix()'],['../classvg_1_1WFAExtender.html#a73ca61152596774e30d6c6f40aeea984',1,'vg::WFAExtender::suffix()'],['../structvg_1_1RecombinatorHaplotype.html#ae22f7c420e3d76d6494f66e817ffb342',1,'vg::RecombinatorHaplotype::suffix()']]],
- ['suffixes_5890',['suffixes',['../classvg_1_1PhaseUnfolder.html#a8e235a2b6022ec40a6e66c63c8dd1df0',1,'vg::PhaseUnfolder']]],
- ['suggest_5fedge_5891',['suggest_edge',['../classvg_1_1DiagramExplainer.html#a5565fd4595e708faa7f82534b1b87380',1,'vg::DiagramExplainer']]],
- ['suggested_5fedge_5ft_5892',['suggested_edge_t',['../classvg_1_1DiagramExplainer.html#ae9907aa970a58c2c6a89829c6f3020ba',1,'vg::DiagramExplainer']]],
- ['suggested_5fedges_5893',['suggested_edges',['../classvg_1_1DiagramExplainer.html#a14bbd52421b049d538e13a357209b9ff',1,'vg::DiagramExplainer']]],
- ['sum_5894',['sum',['../structhaplo_1_1haplo__DP__column.html#aeb237931ba6de582496ded7d42517f3a',1,'haplo::haplo_DP_column::sum()'],['../namespacevg.html#aa70726366aa31b20debdcac41c89490c',1,'vg::sum()']]],
- ['summary_5fstatistics_5895',['summary_statistics',['../namespacevg.html#ae8afe82a05092bbf4bc31c8ead079fe3',1,'vg']]],
- ['summarystatistics_5896',['SummaryStatistics',['../structvg_1_1SummaryStatistics.html',1,'vg']]],
- ['super_5897',['super',['../classvg_1_1PathSubgraph.html#a223501d50e8c102bbd7bf602d19b9400',1,'vg::PathSubgraph::super()'],['../classvg_1_1SubHandleGraph.html#aa17f9e8ba0b1b374b852390a9bf0c56a',1,'vg::SubHandleGraph::super()'],['../classvg_1_1TreeSubgraph.html#a1096d8426347b21730e2d7d81527ffc0',1,'vg::TreeSubgraph::super()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ad63f143f0bebc5d600dca495e9fdff77',1,'handlegraph::algorithms::SubHandleGraph::super()']]],
- ['support_5898',['Support',['../structvg_1_1Support.html',1,'vg::Support'],['../structvg_1_1Locus.html#a42e45ba2fa1310b9fba6774b24cdd447',1,'vg::Locus::support()'],['../structvg_1_1LocationSupport.html#a479f1a778e85f8d3747c0b7c44ad5760',1,'vg::LocationSupport::support()']]],
- ['support_5ffinder_5899',['support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a2af17a0bf619778576c49627563994dc',1,'vg::SupportBasedSnarlCaller']]],
- ['support_5fmax_5900',['support_max',['../namespacevg.html#ac3787b0a7fc02bbfe45dc5eb082d5779',1,'vg']]],
- ['support_5fmin_5901',['support_min',['../namespacevg.html#a3c2ae4c37201ebbc6f6d4faaf27fe4de',1,'vg']]],
- ['support_5fval_5902',['support_val',['../classvg_1_1SupportBasedSnarlCaller.html#a84da98787b002a2ed9c8c1da6661cebd',1,'vg::SupportBasedSnarlCaller::support_val()'],['../classvg_1_1TraversalSupportFinder.html#a3a128da202bd6889a2e5fd92ba3227dc',1,'vg::TraversalSupportFinder::support_val()']]],
- ['supportaugmentedgraph_5903',['SupportAugmentedGraph',['../structvg_1_1SupportAugmentedGraph.html',1,'vg']]],
- ['supportbasedsnarlcaller_5904',['SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html',1,'vg::SupportBasedSnarlCaller'],['../classvg_1_1SupportBasedSnarlCaller.html#adff4e7045e950e7caea2858569afec02',1,'vg::SupportBasedSnarlCaller::SupportBasedSnarlCaller()']]],
- ['supportmap_5905',['SupportMap',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af8ae65b6009d1f121c27fb3ab969ef90',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
- ['supportrestrictedtraversalfinder_5906',['SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html',1,'vg::SupportRestrictedTraversalFinder'],['../classvg_1_1SupportRestrictedTraversalFinder.html#aceeb94d7e05fdbc113557b61448f6b2a',1,'vg::SupportRestrictedTraversalFinder::SupportRestrictedTraversalFinder()']]],
- ['suppress_5fcluster_5fmerging_5907',['suppress_cluster_merging',['../classvg_1_1MultipathMapper.html#ad25f17a8c485548abf5f63517937067f',1,'vg::MultipathMapper']]],
- ['suppress_5fmismapping_5fdetection_5908',['suppress_mismapping_detection',['../classvg_1_1MultipathMapper.html#a514a648b0822a7c74e853ab78aed7d95',1,'vg::MultipathMapper']]],
- ['suppress_5fmulticomponent_5fsplitting_5909',['suppress_multicomponent_splitting',['../classvg_1_1MultipathMapper.html#a2dae3baa09f211a0762d121a6c48dc58',1,'vg::MultipathMapper']]],
- ['suppress_5fp_5fvalue_5fmemoization_5910',['suppress_p_value_memoization',['../classvg_1_1MultipathMapper.html#afd6fee3779079af7a2932c7c29098b2d',1,'vg::MultipathMapper']]],
- ['suppress_5ftail_5fanchors_5911',['suppress_tail_anchors',['../classvg_1_1MultipathMapper.html#ad4c0e1fea285f378ef5c7eb23e9baf89',1,'vg::MultipathMapper']]],
- ['surface_5912',['surface',['../classvg_1_1Viz.html#ad93aa239a30c3b7a017348e22f184b85',1,'vg::Viz']]],
- ['surject_5913',['surject',['../classvg_1_1Surjector.html#a4e4e4c28b1313850e647f4d258a0ea82',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a265cf90a6fb12021a70b87ec647c0867',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a80afa331fde9e8bcff66c4e87400217a',1,'vg::Surjector::surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
- ['surject_5falignments_5fin_5fplace_5914',['surject_alignments_in_place',['../classvg_1_1SurjectingAlignmentEmitter.html#a5ba8aab649ae5f31c64be2c5461c743c',1,'vg::SurjectingAlignmentEmitter']]],
- ['surject_5finternal_5915',['surject_internal',['../classvg_1_1Surjector.html#a6474f90fe3cf3ea098a553916bd47ae9',1,'vg::Surjector']]],
- ['surject_5fmain_2ecpp_5916',['surject_main.cpp',['../surject__main_8cpp.html',1,'']]],
- ['surject_5fsubpath_5fglobal_5917',['surject_subpath_global',['../classvg_1_1SurjectingAlignmentEmitter.html#a730237d7e198244c27b29aff8a7d8b7d',1,'vg::SurjectingAlignmentEmitter']]],
- ['surjecting_5falignment_5femitter_2ecpp_5918',['surjecting_alignment_emitter.cpp',['../surjecting__alignment__emitter_8cpp.html',1,'']]],
- ['surjecting_5falignment_5femitter_2ehpp_5919',['surjecting_alignment_emitter.hpp',['../surjecting__alignment__emitter_8hpp.html',1,'']]],
- ['surjectingalignmentemitter_5920',['SurjectingAlignmentEmitter',['../classvg_1_1SurjectingAlignmentEmitter.html',1,'vg::SurjectingAlignmentEmitter'],['../classvg_1_1SurjectingAlignmentEmitter.html#acf03c9f7eedb8d8dd58d6ffab24f139f',1,'vg::SurjectingAlignmentEmitter::SurjectingAlignmentEmitter()']]],
- ['surjector_5921',['Surjector',['../classvg_1_1Surjector.html',1,'vg::Surjector'],['../classvg_1_1Surjector.html#a4b083231c3ae02e3e14c3efb2a72eb1d',1,'vg::Surjector::Surjector()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a7ff6c0ffab9177150fe4941a8ae71c70',1,'vg::SurjectingAlignmentEmitter::surjector()']]],
- ['surjector_2ecpp_5922',['surjector.cpp',['../surjector_8cpp.html',1,'']]],
- ['surjector_2ehpp_5923',['surjector.hpp',['../surjector_8hpp.html',1,'']]],
- ['sv_5ftype_5924',['SV_TYPE',['../structvg_1_1BREAKPOINT.html#a52c38d41e036406a3c2e79d9f4bbfc50',1,'vg::BREAKPOINT']]],
- ['swap_5925',['swap',['../classvg_1_1SnarlState.html#a4e3f0d0c720ea665b3db9542d07f7ec1',1,'vg::SnarlState::swap()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a1466c6e58d54f775b27680dbe5e7fe4d',1,'vg::ZipCodeTree::reverse_iterator::swap()']]],
- ['swap_5falleles_5926',['swap_alleles',['../classvg_1_1PhasedGenome.html#ae325c8488e737b75b980796aacf37246',1,'vg::PhasedGenome']]],
- ['swap_5fendianness_5927',['swap_endianness',['../structvg_1_1endianness.html#a0a3eec44ef047d7771ad9804c5b51c85',1,'vg::endianness']]],
- ['swap_5fhandles_5928',['swap_handles',['../classvg_1_1VG.html#a3d4db6ea2a99bda9a48411491aa6ed4e',1,'vg::VG']]],
- ['swap_5fhaplotypes_5929',['swap_haplotypes',['../classvg_1_1GenomeState.html#aee2aa05cdf5226983f8f25d783da528e',1,'vg::GenomeState']]],
- ['swap_5flabel_5930',['swap_label',['../classvg_1_1PhasedGenome.html#a181b4e71f8debc78ceccf476ce36abcd',1,'vg::PhasedGenome']]],
- ['swap_5fnode_5fid_5931',['swap_node_id',['../classvg_1_1VG.html#afee31880eaf65a1a6d1a250663271b54',1,'vg::VG::swap_node_id(nid_t node_id, nid_t new_id)'],['../classvg_1_1VG.html#a63f2ffa39d84f80e5ab8068a25a03ee9',1,'vg::VG::swap_node_id(Node *node, nid_t new_id)']]],
- ['swap_5fnode_5fids_5932',['swap_node_ids',['../classvg_1_1Paths.html#a3190f22ab39a9039ec9288e1c065ca9c',1,'vg::Paths::swap_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)'],['../classvg_1_1Paths.html#aba01c4d1b1d415622634db97f62b1188',1,'vg::Paths::swap_node_ids(hash_map< id_t, id_t > &id_mapping)']]],
- ['swap_5fnodes_5933',['swap_nodes',['../classvg_1_1VG.html#aa402d1cf817f83ca44f72f6112b6a2e3',1,'vg::VG']]],
- ['swap_5fremove_5934',['swap_remove',['../swap__remove_8hpp.html#a403d9325a22306c4dfefd9202bd3bd00',1,'swap_remove.hpp']]],
- ['swap_5fremove_2ehpp_5935',['swap_remove.hpp',['../swap__remove_8hpp.html',1,'']]],
- ['swaphaplotypescommand_5936',['SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html',1,'vg']]],
- ['symbol_5fcount_5937',['symbol_count',['../classvg_1_1Pictographs.html#a38abbb70a4bdb0b40e5beb2b43cee1d5',1,'vg::Pictographs']]],
- ['symbolic_5fallele_5fwarnings_5938',['symbolic_allele_warnings',['../classvg_1_1Constructor.html#a245d775942ede32387b95497803e114c',1,'vg::Constructor']]],
- ['symbols_5939',['symbols',['../classvg_1_1Pictographs.html#a2504adc26acf0c09e9cccb06e80e1d7b',1,'vg::Pictographs']]],
- ['sync_5940',['sync',['../classvg_1_1VariantAdder.html#abc5742437534663752fccb79b5302b42',1,'vg::VariantAdder']]],
- ['sync_5foffsets_5941',['sync_offsets',['../classxg_1_1XGPath.html#af7e2c286ed51c4422b1b615e4f327b9d',1,'xg::XGPath']]],
- ['sync_5fpaths_5942',['sync_paths',['../classvg_1_1VG.html#a124188a9e0cd68c87c2bc009ea7bd799',1,'vg::VG']]],
- ['synchronizer_5943',['synchronizer',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad2fcccf51dbd2136c680322341847b78',1,'vg::GraphSynchronizer::Lock']]],
- ['syntax_5944',['syntax',['../vg_8proto.html#adbedb258e13546cc707a6ebb073a3d8a',1,'vg.proto']]],
- ['synthesize_5ftail_5fanchors_5945',['synthesize_tail_anchors',['../classvg_1_1MultipathAlignmentGraph.html#a3c34e5d02c2b81614ccd602351b81ed9',1,'vg::MultipathAlignmentGraph']]]
+ ['s_5fbv_5246',['s_bv',['../classxg_1_1XG.html#ac8f0eaf8d0d58d489a6da321d8303c46',1,'xg::XG']]],
+ ['s_5fbv_5frank_5247',['s_bv_rank',['../classxg_1_1XG.html#a14eb778ecdf51cca8ced32eb42112200',1,'xg::XG']]],
+ ['s_5fbv_5fselect_5248',['s_bv_select',['../classxg_1_1XG.html#a45b6e0fcf1dd90f451df245f0ffc3e1c',1,'xg::XG']]],
+ ['s_5fiv_5249',['s_iv',['../classxg_1_1XG.html#aa8e40fcbfa8174b689067d87acd818be',1,'xg::XG']]],
+ ['s_5fscan_5fchain_5250',['S_SCAN_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a5a2a20c895df5cb7d5b27e3335827d84',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fscan_5fsnarl_5251',['S_SCAN_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a3eb7a4cb13ea66f6f4e7e44d06aa41bc',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fskip_5fchain_5252',['S_SKIP_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a98d325e41f9d476ccc2b82e79c873341',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fstack_5fsnarl_5253',['S_STACK_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a45d7d8cf2973c828ad7bd10774a879e4',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fstart_5254',['S_START',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a159863dec1d44845928b1b3df0d24a2a',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['sa_5fto_5fda_5255',['sa_to_da',['../namespacevg.html#aaac16668663556af1aea74159a73d4ed',1,'vg']]],
+ ['safe_5fto_5fget_5256',['safe_to_get',['../classvg_1_1VcfBuffer.html#ac280837b05f233e4420c6e8a7bbef32b',1,'vg::VcfBuffer']]],
+ ['sam_5257',['SAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baa4f1866efe56ebd234e7d5135ecca03e',1,'vg::MultipathAlignmentEmitter']]],
+ ['sam_5ffiles_5258',['sam_files',['../classvg_1_1HTSWriter.html#a57a7f16757fc6ce944636d69c48903cb',1,'vg::HTSWriter']]],
+ ['sam_5fflag_5259',['sam_flag',['../namespacevg.html#ae37c6d66a01cef6f92707d367ebf4cdb',1,'vg']]],
+ ['sam_5fheader_5260',['sam_header',['../classvg_1_1HTSWriter.html#a95cd5874834de9191faf18d39fef9534',1,'vg::HTSWriter']]],
+ ['same_5fcontext_5261',['same_context',['../classvg_1_1VG.html#a96f99984ada5a3a13332ddb2ab0a1c97',1,'vg::VG']]],
+ ['sample_5fcounter_5262',['sample_counter',['../classvg_1_1NGSSimulator.html#ab162ca660d69f66c18c41516a1a69d24',1,'vg::NGSSimulator']]],
+ ['sample_5fgam_5fdepth_5263',['sample_gam_depth',['../namespacevg_1_1algorithms.html#a80703607cfe21f1f593f7b2f03c08b40',1,'vg::algorithms']]],
+ ['sample_5fhaplotypes_5264',['sample_haplotypes',['../giraffe__main_8cpp.html#a6343c45d56779ead6309ffefbf066fdc',1,'sample_haplotypes(const vector< pair< string, string >> &indexes, string &basename, string &sample_name, string &haplotype_file, string &kff_file, bool progress): giraffe_main.cpp'],['../haplotypes__main_8cpp.html#a13d462ac627c7beb00b431280ac9b0c6',1,'sample_haplotypes(const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, const HaplotypesConfig &config): haplotypes_main.cpp']]],
+ ['sample_5finterval_5265',['sample_interval',['../structvg_1_1RebuildParameters.html#aa4adeffb1f91f55c6f1709e6d1c9cfcb',1,'vg::RebuildParameters']]],
+ ['sample_5fmapping_5fdepth_5266',['sample_mapping_depth',['../namespacevg_1_1algorithms.html#a16bd0de261a829b2d81ec48eed9d6482',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const string &input_filename, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq, const string &format)'],['../namespacevg_1_1algorithms.html#a244822514c71473756cfd5ad87f79e08',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const vector< Alignment > &alignments, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq)']]],
+ ['sample_5fminimal_5267',['sample_minimal',['../namespacevg_1_1algorithms.html#a175ee345e226732cb1c37da13a2f045e',1,'vg::algorithms']]],
+ ['sample_5fminimal_2ecpp_5268',['sample_minimal.cpp',['../sample__minimal_8cpp.html',1,'']]],
+ ['sample_5fminimal_2ehpp_5269',['sample_minimal.hpp',['../sample__minimal_8hpp.html',1,'']]],
+ ['sample_5fname_5270',['sample_name',['../classvg_1_1VCFOutputCaller.html#a70e8288543e7facfb79f5211ce33fa7f',1,'vg::VCFOutputCaller::sample_name()'],['../classvg_1_1MCMCCaller.html#a59582bcf7ba0dc3ae52f3f9a7c8eb80c',1,'vg::MCMCCaller::sample_name()'],['../classvg_1_1MinimizerMapper.html#a2f47382b14baf0482c43034e6484d086',1,'vg::MinimizerMapper::sample_name()'],['../classvg_1_1MultipathAlignmentEmitter.html#a6fa324b9dee313b1fceab7bafa62db24',1,'vg::MultipathAlignmentEmitter::sample_name()'],['../structvg_1_1Alignment.html#ad823d9ed3f413faaf35700a41cfab6e7',1,'vg::Alignment::sample_name()'],['../structvg_1_1MultipathAlignment.html#a90d675553385456c66b572a88fa88650',1,'vg::MultipathAlignment::sample_name()']]],
+ ['sample_5fnames_5271',['sample_names',['../classvg_1_1Deconstructor.html#a56f3119a427b1076d0d0d5ca7f478832',1,'vg::Deconstructor']]],
+ ['sample_5fpath_5272',['sample_path',['../classvg_1_1NGSSimulator.html#a57ee602010b5295685556acc30e0355a',1,'vg::NGSSimulator']]],
+ ['sample_5fploidys_5273',['sample_ploidys',['../classvg_1_1Deconstructor.html#a337113fedde38a57458c9329ffd86aac',1,'vg::Deconstructor']]],
+ ['sample_5frange_5274',['sample_range',['../classvg_1_1HaplotypeIndexer.html#a53cb273305c8fb1c039581c1a1b3d76e',1,'vg::HaplotypeIndexer']]],
+ ['sample_5fread_5275',['sample_read',['../classvg_1_1ReadFilter.html#aa592c88e758fc257fdf17418b0f189a8',1,'vg::ReadFilter::sample_read()'],['../classvg_1_1Sampler.html#ab48bd0062b357dfe0cf418beb1e18ad4',1,'vg::Sampler::sample_read()'],['../classvg_1_1NGSSimulator.html#a50a20af9dd3edd86233edf1de13a5cda',1,'vg::NGSSimulator::sample_read()']]],
+ ['sample_5fread_5finternal_5276',['sample_read_internal',['../classvg_1_1NGSSimulator.html#a957be55e0adcf59449587ccb1f8db9de',1,'vg::NGSSimulator']]],
+ ['sample_5fread_5fpair_5277',['sample_read_pair',['../classvg_1_1Sampler.html#a598b41433f5bb9a040749e7a2327b78d',1,'vg::Sampler::sample_read_pair()'],['../classvg_1_1NGSSimulator.html#a5b12189ad9dcf0a4656a321fcf5ff840',1,'vg::NGSSimulator::sample_read_pair()']]],
+ ['sample_5fread_5fquality_5278',['sample_read_quality',['../classvg_1_1NGSSimulator.html#a49ad65d878edb1d76518f589aa0bf02c',1,'vg::NGSSimulator']]],
+ ['sample_5fread_5fquality_5finternal_5279',['sample_read_quality_internal',['../classvg_1_1NGSSimulator.html#a03fb08f4267424aca8d8892a403b134a',1,'vg::NGSSimulator']]],
+ ['sample_5fread_5fquality_5fpair_5280',['sample_read_quality_pair',['../classvg_1_1NGSSimulator.html#a71f6e4ba9442273d4cf1588f24578f55',1,'vg::NGSSimulator']]],
+ ['sample_5fstart_5fgraph_5fpos_5281',['sample_start_graph_pos',['../classvg_1_1NGSSimulator.html#ada5f04218c531191b20a8c28cc57d94e',1,'vg::NGSSimulator']]],
+ ['sample_5fstart_5fpath_5fpos_5282',['sample_start_path_pos',['../classvg_1_1NGSSimulator.html#ad2f821c685108e8ee6912713f0ced8d3',1,'vg::NGSSimulator']]],
+ ['sample_5fstart_5fpos_5283',['sample_start_pos',['../classvg_1_1NGSSimulator.html#a889b49669939bfb7832bad23f02cd02c',1,'vg::NGSSimulator']]],
+ ['sample_5fto_5fhaplotypes_5284',['sample_to_haplotypes',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a5e006ad54f202447a37975fa4919481c',1,'vg::Deconstructor::NestingInfo']]],
+ ['sample_5fto_5fploidy_5285',['sample_to_ploidy',['../structvg_1_1ParentGenotypeInfo.html#a5ac680b0203fe3cccab8959c84f5d556',1,'vg::ParentGenotypeInfo']]],
+ ['sample_5ftransition_5286',['sample_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a4434cebe872c32c384c1f916111fc2e1',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['sample_5funsheared_5fpaths_5287',['sample_unsheared_paths',['../classvg_1_1NGSSimulator.html#af7441bd12030f0e189aca5ba2e0b47ef',1,'vg::NGSSimulator']]],
+ ['sampler_5288',['Sampler',['../classvg_1_1Sampler.html',1,'vg::Sampler'],['../classvg_1_1Sampler.html#ab1d1e96bcf702979dfc86a92dcd8d24b',1,'vg::Sampler::Sampler()']]],
+ ['sampler_2ecpp_5289',['sampler.cpp',['../sampler_8cpp.html',1,'']]],
+ ['sampler_2ehpp_5290',['sampler.hpp',['../sampler_8hpp.html',1,'']]],
+ ['samplers_5291',['samplers',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a8d2808d7b690045d11af93fd6619fbf7',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['samples_5292',['samples',['../structGBWTConfig.html#ae5a3dac168e1ea3d38ddd13f5097fa40',1,'GBWTConfig']]],
+ ['samples_5fin_5fbatch_5293',['samples_in_batch',['../classvg_1_1HaplotypeIndexer.html#a681bcf3fb6014ae885adb3dec25ff2fc',1,'vg::HaplotypeIndexer']]],
+ ['sanitize_5fsequence_5fin_5fplace_5294',['sanitize_sequence_in_place',['../classvg_1_1Constructor.html#a1d90ed36989b851bb3c072f4d67b52dd',1,'vg::Constructor']]],
+ ['save_5295',['save',['../classvg_1_1StreamIndexBase.html#a99761d4d917dc5ba1db1e08a36ceb312',1,'vg::StreamIndexBase::save()'],['../classvg_1_1io_1_1VPKG.html#a80551b46351f1e8d47e8b3ebaf028847',1,'vg::io::VPKG::save(const Have &have, ostream &out)'],['../classvg_1_1io_1_1VPKG.html#a0472c51ab91f4b8663a56a150e0e0f12',1,'vg::io::VPKG::save(const Have &have, const string &filename)']]],
+ ['save_5fbed_5296',['save_bed',['../classvg_1_1FeatureSet.html#a2914a7c47c085b00a454df2bfc5eda67',1,'vg::FeatureSet']]],
+ ['save_5fexplanations_5297',['save_explanations',['../classvg_1_1Explainer.html#a3510aece27ab20079a8a3e87fa702596',1,'vg::Explainer']]],
+ ['save_5ffrag_5flens_5fto_5falns_5298',['save_frag_lens_to_alns',['../classvg_1_1FragmentLengthStatistics.html#ab9376051edd07e128f52f57ac2b5a410',1,'vg::FragmentLengthStatistics']]],
+ ['save_5ffunction_5ft_5299',['save_function_t',['../namespacevg_1_1io.html#a161bd20a13c1fd9993bcddd7ea3cbe57',1,'vg::io']]],
+ ['save_5fgbwt_5300',['save_gbwt',['../namespacevg.html#a790122d8b3f28068aaf09f1eb5b966a9',1,'vg::save_gbwt(const gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a8385d575383b7bae35726e90851a2795',1,'vg::save_gbwt(const gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
+ ['save_5fgbwtgraph_5301',['save_gbwtgraph',['../namespacevg.html#aea7640260b1c70795335439f3d6c2eac',1,'vg']]],
+ ['save_5fgbz_5302',['save_gbz',['../namespacevg.html#a017e7cda40a98b4b044507ab78a34da9',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a6beaace0e6d90b654dc9c382afb39ce0',1,'vg::save_gbz(const gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#af7669e457f62e6f197f3120086a091e2',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
+ ['save_5fgcsa_5303',['save_gcsa',['../namespacevg.html#aa2840fc8dbdb12c000769a3baa39b808',1,'vg']]],
+ ['save_5fhandle_5fgraph_5304',['save_handle_graph',['../namespacevg_1_1io.html#af3f5510bd6a0e5514d3083fcd2ffdd32',1,'vg::io::save_handle_graph(HandleGraph *graph, ostream &os)'],['../namespacevg_1_1io.html#a571f402ff74b738d9070a598a41b58da',1,'vg::io::save_handle_graph(HandleGraph *graph, const string &dest_path)']]],
+ ['save_5fhandle_5fgraph_2ehpp_5305',['save_handle_graph.hpp',['../save__handle__graph_8hpp.html',1,'']]],
+ ['save_5flcp_5306',['save_lcp',['../namespacevg.html#a604f783fb59cb6c3e7fcc783a8286822',1,'vg']]],
+ ['save_5fminimizer_5307',['save_minimizer',['../namespacevg.html#af7885143ca20185816afadc669813f12',1,'vg']]],
+ ['save_5fr_5findex_5308',['save_r_index',['../namespacevg.html#a50d4b5eef7efd656daeb423af1f6a3c6',1,'vg']]],
+ ['save_5frecords_5309',['save_records',['../classvg_1_1HTSWriter.html#a4d3f2772a76d36733f1bb1ccf93f498b',1,'vg::HTSWriter']]],
+ ['save_5fto_5ffile_5310',['save_to_file',['../classvg_1_1Packer.html#a936e5283142e2fb3ac089730b217d533',1,'vg::Packer']]],
+ ['scan_5311',['scan',['../classvg_1_1DozeuInterface.html#a73d9afd8c6b52ff715ae0606bbae4b63',1,'vg::DozeuInterface::scan()'],['../classvg_1_1XdropAligner.html#a3bf50d433186476abc2f732525bf1377',1,'vg::XdropAligner::scan()'],['../classvg_1_1QualAdjXdropAligner.html#a2e8adea58e74731765b5c7d0eb54386f',1,'vg::QualAdjXdropAligner::scan()'],['../structvg_1_1PositionIDScanner.html#a32743fa0fd2721702fe8fc34d565c64a',1,'vg::PositionIDScanner::scan()'],['../structvg_1_1IDScanner.html#a36577d4a2c2ac0d7a12383ae6e9e999d',1,'vg::IDScanner::scan()'],['../structvg_1_1WrappingPositionScanner.html#ac9e28c724f1361a03b6a07e0f9e29ada',1,'vg::WrappingPositionScanner::scan()'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)']]],
+ ['scan_5fbackward_5312',['scan_backward',['../classvg_1_1StreamIndexBase.html#addb451cabccc43915ae629925b3ed3ee',1,'vg::StreamIndexBase']]],
+ ['scan_5fcontig_5flengths_5313',['scan_contig_lengths',['../classvg_1_1VCFGenotyper.html#a28f3c05eb4ffefef243a18dc27562b15',1,'vg::VCFGenotyper']]],
+ ['scan_5ffor_5fdeletion_5314',['scan_for_deletion',['../classvg_1_1VCFTraversalFinder.html#a7842cce2da7786e41fbd110c78e45ef6',1,'vg::VCFTraversalFinder']]],
+ ['scan_5fp_5fvisits_5315',['scan_p_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a04d2b3f11fa053b6d6cdbbcae94b4873',1,'vg::algorithms::GFAParser']]],
+ ['scan_5fpath_5316',['scan_path',['../classhandlegraph_1_1PathHandleGraph.html#aa071f31a10a02d8231b029d0a7ddef0b',1,'handlegraph::PathHandleGraph']]],
+ ['scan_5fseed_5fposition_5317',['scan_seed_position',['../classvg_1_1DozeuInterface.html#a472afdc993f32bfa38518a9cfbd14dcb',1,'vg::DozeuInterface']]],
+ ['scan_5fsnarl_5318',['scan_snarl',['../classvg_1_1VCFOutputCaller.html#ad6cbf084906bc4676fae7715495888b3',1,'vg::VCFOutputCaller']]],
+ ['scan_5fvisits_5319',['scan_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a58ceb0c0017e5ea50b35854e5c52f0f4',1,'vg::algorithms::GFAParser']]],
+ ['scan_5fw_5fvisits_5320',['scan_w_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a7e83307cfe42aae91205fa7180b802b4',1,'vg::algorithms::GFAParser']]],
+ ['scanner_2ecpp_5321',['scanner.cpp',['../scanner_8cpp.html',1,'']]],
+ ['scanner_2ehpp_5322',['scanner.hpp',['../scanner_8hpp.html',1,'']]],
+ ['scc_5fcopy_5fcount_5323',['scc_copy_count',['../classvg_1_1DagifiedGraph.html#a780a2eb98c2a1ad1b106283048f95cf0',1,'vg::DagifiedGraph']]],
+ ['scc_5fcopy_5fof_5fhandle_5324',['scc_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a015efe5e782831e59aaa3c2d6f98cbfd',1,'vg::DagifiedGraph']]],
+ ['scc_5fcopy_5fof_5fnode_5fid_5325',['scc_copy_of_node_id',['../classvg_1_1DagifiedGraph.html#a26161bf79e0a6385ff8f6fb67a1e907b',1,'vg::DagifiedGraph']]],
+ ['scc_5fof_5fhandle_5326',['scc_of_handle',['../classvg_1_1DagifiedGraph.html#afc531153860777849e241cd95ac06b03',1,'vg::DagifiedGraph']]],
+ ['score_5327',['score',['../classvg_1_1MEMChainModelVertex.html#a10cf4210b2f802b628111fe2cd1f309b',1,'vg::MEMChainModelVertex::score()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aa0f6834e2a0860792afc6a701d3396c3',1,'vg::MEMClusterer::HitNode::score()'],['../structvg_1_1Funnel_1_1Item.html#a91b9d511109c7c561be120d3346ea3df',1,'vg::Funnel::Item::score()'],['../structvg_1_1WFAPoint.html#a6358c051265bfcc41d857f6df091eebb',1,'vg::WFAPoint::score()'],['../structvg_1_1GaplessExtension.html#a0989b2a97d4403b381dbf68768757d32',1,'vg::GaplessExtension::score()'],['../structvg_1_1WFAAlignment.html#a066d6b546e0308e8df7fc74f42d5de67',1,'vg::WFAAlignment::score()'],['../structvg_1_1Genotyper_1_1Affinity.html#aa0fa1b63d720aa196205be34ee80ee07',1,'vg::Genotyper::Affinity::score()'],['../structvg_1_1GFFRecord.html#aabb70a3b691d378e87cb3fc3fef418ac',1,'vg::GFFRecord::score()'],['../classvg_1_1AlignmentChainModelVertex.html#a207cf7885f1eb8d129d9f599791b0dea',1,'vg::AlignmentChainModelVertex::score()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a002868b55e87a630c4e4f1e1ff213008',1,'vg::MinimizerMapper::Minimizer::score()'],['../structvg_1_1Recombinator_1_1Statistics.html#a348046df697bf6a89261ecfcb6ac6765',1,'vg::Recombinator::Statistics::score()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#abe1c7432c38de20678f5a74798d96bd4',1,'vg::SnarlDistanceIndexClusterer::Cluster::score()'],['../classvg_1_1algorithms_1_1TracedScore.html#a6c63f6d5199ec14c3e912e06f74d9974',1,'vg::algorithms::TracedScore::score()'],['../structvg_1_1Alignment.html#a5c57b95a7ea122139a092427b592ebeb',1,'vg::Alignment::score()'],['../structvg_1_1Subpath.html#acffb5adff6c20c194740186323f1f484',1,'vg::Subpath::score()'],['../structvg_1_1Connection.html#a5e880c9306bb072e08ab6315bdbb1c6f',1,'vg::Connection::score()'],['../structvg_1_1BenchmarkResult.html#a4baad39dafa27d171b65df225666c887',1,'vg::BenchmarkResult::score()'],['../classvg_1_1MEMChainModel.html#aca053d2a91e4ea7ac440edd670893a84',1,'vg::MEMChainModel::score()'],['../classvg_1_1Funnel.html#a9cdacae4561ece776ba90e293299f930',1,'vg::Funnel::score()'],['../structhaplo_1_1haplo__DP.html#aadc492bf7d73b8d551ed56bb62266baa',1,'haplo::haplo_DP::score(const vg::Path &path, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1haplo__DP.html#a3204316e386c183faa191b9ee6f0b34e',1,'haplo::haplo_DP::score(const gbwt_thread_t &thread, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1linear__haplo__structure.html#a100ae7bbb7fa336e7d273c066f251e29',1,'haplo::linear_haplo_structure::score()'],['../classhaplo_1_1ScoreProvider.html#a4dd1edd0db2c92780af0fce9e62e8a1f',1,'haplo::ScoreProvider::score()'],['../classhaplo_1_1GBWTScoreProvider.html#a9970037ed1e272daa0e0bfdf358c9bce',1,'haplo::GBWTScoreProvider::score()'],['../classhaplo_1_1LinearScoreProvider.html#a0d95fe4eff2760404bce49d3aa50e2f0',1,'haplo::LinearScoreProvider::score()'],['../classvg_1_1AlignmentChainModel.html#a562dbec7e2dc602c82b92ad202620429',1,'vg::AlignmentChainModel::score()'],['../classvg_1_1connection__t.html#a8f34943152ac67f59c15ff776da592e8',1,'vg::connection_t::score()'],['../classvg_1_1subpath__t.html#a9e59579440b9a90f5b0c606dc3cf400a',1,'vg::subpath_t::score()'],['../classvg_1_1algorithms_1_1Anchor.html#aff7b7e2c62b7b7154edd3a9f64b0e5a7',1,'vg::algorithms::Anchor::score()']]],
+ ['score_5falignment_5328',['score_alignment',['../classvg_1_1Mapper.html#aa541cae3a3598e10a7baf7d5ed78f644',1,'vg::Mapper']]],
+ ['score_5falignment_5fpair_5329',['score_alignment_pair',['../classvg_1_1MinimizerMapper.html#a99ce46a1525f7be9fa393163ca1eac40',1,'vg::MinimizerMapper']]],
+ ['score_5fbest_5fchain_5330',['score_best_chain',['../namespacevg_1_1algorithms.html#ad91b7ceb67d3923a4c5cace56a5c4f6e',1,'vg::algorithms']]],
+ ['score_5fbound_5331',['score_bound',['../classvg_1_1WFATree.html#afdb599de97d172e2afde161ea0f8efc9',1,'vg::WFATree']]],
+ ['score_5fchain_5fgap_5332',['score_chain_gap',['../namespacevg_1_1algorithms.html#abdc2933db32d78a14a8e439f7e9643ab',1,'vg::algorithms']]],
+ ['score_5fcluster_5333',['score_cluster',['../classvg_1_1MinimizerMapper.html#a12e67c2dfdb80db4080d3675ed6a18d4',1,'vg::MinimizerMapper']]],
+ ['score_5fcontiguous_5falignment_5334',['score_contiguous_alignment',['../classvg_1_1GSSWAligner.html#a95753239b9d5fa388198ea04ac6c559b',1,'vg::GSSWAligner']]],
+ ['score_5fdiscontiguous_5falignment_5335',['score_discontiguous_alignment',['../classvg_1_1GSSWAligner.html#a795072356e28310d80f95bb5f0bb61f3',1,'vg::GSSWAligner']]],
+ ['score_5ferror_5336',['score_error',['../structvg_1_1BenchmarkResult.html#a880a443c67063f66623006cd82b5ec9d',1,'vg::BenchmarkResult']]],
+ ['score_5fexact_5fmatch_5337',['score_exact_match',['../classvg_1_1GSSWAligner.html#ac33af43d7d8d4a3d94a5ef1582c50cc4',1,'vg::GSSWAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const =0'],['../classvg_1_1GSSWAligner.html#ac8e1b97332df85221c6a2be61cbd1b3d',1,'vg::GSSWAligner::score_exact_match(const string &sequence, const string &base_quality) const =0'],['../classvg_1_1GSSWAligner.html#ac2969d865d7cb4652a7476feabd9c9b5',1,'vg::GSSWAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1Aligner.html#a4e087eea3154fc52fff10cbe14d0cd32',1,'vg::Aligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1Aligner.html#ab18b86459ab4471de6361bce2d8e8459',1,'vg::Aligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1Aligner.html#a86b2a95cc4d4de88a78ab6ce8ccc4b79',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#ae88c5b0e7c75fec448d4ed245cebe9b9',1,'vg::Aligner::score_exact_match(const string &sequence) const'],['../classvg_1_1Aligner.html#a2acc9c763d0b7c16ad69472a148ce75b',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end) const'],['../classvg_1_1QualAdjAligner.html#adf03ac873ae9a9cfbc21e589775111be',1,'vg::QualAdjAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1QualAdjAligner.html#a51941e8914296630f63d303c548cee8d',1,'vg::QualAdjAligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1QualAdjAligner.html#a8348afe2de6738fd4cd26e3fd6358818',1,'vg::QualAdjAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const']]],
+ ['score_5fextension_5fgroup_5338',['score_extension_group',['../classvg_1_1MinimizerMapper.html#a2c8ab02743227cb2550fcfd295043253',1,'vg::MinimizerMapper']]],
+ ['score_5fextensions_5339',['score_extensions',['../classvg_1_1MinimizerMapper.html#af9ff5e0a1b8c7925ccdb8a23d29872ef',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::vector< GaplessExtension >> &extensions, const Alignment &aln, Funnel &funnel) const'],['../classvg_1_1MinimizerMapper.html#a421cdd65bac59fac39fd3b87cce0f3ae',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::pair< std::vector< GaplessExtension >, size_t >> &extensions, const Alignment &aln, Funnel &funnel) const']]],
+ ['score_5ffrom_5340',['score_from',['../classvg_1_1algorithms_1_1TracedScore.html#a999c0829c8c11a2d7478630612b60b74',1,'vg::algorithms::TracedScore']]],
+ ['score_5ffull_5flength_5fbonus_5341',['score_full_length_bonus',['../classvg_1_1GSSWAligner.html#ad6bac86acf59cc8edd4969bd671fcf5d',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1GSSWAligner.html#a952bb420992b5e5e4c81388b015caf97',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const =0'],['../classvg_1_1Aligner.html#aaf87ac123c806ef49c509c494b431c9c',1,'vg::Aligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a442d01bf1ed7d011d015d790f0595817',1,'vg::Aligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const'],['../classvg_1_1QualAdjAligner.html#ac4505d206516b2ad51bdc2387309ae9e',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1QualAdjAligner.html#a84b8bacfebeb426d367ec4441800a4e4',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const']]],
+ ['score_5fgap_5342',['score_gap',['../classvg_1_1GSSWAligner.html#a4071f79659899761586807411d5ab767',1,'vg::GSSWAligner::score_gap()'],['../namespacevg.html#aea0e7a0965b967bed3ff54e6ff630f91',1,'vg::score_gap()']]],
+ ['score_5fmatrix_5343',['score_matrix',['../classvg_1_1GSSWAligner.html#a9ad471080a267eb489e31523ef2b5f2b',1,'vg::GSSWAligner']]],
+ ['score_5fmismatch_5344',['score_mismatch',['../classvg_1_1GSSWAligner.html#ab40663f27266555cd2718fca337ac348',1,'vg::GSSWAligner::score_mismatch()'],['../classvg_1_1Aligner.html#a7e359a8a6af31e1fba84a681c751ec23',1,'vg::Aligner::score_mismatch(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a6728bc34b9e4daa49c1045c8ded44553',1,'vg::Aligner::score_mismatch(size_t length) const'],['../classvg_1_1QualAdjAligner.html#ada69f388d291f6c3693812d91c84231a',1,'vg::QualAdjAligner::score_mismatch()']]],
+ ['score_5foutput_5345',['score_output',['../structHaplotypesConfig.html#aea2a24fbc9fbe00f814c1b98d8607079',1,'HaplotypesConfig']]],
+ ['score_5fpartial_5falignment_5346',['score_partial_alignment',['../classvg_1_1GSSWAligner.html#adc950708e8d5ff812a838116c6b50910',1,'vg::GSSWAligner::score_partial_alignment()'],['../classvg_1_1Aligner.html#a4537844a4aa7783f6a41c7cefd758602',1,'vg::Aligner::score_partial_alignment()'],['../classvg_1_1QualAdjAligner.html#aee20bae08e744224825723a878d57bef',1,'vg::QualAdjAligner::score_partial_alignment()']]],
+ ['score_5fsort_5fand_5fdeduplicate_5falignments_5347',['score_sort_and_deduplicate_alignments',['../classvg_1_1Mapper.html#ae820fb3edeac9da2ef475cb6b0e0f0e9',1,'vg::Mapper']]],
+ ['score_5fto_5funnormalized_5flikelihood_5fln_5348',['score_to_unnormalized_likelihood_ln',['../classvg_1_1GSSWAligner.html#a59623587d4dfb1e0310fb608e9def2f0',1,'vg::GSSWAligner']]],
+ ['score_5ftree_5349',['score_tree',['../classvg_1_1MinimizerMapper.html#ad4b6267b5e93d0fb618de0584cf2b213',1,'vg::MinimizerMapper']]],
+ ['scoreproperties_5350',['ScoreProperties',['../structvg_1_1WFATree_1_1ScoreProperties.html',1,'vg::WFATree']]],
+ ['scoreprovider_5351',['ScoreProvider',['../classhaplo_1_1ScoreProvider.html',1,'haplo']]],
+ ['scores_5352',['scores',['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ab466534da431354516132617d0f14e95',1,'vg::Recombinator::LocalHaplotype']]],
+ ['scoringoptions_5353',['ScoringOptions',['../structScoringOptions.html',1,'']]],
+ ['scratch_5354',['scratch',['../structvg_1_1ChainIterator.html#a277447dceb98d18d597a73f2c790e15c',1,'vg::ChainIterator']]],
+ ['search_5fleft_5355',['search_left',['../classvg_1_1NestedTraversalFinder.html#a04465d6248557f427e5d35b657292e25',1,'vg::NestedTraversalFinder']]],
+ ['search_5fmultipath_5falignment_5356',['search_multipath_alignment',['../namespacevg.html#aa9d71371be6972c8284b267d42fac754',1,'vg']]],
+ ['search_5fright_5357',['search_right',['../classvg_1_1NestedTraversalFinder.html#a2b020fead8b7c40b06f9c0e1041b2cb5',1,'vg::NestedTraversalFinder']]],
+ ['search_5fthreads_5358',['search_threads',['../structGBWTConfig.html#a1e999f204cdd3655aac4739f12b3265f',1,'GBWTConfig']]],
+ ['search_5ftype_5359',['search_type',['../classvg_1_1PhaseUnfolder.html#a7484966dc448f4c3b894a53233f46d9f',1,'vg::PhaseUnfolder']]],
+ ['secondary_5frescue_5fattempts_5360',['secondary_rescue_attempts',['../classvg_1_1MultipathMapper.html#a0203a68c7b346ec30bf2854c78bb3434',1,'vg::MultipathMapper']]],
+ ['secondary_5frescue_5fscore_5fdiff_5361',['secondary_rescue_score_diff',['../classvg_1_1MultipathMapper.html#ac5ba763f99c22ff9feccb76333cf1039',1,'vg::MultipathMapper']]],
+ ['secondary_5frescue_5fsubopt_5fdiff_5362',['secondary_rescue_subopt_diff',['../classvg_1_1MultipathMapper.html#aee081b4a0ee6adadb2dff205a24a2c7a',1,'vg::MultipathMapper']]],
+ ['secondary_5fscore_5363',['secondary_score',['../structvg_1_1Alignment.html#a58502a21a2588a5ac8baaa6e31c81eb4',1,'vg::Alignment']]],
+ ['seed_5364',['Seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html',1,'vg::SnarlDistanceIndexClusterer::Seed'],['../classvg_1_1MCMCGenotyper.html#aa2399e6a45d2595e08053cdb66207b37',1,'vg::MCMCGenotyper::seed()'],['../classvg_1_1NGSSimulator.html#a99ce1e3ba72956bbf9d1cbaa0fd89014',1,'vg::NGSSimulator::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a1430e1d0dccc75ffa1962408e6226a21',1,'vg::SnarlDistanceIndexClusterer::SeedCache::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#aae124944787f51e8d8fc23cb274f0350',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::seed()'],['../classvg_1_1SpliceRegion.html#a10732e3be85dbecaf6d046ba52f9f716',1,'vg::SpliceRegion::seed()'],['../classvg_1_1StreamSorter.html#a8875748639a885dfacf261956a9b3ee4',1,'vg::StreamSorter::seed()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a38ffc441fe03ec44c1c089eba2b76ae2',1,'vg::ZipCodeTree::oriented_seed_t::seed()'],['../classvg_1_1MinimizerMapper.html#ab964411462aea4fc777127a887a9a6f7',1,'vg::MinimizerMapper::Seed()'],['../classvg_1_1ZipCodeTree.html#a50817b343d4ad6368df659e16b9a7549',1,'vg::ZipCodeTree::Seed()'],['../classvg_1_1ZipCodeForest.html#a93f9eaa38dd8024a73a2aeca456e5156',1,'vg::ZipCodeForest::Seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#adf405ffb00189f3c469f3fc7e79fde01',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed()=default'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#ad6d85e239a68f94ff5dbf2b0362f3c52',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(pos_t pos, size_t source, ZipCode zipcode)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a7859f190024d96f7182de94f197df881',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(Seed &&other)'],['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adab044c319f32f470727c5c2ba078487f5',1,'vg::ZipCodeTree::SEED()']]],
+ ['seed_5fcount_5fprefix_5fsum_5365',['seed_count_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af787cd3652afaa91cdebf97673456004',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['seed_5fend_5366',['seed_end',['../classvg_1_1algorithms_1_1Anchor.html#a2db67aba40631bb9e462e2ae744a2ddd',1,'vg::algorithms::Anchor']]],
+ ['seed_5findices_5367',['seed_indices',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ad587cbee5a1b577adbc9548a99f857b4',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['seed_5fis_5freversed_5fat_5fdepth_5368',['seed_is_reversed_at_depth',['../classvg_1_1ZipCodeTree.html#a984f21c55ccaf7b053ce0e4fe77f91ff',1,'vg::ZipCodeTree']]],
+ ['seed_5flength_5369',['seed_length',['../classvg_1_1algorithms_1_1Anchor.html#a739e4bcbda94fa20b8d99ad5340b5fc6',1,'vg::algorithms::Anchor']]],
+ ['seed_5fresult_5ft_5370',['seed_result_t',['../structvg_1_1ZipCodeTree_1_1seed__result__t.html',1,'vg::ZipCodeTree']]],
+ ['seed_5fsort_5forder_5371',['seed_sort_order',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ae40d481f31fd4ece290a206482ed5a13',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['seed_5fstart_5372',['seed_start',['../classvg_1_1algorithms_1_1Anchor.html#af68c4af649ee5dfbf4cfff0e0e4493c8',1,'vg::algorithms::Anchor']]],
+ ['seed_5ftype_5373',['seed_type',['../structvg_1_1GaplessExtension.html#a8c8a3d415e13a943e87b4c1e33347081',1,'vg::GaplessExtension::seed_type()'],['../classvg_1_1GaplessExtender.html#a8891a422c7921863c589850636d9f252',1,'vg::GaplessExtender::seed_type()']]],
+ ['seedcache_5374',['SeedCache',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['seeds_5375',['seeds',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a7451a72162f19b00d1bd44fc62be0297',1,'vg::BandedGlobalAligner::BAMatrix::seeds()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a0531ebefe7a686d6624c7b5f60357aeb',1,'vg::SnarlDistanceIndexClusterer::Cluster::seeds()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ac8b2807cb1f656be384407ed36b1c926',1,'vg::ZipCodeForest::forest_growing_state_t::seeds()']]],
+ ['seeds_5fin_5fsubgraph_5376',['seeds_in_subgraph',['../classvg_1_1MinimizerMapper.html#a98117858da937a277f445898bcc2d125',1,'vg::MinimizerMapper']]],
+ ['seek_5377',['seek',['../structhFILE__backend.html#a93b5b1dcb35560b106e1cccb38476ddb',1,'hFILE_backend::seek()'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa221be19182d88b7caa36ead3e63c829',1,'vg::io::BlockedGzipInputStream::Seek()']]],
+ ['seek_5fgroup_5378',['seek_group',['../classvg_1_1io_1_1MessageIterator.html#a97a1561c82f55827a208b2bea5e8da71',1,'vg::io::MessageIterator::seek_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#aad5921d9a10314f8060b0835225fc3cd',1,'vg::io::ProtobufIterator::seek_group()']]],
+ ['seen_5fread_5fnames_5379',['seen_read_names',['../classvg_1_1ReadFilter.html#a613b00bb83a119d89911ed4315e4e24a',1,'vg::ReadFilter']]],
+ ['segment_5fto_5fname_5380',['segment_to_name',['../classvg_1_1FlatFileBackTranslation.html#a09f2373723a0f9901698cf8315a3f813',1,'vg::FlatFileBackTranslation']]],
+ ['segment_5ftranslation_5381',['segment_translation',['../structGBWTConfig.html#a8415ef08abc7ef4e9d854dc100d0df15',1,'GBWTConfig']]],
+ ['select_5fdiploid_5382',['select_diploid',['../namespacevg.html#a5b634a10b029be9c22dccc3ef362f61c',1,'vg']]],
+ ['select_5fhaplotypes_5383',['select_haplotypes',['../namespacevg.html#af2de3a2f2b77abef4336df983356fc23',1,'vg']]],
+ ['sense_5fto_5fstring_5384',['SENSE_TO_STRING',['../paths__main_8cpp.html#a16ad253f4e8c46b88b363e1ffc613c51',1,'paths_main.cpp']]],
+ ['separator_5385',['SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#ac50cb6403ceaabd3f878e2c4f2195f56',1,'handlegraph::PathMetadata']]],
+ ['seq_5386',['seq',['../structvg_1_1kmer__t.html#a98b04ac70a36cf6feae80b03b3a32eb2',1,'vg::kmer_t::seq()'],['../structvg_1_1Region.html#a938cc852fd08f11656bdfbd204843017',1,'vg::Region::seq()'],['../structvg_1_1VG_1_1Plan.html#a4bb5a9fa8f5bb32c2e94d3c038f9cf95',1,'vg::VG::Plan::seq()'],['../structvg_1_1algorithms_1_1kmer__t.html#a5c235e7c7f3a819e291956d8e307821a',1,'vg::algorithms::kmer_t::seq()'],['../structvg_1_1algorithms_1_1walk__t.html#a65bec2a64da1b8f7c3820d49b5bef09f',1,'vg::algorithms::walk_t::seq()']]],
+ ['seq_5fchain_5ffor_5fpath_5387',['seq_chain_for_path',['../haplotypes__main_8cpp.html#a462a39ecca4a3d1298196a6f23ef24a5',1,'haplotypes_main.cpp']]],
+ ['seq_5fdoes_5fnot_5fmatch_5388',['SEQ_DOES_NOT_MATCH',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9acc8619639d089c16381dd05298fe3df8',1,'vg::AlignmentValidity']]],
+ ['seq_5ffor_5fchain_5389',['seq_for_chain',['../haplotypes__main_8cpp.html#ace19d06b45cb66b44602157c3bc24916',1,'haplotypes_main.cpp']]],
+ ['seq_5flength_5390',['seq_length',['../classvg_1_1Viz.html#a2f5862e76ca098060b503d03de76c024',1,'vg::Viz::seq_length()'],['../classxg_1_1XG.html#a7eadd7681a21479f7f31c240047cdffe',1,'xg::XG::seq_length()']]],
+ ['seq_5foffset_5391',['seq_offset',['../structvg_1_1MatchPos.html#a85fc0d2a7af86db887d649d3c968755e',1,'vg::MatchPos::seq_offset()'],['../structvg_1_1WFAPoint.html#a14ceda5614586a0e3ef44b729ad179c0',1,'vg::WFAPoint::seq_offset()'],['../structvg_1_1WFAAlignment.html#a1fc0e09c8462c5aa10d4f0acbc2a8f2d',1,'vg::WFAAlignment::seq_offset()']]],
+ ['seqcomplexity_5392',['SeqComplexity',['../structvg_1_1SeqComplexity.html',1,'vg::SeqComplexity< MaxOrder >'],['../structvg_1_1SeqComplexity.html#a18ab1a3d85623f42d1e8848fcf94846d',1,'vg::SeqComplexity::SeqComplexity(string::const_iterator begin, string::const_iterator end)'],['../structvg_1_1SeqComplexity.html#ac7a2e970b541883c812fafa7851d6278',1,'vg::SeqComplexity::SeqComplexity(const string &seq)']]],
+ ['sequence_5393',['sequence',['../classvg_1_1ExtraNodeGraph.html#ad485e6609536566720fe5a48f7e2af84',1,'vg::ExtraNodeGraph::sequence()'],['../classvg_1_1WFATree.html#abbd67ff2f910ad5a4c0c1f49b10394a5',1,'vg::WFATree::sequence()'],['../structvg_1_1PathIndex.html#a0b807b5252299d9b0f1c9168079a591f',1,'vg::PathIndex::sequence()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#a2e6f784aa4bde512d84c0f1d3cedd01f',1,'vg::Recombinator::LocalHaplotype::sequence()'],['../structvg_1_1Node.html#a9a0e8995bc48aa5e24977d1bd20e91a3',1,'vg::Node::sequence()'],['../structvg_1_1Edit.html#a4a7726b24b28ed819d37b9c39ae839d1',1,'vg::Edit::sequence()'],['../structvg_1_1Alignment.html#a2ae1f06d48c37997cee72b7cd3210a83',1,'vg::Alignment::sequence()'],['../structvg_1_1MultipathAlignment.html#ae6c263b75effad9b08e514c5852f1221',1,'vg::MultipathAlignment::sequence()'],['../structvg_1_1KmerMatch.html#ab434e30bbaf0fbb10425d5bc35ac50b2',1,'vg::KmerMatch::sequence()'],['../classvg_1_1MaximalExactMatch.html#a9746bd3ef368dbeae05459381223cebc',1,'vg::MaximalExactMatch::sequence()'],['../classvg_1_1multipath__alignment__t.html#a5637161345c2b1a557a40188b564dd55',1,'vg::multipath_alignment_t::sequence()'],['../classvg_1_1edit__t.html#aca5aef83ea5f5195699732c61c44b86d',1,'vg::edit_t::sequence()'],['../classvg_1_1Sampler.html#a355de4870a71a88834406f3e7f297272',1,'vg::Sampler::sequence()']]],
+ ['sequence_5fcomplexity_2ehpp_5394',['sequence_complexity.hpp',['../sequence__complexity_8hpp.html',1,'']]],
+ ['sequence_5fid_5395',['sequence_id',['../structvg_1_1GFFRecord.html#a91b952a4d9d5c4f44e6def80e33073c8',1,'vg::GFFRecord::sequence_id()'],['../structvg_1_1RecombinatorHaplotype.html#a3b372fd165a3e707a50e2a0a1f61cef5',1,'vg::RecombinatorHaplotype::sequence_id()']]],
+ ['sequence_5fpositions_5396',['sequence_positions',['../classvg_1_1BaseMapper.html#a1fc5077e5ea4a236ddf8edcf93288eb9',1,'vg::BaseMapper']]],
+ ['sequence_5fsource_5397',['sequence_source',['../structGraphHandler.html#a1583ae5e2c88d3099b62255a28978316',1,'GraphHandler']]],
+ ['sequence_5ftype_5398',['sequence_type',['../structvg_1_1RecombinatorHaplotype.html#a20c784c55500a6e02c9ad4762be12176',1,'vg::RecombinatorHaplotype::sequence_type()'],['../classvg_1_1Haplotypes.html#aebc70f387d48bd0e5c8f0c607c496535',1,'vg::Haplotypes::sequence_type()'],['../classvg_1_1HaplotypePartitioner.html#aa06fc618c54377342c05b7306b8dec72',1,'vg::HaplotypePartitioner::sequence_type()'],['../classvg_1_1Recombinator.html#a8a1ad77c3ad37fbcfa48dc5f89f591af',1,'vg::Recombinator::sequence_type()']]],
+ ['sequences_5399',['sequences',['../structvg_1_1Haplotypes_1_1Subchain.html#aae0d847a9118ccb4ff178c3ac7c759eb',1,'vg::Haplotypes::Subchain']]],
+ ['serializable_5400',['Serializable',['../classhandlegraph_1_1Serializable.html',1,'handlegraph']]],
+ ['serializable_2ecpp_5401',['serializable.cpp',['../serializable_8cpp.html',1,'']]],
+ ['serializable_2ehpp_5402',['serializable.hpp',['../serializable_8hpp.html',1,'']]],
+ ['serializable_5fhandle_5fgraph_2ehpp_5403',['serializable_handle_graph.hpp',['../serializable__handle__graph_8hpp.html',1,'']]],
+ ['serializablehandlegraph_5404',['SerializableHandleGraph',['../classhandlegraph_1_1SerializableHandleGraph.html',1,'handlegraph::SerializableHandleGraph'],['../namespacevg.html#a7378a177b4ed2e7be87e02a9bfcb7d4e',1,'vg::SerializableHandleGraph()']]],
+ ['serialize_5405',['serialize',['../structvg_1_1GBWTHandler.html#aa855690c481cca126734e20f5d126d04',1,'vg::GBWTHandler::serialize()'],['../classvg_1_1Packer.html#a833e1fa21ac3f5f5f6a001c5c5ee0f4c',1,'vg::Packer::serialize()'],['../classvg_1_1SnarlManager.html#afdcb932a1a891671acbdaaf445aee0b2',1,'vg::SnarlManager::serialize()'],['../classvg_1_1VG.html#a0ee4603518e9cd5915a65e65c2d763b2',1,'vg::VG::serialize()'],['../classvg_1_1ZipCodeCollection.html#afb7d15490acd1b076664049072184914',1,'vg::ZipCodeCollection::serialize()'],['../classxg_1_1XGPath.html#a74e7b70ac4829545e7b48c137808d6e4',1,'xg::XGPath::serialize()'],['../classhandlegraph_1_1Serializable.html#adae323cce9552f03774ab71dd5fb07d0',1,'handlegraph::Serializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1Serializable.html#ac6e9dfc830acdf96fbfe53d83d33802e',1,'handlegraph::Serializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1Serializable.html#a050e6c2b6e2fccd85362e908da60d20b',1,'handlegraph::Serializable::serialize(std::ostream &out)'],['../classhandlegraph_1_1Serializable.html#aa97699c9b50235d5f2439eb57c5df653',1,'handlegraph::Serializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#acaec0b472d85de2ff98b8635b5fbf33c',1,'handlegraph::TriviallySerializable::serialize(const std::function< void(const void *, size_t)> &iteratee) const =0'],['../classhandlegraph_1_1TriviallySerializable.html#a2881d2d598bd35cc68008ad3dc4b82d5',1,'handlegraph::TriviallySerializable::serialize(int fd)=0'],['../classhandlegraph_1_1TriviallySerializable.html#ab04c99b94217a13ce598e8fd484b09c1',1,'handlegraph::TriviallySerializable::serialize(int fd) const'],['../classhandlegraph_1_1TriviallySerializable.html#aaeb37dbdd6e221e2c5ddfba9cb226c56',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1TriviallySerializable.html#a6c306e7cce2dfe6079b093aa2fae77a0',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#a674a89ff2072c5e57c7f5f07d915d049',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1TriviallySerializable.html#a89624195e0d24768774e98c61d17c779',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out)']]],
+ ['serialize_5fand_5fmeasure_5406',['serialize_and_measure',['../classxg_1_1XG.html#aac0ec5744208c54abfc692bf7ff66536',1,'xg::XG']]],
+ ['serialize_5fmembers_5407',['serialize_members',['../classxg_1_1XG.html#a99af109d31808040b7f1819c6a236b05',1,'xg::XG::serialize_members()'],['../classhandlegraph_1_1Serializable.html#a79235728e5f1e8fb1c0e19e275a33fff',1,'handlegraph::Serializable::serialize_members()']]],
+ ['serialize_5fmembers_5fand_5fmeasure_5408',['serialize_members_and_measure',['../classxg_1_1XG.html#af7c089f5d1342620dd573b2aa4197ca8',1,'xg::XG']]],
+ ['serialize_5fsegment_5ftranslation_5409',['serialize_segment_translation',['../structGraphHandler.html#ad8ffb0dac5a43b9c1dee33eba093d02e',1,'GraphHandler']]],
+ ['serialize_5fto_5femitter_5410',['serialize_to_emitter',['../classvg_1_1VG.html#a59121c0226c3fd8c328641490bf2fac6',1,'vg::VG']]],
+ ['serialize_5fto_5ffile_5411',['serialize_to_file',['../classvg_1_1VG.html#a3522042a3a00ac802d6738d0bec6269c',1,'vg::VG']]],
+ ['serialize_5fto_5ffunction_5412',['serialize_to_function',['../classvg_1_1VG.html#ad3187dd6ce750583f6b1a7c32f278d2a',1,'vg::VG']]],
+ ['serialize_5fto_5fostream_5413',['serialize_to_ostream',['../classvg_1_1VG.html#a70e67b525bca0f766d7f0170759ed1d0',1,'vg::VG']]],
+ ['set_5414',['set',['../structvg_1_1subcommand_1_1BaseArgSpec.html#ae73224926db6d8d7730212d2714e1dcf',1,'vg::subcommand::BaseArgSpec::set()'],['../structvg_1_1subcommand_1_1ArgSpec.html#afd6266196b810cf1b11c88e5ad3fd2a2',1,'vg::subcommand::ArgSpec::set()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad81d797abdd9ece7dece847ad979f80c',1,'vg::subcommand::BaseOptionGroup::set()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a667b46c883efd1b60966679f31bb03fe',1,'vg::subcommand::OptionGroup::set()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a72309d1c25433c7e3a6e3e7dac0930fd',1,'vg::subcommand::GroupedOptionGroup::set()']]],
+ ['set_5falignment_5fscores_5415',['set_alignment_scores',['../classvg_1_1AlignerClient.html#a1fde3e4537147030d153d403fd04ec77',1,'vg::AlignerClient::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#adbdd2fabd7a36353526663aede3cb555',1,'vg::AlignerClient::set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#a79424f53b6e4f588da23ea531a600b84',1,'vg::AlignerClient::set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1BaseMapper.html#addc9b0af15050357598c372e135d6a0e',1,'vg::BaseMapper::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1BaseMapper.html#aed94c577ba8f01eb8098d1be74b8d70a',1,'vg::BaseMapper::set_alignment_scores(istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1MinimizerMapper.html#a98a602ac6b9f20d9da825d8a542ceebd',1,'vg::MinimizerMapper::set_alignment_scores()'],['../classvg_1_1MultipathMapper.html#ad897513b9554b2dabebea47cc3f3da9f',1,'vg::MultipathMapper::set_alignment_scores()']]],
+ ['set_5fallele_5416',['set_allele',['../classvg_1_1PhasedGenome.html#ad0fdafbc6cb6fbfb576be92f6f6bc17d',1,'vg::PhasedGenome']]],
+ ['set_5fannotation_5417',['set_annotation',['../classvg_1_1multipath__alignment__t.html#aebfe1bbda50606c4feb85bb674698c4e',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name)'],['../classvg_1_1multipath__alignment__t.html#a1927cf1ca631a6efb5ed6c83072e2e2c',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, double value)'],['../classvg_1_1multipath__alignment__t.html#a37e9679383b80b3a5028017155d04296',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, bool value)'],['../classvg_1_1multipath__alignment__t.html#aca07d0a515d16b62eca1f1c9ad44ffc9',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, const string &value)'],['../namespacevg.html#adea29af7b94ac90b1db0eacd908511c0',1,'vg::set_annotation(Annotated *annotated, const string &name, const AnnotationType &annotation)'],['../namespacevg.html#a54bcd5d5fc5318bbdbe784f224b906bd',1,'vg::set_annotation(Annotated &annotated, const string &name, const AnnotationType &annotation)']]],
+ ['set_5fautomatic_5fmin_5fclustering_5flength_5418',['set_automatic_min_clustering_length',['../classvg_1_1MultipathMapper.html#ac0a6f15f0273faa48ff52a59a08855e1',1,'vg::MultipathMapper']]],
+ ['set_5favg_5419',['set_avg',['../classvg_1_1Filter.html#a3629b0035db72bc575a6f0d440b52288',1,'vg::Filter']]],
+ ['set_5fbaseline_5ferror_5420',['set_baseline_error',['../classvg_1_1PoissonSupportSnarlCaller.html#a41964acba3d81c26b01f9b00cd49257a',1,'vg::PoissonSupportSnarlCaller']]],
+ ['set_5fchain_5fcomponent_5421',['set_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a6d70e8ff87f9e2a2d47511b9aece4980',1,'vg::ZipCode::node_code_t::set_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a05fecca7e22cfd80595143e5b6fe1b74',1,'vg::ZipCode::snarl_code_t::set_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a969b901d95d609ce1a065278ef6bd7fb',1,'vg::ZipCodeForest::sort_value_t::set_chain_component()']]],
+ ['set_5fchain_5forder_5422',['set_chain_order',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a33c2b7d50ccefb836fe376dec56c9c09',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['set_5fchain_5fvalues_5423',['set_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae0c994c6c86ccbc4b32689baa6183349',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['set_5fchild_5fcount_5424',['set_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04d8cd3924cd20476f71d21690530ee6',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fcircularity_5425',['set_circularity',['../classvg_1_1VG.html#a73c97ce0157b90f95b888e4b6983f5c8',1,'vg::VG::set_circularity()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a9172694447503e35d50093d55e845eb8',1,'handlegraph::MutablePathHandleGraph::set_circularity()']]],
+ ['set_5fcode_5ftype_5426',['set_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aeac2169d6f24e91993e1b8c28b8d5a30',1,'vg::ZipCode::snarl_code_t::set_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ab80c26e62009341686000a010bb0d5c3',1,'vg::ZipCodeForest::sort_value_t::set_code_type()']]],
+ ['set_5fcompressed_5fannotation_5427',['set_compressed_annotation',['../namespacevg.html#a3f6c363cc3cb03b7379635741d1b0837',1,'vg::set_compressed_annotation(Annotated *annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)'],['../namespacevg.html#a0efd9e2e5d1ab86647910ccd002109cd',1,'vg::set_compressed_annotation(Annotated &annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)']]],
+ ['set_5fconnection_5428',['set_connection',['../classvg_1_1subpath__t.html#ae0073c7a92ebfc9ea0acfe7e17837bd1',1,'vg::subpath_t']]],
+ ['set_5fconnectivity_5429',['set_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac59bb21ee878d8f2923ac7f8dc857641',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fcrash_5fcontext_5430',['set_crash_context',['../namespacevg.html#ac801de9444375b2f131d3c21d125e83b',1,'vg']]],
+ ['set_5fdir_5431',['set_dir',['../namespacevg_1_1temp__file.html#a13270094cd53cedbd540c7fd4412f0d6',1,'vg::temp_file::set_dir()'],['../namespacexg_1_1temp__file.html#a43d250a4567f29ba269e8a3f4c39dbb6',1,'xg::temp_file::set_dir()']]],
+ ['set_5fdistance_5fend_5fleft_5432',['set_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a9b8478c75baaf1a65691dd2d72f4c54d',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fdistance_5fend_5fright_5433',['set_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#acb835fdaed8979f3faa044171bfcbe8f',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fdistance_5fstart_5fleft_5434',['set_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2a611cd876f68bb23d5a62babde8bdf9',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fdistance_5fstart_5fright_5435',['set_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3a6fa5c7c47f14100596b3384d72d51f',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fedge_5436',['set_edge',['../classvg_1_1VG.html#ae1131c1ff0a94ed2ec9ef35cb678801b',1,'vg::VG']]],
+ ['set_5ffilter_5fmatches_5437',['set_filter_matches',['../classvg_1_1Filter.html#ad45e46ca49dca65ee8e3d838d28d71b6',1,'vg::Filter']]],
+ ['set_5ffragment_5flength_5fdistr_5fparams_5438',['set_fragment_length_distr_params',['../classvg_1_1PairedEndMapper.html#a09e89f6da87d25f0ad66fb9eb3139a98',1,'vg::PairedEndMapper']]],
+ ['set_5ffrom_5flength_5439',['set_from_length',['../classvg_1_1edit__t.html#aba75c7882507dcced8ca80081b4b504b',1,'vg::edit_t']]],
+ ['set_5fhash_5fcolor_5440',['set_hash_color',['../classvg_1_1Viz.html#ab5559043258bf1e1cd4e3a754342cdde',1,'vg::Viz']]],
+ ['set_5fhet_5fbias_5441',['set_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a0cb5e2761e2c2feebc901d54a5891454',1,'vg::RatioSupportSnarlCaller']]],
+ ['set_5fid_5fincrement_5442',['set_id_increment',['../classvg_1_1VG.html#aebe71b82645b85e73342366cea0a4549',1,'vg::VG::set_id_increment()'],['../classhandlegraph_1_1MutableHandleGraph.html#ab844ab426cd9f289414aca4d8b892ca9',1,'handlegraph::MutableHandleGraph::set_id_increment()']]],
+ ['set_5finsertion_5fbias_5443',['set_insertion_bias',['../classvg_1_1PoissonSupportSnarlCaller.html#abeb1d41aaa26a91cb3319cc5fe6b0af0',1,'vg::PoissonSupportSnarlCaller']]],
+ ['set_5fintermediate_5ffile_5fkeeping_5444',['set_intermediate_file_keeping',['../classvg_1_1IndexRegistry.html#a983cdafc1b28ea24def5349f90e415eb',1,'vg::IndexRegistry']]],
+ ['set_5fintersection_5445',['set_intersection',['../namespacevg.html#a234b2ca417edb50a3c738991fcfc269a',1,'vg']]],
+ ['set_5fintron_5flength_5fdistribution_5446',['set_intron_length_distribution',['../classvg_1_1MultipathMapper.html#a8c6768f5299e424b19d569dd077dbafe',1,'vg::MultipathMapper']]],
+ ['set_5finverse_5447',['set_inverse',['../classvg_1_1Filter.html#afb65a7ed6bb059f22196415c631680e9',1,'vg::Filter']]],
+ ['set_5fis_5freverse_5448',['set_is_reverse',['../classvg_1_1mapping__t.html#ad248204841f7ba0ce4c3604ec138556d',1,'vg::mapping_t::set_is_reverse()'],['../classvg_1_1position__t.html#a3d78fabe1cda0e0243071a36ccd73996',1,'vg::position_t::set_is_reverse()']]],
+ ['set_5fis_5freversed_5449',['set_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#aaab7c0874ce7df9a462009840404e8fb',1,'vg::ZipCode::node_code_t::set_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8836324bf0af9142171328634fba592d',1,'vg::ZipCode::snarl_code_t::set_is_reversed()']]],
+ ['set_5flast_5fcomponent_5450',['set_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a98cac9a41d2c53554c96084e35a591b5',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5flength_5451',['set_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a2ef78836b286d95e1ad7d0b88c55cbaf',1,'vg::ZipCode::node_code_t::set_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a138235f7ccb84dcc25134cf6f200aecb',1,'vg::ZipCode::chain_code_t::set_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a51cb4c8c5a89e591cede7c9a27d77c8b',1,'vg::ZipCode::snarl_code_t::set_length()']]],
+ ['set_5flog_5fodds_5fagainst_5fsplice_5452',['set_log_odds_against_splice',['../classvg_1_1MultipathMapper.html#a8902c35e23b24555f94fd2f7d95ef806',1,'vg::MultipathMapper']]],
+ ['set_5fmapping_5fquality_5453',['set_mapping_quality',['../classvg_1_1multipath__alignment__t.html#a492c704bcf2ec27123143b83d8218ad9',1,'vg::multipath_alignment_t']]],
+ ['set_5fmax_5fmerge_5fsupression_5flength_5454',['set_max_merge_supression_length',['../classvg_1_1MultipathMapper.html#a3db9d73e2a4b296df8df495c028a615b',1,'vg::MultipathMapper']]],
+ ['set_5fmin_5fbp_5fedge_5foverride_5455',['set_min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a920ba7030a3946b9b239b1a7f1abbe44',1,'vg::TraversalSupportFinder']]],
+ ['set_5fmin_5fdepth_5456',['set_min_depth',['../classvg_1_1Filter.html#a94d0c4f93831a6faf70411dc6caf0ac3',1,'vg::Filter']]],
+ ['set_5fmin_5fpercent_5fidentity_5457',['set_min_percent_identity',['../classvg_1_1Filter.html#ae1837a93c7c3575c52dcba37538070f8',1,'vg::Filter']]],
+ ['set_5fmin_5fqual_5458',['set_min_qual',['../classvg_1_1Filter.html#a5c3851f5838da69576fd3e59443bb8d3',1,'vg::Filter']]],
+ ['set_5fmin_5fsoftclip_5flength_5ffor_5fsplice_5459',['set_min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#ad3848a9b82e967ca119dd94add068597',1,'vg::MultipathMapper']]],
+ ['set_5fmin_5fsplice_5flength_5460',['set_min_splice_length',['../classvg_1_1MultipathAlignmentEmitter.html#aa6e3289654a2ebe8ed2b934a1fcd6d40',1,'vg::MultipathAlignmentEmitter']]],
+ ['set_5fmin_5fsupports_5461',['set_min_supports',['../classvg_1_1SupportBasedSnarlCaller.html#a3afbd8d1bc78b6716c587b93424db8cb',1,'vg::SupportBasedSnarlCaller']]],
+ ['set_5fmy_5fpath_5fposition_5fgraph_5462',['set_my_path_position_graph',['../classvg_1_1Filter.html#a8986008ebcb92629e17da5ed45a23734',1,'vg::Filter']]],
+ ['set_5fmy_5fvg_5463',['set_my_vg',['../classvg_1_1Filter.html#a8742f0354b0e40a55ba2dd7270bd197d',1,'vg::Filter']]],
+ ['set_5fnested_5464',['set_nested',['../classvg_1_1VCFOutputCaller.html#a35f5b2f9d93ea764e0d8f5f957ba4c3a',1,'vg::VCFOutputCaller']]],
+ ['set_5fnext_5465',['set_next',['../classvg_1_1connection__t.html#adc3fded850671e336763eaa0c6d87e78',1,'vg::connection_t::set_next()'],['../classvg_1_1subpath__t.html#a2f0c0e1b1e509de732a1318919af0177',1,'vg::subpath_t::set_next()']]],
+ ['set_5fnode_5fid_5466',['set_node_id',['../classvg_1_1mapping__t.html#a3101ac21e398f36c0367a89b20360cd0',1,'vg::mapping_t::set_node_id()'],['../classvg_1_1position__t.html#a5e2f0de1d8da70bb8b233522597bd02b',1,'vg::position_t::set_node_id()']]],
+ ['set_5foffset_5467',['set_offset',['../structhaplo_1_1haplo__DP__rectangle.html#a9ca4ea25d72d1a40b9a0e1a170e88274',1,'haplo::haplo_DP_rectangle::set_offset()'],['../classvg_1_1position__t.html#ad34d5af7aab58a425f33faa2358ef57e',1,'vg::position_t::set_offset()']]],
+ ['set_5foption_5fvalue_5468',['set_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abdc58a9c90f9adbcac68d3e18f6c7d36',1,'vg::subcommand::BaseOptionGroup']]],
+ ['set_5fpaired_5fall_5469',['set_paired_all',['../structvg_1_1Counts.html#a038f57bbb1cabd1f83b544c22562a0d9',1,'vg::Counts']]],
+ ['set_5fpaired_5fany_5470',['set_paired_any',['../structvg_1_1Counts.html#ad4e3e7b118ed1ec1286d933a57bdbf23',1,'vg::Counts']]],
+ ['set_5fpath_5fposition_5471',['set_path_position',['../classvg_1_1Surjector.html#ac4e7823cc2ce4b65bb8910ef2c1dcbee',1,'vg::Surjector']]],
+ ['set_5fprefix_5472',['set_prefix',['../classvg_1_1IndexRegistry.html#aefc2da48af951d3b300ee0b5c70559c3',1,'vg::IndexRegistry']]],
+ ['set_5fprefix_5fsum_5for_5fidentifier_5473',['set_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a0c99221572a9dce4051fa68a79bb540f',1,'vg::ZipCode::node_code_t::set_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8a66d4f3fba23bebe13618b0d45988a4',1,'vg::ZipCode::snarl_code_t::set_prefix_sum_or_identifier()']]],
+ ['set_5fprev_5fidx_5474',['set_prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#ad1c78747473f9b8816c459949b8b8e8e',1,'haplo::haplo_DP_rectangle']]],
+ ['set_5fquality_5475',['set_quality',['../classvg_1_1multipath__alignment__t.html#a2ff40ca9f44290aeb5406764ccbb5ebf',1,'vg::multipath_alignment_t']]],
+ ['set_5fraw_5fchain_5fcomponent_5476',['set_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a32b61e2274b266a217cebace47e2907a',1,'vg::ZipCode::node_code_t::set_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab4c8a0b7d2e5b20bab6ff83558581a4d',1,'vg::ZipCode::snarl_code_t::set_raw_chain_component()']]],
+ ['set_5fraw_5fchild_5fcount_5477',['set_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ace304ea5d619189a001274a3c117a97b',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fcode_5ftype_5478',['set_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a4b2441552754d8c09003a86ed412af6e',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fconnectivity_5479',['set_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a7e9fc82b6947464a05b05ad154a706dd',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fraw_5fdistance_5fend_5fleft_5480',['set_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6d9d20da8c7cee397bc621395ebb0595',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fdistance_5fend_5fright_5481',['set_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34782c4f89ca5b5ed549c086d782a49a',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fdistance_5fstart_5fleft_5482',['set_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6ef05afc876f9d157a4a22ece67ec14b',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fdistance_5fstart_5fright_5483',['set_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3c42e8e885b205135c84167f3d0c30f9',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fis_5freversed_5484',['set_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ce29ebd996f8894ed6942633fb387b9',1,'vg::ZipCode::node_code_t::set_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af7cdb5f02946631384bab58c2732c305',1,'vg::ZipCode::snarl_code_t::set_raw_is_reversed()']]],
+ ['set_5fraw_5flast_5fcomponent_5485',['set_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a389422a0482e9a0fe88b77bacc88b2fa',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fraw_5flength_5486',['set_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a9eaa33f8ee594c5fe686c4e5e0bfbe30',1,'vg::ZipCode::node_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a373aeb1528f44cf694a7711ab827d088',1,'vg::ZipCode::chain_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6f15f89fa329bcd06088318bb17bbdb2',1,'vg::ZipCode::snarl_code_t::set_raw_length()']]],
+ ['set_5fraw_5fprefix_5fsum_5for_5fidentifier_5487',['set_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a02b5011800febaebbef6c517fc08320e',1,'vg::ZipCode::node_code_t::set_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a38cb2f04ee15fc31ec69d5ef06f45ac1',1,'vg::ZipCode::snarl_code_t::set_raw_prefix_sum_or_identifier()']]],
+ ['set_5fraw_5frecord_5foffset_5488',['set_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5a5034d3c583b9220450bcc2da59f31f',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fsnarl_5frank_5for_5fidentifier_5489',['set_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a214ccf14cf2a287d7756d10036ce9bff',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fread_5f1_5fadapter_5490',['set_read_1_adapter',['../classvg_1_1MultipathMapper.html#aaf7ee8334193018b945900b00cec8826',1,'vg::MultipathMapper']]],
+ ['set_5fread_5f2_5fadapter_5491',['set_read_2_adapter',['../classvg_1_1MultipathMapper.html#a1c1674e89e4702168e75bca6fdb4d0bd',1,'vg::MultipathMapper']]],
+ ['set_5fread_5fcoverage_5492',['set_read_coverage',['../classvg_1_1MultipathMapper.html#a2ce30f7fe70325b6101356f5eb67df3d',1,'vg::MultipathMapper']]],
+ ['set_5fread_5fgroup_5493',['set_read_group',['../classvg_1_1MultipathAlignmentEmitter.html#ad772e7a7315be2a57899c234116de800',1,'vg::MultipathAlignmentEmitter']]],
+ ['set_5frecord_5foffset_5494',['set_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a33b431da2b73e995db51480fd2e5385b',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5frefpos_5495',['set_refpos',['../classvg_1_1MinimizerMapper.html#a7fe47fe6075b79253609a04601d0995e',1,'vg::MinimizerMapper']]],
+ ['set_5fregion_5496',['set_region',['../classvg_1_1VcfBuffer.html#a0a636a74fef67c3cfd59730db3ed427c',1,'vg::VcfBuffer::set_region()'],['../classvg_1_1WindowedVcfBuffer.html#ab6c81f821d5ddcace1e67e7081793142',1,'vg::WindowedVcfBuffer::set_region()']]],
+ ['set_5fremove_5ffailing_5fedits_5497',['set_remove_failing_edits',['../classvg_1_1Filter.html#ab91fdad4a96917a43f1fed85e11a9645',1,'vg::Filter']]],
+ ['set_5fsample_5fname_5498',['set_sample_name',['../classvg_1_1MultipathAlignmentEmitter.html#a398cd239c156944100299fc5babb6194',1,'vg::MultipathAlignmentEmitter']]],
+ ['set_5fscore_5499',['set_score',['../classvg_1_1connection__t.html#ab7e71cc31834606883ce7fee437bdd7b',1,'vg::connection_t::set_score()'],['../classvg_1_1subpath__t.html#a7229edbbe9e72084b114bd03079cc105',1,'vg::subpath_t::set_score()'],['../namespacevg.html#a3b05a1318d7be5ecf3547a3eca837618',1,'vg::set_score()']]],
+ ['set_5fsequence_5500',['set_sequence',['../classvg_1_1multipath__alignment__t.html#a5cabf8eec673f7aaf7d28add560a7e32',1,'vg::multipath_alignment_t::set_sequence()'],['../classvg_1_1edit__t.html#aa2a77df9db620c8500a3eb4802229f43',1,'vg::edit_t::set_sequence()']]],
+ ['set_5fshow_5fprogress_5501',['set_show_progress',['../classvg_1_1GraphCaller.html#a1005b4de9fde3d23adcd1d35f8fece09',1,'vg::GraphCaller']]],
+ ['set_5fsnarl_5frank_5for_5fidentifier_5502',['set_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a43ebf63adc3f81a82dd4b9bb77be2772',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fsnarl_5fvalues_5503',['set_snarl_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a858ed22ff1cba852000f4815bd03e20f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['set_5fsoft_5fclip_5flimit_5504',['set_soft_clip_limit',['../classvg_1_1Filter.html#a8e69a6bc40641a3377dd60f44ec52816',1,'vg::Filter']]],
+ ['set_5fsort_5fvalue_5505',['set_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aa1ea92740944abf659a9080acc7fa0b3',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['set_5fsource_5fpaths_5506',['set_source_paths',['../classvg_1_1Sampler.html#ab217a74d97bc905480c236ab66d30232',1,'vg::Sampler']]],
+ ['set_5fsplit_5fread_5flimit_5507',['set_split_read_limit',['../classvg_1_1Filter.html#a377d6661a880d4d3798e8780d61d6db0',1,'vg::Filter']]],
+ ['set_5fstart_5508',['set_start',['../classvg_1_1multipath__alignment__t.html#a9230aa70e0c93066e0c8f9f4c4af28fa',1,'vg::multipath_alignment_t']]],
+ ['set_5fsupport_5fswitch_5fthreshold_5509',['set_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a53940205edddd5d3bb379b82ede4f74f',1,'vg::TraversalSupportFinder']]],
+ ['set_5fsystem_5fdir_5510',['set_system_dir',['../namespacevg_1_1temp__file.html#ac061a6d187921157d4e62930445996e8',1,'vg::temp_file']]],
+ ['set_5ftags_5511',['set_tags',['../gbwt__main_8cpp.html#ab3856151a0825f396467961305716704',1,'gbwt_main.cpp']]],
+ ['set_5ftarget_5fmemory_5fusage_5512',['set_target_memory_usage',['../classvg_1_1IndexRegistry.html#aee06106e4888a5a17d12fa10f1e87893',1,'vg::IndexRegistry']]],
+ ['set_5fto_5flength_5513',['set_to_length',['../classvg_1_1edit__t.html#a9b38a79f561f60c377c35e186c5cfd96',1,'vg::edit_t']]],
+ ['set_5ftranslation_5514',['set_translation',['../classvg_1_1VCFOutputCaller.html#a918bfde23f9f6afacec9b10319030414',1,'vg::VCFOutputCaller']]],
+ ['set_5fvalue_5515',['set_value',['../structvg_1_1subcommand_1_1ArgSpec.html#a1e31767c05c4a085a3b8087067af70c4',1,'vg::subcommand::ArgSpec::set_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a25817ff171a0199cf4e21fee15261f14',1,'vg::subcommand::ValueArgSpec::set_value()']]],
+ ['set_5fwindow_5flength_5516',['set_window_length',['../classvg_1_1Filter.html#adb96fca6a301e45c84b010f5461440a9',1,'vg::Filter']]],
+ ['setk_5517',['setK',['../classvg_1_1FlowTraversalFinder.html#adf6216e25b6f61a09aa13816eafcd6e3',1,'vg::FlowTraversalFinder']]],
+ ['settotalbyteslimit_5518',['SetTotalBytesLimit',['../message__iterator_8hpp.html#ad3271079865fad5b2725dab227556443',1,'message_iterator.hpp']]],
+ ['sha1_5fvariant_5fname_5519',['sha1_variant_name',['../classvg_1_1Constructor.html#afafc25fc7021c48463894db9abce2f66',1,'vg::Constructor']]],
+ ['sha1head_5520',['sha1head',['../namespacevg.html#a6821cd887e206752c50c1a7be764d1f5',1,'vg']]],
+ ['sha1sum_5521',['sha1sum',['../namespacevg.html#a0cada7d579d914675f53490e0488ab53',1,'vg']]],
+ ['shallow_5fcontents_5522',['shallow_contents',['../classvg_1_1SnarlManager.html#afb7f6b946d3ec05ed619e09491e0a92d',1,'vg::SnarlManager']]],
+ ['share_5fterminal_5fpositions_5523',['share_terminal_positions',['../classvg_1_1MultipathMapper.html#aaff4140e7e711a25b1eb284d7c830c2c',1,'vg::MultipathMapper']]],
+ ['shift_5fprune_5fdiff_5524',['shift_prune_diff',['../classvg_1_1Surjector.html#a3768ca4fe69ba4c58cdbfe81343c56bd',1,'vg::Surjector']]],
+ ['short_5fmem_5ffilter_5ffactor_5525',['short_mem_filter_factor',['../classvg_1_1BaseMapper.html#ac92eb174ad81e8714bf43e4b08aecdb9',1,'vg::BaseMapper']]],
+ ['short_5fmode_5fname_5526',['short_mode_name',['../prune__main_8cpp.html#adf85e917657920f23dce6cefc2ecd2b9',1,'prune_main.cpp']]],
+ ['short_5foption_5527',['short_option',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a60f696e33fce1e021b3454176ce0885f',1,'vg::subcommand::BaseArgSpec']]],
+ ['short_5foptions_5528',['short_options',['../classvg_1_1ConfigurableParser.html#adfde71f165bbcb110831c12e862aa891',1,'vg::ConfigurableParser']]],
+ ['short_5fopts_5529',['short_opts',['../classvg_1_1BaseOption.html#a04134150cfd3143bf1f43f55af5fd3d6',1,'vg::BaseOption']]],
+ ['short_5fread_5fminimizer_5fk_5530',['short_read_minimizer_k',['../structvg_1_1IndexingParameters.html#a74ed1f6b8e93329efc15654c9eac5749',1,'vg::IndexingParameters']]],
+ ['short_5fread_5fminimizer_5fw_5531',['short_read_minimizer_W',['../structvg_1_1IndexingParameters.html#a882b758e0f629a9cd2e9297b193c42df',1,'vg::IndexingParameters::short_read_minimizer_W()'],['../structvg_1_1IndexingParameters.html#acf0c2287ca7ee00853bd27af02757650',1,'vg::IndexingParameters::short_read_minimizer_w()']]],
+ ['shortest_5fcycle_2ecpp_5532',['shortest_cycle.cpp',['../shortest__cycle_8cpp.html',1,'']]],
+ ['shortest_5fcycle_2ehpp_5533',['shortest_cycle.hpp',['../shortest__cycle_8hpp.html',1,'']]],
+ ['shortest_5fcycle_5flength_5534',['shortest_cycle_length',['../namespacevg_1_1algorithms.html#acfe6f985e8bedbad1b33861c62379772',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph, const handle_t &source)'],['../namespacevg_1_1algorithms.html#a012fced2754c445ec404ff5420018982',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph)']]],
+ ['shortest_5fcycle_5flength_5finternal_5535',['shortest_cycle_length_internal',['../namespacevg_1_1algorithms.html#aa87ca8c58307fdb47d448deb2ec43389',1,'vg::algorithms']]],
+ ['shortest_5fseq_5fpaths_5536',['shortest_seq_paths',['../classvg_1_1BandedGlobalAligner.html#a7156058732c9d6f40226609f650944a2',1,'vg::BandedGlobalAligner']]],
+ ['show_5fcnv_5537',['show_cnv',['../classvg_1_1Viz.html#ace366df624ca2b225d3c8d20d9cb15db',1,'vg::Viz']]],
+ ['show_5fdna_5538',['show_dna',['../classvg_1_1Viz.html#a2b8e6f510bca9925fd39e37feddce251',1,'vg::Viz']]],
+ ['show_5fpath_5finfo_5539',['show_path_info',['../classvg_1_1Deconstructor.html#a6d2894dc3b9ea0fea97e2a78e11e2a51',1,'vg::Deconstructor']]],
+ ['show_5fpaths_5540',['show_paths',['../classvg_1_1Viz.html#a501ab25fb94a4d3abd508af7bc77aac3',1,'vg::Viz']]],
+ ['show_5fprogress_5541',['show_progress',['../structvg_1_1GBWTHandler.html#a7513df04845c0145e6933236346ec8fc',1,'vg::GBWTHandler::show_progress()'],['../structvg_1_1RebuildParameters.html#a4a86fbc222841919a70452f4a6e8c463',1,'vg::RebuildParameters::show_progress()'],['../classvg_1_1Genotyper.html#a72599c00acaed553e0d235e5c73d4b82',1,'vg::Genotyper::show_progress()'],['../classvg_1_1GraphCaller.html#a1179324159b5518ebd0eb7d5fb71edd5',1,'vg::GraphCaller::show_progress()'],['../classvg_1_1Progressive.html#a6653625f496832c4cb8711185d5e04cb',1,'vg::Progressive::show_progress()'],['../classvg_1_1Transcriptome.html#af92e5c3f2b2216b98f30f5518fc3b785',1,'vg::Transcriptome::show_progress()'],['../classvg_1_1VGset.html#aa848e2230f2d5c016c0a816cfa14501e',1,'vg::VGset::show_progress()'],['../structGBWTConfig.html#a075b0013542a10eb0708e94f20cb18a6',1,'GBWTConfig::show_progress()']]],
+ ['show_5fstructure_5542',['show_structure',['../classvg_1_1Packer.html#a4aacf109dc6290d39630e5b25020004e',1,'vg::Packer']]],
+ ['show_5fwork_5543',['show_work',['../classvg_1_1MinimizerMapper.html#a089bb5c8a56a7614a2f494690f3b5acd',1,'vg::MinimizerMapper']]],
+ ['shuffledpairs_5544',['ShuffledPairs',['../classvg_1_1ShuffledPairs.html',1,'vg::ShuffledPairs'],['../classvg_1_1ShuffledPairs_1_1iterator.html#a716354d123e5197d160a8d6c4da7817d',1,'vg::ShuffledPairs::iterator::ShuffledPairs()'],['../classvg_1_1ShuffledPairs.html#a7143ff811c0359854ac091749b1f5642',1,'vg::ShuffledPairs::ShuffledPairs()']]],
+ ['sibling_5findices_5fat_5fdepth_5545',['sibling_indices_at_depth',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a0c95aeef3ec92915788ebf083154e265',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['sides_5fcontext_5546',['sides_context',['../classvg_1_1VG.html#ad363c6c82e88dcb1b88d05ff55074ed6',1,'vg::VG']]],
+ ['sides_5ffrom_5547',['sides_from',['../classvg_1_1VG.html#ac670f3c729f93ebaa7c8bd5063225597',1,'vg::VG::sides_from(NodeSide side)'],['../classvg_1_1VG.html#a95c975ed419a0873c894cef7a2f2d3ba',1,'vg::VG::sides_from(nid_t id)']]],
+ ['sides_5fof_5548',['sides_of',['../classvg_1_1VG.html#a030b75d2ad50905cc01fe4b7223cbb83',1,'vg::VG']]],
+ ['sides_5fto_5549',['sides_to',['../classvg_1_1VG.html#a1a156ac1e1fde520bae82850105c6c66',1,'vg::VG::sides_to(NodeSide side)'],['../classvg_1_1VG.html#a68733706482bf7b2627be32438160af3',1,'vg::VG::sides_to(nid_t id)']]],
+ ['sift_5fmain_2ecpp_5550',['sift_main.cpp',['../sift__main_8cpp.html',1,'']]],
+ ['sigma_5551',['sigma',['../classvg_1_1FragmentLengthDistribution.html#a6462bb11645a893b5dc2de057714d8f6',1,'vg::FragmentLengthDistribution']]],
+ ['signature_5552',['signature',['../namespacevg.html#a2616dde2763b947a15ac562fd631e688',1,'vg::signature(const Alignment &aln)'],['../namespacevg.html#a134fc6762c4b66dd4847078b0ddbfdd6',1,'vg::signature(const Alignment &aln1, const Alignment &aln2)']]],
+ ['sim_5fmain_2ecpp_5553',['sim_main.cpp',['../sim__main_8cpp.html',1,'']]],
+ ['simple_5fcomponents_5554',['simple_components',['../namespacehandlegraph_1_1algorithms.html#acc16afc14f0a9dd0a34a4c173b229a4b',1,'handlegraph::algorithms']]],
+ ['simple_5foffsets_5fin_5fpaths_5555',['simple_offsets_in_paths',['../namespacevg_1_1algorithms.html#a9ddb73ef3cf5a8891aa82001f272c3c4',1,'vg::algorithms']]],
+ ['simple_5fsds_5fload_5556',['simple_sds_load',['../structvg_1_1Haplotypes_1_1Subchain.html#a9dfc087f0bada7635e975b6c8e8479a8',1,'vg::Haplotypes::Subchain::simple_sds_load()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a34163c2bf756a469dd6bba7880836f82',1,'vg::Haplotypes::TopLevelChain::simple_sds_load()'],['../classvg_1_1Haplotypes.html#a908ed1a2f1147a2162051be87e5ba389',1,'vg::Haplotypes::simple_sds_load()']]],
+ ['simple_5fsds_5fserialize_5557',['simple_sds_serialize',['../structvg_1_1Haplotypes_1_1Subchain.html#ab30088a7f754d1bfb579773000ac73e0',1,'vg::Haplotypes::Subchain::simple_sds_serialize()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ad5f88539013b3d1c0caed224550e3a06',1,'vg::Haplotypes::TopLevelChain::simple_sds_serialize()'],['../classvg_1_1Haplotypes.html#a3a5a36c107109c893cf382064ad9ea69',1,'vg::Haplotypes::simple_sds_serialize()']]],
+ ['simple_5fsds_5fsize_5558',['simple_sds_size',['../structvg_1_1Haplotypes_1_1Subchain.html#a5f1258caf8b13bd3880f2db6e2967908',1,'vg::Haplotypes::Subchain::simple_sds_size()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#afb004505c7fcc83e89b15c229da33a03',1,'vg::Haplotypes::TopLevelChain::simple_sds_size()'],['../classvg_1_1Haplotypes.html#ac0ebaa605235ee2b6f62c084cfdc6126',1,'vg::Haplotypes::simple_sds_size()']]],
+ ['simpleconsistencycalculator_5559',['SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html',1,'vg']]],
+ ['simpletraversalsupportcalculator_5560',['SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html',1,'vg']]],
+ ['simplify_5561',['simplify',['../classvg_1_1RareVariantSimplifier.html#af17e24fe2acb6700bb7b6d39514af7af',1,'vg::RareVariantSimplifier::simplify()'],['../classvg_1_1SmallSnarlSimplifier.html#a9abe74e35298d7e22f13039a4c6ea5ba',1,'vg::SmallSnarlSimplifier::simplify()'],['../namespacevg.html#a486054f13a4dc43e37c0f0131f6a51ad',1,'vg::simplify(const Alignment &a, bool trim_internal_deletions)'],['../namespacevg.html#a86653c665afe3c8932f60cc39163e202',1,'vg::simplify(const Path &p, bool trim_internal_deletions)'],['../namespacevg.html#a9514446da89671007ae40e420c1297d7',1,'vg::simplify(const Mapping &m, bool trim_internal_deletions)']]],
+ ['simplify_5fcigar_5562',['simplify_cigar',['../namespacevg.html#a553c3fcfd7de2e51f41a6f174c313947',1,'vg']]],
+ ['simplify_5fcomplicated_5fmultipath_5falignment_5563',['simplify_complicated_multipath_alignment',['../classvg_1_1MultipathMapper.html#a92de908372ba0730cfe40638218d815f',1,'vg::MultipathMapper']]],
+ ['simplify_5ffiltered_5fedits_5564',['simplify_filtered_edits',['../namespacevg.html#ad6a42e8ba843cd728b9f84738756b30e',1,'vg']]],
+ ['simplify_5fmain_2ecpp_5565',['simplify_main.cpp',['../simplify__main_8cpp.html',1,'']]],
+ ['simplify_5fonce_5566',['simplify_once',['../classvg_1_1SmallSnarlSimplifier.html#afc5525b90ddf851ee7d43a6476acd99d',1,'vg::SmallSnarlSimplifier']]],
+ ['simplify_5fsiblings_5567',['simplify_siblings',['../namespacevg_1_1algorithms.html#a9e4cebdfc1e901db4588c4612653df96',1,'vg::algorithms']]],
+ ['simplify_5fsiblings_2ecpp_5568',['simplify_siblings.cpp',['../simplify__siblings_8cpp.html',1,'']]],
+ ['simplify_5fsiblings_2ehpp_5569',['simplify_siblings.hpp',['../simplify__siblings_8hpp.html',1,'']]],
+ ['simplify_5ftopologies_5570',['simplify_topologies',['../classvg_1_1MultipathMapper.html#a5f865a27bd34ffce2e2ea1d05fc02b43',1,'vg::MultipathMapper']]],
+ ['simultaneous_5fpair_5falignment_5571',['simultaneous_pair_alignment',['../classvg_1_1Mapper.html#ae83170a63789f8984e82e225486ca5bd',1,'vg::Mapper']]],
+ ['since_5flast_5ffragment_5flength_5festimate_5572',['since_last_fragment_length_estimate',['../classvg_1_1FragmentLengthStatistics.html#ae79e46e68a3b9aa6c87863a6354c01a2',1,'vg::FragmentLengthStatistics']]],
+ ['single_5fstranded_5forientation_5573',['single_stranded_orientation',['../namespacehandlegraph_1_1algorithms.html#a61255fd1513da53219871ea01283e360',1,'handlegraph::algorithms']]],
+ ['sink_5ffwd_5574',['sink_fwd',['../classvg_1_1SourceSinkOverlay.html#a2718021aade5e48683cdc07c5d5b16f7',1,'vg::SourceSinkOverlay']]],
+ ['sink_5fid_5575',['sink_id',['../classvg_1_1SourceSinkOverlay.html#a02ca8620a0e90dbf0190fe285d11a687',1,'vg::SourceSinkOverlay']]],
+ ['sink_5fnodes_5576',['sink_nodes',['../classvg_1_1BandedGlobalAligner.html#ad3ba4ffebb1e61d6ce59a995eac74f68',1,'vg::BandedGlobalAligner']]],
+ ['sink_5frev_5577',['sink_rev',['../classvg_1_1SourceSinkOverlay.html#a4c00143bd29d3f3adbf571f6333ea761',1,'vg::SourceSinkOverlay']]],
+ ['site_5fends_5578',['site_ends',['../classvg_1_1PhasedGenome.html#afc338c2bf1776ec1ccb29c8efee6aaa3',1,'vg::PhasedGenome']]],
+ ['site_5fmanager_5579',['site_manager',['../classvg_1_1SmallSnarlSimplifier.html#a4991294aedb029a70d1d4f459e009bd3',1,'vg::SmallSnarlSimplifier']]],
+ ['site_5fstarts_5580',['site_starts',['../classvg_1_1PhasedGenome.html#accfaae53e12f924b914623734a68102f',1,'vg::PhasedGenome']]],
+ ['sites_5581',['sites',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a7fee7818b260154898be386649d3bfe7',1,'vg::PhasedGenome::Haplotype']]],
+ ['size_5582',['size',['../classvg_1_1algorithms_1_1Anchor.html#a96921a8307e8e97ba77869b58d6d7292',1,'vg::algorithms::Anchor::size()'],['../structjob__type.html#adbc606f42800cfce3697b017578356b9',1,'job_type::size()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#acdf72785ba0579f5985b227ef1ccd48b',1,'vg::DozeuInterface::OrderedGraph::size()'],['../structvg_1_1MatchPos_1_1PathList.html#aee5bea8ee39007b6bf5be7ea72d3695b',1,'vg::MatchPos::PathList::size()'],['../classvg_1_1WFATree.html#ad5da24b01eb588c58e07419dbd5eaca4',1,'vg::WFATree::size()'],['../classvg_1_1SnarlState.html#a02f1d46e384b6617ad43f2390fe0ef98',1,'vg::SnarlState::size()'],['../structhaplo_1_1int__itvl__t.html#acee0f4db1fc8cdfd535e6d181093f01f',1,'haplo::int_itvl_t::size()'],['../structhaplo_1_1gbwt__thread__t.html#a5d4d9e80558ff8e4dbab247cc9782a0c',1,'haplo::gbwt_thread_t::size()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a979f8d5623d9040439803c13e7ebf9b6',1,'haplo::linear_haplo_structure::SNVvector::size()'],['../classvg_1_1HandleGraphNodeSet.html#ae66b372aeb3110162c4d9b5c85e3a28d',1,'vg::HandleGraphNodeSet::size()'],['../classvg_1_1MultipathAlignmentGraph.html#a4ec09c91391cfb06c1c9eea132ce4246',1,'vg::MultipathAlignmentGraph::size()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a028494e0f37785dc8a39de6c4f2876a4',1,'vg::Option< vector< Item >, Parser >::size()'],['../classvg_1_1Paths.html#ac2fb517ea95acdd1eb378bf104c16912',1,'vg::Paths::size()'],['../classvg_1_1SmallBitset.html#a1b3ff28863a53eae0c4b47ff854b4d2d',1,'vg::SmallBitset::size()'],['../classvg_1_1SparseUnionFind.html#a85bfb663efac82a593533bd58890c615',1,'vg::SparseUnionFind::size()'],['../structvg_1_1VectorView.html#a62ec6d3c6520fa2b6d70a23abc473e44',1,'vg::VectorView::size()'],['../classvg_1_1VG.html#a9e3720ce267c8167ce679a015063dab6',1,'vg::VG::size()'],['../classvg_1_1ZipCodeCollection.html#ae1aab3360a759d00d8c43e921dba92f6',1,'vg::ZipCodeCollection::size()']]],
+ ['size_5ft_5fis_5fnonzero_5583',['size_t_is_nonzero',['../namespacevg_1_1subcommand.html#a62e7f4f685f1aabc28ff82aa02f00f7f',1,'vg::subcommand']]],
+ ['size_5ft_5fis_5fpositive_5584',['size_t_is_positive',['../namespacevg_1_1subcommand.html#ae20ec7174b0b153b2657c4931dcca448',1,'vg::subcommand']]],
+ ['sizelimitexceededexception_5585',['SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html',1,'vg::SizeLimitExceededException'],['../classvg_1_1SizeLimitExceededException.html#aeb5d2801f912937112f0e638717156a8',1,'vg::SizeLimitExceededException::SizeLimitExceededException()']]],
+ ['skip_5586',['Skip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#af3849b5292df406dec93738920615987',1,'vg::io::BlockedGzipInputStream']]],
+ ['skip_5falt_5587',['skip_alt',['../classvg_1_1VCFTraversalFinder.html#acc753182667fd49d9afe5eba697c92da',1,'vg::VCFTraversalFinder']]],
+ ['skip_5fstructural_5fduplications_5588',['skip_structural_duplications',['../classvg_1_1VariantAdder.html#a0c90a9845a662358588f517e2cf91501',1,'vg::VariantAdder']]],
+ ['skippable_5589',['skippable',['../classvg_1_1algorithms_1_1Anchor.html#ade34685bea83f218a9756478bcca25a0',1,'vg::algorithms::Anchor']]],
+ ['slope_5590',['slope',['../namespacevg.html#ad477b45059373004136e69022e802e0b',1,'vg']]],
+ ['slug_5591',['SLUG',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa9c42a12326ffdacf390a8b88c9fe1804',1,'vg::subcommand']]],
+ ['small_5592',['small',['../classvg_1_1SmallBitset.html#a8e787b217e48311220e91f7fd191fe14',1,'vg::SmallBitset']]],
+ ['small_5fbitset_2ehpp_5593',['small_bitset.hpp',['../small__bitset_8hpp.html',1,'']]],
+ ['small_5fsnarl_5fsimplifier_2ecpp_5594',['small_snarl_simplifier.cpp',['../small__snarl__simplifier_8cpp.html',1,'']]],
+ ['small_5fsnarl_5fsimplifier_2ehpp_5595',['small_snarl_simplifier.hpp',['../small__snarl__simplifier_8hpp.html',1,'']]],
+ ['smallbitset_5596',['SmallBitset',['../classvg_1_1SmallBitset.html',1,'vg::SmallBitset'],['../classvg_1_1SmallBitset.html#afcefdbe6a3f708ded8d874537ba0616f',1,'vg::SmallBitset::SmallBitset()'],['../classvg_1_1SmallBitset.html#a5c0e06b1e0482ff98adde62fdf9476f2',1,'vg::SmallBitset::SmallBitset(size_t n)'],['../classvg_1_1SmallBitset.html#ae09de51997e95c9c7c85650748e6d9ab',1,'vg::SmallBitset::SmallBitset(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#a59da25f6a4ae99cc7ff12936930ad5e3',1,'vg::SmallBitset::SmallBitset(SmallBitset &&another)']]],
+ ['smallsnarlsimplifier_5597',['SmallSnarlSimplifier',['../classvg_1_1SmallSnarlSimplifier.html',1,'vg::SmallSnarlSimplifier'],['../classvg_1_1SmallSnarlSimplifier.html#ae19c2fcf37820ed9112671fbc7e64033',1,'vg::SmallSnarlSimplifier::SmallSnarlSimplifier()']]],
+ ['smart_5falign_5598',['smart_align',['../classvg_1_1VariantAdder.html#ad3c7e7030142e70f27bc9f0bc42c2cce',1,'vg::VariantAdder']]],
+ ['smellslikegzip_5599',['SmellsLikeGzip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa45ae9d5a0c1689efa567d573ad5747c',1,'vg::io::BlockedGzipInputStream']]],
+ ['sn_5fdeletion_5fbetween_5fref_5600',['sn_deletion_between_ref',['../structhaplo_1_1linear__haplo__structure.html#aa6e425ddac2acb985a1364dd91a2f948',1,'haplo::linear_haplo_structure']]],
+ ['snarl_5601',['Snarl',['../structvg_1_1Snarl.html',1,'vg::Snarl'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#aee85ad3c21e883f05b67c62fbf05be72',1,'vg::ReplaceSnarlHaplotypeCommand::snarl()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#acad9926afa69d4de3d5424ac1f03582d',1,'vg::SnarlManager::SnarlRecord::snarl()'],['../structvg_1_1Visit.html#a7e671bbc7437a16dd3549a6fc49fd2a9',1,'vg::Visit::snarl()']]],
+ ['snarl_5fboundary_5findex_5602',['snarl_boundary_index',['../classvg_1_1SnarlManager.html#a77a449f2f85f37760da1a7182cc1e08b',1,'vg::SnarlManager']]],
+ ['snarl_5fcaller_5603',['snarl_caller',['../classvg_1_1GraphCaller.html#a4b8c6f32019db8528bb6835fdce12ddb',1,'vg::GraphCaller']]],
+ ['snarl_5fcaller_2ecpp_5604',['snarl_caller.cpp',['../snarl__caller_8cpp.html',1,'']]],
+ ['snarl_5fcaller_2ehpp_5605',['snarl_caller.hpp',['../snarl__caller_8hpp.html',1,'']]],
+ ['snarl_5fchain_5fcomponent_5foffset_5606',['SNARL_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#a807c487a518301d1726f87f7eda443a4',1,'vg::ZipCode']]],
+ ['snarl_5fchild_5fcount_5foffset_5607',['SNARL_CHILD_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a37503629f90af0de452b6bc534ad43f5',1,'vg::ZipCode']]],
+ ['snarl_5fcode_5ft_5608',['snarl_code_t',['../structvg_1_1ZipCode_1_1snarl__code__t.html',1,'vg::ZipCode']]],
+ ['snarl_5fdecomposition_2ecpp_5609',['snarl_decomposition.cpp',['../snarl__decomposition_8cpp.html',1,'']]],
+ ['snarl_5fdecomposition_2ehpp_5610',['snarl_decomposition.hpp',['../snarl__decomposition_8hpp.html',1,'']]],
+ ['snarl_5fdistance_5findex_2ecpp_5611',['snarl_distance_index.cpp',['../snarl__distance__index_8cpp.html',1,'']]],
+ ['snarl_5fdistance_5findex_2ehpp_5612',['snarl_distance_index.hpp',['../snarl__distance__index_8hpp.html',1,'']]],
+ ['snarl_5fend_5613',['SNARL_END',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adaaa317dff9d3024c633f537d3b8b08cc7',1,'vg::ZipCodeTree']]],
+ ['snarl_5fend_5findex_5614',['snarl_end_index',['../classvg_1_1SnarlManager.html#a1fd57d0de5eec34fc037ad0afbdfcb77',1,'vg::SnarlManager']]],
+ ['snarl_5finto_5615',['snarl_into',['../classvg_1_1SnarlManager.html#a0f1d327aa074d59976802999d0d179d1',1,'vg::SnarlManager']]],
+ ['snarl_5fis_5fregular_5foffset_5616',['SNARL_IS_REGULAR_OFFSET',['../classvg_1_1ZipCode.html#ad56c1879d223a2151795d2532932d1c8',1,'vg::ZipCode']]],
+ ['snarl_5flength_5foffset_5617',['SNARL_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#ade2f247378ce48537e06399e215013d5',1,'vg::ZipCode']]],
+ ['snarl_5fless_5618',['snarl_less',['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
+ ['snarl_5fmanager_5619',['snarl_manager',['../classvg_1_1GraphCaller.html#a55afa68762956066ccbea2e332342266',1,'vg::GraphCaller::snarl_manager()'],['../classvg_1_1SnarlGraph.html#a292ca2c610a5f06fd06325f193557823',1,'vg::SnarlGraph::snarl_manager()'],['../classvg_1_1Masker.html#a4554deca5d95bdb68843ca7a656170fa',1,'vg::Masker::snarl_manager()'],['../classvg_1_1MCMCCaller.html#a4dad48c8bc658476ff4a6b0ed22817de',1,'vg::MCMCCaller::snarl_manager()'],['../classvg_1_1MultipathMapper.html#a82e1a1af4b8ba0170cf7817cd44f1008',1,'vg::MultipathMapper::snarl_manager()'],['../classvg_1_1NestedTraversalFinder.html#a3b15745919bd3bd7427d487eea14884b',1,'vg::NestedTraversalFinder::snarl_manager()'],['../classvg_1_1PhasedGenome.html#a56494287a449d9b95f24ac7d0e505522',1,'vg::PhasedGenome::snarl_manager()'],['../classvg_1_1RegionExpander.html#ac7c7121e538614d43356e7318769db65',1,'vg::RegionExpander::snarl_manager()'],['../classvg_1_1SupportBasedSnarlCaller.html#a86c40f2d62950d1f484aa6dd84abf60d',1,'vg::SupportBasedSnarlCaller::snarl_manager()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a8e29fb04ba5a9516d74d1da133f06330',1,'vg::ExhaustiveTraversalFinder::snarl_manager()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#a0c4e67f35a6f1e8536a81a781c7cba22',1,'vg::ReadRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a015de241431375a1b43ac32b852246f6',1,'vg::PathRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1RepresentativeTraversalFinder.html#a48de8b31240c6ddda7ff40164ae7708b',1,'vg::RepresentativeTraversalFinder::snarl_manager()'],['../classvg_1_1VCFTraversalFinder.html#ae2fac6aac1b86163b495ef183e3340d9',1,'vg::VCFTraversalFinder::snarl_manager()'],['../classvg_1_1FlowTraversalFinder.html#ab0f619b27f1f2d911e6625ab61ecddeb',1,'vg::FlowTraversalFinder::snarl_manager()'],['../classvg_1_1TraversalSupportFinder.html#adc97ab06de5c4aa553db92bae3879ee5',1,'vg::TraversalSupportFinder::snarl_manager()']]],
+ ['snarl_5fnumber_5620',['snarl_number',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#add50ce54457a4031ed0d8fd0b3b34e9f',1,'vg::SnarlManager::SnarlRecord::snarl_number()'],['../classvg_1_1SnarlManager.html#aa779c0eaea2403d9c36761243a7f9262',1,'vg::SnarlManager::snarl_number()']]],
+ ['snarl_5foffset_5fin_5fchain_5foffset_5621',['SNARL_OFFSET_IN_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a65ff5123c5439118b1b390179cffd818',1,'vg::ZipCode']]],
+ ['snarl_5frank_5for_5fidentifier_5622',['snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4859d74d9e82058d5e6066dd0e99470e',1,'vg::ZipCode::chain_code_t']]],
+ ['snarl_5freference_5flength_5fhistogram_5623',['snarl_reference_length_histogram',['../classvg_1_1Genotyper.html#ac0d4917131823fc2dab43927347d4623',1,'vg::Genotyper']]],
+ ['snarl_5fseed_5fclusterer_2ecpp_5624',['snarl_seed_clusterer.cpp',['../snarl__seed__clusterer_8cpp.html',1,'']]],
+ ['snarl_5fseed_5fclusterer_2ehpp_5625',['snarl_seed_clusterer.hpp',['../snarl__seed__clusterer_8hpp.html',1,'']]],
+ ['snarl_5fsharing_5fend_5626',['snarl_sharing_end',['../classvg_1_1SnarlManager.html#a2ca9eb75908bfcc4cfac8b241236295b',1,'vg::SnarlManager']]],
+ ['snarl_5fsharing_5fstart_5627',['snarl_sharing_start',['../classvg_1_1SnarlManager.html#a43ecf19c495295c45ca828d499651481',1,'vg::SnarlManager']]],
+ ['snarl_5fstart_5628',['SNARL_START',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adad9686e72ac57aa50bd713fce51da5666',1,'vg::ZipCodeTree']]],
+ ['snarl_5fstart_5findex_5629',['snarl_start_index',['../classvg_1_1SnarlManager.html#a10a771b6ada139c76e1b435ee301fdb8',1,'vg::SnarlManager']]],
+ ['snarl_5ftraversals_5630',['snarl_traversals',['../classvg_1_1Genotyper.html#a7ec1915674299d727c61377e91385974',1,'vg::Genotyper']]],
+ ['snarlcaller_5631',['SnarlCaller',['../classvg_1_1SnarlCaller.html',1,'vg']]],
+ ['snarldecomposition_5632',['SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html',1,'handlegraph']]],
+ ['snarldistanceindexclusterer_5633',['SnarlDistanceIndexClusterer',['../classvg_1_1SnarlDistanceIndexClusterer.html',1,'vg::SnarlDistanceIndexClusterer'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a0333d80b03665df71c7d448b7cfb0b06',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a66a56a78a0500f79258057cd3d688966',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a2275f78a71459c60e56929b106d4ed46',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#ae2d9080f0e9ddf775de34ae3aaab7019',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index)']]],
+ ['snarlfinder_5634',['SnarlFinder',['../classvg_1_1SnarlFinder.html',1,'vg']]],
+ ['snarlgraph_5635',['SnarlGraph',['../classvg_1_1SnarlGraph.html',1,'vg::SnarlGraph'],['../classvg_1_1SnarlGraph.html#a0a6e447620c3a37ca37345854330ffd3',1,'vg::SnarlGraph::SnarlGraph()']]],
+ ['snarlmanager_5636',['SnarlManager',['../classvg_1_1SnarlManager.html',1,'vg::SnarlManager'],['../classvg_1_1PathBasedTraversalFinder.html#a905239f50078de78279dd9f0ff82faf3',1,'vg::PathBasedTraversalFinder::snarlmanager()'],['../classvg_1_1SnarlManager.html#a1037a2341484dc7b54a68cd7207d34b8',1,'vg::SnarlManager::SnarlManager(SnarlIterator begin, SnarlIterator end)'],['../classvg_1_1SnarlManager.html#a61b2b80def0128deea2d2da4886b955e',1,'vg::SnarlManager::SnarlManager(istream &in)'],['../classvg_1_1SnarlManager.html#afe16f481e15e098c885d63f47eceb59c',1,'vg::SnarlManager::SnarlManager(const function< void(const function< void(Snarl &)> &)> &for_each_snarl)'],['../classvg_1_1SnarlManager.html#a43b0ecd9e372556380231f29788948d5',1,'vg::SnarlManager::SnarlManager()=default'],['../classvg_1_1SnarlManager.html#a8e61adc170e3d9241a723ca7593883da',1,'vg::SnarlManager::SnarlManager(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#a7549f1ed7e0e02ae36f172ab5f1d3dbd',1,'vg::SnarlManager::SnarlManager(SnarlManager &&other)=default']]],
+ ['snarlmindistance_5637',['SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html',1,'vg::SnarlMinDistance'],['../classvg_1_1SnarlMinDistance.html#adc8c303e683b90d923c522790355abad',1,'vg::SnarlMinDistance::SnarlMinDistance()=delete'],['../classvg_1_1SnarlMinDistance.html#aa8efbd4c363589a72da76621b5b4330d',1,'vg::SnarlMinDistance::SnarlMinDistance(SnarlDistanceIndex &distance_index)']]],
+ ['snarlorienteddistancemeasurer_5638',['SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html',1,'vg::SnarlOrientedDistanceMeasurer'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a81db285adff1ae830dcaf2511652e17a',1,'vg::SnarlOrientedDistanceMeasurer::SnarlOrientedDistanceMeasurer()']]],
+ ['snarlrecord_5639',['SnarlRecord',['../structvg_1_1SnarlManager_1_1SnarlRecord.html',1,'vg::SnarlManager']]],
+ ['snarls_5640',['snarls',['../classvg_1_1SnarlGraph.html#ac9db23e9d10f3c39f25a5397afb9d4fa',1,'vg::SnarlGraph::snarls()'],['../classvg_1_1MCMCGenotyper.html#a23913225e8b2d0d4dfbdb713ccf495c3',1,'vg::MCMCGenotyper::snarls()'],['../classvg_1_1SnarlManager.html#ab56cf756bc65189eeb1d4f1f3f6573b6',1,'vg::SnarlManager::snarls()']]],
+ ['snarls_2ecpp_5641',['snarls.cpp',['../snarls_8cpp.html',1,'']]],
+ ['snarls_2ehpp_5642',['snarls.hpp',['../snarls_8hpp.html',1,'']]],
+ ['snarls_5fmain_2ecpp_5643',['snarls_main.cpp',['../snarls__main_8cpp.html',1,'']]],
+ ['snarlstate_5644',['SnarlState',['../classvg_1_1SnarlState.html',1,'vg::SnarlState'],['../classvg_1_1SnarlState.html#a14db6ed9f20936f71de90d0d12f92468',1,'vg::SnarlState::SnarlState()']]],
+ ['snarltraversal_5645',['SnarlTraversal',['../structvg_1_1SnarlTraversal.html',1,'vg']]],
+ ['snarltreechild_5646',['SnarlTreeChild',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['snarltreenodeproblem_5647',['SnarlTreeNodeProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a119a5148780cd1bf7dd073e91974f255',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, const SnarlDistanceIndex &distance_index, const SeedCache *seed, size_t zipcode_depth)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a26ebc81ba9dff9a498a2d222ff72291c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, bool is_reversed_in_parent, size_t node_length, size_t prefix_sum, size_t component, const SeedCache *seed, size_t zipcode_depth)']]],
+ ['snarltype_5648',['SnarlType',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97',1,'vg']]],
+ ['sniff_5fmagic_5649',['sniff_magic',['../classvg_1_1io_1_1Registry.html#aea2d7b2c4852a48417eeac861974b9c1',1,'vg::io::Registry']]],
+ ['sniff_5ftag_5650',['sniff_tag',['../classvg_1_1io_1_1MessageIterator.html#ac9b3fff8dbbff744fe1ff60805af1c20',1,'vg::io::MessageIterator::sniff_tag(istream &stream)'],['../classvg_1_1io_1_1MessageIterator.html#aabd024a7358bae988de897aebff39645',1,'vg::io::MessageIterator::sniff_tag(::google::protobuf::io::ZeroCopyInputStream &stream)']]],
+ ['snv_5651',['snv',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a80993050ce71b03df8d926cbe0cde822',1,'haplo::linear_haplo_structure']]],
+ ['snvs_5652',['SNVs',['../structhaplo_1_1linear__haplo__structure.html#acde3b4cb1fc9eae479ee626bb0916992',1,'haplo::linear_haplo_structure']]],
+ ['snvvector_5653',['SNVvector',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html',1,'haplo::linear_haplo_structure']]],
+ ['soft_5fclip_5ffilter_5654',['soft_clip_filter',['../classvg_1_1Filter.html#aff62aad43f70cd8de756bdbdf94b962d',1,'vg::Filter']]],
+ ['soft_5fclip_5flimit_5655',['soft_clip_limit',['../classvg_1_1Filter.html#abe44432fa541eee27db7789cc9db066b',1,'vg::Filter']]],
+ ['soft_5fclipped_5656',['soft_clipped',['../structvg_1_1Alignment.html#a6cb12eae3f4fa017bc98b59a91a5414f',1,'vg::Alignment']]],
+ ['softclip_5fend_5657',['softclip_end',['../namespacevg.html#a05d6d0388148a996d9423524fa4bcc91',1,'vg::softclip_end(const Alignment &alignment)'],['../namespacevg.html#aa84e4c417206a9b3a910dfde0fec3857',1,'vg::softclip_end(const Mapping &mapping)']]],
+ ['softclip_5fstart_5658',['softclip_start',['../namespacevg.html#a90f2af92a34fdf5fb4ddfee8f8880b48',1,'vg::softclip_start(const Alignment &alignment)'],['../namespacevg.html#a9fe66eebecbc5017b05c9044413b2b4e',1,'vg::softclip_start(const Mapping &mapping)']]],
+ ['softclip_5fthreshold_5659',['softclip_threshold',['../classvg_1_1Mapper.html#a4320fc9bb3cda3bd7b25ebc5b8644d80',1,'vg::Mapper']]],
+ ['softclip_5ftrim_5660',['softclip_trim',['../namespacevg.html#a947760b26fa8669d55f2f420174a578c',1,'vg']]],
+ ['sort_5661',['sort',['../classvg_1_1StreamSorter.html#a8372ac35036ca7723bfc90a686115166',1,'vg::StreamSorter::sort()'],['../classvg_1_1VG.html#a902d516631c77d074aa2a11ae70a6957',1,'vg::VG::sort()']]],
+ ['sort_5fanchor_5findexes_5662',['sort_anchor_indexes',['../namespacevg_1_1algorithms.html#aaeeaa766337fc50f0a9b4d3214271923',1,'vg::algorithms']]],
+ ['sort_5fand_5fcompute_5fmapping_5fquality_5663',['sort_and_compute_mapping_quality',['../classvg_1_1MultipathMapper.html#a2994778198719e960d1a2875fa0815e8',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< multipath_alignment_t > &multipath_alns, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#afcc5ceaad2a3f21c4c38beb05c59f474',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< pair< size_t, size_t >> *duplicate_pairs_out=nullptr, vector< double > *pair_multiplicities=nullptr) const']]],
+ ['sort_5fby_5fchain_5fscore_5664',['sort_by_chain_score',['../classvg_1_1MinimizerMapper.html#a1006ffeadb8f60e819d8cfbf24e33109',1,'vg::MinimizerMapper']]],
+ ['sort_5fby_5fid_5665',['sort_by_id',['../namespacevg.html#af25c227066a422379ff06d81b5990865',1,'vg']]],
+ ['sort_5fby_5fid_5fdedup_5fand_5fclean_5666',['sort_by_id_dedup_and_clean',['../namespacevg.html#a984c1d2199f90f58677096772b870390',1,'vg']]],
+ ['sort_5fby_5fmapping_5frank_5667',['sort_by_mapping_rank',['../classvg_1_1Paths.html#a2970302cae3a54ef7f4296dbf49266fd',1,'vg::Paths']]],
+ ['sort_5fcompact_5fnodes_5668',['sort_compact_nodes',['../classvg_1_1Transcriptome.html#af7de0784cde3273b344757b81d9bffd5',1,'vg::Transcriptome']]],
+ ['sort_5fedges_5fby_5fid_5669',['sort_edges_by_id',['../namespacevg.html#a90cc117e3ac781c77cf8fdaa7802048b',1,'vg']]],
+ ['sort_5fmain_2ecpp_5670',['sort_main.cpp',['../sort__main_8cpp.html',1,'']]],
+ ['sort_5fminimizers_5fby_5fscore_5671',['sort_minimizers_by_score',['../classvg_1_1MinimizerMapper.html#ad72222c1d644b6f676c91511b4b36789',1,'vg::MinimizerMapper']]],
+ ['sort_5fnodes_5fby_5fid_5672',['sort_nodes_by_id',['../namespacevg.html#afb37b16823e6e26cfd8571a1bb621651',1,'vg']]],
+ ['sort_5fone_5finterval_5673',['sort_one_interval',['../classvg_1_1ZipCodeForest.html#a499f52fbb75374e2dc06ce7998ad8fd6',1,'vg::ZipCodeForest']]],
+ ['sort_5fpair_5fby_5fsecond_5674',['sort_pair_by_second',['../namespacevg.html#a47c7102baf9a07b2c701e9937d53351f',1,'vg']]],
+ ['sort_5fpath_5foffsets_5675',['sort_path_offsets',['../namespacevg_1_1algorithms.html#ad8e5913b682c7c14f119543eca7e7548',1,'vg::algorithms']]],
+ ['sort_5fpermutation_5676',['sort_permutation',['../namespacevg.html#ae031408254f8c4031ba0b632f5456059',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end, const std::function< bool(const typename Iterator::value_type &, const typename Iterator::value_type &)> &comparator)'],['../namespacevg.html#ab03fad9d3c71a090606afbe1ef22ce71',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end)']]],
+ ['sort_5fshuffling_5fties_5677',['sort_shuffling_ties',['../namespacevg.html#afe3de0ca79c815a4eaf63df34805f6d0',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp, LazyRNG &rng)'],['../namespacevg.html#aa071bccfee3a9078930f2c385e8dda20',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp)']]],
+ ['sort_5ftranscript_5fpaths_5fby_5fname_5678',['sort_transcript_paths_by_name',['../namespacevg.html#aaddbcf35ad2ff899bf2ae0caf901f778',1,'vg']]],
+ ['sort_5ftranscript_5fpaths_5fupdate_5fcopy_5fid_5679',['sort_transcript_paths_update_copy_id',['../classvg_1_1Transcriptome.html#af8caf627ac2480d7439231a2d26162eb',1,'vg::Transcriptome']]],
+ ['sort_5fvalue_5680',['sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a0c2510fe5ebea3b2a8cc9105e5a9d9fc',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['sort_5fvalue_5ft_5681',['sort_value_t',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html',1,'vg::ZipCodeForest::sort_value_t'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ac93c5ff7c1b231cd78122b1e1f009aae',1,'vg::ZipCodeForest::sort_value_t::sort_value_t()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a42776d8b3810278dfb5830307fe8190c',1,'vg::ZipCodeForest::sort_value_t::sort_value_t(size_t sort_value, ZipCode::code_type_t code_type, size_t chain_order)']]],
+ ['sort_5fvalues_5fby_5fseed_5682',['sort_values_by_seed',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a94161554748068a953a678af49bc31b7',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['sorted_5fid_5franges_5683',['sorted_id_ranges',['../namespacevg_1_1algorithms.html#a64bd6b3ff0d2e22bf752e29e3522a98d',1,'vg::algorithms']]],
+ ['sorted_5fid_5franges_2ecpp_5684',['sorted_id_ranges.cpp',['../sorted__id__ranges_8cpp.html',1,'']]],
+ ['sorted_5fid_5franges_2ehpp_5685',['sorted_id_ranges.hpp',['../sorted__id__ranges_8hpp.html',1,'']]],
+ ['source_5686',['source',['../structvg_1_1GFFRecord.html#a5bc594d1d69edca2081740dcc5e27bbf',1,'vg::GFFRecord::source()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a440d7f98f38d52de226e584f88784381',1,'vg::SnarlDistanceIndexClusterer::Seed::source()'],['../classvg_1_1algorithms_1_1TracedScore.html#aefa6367efc91b8d4e0964cd66e4f51d7',1,'vg::algorithms::TracedScore::source()']]],
+ ['source_5ffwd_5687',['source_fwd',['../classvg_1_1SourceSinkOverlay.html#ae2d7c52a07eeef273ad95972c158c940',1,'vg::SourceSinkOverlay']]],
+ ['source_5fid_5688',['source_id',['../classvg_1_1SourceSinkOverlay.html#a3bc0ab05f0048a8a6b8a31055b3d35c0',1,'vg::SourceSinkOverlay']]],
+ ['source_5fnodes_5689',['source_nodes',['../classvg_1_1BandedGlobalAligner.html#a15f4ae7556005bd51512b6be93112291',1,'vg::BandedGlobalAligner']]],
+ ['source_5fpaths_5690',['source_paths',['../classvg_1_1Sampler.html#aea2c52dbdae36a6729621fe3279c2d61',1,'vg::Sampler::source_paths()'],['../classvg_1_1NGSSimulator.html#ac377f66a4c6d84f5cb660950d56022ff',1,'vg::NGSSimulator::source_paths()']]],
+ ['source_5frev_5691',['source_rev',['../classvg_1_1SourceSinkOverlay.html#a4ad14a56e07ef3fdc3a0346f4f6e0e05',1,'vg::SourceSinkOverlay']]],
+ ['source_5fsink_5foverlay_2ecpp_5692',['source_sink_overlay.cpp',['../source__sink__overlay_8cpp.html',1,'']]],
+ ['source_5fsink_5foverlay_2ehpp_5693',['source_sink_overlay.hpp',['../source__sink__overlay_8hpp.html',1,'']]],
+ ['sourcesinkoverlay_5694',['SourceSinkOverlay',['../classvg_1_1SourceSinkOverlay.html',1,'vg::SourceSinkOverlay'],['../classvg_1_1SourceSinkOverlay.html#a6eaf260d8530ba866753bb3bcb612e15',1,'vg::SourceSinkOverlay::SourceSinkOverlay()']]],
+ ['space_5fefficient_5fcounting_5695',['space_efficient_counting',['../structvg_1_1IndexingParameters.html#ad22ab98cf3f06bb2c033578dc15ae49e',1,'vg::IndexingParameters']]],
+ ['sparse_5fto_5fdense_5696',['sparse_to_dense',['../classvg_1_1SparseUnionFind.html#a4c161121ec4681cee764e1c261af865d',1,'vg::SparseUnionFind']]],
+ ['sparse_5funion_5ffind_2ecpp_5697',['sparse_union_find.cpp',['../sparse__union__find_8cpp.html',1,'']]],
+ ['sparse_5funion_5ffind_2ehpp_5698',['sparse_union_find.hpp',['../sparse__union__find_8hpp.html',1,'']]],
+ ['sparseunionfind_5699',['SparseUnionFind',['../classvg_1_1SparseUnionFind.html',1,'vg::SparseUnionFind'],['../classvg_1_1SparseUnionFind.html#aabd42adac47a3df51b0dfb55d7cde0f4',1,'vg::SparseUnionFind::SparseUnionFind()']]],
+ ['splice_5frescue_5fgraph_5fstd_5fdevs_5700',['splice_rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#a0fcadd278d752aba5c9bb143f5f3a0d6',1,'vg::MultipathMapper']]],
+ ['splice_5fstats_5701',['splice_stats',['../classvg_1_1MultipathMapper.html#a64556e12bae6880e876d0d16fe44efb9',1,'vg::MultipathMapper']]],
+ ['spliced_5fcigar_5fagainst_5fpath_5702',['spliced_cigar_against_path',['../classvg_1_1SplicedHTSAlignmentEmitter.html#ac447d6f996b11f12c3b8b2267ff4110e',1,'vg::SplicedHTSAlignmentEmitter']]],
+ ['spliced_5fdefault_5fsubgraph_5flimit_5703',['SPLICED_DEFAULT_SUBGRAPH_LIMIT',['../classvg_1_1Surjector.html#a8af3e56b9463fbbf483e78477f4a7172',1,'vg::Surjector']]],
+ ['spliced_5fsurject_5704',['spliced_surject',['../classvg_1_1Surjector.html#a8418e7a55b6b53456c80cbcf937406b5',1,'vg::Surjector']]],
+ ['splicedhtsalignmentemitter_5705',['SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html',1,'vg::SplicedHTSAlignmentEmitter'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#a8e546a34b4f2155fe6fb916123a0135d',1,'vg::SplicedHTSAlignmentEmitter::SplicedHTSAlignmentEmitter()']]],
+ ['spliceregion_5706',['SpliceRegion',['../classvg_1_1SpliceRegion.html',1,'vg::SpliceRegion'],['../classvg_1_1SpliceRegion.html#a3ca49fd7bedbe0b97117f87f7a5edba4',1,'vg::SpliceRegion::SpliceRegion(const pos_t &seed_pos, bool search_left, int64_t search_dist, const HandleGraph &graph, const DinucleotideMachine &dinuc_machine, const SpliceStats &splice_stats)'],['../classvg_1_1SpliceRegion.html#a5935bbc5e17cceae08ee9ef0b91b9abe',1,'vg::SpliceRegion::SpliceRegion()=default']]],
+ ['splicestats_5707',['SpliceStats',['../classvg_1_1SpliceStats.html',1,'vg::SpliceStats'],['../classvg_1_1SpliceStats.html#ac508ff2143cf8296531945e7674702bc',1,'vg::SpliceStats::SpliceStats(const GSSWAligner &scorer)'],['../classvg_1_1SpliceStats.html#a1808c3a4e73d0be56de7caca04142b01',1,'vg::SpliceStats::SpliceStats(const vector< tuple< string, string, double >> &motifs, const vector< double > &lognormal_mixture_weights, const vector< pair< double, double >> &lognormal_component_params, const GSSWAligner &scorer)']]],
+ ['splicestrand_5708',['SpliceStrand',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccd',1,'vg::MultipathMapper']]],
+ ['splicing_2ecpp_5709',['splicing.cpp',['../splicing_8cpp.html',1,'']]],
+ ['splicing_2ehpp_5710',['splicing.hpp',['../splicing_8hpp.html',1,'']]],
+ ['split_5711',['split',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aaf22613489ec859693457e82fd026e3b',1,'vg::Counts::split()'],['../classvg_1_1BitString.html#af826e3c7bce1aeada3f989b1b7d1bcc5',1,'vg::BitString::split()']]],
+ ['split_5fdelims_5712',['split_delims',['../namespacevg.html#acb2577b9163299f775898c17bcd3f72d',1,'vg::split_delims(const std::string &s, const std::string &delims, std::vector< std::string > &elems, size_t max_cuts)'],['../namespacevg.html#a335fce1edcad06f9840edcfad2c53e34',1,'vg::split_delims(const std::string &s, const std::string &delims, size_t max_cuts)']]],
+ ['split_5fext_5713',['split_ext',['../namespacevg.html#a984d142cea24f43a1025bf7bb7b48a53',1,'vg']]],
+ ['split_5fmulticomponent_5falignments_5714',['split_multicomponent_alignments',['../classvg_1_1MultipathMapper.html#af91f97b8331648b4df7587a461ca36b2',1,'vg::MultipathMapper::split_multicomponent_alignments(vector< multipath_alignment_t > &multipath_alns_out, const Alignment *alignment=nullptr, vector< clustergraph_t > *cluster_graphs=nullptr, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#a9257a7f9cc75ddd76a8daef803f2d031',1,'vg::MultipathMapper::split_multicomponent_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &multiplicities) const']]],
+ ['split_5fread_5ffilter_5715',['split_read_filter',['../classvg_1_1Filter.html#a0bc2a72604a0cb134c1f5bad7889a1bf',1,'vg::Filter']]],
+ ['split_5fread_5flimit_5716',['split_read_limit',['../classvg_1_1Filter.html#a0a0eca1fab7afdaec1d6311116dfe4a4',1,'vg::Filter']]],
+ ['split_5fsplice_5fsegment_5717',['split_splice_segment',['../namespacevg.html#aee945465384e60bdda619684ffca2ece',1,'vg']]],
+ ['split_5fstrand_5fgraph_2ecpp_5718',['split_strand_graph.cpp',['../split__strand__graph_8cpp.html',1,'']]],
+ ['split_5fstrand_5fgraph_2ehpp_5719',['split_strand_graph.hpp',['../split__strand__graph_8hpp.html',1,'']]],
+ ['split_5fstrands_5720',['split_strands',['../namespacehandlegraph_1_1algorithms.html#a1a7504e7155f6f9726c772a4b7c0f2c7',1,'handlegraph::algorithms']]],
+ ['split_5fstrands_2ecpp_5721',['split_strands.cpp',['../split__strands_8cpp.html',1,'']]],
+ ['split_5fsupports_5722',['split_supports',['../structvg_1_1BREAKPOINT.html#ad93eef0590346c5658ceb194c78204c5',1,'vg::BREAKPOINT']]],
+ ['ssw_5faligner_2ecpp_5723',['ssw_aligner.cpp',['../ssw__aligner_8cpp.html',1,'']]],
+ ['ssw_5faligner_2ehpp_5724',['ssw_aligner.hpp',['../ssw__aligner_8hpp.html',1,'']]],
+ ['ssw_5fto_5fvg_5725',['ssw_to_vg',['../classvg_1_1SSWAligner.html#a8daaaa17b12f1283c006d633d4c9a8fa',1,'vg::SSWAligner']]],
+ ['sswaligner_5726',['SSWAligner',['../classvg_1_1SSWAligner.html',1,'vg::SSWAligner'],['../classvg_1_1SSWAligner.html#ae91911b3a1357b0d3ae9bcecd51a592a',1,'vg::SSWAligner::SSWAligner()']]],
+ ['stack_5727',['stack',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa26ad54b66a37b0f31fa846c48d59882',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['stack_5fdata_5728',['stack_data',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a8c90da41cf4a8c9beb5794ce8bb0bd1c',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['stack_5fpermutations_5729',['stack_permutations',['../namespacevg.html#a5e9c563a243faef4e5357eca9c7c8500',1,'vg']]],
+ ['stack_5fup_5fvalid_5fwalks_5730',['stack_up_valid_walks',['../classvg_1_1ExhaustiveTraversalFinder.html#ab37a28d916291506bfe78a6818943585',1,'vg::ExhaustiveTraversalFinder']]],
+ ['stacktrace_5fmanually_5731',['stacktrace_manually',['../namespacevg.html#a8d771862cc44504508267240462cb043',1,'vg']]],
+ ['stage_5732',['Stage',['../structvg_1_1Funnel_1_1Stage.html',1,'vg::Funnel::Stage'],['../classvg_1_1Funnel.html#a21b5f8762aa446a64b5ddb3809e5c8e2',1,'vg::Funnel::stage(const string &name)']]],
+ ['stage_5fname_5733',['stage_name',['../classvg_1_1Funnel.html#a832c7d0be58aa6fa1e8dd8e7780e6850',1,'vg::Funnel']]],
+ ['stage_5fstart_5ftime_5734',['stage_start_time',['../classvg_1_1Funnel.html#a74a7f57094e7e1a8040ed9df34932aee',1,'vg::Funnel']]],
+ ['stage_5fstop_5735',['stage_stop',['../classvg_1_1Funnel.html#a87e1b8deccb4438d7f71267ee5f12ced',1,'vg::Funnel']]],
+ ['stages_5736',['stages',['../classvg_1_1Funnel.html#a48bdc3457d5f66a3f454bcde8d42883e',1,'vg::Funnel']]],
+ ['standard_5fextend_5737',['standard_extend',['../structhaplo_1_1haplo__DP__column.html#a5364cc0f365e68434e346c2b48eea996',1,'haplo::haplo_DP_column']]],
+ ['standard_5flibrary_5738',['STANDARD_LIBRARY',['../classvg_1_1Version.html#a679d78a021abc99f587596a38e2fbf84',1,'vg::Version']]],
+ ['star_5fallele_5739',['star_allele',['../classvg_1_1Deconstructor.html#a11591e3c8e54882b5c695f691cec6a62',1,'vg::Deconstructor']]],
+ ['start_5740',['START',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3ab5854c3018055ccefae586f717850711',1,'handlegraph::SnarlDecomposition::START()'],['../structvg_1_1BREAKPOINT.html#a624e7af692ef989d559a3e14e5075d4b',1,'vg::BREAKPOINT::start()'],['../structvg_1_1GFFRecord.html#a1515c4a06b600c34d84b012b0195423a',1,'vg::GFFRecord::start()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#af564269e9eaf8eb68f4c4c3ce1ba3932',1,'vg::GraphSynchronizer::Lock::start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af3baaf52c08ac684ac2571a9f4f56ec0',1,'vg::Haplotypes::Subchain::start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a16932e227f0ac0972fb63bc300a5374d',1,'vg::HaplotypePartitioner::Subchain::start()'],['../structvg_1_1Region.html#a3905a368a833ae5f090f3faafa1b55bc',1,'vg::Region::start()'],['../classvg_1_1NetGraph.html#a2d7b0b659aae1f47312bb76aae43dda0',1,'vg::NetGraph::start()'],['../classvg_1_1algorithms_1_1Anchor.html#a67c31c873448badab1dab33385f290bc',1,'vg::algorithms::Anchor::start()'],['../structMappingRun.html#ae556594581cecb906e1972405df7c460',1,'MappingRun::start()'],['../structReferenceInterval.html#aaeb76d7fd3436409b6bf5500350527dd',1,'ReferenceInterval::start()'],['../structvg_1_1Range.html#a372fbc9ba00e9eb4785fcd049b2451cf',1,'vg::Range::start()'],['../structgafkluge_1_1GafStep.html#abd90c68888f2f19e733a03597e520d2f',1,'gafkluge::GafStep::start()'],['../structvg_1_1MultipathAlignment.html#a8003b8991108e99465d8fd80fc74cc03',1,'vg::MultipathAlignment::start()'],['../structvg_1_1Snarl.html#a2a35b60b251ab2d8429b6afcd387448f',1,'vg::Snarl::start()'],['../classvg_1_1Funnel.html#a4ba2b8db1575820b05d069cd6c802e31',1,'vg::Funnel::start()'],['../classvg_1_1multipath__alignment__t.html#a4cd9b91704e89c799019d9c8962b16bb',1,'vg::multipath_alignment_t::start() const'],['../classvg_1_1multipath__alignment__t.html#ae79344b60aed1577a39391b4b42574f3',1,'vg::multipath_alignment_t::start(size_t i) const']]],
+ ['start_5fbackward_5741',['start_backward',['../namespacevg.html#a43f061abac718e0386965aa537398e74',1,'vg']]],
+ ['start_5fdegree_5742',['start_degree',['../classvg_1_1VG.html#a1ff00edd627e3445eee7f43927bb1518',1,'vg::VG']]],
+ ['start_5fend_5freachable_5743',['start_end_reachable',['../structvg_1_1Snarl.html#acab3c449de2871769eb9a39ba5f9b8f8',1,'vg::Snarl']]],
+ ['start_5fhandle_5744',['start_handle',['../structvg_1_1Haplotypes_1_1Subchain.html#a8b8950af5c76b20ab93ef40dc086da93',1,'vg::Haplotypes::Subchain']]],
+ ['start_5fhint_5745',['start_hint',['../classvg_1_1algorithms_1_1Anchor.html#a1be30d40d8252c36c162bfbb568554a1',1,'vg::algorithms::Anchor']]],
+ ['start_5fhint_5foffset_5746',['start_hint_offset',['../classvg_1_1algorithms_1_1Anchor.html#afe9a192ac276676633aab322189732b0',1,'vg::algorithms::Anchor']]],
+ ['start_5foffset_5747',['start_offset',['../classvg_1_1algorithms_1_1Anchor.html#af25f1f44ad6e51d8f5d318a9b2d816f9',1,'vg::algorithms::Anchor']]],
+ ['start_5fpos_5748',['start_pos',['../classvg_1_1MEMClusterer_1_1HitNode.html#ac1772330432b54080ac41ec1a4302d8d',1,'vg::MEMClusterer::HitNode::start_pos()'],['../classvg_1_1algorithms_1_1Anchor.html#a78487c55bbc790fc1f2a05396ded3530',1,'vg::algorithms::Anchor::start_pos()']]],
+ ['start_5fpos_5fsamplers_5749',['start_pos_samplers',['../classvg_1_1NGSSimulator.html#abe06d132967858ffa36a6f5235a506f2',1,'vg::NGSSimulator']]],
+ ['start_5fseed_5750',['start_seed',['../classvg_1_1algorithms_1_1Anchor.html#a3eb9aa25a9ead7787d829468c571bdd0',1,'vg::algorithms::Anchor']]],
+ ['start_5fself_5freachable_5751',['start_self_reachable',['../structvg_1_1Snarl.html#a9a2de860018e3c8cfd512f6a1904f18c',1,'vg::Snarl']]],
+ ['start_5fsize_5752',['start_size',['../classvg_1_1multipath__alignment__t.html#a8155e732811cdcc1e6fcee417b25bf10',1,'vg::multipath_alignment_t']]],
+ ['start_5ftime_5753',['start_time',['../classvg_1_1Funnel.html#af72a0ecffb7bd38fcd89ee3c71dd638b',1,'vg::Funnel']]],
+ ['start_5fvcf_5754',['start_vcf',['../classvg_1_1Genotyper.html#a8a5aed6de86a488fe78a223d5e4d6bd6',1,'vg::Genotyper']]],
+ ['start_5fzip_5755',['start_zip',['../classvg_1_1algorithms_1_1Anchor.html#a7cd7ad6f5f36dfb5c760ac995a258d88',1,'vg::algorithms::Anchor']]],
+ ['startfile_5756',['StartFile',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaf788a0a0553f9cc0c531fecb941f228',1,'vg::io::BlockedGzipOutputStream']]],
+ ['starting_5fposition_5757',['starting_position',['../structvg_1_1GaplessExtension.html#a2dc9687b1ac33335f593028c981fe494',1,'vg::GaplessExtension']]],
+ ['starts_5fat_5758',['starts_at',['../classhandlegraph_1_1SnarlDecomposition.html#ac6bb78bc95acfd353ff8d6c44915e524',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fat_5fend_5759',['starts_at_end',['../classhandlegraph_1_1SnarlDecomposition.html#aab710270e1997f22d1b09a4fd40a3eaf',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fat_5fstart_5760',['starts_at_start',['../classhandlegraph_1_1SnarlDecomposition.html#adb1c7cccea8188c8e24a4e53c34117bb',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fat_5ftip_5761',['starts_at_tip',['../classhandlegraph_1_1SnarlDecomposition.html#ac47bc288b1c0303d3356e953de4878e2',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fwith_5762',['starts_with',['../namespacevg.html#a7b58d5d004a85a09906301781567970a',1,'vg']]],
+ ['stat_5fcollection_5ft_5763',['stat_collection_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['stat_5fset_5ft_5764',['stat_set_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['state_5765',['state',['../structvg_1_1WFANode.html#ac59b2dd030133cc65cc0bf47af486ef0',1,'vg::WFANode::state()'],['../structvg_1_1GaplessExtension.html#a1b799cab247ae9b2551e902a9f7f2b25',1,'vg::GaplessExtension::state()'],['../classvg_1_1GenomeState.html#ab0f68d58776dcd18a1ef85409a29e452',1,'vg::GenomeState::state()'],['../structhaplo_1_1haplo__DP__rectangle.html#aff798553a0dfd177413b1649e049e574',1,'haplo::haplo_DP_rectangle::state()'],['../classvg_1_1Watchdog.html#a0cecf66da11a5f71e837a9d1b6f6c291',1,'vg::Watchdog::state()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4a2a145b0221202c440cca81c0ba89c9',1,'vg::ZipCodeTree::reverse_iterator::state()'],['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85',1,'vg::Funnel::State()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19',1,'vg::ZipCodeTree::reverse_iterator::State()']]],
+ ['state_5fhash_5766',['state_hash',['../structvg_1_1state__hash.html',1,'vg']]],
+ ['state_5ftype_5767',['state_type',['../classvg_1_1PhaseUnfolder.html#a95529e399d5ef61f6a426e1b5cfe9237',1,'vg::PhaseUnfolder']]],
+ ['states_5768',['states',['../classvg_1_1PhaseUnfolder.html#ac7d3333de41989b2ca10db84ddb1d5a8',1,'vg::PhaseUnfolder']]],
+ ['statistics_5769',['Statistics',['../structvg_1_1Recombinator_1_1Statistics.html',1,'vg::Recombinator']]],
+ ['statistics_2ecpp_5770',['statistics.cpp',['../statistics_8cpp.html',1,'']]],
+ ['statistics_2ehpp_5771',['statistics.hpp',['../statistics_8hpp.html',1,'']]],
+ ['stats_5fmain_2ecpp_5772',['stats_main.cpp',['../stats__main_8cpp.html',1,'']]],
+ ['std_5773',['std',['../namespacestd.html',1,'']]],
+ ['std_5fdev_5774',['std_dev',['../classvg_1_1FragmentLengthDistribution.html#a4da22f6209796ad178bd6ae88a995c03',1,'vg::FragmentLengthDistribution']]],
+ ['stddev_5775',['stddev',['../classvg_1_1normal__distribution.html#aaf593ce22610d686f290face7b5db895',1,'vg::normal_distribution::stddev()'],['../classvg_1_1truncated__normal__distribution.html#a49f7b71f827df31a5590d120e04dcbcf',1,'vg::truncated_normal_distribution::stddev()']]],
+ ['stdev_5776',['stdev',['../structvg_1_1SummaryStatistics.html#abea415bc0808b7714dee7cb6556dcf30',1,'vg::SummaryStatistics::stdev()'],['../namespacevg.html#a11df8bd14dab3c0cfb7ecfa377a362f5',1,'vg::stdev()']]],
+ ['step_5777',['step',['../structvg_1_1Range.html#a05a0a35957e0a0e127b9ef55a305df76',1,'vg::Range::step()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a44f22277ea90f802ae502bdb5bf8e478',1,'handlegraph::PathForEachSocket::iterator::step()']]],
+ ['step_5f1_5fbuild_5fgbwts_5778',['step_1_build_gbwts',['../gbwt__main_8cpp.html#a099d84c7e00d3a536ab0c89a42824a67',1,'gbwt_main.cpp']]],
+ ['step_5f2_5fmerge_5fgbwts_5779',['step_2_merge_gbwts',['../gbwt__main_8cpp.html#a81911b71bc15131cf9f9cc9652cccf0a',1,'gbwt_main.cpp']]],
+ ['step_5f3_5falter_5fgbwt_5780',['step_3_alter_gbwt',['../gbwt__main_8cpp.html#aa89c3d0220f759b0de6756841c3bbfae',1,'gbwt_main.cpp']]],
+ ['step_5f4_5fpath_5fcover_5781',['step_4_path_cover',['../gbwt__main_8cpp.html#ac6ed5f1a6fdf7794797be7ab94278897',1,'gbwt_main.cpp']]],
+ ['step_5f5_5fgbwtgraph_5782',['step_5_gbwtgraph',['../gbwt__main_8cpp.html#a61f18988124c373bf3aa037ad24719f2',1,'gbwt_main.cpp']]],
+ ['step_5f6_5fr_5findex_5783',['step_6_r_index',['../gbwt__main_8cpp.html#a240e0e93804c406946adb930f58c87aa',1,'gbwt_main.cpp']]],
+ ['step_5f7_5fmetadata_5784',['step_7_metadata',['../gbwt__main_8cpp.html#a7d810cefdbee01df4d4fe50406806e30',1,'gbwt_main.cpp']]],
+ ['step_5f8_5fpaths_5785',['step_8_paths',['../gbwt__main_8cpp.html#a859c16083955e4f1ab36c130fe6cce27',1,'gbwt_main.cpp']]],
+ ['step_5fhandle_5ft_5786',['step_handle_t',['../structhandlegraph_1_1step__handle__t.html',1,'handlegraph::step_handle_t'],['../namespacevg.html#a40b137bbd07d198ca2b77962eeeaf7c8',1,'vg::step_handle_t()'],['../namespacevg_1_1io.html#a5473f8a5ac351719453cfd62655beebb',1,'vg::io::step_handle_t()']]],
+ ['step_5fin_5fpath_5787',['step_in_path',['../classvg_1_1VCFTraversalFinder.html#aefa5cf40bc0244f81e52ae2bdb4904d0',1,'vg::VCFTraversalFinder']]],
+ ['step_5frank_5fat_5fposition_5788',['step_rank_at_position',['../classxg_1_1XGPath.html#a92b0745ad293f585d5fb20d1bf20f7cc',1,'xg::XGPath']]],
+ ['steps_5789',['steps',['../classvg_1_1IndexingPlan.html#afe22bdcd727f981fb262b8d29819dee2',1,'vg::IndexingPlan']]],
+ ['steps_5fof_5fhandle_5790',['steps_of_handle',['../classvg_1_1MemoizingGraph.html#ab96deef5a4149f287541058c256a1115',1,'vg::MemoizingGraph::steps_of_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a015b050f33861cbc8e2a0efaaf771a30',1,'handlegraph::PathHandleGraph::steps_of_handle()']]],
+ ['steps_5fof_5fhandle_5fmemo_5791',['steps_of_handle_memo',['../classvg_1_1MemoizingGraph.html#ac2e7cde55ff928b866d7e26caccdd35e',1,'vg::MemoizingGraph']]],
+ ['stop_5792',['stop',['../classvg_1_1Funnel.html#adbe0233346c63f1693fa865eca0083b2',1,'vg::Funnel']]],
+ ['stop_5fon_5fduplicate_5fpaths_5793',['stop_on_duplicate_paths',['../classvg_1_1algorithms_1_1GFAParser.html#abe8f148f7941fc1fbc449687b9623c21',1,'vg::algorithms::GFAParser']]],
+ ['stop_5ftime_5794',['stop_time',['../classvg_1_1Funnel.html#a59b3ea467d461a57b8801c8845b0bdb3',1,'vg::Funnel']]],
+ ['stop_5fwatcher_5795',['stop_watcher',['../classvg_1_1Watchdog.html#a2fbb9a2b514a26515e508ee665295449',1,'vg::Watchdog']]],
+ ['stored_5fcrash_5fcontext_5796',['stored_crash_context',['../namespacevg.html#aeb1b2d0c77858355b8bfbbe4406f0931',1,'vg']]],
+ ['stored_5fedge_5ft_5797',['stored_edge_t',['../classvg_1_1DiagramExplainer.html#a6eca0d51970a6782f49171a354aaeb74',1,'vg::DiagramExplainer']]],
+ ['str_5798',['STR',['../version_8cpp.html#a6a96991688ffe6ae2293f0a4b5f813d2',1,'version.cpp']]],
+ ['strand_5799',['strand',['../structgafkluge_1_1GafRecord.html#a38f3845982a15cf080267890fe7e0b3b',1,'gafkluge::GafRecord']]],
+ ['strand_5fis_5frev_5800',['strand_is_rev',['../structvg_1_1GFFRecord.html#a08edb7d13481c70c0cfbba949e4f81ce',1,'vg::GFFRecord']]],
+ ['strand_5fsampler_5801',['strand_sampler',['../classvg_1_1NGSSimulator.html#a71a4b2c30a477a86d4b7c9f5d6ab3a28',1,'vg::NGSSimulator']]],
+ ['strandsplitgraph_5802',['StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html',1,'vg::StrandSplitGraph'],['../classvg_1_1StrandSplitGraph.html#a0e170b8ad07ca370e31497b804932220',1,'vg::StrandSplitGraph::StrandSplitGraph(const HandleGraph *graph)'],['../classvg_1_1StrandSplitGraph.html#aede16e10fc0b17f2527a62861f155c6d',1,'vg::StrandSplitGraph::StrandSplitGraph()=default']]],
+ ['stream_2ecpp_5803',['stream.cpp',['../stream_8cpp.html',1,'']]],
+ ['stream_2ehpp_5804',['stream.hpp',['../stream_8hpp.html',1,'']]],
+ ['stream_5findex_2ecpp_5805',['stream_index.cpp',['../stream__index_8cpp.html',1,'']]],
+ ['stream_5findex_2ehpp_5806',['stream_index.hpp',['../stream__index_8hpp.html',1,'']]],
+ ['stream_5fmultiplexer_2ecpp_5807',['stream_multiplexer.cpp',['../stream__multiplexer_8cpp.html',1,'']]],
+ ['stream_5fmultiplexer_2ehpp_5808',['stream_multiplexer.hpp',['../stream__multiplexer_8hpp.html',1,'']]],
+ ['stream_5fsort_5809',['stream_sort',['../classvg_1_1StreamSorter.html#a3ef7c0c822f58db91184e6b069c3ce59',1,'vg::StreamSorter']]],
+ ['stream_5fsorter_2ecpp_5810',['stream_sorter.cpp',['../stream__sorter_8cpp.html',1,'']]],
+ ['stream_5fsorter_2ehpp_5811',['stream_sorter.hpp',['../stream__sorter_8hpp.html',1,'']]],
+ ['streamcompressstring_5812',['StreamCompressString',['../namespacezstdutil.html#a64155ae3ce93620ea7868913f4c49ab3',1,'zstdutil']]],
+ ['streamdecompressstring_5813',['StreamDecompressString',['../namespacezstdutil.html#a2b6cfe0b4f483fea633845a8d912e8dd',1,'zstdutil']]],
+ ['streaminbuf_5814',['streaminbuf',['../classvg_1_1io_1_1streaminbuf.html',1,'vg::io::streaminbuf'],['../classvg_1_1io_1_1streaminbuf.html#a611fcbbde05222173c867ea92cf20ed6',1,'vg::io::streaminbuf::streaminbuf()']]],
+ ['streamindex_5815',['StreamIndex',['../classvg_1_1StreamIndex.html',1,'vg::StreamIndex< Message >'],['../classvg_1_1StreamIndex.html#a3508617dbf1b8e8d1df051f4a214fa5e',1,'vg::StreamIndex::StreamIndex()']]],
+ ['streamindex_3c_20vg_3a_3aalgorithms_3a_3agraph_20_3e_5816',['StreamIndex< vg::algorithms::Graph >',['../classvg_1_1StreamIndex.html',1,'vg']]],
+ ['streamindexbase_5817',['StreamIndexBase',['../classvg_1_1StreamIndexBase.html',1,'vg::StreamIndexBase'],['../classvg_1_1StreamIndexBase.html#a2df03d2ee53e9f171e4aa519a079901e',1,'vg::StreamIndexBase::StreamIndexBase()=default'],['../classvg_1_1StreamIndexBase.html#a85207efd00788e14df4df717d88233b7',1,'vg::StreamIndexBase::StreamIndexBase(const StreamIndexBase &other)=delete']]],
+ ['streaming_5fmerge_5818',['streaming_merge',['../classvg_1_1StreamSorter.html#a1c19cdfb158ff9771e471fbbc2b4ac74',1,'vg::StreamSorter::streaming_merge(list< cursor_t > &cursors, emitter_t &emitter, size_t expected_messages=0)'],['../classvg_1_1StreamSorter.html#a77590f7da1d1418fc00e7bdaec2a76e5',1,'vg::StreamSorter::streaming_merge(const vector< string > &temp_names_in, unordered_map< string, size_t > *messages_per_file=nullptr)']]],
+ ['streamistream_5819',['streamistream',['../classvg_1_1io_1_1streamistream.html',1,'vg::io::streamistream'],['../classvg_1_1io_1_1streamistream.html#a0b87c404670f610d20f49f1e2c166648',1,'vg::io::streamistream::streamistream()']]],
+ ['streammultiplexer_5820',['StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html',1,'vg::io::StreamMultiplexer'],['../classvg_1_1io_1_1StreamMultiplexer.html#ae72f4179a6cb14beb1b6460603d88233',1,'vg::io::StreamMultiplexer::StreamMultiplexer(ostream &backing, size_t max_threads)'],['../classvg_1_1io_1_1StreamMultiplexer.html#ad8b06aab5797747b1ce3d544be0cc965',1,'vg::io::StreamMultiplexer::StreamMultiplexer(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#af8352f0fcbb63f162734d48d2ec573ce',1,'vg::io::StreamMultiplexer::StreamMultiplexer(StreamMultiplexer &&other)=delete']]],
+ ['streamsorter_5821',['StreamSorter',['../classvg_1_1StreamSorter.html',1,'vg::StreamSorter< Message >'],['../classvg_1_1StreamSorter.html#a9ef0b8a33f5011eaf655b9420d86b0f5',1,'vg::StreamSorter::StreamSorter()']]],
+ ['strict_5fconflict_5fchecking_5822',['strict_conflict_checking',['../classvg_1_1Deconstructor.html#a565e2bb8d83d007a630f8f3db37c8b43',1,'vg::Deconstructor']]],
+ ['string_5823',['String',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eab41cf4db950b9da3d95a7c1400a5369e',1,'vg::multipath_alignment_t']]],
+ ['string_5fhash_5fmap_5824',['string_hash_map',['../classvg_1_1string__hash__map.html',1,'vg']]],
+ ['string_5fhash_5fset_5825',['string_hash_set',['../classvg_1_1string__hash__set.html',1,'vg']]],
+ ['string_5fquality_5fchar_5fto_5fshort_5826',['string_quality_char_to_short',['../namespacevg_1_1io.html#a4450d95b60550d44cbfe712467e92947',1,'vg::io']]],
+ ['string_5fquality_5fshort_5fto_5fchar_5827',['string_quality_short_to_char',['../namespacevg_1_1io.html#a33f3f10cba44d4ab370628c9579f9ca4',1,'vg::io']]],
+ ['string_5fto_5fint_5828',['string_to_int',['../namespacegafkluge.html#a35bc1201781dd4bab3581189c777a8af',1,'gafkluge']]],
+ ['strip_5fbonuses_5829',['strip_bonuses',['../classvg_1_1BaseMapper.html#a34ab4a12d44f5b17b5b6caa03ea4cd79',1,'vg::BaseMapper']]],
+ ['strip_5ffrom_5fend_5830',['strip_from_end',['../namespacevg.html#adbe45b79675104ebc36691774d4124c4',1,'vg']]],
+ ['strip_5ffrom_5fstart_5831',['strip_from_start',['../namespacevg.html#acd6786ea9551b426f95fba325beff138',1,'vg']]],
+ ['strip_5ffull_5flength_5fbonuses_5832',['strip_full_length_bonuses',['../classvg_1_1MultipathMapper.html#a1147b64d4c4aeffa84403f5341de52bf',1,'vg::MultipathMapper']]],
+ ['strip_5fsubrange_5833',['strip_subrange',['../classvg_1_1Paths.html#aaae6abfe6b12aecfe82457fe8b8b44a8',1,'vg::Paths']]],
+ ['strip_5fsuffixes_5834',['strip_suffixes',['../giraffe__main_8cpp.html#ada042c5c5040b9b72848655d3dc5fcf8',1,'giraffe_main.cpp']]],
+ ['stripped_5fmatch_5falg_5fmax_5flength_5835',['stripped_match_alg_max_length',['../classvg_1_1MultipathMapper.html#aee2a7d30863137faeb2b9925c195262d',1,'vg::MultipathMapper']]],
+ ['stripped_5fmatch_5falg_5fstrip_5flength_5836',['stripped_match_alg_strip_length',['../classvg_1_1MultipathMapper.html#a892c094e2a5b4dcce87b47a0ee27bff8',1,'vg::MultipathMapper']]],
+ ['stripped_5fmatch_5falg_5ftarget_5fcount_5837',['stripped_match_alg_target_count',['../classvg_1_1MultipathMapper.html#a3a8af36f7fbbe431ea804f83e75a684d',1,'vg::MultipathMapper']]],
+ ['strongly_5fconnected_5fcomponents_5838',['strongly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a3c63833d51eac5a3141211367935e9e5',1,'handlegraph::algorithms']]],
+ ['strongly_5fconnected_5fcomponents_2ecpp_5839',['strongly_connected_components.cpp',['../strongly__connected__components_8cpp.html',1,'']]],
+ ['stubbify_5fref_5fpaths_5840',['stubbify_ref_paths',['../namespacevg.html#a9e14750889892e0d70b8bc18fcc9f905',1,'vg']]],
+ ['sub_5fdurations_5841',['sub_durations',['../structvg_1_1Funnel_1_1Stage.html#af090e9aa3d82046a91766e05cdec814d',1,'vg::Funnel::Stage']]],
+ ['sub_5fmem_5fcount_5fthinning_5842',['sub_mem_count_thinning',['../classvg_1_1BaseMapper.html#a8d9a00e1d809346bc62f6f2c1e4fbe32',1,'vg::BaseMapper']]],
+ ['sub_5fmem_5fthinning_5fburn_5fin_5843',['sub_mem_thinning_burn_in',['../classvg_1_1BaseMapper.html#a4e17a40bafbd8832d551acb01298403d',1,'vg::BaseMapper']]],
+ ['sub_5foverlaps_5fof_5ffirst_5faln_5844',['sub_overlaps_of_first_aln',['../namespacevg.html#ab63c41956b73af429507b469108d1759',1,'vg']]],
+ ['sub_5fpoly_5frate_5845',['sub_poly_rate',['../classvg_1_1NGSSimulator.html#a2078f130a3782a67206ad9c2c20067ea',1,'vg::NGSSimulator']]],
+ ['sub_5fscore_5846',['sub_score',['../classvg_1_1ReadFilter.html#a529c0b978b3855bab3dc1074fd18a711',1,'vg::ReadFilter']]],
+ ['subchain_5847',['Subchain',['../structvg_1_1HaplotypePartitioner_1_1Subchain.html',1,'vg::HaplotypePartitioner::Subchain'],['../structvg_1_1Haplotypes_1_1Subchain.html',1,'vg::Haplotypes::Subchain']]],
+ ['subchain_5fid_5848',['subchain_id',['../structHaplotypesConfig.html#ae5e75f47f0768d4e5da28a15baaa702e',1,'HaplotypesConfig']]],
+ ['subchain_5fintervals_5849',['subchain_intervals',['../haplotypes__main_8cpp.html#aed90215616b71a8c576afeeb7a137596',1,'haplotypes_main.cpp']]],
+ ['subchain_5flength_5850',['SUBCHAIN_LENGTH',['../classvg_1_1HaplotypePartitioner.html#a3343e960c394c9c092d08ff931f37081',1,'vg::HaplotypePartitioner::SUBCHAIN_LENGTH()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#ac912479fc22acc7c9078978e71597ad9',1,'vg::HaplotypePartitioner::Parameters::subchain_length()'],['../namespacehaplotypes__defaults.html#af6cc9d47b0c3862d9c0cdea27b55f477',1,'haplotypes_defaults::subchain_length()']]],
+ ['subchain_5fstatistics_5851',['subchain_statistics',['../haplotypes__main_8cpp.html#a559cad6ab46d0a7dc260987e61ed1175',1,'haplotypes_main.cpp']]],
+ ['subchain_5ft_5852',['subchain_t',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbde',1,'vg::Haplotypes::Subchain']]],
+ ['subchain_5fto_5fstring_5853',['subchain_to_string',['../haplotypes__main_8cpp.html#ae88c7a2ca3744f1826af903b27b2df53',1,'haplotypes_main.cpp']]],
+ ['subchains_5854',['subchains',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ae31e41720bb3a859e4762aa9e2c5318b',1,'vg::Haplotypes::TopLevelChain::subchains()'],['../structvg_1_1Recombinator_1_1Statistics.html#ab6d38eac9e036f7b2b0f19736529e3a9',1,'vg::Recombinator::Statistics::subchains()']]],
+ ['subcommand_5855',['Subcommand',['../classvg_1_1subcommand_1_1Subcommand.html',1,'vg::subcommand::Subcommand'],['../classvg_1_1subcommand_1_1Subcommand.html#ad5faf589dd98c3ff0c0d1071fcf90090',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, int priority, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#a38458556194aa9d47b1a49fc8958f345',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#ad2cb9a00761644300914d9ed8439cbe1',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, std::function< int(int, char **)> main_function)']]],
+ ['subcommand_2ecpp_5856',['subcommand.cpp',['../subcommand_8cpp.html',1,'']]],
+ ['subcommand_2ehpp_5857',['subcommand.hpp',['../subcommand_8hpp.html',1,'']]],
+ ['subgraph_5858',['subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aae76f24549ed2f49dc12176f46dfea8d',1,'vg::GraphSynchronizer::Lock::subgraph()'],['../classvg_1_1SpliceRegion.html#aa12379182f8abfc5239c38b433d1b4b8',1,'vg::SpliceRegion::subgraph()'],['../classvg_1_1SubgraphExplainer.html#a6a8bb147fa3f638f7bc0c2a098475999',1,'vg::SubgraphExplainer::subgraph()']]],
+ ['subgraph_2ecpp_5859',['subgraph.cpp',['../subgraph_8cpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8cpp.html',1,'(Global Namespace)']]],
+ ['subgraph_2ehpp_5860',['subgraph.hpp',['../subgraph_8hpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8hpp.html',1,'(Global Namespace)']]],
+ ['subgraph_5fcontaining_5fpath_5fsnarls_5861',['subgraph_containing_path_snarls',['../namespacevg.html#acc960c295c1e3088dc8e71ab1af5c4d6',1,'vg']]],
+ ['subgraph_5fin_5fdistance_5frange_5862',['subgraph_in_distance_range',['../namespacevg.html#aff8a7aca57dd525bc2def1369abae3fe',1,'vg']]],
+ ['subgraph_5fin_5fdistance_5frange_5fwalk_5facross_5fchain_5863',['subgraph_in_distance_range_walk_across_chain',['../namespacevg.html#a30f08b56f8c117103357ed4b8ebc08b8',1,'vg']]],
+ ['subgraph_5fin_5fdistance_5frange_5fwalk_5fgraph_5864',['subgraph_in_distance_range_walk_graph',['../namespacevg.html#a0312bffc43a4f4176aad1c37073b59df',1,'vg']]],
+ ['subgraph_5fmin_5865',['subgraph_min',['../structPruningParameters.html#ada52c2750edf0333574238f15adb1c84',1,'PruningParameters']]],
+ ['subgraph_5foverlay_2ecpp_5866',['subgraph_overlay.cpp',['../subgraph__overlay_8cpp.html',1,'']]],
+ ['subgraph_5foverlay_2ehpp_5867',['subgraph_overlay.hpp',['../subgraph__overlay_8hpp.html',1,'']]],
+ ['subgraph_5fprune_5868',['subgraph_prune',['../classvg_1_1VariantAdder.html#a39e87cff1b1cf12920a36b78bdcc2ddc',1,'vg::VariantAdder']]],
+ ['subgraphexplainer_5869',['SubgraphExplainer',['../classvg_1_1SubgraphExplainer.html',1,'vg::SubgraphExplainer'],['../classvg_1_1SubgraphExplainer.html#adbcee01cfe7c72e36071da4ed5aa1aec',1,'vg::SubgraphExplainer::SubgraphExplainer()']]],
+ ['subgraphoverlay_5870',['SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html',1,'vg::SubgraphOverlay'],['../classvg_1_1SubgraphOverlay.html#ac9ffa71f1e615eb30efc626006c11242',1,'vg::SubgraphOverlay::SubgraphOverlay()']]],
+ ['subgroups_5871',['subgroups',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a17a3b23ed098272dfa4f3a9226ac5bef',1,'vg::subcommand::GroupedOptionGroup']]],
+ ['subhandlegraph_5872',['SubHandleGraph',['../classvg_1_1SubHandleGraph.html',1,'vg::SubHandleGraph'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html',1,'handlegraph::algorithms::SubHandleGraph'],['../classvg_1_1SubHandleGraph.html#ae02101c50fc316637a11ed674637e6a4',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super, HandleIter begin, HandleIter end)'],['../classvg_1_1SubHandleGraph.html#a1426a494a5d412485f5c4959f3b853c8',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super)'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4455c7d0983b1fcce544022a60fa76ab',1,'handlegraph::algorithms::SubHandleGraph::SubHandleGraph()']]],
+ ['subpath_5873',['Subpath',['../structvg_1_1Subpath.html',1,'vg::Subpath'],['../structvg_1_1MultipathAlignment.html#aa92c4cbfee9b5e076c41ca466b44617c',1,'vg::MultipathAlignment::subpath()'],['../classvg_1_1multipath__alignment__t.html#a87bb864c7cd6e424fe9487cc662cade6',1,'vg::multipath_alignment_t::subpath() const'],['../classvg_1_1multipath__alignment__t.html#a5544e1c157233fda1b528bdd3e426f90',1,'vg::multipath_alignment_t::subpath(size_t i) const']]],
+ ['subpath_5fhandles_5874',['subpath_handles',['../classvg_1_1SubpathOverlay.html#ab1edd258ddd2cce726bfbc79b32b2476',1,'vg::SubpathOverlay']]],
+ ['subpath_5foverlay_2ecpp_5875',['subpath_overlay.cpp',['../subpath__overlay_8cpp.html',1,'']]],
+ ['subpath_5foverlay_2ehpp_5876',['subpath_overlay.hpp',['../subpath__overlay_8hpp.html',1,'']]],
+ ['subpath_5fsize_5877',['subpath_size',['../classvg_1_1multipath__alignment__t.html#a3b6820ac77fa5438c55300ba1eb7a97d',1,'vg::multipath_alignment_t']]],
+ ['subpath_5ft_5878',['subpath_t',['../classvg_1_1subpath__t.html',1,'vg::subpath_t'],['../classvg_1_1subpath__t.html#a17ac16fd98564bfa3ab34e9b9b20517e',1,'vg::subpath_t::subpath_t()=default'],['../classvg_1_1subpath__t.html#a31254046fc840d936d42012b2c7b23b5',1,'vg::subpath_t::subpath_t(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a096b12ec158dd2cf139dbe38f55ca2f3',1,'vg::subpath_t::subpath_t(subpath_t &&)=default']]],
+ ['subpath_5fto_5flength_5879',['subpath_to_length',['../classvg_1_1HTSWriter.html#a24dca4e57dcfb498da8f18946194f600',1,'vg::HTSWriter']]],
+ ['subpath_5ftopological_5forder_5880',['subpath_topological_order',['../namespacevg.html#ab1dcbe73351c8eaeea745f4b5191b8f0',1,'vg']]],
+ ['subpathoverlay_5881',['SubpathOverlay',['../classvg_1_1SubpathOverlay.html',1,'vg::SubpathOverlay'],['../classvg_1_1SubpathOverlay.html#a63691d737697292e0a2fd4233024dfb8',1,'vg::SubpathOverlay::SubpathOverlay(const PathHandleGraph *backing, const step_handle_t &begin, const step_handle_t &end)'],['../classvg_1_1SubpathOverlay.html#aa3cc8559a68870f144d69eb44829c95a',1,'vg::SubpathOverlay::SubpathOverlay()=default']]],
+ ['subrange_5ft_5882',['subrange_t',['../namespacevg.html#ae28b502adf2ce7302acbb3138280f06c',1,'vg::subrange_t()'],['../namespacehandlegraph.html#a097e656b1ffb02a80c0b530b1987984a',1,'handlegraph::subrange_t()']]],
+ ['subsequence_5883',['subsequence',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9acf76097b099973339661134c01b30e59',1,'vg::Counts']]],
+ ['subsequences_5884',['subsequences',['../classvg_1_1ReadFilter.html#a98cd220c402ec88c512121825ed690df',1,'vg::ReadFilter']]],
+ ['substage_5885',['substage',['../classvg_1_1Funnel.html#a0520d00fd1dcd9fa4af18d715580c900',1,'vg::Funnel']]],
+ ['substage_5fname_5886',['substage_name',['../classvg_1_1Funnel.html#a4cfa61145fcd97f5710c3d609e72a997',1,'vg::Funnel']]],
+ ['substage_5fstart_5ftime_5887',['substage_start_time',['../classvg_1_1Funnel.html#ae8b9248bf65562b44ac8b65f50619c70',1,'vg::Funnel']]],
+ ['substage_5fstop_5888',['substage_stop',['../classvg_1_1Funnel.html#ab5934891f37d57dc9309e5b0e9f80d9e',1,'vg::Funnel']]],
+ ['subtract_5flog_5889',['subtract_log',['../namespacevg.html#a33c8f5153ad0766df2c72bbec623aa19',1,'vg']]],
+ ['successor_5foffset_5890',['successor_offset',['../classvg_1_1WFATree.html#a33c5e80cc73d5367a95343deb20d8dac',1,'vg::WFATree']]],
+ ['suffix_5891',['suffix',['../classvg_1_1IndexFile.html#acc1a7b94cb2a464d4941e7092aa83612',1,'vg::IndexFile::suffix()'],['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea831a2ebb5fe5a6b08270dfa5b9b6c7ac',1,'vg::Haplotypes::Subchain::suffix()'],['../classvg_1_1WFAExtender.html#a73ca61152596774e30d6c6f40aeea984',1,'vg::WFAExtender::suffix()'],['../structvg_1_1RecombinatorHaplotype.html#ae22f7c420e3d76d6494f66e817ffb342',1,'vg::RecombinatorHaplotype::suffix()']]],
+ ['suffixes_5892',['suffixes',['../classvg_1_1PhaseUnfolder.html#a8e235a2b6022ec40a6e66c63c8dd1df0',1,'vg::PhaseUnfolder']]],
+ ['suggest_5fedge_5893',['suggest_edge',['../classvg_1_1DiagramExplainer.html#a5565fd4595e708faa7f82534b1b87380',1,'vg::DiagramExplainer']]],
+ ['suggested_5fedge_5ft_5894',['suggested_edge_t',['../classvg_1_1DiagramExplainer.html#ae9907aa970a58c2c6a89829c6f3020ba',1,'vg::DiagramExplainer']]],
+ ['suggested_5fedges_5895',['suggested_edges',['../classvg_1_1DiagramExplainer.html#a14bbd52421b049d538e13a357209b9ff',1,'vg::DiagramExplainer']]],
+ ['sum_5896',['sum',['../structhaplo_1_1haplo__DP__column.html#aeb237931ba6de582496ded7d42517f3a',1,'haplo::haplo_DP_column::sum()'],['../namespacevg.html#aa70726366aa31b20debdcac41c89490c',1,'vg::sum()']]],
+ ['summary_5fstatistics_5897',['summary_statistics',['../namespacevg.html#ae8afe82a05092bbf4bc31c8ead079fe3',1,'vg']]],
+ ['summarystatistics_5898',['SummaryStatistics',['../structvg_1_1SummaryStatistics.html',1,'vg']]],
+ ['super_5899',['super',['../classvg_1_1PathSubgraph.html#a223501d50e8c102bbd7bf602d19b9400',1,'vg::PathSubgraph::super()'],['../classvg_1_1SubHandleGraph.html#aa17f9e8ba0b1b374b852390a9bf0c56a',1,'vg::SubHandleGraph::super()'],['../classvg_1_1TreeSubgraph.html#a1096d8426347b21730e2d7d81527ffc0',1,'vg::TreeSubgraph::super()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ad63f143f0bebc5d600dca495e9fdff77',1,'handlegraph::algorithms::SubHandleGraph::super()']]],
+ ['support_5900',['Support',['../structvg_1_1Support.html',1,'vg::Support'],['../structvg_1_1Locus.html#a42e45ba2fa1310b9fba6774b24cdd447',1,'vg::Locus::support()'],['../structvg_1_1LocationSupport.html#a479f1a778e85f8d3747c0b7c44ad5760',1,'vg::LocationSupport::support()']]],
+ ['support_5ffinder_5901',['support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a2af17a0bf619778576c49627563994dc',1,'vg::SupportBasedSnarlCaller']]],
+ ['support_5fmax_5902',['support_max',['../namespacevg.html#ac3787b0a7fc02bbfe45dc5eb082d5779',1,'vg']]],
+ ['support_5fmin_5903',['support_min',['../namespacevg.html#a3c2ae4c37201ebbc6f6d4faaf27fe4de',1,'vg']]],
+ ['support_5fval_5904',['support_val',['../classvg_1_1SupportBasedSnarlCaller.html#a84da98787b002a2ed9c8c1da6661cebd',1,'vg::SupportBasedSnarlCaller::support_val()'],['../classvg_1_1TraversalSupportFinder.html#a3a128da202bd6889a2e5fd92ba3227dc',1,'vg::TraversalSupportFinder::support_val()']]],
+ ['supportaugmentedgraph_5905',['SupportAugmentedGraph',['../structvg_1_1SupportAugmentedGraph.html',1,'vg']]],
+ ['supportbasedsnarlcaller_5906',['SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html',1,'vg::SupportBasedSnarlCaller'],['../classvg_1_1SupportBasedSnarlCaller.html#adff4e7045e950e7caea2858569afec02',1,'vg::SupportBasedSnarlCaller::SupportBasedSnarlCaller()']]],
+ ['supportmap_5907',['SupportMap',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af8ae65b6009d1f121c27fb3ab969ef90',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
+ ['supportrestrictedtraversalfinder_5908',['SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html',1,'vg::SupportRestrictedTraversalFinder'],['../classvg_1_1SupportRestrictedTraversalFinder.html#aceeb94d7e05fdbc113557b61448f6b2a',1,'vg::SupportRestrictedTraversalFinder::SupportRestrictedTraversalFinder()']]],
+ ['suppress_5fcluster_5fmerging_5909',['suppress_cluster_merging',['../classvg_1_1MultipathMapper.html#ad25f17a8c485548abf5f63517937067f',1,'vg::MultipathMapper']]],
+ ['suppress_5fmismapping_5fdetection_5910',['suppress_mismapping_detection',['../classvg_1_1MultipathMapper.html#a514a648b0822a7c74e853ab78aed7d95',1,'vg::MultipathMapper']]],
+ ['suppress_5fmulticomponent_5fsplitting_5911',['suppress_multicomponent_splitting',['../classvg_1_1MultipathMapper.html#a2dae3baa09f211a0762d121a6c48dc58',1,'vg::MultipathMapper']]],
+ ['suppress_5fp_5fvalue_5fmemoization_5912',['suppress_p_value_memoization',['../classvg_1_1MultipathMapper.html#afd6fee3779079af7a2932c7c29098b2d',1,'vg::MultipathMapper']]],
+ ['suppress_5ftail_5fanchors_5913',['suppress_tail_anchors',['../classvg_1_1MultipathMapper.html#ad4c0e1fea285f378ef5c7eb23e9baf89',1,'vg::MultipathMapper']]],
+ ['surface_5914',['surface',['../classvg_1_1Viz.html#ad93aa239a30c3b7a017348e22f184b85',1,'vg::Viz']]],
+ ['surject_5915',['surject',['../classvg_1_1Surjector.html#a4e4e4c28b1313850e647f4d258a0ea82',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a265cf90a6fb12021a70b87ec647c0867',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a80afa331fde9e8bcff66c4e87400217a',1,'vg::Surjector::surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
+ ['surject_5falignments_5fin_5fplace_5916',['surject_alignments_in_place',['../classvg_1_1SurjectingAlignmentEmitter.html#a5ba8aab649ae5f31c64be2c5461c743c',1,'vg::SurjectingAlignmentEmitter']]],
+ ['surject_5finternal_5917',['surject_internal',['../classvg_1_1Surjector.html#a6474f90fe3cf3ea098a553916bd47ae9',1,'vg::Surjector']]],
+ ['surject_5fmain_2ecpp_5918',['surject_main.cpp',['../surject__main_8cpp.html',1,'']]],
+ ['surject_5fsubpath_5fglobal_5919',['surject_subpath_global',['../classvg_1_1SurjectingAlignmentEmitter.html#a730237d7e198244c27b29aff8a7d8b7d',1,'vg::SurjectingAlignmentEmitter']]],
+ ['surjecting_5falignment_5femitter_2ecpp_5920',['surjecting_alignment_emitter.cpp',['../surjecting__alignment__emitter_8cpp.html',1,'']]],
+ ['surjecting_5falignment_5femitter_2ehpp_5921',['surjecting_alignment_emitter.hpp',['../surjecting__alignment__emitter_8hpp.html',1,'']]],
+ ['surjectingalignmentemitter_5922',['SurjectingAlignmentEmitter',['../classvg_1_1SurjectingAlignmentEmitter.html',1,'vg::SurjectingAlignmentEmitter'],['../classvg_1_1SurjectingAlignmentEmitter.html#acf03c9f7eedb8d8dd58d6ffab24f139f',1,'vg::SurjectingAlignmentEmitter::SurjectingAlignmentEmitter()']]],
+ ['surjector_5923',['Surjector',['../classvg_1_1Surjector.html',1,'vg::Surjector'],['../classvg_1_1Surjector.html#a4b083231c3ae02e3e14c3efb2a72eb1d',1,'vg::Surjector::Surjector()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a7ff6c0ffab9177150fe4941a8ae71c70',1,'vg::SurjectingAlignmentEmitter::surjector()']]],
+ ['surjector_2ecpp_5924',['surjector.cpp',['../surjector_8cpp.html',1,'']]],
+ ['surjector_2ehpp_5925',['surjector.hpp',['../surjector_8hpp.html',1,'']]],
+ ['sv_5ftype_5926',['SV_TYPE',['../structvg_1_1BREAKPOINT.html#a52c38d41e036406a3c2e79d9f4bbfc50',1,'vg::BREAKPOINT']]],
+ ['swap_5927',['swap',['../classvg_1_1SnarlState.html#a4e3f0d0c720ea665b3db9542d07f7ec1',1,'vg::SnarlState::swap()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a1466c6e58d54f775b27680dbe5e7fe4d',1,'vg::ZipCodeTree::reverse_iterator::swap()']]],
+ ['swap_5falleles_5928',['swap_alleles',['../classvg_1_1PhasedGenome.html#ae325c8488e737b75b980796aacf37246',1,'vg::PhasedGenome']]],
+ ['swap_5fendianness_5929',['swap_endianness',['../structvg_1_1endianness.html#a0a3eec44ef047d7771ad9804c5b51c85',1,'vg::endianness']]],
+ ['swap_5fhandles_5930',['swap_handles',['../classvg_1_1VG.html#a3d4db6ea2a99bda9a48411491aa6ed4e',1,'vg::VG']]],
+ ['swap_5fhaplotypes_5931',['swap_haplotypes',['../classvg_1_1GenomeState.html#aee2aa05cdf5226983f8f25d783da528e',1,'vg::GenomeState']]],
+ ['swap_5flabel_5932',['swap_label',['../classvg_1_1PhasedGenome.html#a181b4e71f8debc78ceccf476ce36abcd',1,'vg::PhasedGenome']]],
+ ['swap_5fnode_5fid_5933',['swap_node_id',['../classvg_1_1VG.html#afee31880eaf65a1a6d1a250663271b54',1,'vg::VG::swap_node_id(nid_t node_id, nid_t new_id)'],['../classvg_1_1VG.html#a63f2ffa39d84f80e5ab8068a25a03ee9',1,'vg::VG::swap_node_id(Node *node, nid_t new_id)']]],
+ ['swap_5fnode_5fids_5934',['swap_node_ids',['../classvg_1_1Paths.html#a3190f22ab39a9039ec9288e1c065ca9c',1,'vg::Paths::swap_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)'],['../classvg_1_1Paths.html#aba01c4d1b1d415622634db97f62b1188',1,'vg::Paths::swap_node_ids(hash_map< id_t, id_t > &id_mapping)']]],
+ ['swap_5fnodes_5935',['swap_nodes',['../classvg_1_1VG.html#aa402d1cf817f83ca44f72f6112b6a2e3',1,'vg::VG']]],
+ ['swap_5fremove_5936',['swap_remove',['../swap__remove_8hpp.html#a403d9325a22306c4dfefd9202bd3bd00',1,'swap_remove.hpp']]],
+ ['swap_5fremove_2ehpp_5937',['swap_remove.hpp',['../swap__remove_8hpp.html',1,'']]],
+ ['swaphaplotypescommand_5938',['SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html',1,'vg']]],
+ ['symbol_5fcount_5939',['symbol_count',['../classvg_1_1Pictographs.html#a38abbb70a4bdb0b40e5beb2b43cee1d5',1,'vg::Pictographs']]],
+ ['symbolic_5fallele_5fwarnings_5940',['symbolic_allele_warnings',['../classvg_1_1Constructor.html#a245d775942ede32387b95497803e114c',1,'vg::Constructor']]],
+ ['symbols_5941',['symbols',['../classvg_1_1Pictographs.html#a2504adc26acf0c09e9cccb06e80e1d7b',1,'vg::Pictographs']]],
+ ['sync_5942',['sync',['../classvg_1_1VariantAdder.html#abc5742437534663752fccb79b5302b42',1,'vg::VariantAdder']]],
+ ['sync_5foffsets_5943',['sync_offsets',['../classxg_1_1XGPath.html#af7e2c286ed51c4422b1b615e4f327b9d',1,'xg::XGPath']]],
+ ['sync_5fpaths_5944',['sync_paths',['../classvg_1_1VG.html#a124188a9e0cd68c87c2bc009ea7bd799',1,'vg::VG']]],
+ ['synchronizer_5945',['synchronizer',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad2fcccf51dbd2136c680322341847b78',1,'vg::GraphSynchronizer::Lock']]],
+ ['syntax_5946',['syntax',['../vg_8proto.html#adbedb258e13546cc707a6ebb073a3d8a',1,'vg.proto']]],
+ ['synthesize_5ftail_5fanchors_5947',['synthesize_tail_anchors',['../classvg_1_1MultipathAlignmentGraph.html#a3c34e5d02c2b81614ccd602351b81ed9',1,'vg::MultipathAlignmentGraph']]]
];
diff --git a/search/all_14.js b/search/all_14.js
index 53078db3c3..927603b60c 100644
--- a/search/all_14.js
+++ b/search/all_14.js
@@ -1,284 +1,284 @@
var searchData=
[
- ['t_5946',['T',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a830a224fa9ca0c0f9e4027f98537ddd0',1,'vg::subcommand::FlagArgSpec']]],
- ['tables_5947',['Tables',['../structvg_1_1io_1_1Registry_1_1Tables.html',1,'vg::io::Registry']]],
- ['tag_5948',['tag',['../structvg_1_1Funnel_1_1Item.html#acba00ec4fad9a9b3f1a0f9c8dcb4484c',1,'vg::Funnel::Item::tag()'],['../structvg_1_1Funnel_1_1Stage.html#a9efc6bb2afa857b7c8d5c055a3adaae6',1,'vg::Funnel::Stage::tag()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a17e22f4ea8e69209b9aff2c00deb9ba4',1,'vg::io::ProtobufEmitter::tag()'],['../classvg_1_1Funnel.html#abd3cf8783612cccf4faf96f25fc4f17c',1,'vg::Funnel::tag()']]],
- ['tag_5fcorrect_5949',['tag_correct',['../classvg_1_1Funnel.html#aa725f066e32a967c8d482f50c1606f08',1,'vg::Funnel']]],
- ['tag_5flength_5950',['tag_length',['../structvg_1_1Funnel_1_1Item.html#a965c4d888554644e3cbfc5deae970b92',1,'vg::Funnel::Item']]],
- ['tag_5flist_5ft_5951',['tag_list_t',['../classvg_1_1algorithms_1_1GFAParser.html#ad6ed4063154c14a6e348a5c646bae1f1',1,'vg::algorithms::GFAParser']]],
- ['tag_5fseeds_5952',['tag_seeds',['../classvg_1_1MinimizerMapper.html#a59d91d716447b3971fd13e7a1920ab8b',1,'vg::MinimizerMapper']]],
- ['tag_5fspace_5953',['tag_space',['../structvg_1_1Funnel_1_1Stage.html#a582d8a4caf1dbfda777913e2032fa403',1,'vg::Funnel::Stage']]],
- ['tag_5fstart_5954',['tag_start',['../structvg_1_1Funnel_1_1Item.html#a40097e3acf4a20046f5679c5601f823f',1,'vg::Funnel::Item']]],
- ['tag_5fto_5floader_5955',['tag_to_loader',['../structvg_1_1io_1_1Registry_1_1Tables.html#a965e60de0073226a98deef0757d7dfa8',1,'vg::io::Registry::Tables']]],
- ['tag_5fto_5fprotobuf_5956',['tag_to_protobuf',['../structvg_1_1io_1_1Registry_1_1Tables.html#abac3d9be375a86c8f55e5777e97fe323',1,'vg::io::Registry::Tables']]],
- ['taggedmessage_5957',['TaggedMessage',['../classvg_1_1io_1_1MessageIterator.html#ac914a651c928eedea34171366c9f62e8',1,'vg::io::MessageIterator']]],
- ['tags_5958',['tags',['../structGBWTConfig.html#af72aa6461315f4e981c6308ede36fc64',1,'GBWTConfig']]],
- ['tags_5fto_5fset_5959',['tags_to_set',['../structGBWTConfig.html#abf5b058641892fe0532de896d8a6cdeb',1,'GBWTConfig']]],
- ['tail_5fgap_5fmemo_5fmax_5fsize_5960',['tail_gap_memo_max_size',['../classvg_1_1MultipathAlignmentGraph.html#a12e62ccfd7e7adb135d169f7e2671509',1,'vg::MultipathAlignmentGraph']]],
- ['tail_5fnodes_5961',['tail_nodes',['../classvg_1_1VG.html#a25bd74b77e139691555c8d48ecf67d9f',1,'vg::VG::tail_nodes(void)'],['../classvg_1_1VG.html#a47fbc525ed5e9f2a7b00c333f03fe6c8',1,'vg::VG::tail_nodes(vector< Node * > &nodes)'],['../namespacehandlegraph_1_1algorithms.html#ad3eb2f190153333cdee10e6624df34c6',1,'handlegraph::algorithms::tail_nodes()']]],
- ['tail_5foffset_5962',['tail_offset',['../structvg_1_1GaplessExtension.html#a94628e41ab7556750c6ab841ca76fafd',1,'vg::GaplessExtension']]],
- ['tail_5fposition_5963',['tail_position',['../structvg_1_1GaplessExtension.html#adb0c7cc3eee2f406d20fde6db08717b1',1,'vg::GaplessExtension']]],
- ['take_5964',['take',['../structvg_1_1RecombinatorHaplotype.html#aec852acffc1ac8250b5c34aada44b980',1,'vg::RecombinatorHaplotype::take()'],['../classvg_1_1io_1_1MessageIterator.html#ab97d50a333e4f27419f0d661e8669774',1,'vg::io::MessageIterator::take()'],['../classvg_1_1io_1_1ProtobufIterator.html#a32bfe2fea01e8bae7759dff71eb64db8',1,'vg::io::ProtobufIterator::take()']]],
- ['take_5funique_5fminimizers_5965',['take_unique_minimizers',['../namespacevg.html#aced59c99c3795653e7d70f176edf9c82',1,'vg']]],
- ['target_5966',['target',['../classvg_1_1InsufficientInputException.html#aa40303513d2f82efe6690afe9b8a75ce',1,'vg::InsufficientInputException']]],
- ['target_5falignment_5967',['target_alignment',['../namespacevg.html#ac712c04180499746dab8cdc6c8795c56',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse, Mapping &cigar_mapping)'],['../namespacevg.html#a08575acb0012ffaabd9859324e404562',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse)']]],
- ['target_5flength_5968',['TARGET_LENGTH',['../structvg_1_1WFANode.html#a761a104c95d2f39fa286c39c4aeaa6ba',1,'vg::WFANode']]],
- ['target_5fmemory_5fusage_5969',['target_memory_usage',['../classvg_1_1IndexRegistry.html#a6d6ef1d1e1488c9a32feaddca19cdb1a',1,'vg::IndexRegistry::target_memory_usage()'],['../classvg_1_1IndexingPlan.html#a1fd91843fb2c901d9db661e6bc50f07a',1,'vg::IndexingPlan::target_memory_usage()']]],
- ['target_5foffset_5970',['target_offset',['../structvg_1_1WFANode.html#ab230231efd27b35e2db2b6055e187f50',1,'vg::WFANode::target_offset()'],['../structvg_1_1WFAPoint.html#a1ffb5ef3c0d0e64eaeeb2290468bb53f',1,'vg::WFAPoint::target_offset()']]],
- ['targets_5971',['targets',['../classvg_1_1IndexingPlan.html#adda5d82310890614f02b317e46e702a1',1,'vg::IndexingPlan']]],
- ['targetvaluesearch_5972',['TargetValueSearch',['../classvg_1_1TargetValueSearch.html',1,'vg::TargetValueSearch'],['../classvg_1_1TargetValueSearch.html#afaa00740b29b96fd3c0c561898c3330a',1,'vg::TargetValueSearch::TargetValueSearch()=delete'],['../classvg_1_1TargetValueSearch.html#a66c7161857ea38dab47c4da883435ac4',1,'vg::TargetValueSearch::TargetValueSearch(const HandleGraph &handle_graph, DistanceHeuristic *upper_bound_heuristic, DistanceHeuristic *lower_bound_heuristic)']]],
- ['task_5fname_5973',['task_name',['../structvg_1_1Watchdog_1_1thread__state__t.html#a797bf67f4267c5ffeda247c041f7cd14',1,'vg::Watchdog::thread_state_t']]],
- ['tell_5974',['Tell',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a4b34e76da81d5a09d5ab2634a864d401',1,'vg::io::BlockedGzipInputStream::Tell()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a84bb042b0a5df4ecbdadb3852fa04f91',1,'vg::io::BlockedGzipOutputStream::Tell()']]],
- ['tell_5fgroup_5975',['tell_group',['../classvg_1_1io_1_1MessageIterator.html#afc6ab71583004ebdeb7aa24553817936',1,'vg::io::MessageIterator::tell_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6b51328b5c897e36803b63a7058b6c61',1,'vg::io::ProtobufIterator::tell_group()']]],
- ['telomere_5fpair_5976',['telomere_pair',['../structvg_1_1SwapHaplotypesCommand.html#a6a5922c2e74c8227f07631fd2f8cc5f9',1,'vg::SwapHaplotypesCommand']]],
- ['telomeres_5977',['telomeres',['../classvg_1_1GenomeState.html#a2e1564254538fec6438c931a5263ab8a',1,'vg::GenomeState']]],
- ['test_5fmain_2ecpp_5978',['test_main.cpp',['../test__main_8cpp.html',1,'']]],
- ['test_5fmean_5979',['test_mean',['../structvg_1_1BenchmarkResult.html#a7bd2a14daeee009dd5845ba44454d7b5',1,'vg::BenchmarkResult']]],
- ['test_5fsplice_5fcandidates_5980',['test_splice_candidates',['../classvg_1_1MultipathMapper.html#ac45ca6502977ffa0640b3d5cdf21fae1',1,'vg::MultipathMapper']]],
- ['test_5fstddev_5981',['test_stddev',['../structvg_1_1BenchmarkResult.html#a54499cba0e5b1927efb68c3cf4adcff3',1,'vg::BenchmarkResult']]],
- ['testminimizermapper_5982',['TestMinimizerMapper',['../classvg_1_1MinimizerMapper.html#a8239430f869fd4cc597359f38a1ab29e',1,'vg::MinimizerMapper']]],
- ['thin_5falignment_5fcutoff_5983',['thin_alignment_cutoff',['../classvg_1_1VariantAdder.html#a12ef17f5d02d950a436d20e651588a81',1,'vg::VariantAdder']]],
- ['thread_5fbreakpoint_5fcursors_5984',['thread_breakpoint_cursors',['../classvg_1_1io_1_1StreamMultiplexer.html#a836843731535676ddd71a68cd3cd6d7f',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fchunk_5finflation_5ffactor_5985',['thread_chunk_inflation_factor',['../structvg_1_1IndexingParameters.html#a4eb6ab42c2e0c51a9a8891ec24ab9433',1,'vg::IndexingParameters']]],
- ['thread_5fextension_5986',['thread_extension',['../classvg_1_1Mapper.html#ad2f2408aba30a38eda90a10c28cbf410',1,'vg::Mapper']]],
- ['thread_5fids_5ft_5987',['thread_ids_t',['../namespacevg.html#a5c7b3ebb9ad8d6c01a0c54668b102c26',1,'vg']]],
- ['thread_5fmax_5fretained_5fbytes_5988',['THREAD_MAX_RETAINED_BYTES',['../classvg_1_1DozeuInterface.html#a7f00debc965248ba99fc5450ed35e24d',1,'vg::DozeuInterface']]],
- ['thread_5fqueue_5fbyte_5fcounts_5989',['thread_queue_byte_counts',['../classvg_1_1io_1_1StreamMultiplexer.html#a9ec3374dee16f6ee0ce853b04a4d6967',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueue_5fempty_5fslots_5990',['thread_queue_empty_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#a62843d99c1215b3d01109142f2356327',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueue_5ffilled_5fslots_5991',['thread_queue_filled_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#ad34283d480d468d52412bce3daeae5c4',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueue_5fmutexes_5992',['thread_queue_mutexes',['../classvg_1_1io_1_1StreamMultiplexer.html#ae0404331337813a02b7bafd0fb95e10a',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueues_5993',['thread_queues',['../classvg_1_1io_1_1StreamMultiplexer.html#aa4bc760981467acc3bff684653ffebd5',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fstate_5ft_5994',['thread_state_t',['../structvg_1_1Watchdog_1_1thread__state__t.html',1,'vg::Watchdog']]],
- ['thread_5fstreams_5995',['thread_streams',['../classvg_1_1io_1_1StreamMultiplexer.html#a9e75e8ebd9b414f7438dea9b43af3b56',1,'vg::io::StreamMultiplexer']]],
- ['thread_5ft_5996',['thread_t',['../namespacevg.html#a31b8b476fb46de6667b26514b7b24fd2',1,'vg']]],
- ['thread_5fto_5fgraph_5fspanned_5997',['thread_to_graph_spanned',['../namespacevg.html#aa24cc1f72643cab5fa0dfcc551f61d50',1,'vg']]],
- ['threads_5998',['threads',['../classvg_1_1ReadFilter.html#a41808c4d5db46d1405ac906a01bbf794',1,'vg::ReadFilter::threads()'],['../structHaplotypesConfig.html#a179bec8b7054c7eaa5aaf9e055322d63',1,'HaplotypesConfig::threads()'],['../namespacehaplotypes__defaults.html#aa204b98aebcd769c098b7842428b94d6',1,'haplotypes_defaults::threads()']]],
- ['threads_5ffor_5fcontig_5999',['threads_for_contig',['../namespacevg.html#a5813ee7997572d371f9ff7b45bbe4843',1,'vg']]],
- ['threads_5ffor_5fsample_6000',['threads_for_sample',['../namespacevg.html#a2d4b0a9961f932a8caccb1d0723fd171',1,'vg']]],
- ['threads_5fto_5fjobs_6001',['threads_to_jobs',['../haplotypes__main_8cpp.html#a9f628e188cebb5384d8b2b236a745866',1,'haplotypes_main.cpp']]],
- ['three_5fedge_5fconnected_5fcomponent_5fmerges_6002',['three_edge_connected_component_merges',['../namespacevg_1_1algorithms.html#a7215192f2cc6536b6b3aadef4e95c64a',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponent_5fmerges_5fdense_6003',['three_edge_connected_component_merges_dense',['../namespacevg_1_1algorithms.html#a4d4b7c6814fb1f53a83c2e8355d72efa',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponents_6004',['three_edge_connected_components',['../namespacevg_1_1algorithms.html#ae4677e69f0b8ceb8580bc019cc8fbea8',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponents_2ecpp_6005',['three_edge_connected_components.cpp',['../three__edge__connected__components_8cpp.html',1,'']]],
- ['three_5fedge_5fconnected_5fcomponents_2ehpp_6006',['three_edge_connected_components.hpp',['../three__edge__connected__components_8hpp.html',1,'']]],
- ['three_5fedge_5fconnected_5fcomponents_5fdense_6007',['three_edge_connected_components_dense',['../namespacevg_1_1algorithms.html#a34c4a74208a88c0f956e697d5e183f5c',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponents_5fdense_5fcactus_6008',['three_edge_connected_components_dense_cactus',['../namespacevg_1_1algorithms.html#a57de725b70b138394479863428f9d2eb',1,'vg::algorithms']]],
- ['tick_6009',['tick',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa1729ac6451d805cfb67301c5aff03b6',1,'vg::ZipCodeTree::reverse_iterator::tick()'],['../structvg_1_1Range.html#a10f700e0447a5a922611122fa1811b61',1,'vg::Range::tick()']]],
- ['tick_5falong_5fchain_6010',['tick_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a1d1a3f2903fbcc9be3d9725b7d27dba8',1,'vg::subcommand::TickChainLink::tick_along_chain()'],['../structvg_1_1Range.html#a66d38c47018ce4cd2589be167588affe',1,'vg::Range::tick_along_chain()']]],
- ['tick_5falong_5fchain_5fparent_6011',['tick_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#ad9ae4a6d3f61a4d18c56fe85f0259fb8',1,'vg::subcommand::TickChainLink']]],
- ['tick_5fchain_6012',['tick_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a90c9bb7ca4ab9e7f91bb246c5949eae4',1,'vg::subcommand::TickChainLink::tick_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aee28025b35a1a448183eb4957d697e62',1,'vg::subcommand::OptionGroup::tick_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ad0a0fc373e9e599842dbf6e1d67b4271',1,'vg::subcommand::GroupedOptionGroup::tick_chain()']]],
- ['tickchainlink_6013',['TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html',1,'vg::subcommand::TickChainLink'],['../structvg_1_1subcommand_1_1TickChainLink.html#a3a814506ba062fcf389d57efa4304d4a',1,'vg::subcommand::TickChainLink::TickChainLink()=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a46213933eb07d96326cdb848f6dcd066',1,'vg::subcommand::TickChainLink::TickChainLink(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#afe9e76f6721953c97baed84957f6c1fe',1,'vg::subcommand::TickChainLink::TickChainLink(TickChainLink &&other)=delete']]],
- ['time_6014',['time',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#a92a84b5696522b5290e1407cd55dff83',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['time_5fpoint_6015',['time_point',['../classvg_1_1Funnel.html#a573543e4560aee58697f78cc266f22c7',1,'vg::Funnel::time_point()'],['../classvg_1_1Watchdog.html#adbdb9378ef086d2e9255f22ff9ef454d',1,'vg::Watchdog::time_point()']]],
- ['time_5fused_6016',['time_used',['../structvg_1_1Alignment.html#a0c8b04a220715a894a19dcc70ed581c0',1,'vg::Alignment']]],
- ['timed_5fout_6017',['timed_out',['../structvg_1_1Watchdog_1_1thread__state__t.html#a0a1e9d9760eaa0803da68a1ef3a0cdb0',1,'vg::Watchdog::thread_state_t']]],
- ['timeout_6018',['timeout',['../classvg_1_1Watchdog.html#aff48af7cbc77f123d30fefd9aa005181',1,'vg::Watchdog']]],
- ['tip_6019',['TIP',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3a41062278414d99cdb309732619f1ce5f',1,'handlegraph::SnarlDecomposition']]],
- ['tipanchoredmaxdistance_6020',['TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html',1,'vg::TipAnchoredMaxDistance'],['../classvg_1_1TipAnchoredMaxDistance.html#a7a47ea386b37e4e738f71709184fce75',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance()=delete'],['../classvg_1_1TipAnchoredMaxDistance.html#a2658eecf16503163b9c39c44c7468bcc',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance(SnarlDistanceIndex &distance_index)']]],
- ['tmpfstream_5flocks_6021',['tmpfstream_locks',['../classvg_1_1Packer.html#a0f98b46ac443166dc94b2bd3c6b8d5a9',1,'vg::Packer']]],
- ['tmpfstreams_6022',['tmpfstreams',['../classvg_1_1Packer.html#a12c9d820a3b4ba6fdec28b9f05677f64',1,'vg::Packer']]],
- ['to_6023',['to',['../classvg_1_1WFATree.html#abb28a51f09daa96b500ce7a030876f0e',1,'vg::WFATree::to()'],['../structvg_1_1RecombinatorFragment.html#a73179f74032a4ca87c8e4c4a35b78a7c',1,'vg::RecombinatorFragment::to()'],['../structvg_1_1Edge.html#affb3decf0a8b18ad319405c303cdf6a5',1,'vg::Edge::to()'],['../structvg_1_1Alignment.html#a9db86772c1bd48808c0588f96f3c0865',1,'vg::Alignment::to()'],['../structvg_1_1Translation.html#a25a5dc4de6c11119522e319af3639e30',1,'vg::Translation::to()']]],
- ['to_5falignment_6024',['to_alignment',['../classvg_1_1ReadFilter.html#a21b0bf11e5636b41cf6dfc4a61441c4e',1,'vg::ReadFilter::to_alignment()'],['../namespacevg.html#a10bcb19d45af37e8a58129b939b86f21',1,'vg::to_alignment()']]],
- ['to_5fanchor_6025',['to_anchor',['../classvg_1_1MinimizerMapper.html#ae7509b53b63ffb61b768c80f79f04a4d',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, const VectorView< Minimizer > &minimizers, std::vector< Seed > &seeds, size_t seed_number, const HandleGraph &graph, const Aligner *aligner)'],['../classvg_1_1MinimizerMapper.html#a750d65dcbba1734ca9855225090d0149',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, size_t read_start, size_t read_end, const std::vector< size_t > &sorted_seeds, const std::vector< algorithms::Anchor > &seed_anchors, const std::vector< size_t >::const_iterator &mismatch_begin, const std::vector< size_t >::const_iterator &mismatch_end, const HandleGraph &graph, const Aligner *aligner)']]],
- ['to_5fanchors_6026',['to_anchors',['../classvg_1_1MinimizerMapper.html#aaaabeeaf994436a22232bd59af97ea39',1,'vg::MinimizerMapper']]],
- ['to_5fbacking_6027',['to_backing',['../classvg_1_1ExtraNodeGraph.html#ae3c321717804ea0d0762fb4a8f71a7db',1,'vg::ExtraNodeGraph::to_backing()'],['../classvg_1_1SourceSinkOverlay.html#ada12ceaf3a0ed960ea42cf5a1f5de42a',1,'vg::SourceSinkOverlay::to_backing()']]],
- ['to_5fbig_5fendian_6028',['to_big_endian',['../structvg_1_1endianness.html#a5397898b5e413c0c4d09577952b80984',1,'vg::endianness']]],
- ['to_5fcorrect_6029',['to_correct',['../structvg_1_1Alignment.html#a8957ee4a5a3ef66c93f6b6b685774df2',1,'vg::Alignment']]],
- ['to_5fdot_6030',['to_dot',['../classvg_1_1Funnel.html#ad4a9374a423b2b87a15355ffac7a1935',1,'vg::Funnel::to_dot()'],['../classvg_1_1IndexRegistry.html#ad7ff998ac4404629ef683795a9170116',1,'vg::IndexRegistry::to_dot() const'],['../classvg_1_1IndexRegistry.html#a53573d21c79b060ebb0c643b1d395a7f',1,'vg::IndexRegistry::to_dot(const vector< IndexName > &targets) const'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a5eabcd913cf0ba46947d0554eab790fb',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::to_dot()'],['../classvg_1_1MultipathAlignmentGraph.html#a90ff13eb09622a6f5fa9238f6ec4950b',1,'vg::MultipathAlignmentGraph::to_dot()'],['../classvg_1_1VG.html#af502bd29a58e62ff70f8f963d47401a4',1,'vg::VG::to_dot()']]],
- ['to_5fedge_6031',['to_edge',['../namespacevg.html#a1da5277daea16b80ffc4ab75175b1882',1,'vg']]],
- ['to_5fend_6032',['to_end',['../structvg_1_1Edge.html#af1538e8b7416c9af6aae7b3d587182dd',1,'vg::Edge']]],
- ['to_5fgfa_6033',['to_gfa',['../classxg_1_1XG.html#a7cc1d24330a708afd24e768514c474c6',1,'xg::XG']]],
- ['to_5fgraph_6034',['to_graph',['../classvg_1_1Paths.html#ad215b2c7475b7048a073ce6fa805e709',1,'vg::Paths']]],
- ['to_5fidx_6035',['to_idx',['../classvg_1_1MEMClusterer_1_1HitEdge.html#a94b63347e0a6a9907b5573fae257aace',1,'vg::MEMClusterer::HitEdge']]],
- ['to_5fjson_6036',['to_json',['../classvg_1_1Paths.html#ad98bff3b628d499252c7b5fb29191fdc',1,'vg::Paths']]],
- ['to_5fleft_5fside_6037',['to_left_side',['../namespacevg.html#a84d646b72482de0145745a64414ca5df',1,'vg']]],
- ['to_5flength_6038',['to_length',['../structvg_1_1Edit.html#a4f9854d5ba5503280306f1a06bfb3c89',1,'vg::Edit::to_length()'],['../classvg_1_1edit__t.html#ad90d417ef77001a113ab3d1912e76954',1,'vg::edit_t::to_length()'],['../namespacevg.html#a5ed83dc32e575ae68b591d142eb38912',1,'vg::to_length()']]],
- ['to_5flength_5fafter_5fpos_6039',['to_length_after_pos',['../namespacevg.html#ad47f373b3433b3190f9f1c0f5f17274d',1,'vg']]],
- ['to_5flength_5fbefore_5fpos_6040',['to_length_before_pos',['../namespacevg.html#aa40f0cfd74a9eeaa7b6ffecbc0926a6d',1,'vg']]],
- ['to_5fmapping_6041',['to_mapping',['../classvg_1_1mapping__t.html#ab60b07378892ab57a661e27d19cef194',1,'vg::mapping_t::to_mapping()'],['../namespacevg.html#a28be7f9898d5ad6e075e25b81df512e8',1,'vg::to_mapping(const Visit &visit, std::function< size_t(id_t)> node_length)'],['../namespacevg.html#a128ffce6142542678bbbdc6e2e0b40cd',1,'vg::to_mapping(const Visit &visit, const HandleGraph &vg)']]],
- ['to_5fmatrix_6042',['to_matrix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a6d6778356b79ef4f4831acafc090f566',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['to_5fmultipath_5falignment_6043',['to_multipath_alignment',['../namespacevg.html#a27656a1e271730b6a62263dc2af8055d',1,'vg']]],
- ['to_5fnode_5fid_6044',['to_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a3ebf9c322668234f32083e3f9d42b38f',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['to_5fnode_5ftraversal_6045',['to_node_traversal',['../namespacevg.html#a5a2e772d69c9e45cbc1c1d1a9e6df842',1,'vg::to_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#a2c04918053577c402e4f2cab61abd754',1,'vg::to_node_traversal(const Visit &visit, VG &graph)']]],
- ['to_5fnumber_6046',['to_number',['../classvg_1_1BitString.html#a2d6824816926cd463e586bb32ca3debc',1,'vg::BitString']]],
- ['to_5fpath_6047',['to_path',['../structvg_1_1GaplessExtension.html#ade804b684aa81b0b2f95033ead5930a2',1,'vg::GaplessExtension::to_path()'],['../structvg_1_1WFAAlignment.html#a4d90b156bc529bf52019201f30e12842',1,'vg::WFAAlignment::to_path()'],['../classvg_1_1MinimizerMapper.html#ae1565adcd1bdf28aca55134d7482b1af',1,'vg::MinimizerMapper::to_path()']]],
- ['to_5fproto_5fedit_6048',['to_proto_edit',['../namespacevg.html#a84c5dd6c830450f9100b5e9c11522050',1,'vg']]],
- ['to_5fproto_5fmapping_6049',['to_proto_mapping',['../namespacevg.html#a3da977cb90bf3ffd94166edb2fdb980a',1,'vg']]],
- ['to_5fproto_5fmultipath_5falignment_6050',['to_proto_multipath_alignment',['../namespacevg.html#a8f8f0e54cfa0c3279c18748c503ccbe9',1,'vg']]],
- ['to_5fproto_5fpath_6051',['to_proto_path',['../namespacevg.html#a9473b834c584544cc90c819d6b5bb222',1,'vg']]],
- ['to_5fremove_6052',['to_remove',['../structGBWTConfig.html#aa7b2d855903feadc683c6f1379374dbe',1,'GBWTConfig']]],
- ['to_5frev_5fnode_5ftraversal_6053',['to_rev_node_traversal',['../namespacevg.html#a0b4a5c32294bf49aa7f0a6d180cc2832',1,'vg::to_rev_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#ae64d7810e64af7119f1b1b3a2d08d797',1,'vg::to_rev_node_traversal(const Visit &visit, VG &graph)']]],
- ['to_5frev_5fvisit_6054',['to_rev_visit',['../namespacevg.html#a7164ae8636d1ca7783d6202c8ce316ca',1,'vg']]],
- ['to_5fright_5fside_6055',['to_right_side',['../namespacevg.html#a74fab09b3ae1d9f799742a31b5206a35',1,'vg']]],
- ['to_5fseed_6056',['to_seed',['../classvg_1_1GaplessExtender.html#a5b141ee05b0f704d29e9f34de8c67a32',1,'vg::GaplessExtender']]],
- ['to_5fsimple_5freverse_6057',['to_simple_reverse',['../classvg_1_1FlowSort.html#ac49c6a1c8605c7e55d532aac7959611c',1,'vg::FlowSort']]],
- ['to_5fsimple_5freverse_5forientation_6058',['to_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a4d4defd602249dfd58abbaea8058ff5a',1,'vg::FlowSort']]],
- ['to_5fstring_6059',['to_string',['../structvg_1_1BREAKPOINT.html#a889fc9b9ff7feec9847c28eaf17ae6ee',1,'vg::BREAKPOINT::to_string()'],['../structvg_1_1Haplotypes_1_1Subchain.html#aa409e312b588c1b48f3855bf8dfbb3c1',1,'vg::Haplotypes::Subchain::to_string()'],['../structReferenceInterval.html#a91983a3892caceab4288482288f76154',1,'ReferenceInterval::to_string()'],['../namespacestd.html#aec6a9d59586ce5d9e0acc951c9c355c8',1,'std::to_string()'],['../namespacevg.html#ae9aadb20454b27a0819f40006556ffe6',1,'vg::to_string(handle_t handle)'],['../namespacevg.html#ad7ec65dd3bb34f37cff811f49c1b9599',1,'vg::to_string(const HandleGraph &graph, handle_t handle)'],['../namespacevg.html#a75bc48248af00118bc7cdacc00e37db1',1,'vg::to_string(const HandleGraph &graph, edge_t edge)'],['../namespacestd.html#af92da72517d799416d58a59067b6afd9',1,'std::to_string(const vg::pos_t &pos)'],['../namespacestd.html#a4d710aefadc1fdcd0988b913096651a8',1,'std::to_string(const vg::ZipCodeTree::tree_item_type_t &type)'],['../namespacestd.html#a0fcc699939402d5652d7dde38fd615fd',1,'std::to_string(const vg::ZipCodeTree::reverse_iterator::State &state)']]],
- ['to_5fstring_5fgbwtgraph_6060',['to_string_gbwtgraph',['../namespacevg.html#adc47f14b546282cf0818ba47826a9110',1,'vg::to_string_gbwtgraph(handle_t handle)'],['../namespacevg.html#a93282dbd7c3a7daaf92b75f77c28dc29',1,'vg::to_string_gbwtgraph(gbwt::node_type node)']]],
- ['to_5fswap_6061',['to_swap',['../structvg_1_1SwapHaplotypesCommand.html#a89b3e32d9f79d7e50bce707c47a18962',1,'vg::SwapHaplotypesCommand']]],
- ['to_5fturtle_6062',['to_turtle',['../classvg_1_1VG.html#a582500a3d49fe231faa49a5c2e467cc8',1,'vg::VG']]],
- ['to_5fvcf_5fgenotype_6063',['to_vcf_genotype',['../namespacevg.html#a420f2fd8ef6d04f1a34a08af2a3dee0e',1,'vg']]],
- ['to_5fvector_6064',['to_vector',['../structvg_1_1varint__vector__t.html#a00af7863b11453e9e958375476ff8d4a',1,'vg::varint_vector_t::to_vector()'],['../classvg_1_1ZipCode.html#a43c4b30e62f754722d730d47306e76cd',1,'vg::ZipCode::to_vector()']]],
- ['to_5fvisit_6065',['to_visit',['../classvg_1_1NodeSide.html#af9b1413c4dcef8615892989c6e8b6232',1,'vg::NodeSide::to_visit()'],['../namespacevg.html#a827ce532cdbd4710e86a21ebd986e1cc',1,'vg::to_visit(const NodeTraversal &node_traversal)'],['../namespacevg.html#acd53873bb85623cbf5b797f09bf88dc4',1,'vg::to_visit(const Mapping &mapping, bool make_full_node_match=false)'],['../namespacevg.html#aa76433c3398610bc58b842f2a4b462c7',1,'vg::to_visit(id_t node_id, bool is_reverse)'],['../namespacevg.html#a0a18238f71586af9b3eba2ba1dac2a6e',1,'vg::to_visit(const Snarl &snarl)'],['../namespacevg.html#ae7d774bd39780563236dbf2badfc804b',1,'vg::to_visit(const handlegraph::HandleGraph &graph, const handle_t &handle)']]],
- ['to_5fwfa_5falignment_6066',['to_wfa_alignment',['../classvg_1_1MinimizerMapper.html#a41db60efc7634f542cea078a00f18379',1,'vg::MinimizerMapper']]],
- ['to_5fxg_6067',['to_xg',['../classvg_1_1VGset.html#ab26412de51ff980342dea8aceaca6a6c',1,'vg::VGset::to_xg(xg::XG &index)'],['../classvg_1_1VGset.html#ab7d9649e1ae4cc62b05af39c97cf7b06',1,'vg::VGset::to_xg(xg::XG &index, const function< bool(const string &)> &paths_to_take, map< string, Path > *removed_paths=nullptr)']]],
- ['toggle_5fbit_6068',['toggle_bit',['../structhandlegraph_1_1number__bool__packing.html#a7b54fcfbc7ad7e61d67d637374344a7e',1,'handlegraph::number_bool_packing']]],
- ['toolkit_6069',['TOOLKIT',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838af5626d22da713c4acb1ccc508f2816d2',1,'vg::subcommand']]],
- ['top_6070',['top',['../structhaplo_1_1int__itvl__t.html#a28cb4dd08f57cf179227ae76784bdbde',1,'haplo::int_itvl_t::top()'],['../structvg_1_1MatchPos_1_1PathList.html#ac50ec1cafee2fd491fb6d0a10e82835a',1,'vg::MatchPos::PathList::top() const'],['../structvg_1_1MatchPos_1_1PathList.html#a62397e20a1f6c4c50e9e1cec60030685',1,'vg::MatchPos::PathList::top()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa83523c6259341473ec281be15ad2046',1,'vg::ZipCodeTree::reverse_iterator::top()']]],
- ['top_5fborder_6071',['top_border',['../classvg_1_1Viz.html#a9e044e100116d5fe502953643f07d2d2',1,'vg::Viz']]],
- ['top_5fdiag_6072',['top_diag',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a76c5471f0be987920ff0076101367fbc',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['top_5fdown_5fgenotype_6073',['top_down_genotype',['../classvg_1_1LegacyCaller.html#a01e3b84cc03599fbc8cef1df4fcf43c7',1,'vg::LegacyCaller']]],
- ['top_5fk_6074',['top_k',['../classvg_1_1PoissonSupportSnarlCaller.html#a4610e26e36319f7b2620566c7b655c63',1,'vg::PoissonSupportSnarlCaller']]],
- ['top_5flevel_5fchains_6075',['top_level_chains',['../structvg_1_1Haplotypes_1_1Header.html#a8223ce0e3fe99009151debc39caf9c0b',1,'vg::Haplotypes::Header']]],
- ['top_5flevel_5fsnarls_6076',['top_level_snarls',['../classvg_1_1SnarlManager.html#af31a29d8e7836bca46b389c01c625339',1,'vg::SnarlManager']]],
- ['top_5fm_6077',['top_m',['../classvg_1_1PoissonSupportSnarlCaller.html#af61d6e6931ba127537e41cfdbf258d38',1,'vg::PoissonSupportSnarlCaller']]],
- ['top_5ftracebacks_6078',['top_tracebacks',['../classvg_1_1MultipathMapper.html#a122b1eaa39c84e9b18a971ebe6566030',1,'vg::MultipathMapper']]],
- ['toplevelchain_6079',['TopLevelChain',['../structvg_1_1Haplotypes_1_1TopLevelChain.html',1,'vg::Haplotypes']]],
- ['topological_5forder_6080',['topological_order',['../classvg_1_1BandedGlobalAligner.html#a45b4ad348f9232013df241afece68afc',1,'vg::BandedGlobalAligner::topological_order()'],['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab277385bc0c8b0cd52c850f5368f0339',1,'vg::MEMClusterer::HitGraph::topological_order()'],['../namespacehandlegraph_1_1algorithms.html#a7063506d0cc176b808808147b83d7e33',1,'handlegraph::algorithms::topological_order()']]],
- ['topological_5fsort_6081',['topological_sort',['../classvg_1_1MultipathAlignmentGraph.html#a565b45f37d5be97cd30bce1d29c134fc',1,'vg::MultipathAlignmentGraph']]],
- ['topological_5fsort_2ecpp_6082',['topological_sort.cpp',['../topological__sort_8cpp.html',1,'']]],
- ['topologically_5forder_5fsubpaths_6083',['topologically_order_subpaths',['../namespacevg.html#a3ca9ccb5a2301ed1ce48f6334b3c4937',1,'vg']]],
- ['total_6084',['total',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#acb07aae84ec439512a012ee80829c357',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::total()'],['../namespacevg.html#a0a064dd8829b2100c6a38780311073f3',1,'vg::total()']]],
- ['total_5fbits_6085',['TOTAL_BITS',['../classvg_1_1BitString.html#a881dbf42b0dc52a67f0c1edfa4e971f8',1,'vg::BitString']]],
- ['total_5fkmers_6086',['total_kmers',['../structvg_1_1Haplotypes_1_1Header.html#a491f20acd55ad36b6b9b3c24f5b6a39e',1,'vg::Haplotypes::Header']]],
- ['total_5fnode_5fquality_6087',['total_node_quality',['../classvg_1_1Packer.html#a67a80245fcdbc4f5788b1062ee6b55f9',1,'vg::Packer']]],
- ['total_5fseq_5flength_6088',['total_seq_length',['../classvg_1_1BaseMapper.html#a45439a16e3d38573e5cc59cb95462878',1,'vg::BaseMapper::total_seq_length()'],['../classvg_1_1Sampler.html#a1e14636749c41aa2d525177bf1a68cf5',1,'vg::Sampler::total_seq_length()'],['../classvg_1_1NGSSimulator.html#ac83d417596d2d157ddc5903d41be1fef',1,'vg::NGSSimulator::total_seq_length()']]],
- ['total_5fsize_6089',['total_size',['../structvg_1_1RebuildJob.html#aefe022edfe253c6c08690bd0e41dbaa1',1,'vg::RebuildJob']]],
- ['total_5fsubchains_6090',['total_subchains',['../structvg_1_1Haplotypes_1_1Header.html#a64217b5f412fcf46e65dee628abec4dc',1,'vg::Haplotypes::Header']]],
- ['total_5fsupports_6091',['total_supports',['../structvg_1_1BREAKPOINT.html#afc10d66ae6dad31e2086963bc6e34a06',1,'vg::BREAKPOINT']]],
- ['touppercase_6092',['toUppercase',['../namespacevg.html#a00a949105ae94b18ca72452a442b8ddb',1,'vg']]],
- ['touppercaseinplace_6093',['toUppercaseInPlace',['../namespacevg.html#adcf3d4a70f85f067842ccf34a82a4a46',1,'vg']]],
- ['trace_6094',['trace',['../classvg_1_1DozeuInterface.html#a82634289dc80707e1ba8bb1a94503027',1,'vg::DozeuInterface::trace()'],['../classvg_1_1XdropAligner.html#adb3c7fa9b6b7c272ab687e0693a1dc47',1,'vg::XdropAligner::trace()'],['../classvg_1_1QualAdjXdropAligner.html#a8a382e7378bfeb43954a9436cf9d3b09',1,'vg::QualAdjXdropAligner::trace()'],['../classvg_1_1SnarlState.html#a6b13fa6a070139c5d123983265d440bc',1,'vg::SnarlState::trace()']]],
- ['trace_5fhaplotype_6095',['trace_haplotype',['../classvg_1_1GenomeState.html#af167a6237410b8da2c839820e6c804a7',1,'vg::GenomeState']]],
- ['trace_5fhaplotypes_5fand_5fpaths_6096',['trace_haplotypes_and_paths',['../namespacevg.html#a2d9774c4df98285526a427ba54e970ba',1,'vg']]],
- ['trace_5fmain_2ecpp_6097',['trace_main.cpp',['../trace__main_8cpp.html',1,'']]],
- ['trace_5fpath_6098',['trace_path',['../namespacevg.html#a83257be63a821ae991e1b332b62facd4',1,'vg::trace_path()'],['../haplotypes__main_8cpp.html#a8e6fb3993622a6541d6e6beb41ed1c72',1,'trace_path(): haplotypes_main.cpp']]],
- ['trace_5fto_5falignment_6099',['trace_to_alignment',['../classvg_1_1DeletionAligner.html#a1916d488f7ed7e9ad0452a1c6138bc27',1,'vg::DeletionAligner']]],
- ['traceback_6100',['traceback',['../classvg_1_1BandedGlobalAligner.html#a2a2b4909d5eb88633680ea071c5551f4',1,'vg::BandedGlobalAligner::traceback()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a1366942f6ff4eecbebad9b29e9ef2c94',1,'vg::BandedGlobalAligner::BAMatrix::traceback()'],['../classvg_1_1MEMChainModel.html#ae142b05be3a27922e9387108bb052706',1,'vg::MEMChainModel::traceback()'],['../classvg_1_1DeletionAligner.html#aeaa43fcc2267e2aab5ebde031e3852c3',1,'vg::DeletionAligner::traceback()'],['../classvg_1_1AlignmentChainModel.html#ac774ed2018837e64c7ef88ae28c2794a',1,'vg::AlignmentChainModel::traceback()']]],
- ['traceback_5fover_5fedge_6101',['traceback_over_edge',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a0210e1c9a9da04e28e253e2963dd96ad',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['tracedscore_6102',['TracedScore',['../classvg_1_1algorithms_1_1TracedScore.html',1,'vg::algorithms']]],
- ['track_5fcomponents_6103',['track_components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6bc63fbe77aee54235636bbc228a9e96',1,'vg::MEMClusterer::HitGraph']]],
- ['track_5fcorrectness_6104',['track_correctness',['../classvg_1_1MinimizerMapper.html#a7896c6cccfa011c4fbad1b916d30052e',1,'vg::MinimizerMapper']]],
- ['track_5fposition_6105',['track_position',['../classvg_1_1MinimizerMapper.html#a35a153c8cd62696021e17fe9d970b2b3',1,'vg::MinimizerMapper']]],
- ['track_5fprovenance_6106',['track_provenance',['../classvg_1_1MinimizerMapper.html#aeabec85347521c1f42ef51e0453c4e5f',1,'vg::MinimizerMapper']]],
- ['trailing_5fzeros_6107',['trailing_zeros',['../minimizer__main_8cpp.html#a82ed012045f022c7d023ef32c84a9df3',1,'minimizer_main.cpp']]],
- ['transcript_6108',['Transcript',['../structvg_1_1Transcript.html',1,'vg::Transcript'],['../structvg_1_1Transcript.html#a151337b8595bb8b0041ed64a325a7650',1,'vg::Transcript::Transcript()']]],
- ['transcript_5ffile_5fnonempty_6109',['transcript_file_nonempty',['../namespacevg.html#aa44c63a293d251b1bffbbeee59d2b7fe',1,'vg']]],
- ['transcript_5fnames_6110',['transcript_names',['../structvg_1_1TranscriptPath.html#a325799db73bd6e750d5f4ee45014861c',1,'vg::TranscriptPath']]],
- ['transcript_5fpaths_6111',['transcript_paths',['../classvg_1_1Transcriptome.html#a52ca431b737b92befedebee4e71b0f0c',1,'vg::Transcriptome']]],
- ['transcript_5ftag_6112',['transcript_tag',['../classvg_1_1Transcriptome.html#a56a00bd350c02600e5474fc89791d5bd',1,'vg::Transcriptome']]],
- ['transcriptome_6113',['Transcriptome',['../classvg_1_1Transcriptome.html',1,'vg::Transcriptome'],['../classvg_1_1Transcriptome.html#a041373349b45b5d190316229a5b8c562',1,'vg::Transcriptome::Transcriptome()']]],
- ['transcriptome_2ecpp_6114',['transcriptome.cpp',['../transcriptome_8cpp.html',1,'']]],
- ['transcriptome_2ehpp_6115',['transcriptome.hpp',['../transcriptome_8hpp.html',1,'']]],
- ['transcriptpath_6116',['TranscriptPath',['../structvg_1_1TranscriptPath.html',1,'vg::TranscriptPath'],['../structvg_1_1TranscriptPath.html#ad87c876af2acb7bcbbbb52b33ad25e8d',1,'vg::TranscriptPath::TranscriptPath()'],['../structvg_1_1TranscriptPath.html#aef6b201d9d87a24f2c9e7ed6e9e9e1e7',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const string &embedded_path_name, const bool is_reference_in, const bool is_haplotype_in)'],['../structvg_1_1TranscriptPath.html#a1b9b94ca6d527d0f197d98faf2a6a4b5',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const gbwt::size_type &haplotype_gbwt_id, const bool is_reference_in, const bool is_haplotype_in)']]],
- ['transfer_5fbetween_5fproto_5fannotation_6117',['transfer_between_proto_annotation',['../namespacevg.html#ac0534767a787eae1a5f93444bf21b2a1',1,'vg']]],
- ['transfer_5fboundary_5finfo_6118',['transfer_boundary_info',['../namespacevg.html#a82a83d7c54d733abee06d328f91ef5ee',1,'vg']]],
- ['transfer_5ffrom_5fproto_5fannotation_6119',['transfer_from_proto_annotation',['../namespacevg.html#a57c3f88ce9f85ceae2d77c32fd9de04d',1,'vg']]],
- ['transfer_5fproto_5fmetadata_6120',['transfer_proto_metadata',['../namespacevg.html#a0582a68dfa130c9f0a2bdaa1c7ac5ef5',1,'vg::transfer_proto_metadata(const Alignment &from, MultipathAlignment &to)'],['../namespacevg.html#ad6476e86221a660dda1fa85254e9436d',1,'vg::transfer_proto_metadata(const MultipathAlignment &from, Alignment &to)']]],
- ['transfer_5fread_5fmetadata_6121',['transfer_read_metadata',['../namespacevg.html#a195fc7fa6da6fecfa7e9fa31e5cf6f0c',1,'vg::transfer_read_metadata(const MultipathAlignment &from, multipath_alignment_t &to)'],['../namespacevg.html#acac375591689f0066f6c723dc25fb834',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, MultipathAlignment &to)'],['../namespacevg.html#ad0995c3042ff642b9e8aeaa1727dccb5',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, multipath_alignment_t &to)'],['../namespacevg.html#a54b4f608ad692caffd8fce4df9a1e4ef',1,'vg::transfer_read_metadata(const Alignment &from, multipath_alignment_t &to)'],['../namespacevg.html#a2d8929c8f610705661da889830b0b7b9',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, Alignment &to)'],['../namespacevg.html#af48acb91edce241c75a9a4fd02745620',1,'vg::transfer_read_metadata(const Alignment &from, Alignment &to)']]],
- ['transfer_5fto_5fproto_5fannotation_6122',['transfer_to_proto_annotation',['../namespacevg.html#a90a76dfce70406755151cf45e6990848',1,'vg']]],
- ['transfer_5funiform_5fmetadata_6123',['transfer_uniform_metadata',['../namespacevg.html#adbf827b04e42865ece378b51482df898',1,'vg']]],
- ['transform_6124',['transform',['../classvg_1_1VGset.html#aaa5f1b0e3e71bb00a5ad82f210065e81',1,'vg::VGset']]],
- ['transition_5fdistrs_5f1_6125',['transition_distrs_1',['../classvg_1_1NGSSimulator.html#a571f3ff879e38077e8d7dad879157d55',1,'vg::NGSSimulator']]],
- ['transition_5fdistrs_5f2_6126',['transition_distrs_2',['../classvg_1_1NGSSimulator.html#ad3d0c480b5ecd2fa7c5209d86b41911d',1,'vg::NGSSimulator']]],
- ['transition_5fiteratee_6127',['transition_iteratee',['../namespacevg_1_1algorithms.html#ad64245b7dca5a8144ae8720a92b65685',1,'vg::algorithms']]],
- ['transition_5fiterator_6128',['transition_iterator',['../namespacevg_1_1algorithms.html#a79c214c1e7f1d7cc5fe322b8c9fb260c',1,'vg::algorithms']]],
- ['transition_5ftable_6129',['transition_table',['../classvg_1_1DinucleotideMachine.html#a6a81eedb016f3d90fa5b0e2757537531',1,'vg::DinucleotideMachine']]],
- ['transitive_5freduction_6130',['transitive_reduction',['../classvg_1_1Surjector.html#a2149d1e5e6aba2e07b92030e6afc617d',1,'vg::Surjector']]],
- ['translate_6131',['translate',['../classvg_1_1Translator.html#a3407f68503febdc2bd4366947e96d003',1,'vg::Translator::translate(const Position &position)'],['../classvg_1_1Translator.html#a6e27eb192e227afe777de2dc6488eb26',1,'vg::Translator::translate(const Position &position, const Translation &translation)'],['../classvg_1_1Translator.html#a1a8657e279942f5b4a802aad9e0baab6',1,'vg::Translator::translate(const Edge &edge)'],['../classvg_1_1Translator.html#a9ea3b0a85f25159214b34041b20a5cd3',1,'vg::Translator::translate(const Mapping &mapping)'],['../classvg_1_1Translator.html#a28ee9ca0de37d9d83f24b33639f0893c',1,'vg::Translator::translate(const Path &path)'],['../classvg_1_1Translator.html#af2f3e933feb2e28acf713316840b03c4',1,'vg::Translator::translate(const Alignment &aln)'],['../classvg_1_1Translator.html#ab4dffeb58e1c441c82039c6dd17445f5',1,'vg::Translator::translate(const Locus &locus)']]],
- ['translate_5fback_6132',['translate_back',['../classvg_1_1FlatFileBackTranslation.html#a44128954132be459c4229001b0441add',1,'vg::FlatFileBackTranslation::translate_back()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a762d6c9b1ad1762f3521c3a24cf82f55',1,'vg::algorithms::GFAIDMapInfo::translate_back()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#a4005088073dfdd8d3da33803198ee737',1,'handlegraph::NamedNodeBackTranslation::translate_back()']]],
- ['translate_5fdown_6133',['translate_down',['../classvg_1_1PathSubgraph.html#a7fa974235481756de3a7bb3c04f58ef7',1,'vg::PathSubgraph::translate_down()'],['../classvg_1_1TreeSubgraph.html#a71ab7a4ca370f712cf7c4912ccb5ab25',1,'vg::TreeSubgraph::translate_down()']]],
- ['translate_5fmain_2ecpp_6134',['translate_main.cpp',['../translate__main_8cpp.html',1,'']]],
- ['translate_5fmems_6135',['translate_mems',['../namespacevg.html#a4bc1837d8c1cca33ab223957402b70ba',1,'vg']]],
- ['translate_5fnode_5fids_6136',['translate_node_ids',['../classvg_1_1JoinedSpliceGraph.html#a535cf652e7e39598979b003b7155ae4f',1,'vg::JoinedSpliceGraph::translate_node_ids()'],['../namespacevg.html#af71770196fc31c2e3c9c2a83f3497177',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator)'],['../namespacevg.html#aa49e4506c94e5747c88805e39aa18090',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator, id_t cut_node, size_t bases_removed, bool from_right)'],['../namespacevg.html#a322ec292675d4891ecc265e56a836db7',1,'vg::translate_node_ids(path_t &path, const unordered_map< id_t, id_t > &translator)']]],
- ['translate_5fnodes_6137',['translate_nodes',['../namespacevg.html#a98dcd16f2a4eae4c223a374dd2ab2da4',1,'vg']]],
- ['translate_5foriented_5fnode_5fids_6138',['translate_oriented_node_ids',['../namespacevg.html#a2b0ba7a1d0cf7630b79d03ba0ab65c53',1,'vg::translate_oriented_node_ids(Path &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#acb86c984b743e10c6ddaa57612ca3991',1,'vg::translate_oriented_node_ids(Path &path, const function< pair< id_t, bool >(id_t)> &translator)'],['../namespacevg.html#a449dd4b0d7106c6ee7afceb4f7412d6d',1,'vg::translate_oriented_node_ids(path_t &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#abfebb6e72326ea81b2ed13b4c3b57885',1,'vg::translate_oriented_node_ids(path_t &path, const function< pair< id_t, bool >(id_t)> &translator)']]],
- ['translate_5fsnarl_5fnum_6139',['translate_snarl_num',['../classvg_1_1SnarlManager.html#afdd078898493f277dc1aa5dc3dae5d56',1,'vg::SnarlManager']]],
- ['translate_5fthrough_6140',['translate_through',['../classvg_1_1io_1_1GafAlignmentEmitter.html#a2e7cff4276d5f1cd7857f91d8970be0e',1,'vg::io::GafAlignmentEmitter']]],
- ['translation_6141',['Translation',['../structvg_1_1Translation.html',1,'vg::Translation'],['../classvg_1_1BackTranslatingAlignmentEmitter.html#a7bbe9fc362769137eb5446c5ba9d4e49',1,'vg::BackTranslatingAlignmentEmitter::translation()'],['../classvg_1_1VCFOutputCaller.html#a212346d7a629ae3280ce3eb39606237b',1,'vg::VCFOutputCaller::translation()']]],
- ['translations_6142',['translations',['../classvg_1_1Translator.html#aba17cd4fd008c2dbee1da376db1807be',1,'vg::Translator']]],
- ['translator_6143',['Translator',['../classvg_1_1Translator.html',1,'vg::Translator'],['../classvg_1_1Translator.html#ac23acdcea38566f2e68005eca4afff73',1,'vg::Translator::Translator(void)'],['../classvg_1_1Translator.html#aeab811097e483365bbd273efc4c4445e',1,'vg::Translator::Translator(istream &in)'],['../classvg_1_1Translator.html#a99602b3868ae6f8f1efc6bf7adcde6f6',1,'vg::Translator::Translator(const vector< Translation > &trans)'],['../structvg_1_1AugmentedGraph.html#a3ac035d37452eb611b943cfa4754d6c6',1,'vg::AugmentedGraph::translator()'],['../classvg_1_1Genotyper.html#ad14928554aace83524e80d8c109e17b2',1,'vg::Genotyper::translator()']]],
- ['translator_2ecpp_6144',['translator.cpp',['../translator_8cpp.html',1,'']]],
- ['translator_2ehpp_6145',['translator.hpp',['../translator_8hpp.html',1,'']]],
- ['transpose_6146',['transpose',['../namespacevg.html#a1409ac23ce33abd463dcd46093079023',1,'vg']]],
- ['trav_6147',['trav',['../classvg_1_1MCMCCaller.html#a44187bff29621c4b3ff13560ea748223',1,'vg::MCMCCaller']]],
- ['trav_5fpadding_6148',['trav_padding',['../classvg_1_1GAFOutputCaller.html#a1ef9a3f2df7cfbd1a35e3ee8f56f4657',1,'vg::GAFOutputCaller']]],
- ['trav_5fsequence_6149',['trav_sequence',['../classvg_1_1VG.html#a57296ecbcfce10f95b86233e10c35d7d',1,'vg::VG']]],
- ['trav_5fstring_6150',['trav_string',['../classvg_1_1VCFOutputCaller.html#ae4b896a68da613eb2e8e509279e4e1b9',1,'vg::VCFOutputCaller']]],
- ['traversal_6151',['traversal',['../classvg_1_1mapping__t.html#a9ef6e5278c0ac9ce077ea2c8e0902674',1,'vg::mapping_t::traversal()'],['../namespacevg.html#a4ea210eff71c5a1039378130f98de166',1,'vg::Traversal()']]],
- ['traversal_5falg_6152',['traversal_alg',['../classvg_1_1Genotyper.html#a5b040c1636f479b52dbdb641e82f74dd',1,'vg::Genotyper']]],
- ['traversal_5fclusters_2ecpp_6153',['traversal_clusters.cpp',['../traversal__clusters_8cpp.html',1,'']]],
- ['traversal_5fclusters_2ehpp_6154',['traversal_clusters.hpp',['../traversal__clusters_8hpp.html',1,'']]],
- ['traversal_5ffinder_6155',['traversal_finder',['../classvg_1_1VCFGenotyper.html#afa0dd907b77ec7bd5d33f972c06ab131',1,'vg::VCFGenotyper::traversal_finder()'],['../classvg_1_1LegacyCaller.html#ada2c8e9befb0cbe8043779758468664a',1,'vg::LegacyCaller::traversal_finder()'],['../classvg_1_1FlowCaller.html#ad55a5eccba503ff1543b553ce5cd813f',1,'vg::FlowCaller::traversal_finder()'],['../classvg_1_1NestedFlowCaller.html#aaf2b6c922dfa6c16913325243496a126',1,'vg::NestedFlowCaller::traversal_finder()'],['../classvg_1_1SmallSnarlSimplifier.html#aaf858ca21b486fe45acbf92a4cbea5ba',1,'vg::SmallSnarlSimplifier::traversal_finder()']]],
- ['traversal_5ffinder_2ecpp_6156',['traversal_finder.cpp',['../traversal__finder_8cpp.html',1,'']]],
- ['traversal_5ffinder_2ehpp_6157',['traversal_finder.hpp',['../traversal__finder_8hpp.html',1,'']]],
- ['traversal_5fsupport_2ecpp_6158',['traversal_support.cpp',['../traversal__support_8cpp.html',1,'']]],
- ['traversal_5fsupport_2ehpp_6159',['traversal_support.hpp',['../traversal__support_8hpp.html',1,'']]],
- ['traversal_5fto_5fstring_6160',['traversal_to_string',['../namespacevg.html#a94385b32246fc81a0a44ea1b47d994ee',1,'vg::traversal_to_string(VG &graph, const SnarlTraversal &path)'],['../namespacevg.html#a6a885124cc3018dc7cd6d2001b6b54f5',1,'vg::traversal_to_string(const PathHandleGraph *graph, const Traversal &traversal, int64_t max_steps)']]],
- ['traversalalg_6161',['TraversalAlg',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4',1,'vg::Genotyper']]],
- ['traversalfinder_6162',['TraversalFinder',['../classvg_1_1TraversalFinder.html',1,'vg']]],
- ['traversals_5fonly_6163',['traversals_only',['../classvg_1_1VCFGenotyper.html#a61906c71880dba31065f8cf04b95b60d',1,'vg::VCFGenotyper::traversals_only()'],['../classvg_1_1FlowCaller.html#ad20a95ea02344c6b21a4912381e7b984',1,'vg::FlowCaller::traversals_only()'],['../classvg_1_1NestedFlowCaller.html#a5012c7a944e3c3d57148ff11d0a7a174',1,'vg::NestedFlowCaller::traversals_only()']]],
- ['traversalsupportcalculator_6164',['TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html',1,'vg']]],
- ['traversalsupportfinder_6165',['TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html',1,'vg::TraversalSupportFinder'],['../classvg_1_1TraversalSupportFinder.html#ab281113b3cdf2992299a2768ce1be832',1,'vg::TraversalSupportFinder::TraversalSupportFinder()']]],
- ['traverse_5fcomponents_6166',['traverse_components',['../namespacevg_1_1algorithms.html#a6341683f1b89495d2ac1558ed2875343',1,'vg::algorithms']]],
- ['traverse_5fcomputed_5fdecomposition_6167',['traverse_computed_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#ab843403935c08e4d1764b693a897c16c',1,'vg::IntegratedSnarlFinder']]],
- ['traverse_5fdecomposition_6168',['traverse_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#a31a75674d1cc7d5f2b6a028161c6038f',1,'vg::IntegratedSnarlFinder::traverse_decomposition()'],['../classvg_1_1HandleGraphSnarlFinder.html#a9cba8688e5dd28b23ed3529af122f308',1,'vg::HandleGraphSnarlFinder::traverse_decomposition()']]],
- ['traverse_5fedge_5fhandle_6169',['traverse_edge_handle',['../classhandlegraph_1_1HandleGraph.html#af167b0664299cfd4eac610f129fa5fee',1,'handlegraph::HandleGraph']]],
- ['traverse_5fin_5forder_6170',['traverse_in_order',['../classvg_1_1BitStringTree.html#a5f825ebeb38c6d1572fa73692810c273',1,'vg::BitStringTree::traverse_in_order()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#aa89c88fbab67819e3f072da4bc82e253',1,'vg::BitStringTree::TreeNode::traverse_in_order()']]],
- ['traverse_5fleft_6171',['traverse_left',['../classvg_1_1Paths.html#a861618af488874863197ad48f17a9ae4',1,'vg::Paths']]],
- ['traverse_5fright_6172',['traverse_right',['../classvg_1_1Paths.html#aabda0fb1288e7681b317cd5b4cfad242',1,'vg::Paths']]],
- ['traverse_5fup_6173',['traverse_up',['../classvg_1_1BitStringTree.html#aefd44d9f67d266cb206724b8516c001c',1,'vg::BitStringTree::traverse_up()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#ae67c2a504203ce10bbc6cc33d94c2e3b',1,'vg::BitStringTree::TreeNode::traverse_up()']]],
- ['travs_6174',['travs',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a1ee05f25a4d87f1d40abfdea92d9d942',1,'vg::NestedFlowCaller::CallRecord']]],
- ['travs_5ffrom_6175',['travs_from',['../classvg_1_1VG.html#a34a493a0628857a3bfae181295ba541d',1,'vg::VG']]],
- ['travs_5fof_6176',['travs_of',['../classvg_1_1VG.html#ae065082f817e9bc0e278cf71f31af1e2',1,'vg::VG']]],
- ['travs_5fto_6177',['travs_to',['../classvg_1_1VG.html#a0a962957210c079fa242b383d5c65de3',1,'vg::VG']]],
- ['tree_6178',['Tree',['../structvg_1_1Tree.html',1,'vg::Tree< T >'],['../classvg_1_1TreeSubgraph.html#a91ef2cd31f18ada628b0990faae105a1',1,'vg::TreeSubgraph::tree()'],['../structvg_1_1Tree.html#a2583e3d479b8b3fa66e8eb0065417934',1,'vg::Tree::Tree()']]],
- ['tree_5fitem_5ft_6179',['tree_item_t',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html',1,'vg::ZipCodeTree::tree_item_t'],['../classvg_1_1ZipCodeForest.html#a6f4d116fc7bbdf877de9a8968133f5d5',1,'vg::ZipCodeForest::tree_item_t()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a5740e0956ab1ddcb8148d70702c2000f',1,'vg::ZipCodeTree::tree_item_t::tree_item_t()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a895703befafce6654f476cc86bdc33ed',1,'vg::ZipCodeTree::tree_item_t::tree_item_t(tree_item_type_t type, size_t raw_value, bool is_reversed)']]],
- ['tree_5fitem_5ftype_5ft_6180',['tree_item_type_t',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ad',1,'vg::ZipCodeTree::tree_item_type_t()'],['../classvg_1_1ZipCodeForest.html#a21bc3d5c8b89cd4260cdacbcd3e853df',1,'vg::ZipCodeForest::tree_item_type_t()']]],
- ['tree_5fsubgraph_2ecpp_6181',['tree_subgraph.cpp',['../tree__subgraph_8cpp.html',1,'']]],
- ['tree_5fsubgraph_2ehpp_6182',['tree_subgraph.hpp',['../tree__subgraph_8hpp.html',1,'']]],
- ['treenode_6183',['TreeNode',['../structvg_1_1BitStringTree_1_1TreeNode.html',1,'vg::BitStringTree< Item >::TreeNode'],['../structvg_1_1TreeNode.html',1,'vg::TreeNode< T >'],['../structvg_1_1TreeNode.html#a386f7b2ec0948165140022155dda8c04',1,'vg::TreeNode::TreeNode()']]],
- ['trees_6184',['trees',['../classvg_1_1ZipCodeForest.html#af85d4ca7594aee84b37f7864e24e5ce6',1,'vg::ZipCodeForest']]],
- ['treesubgraph_6185',['TreeSubgraph',['../classvg_1_1TreeSubgraph.html',1,'vg::TreeSubgraph'],['../classvg_1_1TreeSubgraph.html#aa43b054cfbc6f2f96fbc8fcef42887c5',1,'vg::TreeSubgraph::TreeSubgraph()']]],
- ['trim_6186',['trim',['../classvg_1_1WFATree.html#aa4c7ff4d5620d1a75545bef9357096f3',1,'vg::WFATree']]],
- ['trim_5falignment_6187',['trim_alignment',['../namespacevg.html#ad83da8607e104967dd51d9230f4b51bb',1,'vg']]],
- ['trim_5fambiguous_5fend_6188',['trim_ambiguous_end',['../classvg_1_1ReadFilter.html#ac5d77581ac1d34661c62f446692217ab',1,'vg::ReadFilter']]],
- ['trim_5fambiguous_5fends_6189',['trim_ambiguous_ends',['../classvg_1_1ReadFilter.html#a265a2c2d5e5af4924c406b97d764d9aa',1,'vg::ReadFilter::trim_ambiguous_ends(Read &read, int k) const'],['../classvg_1_1ReadFilter.html#ac49bf695fadbdaf8b41c972587493630',1,'vg::ReadFilter::trim_ambiguous_ends(Alignment &alignment, int k) const'],['../classvg_1_1ReadFilter.html#a266b5aeeb2081d2bd5f29ae43fdc00f8',1,'vg::ReadFilter::trim_ambiguous_ends(MultipathAlignment &aln, int k) const']]],
- ['trim_5fand_5fcheck_5ffor_5fempty_6190',['trim_and_check_for_empty',['../classvg_1_1MultipathAlignmentGraph.html#a114d073d4422c085a2c5768b6f165001',1,'vg::MultipathAlignmentGraph']]],
- ['trim_5fhanging_5fends_6191',['trim_hanging_ends',['../namespacevg.html#a990f54fb0e09dc439dace1519aff5e9f',1,'vg']]],
- ['trim_5fhanging_5findels_6192',['trim_hanging_indels',['../classvg_1_1MultipathAlignmentGraph.html#aca7bc3f6c3de6fc3df3adabf3161260c',1,'vg::MultipathAlignmentGraph']]],
- ['trim_5findels_6193',['trim_indels',['../classvg_1_1Constructor.html#a130c318e05428ee7973135ac5ea26b50',1,'vg::Constructor']]],
- ['trim_5fmismatches_6194',['trim_mismatches',['../namespacevg.html#a77211f457b4e1f61915d771faf06cda0',1,'vg']]],
- ['trim_5fpath_6195',['trim_path',['../namespacevg.html#ab8d0345d2d7cea79ffdca38d33ed0c7f',1,'vg']]],
- ['trim_5fto_5fbranch_5fpoints_6196',['trim_to_branch_points',['../classvg_1_1MultipathAlignmentGraph.html#ac3199fb5e097873e2635e3fb34a8eafe',1,'vg::MultipathAlignmentGraph']]],
- ['trim_5fto_5fvariable_6197',['trim_to_variable',['../classvg_1_1Constructor.html#a428cf1b27e402a304c18e40f87e9dc02',1,'vg::Constructor']]],
- ['trimmed_5fend_6198',['trimmed_end',['../namespacevg.html#a9e61398cd459bb9ba3a1ced205491712',1,'vg']]],
- ['trivially_5fserializable_2ecpp_6199',['trivially_serializable.cpp',['../trivially__serializable_8cpp.html',1,'']]],
- ['trivially_5fserializable_2ehpp_6200',['trivially_serializable.hpp',['../trivially__serializable_8hpp.html',1,'']]],
- ['triviallyserializable_6201',['TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html',1,'handlegraph::TriviallySerializable'],['../classhandlegraph_1_1TriviallySerializable.html#a209a7ede82e8ad286a8a3fb1e51c3604',1,'handlegraph::TriviallySerializable::TriviallySerializable()']]],
- ['trivialtraversalfinder_6202',['TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html',1,'vg::TrivialTraversalFinder'],['../classvg_1_1TrivialTraversalFinder.html#a46403401b7efaec8d99b63b2013f7e60',1,'vg::TrivialTraversalFinder::TrivialTraversalFinder()']]],
- ['truncate_5fhandle_6203',['truncate_handle',['../classhandlegraph_1_1DeletableHandleGraph.html#aa65cef3b3261f8d1bc2057c5f2ee100a',1,'handlegraph::DeletableHandleGraph']]],
- ['truncated_5fnormal_5fdistribution_6204',['truncated_normal_distribution',['../classvg_1_1truncated__normal__distribution.html',1,'vg::truncated_normal_distribution< T >'],['../classvg_1_1truncated__normal__distribution.html#aa48544711e2d4a11ffe876366898e463',1,'vg::truncated_normal_distribution::truncated_normal_distribution()']]],
- ['truncation_5fmultiplicity_5fmq_5flimit_6205',['truncation_multiplicity_mq_limit',['../classvg_1_1MultipathMapper.html#a2f61a2ded5875ca3e7bf656d2198522a',1,'vg::MultipathMapper']]],
- ['try_5fload_5fbare_6206',['try_load_bare',['../classvg_1_1io_1_1VPKG.html#ad5d2bad9c95479a3f1520c5fadcba1b2',1,'vg::io::VPKG']]],
- ['try_5fload_5fencapsulated_6207',['try_load_encapsulated',['../classvg_1_1io_1_1VPKG.html#a695e5a53bfbc9a5b36c5ea2306f253db',1,'vg::io::VPKG::try_load_encapsulated(istream &in)'],['../classvg_1_1io_1_1VPKG.html#a860f50291f4b5a6be232e5312eb884ab',1,'vg::io::VPKG::try_load_encapsulated(MessageIterator &it)']]],
- ['try_5fload_5ffirst_6208',['try_load_first',['../classvg_1_1io_1_1VPKG.html#a58ed1c37748fed4b15d4e611659ce4c3',1,'vg::io::VPKG::try_load_first(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a504e965a2a019ce27267ea85c106a91b',1,'vg::io::VPKG::try_load_first(const string &filename)']]],
- ['try_5fload_5ffirst_5fbare_6209',['try_load_first_bare',['../classvg_1_1io_1_1VPKG.html#acfc929254f523522f369c4a17c8f0941',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a2707edbb6b28a6623ea8ae11e607c861',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)']]],
- ['try_5fload_5ffirst_5fencapsulated_6210',['try_load_first_encapsulated',['../classvg_1_1io_1_1VPKG.html#a12f9922d4b17194d248dc3f19a449f60',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a186f277ebf475632f1b4d1eac4c48139',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)']]],
- ['try_5fload_5fone_6211',['try_load_one',['../classvg_1_1io_1_1VPKG.html#a0d7f96d4dd7fe5b1fe47b330ca617623',1,'vg::io::VPKG::try_load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#ab3a2026ac79ee1539271ba1791108c66',1,'vg::io::VPKG::try_load_one(const string &filename)']]],
- ['tsvalignmentemitter_6212',['TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html',1,'vg::io::TSVAlignmentEmitter'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#aa8778347f51972fcb03f74565c5e3117',1,'vg::io::TSVAlignmentEmitter::TSVAlignmentEmitter()']]],
- ['tsvexplainer_6213',['TSVExplainer',['../classvg_1_1TSVExplainer.html',1,'vg::TSVExplainer'],['../classvg_1_1TSVExplainer.html#a3a9d31e471d1808b30dfdc6c995660b4',1,'vg::TSVExplainer::TSVExplainer()']]],
- ['tumor_5fsupports_6214',['tumor_supports',['../structvg_1_1BREAKPOINT.html#a66f75cad38b9fa5a3aab6b09b7a4ef8a',1,'vg::BREAKPOINT']]],
- ['tv_5fpath_6215',['tv_path',['../classvg_1_1TargetValueSearch.html#a9ab66a82967803031203885c18291c6f',1,'vg::TargetValueSearch']]],
- ['tv_5fpath_5fexists_6216',['tv_path_exists',['../classvg_1_1TargetValueSearch.html#a407607bcab4cfd14e283386bac418636',1,'vg::TargetValueSearch']]],
- ['tv_5fpath_5flength_6217',['tv_path_length',['../classvg_1_1TargetValueSearch.html#a7dc599c6d4a317999890c81634d9ddf5',1,'vg::TargetValueSearch']]],
- ['tv_5fphase2_6218',['tv_phase2',['../classvg_1_1TargetValueSearch.html#a794b8271df6bcf349db5e6d605402744',1,'vg::TargetValueSearch']]],
- ['tvs_6219',['tvs',['../classvg_1_1TVSClusterer.html#ad59ad1a2a88d40a980a7b7fb2cc18a0d',1,'vg::TVSClusterer']]],
- ['tvsclusterer_6220',['TVSClusterer',['../classvg_1_1TVSClusterer.html',1,'vg::TVSClusterer'],['../classvg_1_1TVSClusterer.html#a5b8fdb6006095094e85e6f760b8d0e3d',1,'vg::TVSClusterer::TVSClusterer()']]],
- ['type_6221',['type',['../structvg_1_1Range.html#a5ea713fb16f3d49d94278914668503a9',1,'vg::Range::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html#ac5175c5d84e3de42bbf69d38196d8026',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...) const >::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html#aea61ef0da1a01e10576a705d6d1605ac',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...)>::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html#a579d806514cabd7b397ad5e0c1db94b4',1,'handlegraph::return_type_of< Returns(*)(Args...)>::type()'],['../structvg_1_1GFFRecord.html#a0cc4e99f9e73fafafa9be311151ef0d7',1,'vg::GFFRecord::type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a2710528f0d6c0e15f824b38963a9ffe6',1,'vg::Haplotypes::Subchain::type()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a22b9b6cfc7735eedf7a813234b606761',1,'vg::HaplotypePartitioner::Subchain::type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ad39deee97644fc66b6c0a2514db7622a',1,'vg::ZipCodeTree::tree_item_t::type()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af21cc2ebf18d65a28c08ef24db23eee1',1,'vg::ZipCodeForest::child_info_t::type()'],['../structReferenceInterval.html#af544c6bc00b6fc4653ba71e869bbc4a5',1,'ReferenceInterval::type()'],['../structvg_1_1Snarl.html#a9490890cd7fff85dc32a25cb58d471f6',1,'vg::Snarl::type()']]],
- ['type_5fas_5fchar_6222',['type_as_char',['../structReferenceInterval.html#a9ae0102fab5146105642e388d6bef997',1,'ReferenceInterval']]],
- ['type_5fto_5fbare_5floaders_6223',['type_to_bare_loaders',['../structvg_1_1io_1_1Registry_1_1Tables.html#a6330f82f362346c61bdb1607773e812a',1,'vg::io::Registry::Tables']]],
- ['type_5fto_5fsaver_6224',['type_to_saver',['../structvg_1_1io_1_1Registry_1_1Tables.html#af3921832709101fdc87cfca00da3f2bf',1,'vg::io::Registry::Tables']]],
- ['types_2ecpp_6225',['types.cpp',['../types_8cpp.html',1,'']]],
- ['types_2ehpp_6226',['types.hpp',['../src_2types_8hpp.html',1,'(Global Namespace)'],['../deps_2libhandlegraph_2src_2include_2handlegraph_2types_8hpp.html',1,'(Global Namespace)']]]
+ ['t_5948',['T',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a830a224fa9ca0c0f9e4027f98537ddd0',1,'vg::subcommand::FlagArgSpec']]],
+ ['tables_5949',['Tables',['../structvg_1_1io_1_1Registry_1_1Tables.html',1,'vg::io::Registry']]],
+ ['tag_5950',['tag',['../structvg_1_1Funnel_1_1Item.html#acba00ec4fad9a9b3f1a0f9c8dcb4484c',1,'vg::Funnel::Item::tag()'],['../structvg_1_1Funnel_1_1Stage.html#a9efc6bb2afa857b7c8d5c055a3adaae6',1,'vg::Funnel::Stage::tag()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a17e22f4ea8e69209b9aff2c00deb9ba4',1,'vg::io::ProtobufEmitter::tag()'],['../classvg_1_1Funnel.html#abd3cf8783612cccf4faf96f25fc4f17c',1,'vg::Funnel::tag()']]],
+ ['tag_5fcorrect_5951',['tag_correct',['../classvg_1_1Funnel.html#aa725f066e32a967c8d482f50c1606f08',1,'vg::Funnel']]],
+ ['tag_5flength_5952',['tag_length',['../structvg_1_1Funnel_1_1Item.html#a965c4d888554644e3cbfc5deae970b92',1,'vg::Funnel::Item']]],
+ ['tag_5flist_5ft_5953',['tag_list_t',['../classvg_1_1algorithms_1_1GFAParser.html#ad6ed4063154c14a6e348a5c646bae1f1',1,'vg::algorithms::GFAParser']]],
+ ['tag_5fseeds_5954',['tag_seeds',['../classvg_1_1MinimizerMapper.html#a59d91d716447b3971fd13e7a1920ab8b',1,'vg::MinimizerMapper']]],
+ ['tag_5fspace_5955',['tag_space',['../structvg_1_1Funnel_1_1Stage.html#a582d8a4caf1dbfda777913e2032fa403',1,'vg::Funnel::Stage']]],
+ ['tag_5fstart_5956',['tag_start',['../structvg_1_1Funnel_1_1Item.html#a40097e3acf4a20046f5679c5601f823f',1,'vg::Funnel::Item']]],
+ ['tag_5fto_5floader_5957',['tag_to_loader',['../structvg_1_1io_1_1Registry_1_1Tables.html#a965e60de0073226a98deef0757d7dfa8',1,'vg::io::Registry::Tables']]],
+ ['tag_5fto_5fprotobuf_5958',['tag_to_protobuf',['../structvg_1_1io_1_1Registry_1_1Tables.html#abac3d9be375a86c8f55e5777e97fe323',1,'vg::io::Registry::Tables']]],
+ ['taggedmessage_5959',['TaggedMessage',['../classvg_1_1io_1_1MessageIterator.html#ac914a651c928eedea34171366c9f62e8',1,'vg::io::MessageIterator']]],
+ ['tags_5960',['tags',['../structGBWTConfig.html#af72aa6461315f4e981c6308ede36fc64',1,'GBWTConfig']]],
+ ['tags_5fto_5fset_5961',['tags_to_set',['../structGBWTConfig.html#abf5b058641892fe0532de896d8a6cdeb',1,'GBWTConfig']]],
+ ['tail_5fgap_5fmemo_5fmax_5fsize_5962',['tail_gap_memo_max_size',['../classvg_1_1MultipathAlignmentGraph.html#a12e62ccfd7e7adb135d169f7e2671509',1,'vg::MultipathAlignmentGraph']]],
+ ['tail_5fnodes_5963',['tail_nodes',['../classvg_1_1VG.html#a25bd74b77e139691555c8d48ecf67d9f',1,'vg::VG::tail_nodes(void)'],['../classvg_1_1VG.html#a47fbc525ed5e9f2a7b00c333f03fe6c8',1,'vg::VG::tail_nodes(vector< Node * > &nodes)'],['../namespacehandlegraph_1_1algorithms.html#ad3eb2f190153333cdee10e6624df34c6',1,'handlegraph::algorithms::tail_nodes()']]],
+ ['tail_5foffset_5964',['tail_offset',['../structvg_1_1GaplessExtension.html#a94628e41ab7556750c6ab841ca76fafd',1,'vg::GaplessExtension']]],
+ ['tail_5fposition_5965',['tail_position',['../structvg_1_1GaplessExtension.html#adb0c7cc3eee2f406d20fde6db08717b1',1,'vg::GaplessExtension']]],
+ ['take_5966',['take',['../structvg_1_1RecombinatorHaplotype.html#aec852acffc1ac8250b5c34aada44b980',1,'vg::RecombinatorHaplotype::take()'],['../classvg_1_1io_1_1MessageIterator.html#ab97d50a333e4f27419f0d661e8669774',1,'vg::io::MessageIterator::take()'],['../classvg_1_1io_1_1ProtobufIterator.html#a32bfe2fea01e8bae7759dff71eb64db8',1,'vg::io::ProtobufIterator::take()']]],
+ ['take_5funique_5fminimizers_5967',['take_unique_minimizers',['../namespacevg.html#aced59c99c3795653e7d70f176edf9c82',1,'vg']]],
+ ['target_5968',['target',['../classvg_1_1InsufficientInputException.html#aa40303513d2f82efe6690afe9b8a75ce',1,'vg::InsufficientInputException']]],
+ ['target_5falignment_5969',['target_alignment',['../namespacevg.html#ac712c04180499746dab8cdc6c8795c56',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse, Mapping &cigar_mapping)'],['../namespacevg.html#a08575acb0012ffaabd9859324e404562',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse)']]],
+ ['target_5flength_5970',['TARGET_LENGTH',['../structvg_1_1WFANode.html#a761a104c95d2f39fa286c39c4aeaa6ba',1,'vg::WFANode']]],
+ ['target_5fmemory_5fusage_5971',['target_memory_usage',['../classvg_1_1IndexRegistry.html#a6d6ef1d1e1488c9a32feaddca19cdb1a',1,'vg::IndexRegistry::target_memory_usage()'],['../classvg_1_1IndexingPlan.html#a1fd91843fb2c901d9db661e6bc50f07a',1,'vg::IndexingPlan::target_memory_usage()']]],
+ ['target_5foffset_5972',['target_offset',['../structvg_1_1WFANode.html#ab230231efd27b35e2db2b6055e187f50',1,'vg::WFANode::target_offset()'],['../structvg_1_1WFAPoint.html#a1ffb5ef3c0d0e64eaeeb2290468bb53f',1,'vg::WFAPoint::target_offset()']]],
+ ['targets_5973',['targets',['../classvg_1_1IndexingPlan.html#adda5d82310890614f02b317e46e702a1',1,'vg::IndexingPlan']]],
+ ['targetvaluesearch_5974',['TargetValueSearch',['../classvg_1_1TargetValueSearch.html',1,'vg::TargetValueSearch'],['../classvg_1_1TargetValueSearch.html#afaa00740b29b96fd3c0c561898c3330a',1,'vg::TargetValueSearch::TargetValueSearch()=delete'],['../classvg_1_1TargetValueSearch.html#a66c7161857ea38dab47c4da883435ac4',1,'vg::TargetValueSearch::TargetValueSearch(const HandleGraph &handle_graph, DistanceHeuristic *upper_bound_heuristic, DistanceHeuristic *lower_bound_heuristic)']]],
+ ['task_5fname_5975',['task_name',['../structvg_1_1Watchdog_1_1thread__state__t.html#a797bf67f4267c5ffeda247c041f7cd14',1,'vg::Watchdog::thread_state_t']]],
+ ['tell_5976',['Tell',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a4b34e76da81d5a09d5ab2634a864d401',1,'vg::io::BlockedGzipInputStream::Tell()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a84bb042b0a5df4ecbdadb3852fa04f91',1,'vg::io::BlockedGzipOutputStream::Tell()']]],
+ ['tell_5fgroup_5977',['tell_group',['../classvg_1_1io_1_1MessageIterator.html#afc6ab71583004ebdeb7aa24553817936',1,'vg::io::MessageIterator::tell_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6b51328b5c897e36803b63a7058b6c61',1,'vg::io::ProtobufIterator::tell_group()']]],
+ ['telomere_5fpair_5978',['telomere_pair',['../structvg_1_1SwapHaplotypesCommand.html#a6a5922c2e74c8227f07631fd2f8cc5f9',1,'vg::SwapHaplotypesCommand']]],
+ ['telomeres_5979',['telomeres',['../classvg_1_1GenomeState.html#a2e1564254538fec6438c931a5263ab8a',1,'vg::GenomeState']]],
+ ['test_5fmain_2ecpp_5980',['test_main.cpp',['../test__main_8cpp.html',1,'']]],
+ ['test_5fmean_5981',['test_mean',['../structvg_1_1BenchmarkResult.html#a7bd2a14daeee009dd5845ba44454d7b5',1,'vg::BenchmarkResult']]],
+ ['test_5fsplice_5fcandidates_5982',['test_splice_candidates',['../classvg_1_1MultipathMapper.html#ac45ca6502977ffa0640b3d5cdf21fae1',1,'vg::MultipathMapper']]],
+ ['test_5fstddev_5983',['test_stddev',['../structvg_1_1BenchmarkResult.html#a54499cba0e5b1927efb68c3cf4adcff3',1,'vg::BenchmarkResult']]],
+ ['testminimizermapper_5984',['TestMinimizerMapper',['../classvg_1_1MinimizerMapper.html#a8239430f869fd4cc597359f38a1ab29e',1,'vg::MinimizerMapper']]],
+ ['thin_5falignment_5fcutoff_5985',['thin_alignment_cutoff',['../classvg_1_1VariantAdder.html#a12ef17f5d02d950a436d20e651588a81',1,'vg::VariantAdder']]],
+ ['thread_5fbreakpoint_5fcursors_5986',['thread_breakpoint_cursors',['../classvg_1_1io_1_1StreamMultiplexer.html#a836843731535676ddd71a68cd3cd6d7f',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fchunk_5finflation_5ffactor_5987',['thread_chunk_inflation_factor',['../structvg_1_1IndexingParameters.html#a4eb6ab42c2e0c51a9a8891ec24ab9433',1,'vg::IndexingParameters']]],
+ ['thread_5fextension_5988',['thread_extension',['../classvg_1_1Mapper.html#ad2f2408aba30a38eda90a10c28cbf410',1,'vg::Mapper']]],
+ ['thread_5fids_5ft_5989',['thread_ids_t',['../namespacevg.html#a5c7b3ebb9ad8d6c01a0c54668b102c26',1,'vg']]],
+ ['thread_5fmax_5fretained_5fbytes_5990',['THREAD_MAX_RETAINED_BYTES',['../classvg_1_1DozeuInterface.html#a7f00debc965248ba99fc5450ed35e24d',1,'vg::DozeuInterface']]],
+ ['thread_5fqueue_5fbyte_5fcounts_5991',['thread_queue_byte_counts',['../classvg_1_1io_1_1StreamMultiplexer.html#a9ec3374dee16f6ee0ce853b04a4d6967',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueue_5fempty_5fslots_5992',['thread_queue_empty_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#a62843d99c1215b3d01109142f2356327',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueue_5ffilled_5fslots_5993',['thread_queue_filled_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#ad34283d480d468d52412bce3daeae5c4',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueue_5fmutexes_5994',['thread_queue_mutexes',['../classvg_1_1io_1_1StreamMultiplexer.html#ae0404331337813a02b7bafd0fb95e10a',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueues_5995',['thread_queues',['../classvg_1_1io_1_1StreamMultiplexer.html#aa4bc760981467acc3bff684653ffebd5',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fstate_5ft_5996',['thread_state_t',['../structvg_1_1Watchdog_1_1thread__state__t.html',1,'vg::Watchdog']]],
+ ['thread_5fstreams_5997',['thread_streams',['../classvg_1_1io_1_1StreamMultiplexer.html#a9e75e8ebd9b414f7438dea9b43af3b56',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5ft_5998',['thread_t',['../namespacevg.html#a31b8b476fb46de6667b26514b7b24fd2',1,'vg']]],
+ ['thread_5fto_5fgraph_5fspanned_5999',['thread_to_graph_spanned',['../namespacevg.html#aa24cc1f72643cab5fa0dfcc551f61d50',1,'vg']]],
+ ['threads_6000',['threads',['../classvg_1_1ReadFilter.html#a41808c4d5db46d1405ac906a01bbf794',1,'vg::ReadFilter::threads()'],['../structHaplotypesConfig.html#a179bec8b7054c7eaa5aaf9e055322d63',1,'HaplotypesConfig::threads()'],['../namespacehaplotypes__defaults.html#aa204b98aebcd769c098b7842428b94d6',1,'haplotypes_defaults::threads()']]],
+ ['threads_5ffor_5fcontig_6001',['threads_for_contig',['../namespacevg.html#a5813ee7997572d371f9ff7b45bbe4843',1,'vg']]],
+ ['threads_5ffor_5fsample_6002',['threads_for_sample',['../namespacevg.html#a2d4b0a9961f932a8caccb1d0723fd171',1,'vg']]],
+ ['threads_5fto_5fjobs_6003',['threads_to_jobs',['../haplotypes__main_8cpp.html#a9f628e188cebb5384d8b2b236a745866',1,'haplotypes_main.cpp']]],
+ ['three_5fedge_5fconnected_5fcomponent_5fmerges_6004',['three_edge_connected_component_merges',['../namespacevg_1_1algorithms.html#a7215192f2cc6536b6b3aadef4e95c64a',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponent_5fmerges_5fdense_6005',['three_edge_connected_component_merges_dense',['../namespacevg_1_1algorithms.html#a4d4b7c6814fb1f53a83c2e8355d72efa',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponents_6006',['three_edge_connected_components',['../namespacevg_1_1algorithms.html#ae4677e69f0b8ceb8580bc019cc8fbea8',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponents_2ecpp_6007',['three_edge_connected_components.cpp',['../three__edge__connected__components_8cpp.html',1,'']]],
+ ['three_5fedge_5fconnected_5fcomponents_2ehpp_6008',['three_edge_connected_components.hpp',['../three__edge__connected__components_8hpp.html',1,'']]],
+ ['three_5fedge_5fconnected_5fcomponents_5fdense_6009',['three_edge_connected_components_dense',['../namespacevg_1_1algorithms.html#a34c4a74208a88c0f956e697d5e183f5c',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponents_5fdense_5fcactus_6010',['three_edge_connected_components_dense_cactus',['../namespacevg_1_1algorithms.html#a57de725b70b138394479863428f9d2eb',1,'vg::algorithms']]],
+ ['tick_6011',['tick',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa1729ac6451d805cfb67301c5aff03b6',1,'vg::ZipCodeTree::reverse_iterator::tick()'],['../structvg_1_1Range.html#a10f700e0447a5a922611122fa1811b61',1,'vg::Range::tick()']]],
+ ['tick_5falong_5fchain_6012',['tick_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a1d1a3f2903fbcc9be3d9725b7d27dba8',1,'vg::subcommand::TickChainLink::tick_along_chain()'],['../structvg_1_1Range.html#a66d38c47018ce4cd2589be167588affe',1,'vg::Range::tick_along_chain()']]],
+ ['tick_5falong_5fchain_5fparent_6013',['tick_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#ad9ae4a6d3f61a4d18c56fe85f0259fb8',1,'vg::subcommand::TickChainLink']]],
+ ['tick_5fchain_6014',['tick_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a90c9bb7ca4ab9e7f91bb246c5949eae4',1,'vg::subcommand::TickChainLink::tick_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aee28025b35a1a448183eb4957d697e62',1,'vg::subcommand::OptionGroup::tick_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ad0a0fc373e9e599842dbf6e1d67b4271',1,'vg::subcommand::GroupedOptionGroup::tick_chain()']]],
+ ['tickchainlink_6015',['TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html',1,'vg::subcommand::TickChainLink'],['../structvg_1_1subcommand_1_1TickChainLink.html#a3a814506ba062fcf389d57efa4304d4a',1,'vg::subcommand::TickChainLink::TickChainLink()=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a46213933eb07d96326cdb848f6dcd066',1,'vg::subcommand::TickChainLink::TickChainLink(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#afe9e76f6721953c97baed84957f6c1fe',1,'vg::subcommand::TickChainLink::TickChainLink(TickChainLink &&other)=delete']]],
+ ['time_6016',['time',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#a92a84b5696522b5290e1407cd55dff83',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['time_5fpoint_6017',['time_point',['../classvg_1_1Funnel.html#a573543e4560aee58697f78cc266f22c7',1,'vg::Funnel::time_point()'],['../classvg_1_1Watchdog.html#adbdb9378ef086d2e9255f22ff9ef454d',1,'vg::Watchdog::time_point()']]],
+ ['time_5fused_6018',['time_used',['../structvg_1_1Alignment.html#a0c8b04a220715a894a19dcc70ed581c0',1,'vg::Alignment']]],
+ ['timed_5fout_6019',['timed_out',['../structvg_1_1Watchdog_1_1thread__state__t.html#a0a1e9d9760eaa0803da68a1ef3a0cdb0',1,'vg::Watchdog::thread_state_t']]],
+ ['timeout_6020',['timeout',['../classvg_1_1Watchdog.html#aff48af7cbc77f123d30fefd9aa005181',1,'vg::Watchdog']]],
+ ['tip_6021',['TIP',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3a41062278414d99cdb309732619f1ce5f',1,'handlegraph::SnarlDecomposition']]],
+ ['tipanchoredmaxdistance_6022',['TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html',1,'vg::TipAnchoredMaxDistance'],['../classvg_1_1TipAnchoredMaxDistance.html#a7a47ea386b37e4e738f71709184fce75',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance()=delete'],['../classvg_1_1TipAnchoredMaxDistance.html#a2658eecf16503163b9c39c44c7468bcc',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance(SnarlDistanceIndex &distance_index)']]],
+ ['tmpfstream_5flocks_6023',['tmpfstream_locks',['../classvg_1_1Packer.html#a0f98b46ac443166dc94b2bd3c6b8d5a9',1,'vg::Packer']]],
+ ['tmpfstreams_6024',['tmpfstreams',['../classvg_1_1Packer.html#a12c9d820a3b4ba6fdec28b9f05677f64',1,'vg::Packer']]],
+ ['to_6025',['to',['../classvg_1_1WFATree.html#abb28a51f09daa96b500ce7a030876f0e',1,'vg::WFATree::to()'],['../structvg_1_1RecombinatorFragment.html#a73179f74032a4ca87c8e4c4a35b78a7c',1,'vg::RecombinatorFragment::to()'],['../structvg_1_1Edge.html#affb3decf0a8b18ad319405c303cdf6a5',1,'vg::Edge::to()'],['../structvg_1_1Alignment.html#a9db86772c1bd48808c0588f96f3c0865',1,'vg::Alignment::to()'],['../structvg_1_1Translation.html#a25a5dc4de6c11119522e319af3639e30',1,'vg::Translation::to()']]],
+ ['to_5falignment_6026',['to_alignment',['../classvg_1_1ReadFilter.html#a21b0bf11e5636b41cf6dfc4a61441c4e',1,'vg::ReadFilter::to_alignment()'],['../namespacevg.html#a10bcb19d45af37e8a58129b939b86f21',1,'vg::to_alignment()']]],
+ ['to_5fanchor_6027',['to_anchor',['../classvg_1_1MinimizerMapper.html#ae7509b53b63ffb61b768c80f79f04a4d',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, const VectorView< Minimizer > &minimizers, std::vector< Seed > &seeds, size_t seed_number, const HandleGraph &graph, const Aligner *aligner)'],['../classvg_1_1MinimizerMapper.html#a750d65dcbba1734ca9855225090d0149',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, size_t read_start, size_t read_end, const std::vector< size_t > &sorted_seeds, const std::vector< algorithms::Anchor > &seed_anchors, const std::vector< size_t >::const_iterator &mismatch_begin, const std::vector< size_t >::const_iterator &mismatch_end, const HandleGraph &graph, const Aligner *aligner)']]],
+ ['to_5fanchors_6028',['to_anchors',['../classvg_1_1MinimizerMapper.html#aaaabeeaf994436a22232bd59af97ea39',1,'vg::MinimizerMapper']]],
+ ['to_5fbacking_6029',['to_backing',['../classvg_1_1ExtraNodeGraph.html#ae3c321717804ea0d0762fb4a8f71a7db',1,'vg::ExtraNodeGraph::to_backing()'],['../classvg_1_1SourceSinkOverlay.html#ada12ceaf3a0ed960ea42cf5a1f5de42a',1,'vg::SourceSinkOverlay::to_backing()']]],
+ ['to_5fbig_5fendian_6030',['to_big_endian',['../structvg_1_1endianness.html#a5397898b5e413c0c4d09577952b80984',1,'vg::endianness']]],
+ ['to_5fcorrect_6031',['to_correct',['../structvg_1_1Alignment.html#a8957ee4a5a3ef66c93f6b6b685774df2',1,'vg::Alignment']]],
+ ['to_5fdot_6032',['to_dot',['../classvg_1_1Funnel.html#ad4a9374a423b2b87a15355ffac7a1935',1,'vg::Funnel::to_dot()'],['../classvg_1_1IndexRegistry.html#ad7ff998ac4404629ef683795a9170116',1,'vg::IndexRegistry::to_dot() const'],['../classvg_1_1IndexRegistry.html#a53573d21c79b060ebb0c643b1d395a7f',1,'vg::IndexRegistry::to_dot(const vector< IndexName > &targets) const'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a5eabcd913cf0ba46947d0554eab790fb',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::to_dot()'],['../classvg_1_1MultipathAlignmentGraph.html#a90ff13eb09622a6f5fa9238f6ec4950b',1,'vg::MultipathAlignmentGraph::to_dot()'],['../classvg_1_1VG.html#af502bd29a58e62ff70f8f963d47401a4',1,'vg::VG::to_dot()']]],
+ ['to_5fedge_6033',['to_edge',['../namespacevg.html#a1da5277daea16b80ffc4ab75175b1882',1,'vg']]],
+ ['to_5fend_6034',['to_end',['../structvg_1_1Edge.html#af1538e8b7416c9af6aae7b3d587182dd',1,'vg::Edge']]],
+ ['to_5fgfa_6035',['to_gfa',['../classxg_1_1XG.html#a7cc1d24330a708afd24e768514c474c6',1,'xg::XG']]],
+ ['to_5fgraph_6036',['to_graph',['../classvg_1_1Paths.html#ad215b2c7475b7048a073ce6fa805e709',1,'vg::Paths']]],
+ ['to_5fidx_6037',['to_idx',['../classvg_1_1MEMClusterer_1_1HitEdge.html#a94b63347e0a6a9907b5573fae257aace',1,'vg::MEMClusterer::HitEdge']]],
+ ['to_5fjson_6038',['to_json',['../classvg_1_1Paths.html#ad98bff3b628d499252c7b5fb29191fdc',1,'vg::Paths']]],
+ ['to_5fleft_5fside_6039',['to_left_side',['../namespacevg.html#a84d646b72482de0145745a64414ca5df',1,'vg']]],
+ ['to_5flength_6040',['to_length',['../structvg_1_1Edit.html#a4f9854d5ba5503280306f1a06bfb3c89',1,'vg::Edit::to_length()'],['../classvg_1_1edit__t.html#ad90d417ef77001a113ab3d1912e76954',1,'vg::edit_t::to_length()'],['../namespacevg.html#a5ed83dc32e575ae68b591d142eb38912',1,'vg::to_length()']]],
+ ['to_5flength_5fafter_5fpos_6041',['to_length_after_pos',['../namespacevg.html#ad47f373b3433b3190f9f1c0f5f17274d',1,'vg']]],
+ ['to_5flength_5fbefore_5fpos_6042',['to_length_before_pos',['../namespacevg.html#aa40f0cfd74a9eeaa7b6ffecbc0926a6d',1,'vg']]],
+ ['to_5fmapping_6043',['to_mapping',['../classvg_1_1mapping__t.html#ab60b07378892ab57a661e27d19cef194',1,'vg::mapping_t::to_mapping()'],['../namespacevg.html#a28be7f9898d5ad6e075e25b81df512e8',1,'vg::to_mapping(const Visit &visit, std::function< size_t(id_t)> node_length)'],['../namespacevg.html#a128ffce6142542678bbbdc6e2e0b40cd',1,'vg::to_mapping(const Visit &visit, const HandleGraph &vg)']]],
+ ['to_5fmatrix_6044',['to_matrix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a6d6778356b79ef4f4831acafc090f566',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['to_5fmultipath_5falignment_6045',['to_multipath_alignment',['../namespacevg.html#a27656a1e271730b6a62263dc2af8055d',1,'vg']]],
+ ['to_5fnode_5fid_6046',['to_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a3ebf9c322668234f32083e3f9d42b38f',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['to_5fnode_5ftraversal_6047',['to_node_traversal',['../namespacevg.html#a5a2e772d69c9e45cbc1c1d1a9e6df842',1,'vg::to_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#a2c04918053577c402e4f2cab61abd754',1,'vg::to_node_traversal(const Visit &visit, VG &graph)']]],
+ ['to_5fnumber_6048',['to_number',['../classvg_1_1BitString.html#a2d6824816926cd463e586bb32ca3debc',1,'vg::BitString']]],
+ ['to_5fpath_6049',['to_path',['../structvg_1_1GaplessExtension.html#ade804b684aa81b0b2f95033ead5930a2',1,'vg::GaplessExtension::to_path()'],['../structvg_1_1WFAAlignment.html#a4d90b156bc529bf52019201f30e12842',1,'vg::WFAAlignment::to_path()'],['../classvg_1_1MinimizerMapper.html#ae1565adcd1bdf28aca55134d7482b1af',1,'vg::MinimizerMapper::to_path()']]],
+ ['to_5fproto_5fedit_6050',['to_proto_edit',['../namespacevg.html#a84c5dd6c830450f9100b5e9c11522050',1,'vg']]],
+ ['to_5fproto_5fmapping_6051',['to_proto_mapping',['../namespacevg.html#a3da977cb90bf3ffd94166edb2fdb980a',1,'vg']]],
+ ['to_5fproto_5fmultipath_5falignment_6052',['to_proto_multipath_alignment',['../namespacevg.html#a8f8f0e54cfa0c3279c18748c503ccbe9',1,'vg']]],
+ ['to_5fproto_5fpath_6053',['to_proto_path',['../namespacevg.html#a9473b834c584544cc90c819d6b5bb222',1,'vg']]],
+ ['to_5fremove_6054',['to_remove',['../structGBWTConfig.html#aa7b2d855903feadc683c6f1379374dbe',1,'GBWTConfig']]],
+ ['to_5frev_5fnode_5ftraversal_6055',['to_rev_node_traversal',['../namespacevg.html#a0b4a5c32294bf49aa7f0a6d180cc2832',1,'vg::to_rev_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#ae64d7810e64af7119f1b1b3a2d08d797',1,'vg::to_rev_node_traversal(const Visit &visit, VG &graph)']]],
+ ['to_5frev_5fvisit_6056',['to_rev_visit',['../namespacevg.html#a7164ae8636d1ca7783d6202c8ce316ca',1,'vg']]],
+ ['to_5fright_5fside_6057',['to_right_side',['../namespacevg.html#a74fab09b3ae1d9f799742a31b5206a35',1,'vg']]],
+ ['to_5fseed_6058',['to_seed',['../classvg_1_1GaplessExtender.html#a5b141ee05b0f704d29e9f34de8c67a32',1,'vg::GaplessExtender']]],
+ ['to_5fsimple_5freverse_6059',['to_simple_reverse',['../classvg_1_1FlowSort.html#ac49c6a1c8605c7e55d532aac7959611c',1,'vg::FlowSort']]],
+ ['to_5fsimple_5freverse_5forientation_6060',['to_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a4d4defd602249dfd58abbaea8058ff5a',1,'vg::FlowSort']]],
+ ['to_5fstring_6061',['to_string',['../structvg_1_1BREAKPOINT.html#a889fc9b9ff7feec9847c28eaf17ae6ee',1,'vg::BREAKPOINT::to_string()'],['../structvg_1_1Haplotypes_1_1Subchain.html#aa409e312b588c1b48f3855bf8dfbb3c1',1,'vg::Haplotypes::Subchain::to_string()'],['../structReferenceInterval.html#a91983a3892caceab4288482288f76154',1,'ReferenceInterval::to_string()'],['../namespacestd.html#aec6a9d59586ce5d9e0acc951c9c355c8',1,'std::to_string()'],['../namespacevg.html#ae9aadb20454b27a0819f40006556ffe6',1,'vg::to_string(handle_t handle)'],['../namespacevg.html#ad7ec65dd3bb34f37cff811f49c1b9599',1,'vg::to_string(const HandleGraph &graph, handle_t handle)'],['../namespacevg.html#a75bc48248af00118bc7cdacc00e37db1',1,'vg::to_string(const HandleGraph &graph, edge_t edge)'],['../namespacestd.html#af92da72517d799416d58a59067b6afd9',1,'std::to_string(const vg::pos_t &pos)'],['../namespacestd.html#a4d710aefadc1fdcd0988b913096651a8',1,'std::to_string(const vg::ZipCodeTree::tree_item_type_t &type)'],['../namespacestd.html#a0fcc699939402d5652d7dde38fd615fd',1,'std::to_string(const vg::ZipCodeTree::reverse_iterator::State &state)']]],
+ ['to_5fstring_5fgbwtgraph_6062',['to_string_gbwtgraph',['../namespacevg.html#adc47f14b546282cf0818ba47826a9110',1,'vg::to_string_gbwtgraph(handle_t handle)'],['../namespacevg.html#a93282dbd7c3a7daaf92b75f77c28dc29',1,'vg::to_string_gbwtgraph(gbwt::node_type node)']]],
+ ['to_5fswap_6063',['to_swap',['../structvg_1_1SwapHaplotypesCommand.html#a89b3e32d9f79d7e50bce707c47a18962',1,'vg::SwapHaplotypesCommand']]],
+ ['to_5fturtle_6064',['to_turtle',['../classvg_1_1VG.html#a582500a3d49fe231faa49a5c2e467cc8',1,'vg::VG']]],
+ ['to_5fvcf_5fgenotype_6065',['to_vcf_genotype',['../namespacevg.html#a420f2fd8ef6d04f1a34a08af2a3dee0e',1,'vg']]],
+ ['to_5fvector_6066',['to_vector',['../structvg_1_1varint__vector__t.html#a00af7863b11453e9e958375476ff8d4a',1,'vg::varint_vector_t::to_vector()'],['../classvg_1_1ZipCode.html#a43c4b30e62f754722d730d47306e76cd',1,'vg::ZipCode::to_vector()']]],
+ ['to_5fvisit_6067',['to_visit',['../classvg_1_1NodeSide.html#af9b1413c4dcef8615892989c6e8b6232',1,'vg::NodeSide::to_visit()'],['../namespacevg.html#a827ce532cdbd4710e86a21ebd986e1cc',1,'vg::to_visit(const NodeTraversal &node_traversal)'],['../namespacevg.html#acd53873bb85623cbf5b797f09bf88dc4',1,'vg::to_visit(const Mapping &mapping, bool make_full_node_match=false)'],['../namespacevg.html#aa76433c3398610bc58b842f2a4b462c7',1,'vg::to_visit(id_t node_id, bool is_reverse)'],['../namespacevg.html#a0a18238f71586af9b3eba2ba1dac2a6e',1,'vg::to_visit(const Snarl &snarl)'],['../namespacevg.html#ae7d774bd39780563236dbf2badfc804b',1,'vg::to_visit(const handlegraph::HandleGraph &graph, const handle_t &handle)']]],
+ ['to_5fwfa_5falignment_6068',['to_wfa_alignment',['../classvg_1_1MinimizerMapper.html#a41db60efc7634f542cea078a00f18379',1,'vg::MinimizerMapper']]],
+ ['to_5fxg_6069',['to_xg',['../classvg_1_1VGset.html#ab26412de51ff980342dea8aceaca6a6c',1,'vg::VGset::to_xg(xg::XG &index)'],['../classvg_1_1VGset.html#ab7d9649e1ae4cc62b05af39c97cf7b06',1,'vg::VGset::to_xg(xg::XG &index, const function< bool(const string &)> &paths_to_take, map< string, Path > *removed_paths=nullptr)']]],
+ ['toggle_5fbit_6070',['toggle_bit',['../structhandlegraph_1_1number__bool__packing.html#a7b54fcfbc7ad7e61d67d637374344a7e',1,'handlegraph::number_bool_packing']]],
+ ['toolkit_6071',['TOOLKIT',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838af5626d22da713c4acb1ccc508f2816d2',1,'vg::subcommand']]],
+ ['top_6072',['top',['../structhaplo_1_1int__itvl__t.html#a28cb4dd08f57cf179227ae76784bdbde',1,'haplo::int_itvl_t::top()'],['../structvg_1_1MatchPos_1_1PathList.html#ac50ec1cafee2fd491fb6d0a10e82835a',1,'vg::MatchPos::PathList::top() const'],['../structvg_1_1MatchPos_1_1PathList.html#a62397e20a1f6c4c50e9e1cec60030685',1,'vg::MatchPos::PathList::top()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa83523c6259341473ec281be15ad2046',1,'vg::ZipCodeTree::reverse_iterator::top()']]],
+ ['top_5fborder_6073',['top_border',['../classvg_1_1Viz.html#a9e044e100116d5fe502953643f07d2d2',1,'vg::Viz']]],
+ ['top_5fdiag_6074',['top_diag',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a76c5471f0be987920ff0076101367fbc',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['top_5fdown_5fgenotype_6075',['top_down_genotype',['../classvg_1_1LegacyCaller.html#a01e3b84cc03599fbc8cef1df4fcf43c7',1,'vg::LegacyCaller']]],
+ ['top_5fk_6076',['top_k',['../classvg_1_1PoissonSupportSnarlCaller.html#a4610e26e36319f7b2620566c7b655c63',1,'vg::PoissonSupportSnarlCaller']]],
+ ['top_5flevel_5fchains_6077',['top_level_chains',['../structvg_1_1Haplotypes_1_1Header.html#a8223ce0e3fe99009151debc39caf9c0b',1,'vg::Haplotypes::Header']]],
+ ['top_5flevel_5fsnarls_6078',['top_level_snarls',['../classvg_1_1SnarlManager.html#af31a29d8e7836bca46b389c01c625339',1,'vg::SnarlManager']]],
+ ['top_5fm_6079',['top_m',['../classvg_1_1PoissonSupportSnarlCaller.html#af61d6e6931ba127537e41cfdbf258d38',1,'vg::PoissonSupportSnarlCaller']]],
+ ['top_5ftracebacks_6080',['top_tracebacks',['../classvg_1_1MultipathMapper.html#a122b1eaa39c84e9b18a971ebe6566030',1,'vg::MultipathMapper']]],
+ ['toplevelchain_6081',['TopLevelChain',['../structvg_1_1Haplotypes_1_1TopLevelChain.html',1,'vg::Haplotypes']]],
+ ['topological_5forder_6082',['topological_order',['../classvg_1_1BandedGlobalAligner.html#a45b4ad348f9232013df241afece68afc',1,'vg::BandedGlobalAligner::topological_order()'],['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab277385bc0c8b0cd52c850f5368f0339',1,'vg::MEMClusterer::HitGraph::topological_order()'],['../namespacehandlegraph_1_1algorithms.html#a7063506d0cc176b808808147b83d7e33',1,'handlegraph::algorithms::topological_order()']]],
+ ['topological_5fsort_6083',['topological_sort',['../classvg_1_1MultipathAlignmentGraph.html#a565b45f37d5be97cd30bce1d29c134fc',1,'vg::MultipathAlignmentGraph']]],
+ ['topological_5fsort_2ecpp_6084',['topological_sort.cpp',['../topological__sort_8cpp.html',1,'']]],
+ ['topologically_5forder_5fsubpaths_6085',['topologically_order_subpaths',['../namespacevg.html#a3ca9ccb5a2301ed1ce48f6334b3c4937',1,'vg']]],
+ ['total_6086',['total',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#acb07aae84ec439512a012ee80829c357',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::total()'],['../namespacevg.html#a0a064dd8829b2100c6a38780311073f3',1,'vg::total()']]],
+ ['total_5fbits_6087',['TOTAL_BITS',['../classvg_1_1BitString.html#a881dbf42b0dc52a67f0c1edfa4e971f8',1,'vg::BitString']]],
+ ['total_5fkmers_6088',['total_kmers',['../structvg_1_1Haplotypes_1_1Header.html#a491f20acd55ad36b6b9b3c24f5b6a39e',1,'vg::Haplotypes::Header']]],
+ ['total_5fnode_5fquality_6089',['total_node_quality',['../classvg_1_1Packer.html#a67a80245fcdbc4f5788b1062ee6b55f9',1,'vg::Packer']]],
+ ['total_5fseq_5flength_6090',['total_seq_length',['../classvg_1_1BaseMapper.html#a45439a16e3d38573e5cc59cb95462878',1,'vg::BaseMapper::total_seq_length()'],['../classvg_1_1Sampler.html#a1e14636749c41aa2d525177bf1a68cf5',1,'vg::Sampler::total_seq_length()'],['../classvg_1_1NGSSimulator.html#ac83d417596d2d157ddc5903d41be1fef',1,'vg::NGSSimulator::total_seq_length()']]],
+ ['total_5fsize_6091',['total_size',['../structvg_1_1RebuildJob.html#aefe022edfe253c6c08690bd0e41dbaa1',1,'vg::RebuildJob']]],
+ ['total_5fsubchains_6092',['total_subchains',['../structvg_1_1Haplotypes_1_1Header.html#a64217b5f412fcf46e65dee628abec4dc',1,'vg::Haplotypes::Header']]],
+ ['total_5fsupports_6093',['total_supports',['../structvg_1_1BREAKPOINT.html#afc10d66ae6dad31e2086963bc6e34a06',1,'vg::BREAKPOINT']]],
+ ['touppercase_6094',['toUppercase',['../namespacevg.html#a00a949105ae94b18ca72452a442b8ddb',1,'vg']]],
+ ['touppercaseinplace_6095',['toUppercaseInPlace',['../namespacevg.html#adcf3d4a70f85f067842ccf34a82a4a46',1,'vg']]],
+ ['trace_6096',['trace',['../classvg_1_1DozeuInterface.html#a82634289dc80707e1ba8bb1a94503027',1,'vg::DozeuInterface::trace()'],['../classvg_1_1XdropAligner.html#adb3c7fa9b6b7c272ab687e0693a1dc47',1,'vg::XdropAligner::trace()'],['../classvg_1_1QualAdjXdropAligner.html#a8a382e7378bfeb43954a9436cf9d3b09',1,'vg::QualAdjXdropAligner::trace()'],['../classvg_1_1SnarlState.html#a6b13fa6a070139c5d123983265d440bc',1,'vg::SnarlState::trace()']]],
+ ['trace_5fhaplotype_6097',['trace_haplotype',['../classvg_1_1GenomeState.html#af167a6237410b8da2c839820e6c804a7',1,'vg::GenomeState']]],
+ ['trace_5fhaplotypes_5fand_5fpaths_6098',['trace_haplotypes_and_paths',['../namespacevg.html#a2d9774c4df98285526a427ba54e970ba',1,'vg']]],
+ ['trace_5fmain_2ecpp_6099',['trace_main.cpp',['../trace__main_8cpp.html',1,'']]],
+ ['trace_5fpath_6100',['trace_path',['../namespacevg.html#a83257be63a821ae991e1b332b62facd4',1,'vg::trace_path()'],['../haplotypes__main_8cpp.html#a8e6fb3993622a6541d6e6beb41ed1c72',1,'trace_path(): haplotypes_main.cpp']]],
+ ['trace_5fto_5falignment_6101',['trace_to_alignment',['../classvg_1_1DeletionAligner.html#a1916d488f7ed7e9ad0452a1c6138bc27',1,'vg::DeletionAligner']]],
+ ['traceback_6102',['traceback',['../classvg_1_1BandedGlobalAligner.html#a2a2b4909d5eb88633680ea071c5551f4',1,'vg::BandedGlobalAligner::traceback()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a1366942f6ff4eecbebad9b29e9ef2c94',1,'vg::BandedGlobalAligner::BAMatrix::traceback()'],['../classvg_1_1MEMChainModel.html#ae142b05be3a27922e9387108bb052706',1,'vg::MEMChainModel::traceback()'],['../classvg_1_1DeletionAligner.html#aeaa43fcc2267e2aab5ebde031e3852c3',1,'vg::DeletionAligner::traceback()'],['../classvg_1_1AlignmentChainModel.html#ac774ed2018837e64c7ef88ae28c2794a',1,'vg::AlignmentChainModel::traceback()']]],
+ ['traceback_5fover_5fedge_6103',['traceback_over_edge',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a0210e1c9a9da04e28e253e2963dd96ad',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['tracedscore_6104',['TracedScore',['../classvg_1_1algorithms_1_1TracedScore.html',1,'vg::algorithms']]],
+ ['track_5fcomponents_6105',['track_components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6bc63fbe77aee54235636bbc228a9e96',1,'vg::MEMClusterer::HitGraph']]],
+ ['track_5fcorrectness_6106',['track_correctness',['../classvg_1_1MinimizerMapper.html#a7896c6cccfa011c4fbad1b916d30052e',1,'vg::MinimizerMapper']]],
+ ['track_5fposition_6107',['track_position',['../classvg_1_1MinimizerMapper.html#a35a153c8cd62696021e17fe9d970b2b3',1,'vg::MinimizerMapper']]],
+ ['track_5fprovenance_6108',['track_provenance',['../classvg_1_1MinimizerMapper.html#aeabec85347521c1f42ef51e0453c4e5f',1,'vg::MinimizerMapper']]],
+ ['trailing_5fzeros_6109',['trailing_zeros',['../minimizer__main_8cpp.html#a82ed012045f022c7d023ef32c84a9df3',1,'minimizer_main.cpp']]],
+ ['transcript_6110',['Transcript',['../structvg_1_1Transcript.html',1,'vg::Transcript'],['../structvg_1_1Transcript.html#a151337b8595bb8b0041ed64a325a7650',1,'vg::Transcript::Transcript()']]],
+ ['transcript_5ffile_5fnonempty_6111',['transcript_file_nonempty',['../namespacevg.html#aa44c63a293d251b1bffbbeee59d2b7fe',1,'vg']]],
+ ['transcript_5fnames_6112',['transcript_names',['../structvg_1_1TranscriptPath.html#a325799db73bd6e750d5f4ee45014861c',1,'vg::TranscriptPath']]],
+ ['transcript_5fpaths_6113',['transcript_paths',['../classvg_1_1Transcriptome.html#a52ca431b737b92befedebee4e71b0f0c',1,'vg::Transcriptome']]],
+ ['transcript_5ftag_6114',['transcript_tag',['../classvg_1_1Transcriptome.html#a56a00bd350c02600e5474fc89791d5bd',1,'vg::Transcriptome']]],
+ ['transcriptome_6115',['Transcriptome',['../classvg_1_1Transcriptome.html',1,'vg::Transcriptome'],['../classvg_1_1Transcriptome.html#a041373349b45b5d190316229a5b8c562',1,'vg::Transcriptome::Transcriptome()']]],
+ ['transcriptome_2ecpp_6116',['transcriptome.cpp',['../transcriptome_8cpp.html',1,'']]],
+ ['transcriptome_2ehpp_6117',['transcriptome.hpp',['../transcriptome_8hpp.html',1,'']]],
+ ['transcriptpath_6118',['TranscriptPath',['../structvg_1_1TranscriptPath.html',1,'vg::TranscriptPath'],['../structvg_1_1TranscriptPath.html#ad87c876af2acb7bcbbbb52b33ad25e8d',1,'vg::TranscriptPath::TranscriptPath()'],['../structvg_1_1TranscriptPath.html#aef6b201d9d87a24f2c9e7ed6e9e9e1e7',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const string &embedded_path_name, const bool is_reference_in, const bool is_haplotype_in)'],['../structvg_1_1TranscriptPath.html#a1b9b94ca6d527d0f197d98faf2a6a4b5',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const gbwt::size_type &haplotype_gbwt_id, const bool is_reference_in, const bool is_haplotype_in)']]],
+ ['transfer_5fbetween_5fproto_5fannotation_6119',['transfer_between_proto_annotation',['../namespacevg.html#ac0534767a787eae1a5f93444bf21b2a1',1,'vg']]],
+ ['transfer_5fboundary_5finfo_6120',['transfer_boundary_info',['../namespacevg.html#a82a83d7c54d733abee06d328f91ef5ee',1,'vg']]],
+ ['transfer_5ffrom_5fproto_5fannotation_6121',['transfer_from_proto_annotation',['../namespacevg.html#a57c3f88ce9f85ceae2d77c32fd9de04d',1,'vg']]],
+ ['transfer_5fproto_5fmetadata_6122',['transfer_proto_metadata',['../namespacevg.html#a0582a68dfa130c9f0a2bdaa1c7ac5ef5',1,'vg::transfer_proto_metadata(const Alignment &from, MultipathAlignment &to)'],['../namespacevg.html#ad6476e86221a660dda1fa85254e9436d',1,'vg::transfer_proto_metadata(const MultipathAlignment &from, Alignment &to)']]],
+ ['transfer_5fread_5fmetadata_6123',['transfer_read_metadata',['../namespacevg.html#a195fc7fa6da6fecfa7e9fa31e5cf6f0c',1,'vg::transfer_read_metadata(const MultipathAlignment &from, multipath_alignment_t &to)'],['../namespacevg.html#acac375591689f0066f6c723dc25fb834',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, MultipathAlignment &to)'],['../namespacevg.html#ad0995c3042ff642b9e8aeaa1727dccb5',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, multipath_alignment_t &to)'],['../namespacevg.html#a54b4f608ad692caffd8fce4df9a1e4ef',1,'vg::transfer_read_metadata(const Alignment &from, multipath_alignment_t &to)'],['../namespacevg.html#a2d8929c8f610705661da889830b0b7b9',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, Alignment &to)'],['../namespacevg.html#af48acb91edce241c75a9a4fd02745620',1,'vg::transfer_read_metadata(const Alignment &from, Alignment &to)']]],
+ ['transfer_5fto_5fproto_5fannotation_6124',['transfer_to_proto_annotation',['../namespacevg.html#a90a76dfce70406755151cf45e6990848',1,'vg']]],
+ ['transfer_5funiform_5fmetadata_6125',['transfer_uniform_metadata',['../namespacevg.html#adbf827b04e42865ece378b51482df898',1,'vg']]],
+ ['transform_6126',['transform',['../classvg_1_1VGset.html#aaa5f1b0e3e71bb00a5ad82f210065e81',1,'vg::VGset']]],
+ ['transition_5fdistrs_5f1_6127',['transition_distrs_1',['../classvg_1_1NGSSimulator.html#a571f3ff879e38077e8d7dad879157d55',1,'vg::NGSSimulator']]],
+ ['transition_5fdistrs_5f2_6128',['transition_distrs_2',['../classvg_1_1NGSSimulator.html#ad3d0c480b5ecd2fa7c5209d86b41911d',1,'vg::NGSSimulator']]],
+ ['transition_5fiteratee_6129',['transition_iteratee',['../namespacevg_1_1algorithms.html#ad64245b7dca5a8144ae8720a92b65685',1,'vg::algorithms']]],
+ ['transition_5fiterator_6130',['transition_iterator',['../namespacevg_1_1algorithms.html#a79c214c1e7f1d7cc5fe322b8c9fb260c',1,'vg::algorithms']]],
+ ['transition_5ftable_6131',['transition_table',['../classvg_1_1DinucleotideMachine.html#a6a81eedb016f3d90fa5b0e2757537531',1,'vg::DinucleotideMachine']]],
+ ['transitive_5freduction_6132',['transitive_reduction',['../classvg_1_1Surjector.html#a2149d1e5e6aba2e07b92030e6afc617d',1,'vg::Surjector']]],
+ ['translate_6133',['translate',['../classvg_1_1Translator.html#a3407f68503febdc2bd4366947e96d003',1,'vg::Translator::translate(const Position &position)'],['../classvg_1_1Translator.html#a6e27eb192e227afe777de2dc6488eb26',1,'vg::Translator::translate(const Position &position, const Translation &translation)'],['../classvg_1_1Translator.html#a1a8657e279942f5b4a802aad9e0baab6',1,'vg::Translator::translate(const Edge &edge)'],['../classvg_1_1Translator.html#a9ea3b0a85f25159214b34041b20a5cd3',1,'vg::Translator::translate(const Mapping &mapping)'],['../classvg_1_1Translator.html#a28ee9ca0de37d9d83f24b33639f0893c',1,'vg::Translator::translate(const Path &path)'],['../classvg_1_1Translator.html#af2f3e933feb2e28acf713316840b03c4',1,'vg::Translator::translate(const Alignment &aln)'],['../classvg_1_1Translator.html#ab4dffeb58e1c441c82039c6dd17445f5',1,'vg::Translator::translate(const Locus &locus)']]],
+ ['translate_5fback_6134',['translate_back',['../classvg_1_1FlatFileBackTranslation.html#a44128954132be459c4229001b0441add',1,'vg::FlatFileBackTranslation::translate_back()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a762d6c9b1ad1762f3521c3a24cf82f55',1,'vg::algorithms::GFAIDMapInfo::translate_back()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#a4005088073dfdd8d3da33803198ee737',1,'handlegraph::NamedNodeBackTranslation::translate_back()']]],
+ ['translate_5fdown_6135',['translate_down',['../classvg_1_1PathSubgraph.html#a7fa974235481756de3a7bb3c04f58ef7',1,'vg::PathSubgraph::translate_down()'],['../classvg_1_1TreeSubgraph.html#a71ab7a4ca370f712cf7c4912ccb5ab25',1,'vg::TreeSubgraph::translate_down()']]],
+ ['translate_5fmain_2ecpp_6136',['translate_main.cpp',['../translate__main_8cpp.html',1,'']]],
+ ['translate_5fmems_6137',['translate_mems',['../namespacevg.html#a4bc1837d8c1cca33ab223957402b70ba',1,'vg']]],
+ ['translate_5fnode_5fids_6138',['translate_node_ids',['../classvg_1_1JoinedSpliceGraph.html#a535cf652e7e39598979b003b7155ae4f',1,'vg::JoinedSpliceGraph::translate_node_ids()'],['../namespacevg.html#af71770196fc31c2e3c9c2a83f3497177',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator)'],['../namespacevg.html#aa49e4506c94e5747c88805e39aa18090',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator, id_t cut_node, size_t bases_removed, bool from_right)'],['../namespacevg.html#a322ec292675d4891ecc265e56a836db7',1,'vg::translate_node_ids(path_t &path, const unordered_map< id_t, id_t > &translator)']]],
+ ['translate_5fnodes_6139',['translate_nodes',['../namespacevg.html#a98dcd16f2a4eae4c223a374dd2ab2da4',1,'vg']]],
+ ['translate_5foriented_5fnode_5fids_6140',['translate_oriented_node_ids',['../namespacevg.html#a2b0ba7a1d0cf7630b79d03ba0ab65c53',1,'vg::translate_oriented_node_ids(Path &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#acb86c984b743e10c6ddaa57612ca3991',1,'vg::translate_oriented_node_ids(Path &path, const function< pair< id_t, bool >(id_t)> &translator)'],['../namespacevg.html#a449dd4b0d7106c6ee7afceb4f7412d6d',1,'vg::translate_oriented_node_ids(path_t &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#abfebb6e72326ea81b2ed13b4c3b57885',1,'vg::translate_oriented_node_ids(path_t &path, const function< pair< id_t, bool >(id_t)> &translator)']]],
+ ['translate_5fsnarl_5fnum_6141',['translate_snarl_num',['../classvg_1_1SnarlManager.html#afdd078898493f277dc1aa5dc3dae5d56',1,'vg::SnarlManager']]],
+ ['translate_5fthrough_6142',['translate_through',['../classvg_1_1io_1_1GafAlignmentEmitter.html#a2e7cff4276d5f1cd7857f91d8970be0e',1,'vg::io::GafAlignmentEmitter']]],
+ ['translation_6143',['Translation',['../structvg_1_1Translation.html',1,'vg::Translation'],['../classvg_1_1BackTranslatingAlignmentEmitter.html#a7bbe9fc362769137eb5446c5ba9d4e49',1,'vg::BackTranslatingAlignmentEmitter::translation()'],['../classvg_1_1VCFOutputCaller.html#a212346d7a629ae3280ce3eb39606237b',1,'vg::VCFOutputCaller::translation()']]],
+ ['translations_6144',['translations',['../classvg_1_1Translator.html#aba17cd4fd008c2dbee1da376db1807be',1,'vg::Translator']]],
+ ['translator_6145',['Translator',['../classvg_1_1Translator.html',1,'vg::Translator'],['../classvg_1_1Translator.html#ac23acdcea38566f2e68005eca4afff73',1,'vg::Translator::Translator(void)'],['../classvg_1_1Translator.html#aeab811097e483365bbd273efc4c4445e',1,'vg::Translator::Translator(istream &in)'],['../classvg_1_1Translator.html#a99602b3868ae6f8f1efc6bf7adcde6f6',1,'vg::Translator::Translator(const vector< Translation > &trans)'],['../structvg_1_1AugmentedGraph.html#a3ac035d37452eb611b943cfa4754d6c6',1,'vg::AugmentedGraph::translator()'],['../classvg_1_1Genotyper.html#ad14928554aace83524e80d8c109e17b2',1,'vg::Genotyper::translator()']]],
+ ['translator_2ecpp_6146',['translator.cpp',['../translator_8cpp.html',1,'']]],
+ ['translator_2ehpp_6147',['translator.hpp',['../translator_8hpp.html',1,'']]],
+ ['transpose_6148',['transpose',['../namespacevg.html#a1409ac23ce33abd463dcd46093079023',1,'vg']]],
+ ['trav_6149',['trav',['../classvg_1_1MCMCCaller.html#a44187bff29621c4b3ff13560ea748223',1,'vg::MCMCCaller']]],
+ ['trav_5fpadding_6150',['trav_padding',['../classvg_1_1GAFOutputCaller.html#a1ef9a3f2df7cfbd1a35e3ee8f56f4657',1,'vg::GAFOutputCaller']]],
+ ['trav_5fsequence_6151',['trav_sequence',['../classvg_1_1VG.html#a57296ecbcfce10f95b86233e10c35d7d',1,'vg::VG']]],
+ ['trav_5fstring_6152',['trav_string',['../classvg_1_1VCFOutputCaller.html#ae4b896a68da613eb2e8e509279e4e1b9',1,'vg::VCFOutputCaller']]],
+ ['traversal_6153',['traversal',['../classvg_1_1mapping__t.html#a9ef6e5278c0ac9ce077ea2c8e0902674',1,'vg::mapping_t::traversal()'],['../namespacevg.html#a4ea210eff71c5a1039378130f98de166',1,'vg::Traversal()']]],
+ ['traversal_5falg_6154',['traversal_alg',['../classvg_1_1Genotyper.html#a5b040c1636f479b52dbdb641e82f74dd',1,'vg::Genotyper']]],
+ ['traversal_5fclusters_2ecpp_6155',['traversal_clusters.cpp',['../traversal__clusters_8cpp.html',1,'']]],
+ ['traversal_5fclusters_2ehpp_6156',['traversal_clusters.hpp',['../traversal__clusters_8hpp.html',1,'']]],
+ ['traversal_5ffinder_6157',['traversal_finder',['../classvg_1_1VCFGenotyper.html#afa0dd907b77ec7bd5d33f972c06ab131',1,'vg::VCFGenotyper::traversal_finder()'],['../classvg_1_1LegacyCaller.html#ada2c8e9befb0cbe8043779758468664a',1,'vg::LegacyCaller::traversal_finder()'],['../classvg_1_1FlowCaller.html#ad55a5eccba503ff1543b553ce5cd813f',1,'vg::FlowCaller::traversal_finder()'],['../classvg_1_1NestedFlowCaller.html#aaf2b6c922dfa6c16913325243496a126',1,'vg::NestedFlowCaller::traversal_finder()'],['../classvg_1_1SmallSnarlSimplifier.html#aaf858ca21b486fe45acbf92a4cbea5ba',1,'vg::SmallSnarlSimplifier::traversal_finder()']]],
+ ['traversal_5ffinder_2ecpp_6158',['traversal_finder.cpp',['../traversal__finder_8cpp.html',1,'']]],
+ ['traversal_5ffinder_2ehpp_6159',['traversal_finder.hpp',['../traversal__finder_8hpp.html',1,'']]],
+ ['traversal_5fsupport_2ecpp_6160',['traversal_support.cpp',['../traversal__support_8cpp.html',1,'']]],
+ ['traversal_5fsupport_2ehpp_6161',['traversal_support.hpp',['../traversal__support_8hpp.html',1,'']]],
+ ['traversal_5fto_5fstring_6162',['traversal_to_string',['../namespacevg.html#a94385b32246fc81a0a44ea1b47d994ee',1,'vg::traversal_to_string(VG &graph, const SnarlTraversal &path)'],['../namespacevg.html#a6a885124cc3018dc7cd6d2001b6b54f5',1,'vg::traversal_to_string(const PathHandleGraph *graph, const Traversal &traversal, int64_t max_steps)']]],
+ ['traversalalg_6163',['TraversalAlg',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4',1,'vg::Genotyper']]],
+ ['traversalfinder_6164',['TraversalFinder',['../classvg_1_1TraversalFinder.html',1,'vg']]],
+ ['traversals_5fonly_6165',['traversals_only',['../classvg_1_1VCFGenotyper.html#a61906c71880dba31065f8cf04b95b60d',1,'vg::VCFGenotyper::traversals_only()'],['../classvg_1_1FlowCaller.html#ad20a95ea02344c6b21a4912381e7b984',1,'vg::FlowCaller::traversals_only()'],['../classvg_1_1NestedFlowCaller.html#a5012c7a944e3c3d57148ff11d0a7a174',1,'vg::NestedFlowCaller::traversals_only()']]],
+ ['traversalsupportcalculator_6166',['TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html',1,'vg']]],
+ ['traversalsupportfinder_6167',['TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html',1,'vg::TraversalSupportFinder'],['../classvg_1_1TraversalSupportFinder.html#ab281113b3cdf2992299a2768ce1be832',1,'vg::TraversalSupportFinder::TraversalSupportFinder()']]],
+ ['traverse_5fcomponents_6168',['traverse_components',['../namespacevg_1_1algorithms.html#a6341683f1b89495d2ac1558ed2875343',1,'vg::algorithms']]],
+ ['traverse_5fcomputed_5fdecomposition_6169',['traverse_computed_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#ab843403935c08e4d1764b693a897c16c',1,'vg::IntegratedSnarlFinder']]],
+ ['traverse_5fdecomposition_6170',['traverse_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#a31a75674d1cc7d5f2b6a028161c6038f',1,'vg::IntegratedSnarlFinder::traverse_decomposition()'],['../classvg_1_1HandleGraphSnarlFinder.html#a9cba8688e5dd28b23ed3529af122f308',1,'vg::HandleGraphSnarlFinder::traverse_decomposition()']]],
+ ['traverse_5fedge_5fhandle_6171',['traverse_edge_handle',['../classhandlegraph_1_1HandleGraph.html#af167b0664299cfd4eac610f129fa5fee',1,'handlegraph::HandleGraph']]],
+ ['traverse_5fin_5forder_6172',['traverse_in_order',['../classvg_1_1BitStringTree.html#a5f825ebeb38c6d1572fa73692810c273',1,'vg::BitStringTree::traverse_in_order()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#aa89c88fbab67819e3f072da4bc82e253',1,'vg::BitStringTree::TreeNode::traverse_in_order()']]],
+ ['traverse_5fleft_6173',['traverse_left',['../classvg_1_1Paths.html#a861618af488874863197ad48f17a9ae4',1,'vg::Paths']]],
+ ['traverse_5fright_6174',['traverse_right',['../classvg_1_1Paths.html#aabda0fb1288e7681b317cd5b4cfad242',1,'vg::Paths']]],
+ ['traverse_5fup_6175',['traverse_up',['../classvg_1_1BitStringTree.html#aefd44d9f67d266cb206724b8516c001c',1,'vg::BitStringTree::traverse_up()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#ae67c2a504203ce10bbc6cc33d94c2e3b',1,'vg::BitStringTree::TreeNode::traverse_up()']]],
+ ['travs_6176',['travs',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a1ee05f25a4d87f1d40abfdea92d9d942',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['travs_5ffrom_6177',['travs_from',['../classvg_1_1VG.html#a34a493a0628857a3bfae181295ba541d',1,'vg::VG']]],
+ ['travs_5fof_6178',['travs_of',['../classvg_1_1VG.html#ae065082f817e9bc0e278cf71f31af1e2',1,'vg::VG']]],
+ ['travs_5fto_6179',['travs_to',['../classvg_1_1VG.html#a0a962957210c079fa242b383d5c65de3',1,'vg::VG']]],
+ ['tree_6180',['Tree',['../structvg_1_1Tree.html',1,'vg::Tree< T >'],['../classvg_1_1TreeSubgraph.html#a91ef2cd31f18ada628b0990faae105a1',1,'vg::TreeSubgraph::tree()'],['../structvg_1_1Tree.html#a2583e3d479b8b3fa66e8eb0065417934',1,'vg::Tree::Tree()']]],
+ ['tree_5fitem_5ft_6181',['tree_item_t',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html',1,'vg::ZipCodeTree::tree_item_t'],['../classvg_1_1ZipCodeForest.html#a6f4d116fc7bbdf877de9a8968133f5d5',1,'vg::ZipCodeForest::tree_item_t()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a5740e0956ab1ddcb8148d70702c2000f',1,'vg::ZipCodeTree::tree_item_t::tree_item_t()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a895703befafce6654f476cc86bdc33ed',1,'vg::ZipCodeTree::tree_item_t::tree_item_t(tree_item_type_t type, size_t raw_value, bool is_reversed)']]],
+ ['tree_5fitem_5ftype_5ft_6182',['tree_item_type_t',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ad',1,'vg::ZipCodeTree::tree_item_type_t()'],['../classvg_1_1ZipCodeForest.html#a21bc3d5c8b89cd4260cdacbcd3e853df',1,'vg::ZipCodeForest::tree_item_type_t()']]],
+ ['tree_5fsubgraph_2ecpp_6183',['tree_subgraph.cpp',['../tree__subgraph_8cpp.html',1,'']]],
+ ['tree_5fsubgraph_2ehpp_6184',['tree_subgraph.hpp',['../tree__subgraph_8hpp.html',1,'']]],
+ ['treenode_6185',['TreeNode',['../structvg_1_1BitStringTree_1_1TreeNode.html',1,'vg::BitStringTree< Item >::TreeNode'],['../structvg_1_1TreeNode.html',1,'vg::TreeNode< T >'],['../structvg_1_1TreeNode.html#a386f7b2ec0948165140022155dda8c04',1,'vg::TreeNode::TreeNode()']]],
+ ['trees_6186',['trees',['../classvg_1_1ZipCodeForest.html#af85d4ca7594aee84b37f7864e24e5ce6',1,'vg::ZipCodeForest']]],
+ ['treesubgraph_6187',['TreeSubgraph',['../classvg_1_1TreeSubgraph.html',1,'vg::TreeSubgraph'],['../classvg_1_1TreeSubgraph.html#aa43b054cfbc6f2f96fbc8fcef42887c5',1,'vg::TreeSubgraph::TreeSubgraph()']]],
+ ['trim_6188',['trim',['../classvg_1_1WFATree.html#aa4c7ff4d5620d1a75545bef9357096f3',1,'vg::WFATree']]],
+ ['trim_5falignment_6189',['trim_alignment',['../namespacevg.html#ad83da8607e104967dd51d9230f4b51bb',1,'vg']]],
+ ['trim_5fambiguous_5fend_6190',['trim_ambiguous_end',['../classvg_1_1ReadFilter.html#ac5d77581ac1d34661c62f446692217ab',1,'vg::ReadFilter']]],
+ ['trim_5fambiguous_5fends_6191',['trim_ambiguous_ends',['../classvg_1_1ReadFilter.html#a265a2c2d5e5af4924c406b97d764d9aa',1,'vg::ReadFilter::trim_ambiguous_ends(Read &read, int k) const'],['../classvg_1_1ReadFilter.html#ac49bf695fadbdaf8b41c972587493630',1,'vg::ReadFilter::trim_ambiguous_ends(Alignment &alignment, int k) const'],['../classvg_1_1ReadFilter.html#a266b5aeeb2081d2bd5f29ae43fdc00f8',1,'vg::ReadFilter::trim_ambiguous_ends(MultipathAlignment &aln, int k) const']]],
+ ['trim_5fand_5fcheck_5ffor_5fempty_6192',['trim_and_check_for_empty',['../classvg_1_1MultipathAlignmentGraph.html#a114d073d4422c085a2c5768b6f165001',1,'vg::MultipathAlignmentGraph']]],
+ ['trim_5fhanging_5fends_6193',['trim_hanging_ends',['../namespacevg.html#a990f54fb0e09dc439dace1519aff5e9f',1,'vg']]],
+ ['trim_5fhanging_5findels_6194',['trim_hanging_indels',['../classvg_1_1MultipathAlignmentGraph.html#aca7bc3f6c3de6fc3df3adabf3161260c',1,'vg::MultipathAlignmentGraph']]],
+ ['trim_5findels_6195',['trim_indels',['../classvg_1_1Constructor.html#a130c318e05428ee7973135ac5ea26b50',1,'vg::Constructor']]],
+ ['trim_5fmismatches_6196',['trim_mismatches',['../namespacevg.html#a77211f457b4e1f61915d771faf06cda0',1,'vg']]],
+ ['trim_5fpath_6197',['trim_path',['../namespacevg.html#ab8d0345d2d7cea79ffdca38d33ed0c7f',1,'vg']]],
+ ['trim_5fto_5fbranch_5fpoints_6198',['trim_to_branch_points',['../classvg_1_1MultipathAlignmentGraph.html#ac3199fb5e097873e2635e3fb34a8eafe',1,'vg::MultipathAlignmentGraph']]],
+ ['trim_5fto_5fvariable_6199',['trim_to_variable',['../classvg_1_1Constructor.html#a428cf1b27e402a304c18e40f87e9dc02',1,'vg::Constructor']]],
+ ['trimmed_5fend_6200',['trimmed_end',['../namespacevg.html#a9e61398cd459bb9ba3a1ced205491712',1,'vg']]],
+ ['trivially_5fserializable_2ecpp_6201',['trivially_serializable.cpp',['../trivially__serializable_8cpp.html',1,'']]],
+ ['trivially_5fserializable_2ehpp_6202',['trivially_serializable.hpp',['../trivially__serializable_8hpp.html',1,'']]],
+ ['triviallyserializable_6203',['TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html',1,'handlegraph::TriviallySerializable'],['../classhandlegraph_1_1TriviallySerializable.html#a209a7ede82e8ad286a8a3fb1e51c3604',1,'handlegraph::TriviallySerializable::TriviallySerializable()']]],
+ ['trivialtraversalfinder_6204',['TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html',1,'vg::TrivialTraversalFinder'],['../classvg_1_1TrivialTraversalFinder.html#a46403401b7efaec8d99b63b2013f7e60',1,'vg::TrivialTraversalFinder::TrivialTraversalFinder()']]],
+ ['truncate_5fhandle_6205',['truncate_handle',['../classhandlegraph_1_1DeletableHandleGraph.html#aa65cef3b3261f8d1bc2057c5f2ee100a',1,'handlegraph::DeletableHandleGraph']]],
+ ['truncated_5fnormal_5fdistribution_6206',['truncated_normal_distribution',['../classvg_1_1truncated__normal__distribution.html',1,'vg::truncated_normal_distribution< T >'],['../classvg_1_1truncated__normal__distribution.html#aa48544711e2d4a11ffe876366898e463',1,'vg::truncated_normal_distribution::truncated_normal_distribution()']]],
+ ['truncation_5fmultiplicity_5fmq_5flimit_6207',['truncation_multiplicity_mq_limit',['../classvg_1_1MultipathMapper.html#a2f61a2ded5875ca3e7bf656d2198522a',1,'vg::MultipathMapper']]],
+ ['try_5fload_5fbare_6208',['try_load_bare',['../classvg_1_1io_1_1VPKG.html#ad5d2bad9c95479a3f1520c5fadcba1b2',1,'vg::io::VPKG']]],
+ ['try_5fload_5fencapsulated_6209',['try_load_encapsulated',['../classvg_1_1io_1_1VPKG.html#a695e5a53bfbc9a5b36c5ea2306f253db',1,'vg::io::VPKG::try_load_encapsulated(istream &in)'],['../classvg_1_1io_1_1VPKG.html#a860f50291f4b5a6be232e5312eb884ab',1,'vg::io::VPKG::try_load_encapsulated(MessageIterator &it)']]],
+ ['try_5fload_5ffirst_6210',['try_load_first',['../classvg_1_1io_1_1VPKG.html#a58ed1c37748fed4b15d4e611659ce4c3',1,'vg::io::VPKG::try_load_first(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a504e965a2a019ce27267ea85c106a91b',1,'vg::io::VPKG::try_load_first(const string &filename)']]],
+ ['try_5fload_5ffirst_5fbare_6211',['try_load_first_bare',['../classvg_1_1io_1_1VPKG.html#acfc929254f523522f369c4a17c8f0941',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a2707edbb6b28a6623ea8ae11e607c861',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)']]],
+ ['try_5fload_5ffirst_5fencapsulated_6212',['try_load_first_encapsulated',['../classvg_1_1io_1_1VPKG.html#a12f9922d4b17194d248dc3f19a449f60',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a186f277ebf475632f1b4d1eac4c48139',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)']]],
+ ['try_5fload_5fone_6213',['try_load_one',['../classvg_1_1io_1_1VPKG.html#a0d7f96d4dd7fe5b1fe47b330ca617623',1,'vg::io::VPKG::try_load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#ab3a2026ac79ee1539271ba1791108c66',1,'vg::io::VPKG::try_load_one(const string &filename)']]],
+ ['tsvalignmentemitter_6214',['TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html',1,'vg::io::TSVAlignmentEmitter'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#aa8778347f51972fcb03f74565c5e3117',1,'vg::io::TSVAlignmentEmitter::TSVAlignmentEmitter()']]],
+ ['tsvexplainer_6215',['TSVExplainer',['../classvg_1_1TSVExplainer.html',1,'vg::TSVExplainer'],['../classvg_1_1TSVExplainer.html#a3a9d31e471d1808b30dfdc6c995660b4',1,'vg::TSVExplainer::TSVExplainer()']]],
+ ['tumor_5fsupports_6216',['tumor_supports',['../structvg_1_1BREAKPOINT.html#a66f75cad38b9fa5a3aab6b09b7a4ef8a',1,'vg::BREAKPOINT']]],
+ ['tv_5fpath_6217',['tv_path',['../classvg_1_1TargetValueSearch.html#a9ab66a82967803031203885c18291c6f',1,'vg::TargetValueSearch']]],
+ ['tv_5fpath_5fexists_6218',['tv_path_exists',['../classvg_1_1TargetValueSearch.html#a407607bcab4cfd14e283386bac418636',1,'vg::TargetValueSearch']]],
+ ['tv_5fpath_5flength_6219',['tv_path_length',['../classvg_1_1TargetValueSearch.html#a7dc599c6d4a317999890c81634d9ddf5',1,'vg::TargetValueSearch']]],
+ ['tv_5fphase2_6220',['tv_phase2',['../classvg_1_1TargetValueSearch.html#a794b8271df6bcf349db5e6d605402744',1,'vg::TargetValueSearch']]],
+ ['tvs_6221',['tvs',['../classvg_1_1TVSClusterer.html#ad59ad1a2a88d40a980a7b7fb2cc18a0d',1,'vg::TVSClusterer']]],
+ ['tvsclusterer_6222',['TVSClusterer',['../classvg_1_1TVSClusterer.html',1,'vg::TVSClusterer'],['../classvg_1_1TVSClusterer.html#a5b8fdb6006095094e85e6f760b8d0e3d',1,'vg::TVSClusterer::TVSClusterer()']]],
+ ['type_6223',['type',['../structvg_1_1Range.html#a5ea713fb16f3d49d94278914668503a9',1,'vg::Range::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html#ac5175c5d84e3de42bbf69d38196d8026',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...) const >::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html#aea61ef0da1a01e10576a705d6d1605ac',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...)>::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html#a579d806514cabd7b397ad5e0c1db94b4',1,'handlegraph::return_type_of< Returns(*)(Args...)>::type()'],['../structvg_1_1GFFRecord.html#a0cc4e99f9e73fafafa9be311151ef0d7',1,'vg::GFFRecord::type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a2710528f0d6c0e15f824b38963a9ffe6',1,'vg::Haplotypes::Subchain::type()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a22b9b6cfc7735eedf7a813234b606761',1,'vg::HaplotypePartitioner::Subchain::type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ad39deee97644fc66b6c0a2514db7622a',1,'vg::ZipCodeTree::tree_item_t::type()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af21cc2ebf18d65a28c08ef24db23eee1',1,'vg::ZipCodeForest::child_info_t::type()'],['../structReferenceInterval.html#af544c6bc00b6fc4653ba71e869bbc4a5',1,'ReferenceInterval::type()'],['../structvg_1_1Snarl.html#a9490890cd7fff85dc32a25cb58d471f6',1,'vg::Snarl::type()']]],
+ ['type_5fas_5fchar_6224',['type_as_char',['../structReferenceInterval.html#a9ae0102fab5146105642e388d6bef997',1,'ReferenceInterval']]],
+ ['type_5fto_5fbare_5floaders_6225',['type_to_bare_loaders',['../structvg_1_1io_1_1Registry_1_1Tables.html#a6330f82f362346c61bdb1607773e812a',1,'vg::io::Registry::Tables']]],
+ ['type_5fto_5fsaver_6226',['type_to_saver',['../structvg_1_1io_1_1Registry_1_1Tables.html#af3921832709101fdc87cfca00da3f2bf',1,'vg::io::Registry::Tables']]],
+ ['types_2ecpp_6227',['types.cpp',['../types_8cpp.html',1,'']]],
+ ['types_2ehpp_6228',['types.hpp',['../src_2types_8hpp.html',1,'(Global Namespace)'],['../deps_2libhandlegraph_2src_2include_2handlegraph_2types_8hpp.html',1,'(Global Namespace)']]]
];
diff --git a/search/all_15.js b/search/all_15.js
index c75be07adb..09d3557dd9 100644
--- a/search/all_15.js
+++ b/search/all_15.js
@@ -1,101 +1,101 @@
var searchData=
[
- ['uf_6227',['uf',['../classvg_1_1ContractingGraph.html#a0397c367ca4856e715fe3400b351d715',1,'vg::ContractingGraph']]],
- ['uf_5fhandle_6228',['uf_handle',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a84a5d20d03e165edd89bdddf7ccfa25f',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['uf_5frank_6229',['uf_rank',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a7d285e6a4baec754e89edd5338589f3e',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['ultrabubble_6230',['ULTRABUBBLE',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97aea6b4b85aa567a940c7434df2fcb56fb',1,'vg']]],
- ['unaligned_5fbands_6231',['unaligned_bands',['../classvg_1_1AlignmentChainModel.html#a86bcd77b21cc9b8b9c2b9f100fb9ce71',1,'vg::AlignmentChainModel']]],
- ['unaltered_5fmotif_5fdata_6232',['unaltered_motif_data',['../classvg_1_1SpliceStats.html#a8958ca644d2a270c59a67d2038ce85eb',1,'vg::SpliceStats']]],
- ['unary_6233',['UNARY',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a0e62c0ff8521d5960a5cc819a7bf7230',1,'vg']]],
- ['unary_5fboundaries_6234',['unary_boundaries',['../classvg_1_1NetGraph.html#ae573871a7c3cd0be507222751f870f72',1,'vg::NetGraph']]],
- ['unbacked_6235',['unbacked',['../structvg_1_1GBWTHandler.html#aed5e6775de6c9c96c78a752903a5a3ac',1,'vg::GBWTHandler']]],
- ['uncanonicalizable_5fsv_5fwarned_6236',['uncanonicalizable_sv_warned',['../classvg_1_1Constructor.html#ac7747658550e74b383a491a06e04ea99',1,'vg::Constructor']]],
- ['unchop_6237',['unchop',['../namespacehandlegraph_1_1algorithms.html#a407196811333767aa7f89b7ecc231564',1,'handlegraph::algorithms']]],
- ['unclassified_6238',['UNCLASSIFIED',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a7db3292851220acc20f75deebe0924ff',1,'vg']]],
- ['uncompressed_5fout_6239',['uncompressed_out',['../classvg_1_1io_1_1MessageEmitter.html#a19f6d714ad67ec55346998140ce79258',1,'vg::io::MessageEmitter']]],
- ['uncompressed_5fout_5fostream_6240',['uncompressed_out_ostream',['../classvg_1_1io_1_1MessageEmitter.html#aeb08e36bd3266eabc11d2d27e6336812',1,'vg::io::MessageEmitter']]],
- ['uncompressed_5fout_5fwritten_6241',['uncompressed_out_written',['../classvg_1_1io_1_1MessageEmitter.html#ae75aa23f1b6b85340f7bc586282e7c55',1,'vg::io::MessageEmitter']]],
- ['underflow_6242',['underflow',['../classvg_1_1io_1_1fdinbuf.html#a67ea7aab3e21cacec9fb836d4a70673e',1,'vg::io::fdinbuf::underflow()'],['../classvg_1_1io_1_1streaminbuf.html#afa7f9b8f4f3159d819b2c9a2eb6a05cb',1,'vg::io::streaminbuf::underflow()']]],
- ['underlying_5finterval_6243',['underlying_interval',['../classvg_1_1IncrementalSubgraph.html#ab6537f375ee27409fee46bd4dfdcb1a3',1,'vg::IncrementalSubgraph::underlying_interval()'],['../classvg_1_1JoinedSpliceGraph.html#ad9a0c6d572cb5052efa79e66d8cd29ab',1,'vg::JoinedSpliceGraph::underlying_interval()']]],
- ['undetermined_6244',['Undetermined',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda6fa550428b55152a0c55175786170a75',1,'vg::MultipathMapper']]],
- ['unescape_5fdelim_6245',['unescape_delim',['../classvg_1_1Packer.html#a32f8697cf4c222f5e207a4b15a1f0883',1,'vg::Packer']]],
- ['unescape_5fdelims_6246',['unescape_delims',['../classvg_1_1Packer.html#a92b44e965dd5da9da72e1a9196290d94',1,'vg::Packer']]],
- ['unfold_6247',['unfold',['../classvg_1_1PhaseUnfolder.html#a39a286ab3746a9a175a898bead3d2612',1,'vg::PhaseUnfolder::unfold()'],['../classvg_1_1VG.html#a6552b9da8cff82802ee24090064eb3a8',1,'vg::VG::unfold()']]],
- ['unfold_5fcomponent_6248',['unfold_component',['../classvg_1_1PhaseUnfolder.html#a84543fbc3521c9da70838339613ac3b9',1,'vg::PhaseUnfolder']]],
- ['unfold_5fmax_5flength_6249',['unfold_max_length',['../classvg_1_1Genotyper.html#ab3e4270419b361c9455125ca305709e2',1,'vg::Genotyper']]],
- ['uniform_5fint_5fdistribution_6250',['uniform_int_distribution',['../classvg_1_1uniform__int__distribution.html',1,'vg::uniform_int_distribution< T >'],['../classvg_1_1uniform__int__distribution.html#ab8d23ee7f2beacc01804f3206c3bc663',1,'vg::uniform_int_distribution::uniform_int_distribution()']]],
- ['uniform_5fint_5fdistribution_3c_20size_5ft_20_3e_6251',['uniform_int_distribution< size_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
- ['uniform_5fint_5fdistribution_3c_20uint8_5ft_20_3e_6252',['uniform_int_distribution< uint8_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
- ['uniform_5freal_5fdistribution_6253',['uniform_real_distribution',['../classvg_1_1uniform__real__distribution.html',1,'vg::uniform_real_distribution< T >'],['../classvg_1_1uniform__real__distribution.html#aaa8046adecf3b01e7e702df2e4fe3abd',1,'vg::uniform_real_distribution::uniform_real_distribution()']]],
- ['uniform_5freal_5fdistribution_3c_20double_20_3e_6254',['uniform_real_distribution< double >',['../classvg_1_1uniform__real__distribution.html',1,'vg']]],
- ['unindex_5fedge_5fby_5fnode_5fsides_6255',['unindex_edge_by_node_sides',['../classvg_1_1VG.html#a1c0b7db8d3043747e8b9a44cba4eaac9',1,'vg::VG::unindex_edge_by_node_sides(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a5677da9ff22052f6c6a85bfe66e1256d',1,'vg::VG::unindex_edge_by_node_sides(Edge *edge)']]],
- ['union_5ffind_6256',['union_find',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a6bcd65e92edd9e1bf925a9e4a8c7cc01',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['union_5fgroups_6257',['union_groups',['../classvg_1_1SparseUnionFind.html#ac3fdf36c05a3145bc8c309d4ec3bd2d6',1,'vg::SparseUnionFind']]],
- ['unique_5fminimizers_6258',['unique_minimizers',['../classvg_1_1HaplotypePartitioner.html#a16638525e7b8ceca27c326af457519b6',1,'vg::HaplotypePartitioner::unique_minimizers(gbwt::size_type sequence_id) const'],['../classvg_1_1HaplotypePartitioner.html#aa846481b6e9014761d65a430179e5d80',1,'vg::HaplotypePartitioner::unique_minimizers(sequence_type sequence, Subchain subchain) const']]],
- ['uniqueness_6259',['uniqueness',['../structvg_1_1Alignment.html#a2d744ce39b375cdeb8adfc3721a18eb0',1,'vg::Alignment']]],
- ['universe_5fsize_6260',['universe_size',['../classvg_1_1SmallBitset.html#aa8dbf9601e90ce99f26895d8a4d79de0',1,'vg::SmallBitset']]],
- ['unlocalized_5finsertion_6261',['unlocalized_insertion',['../structvg_1_1WFAAlignment.html#a5f48d4dc6b6001b37549054ad20b9b47',1,'vg::WFAAlignment']]],
- ['unlock_6262',['unlock',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1cfc8d66ced1ef3d435f99579ac44ca6',1,'vg::GraphSynchronizer::Lock']]],
- ['unmapped_6263',['unmapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aa653bbbb9be3aa57e63377efbf2122bb',1,'vg::Counts']]],
- ['unmapped_5ffilter_6264',['unmapped_filter',['../classvg_1_1Filter.html#a3a02d37cb7cf0b042aa5933186a76061',1,'vg::Filter']]],
- ['unoriented_5fdistance_5fbetween_6265',['unoriented_distance_between',['../classvg_1_1MinimizerMapper.html#a6fc70b73ed8c2aa3505a483b074671b8',1,'vg::MinimizerMapper']]],
- ['unoriented_5fmotif_6266',['unoriented_motif',['../classvg_1_1SpliceStats.html#aaeeab4dee70e8e231fa92646267ccbff',1,'vg::SpliceStats']]],
- ['unpack_5fbit_6267',['unpack_bit',['../structhandlegraph_1_1number__bool__packing.html#a52f57c83e66ad6f09b519dff55be71d9',1,'handlegraph::number_bool_packing']]],
- ['unpack_5fchain_5fcode_6268',['unpack_chain_code',['../classvg_1_1ZipCode.html#a66e91c21e0b8a818b6de6a620ee0bdf5',1,'vg::ZipCode']]],
- ['unpack_5fnode_5fcode_6269',['unpack_node_code',['../classvg_1_1ZipCode.html#a7e7cd0b16ad1b9ac447b6eb0458f289d',1,'vg::ZipCode']]],
- ['unpack_5fnumber_6270',['unpack_number',['../structhandlegraph_1_1number__bool__packing.html#a5f2f610bc0e6819ff0ae3d91d2aff9fc',1,'handlegraph::number_bool_packing']]],
- ['unpack_5fsnarl_5fcode_6271',['unpack_snarl_code',['../classvg_1_1ZipCode.html#a4b76c5d63d72f9938352327e6d7b06c0',1,'vg::ZipCode']]],
- ['unpaired_5ffor_5feach_5fparallel_6272',['unpaired_for_each_parallel',['../namespacevg_1_1io.html#ac3daebbee97f2451b25aec3c642c06c8',1,'vg::io']]],
- ['unpaired_5fpenalty_6273',['unpaired_penalty',['../classvg_1_1BaseMapper.html#ad20ea9a68bcaca157350595f03b4601c',1,'vg::BaseMapper']]],
- ['unparse_6274',['unparse',['../classvg_1_1OptionValueParser.html#a816cf0ccd1d8b95f6f8f47434e1af376',1,'vg::OptionValueParser::unparse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a57f771079219ffb85ea0cebc6b024045',1,'vg::OptionValueParser< vector< Item > >::unparse()'],['../classvg_1_1OptionValueParser.html#aa72adfa088347d83a7019da414c4b8a7',1,'vg::OptionValueParser::unparse()']]],
- ['unrecord_6275',['unrecord',['../classvg_1_1SnarlManager.html#a40be4db13bf881c882f3be70c067c111',1,'vg::SnarlManager::unrecord(const SnarlRecord *record) const'],['../classvg_1_1SnarlManager.html#aeeb8bf1eb342004f69b33caadad5a713',1,'vg::SnarlManager::unrecord(SnarlRecord *record)']]],
- ['unreverse_5fgraph_6276',['unreverse_graph',['../classvg_1_1GSSWAligner.html#aeb2785609201c50f8e7addde7eeddb0a',1,'vg::GSSWAligner']]],
- ['unreverse_5fgraph_5fmapping_6277',['unreverse_graph_mapping',['../classvg_1_1GSSWAligner.html#aa00b750624c67e2cfa4d98193acf8dd9',1,'vg::GSSWAligner']]],
- ['unset_6278',['unset',['../classvg_1_1algorithms_1_1TracedScore.html#a5ba55d94d11446319300052e02df1b23',1,'vg::algorithms::TracedScore']]],
- ['unstranded_6279',['unstranded',['../classvg_1_1OrientedDistanceClusterer.html#a34e43333ce3f5294f28b3cadc18c54ac',1,'vg::OrientedDistanceClusterer']]],
- ['untangle_5fallele_5ftraversals_6280',['untangle_allele_traversals',['../classvg_1_1Deconstructor.html#a3be6aea7084e6875585939a3cd40476e',1,'vg::Deconstructor']]],
- ['update_6281',['update',['../structvg_1_1WFANode.html#a3ca9cee0c921c093c9c9b88506f1e58a',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, const MatchPos &pos)'],['../structvg_1_1WFANode.html#a8577faa0410e723fa6c5a2de7f4e452c',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, uint32_t seq_offset, uint32_t node_offset)']]],
- ['update_5fdiagonal_5frange_6282',['update_diagonal_range',['../classvg_1_1WFATree.html#a923bbbd53962ce4121989e66291afa5a',1,'vg::WFATree']]],
- ['update_5fhaplotype_5findex_6283',['update_haplotype_index',['../classvg_1_1Transcriptome.html#a5b33f790ea79988af1d05ba0b1fd1cea',1,'vg::Transcriptome']]],
- ['update_5fin_5fout_5fedges_6284',['update_in_out_edges',['../classvg_1_1FlowSort.html#a09b6782a1ab4d5c5ed7fa23cf83083d8',1,'vg::FlowSort']]],
- ['update_5finner_5fvalues_6285',['update_inner_values',['../structhaplo_1_1haplo__DP__column.html#ae5860a155f8e49360b2fb2289e2555b8',1,'haplo::haplo_DP_column']]],
- ['update_5fintron_5flength_5fdistribution_6286',['update_intron_length_distribution',['../classvg_1_1SpliceStats.html#a984c94dae240b73a92d40f4d36d39fb6',1,'vg::SpliceStats']]],
- ['update_5fmapping_5fpositions_6287',['update_mapping_positions',['../structvg_1_1PathIndex.html#a783b7aafb86a509a3434c10b5ae9355f',1,'vg::PathIndex']]],
- ['update_5fmotifs_6288',['update_motifs',['../classvg_1_1SpliceStats.html#a26085c886cc27966f45c239fb13e0136',1,'vg::SpliceStats']]],
- ['update_5fnesting_5finfo_5ftags_6289',['update_nesting_info_tags',['../classvg_1_1VCFOutputCaller.html#a131c6d35d0722a64bd18b4a646efac5a',1,'vg::VCFOutputCaller']]],
- ['update_5fpath_5findexes_6290',['update_path_indexes',['../classvg_1_1GraphSynchronizer.html#a056cd54145b467de24d6ce128749af27',1,'vg::GraphSynchronizer']]],
- ['update_5fprogress_6291',['update_progress',['../classvg_1_1Progressive.html#a0d64e6aa69bc094c163f4827602a302c',1,'vg::Progressive']]],
- ['update_5fscore_5fvector_6292',['update_score_vector',['../structhaplo_1_1haplo__DP__column.html#a40859e4ede0d3829b5e7dca9a89af660',1,'haplo::haplo_DP_column']]],
- ['update_5fscoring_6293',['update_scoring',['../classvg_1_1SpliceStats.html#a23dd768b9e57750de42c5f88a2b2d8d4',1,'vg::SpliceStats']]],
- ['update_5fstate_6294',['update_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#afb76a0ce92c750ae8cb12eaf2c0ae7fd',1,'vg::BandedGlobalAligner::BABuilder::update_state()'],['../classvg_1_1DinucleotideMachine.html#a9b246cec10b2a7e45ed7f3a3261427e5',1,'vg::DinucleotideMachine::update_state()']]],
- ['update_5ftranscript_5fpaths_6295',['update_transcript_paths',['../classvg_1_1Transcriptome.html#a9f55d0f16470ee2750fe09986c85b464',1,'vg::Transcriptome']]],
- ['update_5fvcf_5fheader_6296',['update_vcf_header',['../classvg_1_1SnarlCaller.html#a7fb3205d6e94505aadf0c9944fac7eb4',1,'vg::SnarlCaller::update_vcf_header()'],['../classvg_1_1RatioSupportSnarlCaller.html#ac7a153c3c35bc7d314f69f8ccbc30ae1',1,'vg::RatioSupportSnarlCaller::update_vcf_header()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a2872f6728e288de01d5403fcdb76a05b',1,'vg::PoissonSupportSnarlCaller::update_vcf_header()']]],
- ['update_5fvcf_5finfo_6297',['update_vcf_info',['../classvg_1_1MCMCCaller.html#a8deeb18605436556136403261715155e',1,'vg::MCMCCaller::update_vcf_info()'],['../classvg_1_1SnarlCaller.html#a5098383d371e037c79e4c278e3fbbea1',1,'vg::SnarlCaller::update_vcf_info()'],['../classvg_1_1SupportBasedSnarlCaller.html#a3ddd1e17537734b984fa0befe9f0d7f6',1,'vg::SupportBasedSnarlCaller::update_vcf_info()'],['../classvg_1_1RatioSupportSnarlCaller.html#a3dc6a3524e755fba03211f0f0dd3483f',1,'vg::RatioSupportSnarlCaller::update_vcf_info()'],['../classvg_1_1PoissonSupportSnarlCaller.html#abe1990823417defcd0c6f68132680db1',1,'vg::PoissonSupportSnarlCaller::update_vcf_info()']]],
- ['upper_5fbound_6298',['upper_bound',['../structvg_1_1BREAKPOINT.html#add7be6a634fda8c98ff9627ecd454683',1,'vg::BREAKPOINT']]],
- ['upper_5fbound_5fheuristic_6299',['upper_bound_heuristic',['../classvg_1_1TargetValueSearch.html#ac3930066893407bf6fd3e57a717bba0c',1,'vg::TargetValueSearch']]],
- ['usable_5fbits_6300',['USABLE_BITS',['../structvg_1_1varint__vector__t.html#a86e608e634d04476754226a796122066',1,'vg::varint_vector_t']]],
- ['use_6301',['use',['../structvg_1_1GBWTHandler.html#a8062238f984f4c521cef46cfc2961626',1,'vg::GBWTHandler::use(gbwt::GBWT &new_index)'],['../structvg_1_1GBWTHandler.html#a574972e799a708837a0e2e481926f87a',1,'vg::GBWTHandler::use(gbwt::DynamicGBWT &new_index)'],['../structGraphHandler.html#a4ccfddaf318c987155ab13de16dcfc2c',1,'GraphHandler::use()']]],
- ['use_5fapprox_5fsub_5fmem_5fcount_6302',['use_approx_sub_mem_count',['../classvg_1_1BaseMapper.html#abf1a0a71b2bcc7763690fed623383fb3',1,'vg::BaseMapper']]],
- ['use_5favg_6303',['use_avg',['../classvg_1_1Filter.html#a271fe98c839b17295ecef0dc54cb7d7e',1,'vg::Filter']]],
- ['use_5fbounded_5fsyncmers_6304',['use_bounded_syncmers',['../structvg_1_1IndexingParameters.html#ae034b19e5a2e71bccc1bf35addbe0b45',1,'vg::IndexingParameters']]],
- ['use_5fcluster_5fmq_6305',['use_cluster_mq',['../classvg_1_1Mapper.html#a2c4c837c39fa708de934f5c24c3c371e',1,'vg::Mapper']]],
- ['use_5fcompressed_6306',['use_compressed',['../structvg_1_1GBWTHandler.html#a40007a32d020290a72aaef0e830454c4',1,'vg::GBWTHandler']]],
- ['use_5fdynamic_6307',['use_dynamic',['../structvg_1_1GBWTHandler.html#a88de75253b3b9b54e844d0a20ff9a5c7',1,'vg::GBWTHandler']]],
- ['use_5fexplored_5fcap_6308',['use_explored_cap',['../classvg_1_1MinimizerMapper.html#a84b734b0d1be3a5015eb92f8c331b6f3',1,'vg::MinimizerMapper']]],
- ['use_5ffanout_5fmatch_5falg_6309',['use_fanout_match_alg',['../classvg_1_1MultipathMapper.html#ac02b5155c59ad4603f0cc633b2dfad8a',1,'vg::MultipathMapper']]],
- ['use_5fgreedy_5fmem_5frestarts_6310',['use_greedy_mem_restarts',['../classvg_1_1BaseMapper.html#ad95c004337db9d7de612c3cffe4f90f8',1,'vg::BaseMapper']]],
- ['use_5finternal_5fconnectivity_6311',['use_internal_connectivity',['../classvg_1_1NetGraph.html#a57dedbbe009595f748dc3c4deae2dc72',1,'vg::NetGraph']]],
- ['use_5fmapq_6312',['use_mapq',['../classvg_1_1Genotyper.html#a5991ce66cc2a9ea45bd27d288dd7d9b8',1,'vg::Genotyper::use_mapq()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a0588ea9ea69bf3c4c3f9108549e6102b',1,'vg::PoissonSupportSnarlCaller::use_mapq()']]],
- ['use_5fmin_5fdist_5fclusterer_6313',['use_min_dist_clusterer',['../classvg_1_1MultipathMapper.html#aed5898444e134f0fb95ae527d215e88f',1,'vg::MultipathMapper']]],
- ['use_5for_5fsave_6314',['use_or_save',['../gbwt__main_8cpp.html#ab82463d53fb85eaec6c4e581e009d9e6',1,'gbwt_main.cpp']]],
- ['use_5fpessimistic_5ftail_5falignment_6315',['use_pessimistic_tail_alignment',['../classvg_1_1MultipathMapper.html#a552098fc2ac26aa17929d31f7a0f1ecd',1,'vg::MultipathMapper']]],
- ['use_5fpopulation_5fmapqs_6316',['use_population_mapqs',['../classvg_1_1MultipathMapper.html#aaaecbb0881e444042662a72907442fc1',1,'vg::MultipathMapper']]],
- ['use_5fpreset_6317',['use_preset',['../gbwt__main_8cpp.html#ad246795d44cf23172412ae1c6a7a86e6',1,'gbwt_main.cpp']]],
- ['use_5fstripped_5fmatch_5falg_6318',['use_stripped_match_alg',['../classvg_1_1MultipathMapper.html#ac9ea306291983b4c10ff1ec97b6d1adc',1,'vg::MultipathMapper']]],
- ['use_5ftvs_5fclusterer_6319',['use_tvs_clusterer',['../classvg_1_1MultipathMapper.html#afaa33d747ce1393304aa96bc5245a4f8',1,'vg::MultipathMapper']]],
- ['used_5fbins_5fof_5frange_6320',['used_bins_of_range',['../classvg_1_1StreamIndexBase.html#a94777b19236dfb74d66ba8c484bf663f',1,'vg::StreamIndexBase']]],
- ['uses_5fus_6321',['uses_Us',['../namespacevg.html#acd966c42f332957a1b9317faa3d26407',1,'vg']]],
- ['util_2ehpp_6322',['util.hpp',['../util_8hpp.html',1,'']]],
- ['utility_2ecpp_6323',['utility.cpp',['../utility_8cpp.html',1,'']]],
- ['utility_2ehpp_6324',['utility.hpp',['../utility_8hpp.html',1,'']]]
+ ['uf_6229',['uf',['../classvg_1_1ContractingGraph.html#a0397c367ca4856e715fe3400b351d715',1,'vg::ContractingGraph']]],
+ ['uf_5fhandle_6230',['uf_handle',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a84a5d20d03e165edd89bdddf7ccfa25f',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['uf_5frank_6231',['uf_rank',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a7d285e6a4baec754e89edd5338589f3e',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['ultrabubble_6232',['ULTRABUBBLE',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97aea6b4b85aa567a940c7434df2fcb56fb',1,'vg']]],
+ ['unaligned_5fbands_6233',['unaligned_bands',['../classvg_1_1AlignmentChainModel.html#a86bcd77b21cc9b8b9c2b9f100fb9ce71',1,'vg::AlignmentChainModel']]],
+ ['unaltered_5fmotif_5fdata_6234',['unaltered_motif_data',['../classvg_1_1SpliceStats.html#a8958ca644d2a270c59a67d2038ce85eb',1,'vg::SpliceStats']]],
+ ['unary_6235',['UNARY',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a0e62c0ff8521d5960a5cc819a7bf7230',1,'vg']]],
+ ['unary_5fboundaries_6236',['unary_boundaries',['../classvg_1_1NetGraph.html#ae573871a7c3cd0be507222751f870f72',1,'vg::NetGraph']]],
+ ['unbacked_6237',['unbacked',['../structvg_1_1GBWTHandler.html#aed5e6775de6c9c96c78a752903a5a3ac',1,'vg::GBWTHandler']]],
+ ['uncanonicalizable_5fsv_5fwarned_6238',['uncanonicalizable_sv_warned',['../classvg_1_1Constructor.html#ac7747658550e74b383a491a06e04ea99',1,'vg::Constructor']]],
+ ['unchop_6239',['unchop',['../namespacehandlegraph_1_1algorithms.html#a407196811333767aa7f89b7ecc231564',1,'handlegraph::algorithms']]],
+ ['unclassified_6240',['UNCLASSIFIED',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a7db3292851220acc20f75deebe0924ff',1,'vg']]],
+ ['uncompressed_5fout_6241',['uncompressed_out',['../classvg_1_1io_1_1MessageEmitter.html#a19f6d714ad67ec55346998140ce79258',1,'vg::io::MessageEmitter']]],
+ ['uncompressed_5fout_5fostream_6242',['uncompressed_out_ostream',['../classvg_1_1io_1_1MessageEmitter.html#aeb08e36bd3266eabc11d2d27e6336812',1,'vg::io::MessageEmitter']]],
+ ['uncompressed_5fout_5fwritten_6243',['uncompressed_out_written',['../classvg_1_1io_1_1MessageEmitter.html#ae75aa23f1b6b85340f7bc586282e7c55',1,'vg::io::MessageEmitter']]],
+ ['underflow_6244',['underflow',['../classvg_1_1io_1_1fdinbuf.html#a67ea7aab3e21cacec9fb836d4a70673e',1,'vg::io::fdinbuf::underflow()'],['../classvg_1_1io_1_1streaminbuf.html#afa7f9b8f4f3159d819b2c9a2eb6a05cb',1,'vg::io::streaminbuf::underflow()']]],
+ ['underlying_5finterval_6245',['underlying_interval',['../classvg_1_1IncrementalSubgraph.html#ab6537f375ee27409fee46bd4dfdcb1a3',1,'vg::IncrementalSubgraph::underlying_interval()'],['../classvg_1_1JoinedSpliceGraph.html#ad9a0c6d572cb5052efa79e66d8cd29ab',1,'vg::JoinedSpliceGraph::underlying_interval()']]],
+ ['undetermined_6246',['Undetermined',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda6fa550428b55152a0c55175786170a75',1,'vg::MultipathMapper']]],
+ ['unescape_5fdelim_6247',['unescape_delim',['../classvg_1_1Packer.html#a32f8697cf4c222f5e207a4b15a1f0883',1,'vg::Packer']]],
+ ['unescape_5fdelims_6248',['unescape_delims',['../classvg_1_1Packer.html#a92b44e965dd5da9da72e1a9196290d94',1,'vg::Packer']]],
+ ['unfold_6249',['unfold',['../classvg_1_1PhaseUnfolder.html#a39a286ab3746a9a175a898bead3d2612',1,'vg::PhaseUnfolder::unfold()'],['../classvg_1_1VG.html#a6552b9da8cff82802ee24090064eb3a8',1,'vg::VG::unfold()']]],
+ ['unfold_5fcomponent_6250',['unfold_component',['../classvg_1_1PhaseUnfolder.html#a84543fbc3521c9da70838339613ac3b9',1,'vg::PhaseUnfolder']]],
+ ['unfold_5fmax_5flength_6251',['unfold_max_length',['../classvg_1_1Genotyper.html#ab3e4270419b361c9455125ca305709e2',1,'vg::Genotyper']]],
+ ['uniform_5fint_5fdistribution_6252',['uniform_int_distribution',['../classvg_1_1uniform__int__distribution.html',1,'vg::uniform_int_distribution< T >'],['../classvg_1_1uniform__int__distribution.html#ab8d23ee7f2beacc01804f3206c3bc663',1,'vg::uniform_int_distribution::uniform_int_distribution()']]],
+ ['uniform_5fint_5fdistribution_3c_20size_5ft_20_3e_6253',['uniform_int_distribution< size_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
+ ['uniform_5fint_5fdistribution_3c_20uint8_5ft_20_3e_6254',['uniform_int_distribution< uint8_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
+ ['uniform_5freal_5fdistribution_6255',['uniform_real_distribution',['../classvg_1_1uniform__real__distribution.html',1,'vg::uniform_real_distribution< T >'],['../classvg_1_1uniform__real__distribution.html#aaa8046adecf3b01e7e702df2e4fe3abd',1,'vg::uniform_real_distribution::uniform_real_distribution()']]],
+ ['uniform_5freal_5fdistribution_3c_20double_20_3e_6256',['uniform_real_distribution< double >',['../classvg_1_1uniform__real__distribution.html',1,'vg']]],
+ ['unindex_5fedge_5fby_5fnode_5fsides_6257',['unindex_edge_by_node_sides',['../classvg_1_1VG.html#a1c0b7db8d3043747e8b9a44cba4eaac9',1,'vg::VG::unindex_edge_by_node_sides(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a5677da9ff22052f6c6a85bfe66e1256d',1,'vg::VG::unindex_edge_by_node_sides(Edge *edge)']]],
+ ['union_5ffind_6258',['union_find',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a6bcd65e92edd9e1bf925a9e4a8c7cc01',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['union_5fgroups_6259',['union_groups',['../classvg_1_1SparseUnionFind.html#ac3fdf36c05a3145bc8c309d4ec3bd2d6',1,'vg::SparseUnionFind']]],
+ ['unique_5fminimizers_6260',['unique_minimizers',['../classvg_1_1HaplotypePartitioner.html#a16638525e7b8ceca27c326af457519b6',1,'vg::HaplotypePartitioner::unique_minimizers(gbwt::size_type sequence_id) const'],['../classvg_1_1HaplotypePartitioner.html#aa846481b6e9014761d65a430179e5d80',1,'vg::HaplotypePartitioner::unique_minimizers(sequence_type sequence, Subchain subchain) const']]],
+ ['uniqueness_6261',['uniqueness',['../structvg_1_1Alignment.html#a2d744ce39b375cdeb8adfc3721a18eb0',1,'vg::Alignment']]],
+ ['universe_5fsize_6262',['universe_size',['../classvg_1_1SmallBitset.html#aa8dbf9601e90ce99f26895d8a4d79de0',1,'vg::SmallBitset']]],
+ ['unlocalized_5finsertion_6263',['unlocalized_insertion',['../structvg_1_1WFAAlignment.html#a5f48d4dc6b6001b37549054ad20b9b47',1,'vg::WFAAlignment']]],
+ ['unlock_6264',['unlock',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1cfc8d66ced1ef3d435f99579ac44ca6',1,'vg::GraphSynchronizer::Lock']]],
+ ['unmapped_6265',['unmapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aa653bbbb9be3aa57e63377efbf2122bb',1,'vg::Counts']]],
+ ['unmapped_5ffilter_6266',['unmapped_filter',['../classvg_1_1Filter.html#a3a02d37cb7cf0b042aa5933186a76061',1,'vg::Filter']]],
+ ['unoriented_5fdistance_5fbetween_6267',['unoriented_distance_between',['../classvg_1_1MinimizerMapper.html#a6fc70b73ed8c2aa3505a483b074671b8',1,'vg::MinimizerMapper']]],
+ ['unoriented_5fmotif_6268',['unoriented_motif',['../classvg_1_1SpliceStats.html#aaeeab4dee70e8e231fa92646267ccbff',1,'vg::SpliceStats']]],
+ ['unpack_5fbit_6269',['unpack_bit',['../structhandlegraph_1_1number__bool__packing.html#a52f57c83e66ad6f09b519dff55be71d9',1,'handlegraph::number_bool_packing']]],
+ ['unpack_5fchain_5fcode_6270',['unpack_chain_code',['../classvg_1_1ZipCode.html#a66e91c21e0b8a818b6de6a620ee0bdf5',1,'vg::ZipCode']]],
+ ['unpack_5fnode_5fcode_6271',['unpack_node_code',['../classvg_1_1ZipCode.html#a7e7cd0b16ad1b9ac447b6eb0458f289d',1,'vg::ZipCode']]],
+ ['unpack_5fnumber_6272',['unpack_number',['../structhandlegraph_1_1number__bool__packing.html#a5f2f610bc0e6819ff0ae3d91d2aff9fc',1,'handlegraph::number_bool_packing']]],
+ ['unpack_5fsnarl_5fcode_6273',['unpack_snarl_code',['../classvg_1_1ZipCode.html#a4b76c5d63d72f9938352327e6d7b06c0',1,'vg::ZipCode']]],
+ ['unpaired_5ffor_5feach_5fparallel_6274',['unpaired_for_each_parallel',['../namespacevg_1_1io.html#ac3daebbee97f2451b25aec3c642c06c8',1,'vg::io']]],
+ ['unpaired_5fpenalty_6275',['unpaired_penalty',['../classvg_1_1BaseMapper.html#ad20ea9a68bcaca157350595f03b4601c',1,'vg::BaseMapper']]],
+ ['unparse_6276',['unparse',['../classvg_1_1OptionValueParser.html#a816cf0ccd1d8b95f6f8f47434e1af376',1,'vg::OptionValueParser::unparse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a57f771079219ffb85ea0cebc6b024045',1,'vg::OptionValueParser< vector< Item > >::unparse()'],['../classvg_1_1OptionValueParser.html#aa72adfa088347d83a7019da414c4b8a7',1,'vg::OptionValueParser::unparse()']]],
+ ['unrecord_6277',['unrecord',['../classvg_1_1SnarlManager.html#a40be4db13bf881c882f3be70c067c111',1,'vg::SnarlManager::unrecord(const SnarlRecord *record) const'],['../classvg_1_1SnarlManager.html#aeeb8bf1eb342004f69b33caadad5a713',1,'vg::SnarlManager::unrecord(SnarlRecord *record)']]],
+ ['unreverse_5fgraph_6278',['unreverse_graph',['../classvg_1_1GSSWAligner.html#aeb2785609201c50f8e7addde7eeddb0a',1,'vg::GSSWAligner']]],
+ ['unreverse_5fgraph_5fmapping_6279',['unreverse_graph_mapping',['../classvg_1_1GSSWAligner.html#aa00b750624c67e2cfa4d98193acf8dd9',1,'vg::GSSWAligner']]],
+ ['unset_6280',['unset',['../classvg_1_1algorithms_1_1TracedScore.html#a5ba55d94d11446319300052e02df1b23',1,'vg::algorithms::TracedScore']]],
+ ['unstranded_6281',['unstranded',['../classvg_1_1OrientedDistanceClusterer.html#a34e43333ce3f5294f28b3cadc18c54ac',1,'vg::OrientedDistanceClusterer']]],
+ ['untangle_5fallele_5ftraversals_6282',['untangle_allele_traversals',['../classvg_1_1Deconstructor.html#a3be6aea7084e6875585939a3cd40476e',1,'vg::Deconstructor']]],
+ ['update_6283',['update',['../structvg_1_1WFANode.html#a3ca9cee0c921c093c9c9b88506f1e58a',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, const MatchPos &pos)'],['../structvg_1_1WFANode.html#a8577faa0410e723fa6c5a2de7f4e452c',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, uint32_t seq_offset, uint32_t node_offset)']]],
+ ['update_5fdiagonal_5frange_6284',['update_diagonal_range',['../classvg_1_1WFATree.html#a923bbbd53962ce4121989e66291afa5a',1,'vg::WFATree']]],
+ ['update_5fhaplotype_5findex_6285',['update_haplotype_index',['../classvg_1_1Transcriptome.html#a5b33f790ea79988af1d05ba0b1fd1cea',1,'vg::Transcriptome']]],
+ ['update_5fin_5fout_5fedges_6286',['update_in_out_edges',['../classvg_1_1FlowSort.html#a09b6782a1ab4d5c5ed7fa23cf83083d8',1,'vg::FlowSort']]],
+ ['update_5finner_5fvalues_6287',['update_inner_values',['../structhaplo_1_1haplo__DP__column.html#ae5860a155f8e49360b2fb2289e2555b8',1,'haplo::haplo_DP_column']]],
+ ['update_5fintron_5flength_5fdistribution_6288',['update_intron_length_distribution',['../classvg_1_1SpliceStats.html#a984c94dae240b73a92d40f4d36d39fb6',1,'vg::SpliceStats']]],
+ ['update_5fmapping_5fpositions_6289',['update_mapping_positions',['../structvg_1_1PathIndex.html#a783b7aafb86a509a3434c10b5ae9355f',1,'vg::PathIndex']]],
+ ['update_5fmotifs_6290',['update_motifs',['../classvg_1_1SpliceStats.html#a26085c886cc27966f45c239fb13e0136',1,'vg::SpliceStats']]],
+ ['update_5fnesting_5finfo_5ftags_6291',['update_nesting_info_tags',['../classvg_1_1VCFOutputCaller.html#a131c6d35d0722a64bd18b4a646efac5a',1,'vg::VCFOutputCaller']]],
+ ['update_5fpath_5findexes_6292',['update_path_indexes',['../classvg_1_1GraphSynchronizer.html#a056cd54145b467de24d6ce128749af27',1,'vg::GraphSynchronizer']]],
+ ['update_5fprogress_6293',['update_progress',['../classvg_1_1Progressive.html#a0d64e6aa69bc094c163f4827602a302c',1,'vg::Progressive']]],
+ ['update_5fscore_5fvector_6294',['update_score_vector',['../structhaplo_1_1haplo__DP__column.html#a40859e4ede0d3829b5e7dca9a89af660',1,'haplo::haplo_DP_column']]],
+ ['update_5fscoring_6295',['update_scoring',['../classvg_1_1SpliceStats.html#a23dd768b9e57750de42c5f88a2b2d8d4',1,'vg::SpliceStats']]],
+ ['update_5fstate_6296',['update_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#afb76a0ce92c750ae8cb12eaf2c0ae7fd',1,'vg::BandedGlobalAligner::BABuilder::update_state()'],['../classvg_1_1DinucleotideMachine.html#a9b246cec10b2a7e45ed7f3a3261427e5',1,'vg::DinucleotideMachine::update_state()']]],
+ ['update_5ftranscript_5fpaths_6297',['update_transcript_paths',['../classvg_1_1Transcriptome.html#a9f55d0f16470ee2750fe09986c85b464',1,'vg::Transcriptome']]],
+ ['update_5fvcf_5fheader_6298',['update_vcf_header',['../classvg_1_1SnarlCaller.html#a7fb3205d6e94505aadf0c9944fac7eb4',1,'vg::SnarlCaller::update_vcf_header()'],['../classvg_1_1RatioSupportSnarlCaller.html#ac7a153c3c35bc7d314f69f8ccbc30ae1',1,'vg::RatioSupportSnarlCaller::update_vcf_header()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a2872f6728e288de01d5403fcdb76a05b',1,'vg::PoissonSupportSnarlCaller::update_vcf_header()']]],
+ ['update_5fvcf_5finfo_6299',['update_vcf_info',['../classvg_1_1MCMCCaller.html#a8deeb18605436556136403261715155e',1,'vg::MCMCCaller::update_vcf_info()'],['../classvg_1_1SnarlCaller.html#a5098383d371e037c79e4c278e3fbbea1',1,'vg::SnarlCaller::update_vcf_info()'],['../classvg_1_1SupportBasedSnarlCaller.html#a3ddd1e17537734b984fa0befe9f0d7f6',1,'vg::SupportBasedSnarlCaller::update_vcf_info()'],['../classvg_1_1RatioSupportSnarlCaller.html#a3dc6a3524e755fba03211f0f0dd3483f',1,'vg::RatioSupportSnarlCaller::update_vcf_info()'],['../classvg_1_1PoissonSupportSnarlCaller.html#abe1990823417defcd0c6f68132680db1',1,'vg::PoissonSupportSnarlCaller::update_vcf_info()']]],
+ ['upper_5fbound_6300',['upper_bound',['../structvg_1_1BREAKPOINT.html#add7be6a634fda8c98ff9627ecd454683',1,'vg::BREAKPOINT']]],
+ ['upper_5fbound_5fheuristic_6301',['upper_bound_heuristic',['../classvg_1_1TargetValueSearch.html#ac3930066893407bf6fd3e57a717bba0c',1,'vg::TargetValueSearch']]],
+ ['usable_5fbits_6302',['USABLE_BITS',['../structvg_1_1varint__vector__t.html#a86e608e634d04476754226a796122066',1,'vg::varint_vector_t']]],
+ ['use_6303',['use',['../structvg_1_1GBWTHandler.html#a8062238f984f4c521cef46cfc2961626',1,'vg::GBWTHandler::use(gbwt::GBWT &new_index)'],['../structvg_1_1GBWTHandler.html#a574972e799a708837a0e2e481926f87a',1,'vg::GBWTHandler::use(gbwt::DynamicGBWT &new_index)'],['../structGraphHandler.html#a4ccfddaf318c987155ab13de16dcfc2c',1,'GraphHandler::use()']]],
+ ['use_5fapprox_5fsub_5fmem_5fcount_6304',['use_approx_sub_mem_count',['../classvg_1_1BaseMapper.html#abf1a0a71b2bcc7763690fed623383fb3',1,'vg::BaseMapper']]],
+ ['use_5favg_6305',['use_avg',['../classvg_1_1Filter.html#a271fe98c839b17295ecef0dc54cb7d7e',1,'vg::Filter']]],
+ ['use_5fbounded_5fsyncmers_6306',['use_bounded_syncmers',['../structvg_1_1IndexingParameters.html#ae034b19e5a2e71bccc1bf35addbe0b45',1,'vg::IndexingParameters']]],
+ ['use_5fcluster_5fmq_6307',['use_cluster_mq',['../classvg_1_1Mapper.html#a2c4c837c39fa708de934f5c24c3c371e',1,'vg::Mapper']]],
+ ['use_5fcompressed_6308',['use_compressed',['../structvg_1_1GBWTHandler.html#a40007a32d020290a72aaef0e830454c4',1,'vg::GBWTHandler']]],
+ ['use_5fdynamic_6309',['use_dynamic',['../structvg_1_1GBWTHandler.html#a88de75253b3b9b54e844d0a20ff9a5c7',1,'vg::GBWTHandler']]],
+ ['use_5fexplored_5fcap_6310',['use_explored_cap',['../classvg_1_1MinimizerMapper.html#a84b734b0d1be3a5015eb92f8c331b6f3',1,'vg::MinimizerMapper']]],
+ ['use_5ffanout_5fmatch_5falg_6311',['use_fanout_match_alg',['../classvg_1_1MultipathMapper.html#ac02b5155c59ad4603f0cc633b2dfad8a',1,'vg::MultipathMapper']]],
+ ['use_5fgreedy_5fmem_5frestarts_6312',['use_greedy_mem_restarts',['../classvg_1_1BaseMapper.html#ad95c004337db9d7de612c3cffe4f90f8',1,'vg::BaseMapper']]],
+ ['use_5finternal_5fconnectivity_6313',['use_internal_connectivity',['../classvg_1_1NetGraph.html#a57dedbbe009595f748dc3c4deae2dc72',1,'vg::NetGraph']]],
+ ['use_5fmapq_6314',['use_mapq',['../classvg_1_1Genotyper.html#a5991ce66cc2a9ea45bd27d288dd7d9b8',1,'vg::Genotyper::use_mapq()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a0588ea9ea69bf3c4c3f9108549e6102b',1,'vg::PoissonSupportSnarlCaller::use_mapq()']]],
+ ['use_5fmin_5fdist_5fclusterer_6315',['use_min_dist_clusterer',['../classvg_1_1MultipathMapper.html#aed5898444e134f0fb95ae527d215e88f',1,'vg::MultipathMapper']]],
+ ['use_5for_5fsave_6316',['use_or_save',['../gbwt__main_8cpp.html#ab82463d53fb85eaec6c4e581e009d9e6',1,'gbwt_main.cpp']]],
+ ['use_5fpessimistic_5ftail_5falignment_6317',['use_pessimistic_tail_alignment',['../classvg_1_1MultipathMapper.html#a552098fc2ac26aa17929d31f7a0f1ecd',1,'vg::MultipathMapper']]],
+ ['use_5fpopulation_5fmapqs_6318',['use_population_mapqs',['../classvg_1_1MultipathMapper.html#aaaecbb0881e444042662a72907442fc1',1,'vg::MultipathMapper']]],
+ ['use_5fpreset_6319',['use_preset',['../gbwt__main_8cpp.html#ad246795d44cf23172412ae1c6a7a86e6',1,'gbwt_main.cpp']]],
+ ['use_5fstripped_5fmatch_5falg_6320',['use_stripped_match_alg',['../classvg_1_1MultipathMapper.html#ac9ea306291983b4c10ff1ec97b6d1adc',1,'vg::MultipathMapper']]],
+ ['use_5ftvs_5fclusterer_6321',['use_tvs_clusterer',['../classvg_1_1MultipathMapper.html#afaa33d747ce1393304aa96bc5245a4f8',1,'vg::MultipathMapper']]],
+ ['used_5fbins_5fof_5frange_6322',['used_bins_of_range',['../classvg_1_1StreamIndexBase.html#a94777b19236dfb74d66ba8c484bf663f',1,'vg::StreamIndexBase']]],
+ ['uses_5fus_6323',['uses_Us',['../namespacevg.html#acd966c42f332957a1b9317faa3d26407',1,'vg']]],
+ ['util_2ehpp_6324',['util.hpp',['../util_8hpp.html',1,'']]],
+ ['utility_2ecpp_6325',['utility.cpp',['../utility_8cpp.html',1,'']]],
+ ['utility_2ehpp_6326',['utility.hpp',['../utility_8hpp.html',1,'']]]
];
diff --git a/search/all_16.js b/search/all_16.js
index 0551987429..b2da736206 100644
--- a/search/all_16.js
+++ b/search/all_16.js
@@ -1,140 +1,140 @@
var searchData=
[
- ['algorithms_6325',['algorithms',['../namespacevg_1_1algorithms.html',1,'vg']]],
- ['io_6326',['io',['../namespacevg_1_1io.html',1,'vg']]],
- ['subcommand_6327',['subcommand',['../namespacevg_1_1subcommand.html',1,'vg']]],
- ['temp_5ffile_6328',['temp_file',['../namespacevg_1_1temp__file.html',1,'vg']]],
- ['v_6329',['v',['../structvg_1_1TreeNode.html#aa4855443d5325cd35ff3d1d5a6855190',1,'vg::TreeNode']]],
- ['valid_5foutput_5fformat_6330',['valid_output_format',['../namespacevg_1_1io.html#accd0bfdce54ff793cf2fae6b1122ec54',1,'vg::io']]],
- ['validate_6331',['validate',['../structHaplotypesConfig.html#a6eeffe1089fb8292af1674eacc00e8a4',1,'HaplotypesConfig']]],
- ['validate_5fchain_6332',['validate_chain',['../haplotypes__main_8cpp.html#a3a45e87bba0a989b6090009d4625b7be',1,'haplotypes_main.cpp']]],
- ['validate_5fclusters_6333',['validate_clusters',['../classvg_1_1MinimizerMapper.html#a6570c2ad670d859a7968185b9ca4766b',1,'vg::MinimizerMapper']]],
- ['validate_5fedges_6334',['validate_edges',['../haplotypes__main_8cpp.html#a999c98d1ee58048171f7dcecf358d2d3',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_6335',['validate_error',['../haplotypes__main_8cpp.html#a0ea019c2395c52022f514fa4f82cf160',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_5fchain_6336',['validate_error_chain',['../haplotypes__main_8cpp.html#afdc6618a23f46fd617c11c59dc002c49',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_5fsequence_6337',['validate_error_sequence',['../haplotypes__main_8cpp.html#a2d43c126781548ac00da14e8e01adcb2',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_5fsubchain_6338',['validate_error_subchain',['../haplotypes__main_8cpp.html#a89350da9375f069d78273ad1f90779f7',1,'haplotypes_main.cpp']]],
- ['validate_5fgbwt_5fconfig_6339',['validate_gbwt_config',['../gbwt__main_8cpp.html#af5ed19bfdb99fb96253ad3871e87fe21',1,'gbwt_main.cpp']]],
- ['validate_5fhaplotypes_6340',['validate_haplotypes',['../haplotypes__main_8cpp.html#a32b60c224f945b606e8ad835badd30e0',1,'haplotypes_main.cpp']]],
- ['validate_5fmain_2ecpp_6341',['validate_main.cpp',['../validate__main_8cpp.html',1,'']]],
- ['validate_5fmultipath_5falignment_6342',['validate_multipath_alignment',['../namespacevg.html#a026842b7758f60f2be6a474cf41d3fe1',1,'vg']]],
- ['validate_5fnodes_6343',['validate_nodes',['../haplotypes__main_8cpp.html#aacf025eb707a93ff8273d2030a917941',1,'haplotypes_main.cpp']]],
- ['validate_5fsnarl_6344',['validate_snarl',['../classvg_1_1ZipCodeTree.html#a8650ce6bcf5e49fe2cdcda115907a6a4',1,'vg::ZipCodeTree']]],
- ['validate_5fsubgraph_6345',['validate_subgraph',['../haplotypes__main_8cpp.html#a34f1931e5c2978decef6f1b46cfe5808',1,'haplotypes_main.cpp']]],
- ['validate_5funary_5fpath_6346',['validate_unary_path',['../haplotypes__main_8cpp.html#a5ec83acb4aef7e3600194a474bf7503c',1,'haplotypes_main.cpp']]],
- ['validate_5fzip_5fforest_6347',['validate_zip_forest',['../classvg_1_1ZipCodeForest.html#a61e851b424a075f606092a97d0106845',1,'vg::ZipCodeForest']]],
- ['validate_5fzip_5ftree_6348',['validate_zip_tree',['../classvg_1_1ZipCodeTree.html#aae99837c7693b5ee6bdc2a2b0dd053ec',1,'vg::ZipCodeTree']]],
- ['validator_6349',['validator',['../structvg_1_1subcommand_1_1ArgSpec.html#a542e2d18276cafc5c6219a47be001197',1,'vg::subcommand::ArgSpec']]],
- ['validatorfunction_6350',['ValidatorFunction',['../namespacevg_1_1subcommand.html#a2b4313825cf18541121dd65b08b066e9',1,'vg::subcommand']]],
- ['valuation_6351',['Valuation',['../structvg_1_1subcommand_1_1Valuation.html',1,'vg::subcommand::Valuation< T >'],['../structvg_1_1subcommand_1_1Valuation.html#aa6eadc2e42b34b522bfd972d37ffec72',1,'vg::subcommand::Valuation::Valuation()']]],
- ['value_6352',['Value',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a74a157bf3bce2696b04754f1c6dd72b9',1,'vg::Option< vector< Item >, Parser >::Value()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#abaad50c48424395686b10a95dfc16ab7',1,'vg::MinimizerMapper::Minimizer::value()'],['../classvg_1_1BaseOption.html#aa74c66fcf0f363ce08bb6e5060fd42e5',1,'vg::BaseOption::value()'],['../classvg_1_1SmallBitset.html#a486a8a8a5a30fab268ae96a9cf464fdd',1,'vg::SmallBitset::value()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#af141b75a2e3f2014b3289b3cffe99c44',1,'vg::ZipCodeTree::tree_item_t::value()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#a5d3fb39613dc2935ea316d87d2244f7b',1,'vg::ZipCodeForest::child_info_t::value()'],['../structvg_1_1subcommand_1_1Valuation.html#a88e369b92873968c8d7b68cc78ce1b1d',1,'vg::subcommand::Valuation::value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a518e378dc3759f070912c8cf42ae83cd',1,'vg::subcommand::ValueArgSpec::value()'],['../classvg_1_1io_1_1MessageIterator.html#a698864a67e1e721c06a97875f6cbcbde',1,'vg::io::MessageIterator::value()'],['../classvg_1_1io_1_1ProtobufIterator.html#aa66494ab08ee29d36b1aa04f0213f566',1,'vg::io::ProtobufIterator::value()'],['../classvg_1_1ProblemDumpExplainer.html#a27164f7c9d1bd3f25bafed94b745444c',1,'vg::ProblemDumpExplainer::value(const std::string &v)'],['../classvg_1_1ProblemDumpExplainer.html#a6b948ca538c47cc4042d039fcb6381d7',1,'vg::ProblemDumpExplainer::value(double v)'],['../classvg_1_1ProblemDumpExplainer.html#a97c2e3c2f810e01cf79d3e4c0cf4ae47',1,'vg::ProblemDumpExplainer::value(size_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a9847ed10905a3633101e1c71f36abc7a',1,'vg::ProblemDumpExplainer::value(int v)'],['../classvg_1_1ProblemDumpExplainer.html#aca748cde7cbb1763ef518d5715a9855b',1,'vg::ProblemDumpExplainer::value(bool v)'],['../classvg_1_1ProblemDumpExplainer.html#a5617b0887736bf19ffbc177f43f3807f',1,'vg::ProblemDumpExplainer::value(vg::id_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a327bd602828aca8f102f1ca46f1e6115',1,'vg::ProblemDumpExplainer::value(const pos_t &v)'],['../classvg_1_1ProblemDumpExplainer.html#aad49d76e8e8442d74b8b987906dd0bc3',1,'vg::ProblemDumpExplainer::value(const HandleGraph &v)'],['../classvg_1_1ProblemDumpExplainer.html#a2c21785e31b448b21733c4dc53729823',1,'vg::ProblemDumpExplainer::value(const handle_t &v, const HandleGraph &context)'],['../structvg_1_1WFAPoint.html#aeae29642d758fc5ca9c308b094ff3c53',1,'vg::WFAPoint::value()']]],
- ['value_5fat_6353',['value_at',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a2146c37988fd520600d806d1606f0f3f',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['value_5fbits_6354',['VALUE_BITS',['../classvg_1_1SmallBitset.html#a1570694b6aa163d390bc65f3ad2e015d',1,'vg::SmallBitset']]],
- ['value_5fcast_6355',['value_cast',['../namespacevg.html#a76fc86953f8c080621c080cd35bc9ae0',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#ac84a9621d5108f53976d51f1188e7214',1,'vg::value_cast(const T &wrap)'],['../namespacevg.html#a12109d27c9801031e32a408e75af2bd1',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#aca53457219a2ced000f439df5bd0d71f',1,'vg::value_cast(const Container &wrap)']]],
- ['value_5fcast_3c_20bool_20_3e_6356',['value_cast< bool >',['../namespacevg.html#ac90d23f22ad3ec78da4e03dc011cabf8',1,'vg::value_cast< bool >(const google::protobuf::Value &value)'],['../namespacevg.html#ab572dfa4b65db43984f1572d74a94036',1,'vg::value_cast< bool >(const bool &wrap)']]],
- ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3astruct_20_2a_20_3e_6357',['value_cast< const google::protobuf::Struct * >',['../namespacevg.html#a2683b1d5f38a8b34051fec41d7c011f0',1,'vg']]],
- ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3avalue_20_2a_20_3e_6358',['value_cast< const google::protobuf::Value * >',['../namespacevg.html#a248b5f3265dbbdde641fee26c075842a',1,'vg']]],
- ['value_5fcast_3c_20double_20_3e_6359',['value_cast< double >',['../namespacevg.html#a13a0cc45e4277281efeedb821c1444f6',1,'vg::value_cast< double >(const google::protobuf::Value &value)'],['../namespacevg.html#ac16fdb4078f95e252450a80a1e9e14f2',1,'vg::value_cast< double >(const double &wrap)']]],
- ['value_5fcast_3c_20int_20_3e_6360',['value_cast< int >',['../namespacevg.html#ad1ca627c13de536f96efbc08934edb62',1,'vg']]],
- ['value_5fcast_3c_20size_5ft_20_3e_6361',['value_cast< size_t >',['../namespacevg.html#a2a12578ee636d9d929a9c1205e7c8525',1,'vg']]],
- ['value_5fcast_3c_20string_20_3e_6362',['value_cast< string >',['../namespacevg.html#a16575a017d153499fe4a0976e801be61',1,'vg::value_cast< string >(const google::protobuf::Value &value)'],['../namespacevg.html#a51e6a112ff1115272420d46ca4316f63',1,'vg::value_cast< string >(const string &wrap)']]],
- ['value_5fmask_6363',['VALUE_MASK',['../classvg_1_1SmallBitset.html#a0d940c085d362391f5bc531bd948623a',1,'vg::SmallBitset']]],
- ['value_5fset_6364',['value_set',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a215243ebe6068e28cb2ad00472a9a4d9',1,'vg::subcommand::ValueArgSpec']]],
- ['value_5fshift_6365',['VALUE_SHIFT',['../classvg_1_1SmallBitset.html#ad5a1d72bf8ad3ce5c8341da2fa78eafb',1,'vg::SmallBitset']]],
- ['value_5ftype_6366',['value_type',['../structvg_1_1WFAPoint.html#a783bd5a58352f7be967ed9556c99f95b',1,'vg::WFAPoint::value_type()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a93f9129d2273ed4e7475456485be17b1',1,'vg::PhasedGenome::iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#a5d5cc51db9a7bee260aa4b303b8d593a',1,'std::iterator_traits< vg::PhasedGenome::iterator >::value_type()'],['../classvg_1_1SmallBitset.html#a424751e879964b97d81879b1c2ef2e25',1,'vg::SmallBitset::value_type()'],['../classvg_1_1count__back__inserter.html#a18a57c061e584b32ad1cc805c59b8a84',1,'vg::count_back_inserter::value_type()'],['../structvg_1_1VectorView_1_1const__iterator.html#a9dbd79edd9a90a030c98fe15df98749c',1,'vg::VectorView::const_iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#ae6286581a32d15a3a27ea7413e38cf4c',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a4864777b7b0405f28848b8a478867cb3',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::value_type()']]],
- ['valueargspec_6367',['ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand::ValueArgSpec< T, Receiver, Holder >'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#af9860ac96dc38b06b5de9b00ae31ffbe',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, char short_option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a10b4640232a0e4ece857459d903c3809',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)']]],
- ['valueargspec_3c_20bool_2c_20receiver_20_3e_6368',['ValueArgSpec< bool, Receiver >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
- ['valueargspec_3c_20t_2c_20receiver_2c_20range_3c_20t_20_3e_20_3e_6369',['ValueArgSpec< T, Receiver, Range< T > >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
- ['values_6370',['values',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a341b8cdfa0d90adaea6f9c52196b5de6',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t']]],
- ['var_6371',['var',['../namespacevg.html#afe7fae89b379b5411189ac0ac74b2dd4',1,'vg']]],
- ['variant_5fadder_2ecpp_6372',['variant_adder.cpp',['../variant__adder_8cpp.html',1,'']]],
- ['variant_5fadder_2ehpp_6373',['variant_adder.hpp',['../variant__adder_8hpp.html',1,'']]],
- ['variant_5falts_6374',['variant_alts',['../structvg_1_1VG_1_1Plan.html#ad2b28e3a651018396d6c0a1b3377e161',1,'vg::VG::Plan']]],
- ['variant_5frange_6375',['variant_range',['../classvg_1_1VariantAdder.html#aa23751086259b5976ffe78169a6000b9',1,'vg::VariantAdder']]],
- ['variant_5frecall_6376',['variant_recall',['../namespacevg.html#a96096594534e59d12b7a2cff3c400ef0',1,'vg']]],
- ['variant_5frecall_2ecpp_6377',['variant_recall.cpp',['../variant__recall_8cpp.html',1,'']]],
- ['variant_5frecall_2ehpp_6378',['variant_recall.hpp',['../variant__recall_8hpp.html',1,'']]],
- ['variant_5fsource_6379',['variant_source',['../classvg_1_1RareVariantSimplifier.html#afd96f926d4135c8c1ae967ad22aad03a',1,'vg::RareVariantSimplifier']]],
- ['variant_5fto_5ftraversal_6380',['variant_to_traversal',['../classvg_1_1VG.html#ac697184acf2edadca58ddc776f9f4e7e',1,'vg::VG']]],
- ['variantadder_6381',['VariantAdder',['../classvg_1_1VariantAdder.html',1,'vg::VariantAdder'],['../classvg_1_1VariantAdder.html#a267056ae90838d3aef2ddfe992a045ff',1,'vg::VariantAdder::VariantAdder()']]],
- ['variants_5fafter_6382',['variants_after',['../classvg_1_1WindowedVcfBuffer.html#a8c0bf4d78e07bcc7ec8f58287452ad9e',1,'vg::WindowedVcfBuffer']]],
- ['variants_5fbefore_6383',['variants_before',['../classvg_1_1WindowedVcfBuffer.html#a24156cab3205fcb845418259a91ada3a',1,'vg::WindowedVcfBuffer']]],
- ['varint_2ecpp_6384',['varint.cpp',['../varint_8cpp.html',1,'']]],
- ['varint_2ehpp_6385',['varint.hpp',['../varint_8hpp.html',1,'']]],
- ['varint_5fvector_5ft_6386',['varint_vector_t',['../structvg_1_1varint__vector__t.html',1,'vg']]],
- ['vars_5fper_5fchunk_6387',['vars_per_chunk',['../classvg_1_1Constructor.html#a7cc8ae0e38492082ba8e886ea174944f',1,'vg::Constructor']]],
- ['vcf_5fbuffer_2ecpp_6388',['vcf_buffer.cpp',['../vcf__buffer_8cpp.html',1,'']]],
- ['vcf_5fbuffer_2ehpp_6389',['vcf_buffer.hpp',['../vcf__buffer_8hpp.html',1,'']]],
- ['vcf_5fcontigs_6390',['vcf_contigs',['../namespacevg.html#a691144860bc63559aaf088d2e052af62',1,'vg']]],
- ['vcf_5ffixup_6391',['vcf_fixup',['../classvg_1_1VCFOutputCaller.html#ab063824a02c65e499cac3d2ca96ca504',1,'vg::VCFOutputCaller']]],
- ['vcf_5fheader_6392',['vcf_header',['../classvg_1_1VCFOutputCaller.html#aeb9a75eed0ba2a369439abddf1ac3f65',1,'vg::VCFOutputCaller::vcf_header()'],['../classvg_1_1VCFGenotyper.html#a8dae0df9c45f88aadca9fcaa8d0e7214',1,'vg::VCFGenotyper::vcf_header()'],['../classvg_1_1LegacyCaller.html#a4536625fdb753727a7d8321cadc6946b',1,'vg::LegacyCaller::vcf_header()'],['../classvg_1_1FlowCaller.html#a2c4e7365e43593313a30d7d4ea03c4a9',1,'vg::FlowCaller::vcf_header()'],['../classvg_1_1NestedFlowCaller.html#a38c3758ea8fd04852eb62c40ec9be010',1,'vg::NestedFlowCaller::vcf_header()'],['../classvg_1_1MCMCCaller.html#af67e8bf51b99831bd5b9f67c2581d084',1,'vg::MCMCCaller::vcf_header()']]],
- ['vcf_5finput_6393',['vcf_input',['../structHaplotypesConfig.html#a8d58855b93c6c570420598f99f2d8ea2',1,'HaplotypesConfig']]],
- ['vcf_5fis_5fphased_6394',['vcf_is_phased',['../classvg_1_1IndexRegistry.html#abeceb0062997804e84372c7bca76c8ae',1,'vg::IndexRegistry']]],
- ['vcf_5fto_5ffasta_6395',['vcf_to_fasta',['../classvg_1_1NameMapper.html#a6e8c36e6207dbc905170bde6a5c396b3',1,'vg::NameMapper']]],
- ['vcf_5fto_5ffasta_5frenames_6396',['vcf_to_fasta_renames',['../classvg_1_1NameMapper.html#afd130381fc9ad1a930932e672fda80d1',1,'vg::NameMapper']]],
- ['vcfbuffer_6397',['VcfBuffer',['../classvg_1_1VcfBuffer.html',1,'vg::VcfBuffer'],['../classvg_1_1VcfBuffer.html#a402d5cadd95f5725876b22b8c9bd830b',1,'vg::VcfBuffer::VcfBuffer(vcflib::VariantCallFile *file=nullptr)'],['../classvg_1_1VcfBuffer.html#ad388f47df62ebab69ab9188efd37be1e',1,'vg::VcfBuffer::VcfBuffer(const VcfBuffer &other)=delete']]],
- ['vcfgenotyper_6398',['VCFGenotyper',['../classvg_1_1VCFGenotyper.html',1,'vg::VCFGenotyper'],['../classvg_1_1VCFGenotyper.html#a8c65e87515bd32e6f90bba45712175bf',1,'vg::VCFGenotyper::VCFGenotyper()']]],
- ['vcfoutputcaller_6399',['VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html',1,'vg::VCFOutputCaller'],['../classvg_1_1VCFOutputCaller.html#ad758f9180a51784374ef044b54883f87',1,'vg::VCFOutputCaller::VCFOutputCaller()']]],
- ['vcfrecordconverter_6400',['VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html',1,'vg']]],
- ['vcfrecordfilter_6401',['VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html',1,'vg']]],
- ['vcftraversalfinder_6402',['VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html',1,'vg::VCFTraversalFinder'],['../classvg_1_1VCFTraversalFinder.html#aaa8aa0b5cbe8a0e2ff664b6b385339da',1,'vg::VCFTraversalFinder::VCFTraversalFinder()']]],
- ['vectorizablehandlegraph_6403',['VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html',1,'handlegraph::VectorizableHandleGraph'],['../namespacevg.html#a449aa64ac606119e59f71cecb8a3b218',1,'vg::VectorizableHandleGraph()']]],
- ['vectorize_5fmain_2ecpp_6404',['vectorize_main.cpp',['../vectorize__main_8cpp.html',1,'']]],
- ['vectorizer_6405',['Vectorizer',['../classVectorizer.html',1,'Vectorizer'],['../classVectorizer.html#ac6f2b56806bc2e8444492cb3d32f42be',1,'Vectorizer::Vectorizer()']]],
- ['vectorizer_2ecpp_6406',['vectorizer.cpp',['../vectorizer_8cpp.html',1,'']]],
- ['vectorizer_2ehpp_6407',['vectorizer.hpp',['../vectorizer_8hpp.html',1,'']]],
- ['vectorview_6408',['VectorView',['../structvg_1_1VectorView.html',1,'vg::VectorView< Item >'],['../structvg_1_1VectorView.html#aefb5d25c5ced8c23549c605abb29c09f',1,'vg::VectorView::VectorView()'],['../structvg_1_1VectorView.html#adaf1a835fd36e7c4194d4ee53adc4528',1,'vg::VectorView::VectorView(const VectorView &other)=default'],['../structvg_1_1VectorView.html#ac6ad816ef159fe1b9dad8c9539a5b8de',1,'vg::VectorView::VectorView(VectorView &&other)=default'],['../structvg_1_1VectorView.html#ace693cb938bdc8545ff2d00faf2c9136',1,'vg::VectorView::VectorView(const vector< Item > &items)'],['../structvg_1_1VectorView.html#a5e4711cb47476cfe22eccef4823d4fa8',1,'vg::VectorView::VectorView(const vector< Item > &items, const vector< size_t > &indexes)']]],
- ['vectorviewinverse_6409',['VectorViewInverse',['../classvg_1_1VectorViewInverse.html',1,'vg::VectorViewInverse'],['../classvg_1_1VectorViewInverse.html#a6f4c737e0dc739eca4f09a472e520335',1,'vg::VectorViewInverse::VectorViewInverse()'],['../classvg_1_1VectorViewInverse.html#ab87205a1d88681364f2768e778e87c8d',1,'vg::VectorViewInverse::VectorViewInverse(const VectorView< Item > &view)']]],
- ['verbose_6410',['verbose',['../classvg_1_1NestedTraversalFinder.html#a67980934b7315e90dcd63fa046b465b7',1,'vg::NestedTraversalFinder::verbose()'],['../classvg_1_1ReadFilter.html#aa207b19d222c64919714bae506b726a6',1,'vg::ReadFilter::verbose()'],['../classvg_1_1RepresentativeTraversalFinder.html#a6af3519805d1115b006ad8b3bf2d3a3e',1,'vg::RepresentativeTraversalFinder::verbose()'],['../classvg_1_1io_1_1MessageIterator.html#af3f1540514c644f1d01212d515f603e6',1,'vg::io::MessageIterator::verbose()']]],
- ['verbosity_6411',['verbosity',['../structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579',1,'vg::IndexingParameters::verbosity()'],['../classvg_1_1HaplotypePartitioner.html#ac5d1210d753c0fe6ed936f18f02e2cd2',1,'vg::HaplotypePartitioner::verbosity()'],['../classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12',1,'vg::Recombinator::verbosity()'],['../structHaplotypesConfig.html#ad04e07b242265b989bc2b93479676b84',1,'HaplotypesConfig::verbosity()'],['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3',1,'vg::IndexingParameters::Verbosity()'],['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28a',1,'vg::Haplotypes::Verbosity()'],['../classvg_1_1HaplotypePartitioner.html#a7b5fa99a041f7c61f73644541dd926b1',1,'vg::HaplotypePartitioner::Verbosity()'],['../classvg_1_1Recombinator.html#a097faaea0512d01e5e7732dd1991f129',1,'vg::Recombinator::Verbosity()']]],
- ['verbosity_5fbasic_6412',['verbosity_basic',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa718364c23222ec5e7444240be0799449',1,'vg::Haplotypes']]],
- ['verbosity_5fdebug_6413',['verbosity_debug',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aaa92669d64637a1583a113eb279234241',1,'vg::Haplotypes']]],
- ['verbosity_5fdetailed_6414',['verbosity_detailed',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa8c3562efded9b2b9ae9fd7ee05594ce0',1,'vg::Haplotypes']]],
- ['verbosity_5fsilent_6415',['verbosity_silent',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aadd4472c60bf6446f52a09a0d41140a21',1,'vg::Haplotypes']]],
- ['verify_5fpath_6416',['verify_path',['../namespacevg.html#a3ed0a4f26673002b2081832a7602e9bd',1,'vg']]],
- ['verify_5fpaths_6417',['verify_paths',['../classvg_1_1PhaseUnfolder.html#a910deba7dd5b5f9bce7a1da4e53cfeb1',1,'vg::PhaseUnfolder']]],
- ['verify_5fvalid_5flog_5fodds_5fscore_5fmatrix_6418',['verify_valid_log_odds_score_matrix',['../classvg_1_1GSSWAligner.html#acc5d3a8c0c22cbd966e96a42eb095cd8',1,'vg::GSSWAligner']]],
- ['version_6419',['Version',['../classvg_1_1Version.html',1,'vg::Version'],['../structvg_1_1Haplotypes_1_1Header.html#ac2e1810f289c24ac4c2f74d8df9df5ec',1,'vg::Haplotypes::Header::version()'],['../classvg_1_1ZipCodeCollection.html#ad97d400ad51f2d7d1a880d81bbf8993d',1,'vg::ZipCodeCollection::version()'],['../structvg_1_1Haplotypes_1_1Header.html#a68bfc0fe68e8fc1b42ad078eaa234777',1,'vg::Haplotypes::Header::VERSION()'],['../classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222',1,'vg::Version::VERSION()'],['../classvg_1_1Version.html#a05bb9f14c7597bf90a2981db7e59b058',1,'vg::Version::Version()=delete']]],
- ['version_2ecpp_6420',['version.cpp',['../version_8cpp.html',1,'']]],
- ['version_2ehpp_6421',['version.hpp',['../version_8hpp.html',1,'']]],
- ['version_5fmain_2ecpp_6422',['version_main.cpp',['../version__main_8cpp.html',1,'']]],
- ['vg_6423',['VG',['../classvg_1_1VG.html',1,'vg::VG'],['../namespacevg.html',1,'vg'],['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a5e978449ccc729202c33e2dc543b8327',1,'vg::IndexingParameters::VG()'],['../classvg_1_1VG.html#ac2399de59931e282fb1f4d3da9a8dcb1',1,'vg::VG::VG(void)'],['../classvg_1_1VG.html#a2dc9648985454d3aedd9a477ff0c52b2',1,'vg::VG::VG(istream &in, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#a0fbb777fd8ab6050124a6eaf9eca9133',1,'vg::VG::VG(const function< void(const function< void(Graph &)> &)> &send_graphs, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#af4d321b31b873153431c261090d052af',1,'vg::VG::VG(const Graph &from, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#abeafee2d3bc6e0039e99fccdea10f4f9',1,'vg::VG::VG(set< Node * > &nodes, set< Edge * > &edges)'],['../classvg_1_1VG.html#a3148455330df9ac055c6bd1eb7da3167',1,'vg::VG::VG(const VG &other)'],['../classvg_1_1VG.html#ab8365ccd6a093ec50f7d54b1c7a7c672',1,'vg::VG::VG(VG &&other) noexcept'],['../classvg_1_1FlowSort.html#abd481c5b9e6c9c5aeaf846652dd3c76f',1,'vg::FlowSort::vg()']]],
- ['vg_2ecpp_6424',['vg.cpp',['../vg_8cpp.html',1,'']]],
- ['vg_2ehpp_6425',['vg.hpp',['../vg_8hpp.html',1,'']]],
- ['vg_2eproto_6426',['vg.proto',['../vg_8proto.html',1,'']]],
- ['vg_5fbuild_5fhost_6427',['VG_BUILD_HOST',['../vg__environment__version_8hpp.html#a2baea5938fa1a9b70e6a27ccc59c65d9',1,'vg_environment_version.hpp']]],
- ['vg_5fbuild_5fuser_6428',['VG_BUILD_USER',['../vg__environment__version_8hpp.html#a95dd87e623e9d0c99f662e3d2ca6676d',1,'vg_environment_version.hpp']]],
- ['vg_5fcompiler_5fversion_6429',['VG_COMPILER_VERSION',['../vg__environment__version_8hpp.html#a018858ebcbef9ca466d11e0f9effd990',1,'vg_environment_version.hpp']]],
- ['vg_5fenvironment_5fversion_2ehpp_6430',['vg_environment_version.hpp',['../vg__environment__version_8hpp.html',1,'']]],
- ['vg_5ffilename_6431',['vg_filename',['../classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0',1,'vg::IndexedVG']]],
- ['vg_5fgit_5fversion_6432',['VG_GIT_VERSION',['../vg__git__version_8hpp.html#a5df50394a80dec8f6151eb57db04a38a',1,'vg_git_version.hpp']]],
- ['vg_5fgit_5fversion_2ehpp_6433',['vg_git_version.hpp',['../vg__git__version_8hpp.html',1,'']]],
- ['vg_5fhelp_6434',['vg_help',['../main_8cpp.html#aae3a18cc6fba2e4bf97e9a01f4734f4f',1,'main.cpp']]],
- ['vg_5fhtslib_5fversion_6435',['VG_HTSLIB_VERSION',['../version_8cpp.html#a0b12716ad9e947816319b2c448b942f3',1,'version.cpp']]],
- ['vg_5fmain_6436',['vg_main',['../main_8cpp.html#a8b9f48d3aed7bbfe82cdc4f092867c50',1,'main.cpp']]],
- ['vg_5fos_6437',['VG_OS',['../vg__environment__version_8hpp.html#a4b1110f54b4fd6d1242837dee0dbc820',1,'vg_environment_version.hpp']]],
- ['vg_5fpreflight_5feverywhere_6438',['VG_PREFLIGHT_EVERYWHERE',['../preflight_8hpp.html#a15a8edc41d783e0cc08568efe26a83fd',1,'preflight.hpp']]],
- ['vg_5fset_2ecpp_6439',['vg_set.cpp',['../vg__set_8cpp.html',1,'']]],
- ['vg_5fset_2ehpp_6440',['vg_set.hpp',['../vg__set_8hpp.html',1,'']]],
- ['vg_5fstandard_5flibrary_5fversion_6441',['VG_STANDARD_LIBRARY_VERSION',['../version_8cpp.html#a923fcc9a50a1ddbec3aa567d4f91d576',1,'version.cpp']]],
- ['vgalignmentemitter_6442',['VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html',1,'vg::io::VGAlignmentEmitter'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#af278878b244808a182eae17640f23a45',1,'vg::io::VGAlignmentEmitter::VGAlignmentEmitter()']]],
- ['vgindexes_6443',['VGIndexes',['../structvg_1_1VGIndexes.html',1,'vg']]],
- ['vgset_6444',['VGset',['../classvg_1_1VGset.html',1,'vg::VGset'],['../classvg_1_1VGset.html#a5ff9a6c4fa0223bcee7072f86a657751',1,'vg::VGset::VGset()'],['../classvg_1_1VGset.html#a6adbb25be82de20911fd901da4e9fe41',1,'vg::VGset::VGset(vector< string > &files)']]],
- ['view_5fmain_2ecpp_6445',['view_main.cpp',['../view__main_8cpp.html',1,'']]],
- ['view_5fmultipath_5falignment_6446',['view_multipath_alignment',['../namespacevg.html#a411a023efbe439f069829603a2775673',1,'vg']]],
- ['view_5fmultipath_5falignment_5fas_5fdot_6447',['view_multipath_alignment_as_dot',['../namespacevg.html#a716909fc23ddaab59e0d2bf89fdd1ae3',1,'vg']]],
- ['visit_6448',['Visit',['../structvg_1_1Visit.html',1,'vg::Visit'],['../structvg_1_1SnarlTraversal.html#aff14559c1e4fb55bdf87320f3a4ee636',1,'vg::SnarlTraversal::visit()']]],
- ['visit_5fcontained_5fsnarls_6449',['visit_contained_snarls',['../namespacevg.html#ae3a49e3aea82c8e552e4cf9fd8396ad4',1,'vg']]],
- ['visit_5fnext_5fnode_6450',['visit_next_node',['../classvg_1_1ExhaustiveTraversalFinder.html#a2cec9de94838e3575a20271db01a1a4f',1,'vg::ExhaustiveTraversalFinder::visit_next_node()'],['../classvg_1_1SupportRestrictedTraversalFinder.html#a9cdb3b8f554e58cba6fea9c2ccb40e14',1,'vg::SupportRestrictedTraversalFinder::visit_next_node()']]],
- ['visited_6451',['visited',['../classvg_1_1HandleGraphNodeSet.html#a6a1318a8e451562f282bf960032634f4',1,'vg::HandleGraphNodeSet']]],
- ['visits_5fleft_6452',['visits_left',['../classvg_1_1SnarlManager.html#a27e95077ab5c9a7288f2833d5e66433e',1,'vg::SnarlManager']]],
- ['visits_5fright_6453',['visits_right',['../classvg_1_1SnarlManager.html#a567554948e5dc03604a46972eb42d295',1,'vg::SnarlManager']]],
- ['viz_6454',['Viz',['../classvg_1_1Viz.html',1,'vg::Viz'],['../classvg_1_1Viz.html#a8e9440d6c67fde7f10fe9c0366759041',1,'vg::Viz::Viz(void)'],['../classvg_1_1Viz.html#a5d343eb2d20b2db1eb66def4b8d3081c',1,'vg::Viz::Viz(PathHandleGraph *x, vector< Packer > *p, const vector< string > &n, const string &o, int w, int h, bool c, bool d, bool t)']]],
- ['viz_2ecpp_6455',['viz.cpp',['../viz_8cpp.html',1,'']]],
- ['viz_2ehpp_6456',['viz.hpp',['../viz_8hpp.html',1,'']]],
- ['viz_5fmain_2ecpp_6457',['viz_main.cpp',['../viz__main_8cpp.html',1,'']]],
- ['vpkg_6458',['VPKG',['../classvg_1_1io_1_1VPKG.html',1,'vg::io']]],
- ['vpkg_2ecpp_6459',['vpkg.cpp',['../vpkg_8cpp.html',1,'']]],
- ['vpkg_2ehpp_6460',['vpkg.hpp',['../vpkg_8hpp.html',1,'']]],
- ['vpmax_6461',['vpmax',['../namespacevg.html#aec4813274fc2af3d83679e128fdeb32f',1,'vg']]]
+ ['algorithms_6327',['algorithms',['../namespacevg_1_1algorithms.html',1,'vg']]],
+ ['io_6328',['io',['../namespacevg_1_1io.html',1,'vg']]],
+ ['subcommand_6329',['subcommand',['../namespacevg_1_1subcommand.html',1,'vg']]],
+ ['temp_5ffile_6330',['temp_file',['../namespacevg_1_1temp__file.html',1,'vg']]],
+ ['v_6331',['v',['../structvg_1_1TreeNode.html#aa4855443d5325cd35ff3d1d5a6855190',1,'vg::TreeNode']]],
+ ['valid_5foutput_5fformat_6332',['valid_output_format',['../namespacevg_1_1io.html#accd0bfdce54ff793cf2fae6b1122ec54',1,'vg::io']]],
+ ['validate_6333',['validate',['../structHaplotypesConfig.html#a6eeffe1089fb8292af1674eacc00e8a4',1,'HaplotypesConfig']]],
+ ['validate_5fchain_6334',['validate_chain',['../haplotypes__main_8cpp.html#a3a45e87bba0a989b6090009d4625b7be',1,'haplotypes_main.cpp']]],
+ ['validate_5fclusters_6335',['validate_clusters',['../classvg_1_1MinimizerMapper.html#a6570c2ad670d859a7968185b9ca4766b',1,'vg::MinimizerMapper']]],
+ ['validate_5fedges_6336',['validate_edges',['../haplotypes__main_8cpp.html#a999c98d1ee58048171f7dcecf358d2d3',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_6337',['validate_error',['../haplotypes__main_8cpp.html#a0ea019c2395c52022f514fa4f82cf160',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_5fchain_6338',['validate_error_chain',['../haplotypes__main_8cpp.html#afdc6618a23f46fd617c11c59dc002c49',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_5fsequence_6339',['validate_error_sequence',['../haplotypes__main_8cpp.html#a2d43c126781548ac00da14e8e01adcb2',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_5fsubchain_6340',['validate_error_subchain',['../haplotypes__main_8cpp.html#a89350da9375f069d78273ad1f90779f7',1,'haplotypes_main.cpp']]],
+ ['validate_5fgbwt_5fconfig_6341',['validate_gbwt_config',['../gbwt__main_8cpp.html#af5ed19bfdb99fb96253ad3871e87fe21',1,'gbwt_main.cpp']]],
+ ['validate_5fhaplotypes_6342',['validate_haplotypes',['../haplotypes__main_8cpp.html#a32b60c224f945b606e8ad835badd30e0',1,'haplotypes_main.cpp']]],
+ ['validate_5fmain_2ecpp_6343',['validate_main.cpp',['../validate__main_8cpp.html',1,'']]],
+ ['validate_5fmultipath_5falignment_6344',['validate_multipath_alignment',['../namespacevg.html#a026842b7758f60f2be6a474cf41d3fe1',1,'vg']]],
+ ['validate_5fnodes_6345',['validate_nodes',['../haplotypes__main_8cpp.html#aacf025eb707a93ff8273d2030a917941',1,'haplotypes_main.cpp']]],
+ ['validate_5fsnarl_6346',['validate_snarl',['../classvg_1_1ZipCodeTree.html#a8650ce6bcf5e49fe2cdcda115907a6a4',1,'vg::ZipCodeTree']]],
+ ['validate_5fsubgraph_6347',['validate_subgraph',['../haplotypes__main_8cpp.html#a34f1931e5c2978decef6f1b46cfe5808',1,'haplotypes_main.cpp']]],
+ ['validate_5funary_5fpath_6348',['validate_unary_path',['../haplotypes__main_8cpp.html#a5ec83acb4aef7e3600194a474bf7503c',1,'haplotypes_main.cpp']]],
+ ['validate_5fzip_5fforest_6349',['validate_zip_forest',['../classvg_1_1ZipCodeForest.html#a61e851b424a075f606092a97d0106845',1,'vg::ZipCodeForest']]],
+ ['validate_5fzip_5ftree_6350',['validate_zip_tree',['../classvg_1_1ZipCodeTree.html#aae99837c7693b5ee6bdc2a2b0dd053ec',1,'vg::ZipCodeTree']]],
+ ['validator_6351',['validator',['../structvg_1_1subcommand_1_1ArgSpec.html#a542e2d18276cafc5c6219a47be001197',1,'vg::subcommand::ArgSpec']]],
+ ['validatorfunction_6352',['ValidatorFunction',['../namespacevg_1_1subcommand.html#a2b4313825cf18541121dd65b08b066e9',1,'vg::subcommand']]],
+ ['valuation_6353',['Valuation',['../structvg_1_1subcommand_1_1Valuation.html',1,'vg::subcommand::Valuation< T >'],['../structvg_1_1subcommand_1_1Valuation.html#aa6eadc2e42b34b522bfd972d37ffec72',1,'vg::subcommand::Valuation::Valuation()']]],
+ ['value_6354',['Value',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a74a157bf3bce2696b04754f1c6dd72b9',1,'vg::Option< vector< Item >, Parser >::Value()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#abaad50c48424395686b10a95dfc16ab7',1,'vg::MinimizerMapper::Minimizer::value()'],['../classvg_1_1BaseOption.html#aa74c66fcf0f363ce08bb6e5060fd42e5',1,'vg::BaseOption::value()'],['../classvg_1_1SmallBitset.html#a486a8a8a5a30fab268ae96a9cf464fdd',1,'vg::SmallBitset::value()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#af141b75a2e3f2014b3289b3cffe99c44',1,'vg::ZipCodeTree::tree_item_t::value()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#a5d3fb39613dc2935ea316d87d2244f7b',1,'vg::ZipCodeForest::child_info_t::value()'],['../structvg_1_1subcommand_1_1Valuation.html#a88e369b92873968c8d7b68cc78ce1b1d',1,'vg::subcommand::Valuation::value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a518e378dc3759f070912c8cf42ae83cd',1,'vg::subcommand::ValueArgSpec::value()'],['../classvg_1_1io_1_1MessageIterator.html#a698864a67e1e721c06a97875f6cbcbde',1,'vg::io::MessageIterator::value()'],['../classvg_1_1io_1_1ProtobufIterator.html#aa66494ab08ee29d36b1aa04f0213f566',1,'vg::io::ProtobufIterator::value()'],['../classvg_1_1ProblemDumpExplainer.html#a27164f7c9d1bd3f25bafed94b745444c',1,'vg::ProblemDumpExplainer::value(const std::string &v)'],['../classvg_1_1ProblemDumpExplainer.html#a6b948ca538c47cc4042d039fcb6381d7',1,'vg::ProblemDumpExplainer::value(double v)'],['../classvg_1_1ProblemDumpExplainer.html#a97c2e3c2f810e01cf79d3e4c0cf4ae47',1,'vg::ProblemDumpExplainer::value(size_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a9847ed10905a3633101e1c71f36abc7a',1,'vg::ProblemDumpExplainer::value(int v)'],['../classvg_1_1ProblemDumpExplainer.html#aca748cde7cbb1763ef518d5715a9855b',1,'vg::ProblemDumpExplainer::value(bool v)'],['../classvg_1_1ProblemDumpExplainer.html#a5617b0887736bf19ffbc177f43f3807f',1,'vg::ProblemDumpExplainer::value(vg::id_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a327bd602828aca8f102f1ca46f1e6115',1,'vg::ProblemDumpExplainer::value(const pos_t &v)'],['../classvg_1_1ProblemDumpExplainer.html#aad49d76e8e8442d74b8b987906dd0bc3',1,'vg::ProblemDumpExplainer::value(const HandleGraph &v)'],['../classvg_1_1ProblemDumpExplainer.html#a2c21785e31b448b21733c4dc53729823',1,'vg::ProblemDumpExplainer::value(const handle_t &v, const HandleGraph &context)'],['../structvg_1_1WFAPoint.html#aeae29642d758fc5ca9c308b094ff3c53',1,'vg::WFAPoint::value()']]],
+ ['value_5fat_6355',['value_at',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a2146c37988fd520600d806d1606f0f3f',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['value_5fbits_6356',['VALUE_BITS',['../classvg_1_1SmallBitset.html#a1570694b6aa163d390bc65f3ad2e015d',1,'vg::SmallBitset']]],
+ ['value_5fcast_6357',['value_cast',['../namespacevg.html#a76fc86953f8c080621c080cd35bc9ae0',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#ac84a9621d5108f53976d51f1188e7214',1,'vg::value_cast(const T &wrap)'],['../namespacevg.html#a12109d27c9801031e32a408e75af2bd1',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#aca53457219a2ced000f439df5bd0d71f',1,'vg::value_cast(const Container &wrap)']]],
+ ['value_5fcast_3c_20bool_20_3e_6358',['value_cast< bool >',['../namespacevg.html#ac90d23f22ad3ec78da4e03dc011cabf8',1,'vg::value_cast< bool >(const google::protobuf::Value &value)'],['../namespacevg.html#ab572dfa4b65db43984f1572d74a94036',1,'vg::value_cast< bool >(const bool &wrap)']]],
+ ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3astruct_20_2a_20_3e_6359',['value_cast< const google::protobuf::Struct * >',['../namespacevg.html#a2683b1d5f38a8b34051fec41d7c011f0',1,'vg']]],
+ ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3avalue_20_2a_20_3e_6360',['value_cast< const google::protobuf::Value * >',['../namespacevg.html#a248b5f3265dbbdde641fee26c075842a',1,'vg']]],
+ ['value_5fcast_3c_20double_20_3e_6361',['value_cast< double >',['../namespacevg.html#a13a0cc45e4277281efeedb821c1444f6',1,'vg::value_cast< double >(const google::protobuf::Value &value)'],['../namespacevg.html#ac16fdb4078f95e252450a80a1e9e14f2',1,'vg::value_cast< double >(const double &wrap)']]],
+ ['value_5fcast_3c_20int_20_3e_6362',['value_cast< int >',['../namespacevg.html#ad1ca627c13de536f96efbc08934edb62',1,'vg']]],
+ ['value_5fcast_3c_20size_5ft_20_3e_6363',['value_cast< size_t >',['../namespacevg.html#a2a12578ee636d9d929a9c1205e7c8525',1,'vg']]],
+ ['value_5fcast_3c_20string_20_3e_6364',['value_cast< string >',['../namespacevg.html#a16575a017d153499fe4a0976e801be61',1,'vg::value_cast< string >(const google::protobuf::Value &value)'],['../namespacevg.html#a51e6a112ff1115272420d46ca4316f63',1,'vg::value_cast< string >(const string &wrap)']]],
+ ['value_5fmask_6365',['VALUE_MASK',['../classvg_1_1SmallBitset.html#a0d940c085d362391f5bc531bd948623a',1,'vg::SmallBitset']]],
+ ['value_5fset_6366',['value_set',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a215243ebe6068e28cb2ad00472a9a4d9',1,'vg::subcommand::ValueArgSpec']]],
+ ['value_5fshift_6367',['VALUE_SHIFT',['../classvg_1_1SmallBitset.html#ad5a1d72bf8ad3ce5c8341da2fa78eafb',1,'vg::SmallBitset']]],
+ ['value_5ftype_6368',['value_type',['../structvg_1_1WFAPoint.html#a783bd5a58352f7be967ed9556c99f95b',1,'vg::WFAPoint::value_type()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a93f9129d2273ed4e7475456485be17b1',1,'vg::PhasedGenome::iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#a5d5cc51db9a7bee260aa4b303b8d593a',1,'std::iterator_traits< vg::PhasedGenome::iterator >::value_type()'],['../classvg_1_1SmallBitset.html#a424751e879964b97d81879b1c2ef2e25',1,'vg::SmallBitset::value_type()'],['../classvg_1_1count__back__inserter.html#a18a57c061e584b32ad1cc805c59b8a84',1,'vg::count_back_inserter::value_type()'],['../structvg_1_1VectorView_1_1const__iterator.html#a9dbd79edd9a90a030c98fe15df98749c',1,'vg::VectorView::const_iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#ae6286581a32d15a3a27ea7413e38cf4c',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a4864777b7b0405f28848b8a478867cb3',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::value_type()']]],
+ ['valueargspec_6369',['ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand::ValueArgSpec< T, Receiver, Holder >'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#af9860ac96dc38b06b5de9b00ae31ffbe',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, char short_option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a10b4640232a0e4ece857459d903c3809',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)']]],
+ ['valueargspec_3c_20bool_2c_20receiver_20_3e_6370',['ValueArgSpec< bool, Receiver >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
+ ['valueargspec_3c_20t_2c_20receiver_2c_20range_3c_20t_20_3e_20_3e_6371',['ValueArgSpec< T, Receiver, Range< T > >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
+ ['values_6372',['values',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a341b8cdfa0d90adaea6f9c52196b5de6',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t']]],
+ ['var_6373',['var',['../namespacevg.html#afe7fae89b379b5411189ac0ac74b2dd4',1,'vg']]],
+ ['variant_5fadder_2ecpp_6374',['variant_adder.cpp',['../variant__adder_8cpp.html',1,'']]],
+ ['variant_5fadder_2ehpp_6375',['variant_adder.hpp',['../variant__adder_8hpp.html',1,'']]],
+ ['variant_5falts_6376',['variant_alts',['../structvg_1_1VG_1_1Plan.html#ad2b28e3a651018396d6c0a1b3377e161',1,'vg::VG::Plan']]],
+ ['variant_5frange_6377',['variant_range',['../classvg_1_1VariantAdder.html#aa23751086259b5976ffe78169a6000b9',1,'vg::VariantAdder']]],
+ ['variant_5frecall_6378',['variant_recall',['../namespacevg.html#a96096594534e59d12b7a2cff3c400ef0',1,'vg']]],
+ ['variant_5frecall_2ecpp_6379',['variant_recall.cpp',['../variant__recall_8cpp.html',1,'']]],
+ ['variant_5frecall_2ehpp_6380',['variant_recall.hpp',['../variant__recall_8hpp.html',1,'']]],
+ ['variant_5fsource_6381',['variant_source',['../classvg_1_1RareVariantSimplifier.html#afd96f926d4135c8c1ae967ad22aad03a',1,'vg::RareVariantSimplifier']]],
+ ['variant_5fto_5ftraversal_6382',['variant_to_traversal',['../classvg_1_1VG.html#ac697184acf2edadca58ddc776f9f4e7e',1,'vg::VG']]],
+ ['variantadder_6383',['VariantAdder',['../classvg_1_1VariantAdder.html',1,'vg::VariantAdder'],['../classvg_1_1VariantAdder.html#a267056ae90838d3aef2ddfe992a045ff',1,'vg::VariantAdder::VariantAdder()']]],
+ ['variants_5fafter_6384',['variants_after',['../classvg_1_1WindowedVcfBuffer.html#a8c0bf4d78e07bcc7ec8f58287452ad9e',1,'vg::WindowedVcfBuffer']]],
+ ['variants_5fbefore_6385',['variants_before',['../classvg_1_1WindowedVcfBuffer.html#a24156cab3205fcb845418259a91ada3a',1,'vg::WindowedVcfBuffer']]],
+ ['varint_2ecpp_6386',['varint.cpp',['../varint_8cpp.html',1,'']]],
+ ['varint_2ehpp_6387',['varint.hpp',['../varint_8hpp.html',1,'']]],
+ ['varint_5fvector_5ft_6388',['varint_vector_t',['../structvg_1_1varint__vector__t.html',1,'vg']]],
+ ['vars_5fper_5fchunk_6389',['vars_per_chunk',['../classvg_1_1Constructor.html#a7cc8ae0e38492082ba8e886ea174944f',1,'vg::Constructor']]],
+ ['vcf_5fbuffer_2ecpp_6390',['vcf_buffer.cpp',['../vcf__buffer_8cpp.html',1,'']]],
+ ['vcf_5fbuffer_2ehpp_6391',['vcf_buffer.hpp',['../vcf__buffer_8hpp.html',1,'']]],
+ ['vcf_5fcontigs_6392',['vcf_contigs',['../namespacevg.html#a691144860bc63559aaf088d2e052af62',1,'vg']]],
+ ['vcf_5ffixup_6393',['vcf_fixup',['../classvg_1_1VCFOutputCaller.html#ab063824a02c65e499cac3d2ca96ca504',1,'vg::VCFOutputCaller']]],
+ ['vcf_5fheader_6394',['vcf_header',['../classvg_1_1VCFOutputCaller.html#aeb9a75eed0ba2a369439abddf1ac3f65',1,'vg::VCFOutputCaller::vcf_header()'],['../classvg_1_1VCFGenotyper.html#a8dae0df9c45f88aadca9fcaa8d0e7214',1,'vg::VCFGenotyper::vcf_header()'],['../classvg_1_1LegacyCaller.html#a4536625fdb753727a7d8321cadc6946b',1,'vg::LegacyCaller::vcf_header()'],['../classvg_1_1FlowCaller.html#a2c4e7365e43593313a30d7d4ea03c4a9',1,'vg::FlowCaller::vcf_header()'],['../classvg_1_1NestedFlowCaller.html#a38c3758ea8fd04852eb62c40ec9be010',1,'vg::NestedFlowCaller::vcf_header()'],['../classvg_1_1MCMCCaller.html#af67e8bf51b99831bd5b9f67c2581d084',1,'vg::MCMCCaller::vcf_header()']]],
+ ['vcf_5finput_6395',['vcf_input',['../structHaplotypesConfig.html#a8d58855b93c6c570420598f99f2d8ea2',1,'HaplotypesConfig']]],
+ ['vcf_5fis_5fphased_6396',['vcf_is_phased',['../classvg_1_1IndexRegistry.html#abeceb0062997804e84372c7bca76c8ae',1,'vg::IndexRegistry']]],
+ ['vcf_5fto_5ffasta_6397',['vcf_to_fasta',['../classvg_1_1NameMapper.html#a6e8c36e6207dbc905170bde6a5c396b3',1,'vg::NameMapper']]],
+ ['vcf_5fto_5ffasta_5frenames_6398',['vcf_to_fasta_renames',['../classvg_1_1NameMapper.html#afd130381fc9ad1a930932e672fda80d1',1,'vg::NameMapper']]],
+ ['vcfbuffer_6399',['VcfBuffer',['../classvg_1_1VcfBuffer.html',1,'vg::VcfBuffer'],['../classvg_1_1VcfBuffer.html#a402d5cadd95f5725876b22b8c9bd830b',1,'vg::VcfBuffer::VcfBuffer(vcflib::VariantCallFile *file=nullptr)'],['../classvg_1_1VcfBuffer.html#ad388f47df62ebab69ab9188efd37be1e',1,'vg::VcfBuffer::VcfBuffer(const VcfBuffer &other)=delete']]],
+ ['vcfgenotyper_6400',['VCFGenotyper',['../classvg_1_1VCFGenotyper.html',1,'vg::VCFGenotyper'],['../classvg_1_1VCFGenotyper.html#a8c65e87515bd32e6f90bba45712175bf',1,'vg::VCFGenotyper::VCFGenotyper()']]],
+ ['vcfoutputcaller_6401',['VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html',1,'vg::VCFOutputCaller'],['../classvg_1_1VCFOutputCaller.html#ad758f9180a51784374ef044b54883f87',1,'vg::VCFOutputCaller::VCFOutputCaller()']]],
+ ['vcfrecordconverter_6402',['VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html',1,'vg']]],
+ ['vcfrecordfilter_6403',['VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html',1,'vg']]],
+ ['vcftraversalfinder_6404',['VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html',1,'vg::VCFTraversalFinder'],['../classvg_1_1VCFTraversalFinder.html#aaa8aa0b5cbe8a0e2ff664b6b385339da',1,'vg::VCFTraversalFinder::VCFTraversalFinder()']]],
+ ['vectorizablehandlegraph_6405',['VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html',1,'handlegraph::VectorizableHandleGraph'],['../namespacevg.html#a449aa64ac606119e59f71cecb8a3b218',1,'vg::VectorizableHandleGraph()']]],
+ ['vectorize_5fmain_2ecpp_6406',['vectorize_main.cpp',['../vectorize__main_8cpp.html',1,'']]],
+ ['vectorizer_6407',['Vectorizer',['../classVectorizer.html',1,'Vectorizer'],['../classVectorizer.html#ac6f2b56806bc2e8444492cb3d32f42be',1,'Vectorizer::Vectorizer()']]],
+ ['vectorizer_2ecpp_6408',['vectorizer.cpp',['../vectorizer_8cpp.html',1,'']]],
+ ['vectorizer_2ehpp_6409',['vectorizer.hpp',['../vectorizer_8hpp.html',1,'']]],
+ ['vectorview_6410',['VectorView',['../structvg_1_1VectorView.html',1,'vg::VectorView< Item >'],['../structvg_1_1VectorView.html#aefb5d25c5ced8c23549c605abb29c09f',1,'vg::VectorView::VectorView()'],['../structvg_1_1VectorView.html#adaf1a835fd36e7c4194d4ee53adc4528',1,'vg::VectorView::VectorView(const VectorView &other)=default'],['../structvg_1_1VectorView.html#ac6ad816ef159fe1b9dad8c9539a5b8de',1,'vg::VectorView::VectorView(VectorView &&other)=default'],['../structvg_1_1VectorView.html#ace693cb938bdc8545ff2d00faf2c9136',1,'vg::VectorView::VectorView(const vector< Item > &items)'],['../structvg_1_1VectorView.html#a5e4711cb47476cfe22eccef4823d4fa8',1,'vg::VectorView::VectorView(const vector< Item > &items, const vector< size_t > &indexes)']]],
+ ['vectorviewinverse_6411',['VectorViewInverse',['../classvg_1_1VectorViewInverse.html',1,'vg::VectorViewInverse'],['../classvg_1_1VectorViewInverse.html#a6f4c737e0dc739eca4f09a472e520335',1,'vg::VectorViewInverse::VectorViewInverse()'],['../classvg_1_1VectorViewInverse.html#ab87205a1d88681364f2768e778e87c8d',1,'vg::VectorViewInverse::VectorViewInverse(const VectorView< Item > &view)']]],
+ ['verbose_6412',['verbose',['../classvg_1_1NestedTraversalFinder.html#a67980934b7315e90dcd63fa046b465b7',1,'vg::NestedTraversalFinder::verbose()'],['../classvg_1_1ReadFilter.html#aa207b19d222c64919714bae506b726a6',1,'vg::ReadFilter::verbose()'],['../classvg_1_1RepresentativeTraversalFinder.html#a6af3519805d1115b006ad8b3bf2d3a3e',1,'vg::RepresentativeTraversalFinder::verbose()'],['../classvg_1_1io_1_1MessageIterator.html#af3f1540514c644f1d01212d515f603e6',1,'vg::io::MessageIterator::verbose()']]],
+ ['verbosity_6413',['verbosity',['../structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579',1,'vg::IndexingParameters::verbosity()'],['../classvg_1_1HaplotypePartitioner.html#ac5d1210d753c0fe6ed936f18f02e2cd2',1,'vg::HaplotypePartitioner::verbosity()'],['../classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12',1,'vg::Recombinator::verbosity()'],['../structHaplotypesConfig.html#ad04e07b242265b989bc2b93479676b84',1,'HaplotypesConfig::verbosity()'],['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3',1,'vg::IndexingParameters::Verbosity()'],['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28a',1,'vg::Haplotypes::Verbosity()'],['../classvg_1_1HaplotypePartitioner.html#a7b5fa99a041f7c61f73644541dd926b1',1,'vg::HaplotypePartitioner::Verbosity()'],['../classvg_1_1Recombinator.html#a097faaea0512d01e5e7732dd1991f129',1,'vg::Recombinator::Verbosity()']]],
+ ['verbosity_5fbasic_6414',['verbosity_basic',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa718364c23222ec5e7444240be0799449',1,'vg::Haplotypes']]],
+ ['verbosity_5fdebug_6415',['verbosity_debug',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aaa92669d64637a1583a113eb279234241',1,'vg::Haplotypes']]],
+ ['verbosity_5fdetailed_6416',['verbosity_detailed',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa8c3562efded9b2b9ae9fd7ee05594ce0',1,'vg::Haplotypes']]],
+ ['verbosity_5fsilent_6417',['verbosity_silent',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aadd4472c60bf6446f52a09a0d41140a21',1,'vg::Haplotypes']]],
+ ['verify_5fpath_6418',['verify_path',['../namespacevg.html#a3ed0a4f26673002b2081832a7602e9bd',1,'vg']]],
+ ['verify_5fpaths_6419',['verify_paths',['../classvg_1_1PhaseUnfolder.html#a910deba7dd5b5f9bce7a1da4e53cfeb1',1,'vg::PhaseUnfolder']]],
+ ['verify_5fvalid_5flog_5fodds_5fscore_5fmatrix_6420',['verify_valid_log_odds_score_matrix',['../classvg_1_1GSSWAligner.html#acc5d3a8c0c22cbd966e96a42eb095cd8',1,'vg::GSSWAligner']]],
+ ['version_6421',['Version',['../classvg_1_1Version.html',1,'vg::Version'],['../structvg_1_1Haplotypes_1_1Header.html#ac2e1810f289c24ac4c2f74d8df9df5ec',1,'vg::Haplotypes::Header::version()'],['../classvg_1_1ZipCodeCollection.html#ad97d400ad51f2d7d1a880d81bbf8993d',1,'vg::ZipCodeCollection::version()'],['../structvg_1_1Haplotypes_1_1Header.html#a68bfc0fe68e8fc1b42ad078eaa234777',1,'vg::Haplotypes::Header::VERSION()'],['../classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222',1,'vg::Version::VERSION()'],['../classvg_1_1Version.html#a05bb9f14c7597bf90a2981db7e59b058',1,'vg::Version::Version()=delete']]],
+ ['version_2ecpp_6422',['version.cpp',['../version_8cpp.html',1,'']]],
+ ['version_2ehpp_6423',['version.hpp',['../version_8hpp.html',1,'']]],
+ ['version_5fmain_2ecpp_6424',['version_main.cpp',['../version__main_8cpp.html',1,'']]],
+ ['vg_6425',['VG',['../classvg_1_1VG.html',1,'vg::VG'],['../namespacevg.html',1,'vg'],['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a5e978449ccc729202c33e2dc543b8327',1,'vg::IndexingParameters::VG()'],['../classvg_1_1VG.html#ac2399de59931e282fb1f4d3da9a8dcb1',1,'vg::VG::VG(void)'],['../classvg_1_1VG.html#a2dc9648985454d3aedd9a477ff0c52b2',1,'vg::VG::VG(istream &in, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#a0fbb777fd8ab6050124a6eaf9eca9133',1,'vg::VG::VG(const function< void(const function< void(Graph &)> &)> &send_graphs, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#af4d321b31b873153431c261090d052af',1,'vg::VG::VG(const Graph &from, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#abeafee2d3bc6e0039e99fccdea10f4f9',1,'vg::VG::VG(set< Node * > &nodes, set< Edge * > &edges)'],['../classvg_1_1VG.html#a3148455330df9ac055c6bd1eb7da3167',1,'vg::VG::VG(const VG &other)'],['../classvg_1_1VG.html#ab8365ccd6a093ec50f7d54b1c7a7c672',1,'vg::VG::VG(VG &&other) noexcept'],['../classvg_1_1FlowSort.html#abd481c5b9e6c9c5aeaf846652dd3c76f',1,'vg::FlowSort::vg()']]],
+ ['vg_2ecpp_6426',['vg.cpp',['../vg_8cpp.html',1,'']]],
+ ['vg_2ehpp_6427',['vg.hpp',['../vg_8hpp.html',1,'']]],
+ ['vg_2eproto_6428',['vg.proto',['../vg_8proto.html',1,'']]],
+ ['vg_5fbuild_5fhost_6429',['VG_BUILD_HOST',['../vg__environment__version_8hpp.html#a2baea5938fa1a9b70e6a27ccc59c65d9',1,'vg_environment_version.hpp']]],
+ ['vg_5fbuild_5fuser_6430',['VG_BUILD_USER',['../vg__environment__version_8hpp.html#a95dd87e623e9d0c99f662e3d2ca6676d',1,'vg_environment_version.hpp']]],
+ ['vg_5fcompiler_5fversion_6431',['VG_COMPILER_VERSION',['../vg__environment__version_8hpp.html#a018858ebcbef9ca466d11e0f9effd990',1,'vg_environment_version.hpp']]],
+ ['vg_5fenvironment_5fversion_2ehpp_6432',['vg_environment_version.hpp',['../vg__environment__version_8hpp.html',1,'']]],
+ ['vg_5ffilename_6433',['vg_filename',['../classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0',1,'vg::IndexedVG']]],
+ ['vg_5fgit_5fversion_6434',['VG_GIT_VERSION',['../vg__git__version_8hpp.html#a5df50394a80dec8f6151eb57db04a38a',1,'vg_git_version.hpp']]],
+ ['vg_5fgit_5fversion_2ehpp_6435',['vg_git_version.hpp',['../vg__git__version_8hpp.html',1,'']]],
+ ['vg_5fhelp_6436',['vg_help',['../main_8cpp.html#aae3a18cc6fba2e4bf97e9a01f4734f4f',1,'main.cpp']]],
+ ['vg_5fhtslib_5fversion_6437',['VG_HTSLIB_VERSION',['../version_8cpp.html#a0b12716ad9e947816319b2c448b942f3',1,'version.cpp']]],
+ ['vg_5fmain_6438',['vg_main',['../main_8cpp.html#a8b9f48d3aed7bbfe82cdc4f092867c50',1,'main.cpp']]],
+ ['vg_5fos_6439',['VG_OS',['../vg__environment__version_8hpp.html#a4b1110f54b4fd6d1242837dee0dbc820',1,'vg_environment_version.hpp']]],
+ ['vg_5fpreflight_5feverywhere_6440',['VG_PREFLIGHT_EVERYWHERE',['../preflight_8hpp.html#a15a8edc41d783e0cc08568efe26a83fd',1,'preflight.hpp']]],
+ ['vg_5fset_2ecpp_6441',['vg_set.cpp',['../vg__set_8cpp.html',1,'']]],
+ ['vg_5fset_2ehpp_6442',['vg_set.hpp',['../vg__set_8hpp.html',1,'']]],
+ ['vg_5fstandard_5flibrary_5fversion_6443',['VG_STANDARD_LIBRARY_VERSION',['../version_8cpp.html#a923fcc9a50a1ddbec3aa567d4f91d576',1,'version.cpp']]],
+ ['vgalignmentemitter_6444',['VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html',1,'vg::io::VGAlignmentEmitter'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#af278878b244808a182eae17640f23a45',1,'vg::io::VGAlignmentEmitter::VGAlignmentEmitter()']]],
+ ['vgindexes_6445',['VGIndexes',['../structvg_1_1VGIndexes.html',1,'vg']]],
+ ['vgset_6446',['VGset',['../classvg_1_1VGset.html',1,'vg::VGset'],['../classvg_1_1VGset.html#a5ff9a6c4fa0223bcee7072f86a657751',1,'vg::VGset::VGset()'],['../classvg_1_1VGset.html#a6adbb25be82de20911fd901da4e9fe41',1,'vg::VGset::VGset(vector< string > &files)']]],
+ ['view_5fmain_2ecpp_6447',['view_main.cpp',['../view__main_8cpp.html',1,'']]],
+ ['view_5fmultipath_5falignment_6448',['view_multipath_alignment',['../namespacevg.html#a411a023efbe439f069829603a2775673',1,'vg']]],
+ ['view_5fmultipath_5falignment_5fas_5fdot_6449',['view_multipath_alignment_as_dot',['../namespacevg.html#a716909fc23ddaab59e0d2bf89fdd1ae3',1,'vg']]],
+ ['visit_6450',['Visit',['../structvg_1_1Visit.html',1,'vg::Visit'],['../structvg_1_1SnarlTraversal.html#aff14559c1e4fb55bdf87320f3a4ee636',1,'vg::SnarlTraversal::visit()']]],
+ ['visit_5fcontained_5fsnarls_6451',['visit_contained_snarls',['../namespacevg.html#ae3a49e3aea82c8e552e4cf9fd8396ad4',1,'vg']]],
+ ['visit_5fnext_5fnode_6452',['visit_next_node',['../classvg_1_1ExhaustiveTraversalFinder.html#a2cec9de94838e3575a20271db01a1a4f',1,'vg::ExhaustiveTraversalFinder::visit_next_node()'],['../classvg_1_1SupportRestrictedTraversalFinder.html#a9cdb3b8f554e58cba6fea9c2ccb40e14',1,'vg::SupportRestrictedTraversalFinder::visit_next_node()']]],
+ ['visited_6453',['visited',['../classvg_1_1HandleGraphNodeSet.html#a6a1318a8e451562f282bf960032634f4',1,'vg::HandleGraphNodeSet']]],
+ ['visits_5fleft_6454',['visits_left',['../classvg_1_1SnarlManager.html#a27e95077ab5c9a7288f2833d5e66433e',1,'vg::SnarlManager']]],
+ ['visits_5fright_6455',['visits_right',['../classvg_1_1SnarlManager.html#a567554948e5dc03604a46972eb42d295',1,'vg::SnarlManager']]],
+ ['viz_6456',['Viz',['../classvg_1_1Viz.html',1,'vg::Viz'],['../classvg_1_1Viz.html#a8e9440d6c67fde7f10fe9c0366759041',1,'vg::Viz::Viz(void)'],['../classvg_1_1Viz.html#a5d343eb2d20b2db1eb66def4b8d3081c',1,'vg::Viz::Viz(PathHandleGraph *x, vector< Packer > *p, const vector< string > &n, const string &o, int w, int h, bool c, bool d, bool t)']]],
+ ['viz_2ecpp_6457',['viz.cpp',['../viz_8cpp.html',1,'']]],
+ ['viz_2ehpp_6458',['viz.hpp',['../viz_8hpp.html',1,'']]],
+ ['viz_5fmain_2ecpp_6459',['viz_main.cpp',['../viz__main_8cpp.html',1,'']]],
+ ['vpkg_6460',['VPKG',['../classvg_1_1io_1_1VPKG.html',1,'vg::io']]],
+ ['vpkg_2ecpp_6461',['vpkg.cpp',['../vpkg_8cpp.html',1,'']]],
+ ['vpkg_2ehpp_6462',['vpkg.hpp',['../vpkg_8hpp.html',1,'']]],
+ ['vpmax_6463',['vpmax',['../namespacevg.html#aec4813274fc2af3d83679e128fdeb32f',1,'vg']]]
];
diff --git a/search/all_17.js b/search/all_17.js
index 169c89a6f2..8788e2e243 100644
--- a/search/all_17.js
+++ b/search/all_17.js
@@ -1,144 +1,144 @@
var searchData=
[
- ['w_6462',['w',['../structHaplotypesConfig.html#afc08b5bf2dd526161ebb29c1ea37d1b4',1,'HaplotypesConfig::w()'],['../namespacehaplotypes__defaults.html#a9e7cea9525076e8d069877c9f1a08552',1,'haplotypes_defaults::w()']]],
- ['wabbit_5fmap_6463',['wabbit_map',['../classVectorizer.html#abc8fdb5dcd0ccc39c2b042633ef6820e',1,'Vectorizer']]],
- ['wabbitize_6464',['wabbitize',['../classVectorizer.html#ae4c3627b5c8ec7b066f5735ca6dfb3f1',1,'Vectorizer']]],
- ['wait_5ffor_5fregion_6465',['wait_for_region',['../classvg_1_1GraphSynchronizer.html#a7f9e68c4e2172bc4a5c7040272a59d38',1,'vg::GraphSynchronizer']]],
- ['walk_2ecpp_6466',['walk.cpp',['../walk_8cpp.html',1,'']]],
- ['walk_2ehpp_6467',['walk.hpp',['../walk_8hpp.html',1,'']]],
- ['walk_5fbackwards_6468',['walk_backwards',['../classvg_1_1NGSSimulator.html#a3b87398480be75b240a98d270bfc843c',1,'vg::NGSSimulator']]],
- ['walk_5fbackwards_5falong_5falignment_6469',['walk_backwards_along_alignment',['../classvg_1_1NGSSimulator.html#af033e5bc63e8407c917f151a4311b64d',1,'vg::NGSSimulator']]],
- ['walk_5ffanout_5fpath_6470',['walk_fanout_path',['../classvg_1_1BaseMapper.html#ad52deed127976201bd63b32929b71491',1,'vg::BaseMapper']]],
- ['walk_5fhaplotype_5ffrequency_6471',['walk_haplotype_frequency',['../namespacevg_1_1algorithms.html#a4af5e9c480c0dc7d0843cf981cd52c32',1,'vg::algorithms']]],
- ['walk_5fhaplotype_5fnames_6472',['walk_haplotype_names',['../namespacevg_1_1algorithms.html#abe9cb62b2ae1c6eb08b10f172980788d',1,'vg::algorithms']]],
- ['walk_5flisteners_6473',['walk_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a349711aec5bbd3063812eae72727c170',1,'vg::algorithms::GFAParser']]],
- ['walk_5ft_6474',['walk_t',['../structvg_1_1algorithms_1_1walk__t.html',1,'vg::algorithms::walk_t'],['../structvg_1_1algorithms_1_1walk__t.html#a5a5ed7ca0dac4f9e742ddeeb28e317e1',1,'vg::algorithms::walk_t::walk_t(uint16_t l, const pos_t &b, const pos_t &e, const handle_t &c, uint16_t f)'],['../structvg_1_1algorithms_1_1walk__t.html#af8c4463befc5bb6cec73b3e493acf545',1,'vg::algorithms::walk_t::walk_t(const std::string &s, const pos_t &b, const pos_t &e, const handle_t &c)']]],
- ['wang_5fhash_6475',['wang_hash',['../structvg_1_1wang__hash.html',1,'vg']]],
- ['wang_5fhash_2ehpp_6476',['wang_hash.hpp',['../wang__hash_8hpp.html',1,'']]],
- ['wang_5fhash_3c_20handle_5ft_20_3e_6477',['wang_hash< handle_t >',['../structvg_1_1wang__hash_3_01handle__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_6478',['wang_hash< handlegraph::net_handle_t >',['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20net_5fidentifier_5ft_20_3e_6479',['wang_hash< net_identifier_t >',['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20nodeside_20_3e_6480',['wang_hash< NodeSide >',['../structvg_1_1wang__hash_3_01NodeSide_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20nodetraversal_20_3e_6481',['wang_hash< NodeTraversal >',['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20path_5fhandle_5ft_20_3e_6482',['wang_hash< path_handle_t >',['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20std_3a_3apair_3c_20a_2c_20b_20_3e_20_3e_6483',['wang_hash< std::pair< A, B > >',['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20t_20_2a_20_3e_6484',['wang_hash< T * >',['../structvg_1_1wang__hash_3_01T_01_5_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20t_2c_20typename_20std_3a_3aenable_5fif_3c_20std_3a_3ais_5fintegral_3c_20t_20_3e_3a_3avalue_20_3e_3a_3atype_20_3e_6485',['wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >',['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html',1,'vg']]],
- ['wang_5fhash_5f64_6486',['wang_hash_64',['../namespacevg.html#a38d35bca25e8a6d5fe10f603cb9048c3',1,'vg']]],
- ['want_5fbreakpoint_6487',['want_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#ac0698f3b6387ce47f4e9d5b2929d6cf4',1,'vg::io::StreamMultiplexer']]],
- ['warn_5fon_5fambiguous_6488',['warn_on_ambiguous',['../classvg_1_1Constructor.html#a24e663d6eee52a9f723faf398cf720fa',1,'vg::Constructor']]],
- ['warn_5fon_5flowercase_6489',['warn_on_lowercase',['../classvg_1_1Constructor.html#a9da8d803e6e0c0be942ca2ecc35e9267',1,'vg::Constructor']]],
- ['warn_5fon_5fmissing_5fvariants_6490',['warn_on_missing_variants',['../classvg_1_1HaplotypeIndexer.html#afb3592792a7d781cb6e88fe7949b7bfe',1,'vg::HaplotypeIndexer']]],
- ['warn_5fon_5fscore_5ffail_6491',['warn_on_score_fail',['../namespacehaplo.html#ab22b0954ba9062360178078ce504f1c2',1,'haplo']]],
- ['warned_5fabout_5fbad_5fdistribution_6492',['warned_about_bad_distribution',['../classvg_1_1MinimizerMapper.html#a3915618267605133f2e9144c693e68e5',1,'vg::MinimizerMapper']]],
- ['warned_5fabout_5fchunking_6493',['warned_about_chunking',['../classvg_1_1Mapper.html#a45dffe2dc008aebd254388281034d27f',1,'vg::Mapper']]],
- ['warned_5fabout_5frescue_5fsize_6494',['warned_about_rescue_size',['../classvg_1_1MinimizerMapper.html#a70bd402b25f6008362e82858be9fe9bc',1,'vg::MinimizerMapper']]],
- ['warned_5fabout_5frewrites_6495',['warned_about_rewrites',['../classvg_1_1VG.html#a8f0519dc706937b8b593f803f3d8eac4',1,'vg::VG']]],
- ['warned_5fabout_5fsubgraph_5fsize_6496',['warned_about_subgraph_size',['../classvg_1_1Surjector.html#affb3a5676516b7042d5c2d08734ea3c8',1,'vg::Surjector']]],
- ['warned_5fabout_5ftail_5fsize_6497',['warned_about_tail_size',['../classvg_1_1MinimizerMapper.html#a0b74ef2cf6f1fd04290172a91623584a',1,'vg::MinimizerMapper']]],
- ['was_5fcorrect_6498',['was_correct',['../classvg_1_1Funnel.html#aac71f37530afee1b7e49770aff8cc53b',1,'vg::Funnel::was_correct(size_t prev_stage_item) const'],['../classvg_1_1Funnel.html#a5f0037505a9df13b92e381f5ff108d72',1,'vg::Funnel::was_correct(size_t prev_stage_index, const string &prev_stage_name, size_t prev_stage_item) const']]],
- ['was_5fprovided_5fdirectly_6499',['was_provided_directly',['../classvg_1_1IndexFile.html#afabf00d9034342540b3614dfc7055715',1,'vg::IndexFile']]],
- ['was_5fset_6500',['was_set',['../structvg_1_1subcommand_1_1ArgSpec.html#acfb22902f7ebf4d8053ec39999dd2821',1,'vg::subcommand::ArgSpec::was_set()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aac6bd613601f636c187b684a69fa25ce',1,'vg::subcommand::ValueArgSpec::was_set()']]],
- ['watchdog_6501',['Watchdog',['../classvg_1_1Watchdog.html',1,'vg::Watchdog'],['../classvg_1_1Watchdog.html#a87e679ecbb8461ae6a26a1958216629b',1,'vg::Watchdog::Watchdog(size_t thread_count, const duration &timeout)'],['../classvg_1_1Watchdog.html#a2934cc5c1fc3b7d0ab20343e6bde1a56',1,'vg::Watchdog::Watchdog(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a73aa9888b0017ed46053c75c085f2748',1,'vg::Watchdog::Watchdog(Watchdog &&other)=delete']]],
- ['watchdog_2ecpp_6502',['watchdog.cpp',['../watchdog_8cpp.html',1,'']]],
- ['watchdog_2ehpp_6503',['watchdog.hpp',['../watchdog_8hpp.html',1,'']]],
- ['watchdog_5ftimeout_6504',['watchdog_timeout',['../structGiraffeMainOptions.html#a51b24824ec0a06a5b080f8578090fa56',1,'GiraffeMainOptions']]],
- ['watcher_6505',['watcher',['../classvg_1_1Watchdog.html#a39ef2d296adea6283596aadd48457e02',1,'vg::Watchdog']]],
- ['watcher_5floop_6506',['watcher_loop',['../classvg_1_1Watchdog.html#ad2e2c831258c42fdba7f2d0fa8625cc9',1,'vg::Watchdog']]],
- ['wavefronts_6507',['wavefronts',['../structvg_1_1WFANode.html#a6b8938c80565dd8c9219945b2a5be194',1,'vg::WFANode']]],
- ['weakly_5fconnected_5fcomponents_6508',['weakly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a96c80b09388c6d079754c66d2f7362e5',1,'handlegraph::algorithms']]],
- ['weakly_5fconnected_5fcomponents_2ecpp_6509',['weakly_connected_components.cpp',['../weakly__connected__components_8cpp.html',1,'']]],
- ['weakly_5fconnected_5fcomponents_5fwith_5ftips_6510',['weakly_connected_components_with_tips',['../namespacehandlegraph_1_1algorithms.html#aa5ff9ed76bd82438b3af0c3112437ccd',1,'handlegraph::algorithms']]],
- ['weibull_5fcdf_6511',['weibull_cdf',['../namespacevg.html#a100efe5dfc5bfe434b53416f93d2a0e1',1,'vg']]],
- ['weibull_5flog_5flikelihood_6512',['weibull_log_likelihood',['../namespacevg.html#ad93405cf370e6d92396691fc3320be1c',1,'vg']]],
- ['weight_6513',['weight',['../classvg_1_1MEMChainModelVertex.html#ad73c85aeb85dde48dd3201260720956b',1,'vg::MEMChainModelVertex::weight()'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a5e9984583bd37a31e8b172fea582e6fd',1,'vg::MEMClusterer::HitEdge::weight()'],['../classvg_1_1AlignmentChainModelVertex.html#a874c1b3121234990ab1c1519921b9c6c',1,'vg::AlignmentChainModelVertex::weight()'],['../structvg_1_1algorithms_1_1Edge.html#a25cfc0a5279fb8d40cc7527099449dc1',1,'vg::algorithms::Edge::weight()'],['../structvg_1_1algorithms_1_1Node.html#a38e105d20eb7efa802dd6b07824cd620',1,'vg::algorithms::Node::weight()']]],
- ['weighted_5fjaccard_5fcoefficient_6514',['weighted_jaccard_coefficient',['../namespacevg.html#aa0b9062cb7b053e7823169d589e113d1',1,'vg']]],
- ['weightedgraph_6515',['WeightedGraph',['../structvg_1_1FlowSort_1_1WeightedGraph.html',1,'vg::FlowSort']]],
- ['wellford_5fmean_5fvar_6516',['wellford_mean_var',['../namespacevg.html#a4b96cd801bc780d426db346f80ab2172',1,'vg']]],
- ['wellford_5fupdate_6517',['wellford_update',['../namespacevg.html#a614c672ed69c280b699a278ce0f34ade',1,'vg']]],
- ['wfa_5falignment_5fto_5falignment_6518',['wfa_alignment_to_alignment',['../classvg_1_1MinimizerMapper.html#a597914c2167ca2b06a3dccbb23e21340',1,'vg::MinimizerMapper']]],
- ['wfa_5fdistance_6519',['wfa_distance',['../classvg_1_1MinimizerMapper.html#adde3e90703e3137d7cb8a0e0c217686b',1,'vg::MinimizerMapper']]],
- ['wfa_5fdistance_5fper_5fbase_6520',['wfa_distance_per_base',['../classvg_1_1MinimizerMapper.html#ae77b975a0ba7e7bddf4d01e92074c1de',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fdistance_6521',['wfa_max_distance',['../classvg_1_1MinimizerMapper.html#a99da16075a34ebad4a01fe94f5d7d4cf',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fmax_5fmismatches_6522',['wfa_max_max_mismatches',['../classvg_1_1MinimizerMapper.html#a65d94bb81e375a2affda69e92e131908',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fmismatches_6523',['wfa_max_mismatches',['../classvg_1_1MinimizerMapper.html#a16b9080b48c374fd3a8d927368379bba',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fmismatches_5fper_5fbase_6524',['wfa_max_mismatches_per_base',['../classvg_1_1MinimizerMapper.html#af1800dc292b642aa366730c8f6034475',1,'vg::MinimizerMapper']]],
- ['wfa_5fmiddle_6525',['wfa_middle',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a18a47b29e26174cc24a57f71ec8f5f9c',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
- ['wfa_5ftail_6526',['wfa_tail',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#aaf4d71d87fb51ba736806a35cb6f1bc0',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
- ['wfaalignment_6527',['WFAAlignment',['../structvg_1_1WFAAlignment.html',1,'vg']]],
- ['wfaextender_6528',['WFAExtender',['../classvg_1_1WFAExtender.html',1,'vg::WFAExtender'],['../classvg_1_1WFAExtender.html#a7d7324769e3d80c6acdd68de034c5830',1,'vg::WFAExtender::WFAExtender()'],['../classvg_1_1WFAExtender.html#a9cc09b85da35171c971868e80cfe2938',1,'vg::WFAExtender::WFAExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner, const ErrorModel &error_model=default_error_model)']]],
- ['wfanode_6529',['WFANode',['../structvg_1_1WFANode.html',1,'vg::WFANode'],['../structvg_1_1WFANode.html#a93d02d2b8f73a4cdcbe5a356258cb5e8',1,'vg::WFANode::WFANode()']]],
- ['wfapoint_6530',['WFAPoint',['../structvg_1_1WFAPoint.html',1,'vg']]],
- ['wfatree_6531',['WFATree',['../classvg_1_1WFATree.html',1,'vg::WFATree'],['../classvg_1_1WFATree.html#ad9880bb173f2bd8e2cdc3708cbb8005f',1,'vg::WFATree::WFATree()']]],
- ['what_6532',['what',['../classvg_1_1NoAlignmentInBandException.html#a006dddb79b9d1c6035c2466c35dbcacf',1,'vg::NoAlignmentInBandException::what()'],['../classvg_1_1InsufficientInputException.html#ae9fd64e80e950783955ff7d875138469',1,'vg::InsufficientInputException::what()'],['../classvg_1_1RewindPlanException.html#a5d3526ac6c26a49f65a962f12c246615',1,'vg::RewindPlanException::what()'],['../classvg_1_1SizeLimitExceededException.html#acb8fbb8940007b68bede049fcf19b046',1,'vg::SizeLimitExceededException::what()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#a7fdc5893f8439a8c8c6169865a8c6e0d',1,'vg::algorithms::GFAFormatError::what()'],['../classj2pb__error.html#a4ac3313fff0e2721ca9480b61ebe6a8b',1,'j2pb_error::what()']]],
- ['which_5fhaplotype_6533',['which_haplotype',['../classvg_1_1PhasedGenome_1_1iterator.html#a02b60bd3c0ec6d86a8bec582e717ea15',1,'vg::PhasedGenome::iterator']]],
- ['whitespace_6534',['whitespace',['../namespacevg.html#a466eef41b2208daa1c649e71022cdc44',1,'vg']]],
- ['whole_5falignment_5fcutoff_6535',['whole_alignment_cutoff',['../classvg_1_1VariantAdder.html#ab40df39042e4ce4fee3eeea919be1c96',1,'vg::VariantAdder']]],
- ['whole_5fgraph_5flock_6536',['whole_graph_lock',['../classvg_1_1GraphSynchronizer.html#aa1a7be56b29656fa604b44b37e134c80',1,'vg::GraphSynchronizer']]],
- ['wideningprng_6537',['WideningPRNG',['../classvg_1_1WideningPRNG.html',1,'vg::WideningPRNG< PRNG, OutType >'],['../classvg_1_1WideningPRNG.html#a5437179a5230df00551a618df6bc4c53',1,'vg::WideningPRNG::WideningPRNG()']]],
- ['widest_5fdijkstra_6538',['widest_dijkstra',['../namespacevg_1_1algorithms.html#a08c6d85f2dc09c22c5d14ed81808769e',1,'vg::algorithms']]],
- ['widget_6539',['WIDGET',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838afa639842a4d69790c890c94b80e27792',1,'vg::subcommand']]],
- ['window_5fbreaking_5fquality_6540',['window_breaking_quality',['../classvg_1_1MinimizerMapper.html#a7999b2f0a931930bfa9eddec4065b51b',1,'vg::MinimizerMapper']]],
- ['window_5flength_6541',['window_length',['../classvg_1_1Filter.html#ad719ad4c073cbe1298c9911e1c1cb329',1,'vg::Filter']]],
- ['window_5fof_5fid_6542',['window_of_id',['../classvg_1_1StreamIndexBase.html#a320b27d89fbc1a74574cc00befe1e7fe',1,'vg::StreamIndexBase']]],
- ['window_5fshift_6543',['WINDOW_SHIFT',['../classvg_1_1StreamIndexBase.html#a1f8223f4ff9ca3d9892d13d2708aff73',1,'vg::StreamIndexBase']]],
- ['window_5fsize_6544',['window_size',['../classvg_1_1WindowedVcfBuffer.html#a898deb05050ba62533e294b7cf959fe3',1,'vg::WindowedVcfBuffer::window_size()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a7fb1665349757422a2868159d2b66437',1,'vg::MinimizerMapper::Minimizer::window_size()']]],
- ['window_5ft_6545',['window_t',['../classvg_1_1StreamIndexBase.html#ad94010282265d6d8743f31ed5b3e98ce',1,'vg::StreamIndexBase']]],
- ['window_5fto_5fstart_6546',['window_to_start',['../classvg_1_1StreamIndexBase.html#a47fab2baab7953595105558d0fcba4e2',1,'vg::StreamIndexBase']]],
- ['windowedvcfbuffer_6547',['WindowedVcfBuffer',['../classvg_1_1WindowedVcfBuffer.html',1,'vg::WindowedVcfBuffer'],['../classvg_1_1WindowedVcfBuffer.html#a7d7af1d1441bab6c687bdf1be7fc4675',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(vcflib::VariantCallFile *file, size_t window_size)'],['../classvg_1_1WindowedVcfBuffer.html#aa57da13990d5983d5e8aa787dfe56995',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(const WindowedVcfBuffer &other)=delete']]],
- ['with_5fcache_5fentry_6548',['with_cache_entry',['../classvg_1_1IndexedVG.html#ac14226d9ccd03cb99af9a08cef31d6ff',1,'vg::IndexedVG']]],
- ['with_5fcursor_6549',['with_cursor',['../classvg_1_1IndexedVG.html#af380961c8e8b342ba8f688c2f073de2e',1,'vg::IndexedVG']]],
- ['with_5fdagified_5flocal_5fgraph_6550',['with_dagified_local_graph',['../classvg_1_1MinimizerMapper.html#a96b3c359c5f86557ddccfdedd67af570',1,'vg::MinimizerMapper']]],
- ['with_5fexception_5fhandling_6551',['with_exception_handling',['../namespacevg.html#a1d2cbe5fe5e1b8a33b7d707f7059b3c6',1,'vg']]],
- ['with_5ffunction_5fcalling_5fstream_6552',['with_function_calling_stream',['../namespacevg_1_1io.html#a8b1a63276edf814575b7afb3b2b9844d',1,'vg::io']]],
- ['with_5fpath_5findex_6553',['with_path_index',['../classvg_1_1GraphSynchronizer.html#a336f5828883adce86ee5e536f8c299ea',1,'vg::GraphSynchronizer']]],
- ['with_5fprogress_6554',['with_progress',['../classvg_1_1Progressive.html#ab44ff020fc951b95dfcd1252c015a020',1,'vg::Progressive']]],
- ['with_5fputback_6555',['with_putback',['../classvg_1_1io_1_1VPKG.html#a0bcbb5a28413d3599a642cd5f22d93be',1,'vg::io::VPKG']]],
- ['with_5fsave_5fstream_6556',['with_save_stream',['../classvg_1_1io_1_1VPKG.html#a030910ec652e742dbf98a845b95943a5',1,'vg::io::VPKG']]],
- ['with_5fvector_6557',['with_vector',['../structvg_1_1VectorView.html#af21c3547b8588e6c20f10f5dc67620bf',1,'vg::VectorView::with_vector(const std::function< void(const vector< Item > &)> &callback) const'],['../structvg_1_1VectorView.html#a2e2e6494c350a37135b9c77cd6320f05',1,'vg::VectorView::with_vector(const std::function< void(vector< Item > &)> &callback)']]],
- ['without_5fread_6558',['without_read',['../structvg_1_1alignment__index__t.html#a3df9895a83da6114ae22d5981a83f9a5',1,'vg::alignment_index_t']]],
- ['work_5fdir_6559',['work_dir',['../classvg_1_1IndexRegistry.html#ab2e9084645b146ff321f70a231161d66',1,'vg::IndexRegistry']]],
- ['worst_5falignment_5fscore_6560',['worst_alignment_score',['../namespacevg.html#a8e2c6fbf0d030acabb7dd6b8d428e143',1,'vg']]],
- ['wrap_6561',['wrap',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01true_01_4.html#afdb8a7b86ca03dafaa44a27b573c0c7d',1,'handlegraph::BoolReturningWrapper< Iteratee, true >::wrap()'],['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01false_01_4.html#a2dc122df61cb917d075af250c16931de',1,'handlegraph::BoolReturningWrapper< Iteratee, false >::wrap()']]],
- ['wrap_5fbare_5floader_6562',['wrap_bare_loader',['../namespacevg_1_1io.html#a36870772d6af0c6fbc0a099f6bed2caf',1,'vg::io']]],
- ['wrap_5fbare_5fsaver_6563',['wrap_bare_saver',['../namespacevg_1_1io.html#ae0cd97ec5478403a25e02c9805f3d286',1,'vg::io']]],
- ['wrap_5ftext_6564',['wrap_text',['../namespacevg.html#a57f111dda471f40192704110bae04a0f',1,'vg']]],
- ['wrap_5fwith_5fnull_5fnodes_6565',['wrap_with_null_nodes',['../classvg_1_1VG.html#a2239c89d6ac7e9dec0d76325c2a68f97',1,'vg::VG']]],
- ['wrapped_5fostream_6566',['wrapped_ostream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a14d9a1a0917016a7af46f2960608d302',1,'vg::io::BlockedGzipOutputStream']]],
- ['wrappingpositionscanner_6567',['WrappingPositionScanner',['../structvg_1_1WrappingPositionScanner.html',1,'vg']]],
- ['write_6568',['write',['../structhFILE__backend.html#ada22f61f6280c429aca37d82ef4c31a4',1,'hFILE_backend::write()'],['../classvg_1_1Paths.html#a8a520b4d648c566f4297418025051784',1,'vg::Paths::write()'],['../classvg_1_1io_1_1JSONStreamHelper.html#ad024636dddd28df4afcd78671598203f',1,'vg::io::JSONStreamHelper::write()'],['../classvg_1_1io_1_1MessageEmitter.html#a58bdb39f127ad810b8dc3b5288bf61df',1,'vg::io::MessageEmitter::write(const string &tag)'],['../classvg_1_1io_1_1MessageEmitter.html#afe12ded46a9500d7b51192ce8cbff596',1,'vg::io::MessageEmitter::write(const string &tag, string &&message)'],['../classvg_1_1io_1_1ProtobufEmitter.html#af2956417dd81044bd5134794693942fd',1,'vg::io::ProtobufEmitter::write()'],['../namespacevg_1_1io.html#a1b6b275aeefcf193d8d25a6b3b7b8f11',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T &(size_t)> &lambda, bool compressed=true)'],['../namespacevg_1_1io.html#aa4c230c8fd256d7a5dfd16aa2014a51f',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T(size_t)> &lambda, bool compressed=true)']]],
- ['write_5falignment_5fto_5ffile_6569',['write_alignment_to_file',['../namespacevg.html#a81c8bc6d3b973fd1a34c3457a9d2e401',1,'vg']]],
- ['write_5fannotations_6570',['write_annotations',['../classvg_1_1DiagramExplainer.html#a173f7e3fbc63ca644ed8f540fef7d41c',1,'vg::DiagramExplainer']]],
- ['write_5farray_5fto_5faux_6571',['write_array_to_aux',['../namespacevg.html#ab55dcc8a50b26b55f7fc142678b7ce63',1,'vg']]],
- ['write_5fbuffered_6572',['write_buffered',['../namespacevg_1_1io.html#a482c50dd5f56410de4988931f2510f57',1,'vg::io']]],
- ['write_5fconnected_5fcomponents_6573',['write_connected_components',['../classvg_1_1DiagramExplainer.html#a5a93fe3708e127f400324b3f6abc1afb',1,'vg::DiagramExplainer']]],
- ['write_5fcopy_6574',['write_copy',['../classvg_1_1io_1_1MessageEmitter.html#af50b05f458e958c26ac55f7994d1f573',1,'vg::io::MessageEmitter::write_copy()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a8ded624b6ba6d5dddf1abe668214ce7e',1,'vg::io::ProtobufEmitter::write_copy()']]],
- ['write_5fedge_6575',['write_edge',['../classvg_1_1DiagramExplainer.html#a36ea9fc4006dda44b55ef17696a53ffe',1,'vg::DiagramExplainer']]],
- ['write_5fedits_6576',['write_edits',['../classvg_1_1Packer.html#af63b2387c9139d25cf7084de15fc4b27',1,'vg::Packer::write_edits(vector< ofstream * > &out) const'],['../classvg_1_1Packer.html#adab10cdf7d5776fb59da650f9b469a24',1,'vg::Packer::write_edits(ostream &out, size_t bin) const']]],
- ['write_5ffasta_5fsequence_6577',['write_fasta_sequence',['../namespacevg.html#a239160a6fee7d0af8914c4ebc7275c78',1,'vg']]],
- ['write_5fgcsa_5fkmers_6578',['write_gcsa_kmers',['../namespacevg.html#a6d8c71ff9f77ddd4a366119e83122771',1,'vg']]],
- ['write_5fgcsa_5fkmers_5fascii_6579',['write_gcsa_kmers_ascii',['../classvg_1_1VGset.html#a8f9d1a671c39aa51a768d0733bccecb9',1,'vg::VGset']]],
- ['write_5fgcsa_5fkmers_5fbinary_6580',['write_gcsa_kmers_binary',['../classvg_1_1VGset.html#a7de0f3cd0ccccd60dc0ef4c29840fe0b',1,'vg::VGset::write_gcsa_kmers_binary(ostream &out, int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)'],['../classvg_1_1VGset.html#a0c1615ae5874cbcc4f77d0b224f2e12e',1,'vg::VGset::write_gcsa_kmers_binary(int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)']]],
- ['write_5fgcsa_5fkmers_5fto_5ftmpfile_6581',['write_gcsa_kmers_to_tmpfile',['../namespacevg.html#a38d9326cbc013aed614bc052c8c224e6',1,'vg']]],
- ['write_5fglobals_6582',['write_globals',['../classvg_1_1DiagramExplainer.html#a47b4615506be1350c648a34fe52fcecd',1,'vg::DiagramExplainer']]],
- ['write_5fgraph_6583',['write_graph',['../classvg_1_1Transcriptome.html#a2b11042d0caef33a18a10e5be784e15c',1,'vg::Transcriptome']]],
- ['write_5fmany_6584',['write_many',['../classvg_1_1io_1_1ProtobufEmitter.html#a05abdc0c51cc62b21c849c2ef13e81e0',1,'vg::io::ProtobufEmitter']]],
- ['write_5fmapping_6585',['write_mapping',['../classvg_1_1PhaseUnfolder.html#a708fb760e358eedc63c624c617885548',1,'vg::PhaseUnfolder']]],
- ['write_5fnode_6586',['write_node',['../classvg_1_1DiagramExplainer.html#adcf77caa4c9627dd25c97f1080888291',1,'vg::DiagramExplainer']]],
- ['write_5foutput_6587',['write_output',['../classvg_1_1ReadFilter.html#a249032f1613c12263e7c14d83b4e527e',1,'vg::ReadFilter']]],
- ['write_5fsupports_6588',['write_supports',['../structvg_1_1SupportAugmentedGraph.html#a4f08f8c78bf0ffbfe7e364d4404b97a9',1,'vg::SupportAugmentedGraph']]],
- ['write_5fto_5ffile_6589',['write_to_file',['../namespacevg_1_1io.html#a88cb8e7bbebb78a2ef3bdce1c64ba077',1,'vg::io']]],
- ['write_5ftranscript_5finfo_6590',['write_transcript_info',['../classvg_1_1Transcriptome.html#ada48319a8370ad45364d9bc8241b275a',1,'vg::Transcriptome']]],
- ['write_5ftranscript_5fsequences_6591',['write_transcript_sequences',['../classvg_1_1Transcriptome.html#a4ce90a0e2556b51c62e4a3e550108750',1,'vg::Transcriptome']]],
- ['write_5ftranslations_6592',['write_translations',['../structvg_1_1AugmentedGraph.html#a70ffd6eb24e80cfa265ae48cdde15a45',1,'vg::AugmentedGraph']]],
- ['write_5ftsv_6593',['write_tsv',['../classvg_1_1ReadFilter.html#a9979d9966e9ea82a9cd160dbf38d4b7c',1,'vg::ReadFilter']]],
- ['write_5fvariant_6594',['write_variant',['../classvg_1_1Genotyper.html#af5b580b6db4e727934f964d00b058038',1,'vg::Genotyper']]],
- ['write_5fvariants_6595',['write_variants',['../classvg_1_1VCFOutputCaller.html#afff7887f0111aae8ae3103b990ff54dd',1,'vg::VCFOutputCaller']]],
- ['write_5fvcf_5fheader_6596',['write_vcf_header',['../classvg_1_1Genotyper.html#ad2beb83f750d1deec75b16a60c2ea805',1,'vg::Genotyper']]],
- ['writealiasedraw_6597',['WriteAliasedRaw',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a85d9e1ca69d7bad9e2941b7ecec08a42',1,'vg::io::BlockedGzipOutputStream']]],
- ['writer_5fstop_6598',['writer_stop',['../classvg_1_1io_1_1StreamMultiplexer.html#ae51a3ffdfe9ec988bf732e4904dcbf60',1,'vg::io::StreamMultiplexer']]],
- ['writer_5fthread_6599',['writer_thread',['../classvg_1_1io_1_1StreamMultiplexer.html#a56a9d39b8ccdd13f07e835ad7a967a60',1,'vg::io::StreamMultiplexer']]],
- ['writer_5fthread_5ffunction_6600',['writer_thread_function',['../classvg_1_1io_1_1StreamMultiplexer.html#a29ba6b97591887c453b0cc112cae41e4',1,'vg::io::StreamMultiplexer']]],
- ['wrong_5fname_6601',['wrong_name',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a5d133dedebb885c312dbfca70d5abe15',1,'vg::Counts']]],
- ['wrong_5frefpos_6602',['wrong_refpos',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a069ad2b94f1414f1ba774043f5047d15',1,'vg::Counts']]]
+ ['w_6464',['w',['../structHaplotypesConfig.html#afc08b5bf2dd526161ebb29c1ea37d1b4',1,'HaplotypesConfig::w()'],['../namespacehaplotypes__defaults.html#a9e7cea9525076e8d069877c9f1a08552',1,'haplotypes_defaults::w()']]],
+ ['wabbit_5fmap_6465',['wabbit_map',['../classVectorizer.html#abc8fdb5dcd0ccc39c2b042633ef6820e',1,'Vectorizer']]],
+ ['wabbitize_6466',['wabbitize',['../classVectorizer.html#ae4c3627b5c8ec7b066f5735ca6dfb3f1',1,'Vectorizer']]],
+ ['wait_5ffor_5fregion_6467',['wait_for_region',['../classvg_1_1GraphSynchronizer.html#a7f9e68c4e2172bc4a5c7040272a59d38',1,'vg::GraphSynchronizer']]],
+ ['walk_2ecpp_6468',['walk.cpp',['../walk_8cpp.html',1,'']]],
+ ['walk_2ehpp_6469',['walk.hpp',['../walk_8hpp.html',1,'']]],
+ ['walk_5fbackwards_6470',['walk_backwards',['../classvg_1_1NGSSimulator.html#a3b87398480be75b240a98d270bfc843c',1,'vg::NGSSimulator']]],
+ ['walk_5fbackwards_5falong_5falignment_6471',['walk_backwards_along_alignment',['../classvg_1_1NGSSimulator.html#af033e5bc63e8407c917f151a4311b64d',1,'vg::NGSSimulator']]],
+ ['walk_5ffanout_5fpath_6472',['walk_fanout_path',['../classvg_1_1BaseMapper.html#ad52deed127976201bd63b32929b71491',1,'vg::BaseMapper']]],
+ ['walk_5fhaplotype_5ffrequency_6473',['walk_haplotype_frequency',['../namespacevg_1_1algorithms.html#a4af5e9c480c0dc7d0843cf981cd52c32',1,'vg::algorithms']]],
+ ['walk_5fhaplotype_5fnames_6474',['walk_haplotype_names',['../namespacevg_1_1algorithms.html#abe9cb62b2ae1c6eb08b10f172980788d',1,'vg::algorithms']]],
+ ['walk_5flisteners_6475',['walk_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a349711aec5bbd3063812eae72727c170',1,'vg::algorithms::GFAParser']]],
+ ['walk_5ft_6476',['walk_t',['../structvg_1_1algorithms_1_1walk__t.html',1,'vg::algorithms::walk_t'],['../structvg_1_1algorithms_1_1walk__t.html#a5a5ed7ca0dac4f9e742ddeeb28e317e1',1,'vg::algorithms::walk_t::walk_t(uint16_t l, const pos_t &b, const pos_t &e, const handle_t &c, uint16_t f)'],['../structvg_1_1algorithms_1_1walk__t.html#af8c4463befc5bb6cec73b3e493acf545',1,'vg::algorithms::walk_t::walk_t(const std::string &s, const pos_t &b, const pos_t &e, const handle_t &c)']]],
+ ['wang_5fhash_6477',['wang_hash',['../structvg_1_1wang__hash.html',1,'vg']]],
+ ['wang_5fhash_2ehpp_6478',['wang_hash.hpp',['../wang__hash_8hpp.html',1,'']]],
+ ['wang_5fhash_3c_20handle_5ft_20_3e_6479',['wang_hash< handle_t >',['../structvg_1_1wang__hash_3_01handle__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_6480',['wang_hash< handlegraph::net_handle_t >',['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20net_5fidentifier_5ft_20_3e_6481',['wang_hash< net_identifier_t >',['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20nodeside_20_3e_6482',['wang_hash< NodeSide >',['../structvg_1_1wang__hash_3_01NodeSide_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20nodetraversal_20_3e_6483',['wang_hash< NodeTraversal >',['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20path_5fhandle_5ft_20_3e_6484',['wang_hash< path_handle_t >',['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20std_3a_3apair_3c_20a_2c_20b_20_3e_20_3e_6485',['wang_hash< std::pair< A, B > >',['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20t_20_2a_20_3e_6486',['wang_hash< T * >',['../structvg_1_1wang__hash_3_01T_01_5_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20t_2c_20typename_20std_3a_3aenable_5fif_3c_20std_3a_3ais_5fintegral_3c_20t_20_3e_3a_3avalue_20_3e_3a_3atype_20_3e_6487',['wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >',['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html',1,'vg']]],
+ ['wang_5fhash_5f64_6488',['wang_hash_64',['../namespacevg.html#a38d35bca25e8a6d5fe10f603cb9048c3',1,'vg']]],
+ ['want_5fbreakpoint_6489',['want_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#ac0698f3b6387ce47f4e9d5b2929d6cf4',1,'vg::io::StreamMultiplexer']]],
+ ['warn_5fon_5fambiguous_6490',['warn_on_ambiguous',['../classvg_1_1Constructor.html#a24e663d6eee52a9f723faf398cf720fa',1,'vg::Constructor']]],
+ ['warn_5fon_5flowercase_6491',['warn_on_lowercase',['../classvg_1_1Constructor.html#a9da8d803e6e0c0be942ca2ecc35e9267',1,'vg::Constructor']]],
+ ['warn_5fon_5fmissing_5fvariants_6492',['warn_on_missing_variants',['../classvg_1_1HaplotypeIndexer.html#afb3592792a7d781cb6e88fe7949b7bfe',1,'vg::HaplotypeIndexer']]],
+ ['warn_5fon_5fscore_5ffail_6493',['warn_on_score_fail',['../namespacehaplo.html#ab22b0954ba9062360178078ce504f1c2',1,'haplo']]],
+ ['warned_5fabout_5fbad_5fdistribution_6494',['warned_about_bad_distribution',['../classvg_1_1MinimizerMapper.html#a3915618267605133f2e9144c693e68e5',1,'vg::MinimizerMapper']]],
+ ['warned_5fabout_5fchunking_6495',['warned_about_chunking',['../classvg_1_1Mapper.html#a45dffe2dc008aebd254388281034d27f',1,'vg::Mapper']]],
+ ['warned_5fabout_5frescue_5fsize_6496',['warned_about_rescue_size',['../classvg_1_1MinimizerMapper.html#a70bd402b25f6008362e82858be9fe9bc',1,'vg::MinimizerMapper']]],
+ ['warned_5fabout_5frewrites_6497',['warned_about_rewrites',['../classvg_1_1VG.html#a8f0519dc706937b8b593f803f3d8eac4',1,'vg::VG']]],
+ ['warned_5fabout_5fsubgraph_5fsize_6498',['warned_about_subgraph_size',['../classvg_1_1Surjector.html#affb3a5676516b7042d5c2d08734ea3c8',1,'vg::Surjector']]],
+ ['warned_5fabout_5ftail_5fsize_6499',['warned_about_tail_size',['../classvg_1_1MinimizerMapper.html#a0b74ef2cf6f1fd04290172a91623584a',1,'vg::MinimizerMapper']]],
+ ['was_5fcorrect_6500',['was_correct',['../classvg_1_1Funnel.html#aac71f37530afee1b7e49770aff8cc53b',1,'vg::Funnel::was_correct(size_t prev_stage_item) const'],['../classvg_1_1Funnel.html#a5f0037505a9df13b92e381f5ff108d72',1,'vg::Funnel::was_correct(size_t prev_stage_index, const string &prev_stage_name, size_t prev_stage_item) const']]],
+ ['was_5fprovided_5fdirectly_6501',['was_provided_directly',['../classvg_1_1IndexFile.html#afabf00d9034342540b3614dfc7055715',1,'vg::IndexFile']]],
+ ['was_5fset_6502',['was_set',['../structvg_1_1subcommand_1_1ArgSpec.html#acfb22902f7ebf4d8053ec39999dd2821',1,'vg::subcommand::ArgSpec::was_set()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aac6bd613601f636c187b684a69fa25ce',1,'vg::subcommand::ValueArgSpec::was_set()']]],
+ ['watchdog_6503',['Watchdog',['../classvg_1_1Watchdog.html',1,'vg::Watchdog'],['../classvg_1_1Watchdog.html#a87e679ecbb8461ae6a26a1958216629b',1,'vg::Watchdog::Watchdog(size_t thread_count, const duration &timeout)'],['../classvg_1_1Watchdog.html#a2934cc5c1fc3b7d0ab20343e6bde1a56',1,'vg::Watchdog::Watchdog(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a73aa9888b0017ed46053c75c085f2748',1,'vg::Watchdog::Watchdog(Watchdog &&other)=delete']]],
+ ['watchdog_2ecpp_6504',['watchdog.cpp',['../watchdog_8cpp.html',1,'']]],
+ ['watchdog_2ehpp_6505',['watchdog.hpp',['../watchdog_8hpp.html',1,'']]],
+ ['watchdog_5ftimeout_6506',['watchdog_timeout',['../structGiraffeMainOptions.html#a51b24824ec0a06a5b080f8578090fa56',1,'GiraffeMainOptions']]],
+ ['watcher_6507',['watcher',['../classvg_1_1Watchdog.html#a39ef2d296adea6283596aadd48457e02',1,'vg::Watchdog']]],
+ ['watcher_5floop_6508',['watcher_loop',['../classvg_1_1Watchdog.html#ad2e2c831258c42fdba7f2d0fa8625cc9',1,'vg::Watchdog']]],
+ ['wavefronts_6509',['wavefronts',['../structvg_1_1WFANode.html#a6b8938c80565dd8c9219945b2a5be194',1,'vg::WFANode']]],
+ ['weakly_5fconnected_5fcomponents_6510',['weakly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a96c80b09388c6d079754c66d2f7362e5',1,'handlegraph::algorithms']]],
+ ['weakly_5fconnected_5fcomponents_2ecpp_6511',['weakly_connected_components.cpp',['../weakly__connected__components_8cpp.html',1,'']]],
+ ['weakly_5fconnected_5fcomponents_5fwith_5ftips_6512',['weakly_connected_components_with_tips',['../namespacehandlegraph_1_1algorithms.html#aa5ff9ed76bd82438b3af0c3112437ccd',1,'handlegraph::algorithms']]],
+ ['weibull_5fcdf_6513',['weibull_cdf',['../namespacevg.html#a100efe5dfc5bfe434b53416f93d2a0e1',1,'vg']]],
+ ['weibull_5flog_5flikelihood_6514',['weibull_log_likelihood',['../namespacevg.html#ad93405cf370e6d92396691fc3320be1c',1,'vg']]],
+ ['weight_6515',['weight',['../classvg_1_1MEMChainModelVertex.html#ad73c85aeb85dde48dd3201260720956b',1,'vg::MEMChainModelVertex::weight()'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a5e9984583bd37a31e8b172fea582e6fd',1,'vg::MEMClusterer::HitEdge::weight()'],['../classvg_1_1AlignmentChainModelVertex.html#a874c1b3121234990ab1c1519921b9c6c',1,'vg::AlignmentChainModelVertex::weight()'],['../structvg_1_1algorithms_1_1Edge.html#a25cfc0a5279fb8d40cc7527099449dc1',1,'vg::algorithms::Edge::weight()'],['../structvg_1_1algorithms_1_1Node.html#a38e105d20eb7efa802dd6b07824cd620',1,'vg::algorithms::Node::weight()']]],
+ ['weighted_5fjaccard_5fcoefficient_6516',['weighted_jaccard_coefficient',['../namespacevg.html#aa0b9062cb7b053e7823169d589e113d1',1,'vg']]],
+ ['weightedgraph_6517',['WeightedGraph',['../structvg_1_1FlowSort_1_1WeightedGraph.html',1,'vg::FlowSort']]],
+ ['wellford_5fmean_5fvar_6518',['wellford_mean_var',['../namespacevg.html#a4b96cd801bc780d426db346f80ab2172',1,'vg']]],
+ ['wellford_5fupdate_6519',['wellford_update',['../namespacevg.html#a614c672ed69c280b699a278ce0f34ade',1,'vg']]],
+ ['wfa_5falignment_5fto_5falignment_6520',['wfa_alignment_to_alignment',['../classvg_1_1MinimizerMapper.html#a597914c2167ca2b06a3dccbb23e21340',1,'vg::MinimizerMapper']]],
+ ['wfa_5fdistance_6521',['wfa_distance',['../classvg_1_1MinimizerMapper.html#adde3e90703e3137d7cb8a0e0c217686b',1,'vg::MinimizerMapper']]],
+ ['wfa_5fdistance_5fper_5fbase_6522',['wfa_distance_per_base',['../classvg_1_1MinimizerMapper.html#ae77b975a0ba7e7bddf4d01e92074c1de',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fdistance_6523',['wfa_max_distance',['../classvg_1_1MinimizerMapper.html#a99da16075a34ebad4a01fe94f5d7d4cf',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fmax_5fmismatches_6524',['wfa_max_max_mismatches',['../classvg_1_1MinimizerMapper.html#a65d94bb81e375a2affda69e92e131908',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fmismatches_6525',['wfa_max_mismatches',['../classvg_1_1MinimizerMapper.html#a16b9080b48c374fd3a8d927368379bba',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fmismatches_5fper_5fbase_6526',['wfa_max_mismatches_per_base',['../classvg_1_1MinimizerMapper.html#af1800dc292b642aa366730c8f6034475',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmiddle_6527',['wfa_middle',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a18a47b29e26174cc24a57f71ec8f5f9c',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
+ ['wfa_5ftail_6528',['wfa_tail',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#aaf4d71d87fb51ba736806a35cb6f1bc0',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
+ ['wfaalignment_6529',['WFAAlignment',['../structvg_1_1WFAAlignment.html',1,'vg']]],
+ ['wfaextender_6530',['WFAExtender',['../classvg_1_1WFAExtender.html',1,'vg::WFAExtender'],['../classvg_1_1WFAExtender.html#a7d7324769e3d80c6acdd68de034c5830',1,'vg::WFAExtender::WFAExtender()'],['../classvg_1_1WFAExtender.html#a9cc09b85da35171c971868e80cfe2938',1,'vg::WFAExtender::WFAExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner, const ErrorModel &error_model=default_error_model)']]],
+ ['wfanode_6531',['WFANode',['../structvg_1_1WFANode.html',1,'vg::WFANode'],['../structvg_1_1WFANode.html#a93d02d2b8f73a4cdcbe5a356258cb5e8',1,'vg::WFANode::WFANode()']]],
+ ['wfapoint_6532',['WFAPoint',['../structvg_1_1WFAPoint.html',1,'vg']]],
+ ['wfatree_6533',['WFATree',['../classvg_1_1WFATree.html',1,'vg::WFATree'],['../classvg_1_1WFATree.html#ad9880bb173f2bd8e2cdc3708cbb8005f',1,'vg::WFATree::WFATree()']]],
+ ['what_6534',['what',['../classvg_1_1NoAlignmentInBandException.html#a006dddb79b9d1c6035c2466c35dbcacf',1,'vg::NoAlignmentInBandException::what()'],['../classvg_1_1InsufficientInputException.html#ae9fd64e80e950783955ff7d875138469',1,'vg::InsufficientInputException::what()'],['../classvg_1_1RewindPlanException.html#a5d3526ac6c26a49f65a962f12c246615',1,'vg::RewindPlanException::what()'],['../classvg_1_1SizeLimitExceededException.html#acb8fbb8940007b68bede049fcf19b046',1,'vg::SizeLimitExceededException::what()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#a7fdc5893f8439a8c8c6169865a8c6e0d',1,'vg::algorithms::GFAFormatError::what()'],['../classj2pb__error.html#a4ac3313fff0e2721ca9480b61ebe6a8b',1,'j2pb_error::what()']]],
+ ['which_5fhaplotype_6535',['which_haplotype',['../classvg_1_1PhasedGenome_1_1iterator.html#a02b60bd3c0ec6d86a8bec582e717ea15',1,'vg::PhasedGenome::iterator']]],
+ ['whitespace_6536',['whitespace',['../namespacevg.html#a466eef41b2208daa1c649e71022cdc44',1,'vg']]],
+ ['whole_5falignment_5fcutoff_6537',['whole_alignment_cutoff',['../classvg_1_1VariantAdder.html#ab40df39042e4ce4fee3eeea919be1c96',1,'vg::VariantAdder']]],
+ ['whole_5fgraph_5flock_6538',['whole_graph_lock',['../classvg_1_1GraphSynchronizer.html#aa1a7be56b29656fa604b44b37e134c80',1,'vg::GraphSynchronizer']]],
+ ['wideningprng_6539',['WideningPRNG',['../classvg_1_1WideningPRNG.html',1,'vg::WideningPRNG< PRNG, OutType >'],['../classvg_1_1WideningPRNG.html#a5437179a5230df00551a618df6bc4c53',1,'vg::WideningPRNG::WideningPRNG()']]],
+ ['widest_5fdijkstra_6540',['widest_dijkstra',['../namespacevg_1_1algorithms.html#a08c6d85f2dc09c22c5d14ed81808769e',1,'vg::algorithms']]],
+ ['widget_6541',['WIDGET',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838afa639842a4d69790c890c94b80e27792',1,'vg::subcommand']]],
+ ['window_5fbreaking_5fquality_6542',['window_breaking_quality',['../classvg_1_1MinimizerMapper.html#a7999b2f0a931930bfa9eddec4065b51b',1,'vg::MinimizerMapper']]],
+ ['window_5flength_6543',['window_length',['../classvg_1_1Filter.html#ad719ad4c073cbe1298c9911e1c1cb329',1,'vg::Filter']]],
+ ['window_5fof_5fid_6544',['window_of_id',['../classvg_1_1StreamIndexBase.html#a320b27d89fbc1a74574cc00befe1e7fe',1,'vg::StreamIndexBase']]],
+ ['window_5fshift_6545',['WINDOW_SHIFT',['../classvg_1_1StreamIndexBase.html#a1f8223f4ff9ca3d9892d13d2708aff73',1,'vg::StreamIndexBase']]],
+ ['window_5fsize_6546',['window_size',['../classvg_1_1WindowedVcfBuffer.html#a898deb05050ba62533e294b7cf959fe3',1,'vg::WindowedVcfBuffer::window_size()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a7fb1665349757422a2868159d2b66437',1,'vg::MinimizerMapper::Minimizer::window_size()']]],
+ ['window_5ft_6547',['window_t',['../classvg_1_1StreamIndexBase.html#ad94010282265d6d8743f31ed5b3e98ce',1,'vg::StreamIndexBase']]],
+ ['window_5fto_5fstart_6548',['window_to_start',['../classvg_1_1StreamIndexBase.html#a47fab2baab7953595105558d0fcba4e2',1,'vg::StreamIndexBase']]],
+ ['windowedvcfbuffer_6549',['WindowedVcfBuffer',['../classvg_1_1WindowedVcfBuffer.html',1,'vg::WindowedVcfBuffer'],['../classvg_1_1WindowedVcfBuffer.html#a7d7af1d1441bab6c687bdf1be7fc4675',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(vcflib::VariantCallFile *file, size_t window_size)'],['../classvg_1_1WindowedVcfBuffer.html#aa57da13990d5983d5e8aa787dfe56995',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(const WindowedVcfBuffer &other)=delete']]],
+ ['with_5fcache_5fentry_6550',['with_cache_entry',['../classvg_1_1IndexedVG.html#ac14226d9ccd03cb99af9a08cef31d6ff',1,'vg::IndexedVG']]],
+ ['with_5fcursor_6551',['with_cursor',['../classvg_1_1IndexedVG.html#af380961c8e8b342ba8f688c2f073de2e',1,'vg::IndexedVG']]],
+ ['with_5fdagified_5flocal_5fgraph_6552',['with_dagified_local_graph',['../classvg_1_1MinimizerMapper.html#a96b3c359c5f86557ddccfdedd67af570',1,'vg::MinimizerMapper']]],
+ ['with_5fexception_5fhandling_6553',['with_exception_handling',['../namespacevg.html#a1d2cbe5fe5e1b8a33b7d707f7059b3c6',1,'vg']]],
+ ['with_5ffunction_5fcalling_5fstream_6554',['with_function_calling_stream',['../namespacevg_1_1io.html#a8b1a63276edf814575b7afb3b2b9844d',1,'vg::io']]],
+ ['with_5fpath_5findex_6555',['with_path_index',['../classvg_1_1GraphSynchronizer.html#a336f5828883adce86ee5e536f8c299ea',1,'vg::GraphSynchronizer']]],
+ ['with_5fprogress_6556',['with_progress',['../classvg_1_1Progressive.html#ab44ff020fc951b95dfcd1252c015a020',1,'vg::Progressive']]],
+ ['with_5fputback_6557',['with_putback',['../classvg_1_1io_1_1VPKG.html#a0bcbb5a28413d3599a642cd5f22d93be',1,'vg::io::VPKG']]],
+ ['with_5fsave_5fstream_6558',['with_save_stream',['../classvg_1_1io_1_1VPKG.html#a030910ec652e742dbf98a845b95943a5',1,'vg::io::VPKG']]],
+ ['with_5fvector_6559',['with_vector',['../structvg_1_1VectorView.html#af21c3547b8588e6c20f10f5dc67620bf',1,'vg::VectorView::with_vector(const std::function< void(const vector< Item > &)> &callback) const'],['../structvg_1_1VectorView.html#a2e2e6494c350a37135b9c77cd6320f05',1,'vg::VectorView::with_vector(const std::function< void(vector< Item > &)> &callback)']]],
+ ['without_5fread_6560',['without_read',['../structvg_1_1alignment__index__t.html#a3df9895a83da6114ae22d5981a83f9a5',1,'vg::alignment_index_t']]],
+ ['work_5fdir_6561',['work_dir',['../classvg_1_1IndexRegistry.html#ab2e9084645b146ff321f70a231161d66',1,'vg::IndexRegistry']]],
+ ['worst_5falignment_5fscore_6562',['worst_alignment_score',['../namespacevg.html#a8e2c6fbf0d030acabb7dd6b8d428e143',1,'vg']]],
+ ['wrap_6563',['wrap',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01true_01_4.html#afdb8a7b86ca03dafaa44a27b573c0c7d',1,'handlegraph::BoolReturningWrapper< Iteratee, true >::wrap()'],['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01false_01_4.html#a2dc122df61cb917d075af250c16931de',1,'handlegraph::BoolReturningWrapper< Iteratee, false >::wrap()']]],
+ ['wrap_5fbare_5floader_6564',['wrap_bare_loader',['../namespacevg_1_1io.html#a36870772d6af0c6fbc0a099f6bed2caf',1,'vg::io']]],
+ ['wrap_5fbare_5fsaver_6565',['wrap_bare_saver',['../namespacevg_1_1io.html#ae0cd97ec5478403a25e02c9805f3d286',1,'vg::io']]],
+ ['wrap_5ftext_6566',['wrap_text',['../namespacevg.html#a57f111dda471f40192704110bae04a0f',1,'vg']]],
+ ['wrap_5fwith_5fnull_5fnodes_6567',['wrap_with_null_nodes',['../classvg_1_1VG.html#a2239c89d6ac7e9dec0d76325c2a68f97',1,'vg::VG']]],
+ ['wrapped_5fostream_6568',['wrapped_ostream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a14d9a1a0917016a7af46f2960608d302',1,'vg::io::BlockedGzipOutputStream']]],
+ ['wrappingpositionscanner_6569',['WrappingPositionScanner',['../structvg_1_1WrappingPositionScanner.html',1,'vg']]],
+ ['write_6570',['write',['../structhFILE__backend.html#ada22f61f6280c429aca37d82ef4c31a4',1,'hFILE_backend::write()'],['../classvg_1_1Paths.html#a8a520b4d648c566f4297418025051784',1,'vg::Paths::write()'],['../classvg_1_1io_1_1JSONStreamHelper.html#ad024636dddd28df4afcd78671598203f',1,'vg::io::JSONStreamHelper::write()'],['../classvg_1_1io_1_1MessageEmitter.html#a58bdb39f127ad810b8dc3b5288bf61df',1,'vg::io::MessageEmitter::write(const string &tag)'],['../classvg_1_1io_1_1MessageEmitter.html#afe12ded46a9500d7b51192ce8cbff596',1,'vg::io::MessageEmitter::write(const string &tag, string &&message)'],['../classvg_1_1io_1_1ProtobufEmitter.html#af2956417dd81044bd5134794693942fd',1,'vg::io::ProtobufEmitter::write()'],['../namespacevg_1_1io.html#a1b6b275aeefcf193d8d25a6b3b7b8f11',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T &(size_t)> &lambda, bool compressed=true)'],['../namespacevg_1_1io.html#aa4c230c8fd256d7a5dfd16aa2014a51f',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T(size_t)> &lambda, bool compressed=true)']]],
+ ['write_5falignment_5fto_5ffile_6571',['write_alignment_to_file',['../namespacevg.html#a81c8bc6d3b973fd1a34c3457a9d2e401',1,'vg']]],
+ ['write_5fannotations_6572',['write_annotations',['../classvg_1_1DiagramExplainer.html#a173f7e3fbc63ca644ed8f540fef7d41c',1,'vg::DiagramExplainer']]],
+ ['write_5farray_5fto_5faux_6573',['write_array_to_aux',['../namespacevg.html#ab55dcc8a50b26b55f7fc142678b7ce63',1,'vg']]],
+ ['write_5fbuffered_6574',['write_buffered',['../namespacevg_1_1io.html#a482c50dd5f56410de4988931f2510f57',1,'vg::io']]],
+ ['write_5fconnected_5fcomponents_6575',['write_connected_components',['../classvg_1_1DiagramExplainer.html#a5a93fe3708e127f400324b3f6abc1afb',1,'vg::DiagramExplainer']]],
+ ['write_5fcopy_6576',['write_copy',['../classvg_1_1io_1_1MessageEmitter.html#af50b05f458e958c26ac55f7994d1f573',1,'vg::io::MessageEmitter::write_copy()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a8ded624b6ba6d5dddf1abe668214ce7e',1,'vg::io::ProtobufEmitter::write_copy()']]],
+ ['write_5fedge_6577',['write_edge',['../classvg_1_1DiagramExplainer.html#a36ea9fc4006dda44b55ef17696a53ffe',1,'vg::DiagramExplainer']]],
+ ['write_5fedits_6578',['write_edits',['../classvg_1_1Packer.html#af63b2387c9139d25cf7084de15fc4b27',1,'vg::Packer::write_edits(vector< ofstream * > &out) const'],['../classvg_1_1Packer.html#adab10cdf7d5776fb59da650f9b469a24',1,'vg::Packer::write_edits(ostream &out, size_t bin) const']]],
+ ['write_5ffasta_5fsequence_6579',['write_fasta_sequence',['../namespacevg.html#a239160a6fee7d0af8914c4ebc7275c78',1,'vg']]],
+ ['write_5fgcsa_5fkmers_6580',['write_gcsa_kmers',['../namespacevg.html#a6d8c71ff9f77ddd4a366119e83122771',1,'vg']]],
+ ['write_5fgcsa_5fkmers_5fascii_6581',['write_gcsa_kmers_ascii',['../classvg_1_1VGset.html#a8f9d1a671c39aa51a768d0733bccecb9',1,'vg::VGset']]],
+ ['write_5fgcsa_5fkmers_5fbinary_6582',['write_gcsa_kmers_binary',['../classvg_1_1VGset.html#a7de0f3cd0ccccd60dc0ef4c29840fe0b',1,'vg::VGset::write_gcsa_kmers_binary(ostream &out, int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)'],['../classvg_1_1VGset.html#a0c1615ae5874cbcc4f77d0b224f2e12e',1,'vg::VGset::write_gcsa_kmers_binary(int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)']]],
+ ['write_5fgcsa_5fkmers_5fto_5ftmpfile_6583',['write_gcsa_kmers_to_tmpfile',['../namespacevg.html#a38d9326cbc013aed614bc052c8c224e6',1,'vg']]],
+ ['write_5fglobals_6584',['write_globals',['../classvg_1_1DiagramExplainer.html#a47b4615506be1350c648a34fe52fcecd',1,'vg::DiagramExplainer']]],
+ ['write_5fgraph_6585',['write_graph',['../classvg_1_1Transcriptome.html#a2b11042d0caef33a18a10e5be784e15c',1,'vg::Transcriptome']]],
+ ['write_5fmany_6586',['write_many',['../classvg_1_1io_1_1ProtobufEmitter.html#a05abdc0c51cc62b21c849c2ef13e81e0',1,'vg::io::ProtobufEmitter']]],
+ ['write_5fmapping_6587',['write_mapping',['../classvg_1_1PhaseUnfolder.html#a708fb760e358eedc63c624c617885548',1,'vg::PhaseUnfolder']]],
+ ['write_5fnode_6588',['write_node',['../classvg_1_1DiagramExplainer.html#adcf77caa4c9627dd25c97f1080888291',1,'vg::DiagramExplainer']]],
+ ['write_5foutput_6589',['write_output',['../classvg_1_1ReadFilter.html#a249032f1613c12263e7c14d83b4e527e',1,'vg::ReadFilter']]],
+ ['write_5fsupports_6590',['write_supports',['../structvg_1_1SupportAugmentedGraph.html#a4f08f8c78bf0ffbfe7e364d4404b97a9',1,'vg::SupportAugmentedGraph']]],
+ ['write_5fto_5ffile_6591',['write_to_file',['../namespacevg_1_1io.html#a88cb8e7bbebb78a2ef3bdce1c64ba077',1,'vg::io']]],
+ ['write_5ftranscript_5finfo_6592',['write_transcript_info',['../classvg_1_1Transcriptome.html#ada48319a8370ad45364d9bc8241b275a',1,'vg::Transcriptome']]],
+ ['write_5ftranscript_5fsequences_6593',['write_transcript_sequences',['../classvg_1_1Transcriptome.html#a4ce90a0e2556b51c62e4a3e550108750',1,'vg::Transcriptome']]],
+ ['write_5ftranslations_6594',['write_translations',['../structvg_1_1AugmentedGraph.html#a70ffd6eb24e80cfa265ae48cdde15a45',1,'vg::AugmentedGraph']]],
+ ['write_5ftsv_6595',['write_tsv',['../classvg_1_1ReadFilter.html#a9979d9966e9ea82a9cd160dbf38d4b7c',1,'vg::ReadFilter']]],
+ ['write_5fvariant_6596',['write_variant',['../classvg_1_1Genotyper.html#af5b580b6db4e727934f964d00b058038',1,'vg::Genotyper']]],
+ ['write_5fvariants_6597',['write_variants',['../classvg_1_1VCFOutputCaller.html#afff7887f0111aae8ae3103b990ff54dd',1,'vg::VCFOutputCaller']]],
+ ['write_5fvcf_5fheader_6598',['write_vcf_header',['../classvg_1_1Genotyper.html#ad2beb83f750d1deec75b16a60c2ea805',1,'vg::Genotyper']]],
+ ['writealiasedraw_6599',['WriteAliasedRaw',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a85d9e1ca69d7bad9e2941b7ecec08a42',1,'vg::io::BlockedGzipOutputStream']]],
+ ['writer_5fstop_6600',['writer_stop',['../classvg_1_1io_1_1StreamMultiplexer.html#ae51a3ffdfe9ec988bf732e4904dcbf60',1,'vg::io::StreamMultiplexer']]],
+ ['writer_5fthread_6601',['writer_thread',['../classvg_1_1io_1_1StreamMultiplexer.html#a56a9d39b8ccdd13f07e835ad7a967a60',1,'vg::io::StreamMultiplexer']]],
+ ['writer_5fthread_5ffunction_6602',['writer_thread_function',['../classvg_1_1io_1_1StreamMultiplexer.html#a29ba6b97591887c453b0cc112cae41e4',1,'vg::io::StreamMultiplexer']]],
+ ['wrong_5fname_6603',['wrong_name',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a5d133dedebb885c312dbfca70d5abe15',1,'vg::Counts']]],
+ ['wrong_5frefpos_6604',['wrong_refpos',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a069ad2b94f1414f1ba774043f5047d15',1,'vg::Counts']]]
];
diff --git a/search/all_18.js b/search/all_18.js
index 0558e08135..dc2eed2d83 100644
--- a/search/all_18.js
+++ b/search/all_18.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['temp_5ffile_6603',['temp_file',['../namespacexg_1_1temp__file.html',1,'xg']]],
- ['xdrop_5faligner_2ecpp_6604',['xdrop_aligner.cpp',['../xdrop__aligner_8cpp.html',1,'']]],
- ['xdropaligner_6605',['XdropAligner',['../classvg_1_1XdropAligner.html',1,'vg::XdropAligner'],['../classvg_1_1XdropAligner.html#ae707a0f10732b011cea8aab49913a142',1,'vg::XdropAligner::XdropAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1XdropAligner.html#a553d87ce9c62f404b01490ad0619164a',1,'vg::XdropAligner::XdropAligner()=default'],['../classvg_1_1XdropAligner.html#af42a02f900600c3c375fa0b6644c97a9',1,'vg::XdropAligner::XdropAligner(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a2eb9135c8b9e7534b90124968e4d3f48',1,'vg::XdropAligner::XdropAligner(XdropAligner &&other)']]],
- ['xdrops_6606',['xdrops',['../classvg_1_1Aligner.html#a6379438f31b8f9f5900acb7ba00596f8',1,'vg::Aligner::xdrops()'],['../classvg_1_1QualAdjAligner.html#a996c23b1f8d703c099a376c0bc610a97',1,'vg::QualAdjAligner::xdrops()']]],
- ['xg_6607',['XG',['../classxg_1_1XG.html',1,'xg::XG'],['../namespacexg.html',1,'xg'],['../classxg_1_1XG.html#ab71253786ed61320ec3101a06df3f369',1,'xg::XG::XG(void)=default'],['../classxg_1_1XG.html#a16821ba9ad761dac00ef46a1d9bc7424',1,'xg::XG::XG(const XG &other)=delete'],['../classxg_1_1XG.html#a4bcac3042196387b5c04b6833de7a035',1,'xg::XG::XG(XG &&other)=delete']]],
- ['xg_2ecpp_6608',['xg.cpp',['../xg_8cpp.html',1,'']]],
- ['xg_2ehpp_6609',['xg.hpp',['../xg_8hpp.html',1,'']]],
- ['xg_5findex_5fsize_6610',['xg_index_size',['../namespacevg.html#a07b713793f27ae9eb7f96617e97549f1',1,'vg']]],
- ['xgformaterror_6611',['XGFormatError',['../classxg_1_1XGFormatError.html',1,'xg']]],
- ['xgidx_6612',['xgidx',['../classvg_1_1Viz.html#a1c854dabf978e525e6fab1223927ab2c',1,'vg::Viz']]],
- ['xgpath_6613',['XGPath',['../classxg_1_1XGPath.html',1,'xg::XGPath'],['../classxg_1_1XGPath.html#af623a612337301ad98ed9c45108b9616',1,'xg::XGPath::XGPath(void)=default'],['../classxg_1_1XGPath.html#a7a3d21f2e1ad0f36c25897591b6e31da',1,'xg::XGPath::XGPath(const std::string &path_name, const std::vector< handle_t > &path, bool is_circular, XG &graph)'],['../classxg_1_1XGPath.html#aeb3f65f6d78a0fa02486f0c9c51c97a8',1,'xg::XGPath::XGPath(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a010789a1a74731505b2b8a570f4e7547',1,'xg::XGPath::XGPath(XGPath &&other)=delete']]],
- ['xindex_6614',['xindex',['../classvg_1_1BaseMapper.html#a0afffd854c5bcf69e8bd1125de4c7267',1,'vg::BaseMapper']]],
- ['xsputn_6615',['xsputn',['../classvg_1_1io_1_1fdoutbuf.html#a1eba1fc19d1c9100bc5eb98259cc914b',1,'vg::io::fdoutbuf']]]
+ ['temp_5ffile_6605',['temp_file',['../namespacexg_1_1temp__file.html',1,'xg']]],
+ ['xdrop_5faligner_2ecpp_6606',['xdrop_aligner.cpp',['../xdrop__aligner_8cpp.html',1,'']]],
+ ['xdropaligner_6607',['XdropAligner',['../classvg_1_1XdropAligner.html',1,'vg::XdropAligner'],['../classvg_1_1XdropAligner.html#ae707a0f10732b011cea8aab49913a142',1,'vg::XdropAligner::XdropAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1XdropAligner.html#a553d87ce9c62f404b01490ad0619164a',1,'vg::XdropAligner::XdropAligner()=default'],['../classvg_1_1XdropAligner.html#af42a02f900600c3c375fa0b6644c97a9',1,'vg::XdropAligner::XdropAligner(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a2eb9135c8b9e7534b90124968e4d3f48',1,'vg::XdropAligner::XdropAligner(XdropAligner &&other)']]],
+ ['xdrops_6608',['xdrops',['../classvg_1_1Aligner.html#a6379438f31b8f9f5900acb7ba00596f8',1,'vg::Aligner::xdrops()'],['../classvg_1_1QualAdjAligner.html#a996c23b1f8d703c099a376c0bc610a97',1,'vg::QualAdjAligner::xdrops()']]],
+ ['xg_6609',['XG',['../classxg_1_1XG.html',1,'xg::XG'],['../namespacexg.html',1,'xg'],['../classxg_1_1XG.html#ab71253786ed61320ec3101a06df3f369',1,'xg::XG::XG(void)=default'],['../classxg_1_1XG.html#a16821ba9ad761dac00ef46a1d9bc7424',1,'xg::XG::XG(const XG &other)=delete'],['../classxg_1_1XG.html#a4bcac3042196387b5c04b6833de7a035',1,'xg::XG::XG(XG &&other)=delete']]],
+ ['xg_2ecpp_6610',['xg.cpp',['../xg_8cpp.html',1,'']]],
+ ['xg_2ehpp_6611',['xg.hpp',['../xg_8hpp.html',1,'']]],
+ ['xg_5findex_5fsize_6612',['xg_index_size',['../namespacevg.html#a07b713793f27ae9eb7f96617e97549f1',1,'vg']]],
+ ['xgformaterror_6613',['XGFormatError',['../classxg_1_1XGFormatError.html',1,'xg']]],
+ ['xgidx_6614',['xgidx',['../classvg_1_1Viz.html#a1c854dabf978e525e6fab1223927ab2c',1,'vg::Viz']]],
+ ['xgpath_6615',['XGPath',['../classxg_1_1XGPath.html',1,'xg::XGPath'],['../classxg_1_1XGPath.html#af623a612337301ad98ed9c45108b9616',1,'xg::XGPath::XGPath(void)=default'],['../classxg_1_1XGPath.html#a7a3d21f2e1ad0f36c25897591b6e31da',1,'xg::XGPath::XGPath(const std::string &path_name, const std::vector< handle_t > &path, bool is_circular, XG &graph)'],['../classxg_1_1XGPath.html#aeb3f65f6d78a0fa02486f0c9c51c97a8',1,'xg::XGPath::XGPath(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a010789a1a74731505b2b8a570f4e7547',1,'xg::XGPath::XGPath(XGPath &&other)=delete']]],
+ ['xindex_6616',['xindex',['../classvg_1_1BaseMapper.html#a0afffd854c5bcf69e8bd1125de4c7267',1,'vg::BaseMapper']]],
+ ['xsputn_6617',['xsputn',['../classvg_1_1io_1_1fdoutbuf.html#a1eba1fc19d1c9100bc5eb98259cc914b',1,'vg::io::fdoutbuf']]]
];
diff --git a/search/all_19.js b/search/all_19.js
index 0713e26605..5ced143a73 100644
--- a/search/all_19.js
+++ b/search/all_19.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['yens_5fk_5fwidest_5fpaths_6616',['yens_k_widest_paths',['../namespacevg_1_1algorithms.html#ad9a715606bdd30499dc9db88583c6573',1,'vg::algorithms']]]
+ ['yens_5fk_5fwidest_5fpaths_6618',['yens_k_widest_paths',['../namespacevg_1_1algorithms.html#ad9a715606bdd30499dc9db88583c6573',1,'vg::algorithms']]]
];
diff --git a/search/all_1a.js b/search/all_1a.js
index fcc36eec78..53d245b4ec 100644
--- a/search/all_1a.js
+++ b/search/all_1a.js
@@ -1,28 +1,28 @@
var searchData=
[
- ['fill_5fin_5fforest_3c_20minimizermapper_3a_3aminimizer_20_3e_6617',['fill_in_forest< MinimizerMapper::Minimizer >',['../namespacevg.html#ad4f0e6958b0bfd7c256ee10291a95925',1,'vg']]],
- ['get_5fcyclic_5fsnarl_5fintervals_3c_20minimizermapper_3a_3aminimizer_20_3e_6618',['get_cyclic_snarl_intervals< MinimizerMapper::Minimizer >',['../namespacevg.html#a279d0eb09ed478cc7c6c98e3cbcd9864',1,'vg']]],
- ['print_5fself_3c_20minimizermapper_3a_3aminimizer_20_3e_6619',['print_self< MinimizerMapper::Minimizer >',['../namespacevg.html#a48dec55a9705e1b2a636a90c7c9d9e9d',1,'vg']]],
- ['z_6620',['Z',['../classvg_1_1truncated__normal__distribution.html#aeef658109dfa3a3d4904aea92a93b93d',1,'vg::truncated_normal_distribution']]],
- ['zip_5falignments_6621',['zip_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a96a24f6cbdc09cf0098251f8b61baf4a',1,'vg::MultipathAlignmentGraph']]],
- ['zip_5fcode_2ecpp_6622',['zip_code.cpp',['../zip__code_8cpp.html',1,'']]],
- ['zip_5fcode_2ehpp_6623',['zip_code.hpp',['../zip__code_8hpp.html',1,'']]],
- ['zip_5fcode_5ftree_6624',['zip_code_tree',['../classvg_1_1ZipCodeTree.html#ad2ffc1171ce7791a9c047612efddeeaa',1,'vg::ZipCodeTree']]],
- ['zip_5fcode_5ftree_2ecpp_6625',['zip_code_tree.cpp',['../zip__code__tree_8cpp.html',1,'']]],
- ['zip_5fcode_5ftree_2ehpp_6626',['zip_code_tree.hpp',['../zip__code__tree_8hpp.html',1,'']]],
- ['zip_5fforest_6627',['zip_forest',['../classvg_1_1MinimizerMapper.html#a5e9775389a175cbe4141678d5a4613dd',1,'vg::MinimizerMapper']]],
- ['zip_5ftree_5ftransition_5fiterator_6628',['zip_tree_transition_iterator',['../namespacevg_1_1algorithms.html#a73608f2f497e40cc514deaa74a00cb52',1,'vg::algorithms']]],
- ['zipcode_6629',['ZipCode',['../classvg_1_1ZipCode.html',1,'vg::ZipCode'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a97855edffa7660f988e3f4b7dad3fc9f',1,'vg::SnarlDistanceIndexClusterer::Seed::zipcode()'],['../classvg_1_1ZipCode.html#a4d8456b4edb18c6c6d812b05b5e4783e',1,'vg::ZipCode::zipcode()']]],
- ['zipcode_5fdepth_6630',['zipcode_depth',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d982a3ef3c1a8ec4c0759a6638e00a9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['zipcode_5fmain_2ecpp_6631',['zipcode_main.cpp',['../zipcode__main_8cpp.html',1,'']]],
- ['zipcode_5ftree_5fcoverage_5fthreshold_6632',['zipcode_tree_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a3af651e9d670f2688887a78128db39f5',1,'vg::MinimizerMapper']]],
- ['zipcode_5ftree_5fscale_6633',['zipcode_tree_scale',['../classvg_1_1MinimizerMapper.html#ab88fdcdafabde8c33f21c176f544ab01',1,'vg::MinimizerMapper']]],
- ['zipcode_5ftree_5fscore_5fthreshold_6634',['zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a98bd33607a6fe87a99e24e6ea4388c01',1,'vg::MinimizerMapper']]],
- ['zipcodecollection_6635',['ZipCodeCollection',['../classvg_1_1ZipCodeCollection.html',1,'vg::ZipCodeCollection'],['../classvg_1_1ZipCodeCollection.html#aef34ada27f78937e260e90fb1fe8a1d0',1,'vg::ZipCodeCollection::ZipCodeCollection()']]],
- ['zipcodeforest_6636',['ZipCodeForest',['../classvg_1_1ZipCodeForest.html',1,'vg::ZipCodeForest'],['../classvg_1_1ZipCodeTree.html#ae954dd8e2c990674b2293ddd18ae6517',1,'vg::ZipCodeTree::ZipCodeForest()'],['../classvg_1_1ZipCodeForest.html#ab6f83d5af9f5ab490040e469f38b68df',1,'vg::ZipCodeForest::ZipCodeForest()']]],
- ['zipcodes_6637',['zipcodes',['../classvg_1_1MinimizerMapper.html#adc4e2829dcbe163a606e567373aa10f4',1,'vg::MinimizerMapper::zipcodes()'],['../classvg_1_1ZipCodeCollection.html#a73068c82a1be054f59074d37b63fe74d',1,'vg::ZipCodeCollection::zipcodes()']]],
- ['zipcodetree_6638',['ZipCodeTree',['../classvg_1_1ZipCodeTree.html',1,'vg::ZipCodeTree'],['../classvg_1_1ZipCodeTree.html#a891b100128d123066ee70e97d1374f41',1,'vg::ZipCodeTree::ZipCodeTree()']]],
- ['zstdutil_6639',['zstdutil',['../namespacezstdutil.html',1,'']]],
- ['zstdutil_2ecpp_6640',['zstdutil.cpp',['../zstdutil_8cpp.html',1,'']]],
- ['zstdutil_2ehpp_6641',['zstdutil.hpp',['../zstdutil_8hpp.html',1,'']]]
+ ['fill_5fin_5fforest_3c_20minimizermapper_3a_3aminimizer_20_3e_6619',['fill_in_forest< MinimizerMapper::Minimizer >',['../namespacevg.html#ad4f0e6958b0bfd7c256ee10291a95925',1,'vg']]],
+ ['get_5fcyclic_5fsnarl_5fintervals_3c_20minimizermapper_3a_3aminimizer_20_3e_6620',['get_cyclic_snarl_intervals< MinimizerMapper::Minimizer >',['../namespacevg.html#a279d0eb09ed478cc7c6c98e3cbcd9864',1,'vg']]],
+ ['print_5fself_3c_20minimizermapper_3a_3aminimizer_20_3e_6621',['print_self< MinimizerMapper::Minimizer >',['../namespacevg.html#a48dec55a9705e1b2a636a90c7c9d9e9d',1,'vg']]],
+ ['z_6622',['Z',['../classvg_1_1truncated__normal__distribution.html#aeef658109dfa3a3d4904aea92a93b93d',1,'vg::truncated_normal_distribution']]],
+ ['zip_5falignments_6623',['zip_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a96a24f6cbdc09cf0098251f8b61baf4a',1,'vg::MultipathAlignmentGraph']]],
+ ['zip_5fcode_2ecpp_6624',['zip_code.cpp',['../zip__code_8cpp.html',1,'']]],
+ ['zip_5fcode_2ehpp_6625',['zip_code.hpp',['../zip__code_8hpp.html',1,'']]],
+ ['zip_5fcode_5ftree_6626',['zip_code_tree',['../classvg_1_1ZipCodeTree.html#ad2ffc1171ce7791a9c047612efddeeaa',1,'vg::ZipCodeTree']]],
+ ['zip_5fcode_5ftree_2ecpp_6627',['zip_code_tree.cpp',['../zip__code__tree_8cpp.html',1,'']]],
+ ['zip_5fcode_5ftree_2ehpp_6628',['zip_code_tree.hpp',['../zip__code__tree_8hpp.html',1,'']]],
+ ['zip_5fforest_6629',['zip_forest',['../classvg_1_1MinimizerMapper.html#a5e9775389a175cbe4141678d5a4613dd',1,'vg::MinimizerMapper']]],
+ ['zip_5ftree_5ftransition_5fiterator_6630',['zip_tree_transition_iterator',['../namespacevg_1_1algorithms.html#a73608f2f497e40cc514deaa74a00cb52',1,'vg::algorithms']]],
+ ['zipcode_6631',['ZipCode',['../classvg_1_1ZipCode.html',1,'vg::ZipCode'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a97855edffa7660f988e3f4b7dad3fc9f',1,'vg::SnarlDistanceIndexClusterer::Seed::zipcode()'],['../classvg_1_1ZipCode.html#a4d8456b4edb18c6c6d812b05b5e4783e',1,'vg::ZipCode::zipcode()']]],
+ ['zipcode_5fdepth_6632',['zipcode_depth',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d982a3ef3c1a8ec4c0759a6638e00a9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['zipcode_5fmain_2ecpp_6633',['zipcode_main.cpp',['../zipcode__main_8cpp.html',1,'']]],
+ ['zipcode_5ftree_5fcoverage_5fthreshold_6634',['zipcode_tree_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a3af651e9d670f2688887a78128db39f5',1,'vg::MinimizerMapper']]],
+ ['zipcode_5ftree_5fscale_6635',['zipcode_tree_scale',['../classvg_1_1MinimizerMapper.html#ab88fdcdafabde8c33f21c176f544ab01',1,'vg::MinimizerMapper']]],
+ ['zipcode_5ftree_5fscore_5fthreshold_6636',['zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a98bd33607a6fe87a99e24e6ea4388c01',1,'vg::MinimizerMapper']]],
+ ['zipcodecollection_6637',['ZipCodeCollection',['../classvg_1_1ZipCodeCollection.html',1,'vg::ZipCodeCollection'],['../classvg_1_1ZipCodeCollection.html#aef34ada27f78937e260e90fb1fe8a1d0',1,'vg::ZipCodeCollection::ZipCodeCollection()']]],
+ ['zipcodeforest_6638',['ZipCodeForest',['../classvg_1_1ZipCodeForest.html',1,'vg::ZipCodeForest'],['../classvg_1_1ZipCodeTree.html#ae954dd8e2c990674b2293ddd18ae6517',1,'vg::ZipCodeTree::ZipCodeForest()'],['../classvg_1_1ZipCodeForest.html#ab6f83d5af9f5ab490040e469f38b68df',1,'vg::ZipCodeForest::ZipCodeForest()']]],
+ ['zipcodes_6639',['zipcodes',['../classvg_1_1MinimizerMapper.html#adc4e2829dcbe163a606e567373aa10f4',1,'vg::MinimizerMapper::zipcodes()'],['../classvg_1_1ZipCodeCollection.html#a73068c82a1be054f59074d37b63fe74d',1,'vg::ZipCodeCollection::zipcodes()']]],
+ ['zipcodetree_6640',['ZipCodeTree',['../classvg_1_1ZipCodeTree.html',1,'vg::ZipCodeTree'],['../classvg_1_1ZipCodeTree.html#a891b100128d123066ee70e97d1374f41',1,'vg::ZipCodeTree::ZipCodeTree()']]],
+ ['zstdutil_6641',['zstdutil',['../namespacezstdutil.html',1,'']]],
+ ['zstdutil_2ecpp_6642',['zstdutil.cpp',['../zstdutil_8cpp.html',1,'']]],
+ ['zstdutil_2ehpp_6643',['zstdutil.hpp',['../zstdutil_8hpp.html',1,'']]]
];
diff --git a/search/all_1b.js b/search/all_1b.js
index 1047cbb58f..2623fe4abc 100644
--- a/search/all_1b.js
+++ b/search/all_1b.js
@@ -1,201 +1,201 @@
var searchData=
[
- ['_7eabstractreadsampler_6642',['~AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html#aab2237075e873b1fac2b9d927835dd5d',1,'vg::AbstractReadSampler']]],
- ['_7ealiasgraph_6643',['~AliasGraph',['../classvg_1_1AliasGraph.html#aa6557ac096d2a238b4bde66341fa4bbf',1,'vg::AliasGraph']]],
- ['_7ealigner_6644',['~Aligner',['../classvg_1_1Aligner.html#ab652846ac99c793321f513e80b3567e7',1,'vg::Aligner']]],
- ['_7ealignmentchainmodelvertex_6645',['~AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html#a2956b8c27f6438dda8d392c47c29da59',1,'vg::AlignmentChainModelVertex']]],
- ['_7ealignmentemitter_6646',['~AlignmentEmitter',['../classvg_1_1io_1_1AlignmentEmitter.html#a8a2ed8eecf9bc49b0c82e0276a8c3ecf',1,'vg::io::AlignmentEmitter']]],
- ['_7ealttracebackstack_6647',['~AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a7271beafb4fd9d7d993e7225d0289ee8',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['_7eappendhaplotypecommand_6648',['~AppendHaplotypeCommand',['../structvg_1_1AppendHaplotypeCommand.html#a5890b1f7b3374109bb8326372f3dcd18',1,'vg::AppendHaplotypeCommand']]],
- ['_7eargspec_6649',['~ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html#a85d84f459627dc7d5d476ef600cd4eaa',1,'vg::subcommand::ArgSpec']]],
- ['_7ebabuilder_6650',['~BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#af4852751e6f009ed647f81926b8c6ac0',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['_7ebamatrix_6651',['~BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac174727f3eb7d040f75bbb638e3ef585',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['_7ebandedglobalaligner_6652',['~BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html#ac211fadde52f8cc1312fddb585c021b0',1,'vg::BandedGlobalAligner']]],
- ['_7ebaseargspec_6653',['~BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a6324c7d0c79aece0d2cf73a9bb385377',1,'vg::subcommand::BaseArgSpec']]],
- ['_7ebaseoption_6654',['~BaseOption',['../classvg_1_1BaseOption.html#a877daeaa51e8978827609c35bffa6f7d',1,'vg::BaseOption']]],
- ['_7ebaseoptiongroup_6655',['~BaseOptionGroup',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a65cfafee0415b04533cece4cde5c9b8a',1,'vg::subcommand::BaseOptionGroup']]],
- ['_7ebasevaluation_6656',['~BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html#af8bbcfd7d30f6c358ba91db3be2a7084',1,'vg::subcommand::BaseValuation']]],
- ['_7eblockedgzipinputstream_6657',['~BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a56990712e743be20a39e760309a8934c',1,'vg::io::BlockedGzipInputStream']]],
- ['_7eblockedgzipoutputstream_6658',['~BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaac9002de6d983cb46a36b44620448bb',1,'vg::io::BlockedGzipOutputStream']]],
- ['_7ebuildablesnarldecomposition_6659',['~BuildableSnarlDecomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a04eec535a4ad69c3d57a7733cbb56f23',1,'handlegraph::BuildableSnarlDecomposition']]],
- ['_7ecachedpackedtraversalsupportfinder_6660',['~CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html#ae90902c6346948c1b2ab45dd389b4014',1,'vg::CachedPackedTraversalSupportFinder']]],
- ['_7ecallinfo_6661',['~CallInfo',['../structvg_1_1SnarlCaller_1_1CallInfo.html#a596d13cd23b7d5dd9a24bdea876a286d',1,'vg::SnarlCaller::CallInfo']]],
- ['_7ecolors_6662',['~Colors',['../classvg_1_1Colors.html#ac08aaa9a815d639d327c3ea80b97ed2b',1,'vg::Colors']]],
- ['_7ecompletedtranscriptpath_6663',['~CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html#a885c00ed2c371cddfe7a9a78c00dcd94',1,'vg::CompletedTranscriptPath']]],
- ['_7ecomponentmindistanceclusterer_6664',['~ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html#aa13390387862e6477651a627db8b36b3',1,'vg::ComponentMinDistanceClusterer']]],
- ['_7econnection_5ft_6665',['~connection_t',['../classvg_1_1connection__t.html#ac3664dfd1f422b7a88b2760e9a4ee83d',1,'vg::connection_t']]],
- ['_7econsistencycalculator_6666',['~ConsistencyCalculator',['../classvg_1_1ConsistencyCalculator.html#afb05d4ab7a962df47c62c408d0154ba0',1,'vg::ConsistencyCalculator']]],
- ['_7edagifiedgraph_6667',['~DagifiedGraph',['../classvg_1_1DagifiedGraph.html#acb7989cf7dcc34da6fd11228d36321f7',1,'vg::DagifiedGraph']]],
- ['_7edeconstructor_6668',['~Deconstructor',['../classvg_1_1Deconstructor.html#a875c8006f289ad46470c05c8808bdd73',1,'vg::Deconstructor']]],
- ['_7edeflection_6669',['~Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#af4deb014af190975b2e7fe3540f6f461',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['_7edeletablehandlegraph_6670',['~DeletableHandleGraph',['../classhandlegraph_1_1DeletableHandleGraph.html#a62ed805e124ceb05cfa98d4e631a9ebd',1,'handlegraph::DeletableHandleGraph']]],
- ['_7edeletehaplotypecommand_6671',['~DeleteHaplotypeCommand',['../structvg_1_1DeleteHaplotypeCommand.html#a2049b0eb4e4cf76d42b26fb9b0ecb659',1,'vg::DeleteHaplotypeCommand']]],
- ['_7edeletionaligner_6672',['~DeletionAligner',['../classvg_1_1DeletionAligner.html#a797ac3036e59d5086c0822b90302dd14',1,'vg::DeletionAligner']]],
- ['_7ediagramexplainer_6673',['~DiagramExplainer',['../classvg_1_1DiagramExplainer.html#aacac728ac8712e2d1f803c0735c34990',1,'vg::DiagramExplainer']]],
- ['_7edinucleotidemachine_6674',['~DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html#a927431a787e6f77549850cea55d883b0',1,'vg::DinucleotideMachine']]],
- ['_7edistanceheuristic_6675',['~DistanceHeuristic',['../classvg_1_1DistanceHeuristic.html#abca20b0fc239abad09fabb6d6bad0b50',1,'vg::DistanceHeuristic']]],
- ['_7edozeuinterface_6676',['~DozeuInterface',['../classvg_1_1DozeuInterface.html#a0ac4d30c781e2a2278986ecbb84a34a6',1,'vg::DozeuInterface']]],
- ['_7edozeupinningoverlay_6677',['~DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html#a6fe397bf132beeabd0ed7f830b1f9994',1,'vg::DozeuPinningOverlay']]],
- ['_7edpscorecomparator_6678',['~DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a02c3e3552497f6425a1f3d14682c1d06',1,'vg::MEMClusterer::DPScoreComparator']]],
- ['_7eedit_5ft_6679',['~edit_t',['../classvg_1_1edit__t.html#a43201af48ee260fa83a5bde0ed75a978',1,'vg::edit_t']]],
- ['_7eeditedtranscriptpath_6680',['~EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html#aba2f28b19414c8c3795e60e76a07f807',1,'vg::EditedTranscriptPath']]],
- ['_7eexhaustivetraversalfinder_6681',['~ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html#a7586c1b256f63d9e4295a9f1011b921a',1,'vg::ExhaustiveTraversalFinder']]],
- ['_7eexpandingoverlaygraph_6682',['~ExpandingOverlayGraph',['../classhandlegraph_1_1ExpandingOverlayGraph.html#a9d7cac3cf3b289fe1980d0575e70be72',1,'handlegraph::ExpandingOverlayGraph']]],
- ['_7eexplainer_6683',['~Explainer',['../classvg_1_1Explainer.html#a68991032a4a7fed25227a884f7f76a2a',1,'vg::Explainer']]],
- ['_7efilter_6684',['~Filter',['../classvg_1_1Filter.html#a09073f3ae2d26bc61cf639dfc4072745',1,'vg::Filter']]],
- ['_7efixedgenotypepriorcalculator_6685',['~FixedGenotypePriorCalculator',['../classvg_1_1FixedGenotypePriorCalculator.html#a4adc4bf44587b687076826dffc91ccf0',1,'vg::FixedGenotypePriorCalculator']]],
- ['_7eflagargspec_6686',['~FlagArgSpec',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a7988d073aa24da829c03c9d68ae651f9',1,'vg::subcommand::FlagArgSpec']]],
- ['_7eflatfilebacktranslation_6687',['~FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html#a4330bd5f76951158a1ea50755b43293d',1,'vg::FlatFileBackTranslation']]],
- ['_7eflowcaller_6688',['~FlowCaller',['../classvg_1_1FlowCaller.html#a6fc652c91844cba402eb9e143883eefa',1,'vg::FlowCaller']]],
- ['_7efragmentlengthdistribution_6689',['~FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html#a5ca105be9aca035e59985092d1a6aa79',1,'vg::FragmentLengthDistribution']]],
- ['_7egafalignmentemitter_6690',['~GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html#ab8c76602efdaadba7319ca5103bc9107',1,'vg::io::GafAlignmentEmitter']]],
- ['_7egafoutputcaller_6691',['~GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html#af275fa29f22a94c9c4180280675a160e',1,'vg::GAFOutputCaller']]],
- ['_7egbwttraversalfinder_6692',['~GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html#aaf4b52f7a7807922daa514df94235a3a',1,'vg::GBWTTraversalFinder']]],
- ['_7egenomestatecommand_6693',['~GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html#a951ebc208c74b7ec323de6f517d02527',1,'vg::GenomeStateCommand']]],
- ['_7egenotypelikelihoodcalculator_6694',['~GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html#a295ae8723775d0481023badde359d44c',1,'vg::GenotypeLikelihoodCalculator']]],
- ['_7egenotypepriorcalculator_6695',['~GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html#a63a28c3dff800ddc5ee37efcd836ba4d',1,'vg::GenotypePriorCalculator']]],
- ['_7egfahandlegraph_6696',['~GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html#aeaa72881401798c61af748a47bc4746e',1,'vg::GFAHandleGraph']]],
- ['_7egffreader_6697',['~GFFReader',['../classvg_1_1GFFReader.html#ac13f3d71875c489d9cc9a400d04d6e8e',1,'vg::GFFReader']]],
- ['_7egffrecord_6698',['~GFFRecord',['../structvg_1_1GFFRecord.html#af031304f06fc3a9bdb1f4e7b81695f1a',1,'vg::GFFRecord']]],
- ['_7egraphcaller_6699',['~GraphCaller',['../classvg_1_1GraphCaller.html#a443486cd8ab78a5392b5ed47506ca4c4',1,'vg::GraphCaller']]],
- ['_7egreedymindistanceclusterer_6700',['~GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html#a9d51c4982f45dda3d6da98f182969c6b',1,'vg::GreedyMinDistanceClusterer']]],
- ['_7egroupedoptiongroup_6701',['~GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a03413226481dddd57ccb32b1aa4ef94c',1,'vg::subcommand::GroupedOptionGroup']]],
- ['_7egsswaligner_6702',['~GSSWAligner',['../classvg_1_1GSSWAligner.html#a7a80ce643da0316c9151fab19e8e8581',1,'vg::GSSWAligner']]],
- ['_7ehandlegraph_6703',['~HandleGraph',['../classhandlegraph_1_1HandleGraph.html#a24fb796441c9ad8c870fdb716a82b305',1,'handlegraph::HandleGraph']]],
- ['_7ehandlegraphsnarlfinder_6704',['~HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html#a01f84699fe59b5d360df0ef4a671edb2',1,'vg::HandleGraphSnarlFinder']]],
- ['_7ehandler_6705',['~Handler',['../structvg_1_1temp__file_1_1Handler.html#abefd598acc672c960d80c70fa53c5476',1,'vg::temp_file::Handler::~Handler()'],['../structxg_1_1temp__file_1_1Handler.html#a6a4006456b42c1507d5d3505a8aa93a2',1,'xg::temp_file::Handler::~Handler()']]],
- ['_7ehaplo_5fdp_5fcolumn_6706',['~haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html#a179bfa823f2329b2500fb948bfff30ca',1,'haplo::haplo_DP_column']]],
- ['_7ehaplotype_6707',['~Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a29c3049eebafef23e3ec539093ffe9ce',1,'vg::PhasedGenome::Haplotype']]],
- ['_7ehaplotypenode_6708',['~HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a4e012749eab6e610da87b54036717ec5',1,'vg::PhasedGenome::HaplotypeNode']]],
- ['_7ehitedge_6709',['~HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html#ae1edc6409a97d72b9ae873d4e74d6721',1,'vg::MEMClusterer::HitEdge']]],
- ['_7ehitnode_6710',['~HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html#af253bd2d33cba3d97a13a9a4159c4f41',1,'vg::MEMClusterer::HitNode']]],
- ['_7ehtsalignmentemitter_6711',['~HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html#ab2914f2bdd3ecf8cd230e30479675304',1,'vg::HTSAlignmentEmitter']]],
- ['_7ehtswriter_6712',['~HTSWriter',['../classvg_1_1HTSWriter.html#a8be4096c91ac54b168828071b814104d',1,'vg::HTSWriter']]],
- ['_7eidentityoverlay_6713',['~IdentityOverlay',['../classvg_1_1IdentityOverlay.html#a15e797a8861789f9d2f0ec0f0ca57032',1,'vg::IdentityOverlay']]],
- ['_7eincrementalsubgraph_6714',['~IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html#a330ad1c9229ac053777528cb79efad3e',1,'vg::IncrementalSubgraph']]],
- ['_7eindexingplan_6715',['~IndexingPlan',['../classvg_1_1IndexingPlan.html#adf7d45d963ee4dc8a4ca8c3c3d3ca3ee',1,'vg::IndexingPlan']]],
- ['_7eindexregistry_6716',['~IndexRegistry',['../classvg_1_1IndexRegistry.html#a95e5aa1a57680dd60b599d3735145ac4',1,'vg::IndexRegistry']]],
- ['_7einserthaplotypecommand_6717',['~InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html#a173157b02306f85eb55291107367602e',1,'vg::InsertHaplotypeCommand']]],
- ['_7eiterator_6718',['~iterator',['../classvg_1_1PhasedGenome_1_1iterator.html#a49c0df47c5f5eb7afc45a2978f5dc497',1,'vg::PhasedGenome::iterator::~iterator()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a578e1ae4eb29377b05133e390ad1d4c3',1,'handlegraph::PathForEachSocket::iterator::~iterator()']]],
- ['_7ej2pb_5ferror_6719',['~j2pb_error',['../classj2pb__error.html#a4bf7997e2520c68a3861f9f105132510',1,'j2pb_error']]],
- ['_7ejobschedule_6720',['~JobSchedule',['../classvg_1_1JobSchedule.html#a2c08f9b4c3db46f28c2a44d23524b9aa',1,'vg::JobSchedule']]],
- ['_7ejoinedsplicegraph_6721',['~JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html#a1998a6854f0f56b1fc69476f09ebb5c7',1,'vg::JoinedSpliceGraph']]],
- ['_7ejson_5fautoptr_6722',['~json_autoptr',['../structjson__autoptr.html#a90ed076495793f454cea2f2e8ba3738b',1,'json_autoptr']]],
- ['_7ejsonstreamhelper_6723',['~JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html#a0cb9dd04575adfdb70b5a454a65871a7',1,'vg::io::JSONStreamHelper']]],
- ['_7elegacycaller_6724',['~LegacyCaller',['../classvg_1_1LegacyCaller.html#a10147f341d558b896d91c2180f0361d8',1,'vg::LegacyCaller']]],
- ['_7elinear_5fhaplo_5fstructure_6725',['~linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html#a11b487a3f7b503ed282cd1cfee5ae2f3',1,'haplo::linear_haplo_structure']]],
- ['_7emapper_6726',['~Mapper',['../classvg_1_1Mapper.html#a285dd133a8540553f671b7eac33f6ca0',1,'vg::Mapper']]],
- ['_7emasker_6727',['~Masker',['../classvg_1_1Masker.html#ab8ef1024fde833626e6ef18fbb6fdb9d',1,'vg::Masker']]],
- ['_7emcmccaller_6728',['~MCMCCaller',['../classvg_1_1MCMCCaller.html#a1bd5d1d33ec02a9b5dabcb882996d964',1,'vg::MCMCCaller']]],
- ['_7ememchainmodelvertex_6729',['~MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html#accc20533b5065e34208355797f373a04',1,'vg::MEMChainModelVertex']]],
- ['_7ememclusterer_6730',['~MEMClusterer',['../classvg_1_1MEMClusterer.html#a86a3a3ccd7e416a727118f7aa763db18',1,'vg::MEMClusterer']]],
- ['_7ememoizinggraph_6731',['~MemoizingGraph',['../classvg_1_1MemoizingGraph.html#a7b70d3665f07afcce593013fd4d27170',1,'vg::MemoizingGraph']]],
- ['_7emessageemitter_6732',['~MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html#ae9fa66759101257b58f38ec4f54dabfa',1,'vg::io::MessageEmitter']]],
- ['_7emindistanceclusterer_6733',['~MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html#a92349c1915d207de2c5d3b01df53ce37',1,'vg::MinDistanceClusterer']]],
- ['_7emsaconverter_6734',['~MSAConverter',['../classvg_1_1MSAConverter.html#a3b731a1e51d01aecae26e789fe06b788',1,'vg::MSAConverter']]],
- ['_7emultipath_5falignment_5ft_6735',['~multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html#a732686b480b69ea1a261004c308510e0',1,'vg::multipath_alignment_t']]],
- ['_7emultipathalignmentemitter_6736',['~MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html#a18c81d0a9a77020adca05f0bc5b7fbcb',1,'vg::MultipathAlignmentEmitter']]],
- ['_7emultipathalignmentgraph_6737',['~MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html#a85e2932360f805d5c6353cd25e377e5d',1,'vg::MultipathAlignmentGraph']]],
- ['_7emultipathmapper_6738',['~MultipathMapper',['../classvg_1_1MultipathMapper.html#aae4b40b1c3c0668b884ae3247779f188',1,'vg::MultipathMapper']]],
- ['_7emutablehandlegraph_6739',['~MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html#ace50b9ed07cbbe94f7da963ff02d4141',1,'handlegraph::MutableHandleGraph']]],
- ['_7emutablepathdeletablehandlegraph_6740',['~MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html#a2d936ce540af42363619ebb77c60a4ff',1,'handlegraph::MutablePathDeletableHandleGraph']]],
- ['_7emutablepathhandlegraph_6741',['~MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html#a3b9b032ce45f87e1abd5c175db6f5275',1,'handlegraph::MutablePathHandleGraph']]],
- ['_7emutablepathmetadata_6742',['~MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html#a8be356ab572a35e496b6306a17db4a7e',1,'handlegraph::MutablePathMetadata']]],
- ['_7emutablepathmutablehandlegraph_6743',['~MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html#a55379ced0e4f2952ca3353c558affc44',1,'handlegraph::MutablePathMutableHandleGraph']]],
- ['_7enamednodebacktranslation_6744',['~NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html#ae9fb216bd267d21bf3879b4be822a855',1,'handlegraph::NamedNodeBackTranslation']]],
- ['_7enestedcachedpackedtraversalsupportfinder_6745',['~NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af533ff7a6df4501eedfb085e29ca58d6',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
- ['_7enestedflowcaller_6746',['~NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html#a715d0c0f7ccdca4c4162910ecd75e62e',1,'vg::NestedFlowCaller']]],
- ['_7enestedtraversalfinder_6747',['~NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html#a8ce9c736ca873d86fb63b84c7039dd70',1,'vg::NestedTraversalFinder']]],
- ['_7enullclusterer_6748',['~NullClusterer',['../classvg_1_1NullClusterer.html#a76fedb932d24bd5691d2b8c990abf221',1,'vg::NullClusterer']]],
- ['_7enullmaskinggraph_6749',['~NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html#a2423b2f9fd83988f10edcc70f9df4d51',1,'vg::NullMaskingGraph']]],
- ['_7eoption_6750',['~Option',['../classvg_1_1Option.html#a5e003513f76f5555d0c51b9e61389c22',1,'vg::Option::~Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#acce49922cb0d364a1d3ff4b2db78379a',1,'vg::Option< vector< Item >, Parser >::~Option()']]],
- ['_7eoptiongroup_6751',['~OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html#a8bcbcd0c78cef9c4837dbf77be4f5ad2',1,'vg::subcommand::OptionGroup']]],
- ['_7eoptioninterface_6752',['~OptionInterface',['../classvg_1_1OptionInterface.html#a064598bb6752f1e24c95a91e472448fe',1,'vg::OptionInterface']]],
- ['_7eorienteddistancemeasurer_6753',['~OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html#a5352a20621ca5018d567728fac12a44f',1,'vg::OrientedDistanceMeasurer']]],
- ['_7epackedtraversalsupportfinder_6754',['~PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html#ab5d69efb780653096e7ab6b810db3dcb',1,'vg::PackedTraversalSupportFinder']]],
- ['_7epacker_6755',['~Packer',['../classvg_1_1Packer.html#a771083c86ded80dc5076bc9112a463d7',1,'vg::Packer']]],
- ['_7epath_5fmapping_5ft_6756',['~path_mapping_t',['../classvg_1_1path__mapping__t.html#aa7a0aa3c177f2dff3cf364b78013deac',1,'vg::path_mapping_t']]],
- ['_7epath_5ft_6757',['~path_t',['../classvg_1_1path__t.html#a91a944b05194ede0711911b9235e88d4',1,'vg::path_t']]],
- ['_7epathbasedtraversalfinder_6758',['~PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html#ad60a772a43a10e819d2b2655f1602762',1,'vg::PathBasedTraversalFinder']]],
- ['_7epathchunker_6759',['~PathChunker',['../classvg_1_1PathChunker.html#a49b9500998c8e6faace1206d587ac67d',1,'vg::PathChunker']]],
- ['_7epathforeachsocket_6760',['~PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html#a982a69f458a874ddd5e5feaf61d950f8',1,'handlegraph::PathForEachSocket']]],
- ['_7epathhandlegraph_6761',['~PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html#a49fe5658c5ef27e1d7aba69cd3d7159b',1,'handlegraph::PathHandleGraph']]],
- ['_7epathmetadata_6762',['~PathMetadata',['../classhandlegraph_1_1PathMetadata.html#aee403b8c1269b11877df67ff42b759f3',1,'handlegraph::PathMetadata']]],
- ['_7epathorienteddistancemeasurer_6763',['~PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6ae7fe802887b8e9c1dbd4ab0106a2e3',1,'vg::PathOrientedDistanceMeasurer']]],
- ['_7epathpositionhandlegraph_6764',['~PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html#a2352c6463ffe0b4a279c05a223d8da24',1,'handlegraph::PathPositionHandleGraph']]],
- ['_7epathrestrictedtraversalfinder_6765',['~PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html#a63b53f979b357845cb6a73a9008f4614',1,'vg::PathRestrictedTraversalFinder']]],
- ['_7epathsubgraphoverlay_6766',['~PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html#a2e4550c165f6d744146feff76a7aad89',1,'vg::PathSubgraphOverlay']]],
- ['_7ephasedgenome_6767',['~PhasedGenome',['../classvg_1_1PhasedGenome.html#a08609371573b24264b5f5e14af6d0139',1,'vg::PhasedGenome']]],
- ['_7epictographs_6768',['~Pictographs',['../classvg_1_1Pictographs.html#a0889bee7fb20ed90c52442a614a1648b',1,'vg::Pictographs']]],
- ['_7epoissoncallinfo_6769',['~PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a066ee903413c3c1959ff3de6feeecf5e',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['_7epoissonsupportsnarlcaller_6770',['~PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html#a5bef85e69a8ae047888c4fb72356f215',1,'vg::PoissonSupportSnarlCaller']]],
- ['_7eposition_5ft_6771',['~position_t',['../classvg_1_1position__t.html#a5746bca2e97a32c1f6e941c4775a511f',1,'vg::position_t']]],
- ['_7eproblemdumpexplainer_6772',['~ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html#a649d96d5df14e3276d0b5ef389281fdb',1,'vg::ProblemDumpExplainer']]],
- ['_7eprotobufemitter_6773',['~ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html#ab1994a31484b9a52710a38315adb2bcc',1,'vg::io::ProtobufEmitter']]],
- ['_7equaladjaligner_6774',['~QualAdjAligner',['../classvg_1_1QualAdjAligner.html#a2fb50e162cf507b6feca91f4294c4e1a',1,'vg::QualAdjAligner']]],
- ['_7equaladjxdropaligner_6775',['~QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html#adcaec532a190e022823a64ea56c47d3a',1,'vg::QualAdjXdropAligner']]],
- ['_7erangeargspec_6776',['~RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html#a80afea8df9e2fb8f5b29996e361752f5',1,'vg::subcommand::RangeArgSpec']]],
- ['_7eratiosupportsnarlcaller_6777',['~RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html#a791e985fb18b5fdd13056d609d793eff',1,'vg::RatioSupportSnarlCaller']]],
- ['_7ereadrestrictedtraversalfinder_6778',['~ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html#a8753fffb0d164d41a61de388a148448f',1,'vg::ReadRestrictedTraversalFinder']]],
- ['_7eregionexpander_6779',['~RegionExpander',['../classvg_1_1RegionExpander.html#abf8aece5a42cfe0d0225d04e0fc7836f',1,'vg::RegionExpander']]],
- ['_7ereplacelocalhaplotypecommand_6780',['~ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html#aecd5ab146c17e1e5146cbf6e57c2d3a7',1,'vg::ReplaceLocalHaplotypeCommand']]],
- ['_7ereplacesnarlhaplotypecommand_6781',['~ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a91ce2448ef86a1e7fcb78995b39cbf1a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
- ['_7erepresentativetraversalfinder_6782',['~RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html#ae0f2414849b616e9a027ac675caf462c',1,'vg::RepresentativeTraversalFinder']]],
- ['_7ereversegraph_6783',['~ReverseGraph',['../classvg_1_1ReverseGraph.html#a202906f97f8aa781ed4a7c6ef41cbe85',1,'vg::ReverseGraph']]],
- ['_7erewindplanexception_6784',['~RewindPlanException',['../classvg_1_1RewindPlanException.html#a86b60f1af33c65e62f3cf8f6edffaf67',1,'vg::RewindPlanException']]],
- ['_7escoreprovider_6785',['~ScoreProvider',['../classhaplo_1_1ScoreProvider.html#adc52c96c8d122268f57187010a3eef7f',1,'haplo::ScoreProvider']]],
- ['_7eserializable_6786',['~Serializable',['../classhandlegraph_1_1Serializable.html#ade5618a9c7a93b72550fdbb06ca41518',1,'handlegraph::Serializable']]],
- ['_7esimpleconsistencycalculator_6787',['~SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html#a1b254ae9c4be5dc930b1593bd65fe2a9',1,'vg::SimpleConsistencyCalculator']]],
- ['_7esimpletraversalsupportcalculator_6788',['~SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html#a8b886a386884b9dd13ef5eaeb7eee2fc',1,'vg::SimpleTraversalSupportCalculator']]],
- ['_7esizelimitexceededexception_6789',['~SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html#aeedf0b21d4c09460fb4926ac98fae907',1,'vg::SizeLimitExceededException']]],
- ['_7esmallbitset_6790',['~SmallBitset',['../classvg_1_1SmallBitset.html#ab480cbcce093b352a39bba8404d6ea27',1,'vg::SmallBitset']]],
- ['_7esnarlcaller_6791',['~SnarlCaller',['../classvg_1_1SnarlCaller.html#abda61a55c21f1473db0443293144c96d',1,'vg::SnarlCaller']]],
- ['_7esnarldecomposition_6792',['~SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html#ad5055e48b8816d5785052da55e6da996',1,'handlegraph::SnarlDecomposition']]],
- ['_7esnarlfinder_6793',['~SnarlFinder',['../classvg_1_1SnarlFinder.html#aa2511b024b03f3902ac149f3d6a055d5',1,'vg::SnarlFinder']]],
- ['_7esnarlmanager_6794',['~SnarlManager',['../classvg_1_1SnarlManager.html#a3a6eb9b943f3e1b090e21f23dae5f8ea',1,'vg::SnarlManager']]],
- ['_7esnarlmindistance_6795',['~SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html#af2b84f7d4327621d3def1da80b2853e2',1,'vg::SnarlMinDistance']]],
- ['_7esnarlorienteddistancemeasurer_6796',['~SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#afba648bfa8f3712d2ed3fb698c36cdca',1,'vg::SnarlOrientedDistanceMeasurer']]],
- ['_7esparseunionfind_6797',['~SparseUnionFind',['../classvg_1_1SparseUnionFind.html#a1804e9081d4b8fb2ef37f61a119804aa',1,'vg::SparseUnionFind']]],
- ['_7esplicedhtsalignmentemitter_6798',['~SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a4ecdb4b35322bff73f961e934f4c53f5',1,'vg::SplicedHTSAlignmentEmitter']]],
- ['_7espliceregion_6799',['~SpliceRegion',['../classvg_1_1SpliceRegion.html#a8f4f2d7679069899606445ae1604f9c0',1,'vg::SpliceRegion']]],
- ['_7esswaligner_6800',['~SSWAligner',['../classvg_1_1SSWAligner.html#afccac3a7c1be69feb1602c30749b1b84',1,'vg::SSWAligner']]],
- ['_7estrandsplitgraph_6801',['~StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html#a4ab1bab60dfb53a4e6fd6f2f7efe7e58',1,'vg::StrandSplitGraph']]],
- ['_7estreammultiplexer_6802',['~StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html#ab59b05564e82666f5213863cb2d0af19',1,'vg::io::StreamMultiplexer']]],
- ['_7esubgraphoverlay_6803',['~SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html#ac39107fbe2937cefee3d7a97ba27278b',1,'vg::SubgraphOverlay']]],
- ['_7esubpath_5ft_6804',['~subpath_t',['../classvg_1_1subpath__t.html#a5b759f0b9b9eb1c91cc958ea7f217d73',1,'vg::subpath_t']]],
- ['_7esubpathoverlay_6805',['~SubpathOverlay',['../classvg_1_1SubpathOverlay.html#addf877952378e0897622236387dc4823',1,'vg::SubpathOverlay']]],
- ['_7esupportbasedsnarlcaller_6806',['~SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html#a1bc8a2019ce7e220dbee5b26c4b27211',1,'vg::SupportBasedSnarlCaller']]],
- ['_7esupportrestrictedtraversalfinder_6807',['~SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html#afc63ce9daf884e00c5946d0d133273bd',1,'vg::SupportRestrictedTraversalFinder']]],
- ['_7eswaphaplotypescommand_6808',['~SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html#a1c95200d197a7635ebd54facdf1b2257',1,'vg::SwapHaplotypesCommand']]],
- ['_7etargetvaluesearch_6809',['~TargetValueSearch',['../classvg_1_1TargetValueSearch.html#a11e6bc6d502a87f0bab3ef5cfa012eb6',1,'vg::TargetValueSearch']]],
- ['_7etickchainlink_6810',['~TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html#abe6fcaa01ec5b6b71aa6f956d6c968fd',1,'vg::subcommand::TickChainLink']]],
- ['_7etipanchoredmaxdistance_6811',['~TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html#a7a02421438454a8639035fdecbead5e6',1,'vg::TipAnchoredMaxDistance']]],
- ['_7etranscriptpath_6812',['~TranscriptPath',['../structvg_1_1TranscriptPath.html#a7684fbec1bec3a02319ff8d112f894ff',1,'vg::TranscriptPath']]],
- ['_7etraversalfinder_6813',['~TraversalFinder',['../classvg_1_1TraversalFinder.html#aa42ea2599b925f21244928ad5b997168',1,'vg::TraversalFinder']]],
- ['_7etraversalsupportcalculator_6814',['~TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html#acd55c7b07d365ae00206ac88bf1e3ff9',1,'vg::TraversalSupportCalculator']]],
- ['_7etraversalsupportfinder_6815',['~TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html#a86fe98aaabf74546462d2d52017f69a5',1,'vg::TraversalSupportFinder']]],
- ['_7etree_6816',['~Tree',['../structvg_1_1Tree.html#aa29f56c135efd59c283721181db4f27a',1,'vg::Tree']]],
- ['_7etreenode_6817',['~TreeNode',['../structvg_1_1TreeNode.html#abe3058472100249948412715677d2644',1,'vg::TreeNode']]],
- ['_7etriviallyserializable_6818',['~TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html#ae6c6c81c7b722686ed51bfbff3a2e442',1,'handlegraph::TriviallySerializable']]],
- ['_7etrivialtraversalfinder_6819',['~TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html#a95f1dc0e83e536f4ded43f35982420f3',1,'vg::TrivialTraversalFinder']]],
- ['_7etsvalignmentemitter_6820',['~TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a69a2f7650e4271c33985c5754f6b6f53',1,'vg::io::TSVAlignmentEmitter']]],
- ['_7etsvexplainer_6821',['~TSVExplainer',['../classvg_1_1TSVExplainer.html#ac7c5964711efd7f58c22d6aa9f07884c',1,'vg::TSVExplainer']]],
- ['_7etvsclusterer_6822',['~TVSClusterer',['../classvg_1_1TVSClusterer.html#ad0bd55ec4d0141dbd6b22cab86e2af85',1,'vg::TVSClusterer']]],
- ['_7evaluation_6823',['~Valuation',['../structvg_1_1subcommand_1_1Valuation.html#a299acc17034d0fc8b6107bca001ba49e',1,'vg::subcommand::Valuation']]],
- ['_7evalueargspec_6824',['~ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a97f01678f8355598db5bc6a34a8515af',1,'vg::subcommand::ValueArgSpec']]],
- ['_7evcfgenotyper_6825',['~VCFGenotyper',['../classvg_1_1VCFGenotyper.html#a91aad8f951949331a1753f7e07588381',1,'vg::VCFGenotyper']]],
- ['_7evcfoutputcaller_6826',['~VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html#a61c1441b882dbaaed73154aeae8109d6',1,'vg::VCFOutputCaller']]],
- ['_7evcfrecordconverter_6827',['~VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html#a49013729b000b0fd7c4a380c7ca79da6',1,'vg::VcfRecordConverter']]],
- ['_7evcfrecordfilter_6828',['~VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html#a11f60090fa5e3185bb42ece601457889',1,'vg::VcfRecordFilter']]],
- ['_7evcftraversalfinder_6829',['~VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html#a574fb1c2bdcf2752e75626f4c21bc90c',1,'vg::VCFTraversalFinder']]],
- ['_7evectorizablehandlegraph_6830',['~VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html#ae5986cf718d8f9d98b20f7e819db43f3',1,'handlegraph::VectorizableHandleGraph']]],
- ['_7evectorizer_6831',['~Vectorizer',['../classVectorizer.html#a9e7ee4e6f8a517a85b6e9ed785958104',1,'Vectorizer']]],
- ['_7evectorview_6832',['~VectorView',['../structvg_1_1VectorView.html#af9ec1a56ae0a3d357ccdc67f0958da0c',1,'vg::VectorView']]],
- ['_7evg_6833',['~VG',['../classvg_1_1VG.html#a7513ddb88aeb58bd85a810c2a2ccdf67',1,'vg::VG']]],
- ['_7evgalignmentemitter_6834',['~VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a55e34fab0faf2988c90105e10b33c727',1,'vg::io::VGAlignmentEmitter']]],
- ['_7eviz_6835',['~Viz',['../classvg_1_1Viz.html#ab63af6e73d13224a8a96f0d776cfd248',1,'vg::Viz']]],
- ['_7ewatchdog_6836',['~Watchdog',['../classvg_1_1Watchdog.html#a58772622205b1e7c103612e518a6c995',1,'vg::Watchdog']]],
- ['_7exdropaligner_6837',['~XdropAligner',['../classvg_1_1XdropAligner.html#aaa342dfcc4afb1448b98857fd216044a',1,'vg::XdropAligner']]],
- ['_7exg_6838',['~XG',['../classxg_1_1XG.html#a1670ddfeb5c9c5f04cd14fe725eb0cfd',1,'xg::XG']]],
- ['_7exgpath_6839',['~XGPath',['../classxg_1_1XGPath.html#a831bd85ed9f0db9154a1a8e3b0ad69fd',1,'xg::XGPath']]]
+ ['_7eabstractreadsampler_6644',['~AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html#aab2237075e873b1fac2b9d927835dd5d',1,'vg::AbstractReadSampler']]],
+ ['_7ealiasgraph_6645',['~AliasGraph',['../classvg_1_1AliasGraph.html#aa6557ac096d2a238b4bde66341fa4bbf',1,'vg::AliasGraph']]],
+ ['_7ealigner_6646',['~Aligner',['../classvg_1_1Aligner.html#ab652846ac99c793321f513e80b3567e7',1,'vg::Aligner']]],
+ ['_7ealignmentchainmodelvertex_6647',['~AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html#a2956b8c27f6438dda8d392c47c29da59',1,'vg::AlignmentChainModelVertex']]],
+ ['_7ealignmentemitter_6648',['~AlignmentEmitter',['../classvg_1_1io_1_1AlignmentEmitter.html#a8a2ed8eecf9bc49b0c82e0276a8c3ecf',1,'vg::io::AlignmentEmitter']]],
+ ['_7ealttracebackstack_6649',['~AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a7271beafb4fd9d7d993e7225d0289ee8',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['_7eappendhaplotypecommand_6650',['~AppendHaplotypeCommand',['../structvg_1_1AppendHaplotypeCommand.html#a5890b1f7b3374109bb8326372f3dcd18',1,'vg::AppendHaplotypeCommand']]],
+ ['_7eargspec_6651',['~ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html#a85d84f459627dc7d5d476ef600cd4eaa',1,'vg::subcommand::ArgSpec']]],
+ ['_7ebabuilder_6652',['~BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#af4852751e6f009ed647f81926b8c6ac0',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['_7ebamatrix_6653',['~BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac174727f3eb7d040f75bbb638e3ef585',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['_7ebandedglobalaligner_6654',['~BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html#ac211fadde52f8cc1312fddb585c021b0',1,'vg::BandedGlobalAligner']]],
+ ['_7ebaseargspec_6655',['~BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a6324c7d0c79aece0d2cf73a9bb385377',1,'vg::subcommand::BaseArgSpec']]],
+ ['_7ebaseoption_6656',['~BaseOption',['../classvg_1_1BaseOption.html#a877daeaa51e8978827609c35bffa6f7d',1,'vg::BaseOption']]],
+ ['_7ebaseoptiongroup_6657',['~BaseOptionGroup',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a65cfafee0415b04533cece4cde5c9b8a',1,'vg::subcommand::BaseOptionGroup']]],
+ ['_7ebasevaluation_6658',['~BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html#af8bbcfd7d30f6c358ba91db3be2a7084',1,'vg::subcommand::BaseValuation']]],
+ ['_7eblockedgzipinputstream_6659',['~BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a56990712e743be20a39e760309a8934c',1,'vg::io::BlockedGzipInputStream']]],
+ ['_7eblockedgzipoutputstream_6660',['~BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaac9002de6d983cb46a36b44620448bb',1,'vg::io::BlockedGzipOutputStream']]],
+ ['_7ebuildablesnarldecomposition_6661',['~BuildableSnarlDecomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a04eec535a4ad69c3d57a7733cbb56f23',1,'handlegraph::BuildableSnarlDecomposition']]],
+ ['_7ecachedpackedtraversalsupportfinder_6662',['~CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html#ae90902c6346948c1b2ab45dd389b4014',1,'vg::CachedPackedTraversalSupportFinder']]],
+ ['_7ecallinfo_6663',['~CallInfo',['../structvg_1_1SnarlCaller_1_1CallInfo.html#a596d13cd23b7d5dd9a24bdea876a286d',1,'vg::SnarlCaller::CallInfo']]],
+ ['_7ecolors_6664',['~Colors',['../classvg_1_1Colors.html#ac08aaa9a815d639d327c3ea80b97ed2b',1,'vg::Colors']]],
+ ['_7ecompletedtranscriptpath_6665',['~CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html#a885c00ed2c371cddfe7a9a78c00dcd94',1,'vg::CompletedTranscriptPath']]],
+ ['_7ecomponentmindistanceclusterer_6666',['~ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html#aa13390387862e6477651a627db8b36b3',1,'vg::ComponentMinDistanceClusterer']]],
+ ['_7econnection_5ft_6667',['~connection_t',['../classvg_1_1connection__t.html#ac3664dfd1f422b7a88b2760e9a4ee83d',1,'vg::connection_t']]],
+ ['_7econsistencycalculator_6668',['~ConsistencyCalculator',['../classvg_1_1ConsistencyCalculator.html#afb05d4ab7a962df47c62c408d0154ba0',1,'vg::ConsistencyCalculator']]],
+ ['_7edagifiedgraph_6669',['~DagifiedGraph',['../classvg_1_1DagifiedGraph.html#acb7989cf7dcc34da6fd11228d36321f7',1,'vg::DagifiedGraph']]],
+ ['_7edeconstructor_6670',['~Deconstructor',['../classvg_1_1Deconstructor.html#a875c8006f289ad46470c05c8808bdd73',1,'vg::Deconstructor']]],
+ ['_7edeflection_6671',['~Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#af4deb014af190975b2e7fe3540f6f461',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['_7edeletablehandlegraph_6672',['~DeletableHandleGraph',['../classhandlegraph_1_1DeletableHandleGraph.html#a62ed805e124ceb05cfa98d4e631a9ebd',1,'handlegraph::DeletableHandleGraph']]],
+ ['_7edeletehaplotypecommand_6673',['~DeleteHaplotypeCommand',['../structvg_1_1DeleteHaplotypeCommand.html#a2049b0eb4e4cf76d42b26fb9b0ecb659',1,'vg::DeleteHaplotypeCommand']]],
+ ['_7edeletionaligner_6674',['~DeletionAligner',['../classvg_1_1DeletionAligner.html#a797ac3036e59d5086c0822b90302dd14',1,'vg::DeletionAligner']]],
+ ['_7ediagramexplainer_6675',['~DiagramExplainer',['../classvg_1_1DiagramExplainer.html#aacac728ac8712e2d1f803c0735c34990',1,'vg::DiagramExplainer']]],
+ ['_7edinucleotidemachine_6676',['~DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html#a927431a787e6f77549850cea55d883b0',1,'vg::DinucleotideMachine']]],
+ ['_7edistanceheuristic_6677',['~DistanceHeuristic',['../classvg_1_1DistanceHeuristic.html#abca20b0fc239abad09fabb6d6bad0b50',1,'vg::DistanceHeuristic']]],
+ ['_7edozeuinterface_6678',['~DozeuInterface',['../classvg_1_1DozeuInterface.html#a0ac4d30c781e2a2278986ecbb84a34a6',1,'vg::DozeuInterface']]],
+ ['_7edozeupinningoverlay_6679',['~DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html#a6fe397bf132beeabd0ed7f830b1f9994',1,'vg::DozeuPinningOverlay']]],
+ ['_7edpscorecomparator_6680',['~DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a02c3e3552497f6425a1f3d14682c1d06',1,'vg::MEMClusterer::DPScoreComparator']]],
+ ['_7eedit_5ft_6681',['~edit_t',['../classvg_1_1edit__t.html#a43201af48ee260fa83a5bde0ed75a978',1,'vg::edit_t']]],
+ ['_7eeditedtranscriptpath_6682',['~EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html#aba2f28b19414c8c3795e60e76a07f807',1,'vg::EditedTranscriptPath']]],
+ ['_7eexhaustivetraversalfinder_6683',['~ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html#a7586c1b256f63d9e4295a9f1011b921a',1,'vg::ExhaustiveTraversalFinder']]],
+ ['_7eexpandingoverlaygraph_6684',['~ExpandingOverlayGraph',['../classhandlegraph_1_1ExpandingOverlayGraph.html#a9d7cac3cf3b289fe1980d0575e70be72',1,'handlegraph::ExpandingOverlayGraph']]],
+ ['_7eexplainer_6685',['~Explainer',['../classvg_1_1Explainer.html#a68991032a4a7fed25227a884f7f76a2a',1,'vg::Explainer']]],
+ ['_7efilter_6686',['~Filter',['../classvg_1_1Filter.html#a09073f3ae2d26bc61cf639dfc4072745',1,'vg::Filter']]],
+ ['_7efixedgenotypepriorcalculator_6687',['~FixedGenotypePriorCalculator',['../classvg_1_1FixedGenotypePriorCalculator.html#a4adc4bf44587b687076826dffc91ccf0',1,'vg::FixedGenotypePriorCalculator']]],
+ ['_7eflagargspec_6688',['~FlagArgSpec',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a7988d073aa24da829c03c9d68ae651f9',1,'vg::subcommand::FlagArgSpec']]],
+ ['_7eflatfilebacktranslation_6689',['~FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html#a4330bd5f76951158a1ea50755b43293d',1,'vg::FlatFileBackTranslation']]],
+ ['_7eflowcaller_6690',['~FlowCaller',['../classvg_1_1FlowCaller.html#a6fc652c91844cba402eb9e143883eefa',1,'vg::FlowCaller']]],
+ ['_7efragmentlengthdistribution_6691',['~FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html#a5ca105be9aca035e59985092d1a6aa79',1,'vg::FragmentLengthDistribution']]],
+ ['_7egafalignmentemitter_6692',['~GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html#ab8c76602efdaadba7319ca5103bc9107',1,'vg::io::GafAlignmentEmitter']]],
+ ['_7egafoutputcaller_6693',['~GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html#af275fa29f22a94c9c4180280675a160e',1,'vg::GAFOutputCaller']]],
+ ['_7egbwttraversalfinder_6694',['~GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html#aaf4b52f7a7807922daa514df94235a3a',1,'vg::GBWTTraversalFinder']]],
+ ['_7egenomestatecommand_6695',['~GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html#a951ebc208c74b7ec323de6f517d02527',1,'vg::GenomeStateCommand']]],
+ ['_7egenotypelikelihoodcalculator_6696',['~GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html#a295ae8723775d0481023badde359d44c',1,'vg::GenotypeLikelihoodCalculator']]],
+ ['_7egenotypepriorcalculator_6697',['~GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html#a63a28c3dff800ddc5ee37efcd836ba4d',1,'vg::GenotypePriorCalculator']]],
+ ['_7egfahandlegraph_6698',['~GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html#aeaa72881401798c61af748a47bc4746e',1,'vg::GFAHandleGraph']]],
+ ['_7egffreader_6699',['~GFFReader',['../classvg_1_1GFFReader.html#ac13f3d71875c489d9cc9a400d04d6e8e',1,'vg::GFFReader']]],
+ ['_7egffrecord_6700',['~GFFRecord',['../structvg_1_1GFFRecord.html#af031304f06fc3a9bdb1f4e7b81695f1a',1,'vg::GFFRecord']]],
+ ['_7egraphcaller_6701',['~GraphCaller',['../classvg_1_1GraphCaller.html#a443486cd8ab78a5392b5ed47506ca4c4',1,'vg::GraphCaller']]],
+ ['_7egreedymindistanceclusterer_6702',['~GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html#a9d51c4982f45dda3d6da98f182969c6b',1,'vg::GreedyMinDistanceClusterer']]],
+ ['_7egroupedoptiongroup_6703',['~GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a03413226481dddd57ccb32b1aa4ef94c',1,'vg::subcommand::GroupedOptionGroup']]],
+ ['_7egsswaligner_6704',['~GSSWAligner',['../classvg_1_1GSSWAligner.html#a7a80ce643da0316c9151fab19e8e8581',1,'vg::GSSWAligner']]],
+ ['_7ehandlegraph_6705',['~HandleGraph',['../classhandlegraph_1_1HandleGraph.html#a24fb796441c9ad8c870fdb716a82b305',1,'handlegraph::HandleGraph']]],
+ ['_7ehandlegraphsnarlfinder_6706',['~HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html#a01f84699fe59b5d360df0ef4a671edb2',1,'vg::HandleGraphSnarlFinder']]],
+ ['_7ehandler_6707',['~Handler',['../structvg_1_1temp__file_1_1Handler.html#abefd598acc672c960d80c70fa53c5476',1,'vg::temp_file::Handler::~Handler()'],['../structxg_1_1temp__file_1_1Handler.html#a6a4006456b42c1507d5d3505a8aa93a2',1,'xg::temp_file::Handler::~Handler()']]],
+ ['_7ehaplo_5fdp_5fcolumn_6708',['~haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html#a179bfa823f2329b2500fb948bfff30ca',1,'haplo::haplo_DP_column']]],
+ ['_7ehaplotype_6709',['~Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a29c3049eebafef23e3ec539093ffe9ce',1,'vg::PhasedGenome::Haplotype']]],
+ ['_7ehaplotypenode_6710',['~HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a4e012749eab6e610da87b54036717ec5',1,'vg::PhasedGenome::HaplotypeNode']]],
+ ['_7ehitedge_6711',['~HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html#ae1edc6409a97d72b9ae873d4e74d6721',1,'vg::MEMClusterer::HitEdge']]],
+ ['_7ehitnode_6712',['~HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html#af253bd2d33cba3d97a13a9a4159c4f41',1,'vg::MEMClusterer::HitNode']]],
+ ['_7ehtsalignmentemitter_6713',['~HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html#ab2914f2bdd3ecf8cd230e30479675304',1,'vg::HTSAlignmentEmitter']]],
+ ['_7ehtswriter_6714',['~HTSWriter',['../classvg_1_1HTSWriter.html#a8be4096c91ac54b168828071b814104d',1,'vg::HTSWriter']]],
+ ['_7eidentityoverlay_6715',['~IdentityOverlay',['../classvg_1_1IdentityOverlay.html#a15e797a8861789f9d2f0ec0f0ca57032',1,'vg::IdentityOverlay']]],
+ ['_7eincrementalsubgraph_6716',['~IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html#a330ad1c9229ac053777528cb79efad3e',1,'vg::IncrementalSubgraph']]],
+ ['_7eindexingplan_6717',['~IndexingPlan',['../classvg_1_1IndexingPlan.html#adf7d45d963ee4dc8a4ca8c3c3d3ca3ee',1,'vg::IndexingPlan']]],
+ ['_7eindexregistry_6718',['~IndexRegistry',['../classvg_1_1IndexRegistry.html#a95e5aa1a57680dd60b599d3735145ac4',1,'vg::IndexRegistry']]],
+ ['_7einserthaplotypecommand_6719',['~InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html#a173157b02306f85eb55291107367602e',1,'vg::InsertHaplotypeCommand']]],
+ ['_7eiterator_6720',['~iterator',['../classvg_1_1PhasedGenome_1_1iterator.html#a49c0df47c5f5eb7afc45a2978f5dc497',1,'vg::PhasedGenome::iterator::~iterator()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a578e1ae4eb29377b05133e390ad1d4c3',1,'handlegraph::PathForEachSocket::iterator::~iterator()']]],
+ ['_7ej2pb_5ferror_6721',['~j2pb_error',['../classj2pb__error.html#a4bf7997e2520c68a3861f9f105132510',1,'j2pb_error']]],
+ ['_7ejobschedule_6722',['~JobSchedule',['../classvg_1_1JobSchedule.html#a2c08f9b4c3db46f28c2a44d23524b9aa',1,'vg::JobSchedule']]],
+ ['_7ejoinedsplicegraph_6723',['~JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html#a1998a6854f0f56b1fc69476f09ebb5c7',1,'vg::JoinedSpliceGraph']]],
+ ['_7ejson_5fautoptr_6724',['~json_autoptr',['../structjson__autoptr.html#a90ed076495793f454cea2f2e8ba3738b',1,'json_autoptr']]],
+ ['_7ejsonstreamhelper_6725',['~JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html#a0cb9dd04575adfdb70b5a454a65871a7',1,'vg::io::JSONStreamHelper']]],
+ ['_7elegacycaller_6726',['~LegacyCaller',['../classvg_1_1LegacyCaller.html#a10147f341d558b896d91c2180f0361d8',1,'vg::LegacyCaller']]],
+ ['_7elinear_5fhaplo_5fstructure_6727',['~linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html#a11b487a3f7b503ed282cd1cfee5ae2f3',1,'haplo::linear_haplo_structure']]],
+ ['_7emapper_6728',['~Mapper',['../classvg_1_1Mapper.html#a285dd133a8540553f671b7eac33f6ca0',1,'vg::Mapper']]],
+ ['_7emasker_6729',['~Masker',['../classvg_1_1Masker.html#ab8ef1024fde833626e6ef18fbb6fdb9d',1,'vg::Masker']]],
+ ['_7emcmccaller_6730',['~MCMCCaller',['../classvg_1_1MCMCCaller.html#a1bd5d1d33ec02a9b5dabcb882996d964',1,'vg::MCMCCaller']]],
+ ['_7ememchainmodelvertex_6731',['~MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html#accc20533b5065e34208355797f373a04',1,'vg::MEMChainModelVertex']]],
+ ['_7ememclusterer_6732',['~MEMClusterer',['../classvg_1_1MEMClusterer.html#a86a3a3ccd7e416a727118f7aa763db18',1,'vg::MEMClusterer']]],
+ ['_7ememoizinggraph_6733',['~MemoizingGraph',['../classvg_1_1MemoizingGraph.html#a7b70d3665f07afcce593013fd4d27170',1,'vg::MemoizingGraph']]],
+ ['_7emessageemitter_6734',['~MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html#ae9fa66759101257b58f38ec4f54dabfa',1,'vg::io::MessageEmitter']]],
+ ['_7emindistanceclusterer_6735',['~MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html#a92349c1915d207de2c5d3b01df53ce37',1,'vg::MinDistanceClusterer']]],
+ ['_7emsaconverter_6736',['~MSAConverter',['../classvg_1_1MSAConverter.html#a3b731a1e51d01aecae26e789fe06b788',1,'vg::MSAConverter']]],
+ ['_7emultipath_5falignment_5ft_6737',['~multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html#a732686b480b69ea1a261004c308510e0',1,'vg::multipath_alignment_t']]],
+ ['_7emultipathalignmentemitter_6738',['~MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html#a18c81d0a9a77020adca05f0bc5b7fbcb',1,'vg::MultipathAlignmentEmitter']]],
+ ['_7emultipathalignmentgraph_6739',['~MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html#a85e2932360f805d5c6353cd25e377e5d',1,'vg::MultipathAlignmentGraph']]],
+ ['_7emultipathmapper_6740',['~MultipathMapper',['../classvg_1_1MultipathMapper.html#aae4b40b1c3c0668b884ae3247779f188',1,'vg::MultipathMapper']]],
+ ['_7emutablehandlegraph_6741',['~MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html#ace50b9ed07cbbe94f7da963ff02d4141',1,'handlegraph::MutableHandleGraph']]],
+ ['_7emutablepathdeletablehandlegraph_6742',['~MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html#a2d936ce540af42363619ebb77c60a4ff',1,'handlegraph::MutablePathDeletableHandleGraph']]],
+ ['_7emutablepathhandlegraph_6743',['~MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html#a3b9b032ce45f87e1abd5c175db6f5275',1,'handlegraph::MutablePathHandleGraph']]],
+ ['_7emutablepathmetadata_6744',['~MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html#a8be356ab572a35e496b6306a17db4a7e',1,'handlegraph::MutablePathMetadata']]],
+ ['_7emutablepathmutablehandlegraph_6745',['~MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html#a55379ced0e4f2952ca3353c558affc44',1,'handlegraph::MutablePathMutableHandleGraph']]],
+ ['_7enamednodebacktranslation_6746',['~NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html#ae9fb216bd267d21bf3879b4be822a855',1,'handlegraph::NamedNodeBackTranslation']]],
+ ['_7enestedcachedpackedtraversalsupportfinder_6747',['~NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af533ff7a6df4501eedfb085e29ca58d6',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
+ ['_7enestedflowcaller_6748',['~NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html#a715d0c0f7ccdca4c4162910ecd75e62e',1,'vg::NestedFlowCaller']]],
+ ['_7enestedtraversalfinder_6749',['~NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html#a8ce9c736ca873d86fb63b84c7039dd70',1,'vg::NestedTraversalFinder']]],
+ ['_7enullclusterer_6750',['~NullClusterer',['../classvg_1_1NullClusterer.html#a76fedb932d24bd5691d2b8c990abf221',1,'vg::NullClusterer']]],
+ ['_7enullmaskinggraph_6751',['~NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html#a2423b2f9fd83988f10edcc70f9df4d51',1,'vg::NullMaskingGraph']]],
+ ['_7eoption_6752',['~Option',['../classvg_1_1Option.html#a5e003513f76f5555d0c51b9e61389c22',1,'vg::Option::~Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#acce49922cb0d364a1d3ff4b2db78379a',1,'vg::Option< vector< Item >, Parser >::~Option()']]],
+ ['_7eoptiongroup_6753',['~OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html#a8bcbcd0c78cef9c4837dbf77be4f5ad2',1,'vg::subcommand::OptionGroup']]],
+ ['_7eoptioninterface_6754',['~OptionInterface',['../classvg_1_1OptionInterface.html#a064598bb6752f1e24c95a91e472448fe',1,'vg::OptionInterface']]],
+ ['_7eorienteddistancemeasurer_6755',['~OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html#a5352a20621ca5018d567728fac12a44f',1,'vg::OrientedDistanceMeasurer']]],
+ ['_7epackedtraversalsupportfinder_6756',['~PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html#ab5d69efb780653096e7ab6b810db3dcb',1,'vg::PackedTraversalSupportFinder']]],
+ ['_7epacker_6757',['~Packer',['../classvg_1_1Packer.html#a771083c86ded80dc5076bc9112a463d7',1,'vg::Packer']]],
+ ['_7epath_5fmapping_5ft_6758',['~path_mapping_t',['../classvg_1_1path__mapping__t.html#aa7a0aa3c177f2dff3cf364b78013deac',1,'vg::path_mapping_t']]],
+ ['_7epath_5ft_6759',['~path_t',['../classvg_1_1path__t.html#a91a944b05194ede0711911b9235e88d4',1,'vg::path_t']]],
+ ['_7epathbasedtraversalfinder_6760',['~PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html#ad60a772a43a10e819d2b2655f1602762',1,'vg::PathBasedTraversalFinder']]],
+ ['_7epathchunker_6761',['~PathChunker',['../classvg_1_1PathChunker.html#a49b9500998c8e6faace1206d587ac67d',1,'vg::PathChunker']]],
+ ['_7epathforeachsocket_6762',['~PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html#a982a69f458a874ddd5e5feaf61d950f8',1,'handlegraph::PathForEachSocket']]],
+ ['_7epathhandlegraph_6763',['~PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html#a49fe5658c5ef27e1d7aba69cd3d7159b',1,'handlegraph::PathHandleGraph']]],
+ ['_7epathmetadata_6764',['~PathMetadata',['../classhandlegraph_1_1PathMetadata.html#aee403b8c1269b11877df67ff42b759f3',1,'handlegraph::PathMetadata']]],
+ ['_7epathorienteddistancemeasurer_6765',['~PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6ae7fe802887b8e9c1dbd4ab0106a2e3',1,'vg::PathOrientedDistanceMeasurer']]],
+ ['_7epathpositionhandlegraph_6766',['~PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html#a2352c6463ffe0b4a279c05a223d8da24',1,'handlegraph::PathPositionHandleGraph']]],
+ ['_7epathrestrictedtraversalfinder_6767',['~PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html#a63b53f979b357845cb6a73a9008f4614',1,'vg::PathRestrictedTraversalFinder']]],
+ ['_7epathsubgraphoverlay_6768',['~PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html#a2e4550c165f6d744146feff76a7aad89',1,'vg::PathSubgraphOverlay']]],
+ ['_7ephasedgenome_6769',['~PhasedGenome',['../classvg_1_1PhasedGenome.html#a08609371573b24264b5f5e14af6d0139',1,'vg::PhasedGenome']]],
+ ['_7epictographs_6770',['~Pictographs',['../classvg_1_1Pictographs.html#a0889bee7fb20ed90c52442a614a1648b',1,'vg::Pictographs']]],
+ ['_7epoissoncallinfo_6771',['~PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a066ee903413c3c1959ff3de6feeecf5e',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['_7epoissonsupportsnarlcaller_6772',['~PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html#a5bef85e69a8ae047888c4fb72356f215',1,'vg::PoissonSupportSnarlCaller']]],
+ ['_7eposition_5ft_6773',['~position_t',['../classvg_1_1position__t.html#a5746bca2e97a32c1f6e941c4775a511f',1,'vg::position_t']]],
+ ['_7eproblemdumpexplainer_6774',['~ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html#a649d96d5df14e3276d0b5ef389281fdb',1,'vg::ProblemDumpExplainer']]],
+ ['_7eprotobufemitter_6775',['~ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html#ab1994a31484b9a52710a38315adb2bcc',1,'vg::io::ProtobufEmitter']]],
+ ['_7equaladjaligner_6776',['~QualAdjAligner',['../classvg_1_1QualAdjAligner.html#a2fb50e162cf507b6feca91f4294c4e1a',1,'vg::QualAdjAligner']]],
+ ['_7equaladjxdropaligner_6777',['~QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html#adcaec532a190e022823a64ea56c47d3a',1,'vg::QualAdjXdropAligner']]],
+ ['_7erangeargspec_6778',['~RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html#a80afea8df9e2fb8f5b29996e361752f5',1,'vg::subcommand::RangeArgSpec']]],
+ ['_7eratiosupportsnarlcaller_6779',['~RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html#a791e985fb18b5fdd13056d609d793eff',1,'vg::RatioSupportSnarlCaller']]],
+ ['_7ereadrestrictedtraversalfinder_6780',['~ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html#a8753fffb0d164d41a61de388a148448f',1,'vg::ReadRestrictedTraversalFinder']]],
+ ['_7eregionexpander_6781',['~RegionExpander',['../classvg_1_1RegionExpander.html#abf8aece5a42cfe0d0225d04e0fc7836f',1,'vg::RegionExpander']]],
+ ['_7ereplacelocalhaplotypecommand_6782',['~ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html#aecd5ab146c17e1e5146cbf6e57c2d3a7',1,'vg::ReplaceLocalHaplotypeCommand']]],
+ ['_7ereplacesnarlhaplotypecommand_6783',['~ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a91ce2448ef86a1e7fcb78995b39cbf1a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
+ ['_7erepresentativetraversalfinder_6784',['~RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html#ae0f2414849b616e9a027ac675caf462c',1,'vg::RepresentativeTraversalFinder']]],
+ ['_7ereversegraph_6785',['~ReverseGraph',['../classvg_1_1ReverseGraph.html#a202906f97f8aa781ed4a7c6ef41cbe85',1,'vg::ReverseGraph']]],
+ ['_7erewindplanexception_6786',['~RewindPlanException',['../classvg_1_1RewindPlanException.html#a86b60f1af33c65e62f3cf8f6edffaf67',1,'vg::RewindPlanException']]],
+ ['_7escoreprovider_6787',['~ScoreProvider',['../classhaplo_1_1ScoreProvider.html#adc52c96c8d122268f57187010a3eef7f',1,'haplo::ScoreProvider']]],
+ ['_7eserializable_6788',['~Serializable',['../classhandlegraph_1_1Serializable.html#ade5618a9c7a93b72550fdbb06ca41518',1,'handlegraph::Serializable']]],
+ ['_7esimpleconsistencycalculator_6789',['~SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html#a1b254ae9c4be5dc930b1593bd65fe2a9',1,'vg::SimpleConsistencyCalculator']]],
+ ['_7esimpletraversalsupportcalculator_6790',['~SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html#a8b886a386884b9dd13ef5eaeb7eee2fc',1,'vg::SimpleTraversalSupportCalculator']]],
+ ['_7esizelimitexceededexception_6791',['~SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html#aeedf0b21d4c09460fb4926ac98fae907',1,'vg::SizeLimitExceededException']]],
+ ['_7esmallbitset_6792',['~SmallBitset',['../classvg_1_1SmallBitset.html#ab480cbcce093b352a39bba8404d6ea27',1,'vg::SmallBitset']]],
+ ['_7esnarlcaller_6793',['~SnarlCaller',['../classvg_1_1SnarlCaller.html#abda61a55c21f1473db0443293144c96d',1,'vg::SnarlCaller']]],
+ ['_7esnarldecomposition_6794',['~SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html#ad5055e48b8816d5785052da55e6da996',1,'handlegraph::SnarlDecomposition']]],
+ ['_7esnarlfinder_6795',['~SnarlFinder',['../classvg_1_1SnarlFinder.html#aa2511b024b03f3902ac149f3d6a055d5',1,'vg::SnarlFinder']]],
+ ['_7esnarlmanager_6796',['~SnarlManager',['../classvg_1_1SnarlManager.html#a3a6eb9b943f3e1b090e21f23dae5f8ea',1,'vg::SnarlManager']]],
+ ['_7esnarlmindistance_6797',['~SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html#af2b84f7d4327621d3def1da80b2853e2',1,'vg::SnarlMinDistance']]],
+ ['_7esnarlorienteddistancemeasurer_6798',['~SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#afba648bfa8f3712d2ed3fb698c36cdca',1,'vg::SnarlOrientedDistanceMeasurer']]],
+ ['_7esparseunionfind_6799',['~SparseUnionFind',['../classvg_1_1SparseUnionFind.html#a1804e9081d4b8fb2ef37f61a119804aa',1,'vg::SparseUnionFind']]],
+ ['_7esplicedhtsalignmentemitter_6800',['~SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a4ecdb4b35322bff73f961e934f4c53f5',1,'vg::SplicedHTSAlignmentEmitter']]],
+ ['_7espliceregion_6801',['~SpliceRegion',['../classvg_1_1SpliceRegion.html#a8f4f2d7679069899606445ae1604f9c0',1,'vg::SpliceRegion']]],
+ ['_7esswaligner_6802',['~SSWAligner',['../classvg_1_1SSWAligner.html#afccac3a7c1be69feb1602c30749b1b84',1,'vg::SSWAligner']]],
+ ['_7estrandsplitgraph_6803',['~StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html#a4ab1bab60dfb53a4e6fd6f2f7efe7e58',1,'vg::StrandSplitGraph']]],
+ ['_7estreammultiplexer_6804',['~StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html#ab59b05564e82666f5213863cb2d0af19',1,'vg::io::StreamMultiplexer']]],
+ ['_7esubgraphoverlay_6805',['~SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html#ac39107fbe2937cefee3d7a97ba27278b',1,'vg::SubgraphOverlay']]],
+ ['_7esubpath_5ft_6806',['~subpath_t',['../classvg_1_1subpath__t.html#a5b759f0b9b9eb1c91cc958ea7f217d73',1,'vg::subpath_t']]],
+ ['_7esubpathoverlay_6807',['~SubpathOverlay',['../classvg_1_1SubpathOverlay.html#addf877952378e0897622236387dc4823',1,'vg::SubpathOverlay']]],
+ ['_7esupportbasedsnarlcaller_6808',['~SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html#a1bc8a2019ce7e220dbee5b26c4b27211',1,'vg::SupportBasedSnarlCaller']]],
+ ['_7esupportrestrictedtraversalfinder_6809',['~SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html#afc63ce9daf884e00c5946d0d133273bd',1,'vg::SupportRestrictedTraversalFinder']]],
+ ['_7eswaphaplotypescommand_6810',['~SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html#a1c95200d197a7635ebd54facdf1b2257',1,'vg::SwapHaplotypesCommand']]],
+ ['_7etargetvaluesearch_6811',['~TargetValueSearch',['../classvg_1_1TargetValueSearch.html#a11e6bc6d502a87f0bab3ef5cfa012eb6',1,'vg::TargetValueSearch']]],
+ ['_7etickchainlink_6812',['~TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html#abe6fcaa01ec5b6b71aa6f956d6c968fd',1,'vg::subcommand::TickChainLink']]],
+ ['_7etipanchoredmaxdistance_6813',['~TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html#a7a02421438454a8639035fdecbead5e6',1,'vg::TipAnchoredMaxDistance']]],
+ ['_7etranscriptpath_6814',['~TranscriptPath',['../structvg_1_1TranscriptPath.html#a7684fbec1bec3a02319ff8d112f894ff',1,'vg::TranscriptPath']]],
+ ['_7etraversalfinder_6815',['~TraversalFinder',['../classvg_1_1TraversalFinder.html#aa42ea2599b925f21244928ad5b997168',1,'vg::TraversalFinder']]],
+ ['_7etraversalsupportcalculator_6816',['~TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html#acd55c7b07d365ae00206ac88bf1e3ff9',1,'vg::TraversalSupportCalculator']]],
+ ['_7etraversalsupportfinder_6817',['~TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html#a86fe98aaabf74546462d2d52017f69a5',1,'vg::TraversalSupportFinder']]],
+ ['_7etree_6818',['~Tree',['../structvg_1_1Tree.html#aa29f56c135efd59c283721181db4f27a',1,'vg::Tree']]],
+ ['_7etreenode_6819',['~TreeNode',['../structvg_1_1TreeNode.html#abe3058472100249948412715677d2644',1,'vg::TreeNode']]],
+ ['_7etriviallyserializable_6820',['~TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html#ae6c6c81c7b722686ed51bfbff3a2e442',1,'handlegraph::TriviallySerializable']]],
+ ['_7etrivialtraversalfinder_6821',['~TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html#a95f1dc0e83e536f4ded43f35982420f3',1,'vg::TrivialTraversalFinder']]],
+ ['_7etsvalignmentemitter_6822',['~TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a69a2f7650e4271c33985c5754f6b6f53',1,'vg::io::TSVAlignmentEmitter']]],
+ ['_7etsvexplainer_6823',['~TSVExplainer',['../classvg_1_1TSVExplainer.html#ac7c5964711efd7f58c22d6aa9f07884c',1,'vg::TSVExplainer']]],
+ ['_7etvsclusterer_6824',['~TVSClusterer',['../classvg_1_1TVSClusterer.html#ad0bd55ec4d0141dbd6b22cab86e2af85',1,'vg::TVSClusterer']]],
+ ['_7evaluation_6825',['~Valuation',['../structvg_1_1subcommand_1_1Valuation.html#a299acc17034d0fc8b6107bca001ba49e',1,'vg::subcommand::Valuation']]],
+ ['_7evalueargspec_6826',['~ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a97f01678f8355598db5bc6a34a8515af',1,'vg::subcommand::ValueArgSpec']]],
+ ['_7evcfgenotyper_6827',['~VCFGenotyper',['../classvg_1_1VCFGenotyper.html#a91aad8f951949331a1753f7e07588381',1,'vg::VCFGenotyper']]],
+ ['_7evcfoutputcaller_6828',['~VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html#a61c1441b882dbaaed73154aeae8109d6',1,'vg::VCFOutputCaller']]],
+ ['_7evcfrecordconverter_6829',['~VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html#a49013729b000b0fd7c4a380c7ca79da6',1,'vg::VcfRecordConverter']]],
+ ['_7evcfrecordfilter_6830',['~VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html#a11f60090fa5e3185bb42ece601457889',1,'vg::VcfRecordFilter']]],
+ ['_7evcftraversalfinder_6831',['~VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html#a574fb1c2bdcf2752e75626f4c21bc90c',1,'vg::VCFTraversalFinder']]],
+ ['_7evectorizablehandlegraph_6832',['~VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html#ae5986cf718d8f9d98b20f7e819db43f3',1,'handlegraph::VectorizableHandleGraph']]],
+ ['_7evectorizer_6833',['~Vectorizer',['../classVectorizer.html#a9e7ee4e6f8a517a85b6e9ed785958104',1,'Vectorizer']]],
+ ['_7evectorview_6834',['~VectorView',['../structvg_1_1VectorView.html#af9ec1a56ae0a3d357ccdc67f0958da0c',1,'vg::VectorView']]],
+ ['_7evg_6835',['~VG',['../classvg_1_1VG.html#a7513ddb88aeb58bd85a810c2a2ccdf67',1,'vg::VG']]],
+ ['_7evgalignmentemitter_6836',['~VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a55e34fab0faf2988c90105e10b33c727',1,'vg::io::VGAlignmentEmitter']]],
+ ['_7eviz_6837',['~Viz',['../classvg_1_1Viz.html#ab63af6e73d13224a8a96f0d776cfd248',1,'vg::Viz']]],
+ ['_7ewatchdog_6838',['~Watchdog',['../classvg_1_1Watchdog.html#a58772622205b1e7c103612e518a6c995',1,'vg::Watchdog']]],
+ ['_7exdropaligner_6839',['~XdropAligner',['../classvg_1_1XdropAligner.html#aaa342dfcc4afb1448b98857fd216044a',1,'vg::XdropAligner']]],
+ ['_7exg_6840',['~XG',['../classxg_1_1XG.html#a1670ddfeb5c9c5f04cd14fe725eb0cfd',1,'xg::XG']]],
+ ['_7exgpath_6841',['~XGPath',['../classxg_1_1XGPath.html#a831bd85ed9f0db9154a1a8e3b0ad69fd',1,'xg::XGPath']]]
];
diff --git a/search/all_6.js b/search/all_6.js
index c362555bb7..15fb4ebda3 100644
--- a/search/all_6.js
+++ b/search/all_6.js
@@ -244,125 +244,126 @@ var searchData=
['for_5feach_5fstep_5fon_5fhandle_5fimpl_1842',['for_each_step_on_handle_impl',['../classvg_1_1MemoizingGraph.html#aeff170a12e414f058e658317060798b4',1,'vg::MemoizingGraph::for_each_step_on_handle_impl()'],['../classvg_1_1PathSubgraphOverlay.html#a9e042a3f29d7182fa8510dd46c259b41',1,'vg::PathSubgraphOverlay::for_each_step_on_handle_impl()'],['../classvg_1_1VG.html#a68b4c3665812b5be48d01677367382fd',1,'vg::VG::for_each_step_on_handle_impl()'],['../classxg_1_1XG.html#a0c05acc85982c493ac91b6199ca1cfd4',1,'xg::XG::for_each_step_on_handle_impl()'],['../classhandlegraph_1_1PathHandleGraph.html#a2bbdf56b268001c629cf000f5bd8bb9a',1,'handlegraph::PathHandleGraph::for_each_step_on_handle_impl()'],['../classhandlegraph_1_1PathMetadata.html#a25e78685ad8a987422d9bf6c131c854f',1,'handlegraph::PathMetadata::for_each_step_on_handle_impl()']]],
['for_5feach_5fstep_5fposition_5fon_5fhandle_1843',['for_each_step_position_on_handle',['../classvg_1_1MemoizingGraph.html#aca0068b6da055640d5dbc6034aa6aaa4',1,'vg::MemoizingGraph::for_each_step_position_on_handle()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#a5c30215753a62ebaffcbeffe40009829',1,'handlegraph::PathPositionHandleGraph::for_each_step_position_on_handle()']]],
['for_5feach_5fstream_1844',['for_each_stream',['../classvg_1_1Paths.html#a8ceb67abc89bd22659c751c946906e23',1,'vg::Paths']]],
- ['for_5feach_5ftippy_5fchild_1845',['for_each_tippy_child',['../classhandlegraph_1_1SnarlDecomposition.html#ac28fd7719d52d2148443d31617ae8a3c',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftippy_5fchild_5fimpl_1846',['for_each_tippy_child_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a0f14086d5470e4a95955e9bc3787574a',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftop_5flevel_5fchain_1847',['for_each_top_level_chain',['../classvg_1_1SnarlManager.html#a4bce7b961c24e5a18c834c6a78df8d2e',1,'vg::SnarlManager']]],
- ['for_5feach_5ftop_5flevel_5fchain_5fparallel_1848',['for_each_top_level_chain_parallel',['../classvg_1_1SnarlManager.html#aba6a74d03b6064e29b7ede95ddb2195d',1,'vg::SnarlManager']]],
- ['for_5feach_5ftop_5flevel_5fsnarl_1849',['for_each_top_level_snarl',['../classvg_1_1SnarlManager.html#ac4cf6c9ca0c953ec32bc3677d3171cf0',1,'vg::SnarlManager']]],
- ['for_5feach_5ftop_5flevel_5fsnarl_5fparallel_1850',['for_each_top_level_snarl_parallel',['../classvg_1_1SnarlManager.html#a458f5a996e7352ae749178d08f575a3e',1,'vg::SnarlManager']]],
- ['for_5feach_5ftraversal_1851',['for_each_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a64144f35a85a36bb472044663bd3a618',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fend_1852',['for_each_traversal_end',['../classhandlegraph_1_1SnarlDecomposition.html#ac7ccef73cd4793c0f303b951352b954b',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fend_5fimpl_1853',['for_each_traversal_end_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a5d7c6809f7636d1afae03c34e4747179',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fimpl_1854',['for_each_traversal_impl',['../classhandlegraph_1_1SnarlDecomposition.html#ac5ea5843f70f1550afe868a8fa1bf2ae',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fstart_1855',['for_each_traversal_start',['../classhandlegraph_1_1SnarlDecomposition.html#a0ccdbfddf02159200884e27ae34af0a8',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fstart_5fimpl_1856',['for_each_traversal_start_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a688f4614f5dd84aa01734c5eaf5d0400',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5fwalk_1857',['for_each_walk',['../namespacevg_1_1algorithms.html#ace1ad4f4eccc7041eb1e700463492540',1,'vg::algorithms']]],
- ['for_5fpath_5frange_1858',['for_path_range',['../classxg_1_1XG.html#a2ba1a725e15e5693156a5870701ceac0',1,'xg::XG']]],
- ['force_5fclose_1859',['force_close',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ac677874552857f22f89ee9571eb183db',1,'vg::io::BlockedGzipOutputStream']]],
- ['force_5ffragment_5flength_5fdistr_1860',['force_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ac2731944023ede8d7fb00379ffd8ecbf',1,'vg::PairedEndMapper::force_fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#a7f1925a1c2071ed65c543cc25b4d4f02',1,'vg::MinimizerMapper::force_fragment_length_distr()']]],
- ['force_5fhaplotype_5fcount_1861',['force_haplotype_count',['../classvg_1_1MultipathMapper.html#a4c89cc1e5c4696682c6bc9282de4b034',1,'vg::MultipathMapper']]],
- ['force_5fparameters_1862',['force_parameters',['../classvg_1_1FragmentLengthDistribution.html#a5751543486d54066f30e943ec188b279',1,'vg::FragmentLengthDistribution']]],
- ['force_5fphasing_1863',['force_phasing',['../classvg_1_1HaplotypeIndexer.html#acb44a055288c0a9debed5662e461959e',1,'vg::HaplotypeIndexer']]],
- ['force_5funequal_1864',['force_unequal',['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac1dcdb35b0b8fc51f2aee4abea3ce242',1,'handlegraph::PathForEachSocket::iterator']]],
- ['forest_5fgrowing_5fstate_5ft_1865',['forest_growing_state_t',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html',1,'vg::ZipCodeForest::forest_growing_state_t'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a8617325ab6eae778a65b13a4f21bdd16',1,'vg::ZipCodeForest::forest_growing_state_t::forest_growing_state_t()']]],
- ['forget_1866',['forget',['../namespacevg_1_1temp__file.html#a478c3b30251f8866550b1497bb22ede4',1,'vg::temp_file::forget()'],['../namespacexg_1_1temp__file.html#ab7efd4c620ca53aecb448de975525885',1,'xg::temp_file::forget()']]],
- ['forks_1867',['forks',['../structvg_1_1algorithms_1_1kmer__t.html#ac3f2de8e523f01cdca5d05ffd5a91a4d',1,'vg::algorithms::kmer_t::forks()'],['../structvg_1_1algorithms_1_1walk__t.html#a10f5d30f390ed54e49b4785d3edf7f98',1,'vg::algorithms::walk_t::forks()']]],
- ['format_1868',['FORMAT',['../classhandlegraph_1_1PathMetadata.html#a366a9d88528dcb5a25a44c6984bcaa66',1,'handlegraph::PathMetadata::FORMAT()'],['../classvg_1_1HTSWriter.html#a4c549b347cd3dba4710e1a195445a8b0',1,'vg::HTSWriter::format()'],['../classvg_1_1MultipathAlignmentEmitter.html#acfd964033f896160e64be1710025466c',1,'vg::MultipathAlignmentEmitter::format()'],['../classVectorizer.html#a30aa5bafd8a44b2e1259245b6e046062',1,'Vectorizer::format()']]],
- ['format_5fmultiplier_1869',['format_multiplier',['../namespacevg.html#a3ae70effc22331b3e4667ed48808602c',1,'vg']]],
- ['forward_1870',['forward',['../structvg_1_1Support.html#afe50d5886e57f3ff8594bddb90dfc8fa',1,'vg::Support::forward()'],['../classhandlegraph_1_1HandleGraph.html#a9e946bb4ed53f9423072955cdaab6386',1,'handlegraph::HandleGraph::forward()'],['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda1927367ddd77070a67deacaefa9300a5',1,'vg::MultipathMapper::Forward()']]],
- ['forward_5fgraph_1871',['forward_graph',['../classvg_1_1ReverseGraph.html#ab5cdf413526444fe31d07e3dce91d0f8',1,'vg::ReverseGraph']]],
- ['forward_5fmultiplier_1872',['forward_multiplier',['../classvg_1_1GreedyMinDistanceClusterer.html#a4423fb0153d3e55694c29fea2d5388af',1,'vg::GreedyMinDistanceClusterer']]],
- ['forward_5foffset_1873',['forward_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a3ffe7fc7ef04c67add8a6fae372dcee9',1,'vg::MinimizerMapper::Minimizer']]],
- ['forward_5fonly_1874',['forward_only',['../classvg_1_1Sampler.html#a5d105468c850a483ff1b7696b1da7507',1,'vg::Sampler']]],
- ['forward_5fsequence_1875',['forward_sequence',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ae02ecd440346f71b3d36ab8f291abb82',1,'vg::MinimizerMapper::Minimizer']]],
- ['forwardize_5fbreakpoints_1876',['forwardize_breakpoints',['../namespacevg.html#a9e9c975d7bec4a22a46b72736915ceb1',1,'vg']]],
- ['frac_5fscore_1877',['frac_score',['../classvg_1_1ReadFilter.html#a28e3876fb7401ecf89e9cd75fee37d59',1,'vg::ReadFilter']]],
- ['frag_5fstats_1878',['frag_stats',['../classvg_1_1Mapper.html#a2574eba87f3d7e8e93bf3fee99dacf27',1,'vg::Mapper']]],
- ['fragl_5fsupports_1879',['fragl_supports',['../structvg_1_1BREAKPOINT.html#a282d8840a4a956ce5d76ca1638871df7',1,'vg::BREAKPOINT']]],
- ['fragment_1880',['fragment',['../classvg_1_1MaximalExactMatch.html#aba77f1e25d2845c54f13e2ebc774b0b3',1,'vg::MaximalExactMatch::fragment()'],['../structvg_1_1read__alignment__index__t.html#a068797505b4341843ff1c4899c2c3b23',1,'vg::read_alignment_index_t::fragment()'],['../structvg_1_1alignment__index__t.html#a07b79acb488a39171e138d5593f57d47',1,'vg::alignment_index_t::fragment()'],['../structvg_1_1RecombinatorHaplotype.html#aae088d4a961f202b8cd949e6a6cc7951',1,'vg::RecombinatorHaplotype::fragment()'],['../structvg_1_1RecombinatorFragment.html#a86e6dbf48a53af506e480847a759a8a4',1,'vg::RecombinatorFragment::fragment()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#adabededd78dcfa907533bf94555dd502',1,'vg::SnarlDistanceIndexClusterer::Cluster::fragment()'],['../structvg_1_1Alignment.html#a600fa84d6905316c0964dd035ac48687',1,'vg::Alignment::fragment()']]],
- ['fragment_5fbest_5fleft_1881',['fragment_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af38c9c2b9aaa74591a9724e2d4ec5bd9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['fragment_5fbest_5fright_1882',['fragment_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ac6a766cba9f06e06845ef0d6ba7fb9dc',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['fragment_5fdirection_1883',['fragment_direction',['../classvg_1_1FragmentLengthStatistics.html#af43d1fa0b2d07be1cd3f7d658fa932c5',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fdirections_1884',['fragment_directions',['../classvg_1_1FragmentLengthStatistics.html#a04cfcfa9321c794d2b29c9e88e30cc22',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fdistance_5flimit_1885',['fragment_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a2a5781315318cd19e0ae59cbb9195754',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['fragment_5fdistr_5fis_5ffinalized_1886',['fragment_distr_is_finalized',['../classvg_1_1MinimizerMapper.html#a692470c7551c4966126aa7bf357e60a4',1,'vg::MinimizerMapper']]],
- ['fragment_5fgap_5fscale_1887',['fragment_gap_scale',['../classvg_1_1MinimizerMapper.html#ab8cec4d830d940527099df5cc9ff4b74',1,'vg::MinimizerMapper']]],
- ['fragment_5flength_5fcache_5fsize_1888',['fragment_length_cache_size',['../classvg_1_1FragmentLengthStatistics.html#a8616a97cafb7618fed2b27c08e91afee',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fdistr_1889',['fragment_length_distr',['../classvg_1_1PairedEndMapper.html#a9d232033ef120e15c47d13fab2750bc1',1,'vg::PairedEndMapper::fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#ab019d5888d75bbe36d8eb444d148ac50',1,'vg::MinimizerMapper::fragment_length_distr()']]],
- ['fragment_5flength_5fdistribution_1890',['fragment_length_distribution',['../structvg_1_1Alignment.html#ab13fb82c1707e0c6934d5c5ffd4c3ffa',1,'vg::Alignment']]],
- ['fragment_5flength_5flog_5flikelihood_1891',['fragment_length_log_likelihood',['../classvg_1_1MultipathMapper.html#ac9fbf8240e86c6753e0a55d89752f70d',1,'vg::MultipathMapper']]],
- ['fragment_5flength_5fmean_1892',['fragment_length_mean',['../classvg_1_1FragmentLengthStatistics.html#a0379d61cc368d8f7cea2babfacb24f06',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fpdf_1893',['fragment_length_pdf',['../classvg_1_1FragmentLengthStatistics.html#a929c0b89511551c913882cc65d4de180',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fpval_1894',['fragment_length_pval',['../classvg_1_1FragmentLengthStatistics.html#a5881926df69d005966f59b6dbead8253',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fstdev_1895',['fragment_length_stdev',['../classvg_1_1FragmentLengthStatistics.html#a83626df3ef00fa066df4fcf22a5c9862',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fwarning_5ffactor_1896',['fragment_length_warning_factor',['../classvg_1_1MultipathMapper.html#af0e2a57df540a8eafefc7eec55908b24',1,'vg::MultipathMapper']]],
- ['fragment_5flengths_1897',['fragment_lengths',['../classvg_1_1FragmentLengthStatistics.html#a7640ef7754d2b2b92fc65744e9b25eda',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fmax_1898',['fragment_max',['../classvg_1_1FragmentLengthStatistics.html#a79552864430d5905bc58a388dbc423ef',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fmax_5findel_5fbases_1899',['fragment_max_indel_bases',['../classvg_1_1MinimizerMapper.html#ab1d94c16cfd9cbbdfbc8d8650c07df37',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5findel_5fbases_5fper_5fbase_1900',['fragment_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a464e344d9bd2b5d3cc9b5b5d3a0efd30',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5flookback_5fbases_1901',['fragment_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ac0c7392b8a860133dc2b97a0361e2342',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5flookback_5fbases_5fper_5fbase_1902',['fragment_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a40b63e97284b2f5c18e76df3ed7c2146',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5fmin_5fscore_1903',['fragment_max_min_score',['../classvg_1_1MinimizerMapper.html#a62cd471d896d263d9b6d4cceece17d22',1,'vg::MinimizerMapper']]],
- ['fragment_5fmean_1904',['fragment_mean',['../classvg_1_1NGSSimulator.html#a2a96486c1fa9a2c4ebf4167139898afc',1,'vg::NGSSimulator']]],
- ['fragment_5fmin_5fscore_1905',['fragment_min_score',['../classvg_1_1MinimizerMapper.html#a7d0ae5e86deecd194163f939142c38e9',1,'vg::MinimizerMapper']]],
- ['fragment_5fmodel_5fstr_1906',['fragment_model_str',['../classvg_1_1FragmentLengthStatistics.html#acdcb4761860132d14be1bbe2da236a69',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fmodel_5fupdate_5finterval_1907',['fragment_model_update_interval',['../classvg_1_1FragmentLengthStatistics.html#a37b3e1be0011fae099dd9aef7653c2b6',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fnext_1908',['fragment_next',['../structvg_1_1Alignment.html#a79ace3e74254f2a6e1ed5bdf09eb226f',1,'vg::Alignment']]],
- ['fragment_5forientation_1909',['fragment_orientation',['../classvg_1_1FragmentLengthStatistics.html#aa486f0551d5848bfaaa304cc1c93d636',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5forientations_1910',['fragment_orientations',['../classvg_1_1FragmentLengthStatistics.html#a56a5a981f87edb64149c2b5e5d54df78',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fpoints_5fper_5fpossible_5fmatch_1911',['fragment_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a3b6dbf3556520243639b058698727908',1,'vg::MinimizerMapper']]],
- ['fragment_5fprev_1912',['fragment_prev',['../structvg_1_1Alignment.html#a82a59f4fec8b7fcd069563d99fa04228',1,'vg::Alignment']]],
- ['fragment_5fscore_1913',['fragment_score',['../structvg_1_1Alignment.html#a2a105371920e65f6764f8b723ae6648d',1,'vg::Alignment']]],
- ['fragment_5fscore_5ffraction_1914',['fragment_score_fraction',['../classvg_1_1MinimizerMapper.html#af04f1529476f620ef8c21c15cf44092b',1,'vg::MinimizerMapper']]],
- ['fragment_5fsd_1915',['fragment_sd',['../classvg_1_1NGSSimulator.html#a62d1cb98ae226228eaa9fabc05cf6f47',1,'vg::NGSSimulator']]],
- ['fragment_5fset_5fscore_5fthreshold_1916',['fragment_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a2e064f8ef605db553d7d27d3e05f8a78',1,'vg::MinimizerMapper']]],
- ['fragment_5fsigma_1917',['fragment_sigma',['../classvg_1_1FragmentLengthStatistics.html#aef6f205fdda8e179ef3355218c9c32c1',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fsize_1918',['fragment_size',['../classvg_1_1FragmentLengthStatistics.html#ad703c2e5fc7b03154ec6861a2be1e98b',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5funion_5ffind_1919',['fragment_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a335bcb97a05564c08d4ed9a5f2f25c20',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['fragmentlengthdistribution_1920',['FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html',1,'vg::FragmentLengthDistribution'],['../classvg_1_1FragmentLengthDistribution.html#a8788ddb09653e64eb868cbc942df95c6',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(size_t maximum_sample_size, size_t reestimation_frequency, double robust_estimation_fraction)'],['../classvg_1_1FragmentLengthDistribution.html#a8551fd1f0ad1270145483715f35c7b6b',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(void)']]],
- ['fragmentlengthstatistics_1921',['FragmentLengthStatistics',['../classvg_1_1FragmentLengthStatistics.html',1,'vg']]],
- ['fragments_1922',['fragments',['../structvg_1_1Recombinator_1_1Statistics.html#a8d8a6052fd27254595e54301be1a6f32',1,'vg::Recombinator::Statistics']]],
- ['frequency_1923',['frequency',['../classvg_1_1MCMCGenotyper.html#a4f8407692d3a6657442269ab9356952c',1,'vg::MCMCGenotyper']]],
- ['frequent_1924',['frequent',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa892a529e9382089dc28f99204da4dbaa',1,'vg::Recombinator']]],
- ['from_1925',['from',['../classvg_1_1WFATree.html#a0892abaa48691fcd665163851857a6ba',1,'vg::WFATree::from()'],['../structvg_1_1RecombinatorFragment.html#abb2373fe6dc187291239d57ceff36042',1,'vg::RecombinatorFragment::from()'],['../structvg_1_1Edge.html#a3dfaeceda2846f9b2562d5e6acafd468',1,'vg::Edge::from()'],['../structvg_1_1Translation.html#af19bb0bf7b6d241f3e61f27b83199a1f',1,'vg::Translation::from()']]],
- ['from_5fbacking_1926',['from_backing',['../classvg_1_1ExtraNodeGraph.html#a4d788b60f65afb7c33ae42481d7244ab',1,'vg::ExtraNodeGraph::from_backing()'],['../classvg_1_1ReverseGraph.html#a4f86e4320b018dd684e48250d8c2e455',1,'vg::ReverseGraph::from_backing()'],['../classvg_1_1SourceSinkOverlay.html#ad6d335a0dc7d4d42c7d21a814d79d8eb',1,'vg::SourceSinkOverlay::from_backing()']]],
- ['from_5fbig_5fendian_1927',['from_big_endian',['../structvg_1_1endianness.html#a473244129a68f42dcc05119ffe1132c5',1,'vg::endianness']]],
- ['from_5fenumerators_1928',['from_enumerators',['../classxg_1_1XG.html#a52b214cf4125206aa7d2d43dd3baf4d5',1,'xg::XG']]],
- ['from_5fextension_1929',['from_extension',['../structvg_1_1WFAAlignment.html#ac10be60010c306c84bc522f87e5fd5e5',1,'vg::WFAAlignment']]],
- ['from_5fgfa_1930',['from_gfa',['../classxg_1_1XG.html#a1c89b39930820e72b8365d8984eaf531',1,'xg::XG']]],
- ['from_5fhandle_5fgraph_1931',['from_handle_graph',['../classxg_1_1XG.html#aae49bbd7a7886919ab4adf1629517bb1',1,'xg::XG::from_handle_graph()'],['../namespacevg.html#ae968813905d72a9d49a1822b390cbe5d',1,'vg::from_handle_graph()']]],
- ['from_5fhit_1932',['from_hit',['../namespacevg.html#a61a0d273871a7d0feea0e9f0b1901931',1,'vg']]],
- ['from_5fistream_1933',['from_istream',['../classvg_1_1VG.html#a3c22829197fc65ced4dd2e0f53cb20ff',1,'vg::VG']]],
- ['from_5fkey_5fvalue_1934',['from_key_value',['../structvg_1_1WFAPoint.html#ad32f3fd03ce3f9bb91f2dd7fe1bf52c4',1,'vg::WFAPoint']]],
- ['from_5flength_1935',['from_length',['../structvg_1_1Edit.html#ae9694807752cc5cd06519f498cfba06c',1,'vg::Edit::from_length()'],['../classvg_1_1edit__t.html#a5ff1f97ea22b67b22fbc1c1b54c1d2af',1,'vg::edit_t::from_length()'],['../namespacevg.html#a83d1f079508a3ee8a2705773109a5a8e',1,'vg::from_length()']]],
- ['from_5flength_5fafter_5fpos_1936',['from_length_after_pos',['../namespacevg.html#a59b4e98d0d99a9b58b56f0946f49b1ab',1,'vg']]],
- ['from_5flength_5fbefore_5fpos_1937',['from_length_before_pos',['../namespacevg.html#a21d316f0ae049289cacab5117678d6ab',1,'vg']]],
- ['from_5fmap_5fentry_1938',['from_map_entry',['../structvg_1_1WFAPoint.html#aa547dad190435d35174a40b7ed0094f8',1,'vg::WFAPoint']]],
- ['from_5fnode_5fid_1939',['from_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2084bf098f9ffe829a0de4ca12ae0f3e',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['from_5fpath_5fhandle_5fgraph_1940',['from_path_handle_graph',['../classxg_1_1XG.html#a249328f04690e8022442c0ed845dd042',1,'xg::XG::from_path_handle_graph()'],['../namespacevg.html#a0eaa4d69a029a84c1d3028745c84bc4c',1,'vg::from_path_handle_graph()']]],
- ['from_5fproto_5fedit_1941',['from_proto_edit',['../namespacevg.html#a4b8b4c6f298818989d39189d631980a8',1,'vg']]],
- ['from_5fproto_5fmapping_1942',['from_proto_mapping',['../namespacevg.html#a1e6878ce34057ea3c8e8c0deacc1726b',1,'vg']]],
- ['from_5fproto_5fmultipath_5falignment_1943',['from_proto_multipath_alignment',['../namespacevg.html#a8630566250dfefc57ec84cbf6c22c3e2',1,'vg']]],
- ['from_5fproto_5fpath_1944',['from_proto_path',['../namespacevg.html#a01ce1f20da22c85b09e4bae9bf9a3d1f',1,'vg']]],
- ['from_5fproto_5fposition_1945',['from_proto_position',['../namespacevg.html#ae7d3ba6e34f59b610d86a84d0d6c32d1',1,'vg']]],
- ['from_5fsimple_5freverse_1946',['from_simple_reverse',['../classvg_1_1FlowSort.html#a920aae02af49b5fdd03397b70cda0640',1,'vg::FlowSort']]],
- ['from_5fsimple_5freverse_5forientation_1947',['from_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a7d43a991e41fd1af563ee17bfa82dc06',1,'vg::FlowSort']]],
- ['from_5fstart_1948',['from_start',['../structvg_1_1Edge.html#aadc916440008619a27cdd0c388e8ba86',1,'vg::Edge']]],
- ['from_5fturtle_1949',['from_turtle',['../classvg_1_1VG.html#a8aef48163c0dd4267d24b629de8a04c8',1,'vg::VG']]],
- ['from_5fvector_1950',['from_vector',['../structvg_1_1varint__vector__t.html#a6a568813ee83039d59a8af1dad7b2138',1,'vg::varint_vector_t::from_vector()'],['../classvg_1_1ZipCode.html#acbad7130678653add25cc79639b0f886',1,'vg::ZipCode::from_vector()']]],
- ['frontier_1951',['frontier',['../classvg_1_1IncrementalSubgraph.html#acfc80beeefec7f96a686a85db694985a',1,'vg::IncrementalSubgraph']]],
- ['frontier_5fcopy_5flimit_1952',['frontier_copy_limit',['../classvg_1_1IncrementalSubgraph.html#af136b632b259faac2edc944a06b97011',1,'vg::IncrementalSubgraph']]],
- ['frontier_5fcount_1953',['frontier_count',['../classvg_1_1IncrementalSubgraph.html#aa5becc3ca659a557a83bff4de8643ff4',1,'vg::IncrementalSubgraph']]],
- ['frontier_5findex_1954',['frontier_index',['../classvg_1_1IncrementalSubgraph.html#a877311143c9e9791fa85b29ae7a1351c',1,'vg::IncrementalSubgraph']]],
- ['full_1955',['full',['../structvg_1_1GaplessExtension.html#a1d1eb14643690ee92b30b2f0bdb5d82c',1,'vg::GaplessExtension']]],
- ['full_5fhaplotype_1956',['full_haplotype',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea5f4dff4ab82d6475d46abc492168ad11',1,'vg::Haplotypes::Subchain']]],
- ['full_5fhaplotypes_1957',['full_haplotypes',['../structvg_1_1Recombinator_1_1Statistics.html#a5ae651194a7e9670ae435f46cedf00f3',1,'vg::Recombinator::Statistics']]],
- ['full_5flength_5fbonus_1958',['full_length_bonus',['../classvg_1_1GSSWAligner.html#a24ee1a1d5b84c90c7fc77a4b7d8660bd',1,'vg::GSSWAligner::full_length_bonus()'],['../structScoringOptions.html#a86fa76ce2c5e6a086ea66dd60a8e9701',1,'ScoringOptions::full_length_bonus()']]],
- ['full_5flength_5fextensions_1959',['full_length_extensions',['../classvg_1_1GaplessExtender.html#a0381d55bcbba7e1ea297dc9a915dac1d',1,'vg::GaplessExtender']]],
- ['fulltrace_1960',['fullTrace',['../namespacevg.html#abd1798abb6fcee86ab5b0539fb764eb2',1,'vg']]],
- ['funnel_1961',['Funnel',['../classvg_1_1Funnel.html',1,'vg']]],
- ['funnel_2ecpp_1962',['funnel.cpp',['../funnel_8cpp.html',1,'']]],
- ['funnel_2ehpp_1963',['funnel.hpp',['../funnel_8hpp.html',1,'']]],
- ['funnel_5fname_1964',['funnel_name',['../classvg_1_1Funnel.html#aae00e188df16e84d5ecdb12e6ce5d51e',1,'vg::Funnel']]],
- ['fuse_5fspliced_5falignments_1965',['fuse_spliced_alignments',['../namespacevg.html#a5b37106006a0286045cd12f9159ac245',1,'vg']]]
+ ['for_5feach_5fsubpath_5fof_1845',['for_each_subpath_of',['../namespacevg.html#a9534c53c98412f2d43982fc0b809e7bd',1,'vg']]],
+ ['for_5feach_5ftippy_5fchild_1846',['for_each_tippy_child',['../classhandlegraph_1_1SnarlDecomposition.html#ac28fd7719d52d2148443d31617ae8a3c',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftippy_5fchild_5fimpl_1847',['for_each_tippy_child_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a0f14086d5470e4a95955e9bc3787574a',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftop_5flevel_5fchain_1848',['for_each_top_level_chain',['../classvg_1_1SnarlManager.html#a4bce7b961c24e5a18c834c6a78df8d2e',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftop_5flevel_5fchain_5fparallel_1849',['for_each_top_level_chain_parallel',['../classvg_1_1SnarlManager.html#aba6a74d03b6064e29b7ede95ddb2195d',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftop_5flevel_5fsnarl_1850',['for_each_top_level_snarl',['../classvg_1_1SnarlManager.html#ac4cf6c9ca0c953ec32bc3677d3171cf0',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftop_5flevel_5fsnarl_5fparallel_1851',['for_each_top_level_snarl_parallel',['../classvg_1_1SnarlManager.html#a458f5a996e7352ae749178d08f575a3e',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftraversal_1852',['for_each_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a64144f35a85a36bb472044663bd3a618',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fend_1853',['for_each_traversal_end',['../classhandlegraph_1_1SnarlDecomposition.html#ac7ccef73cd4793c0f303b951352b954b',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fend_5fimpl_1854',['for_each_traversal_end_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a5d7c6809f7636d1afae03c34e4747179',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fimpl_1855',['for_each_traversal_impl',['../classhandlegraph_1_1SnarlDecomposition.html#ac5ea5843f70f1550afe868a8fa1bf2ae',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fstart_1856',['for_each_traversal_start',['../classhandlegraph_1_1SnarlDecomposition.html#a0ccdbfddf02159200884e27ae34af0a8',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fstart_5fimpl_1857',['for_each_traversal_start_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a688f4614f5dd84aa01734c5eaf5d0400',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5fwalk_1858',['for_each_walk',['../namespacevg_1_1algorithms.html#ace1ad4f4eccc7041eb1e700463492540',1,'vg::algorithms']]],
+ ['for_5fpath_5frange_1859',['for_path_range',['../classxg_1_1XG.html#a2ba1a725e15e5693156a5870701ceac0',1,'xg::XG']]],
+ ['force_5fclose_1860',['force_close',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ac677874552857f22f89ee9571eb183db',1,'vg::io::BlockedGzipOutputStream']]],
+ ['force_5ffragment_5flength_5fdistr_1861',['force_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ac2731944023ede8d7fb00379ffd8ecbf',1,'vg::PairedEndMapper::force_fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#a7f1925a1c2071ed65c543cc25b4d4f02',1,'vg::MinimizerMapper::force_fragment_length_distr()']]],
+ ['force_5fhaplotype_5fcount_1862',['force_haplotype_count',['../classvg_1_1MultipathMapper.html#a4c89cc1e5c4696682c6bc9282de4b034',1,'vg::MultipathMapper']]],
+ ['force_5fparameters_1863',['force_parameters',['../classvg_1_1FragmentLengthDistribution.html#a5751543486d54066f30e943ec188b279',1,'vg::FragmentLengthDistribution']]],
+ ['force_5fphasing_1864',['force_phasing',['../classvg_1_1HaplotypeIndexer.html#acb44a055288c0a9debed5662e461959e',1,'vg::HaplotypeIndexer']]],
+ ['force_5funequal_1865',['force_unequal',['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac1dcdb35b0b8fc51f2aee4abea3ce242',1,'handlegraph::PathForEachSocket::iterator']]],
+ ['forest_5fgrowing_5fstate_5ft_1866',['forest_growing_state_t',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html',1,'vg::ZipCodeForest::forest_growing_state_t'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a8617325ab6eae778a65b13a4f21bdd16',1,'vg::ZipCodeForest::forest_growing_state_t::forest_growing_state_t()']]],
+ ['forget_1867',['forget',['../namespacevg_1_1temp__file.html#a478c3b30251f8866550b1497bb22ede4',1,'vg::temp_file::forget()'],['../namespacexg_1_1temp__file.html#ab7efd4c620ca53aecb448de975525885',1,'xg::temp_file::forget()']]],
+ ['forks_1868',['forks',['../structvg_1_1algorithms_1_1kmer__t.html#ac3f2de8e523f01cdca5d05ffd5a91a4d',1,'vg::algorithms::kmer_t::forks()'],['../structvg_1_1algorithms_1_1walk__t.html#a10f5d30f390ed54e49b4785d3edf7f98',1,'vg::algorithms::walk_t::forks()']]],
+ ['format_1869',['FORMAT',['../classhandlegraph_1_1PathMetadata.html#a366a9d88528dcb5a25a44c6984bcaa66',1,'handlegraph::PathMetadata::FORMAT()'],['../classvg_1_1HTSWriter.html#a4c549b347cd3dba4710e1a195445a8b0',1,'vg::HTSWriter::format()'],['../classvg_1_1MultipathAlignmentEmitter.html#acfd964033f896160e64be1710025466c',1,'vg::MultipathAlignmentEmitter::format()'],['../classVectorizer.html#a30aa5bafd8a44b2e1259245b6e046062',1,'Vectorizer::format()']]],
+ ['format_5fmultiplier_1870',['format_multiplier',['../namespacevg.html#a3ae70effc22331b3e4667ed48808602c',1,'vg']]],
+ ['forward_1871',['forward',['../structvg_1_1Support.html#afe50d5886e57f3ff8594bddb90dfc8fa',1,'vg::Support::forward()'],['../classhandlegraph_1_1HandleGraph.html#a9e946bb4ed53f9423072955cdaab6386',1,'handlegraph::HandleGraph::forward()'],['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda1927367ddd77070a67deacaefa9300a5',1,'vg::MultipathMapper::Forward()']]],
+ ['forward_5fgraph_1872',['forward_graph',['../classvg_1_1ReverseGraph.html#ab5cdf413526444fe31d07e3dce91d0f8',1,'vg::ReverseGraph']]],
+ ['forward_5fmultiplier_1873',['forward_multiplier',['../classvg_1_1GreedyMinDistanceClusterer.html#a4423fb0153d3e55694c29fea2d5388af',1,'vg::GreedyMinDistanceClusterer']]],
+ ['forward_5foffset_1874',['forward_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a3ffe7fc7ef04c67add8a6fae372dcee9',1,'vg::MinimizerMapper::Minimizer']]],
+ ['forward_5fonly_1875',['forward_only',['../classvg_1_1Sampler.html#a5d105468c850a483ff1b7696b1da7507',1,'vg::Sampler']]],
+ ['forward_5fsequence_1876',['forward_sequence',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ae02ecd440346f71b3d36ab8f291abb82',1,'vg::MinimizerMapper::Minimizer']]],
+ ['forwardize_5fbreakpoints_1877',['forwardize_breakpoints',['../namespacevg.html#a9e9c975d7bec4a22a46b72736915ceb1',1,'vg']]],
+ ['frac_5fscore_1878',['frac_score',['../classvg_1_1ReadFilter.html#a28e3876fb7401ecf89e9cd75fee37d59',1,'vg::ReadFilter']]],
+ ['frag_5fstats_1879',['frag_stats',['../classvg_1_1Mapper.html#a2574eba87f3d7e8e93bf3fee99dacf27',1,'vg::Mapper']]],
+ ['fragl_5fsupports_1880',['fragl_supports',['../structvg_1_1BREAKPOINT.html#a282d8840a4a956ce5d76ca1638871df7',1,'vg::BREAKPOINT']]],
+ ['fragment_1881',['fragment',['../classvg_1_1MaximalExactMatch.html#aba77f1e25d2845c54f13e2ebc774b0b3',1,'vg::MaximalExactMatch::fragment()'],['../structvg_1_1read__alignment__index__t.html#a068797505b4341843ff1c4899c2c3b23',1,'vg::read_alignment_index_t::fragment()'],['../structvg_1_1alignment__index__t.html#a07b79acb488a39171e138d5593f57d47',1,'vg::alignment_index_t::fragment()'],['../structvg_1_1RecombinatorHaplotype.html#aae088d4a961f202b8cd949e6a6cc7951',1,'vg::RecombinatorHaplotype::fragment()'],['../structvg_1_1RecombinatorFragment.html#a86e6dbf48a53af506e480847a759a8a4',1,'vg::RecombinatorFragment::fragment()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#adabededd78dcfa907533bf94555dd502',1,'vg::SnarlDistanceIndexClusterer::Cluster::fragment()'],['../structvg_1_1Alignment.html#a600fa84d6905316c0964dd035ac48687',1,'vg::Alignment::fragment()']]],
+ ['fragment_5fbest_5fleft_1882',['fragment_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af38c9c2b9aaa74591a9724e2d4ec5bd9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['fragment_5fbest_5fright_1883',['fragment_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ac6a766cba9f06e06845ef0d6ba7fb9dc',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['fragment_5fdirection_1884',['fragment_direction',['../classvg_1_1FragmentLengthStatistics.html#af43d1fa0b2d07be1cd3f7d658fa932c5',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fdirections_1885',['fragment_directions',['../classvg_1_1FragmentLengthStatistics.html#a04cfcfa9321c794d2b29c9e88e30cc22',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fdistance_5flimit_1886',['fragment_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a2a5781315318cd19e0ae59cbb9195754',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['fragment_5fdistr_5fis_5ffinalized_1887',['fragment_distr_is_finalized',['../classvg_1_1MinimizerMapper.html#a692470c7551c4966126aa7bf357e60a4',1,'vg::MinimizerMapper']]],
+ ['fragment_5fgap_5fscale_1888',['fragment_gap_scale',['../classvg_1_1MinimizerMapper.html#ab8cec4d830d940527099df5cc9ff4b74',1,'vg::MinimizerMapper']]],
+ ['fragment_5flength_5fcache_5fsize_1889',['fragment_length_cache_size',['../classvg_1_1FragmentLengthStatistics.html#a8616a97cafb7618fed2b27c08e91afee',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fdistr_1890',['fragment_length_distr',['../classvg_1_1PairedEndMapper.html#a9d232033ef120e15c47d13fab2750bc1',1,'vg::PairedEndMapper::fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#ab019d5888d75bbe36d8eb444d148ac50',1,'vg::MinimizerMapper::fragment_length_distr()']]],
+ ['fragment_5flength_5fdistribution_1891',['fragment_length_distribution',['../structvg_1_1Alignment.html#ab13fb82c1707e0c6934d5c5ffd4c3ffa',1,'vg::Alignment']]],
+ ['fragment_5flength_5flog_5flikelihood_1892',['fragment_length_log_likelihood',['../classvg_1_1MultipathMapper.html#ac9fbf8240e86c6753e0a55d89752f70d',1,'vg::MultipathMapper']]],
+ ['fragment_5flength_5fmean_1893',['fragment_length_mean',['../classvg_1_1FragmentLengthStatistics.html#a0379d61cc368d8f7cea2babfacb24f06',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fpdf_1894',['fragment_length_pdf',['../classvg_1_1FragmentLengthStatistics.html#a929c0b89511551c913882cc65d4de180',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fpval_1895',['fragment_length_pval',['../classvg_1_1FragmentLengthStatistics.html#a5881926df69d005966f59b6dbead8253',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fstdev_1896',['fragment_length_stdev',['../classvg_1_1FragmentLengthStatistics.html#a83626df3ef00fa066df4fcf22a5c9862',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fwarning_5ffactor_1897',['fragment_length_warning_factor',['../classvg_1_1MultipathMapper.html#af0e2a57df540a8eafefc7eec55908b24',1,'vg::MultipathMapper']]],
+ ['fragment_5flengths_1898',['fragment_lengths',['../classvg_1_1FragmentLengthStatistics.html#a7640ef7754d2b2b92fc65744e9b25eda',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fmax_1899',['fragment_max',['../classvg_1_1FragmentLengthStatistics.html#a79552864430d5905bc58a388dbc423ef',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fmax_5findel_5fbases_1900',['fragment_max_indel_bases',['../classvg_1_1MinimizerMapper.html#ab1d94c16cfd9cbbdfbc8d8650c07df37',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5findel_5fbases_5fper_5fbase_1901',['fragment_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a464e344d9bd2b5d3cc9b5b5d3a0efd30',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5flookback_5fbases_1902',['fragment_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ac0c7392b8a860133dc2b97a0361e2342',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5flookback_5fbases_5fper_5fbase_1903',['fragment_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a40b63e97284b2f5c18e76df3ed7c2146',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5fmin_5fscore_1904',['fragment_max_min_score',['../classvg_1_1MinimizerMapper.html#a62cd471d896d263d9b6d4cceece17d22',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmean_1905',['fragment_mean',['../classvg_1_1NGSSimulator.html#a2a96486c1fa9a2c4ebf4167139898afc',1,'vg::NGSSimulator']]],
+ ['fragment_5fmin_5fscore_1906',['fragment_min_score',['../classvg_1_1MinimizerMapper.html#a7d0ae5e86deecd194163f939142c38e9',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmodel_5fstr_1907',['fragment_model_str',['../classvg_1_1FragmentLengthStatistics.html#acdcb4761860132d14be1bbe2da236a69',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fmodel_5fupdate_5finterval_1908',['fragment_model_update_interval',['../classvg_1_1FragmentLengthStatistics.html#a37b3e1be0011fae099dd9aef7653c2b6',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fnext_1909',['fragment_next',['../structvg_1_1Alignment.html#a79ace3e74254f2a6e1ed5bdf09eb226f',1,'vg::Alignment']]],
+ ['fragment_5forientation_1910',['fragment_orientation',['../classvg_1_1FragmentLengthStatistics.html#aa486f0551d5848bfaaa304cc1c93d636',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5forientations_1911',['fragment_orientations',['../classvg_1_1FragmentLengthStatistics.html#a56a5a981f87edb64149c2b5e5d54df78',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fpoints_5fper_5fpossible_5fmatch_1912',['fragment_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a3b6dbf3556520243639b058698727908',1,'vg::MinimizerMapper']]],
+ ['fragment_5fprev_1913',['fragment_prev',['../structvg_1_1Alignment.html#a82a59f4fec8b7fcd069563d99fa04228',1,'vg::Alignment']]],
+ ['fragment_5fscore_1914',['fragment_score',['../structvg_1_1Alignment.html#a2a105371920e65f6764f8b723ae6648d',1,'vg::Alignment']]],
+ ['fragment_5fscore_5ffraction_1915',['fragment_score_fraction',['../classvg_1_1MinimizerMapper.html#af04f1529476f620ef8c21c15cf44092b',1,'vg::MinimizerMapper']]],
+ ['fragment_5fsd_1916',['fragment_sd',['../classvg_1_1NGSSimulator.html#a62d1cb98ae226228eaa9fabc05cf6f47',1,'vg::NGSSimulator']]],
+ ['fragment_5fset_5fscore_5fthreshold_1917',['fragment_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a2e064f8ef605db553d7d27d3e05f8a78',1,'vg::MinimizerMapper']]],
+ ['fragment_5fsigma_1918',['fragment_sigma',['../classvg_1_1FragmentLengthStatistics.html#aef6f205fdda8e179ef3355218c9c32c1',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fsize_1919',['fragment_size',['../classvg_1_1FragmentLengthStatistics.html#ad703c2e5fc7b03154ec6861a2be1e98b',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5funion_5ffind_1920',['fragment_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a335bcb97a05564c08d4ed9a5f2f25c20',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['fragmentlengthdistribution_1921',['FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html',1,'vg::FragmentLengthDistribution'],['../classvg_1_1FragmentLengthDistribution.html#a8788ddb09653e64eb868cbc942df95c6',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(size_t maximum_sample_size, size_t reestimation_frequency, double robust_estimation_fraction)'],['../classvg_1_1FragmentLengthDistribution.html#a8551fd1f0ad1270145483715f35c7b6b',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(void)']]],
+ ['fragmentlengthstatistics_1922',['FragmentLengthStatistics',['../classvg_1_1FragmentLengthStatistics.html',1,'vg']]],
+ ['fragments_1923',['fragments',['../structvg_1_1Recombinator_1_1Statistics.html#a8d8a6052fd27254595e54301be1a6f32',1,'vg::Recombinator::Statistics']]],
+ ['frequency_1924',['frequency',['../classvg_1_1MCMCGenotyper.html#a4f8407692d3a6657442269ab9356952c',1,'vg::MCMCGenotyper']]],
+ ['frequent_1925',['frequent',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa892a529e9382089dc28f99204da4dbaa',1,'vg::Recombinator']]],
+ ['from_1926',['from',['../classvg_1_1WFATree.html#a0892abaa48691fcd665163851857a6ba',1,'vg::WFATree::from()'],['../structvg_1_1RecombinatorFragment.html#abb2373fe6dc187291239d57ceff36042',1,'vg::RecombinatorFragment::from()'],['../structvg_1_1Edge.html#a3dfaeceda2846f9b2562d5e6acafd468',1,'vg::Edge::from()'],['../structvg_1_1Translation.html#af19bb0bf7b6d241f3e61f27b83199a1f',1,'vg::Translation::from()']]],
+ ['from_5fbacking_1927',['from_backing',['../classvg_1_1ExtraNodeGraph.html#a4d788b60f65afb7c33ae42481d7244ab',1,'vg::ExtraNodeGraph::from_backing()'],['../classvg_1_1ReverseGraph.html#a4f86e4320b018dd684e48250d8c2e455',1,'vg::ReverseGraph::from_backing()'],['../classvg_1_1SourceSinkOverlay.html#ad6d335a0dc7d4d42c7d21a814d79d8eb',1,'vg::SourceSinkOverlay::from_backing()']]],
+ ['from_5fbig_5fendian_1928',['from_big_endian',['../structvg_1_1endianness.html#a473244129a68f42dcc05119ffe1132c5',1,'vg::endianness']]],
+ ['from_5fenumerators_1929',['from_enumerators',['../classxg_1_1XG.html#a52b214cf4125206aa7d2d43dd3baf4d5',1,'xg::XG']]],
+ ['from_5fextension_1930',['from_extension',['../structvg_1_1WFAAlignment.html#ac10be60010c306c84bc522f87e5fd5e5',1,'vg::WFAAlignment']]],
+ ['from_5fgfa_1931',['from_gfa',['../classxg_1_1XG.html#a1c89b39930820e72b8365d8984eaf531',1,'xg::XG']]],
+ ['from_5fhandle_5fgraph_1932',['from_handle_graph',['../classxg_1_1XG.html#aae49bbd7a7886919ab4adf1629517bb1',1,'xg::XG::from_handle_graph()'],['../namespacevg.html#ae968813905d72a9d49a1822b390cbe5d',1,'vg::from_handle_graph()']]],
+ ['from_5fhit_1933',['from_hit',['../namespacevg.html#a61a0d273871a7d0feea0e9f0b1901931',1,'vg']]],
+ ['from_5fistream_1934',['from_istream',['../classvg_1_1VG.html#a3c22829197fc65ced4dd2e0f53cb20ff',1,'vg::VG']]],
+ ['from_5fkey_5fvalue_1935',['from_key_value',['../structvg_1_1WFAPoint.html#ad32f3fd03ce3f9bb91f2dd7fe1bf52c4',1,'vg::WFAPoint']]],
+ ['from_5flength_1936',['from_length',['../structvg_1_1Edit.html#ae9694807752cc5cd06519f498cfba06c',1,'vg::Edit::from_length()'],['../classvg_1_1edit__t.html#a5ff1f97ea22b67b22fbc1c1b54c1d2af',1,'vg::edit_t::from_length()'],['../namespacevg.html#a83d1f079508a3ee8a2705773109a5a8e',1,'vg::from_length()']]],
+ ['from_5flength_5fafter_5fpos_1937',['from_length_after_pos',['../namespacevg.html#a59b4e98d0d99a9b58b56f0946f49b1ab',1,'vg']]],
+ ['from_5flength_5fbefore_5fpos_1938',['from_length_before_pos',['../namespacevg.html#a21d316f0ae049289cacab5117678d6ab',1,'vg']]],
+ ['from_5fmap_5fentry_1939',['from_map_entry',['../structvg_1_1WFAPoint.html#aa547dad190435d35174a40b7ed0094f8',1,'vg::WFAPoint']]],
+ ['from_5fnode_5fid_1940',['from_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2084bf098f9ffe829a0de4ca12ae0f3e',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['from_5fpath_5fhandle_5fgraph_1941',['from_path_handle_graph',['../classxg_1_1XG.html#a249328f04690e8022442c0ed845dd042',1,'xg::XG::from_path_handle_graph()'],['../namespacevg.html#a0eaa4d69a029a84c1d3028745c84bc4c',1,'vg::from_path_handle_graph()']]],
+ ['from_5fproto_5fedit_1942',['from_proto_edit',['../namespacevg.html#a4b8b4c6f298818989d39189d631980a8',1,'vg']]],
+ ['from_5fproto_5fmapping_1943',['from_proto_mapping',['../namespacevg.html#a1e6878ce34057ea3c8e8c0deacc1726b',1,'vg']]],
+ ['from_5fproto_5fmultipath_5falignment_1944',['from_proto_multipath_alignment',['../namespacevg.html#a8630566250dfefc57ec84cbf6c22c3e2',1,'vg']]],
+ ['from_5fproto_5fpath_1945',['from_proto_path',['../namespacevg.html#a01ce1f20da22c85b09e4bae9bf9a3d1f',1,'vg']]],
+ ['from_5fproto_5fposition_1946',['from_proto_position',['../namespacevg.html#ae7d3ba6e34f59b610d86a84d0d6c32d1',1,'vg']]],
+ ['from_5fsimple_5freverse_1947',['from_simple_reverse',['../classvg_1_1FlowSort.html#a920aae02af49b5fdd03397b70cda0640',1,'vg::FlowSort']]],
+ ['from_5fsimple_5freverse_5forientation_1948',['from_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a7d43a991e41fd1af563ee17bfa82dc06',1,'vg::FlowSort']]],
+ ['from_5fstart_1949',['from_start',['../structvg_1_1Edge.html#aadc916440008619a27cdd0c388e8ba86',1,'vg::Edge']]],
+ ['from_5fturtle_1950',['from_turtle',['../classvg_1_1VG.html#a8aef48163c0dd4267d24b629de8a04c8',1,'vg::VG']]],
+ ['from_5fvector_1951',['from_vector',['../structvg_1_1varint__vector__t.html#a6a568813ee83039d59a8af1dad7b2138',1,'vg::varint_vector_t::from_vector()'],['../classvg_1_1ZipCode.html#acbad7130678653add25cc79639b0f886',1,'vg::ZipCode::from_vector()']]],
+ ['frontier_1952',['frontier',['../classvg_1_1IncrementalSubgraph.html#acfc80beeefec7f96a686a85db694985a',1,'vg::IncrementalSubgraph']]],
+ ['frontier_5fcopy_5flimit_1953',['frontier_copy_limit',['../classvg_1_1IncrementalSubgraph.html#af136b632b259faac2edc944a06b97011',1,'vg::IncrementalSubgraph']]],
+ ['frontier_5fcount_1954',['frontier_count',['../classvg_1_1IncrementalSubgraph.html#aa5becc3ca659a557a83bff4de8643ff4',1,'vg::IncrementalSubgraph']]],
+ ['frontier_5findex_1955',['frontier_index',['../classvg_1_1IncrementalSubgraph.html#a877311143c9e9791fa85b29ae7a1351c',1,'vg::IncrementalSubgraph']]],
+ ['full_1956',['full',['../structvg_1_1GaplessExtension.html#a1d1eb14643690ee92b30b2f0bdb5d82c',1,'vg::GaplessExtension']]],
+ ['full_5fhaplotype_1957',['full_haplotype',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea5f4dff4ab82d6475d46abc492168ad11',1,'vg::Haplotypes::Subchain']]],
+ ['full_5fhaplotypes_1958',['full_haplotypes',['../structvg_1_1Recombinator_1_1Statistics.html#a5ae651194a7e9670ae435f46cedf00f3',1,'vg::Recombinator::Statistics']]],
+ ['full_5flength_5fbonus_1959',['full_length_bonus',['../classvg_1_1GSSWAligner.html#a24ee1a1d5b84c90c7fc77a4b7d8660bd',1,'vg::GSSWAligner::full_length_bonus()'],['../structScoringOptions.html#a86fa76ce2c5e6a086ea66dd60a8e9701',1,'ScoringOptions::full_length_bonus()']]],
+ ['full_5flength_5fextensions_1960',['full_length_extensions',['../classvg_1_1GaplessExtender.html#a0381d55bcbba7e1ea297dc9a915dac1d',1,'vg::GaplessExtender']]],
+ ['fulltrace_1961',['fullTrace',['../namespacevg.html#abd1798abb6fcee86ab5b0539fb764eb2',1,'vg']]],
+ ['funnel_1962',['Funnel',['../classvg_1_1Funnel.html',1,'vg']]],
+ ['funnel_2ecpp_1963',['funnel.cpp',['../funnel_8cpp.html',1,'']]],
+ ['funnel_2ehpp_1964',['funnel.hpp',['../funnel_8hpp.html',1,'']]],
+ ['funnel_5fname_1965',['funnel_name',['../classvg_1_1Funnel.html#aae00e188df16e84d5ecdb12e6ce5d51e',1,'vg::Funnel']]],
+ ['fuse_5fspliced_5falignments_1966',['fuse_spliced_alignments',['../namespacevg.html#a5b37106006a0286045cd12f9159ac245',1,'vg']]]
];
diff --git a/search/all_7.js b/search/all_7.js
index 3c636c6bb4..30b268f80d 100644
--- a/search/all_7.js
+++ b/search/all_7.js
@@ -1,560 +1,561 @@
var searchData=
[
- ['g_5fbv_1966',['g_bv',['../classxg_1_1XG.html#a7fcb333bb6acf85ce76d81de9735b88a',1,'xg::XG']]],
- ['g_5fbv_5frank_1967',['g_bv_rank',['../classxg_1_1XG.html#abbbc82ab0fe4b0d8abe7e5890a89b952',1,'xg::XG']]],
- ['g_5fbv_5fselect_1968',['g_bv_select',['../classxg_1_1XG.html#a9eb31aaf28e0ab90154233692bdc0c05',1,'xg::XG']]],
- ['g_5fiv_1969',['g_iv',['../classxg_1_1XG.html#a7b4b76e9a150ca86d54cee59a3825f4d',1,'xg::XG']]],
- ['g_5fnode_5fheader_5flength_1970',['G_NODE_HEADER_LENGTH',['../classxg_1_1XG.html#a8a1f38f3430d796f7b2ae452fd80ebbf',1,'xg::XG']]],
- ['g_5fnode_5fid_5foffset_1971',['G_NODE_ID_OFFSET',['../classxg_1_1XG.html#a841f4db9d178690c836a21b6adc9fafe',1,'xg::XG']]],
- ['g_5fnode_5fleft_5fcount_5foffset_1972',['G_NODE_LEFT_COUNT_OFFSET',['../classxg_1_1XG.html#a9028d42350d55a928483b76579549145',1,'xg::XG']]],
- ['g_5fnode_5flength_5foffset_1973',['G_NODE_LENGTH_OFFSET',['../classxg_1_1XG.html#aaf4de09d0f39174f42c793492976acc9',1,'xg::XG']]],
- ['g_5fnode_5fright_5fcount_5foffset_1974',['G_NODE_RIGHT_COUNT_OFFSET',['../classxg_1_1XG.html#ad4aacfc7ad17ddc586566f8d2a5e92e5',1,'xg::XG']]],
- ['g_5fnode_5fseq_5fstart_5foffset_1975',['G_NODE_SEQ_START_OFFSET',['../classxg_1_1XG.html#a19673db503954e65456196d791f7db04',1,'xg::XG']]],
- ['gaf_1976',['GAF',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0bab98a867ffc7b5c1ac2a3e5e171148245',1,'vg::MultipathAlignmentEmitter::GAF()'],['../structGafFile.html#a9dcebeb1a298c34516bdd969dc439560',1,'GafFile::gaf()']]],
- ['gaf_5foutput_1977',['gaf_output',['../classvg_1_1VCFGenotyper.html#ae00bbce9945411dbab0d14e7cdb4b8c2',1,'vg::VCFGenotyper::gaf_output()'],['../classvg_1_1FlowCaller.html#a93037892a9148b952b186852f77f0fa8',1,'vg::FlowCaller::gaf_output()'],['../classvg_1_1NestedFlowCaller.html#a9114ad05033bc7d50becae55041dfae0',1,'vg::NestedFlowCaller::gaf_output()']]],
- ['gaf_5fpaired_5finterleaved_5ffor_5feach_1978',['gaf_paired_interleaved_for_each',['../namespacevg_1_1io.html#a1509c614371533861fa7552febf7af92',1,'vg::io::gaf_paired_interleaved_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda)'],['../namespacevg_1_1io.html#ad242e1399847a5c894201b9e32c13a6d',1,'vg::io::gaf_paired_interleaved_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda)']]],
- ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_1979',['gaf_paired_interleaved_for_each_parallel',['../namespacevg_1_1io.html#a7b473c9f170444107256aa76f522d27a',1,'vg::io::gaf_paired_interleaved_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#a8662ca54b9e1f26e421884a43a4e0e21',1,'vg::io::gaf_paired_interleaved_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)']]],
- ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_5fafter_5fwait_1980',['gaf_paired_interleaved_for_each_parallel_after_wait',['../namespacevg_1_1io.html#a44d7cb48aae7d9c3621fabc6b31faa6e',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)'],['../namespacevg_1_1io.html#a63b12354bf13d6a19b5addc71fc512c7',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)']]],
- ['gaf_5fsample_5fname_1981',['gaf_sample_name',['../classvg_1_1GAFOutputCaller.html#a23554330b3cf641645fe7b3070c6d203',1,'vg::GAFOutputCaller']]],
- ['gaf_5fto_5falignment_1982',['gaf_to_alignment',['../namespacevg_1_1io.html#a44a872a40072dc128fa898a795eeff79',1,'vg::io::gaf_to_alignment(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const gafkluge::GafRecord &gaf, Alignment &aln)'],['../namespacevg_1_1io.html#a363656cc5c1a09f178e3c83785488bad',1,'vg::io::gaf_to_alignment(const HandleGraph &graph, const gafkluge::GafRecord &gaf, Alignment &aln)']]],
- ['gaf_5funpaired_5ffor_5feach_1983',['gaf_unpaired_for_each',['../namespacevg_1_1io.html#a83d5011d88f6ef27ed8837957505284b',1,'vg::io::gaf_unpaired_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda)'],['../namespacevg_1_1io.html#ada4771a7ea674ee9d986af264ab3c00d',1,'vg::io::gaf_unpaired_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda)']]],
- ['gaf_5funpaired_5ffor_5feach_5fparallel_1984',['gaf_unpaired_for_each_parallel',['../namespacevg_1_1io.html#a88d2dffc472bbcfded0b1190fc5bc933',1,'vg::io::gaf_unpaired_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#add46b11d285f6b94896c1f5e91a405a7',1,'vg::io::gaf_unpaired_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)']]],
- ['gafalignmentemitter_1985',['GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html',1,'vg::io::GafAlignmentEmitter'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#ad7b537251b10534375e90a22b795b9cc',1,'vg::io::GafAlignmentEmitter::GafAlignmentEmitter()']]],
- ['gaffile_1986',['GafFile',['../structGafFile.html',1,'']]],
- ['gafkluge_1987',['gafkluge',['../namespacegafkluge.html',1,'']]],
- ['gafkluge_2ehpp_1988',['gafkluge.hpp',['../gafkluge_8hpp.html',1,'']]],
- ['gafoutputcaller_1989',['GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html',1,'vg::GAFOutputCaller'],['../classvg_1_1GAFOutputCaller.html#a2def7ee0c3eb2f0cbfd139ad0eeeec8b',1,'vg::GAFOutputCaller::GAFOutputCaller()']]],
- ['gafrecord_1990',['GafRecord',['../structgafkluge_1_1GafRecord.html',1,'gafkluge::GafRecord'],['../structgafkluge_1_1GafRecord.html#a81394a04ad249c56b3f757484a7663bc',1,'gafkluge::GafRecord::GafRecord()']]],
- ['gafstep_1991',['GafStep',['../structgafkluge_1_1GafStep.html',1,'gafkluge']]],
- ['gam_1992',['GAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baf8d906e37d32ff64beb1baf4c50958fd',1,'vg::MultipathAlignmentEmitter']]],
- ['gam_5fformat_1993',['gam_format',['../structGBWTConfig.html#a1fcbf295cfa998c40744359748fda6c7',1,'GBWTConfig']]],
- ['gamcompare_5fmain_2ecpp_1994',['gamcompare_main.cpp',['../gamcompare__main_8cpp.html',1,'']]],
- ['gamindex_1995',['GAMIndex',['../namespacevg.html#a9b677be2f409ffcbefd5d9f6149c80c1',1,'vg']]],
- ['gamma_5fln_1996',['gamma_ln',['../namespacevg.html#a05748ab256c93e2393252aa8ebbdde3d',1,'vg']]],
- ['gamp_1997',['GAMP',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba00b7d3df4dc1aead7feb32d379bb1a35',1,'vg::MultipathAlignmentEmitter']]],
- ['gampcompare_5fmain_2ecpp_1998',['gampcompare_main.cpp',['../gampcompare__main_8cpp.html',1,'']]],
- ['gamsort_5fmain_2ecpp_1999',['gamsort_main.cpp',['../gamsort__main_8cpp.html',1,'']]],
- ['gamsorter_2000',['GAMSorter',['../namespacevg.html#a6c00bf57d75db83e41ac19a88882c043',1,'vg']]],
- ['gap_5fdistance_5flimit_2001',['gap_distance_limit',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ad9d07441a40519ff349163eb7d87c916',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['gap_5fextend_2002',['gap_extend',['../classvg_1_1WFATree.html#abe47c55fbdfa81f6b0df6ffdb4c3591e',1,'vg::WFATree::gap_extend()'],['../structScoringOptions.html#a8ae3e44719121535cd43560dddc267aa',1,'ScoringOptions::gap_extend()']]],
- ['gap_5fextend_5fpenalty_2003',['gap_extend_penalty',['../classvg_1_1WFATree.html#a705cd842a3204b5dbc0c669f3e1c60c7',1,'vg::WFATree']]],
- ['gap_5fextension_2004',['gap_extension',['../classvg_1_1GSSWAligner.html#afd2379af50d751eee892a10529d64ffb',1,'vg::GSSWAligner::gap_extension()'],['../classvg_1_1DeletionAligner.html#a5fdfc2ac3a633a6e3cd61c2e3beeae97',1,'vg::DeletionAligner::gap_extension()'],['../classvg_1_1SSWAligner.html#a2248e3e561aab8d3b1036d51850b3c2f',1,'vg::SSWAligner::gap_extension()']]],
- ['gap_5flength_2005',['gap_length',['../structvg_1_1WFAExtender_1_1ErrorModel.html#a9cf62e400ef2e4efb434e8e5a452e7e8',1,'vg::WFAExtender::ErrorModel']]],
- ['gap_5fmemo_5fmax_5fsize_2006',['gap_memo_max_size',['../classvg_1_1MultipathMapper.html#a864cc168b7061cf1885ef61785e474d3',1,'vg::MultipathMapper']]],
- ['gap_5fopen_2007',['gap_open',['../classvg_1_1GSSWAligner.html#aa5c0a63b73ad2ff8ec8f05062c768c22',1,'vg::GSSWAligner::gap_open()'],['../classvg_1_1DeletionAligner.html#a7791fe71828711b3208db54db784cf1d',1,'vg::DeletionAligner::gap_open()'],['../classvg_1_1WFATree.html#aec0c57320c07468df3201a106f7e6aa0',1,'vg::WFATree::gap_open()'],['../classvg_1_1SSWAligner.html#a15398a23880418599e81370d485fec0f',1,'vg::SSWAligner::gap_open()'],['../structScoringOptions.html#ab399d0cf09e907906b42d500a54194bc',1,'ScoringOptions::gap_open()']]],
- ['gap_5fpenalty_2008',['gap_penalty',['../classvg_1_1WFATree.html#a46f357dbdd6957c1c08bb82a275a3bcf',1,'vg::WFATree']]],
- ['gap_5fscale_2009',['gap_scale',['../classvg_1_1MinimizerMapper.html#a5e6e66b39ed25c3d81f82546231d790a',1,'vg::MinimizerMapper']]],
- ['gapless_5fextension_5flimit_2010',['gapless_extension_limit',['../classvg_1_1MinimizerMapper.html#af0eb242f1ec9aaaa52e7d03446d09cbf',1,'vg::MinimizerMapper']]],
- ['gaplessextender_2011',['GaplessExtender',['../classvg_1_1GaplessExtender.html',1,'vg::GaplessExtender'],['../classvg_1_1GaplessExtender.html#a497cc4e85c6433a3e41f04895703f271',1,'vg::GaplessExtender::GaplessExtender()'],['../classvg_1_1GaplessExtender.html#aaebc8d221df2787a68023fce2d99290a',1,'vg::GaplessExtender::GaplessExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner)']]],
- ['gaplessextension_2012',['GaplessExtension',['../structvg_1_1GaplessExtension.html',1,'vg']]],
- ['gaps_2013',['gaps',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ac60921b93f505b6731badc2aef7f64f5',1,'vg::WFAExtender::ErrorModel']]],
- ['gbwt_2014',['gbwt',['../classvg_1_1Deconstructor.html#a52b3fcd3d7357f5dd3624d9caa56539f',1,'vg::Deconstructor::gbwt()'],['../classvg_1_1GBWTTraversalFinder.html#a7827a0ee00890a2d8cf1716017e39db7',1,'vg::GBWTTraversalFinder::gbwt()']]],
- ['gbwt_5fbuffer_5fsize_2015',['gbwt_buffer_size',['../classvg_1_1HaplotypeIndexer.html#abc8d5ce81546e16ffb7bf652c098bb11',1,'vg::HaplotypeIndexer']]],
- ['gbwt_5fextender_2ecpp_2016',['gbwt_extender.cpp',['../gbwt__extender_8cpp.html',1,'']]],
- ['gbwt_5fextender_2ehpp_2017',['gbwt_extender.hpp',['../gbwt__extender_8hpp.html',1,'']]],
- ['gbwt_5fgraph_2018',['gbwt_graph',['../classvg_1_1MinimizerMapper.html#abb94c27ed347a36fb38f91cf23a582fb',1,'vg::MinimizerMapper::gbwt_graph()'],['../structGraphHandler.html#ad86c0372b075e6e0c5bfbf61801b3222',1,'GraphHandler::gbwt_graph()']]],
- ['gbwt_5fhelper_2ecpp_2019',['gbwt_helper.cpp',['../gbwt__helper_8cpp.html',1,'']]],
- ['gbwt_5fhelper_2ehpp_2020',['gbwt_helper.hpp',['../gbwt__helper_8hpp.html',1,'']]],
- ['gbwt_5findex_2021',['gbwt_index',['../classvg_1_1PhaseUnfolder.html#abe0ad79b8b65bea2a4f871913c83ee65',1,'vg::PhaseUnfolder']]],
- ['gbwt_5finsert_5fbatch_5fsize_2022',['gbwt_insert_batch_size',['../structvg_1_1IndexingParameters.html#ab408ae73a85875de5dfe376e340f8840',1,'vg::IndexingParameters']]],
- ['gbwt_5finsert_5fbatch_5fsize_5fincrease_5ffactor_2023',['gbwt_insert_batch_size_increase_factor',['../structvg_1_1IndexingParameters.html#a721125abeca5c4755e875f2e3d8c1d2f',1,'vg::IndexingParameters']]],
- ['gbwt_5fmain_2ecpp_2024',['gbwt_main.cpp',['../gbwt__main_8cpp.html',1,'']]],
- ['gbwt_5fname_2025',['gbwt_name',['../structGBWTConfig.html#a5fe3f0a41311811ddf16bcd7dbab4f91',1,'GBWTConfig']]],
- ['gbwt_5fnode_5fwidth_2026',['gbwt_node_width',['../namespacevg.html#ada6300e45d21f1171c5ff2b71f4d173b',1,'vg']]],
- ['gbwt_5foutput_2027',['gbwt_output',['../structGBWTConfig.html#a8d9b4d70bb33f75cb147ee91b75c89af',1,'GBWTConfig']]],
- ['gbwt_5freference_5fsamples_2028',['gbwt_reference_samples',['../classvg_1_1Deconstructor.html#a8f81a59e45aad56aa6edc19756a9eb14',1,'vg::Deconstructor']]],
- ['gbwt_5fsample_5fto_5fphase_5frange_2029',['gbwt_sample_to_phase_range',['../classvg_1_1Deconstructor.html#a5f58aa9a4d3f29e330a9c9e1c9541884',1,'vg::Deconstructor']]],
- ['gbwt_5fsampling_5finterval_2030',['gbwt_sampling_interval',['../structvg_1_1IndexingParameters.html#abd33e81c954cb14ed31455a3950abe64',1,'vg::IndexingParameters']]],
- ['gbwt_5fthread_5ft_2031',['gbwt_thread_t',['../structhaplo_1_1gbwt__thread__t.html',1,'haplo::gbwt_thread_t'],['../structhaplo_1_1gbwt__thread__t.html#a5b148ae0a27b81b4b4af07f200a1255b',1,'haplo::gbwt_thread_t::gbwt_thread_t()'],['../structhaplo_1_1gbwt__thread__t.html#aa52a0e84c11044abd6ce20969629e3a9',1,'haplo::gbwt_thread_t::gbwt_thread_t(const gbwt::vector_type &nodes, const vector< size_t > &node_lengths)']]],
- ['gbwt_5fto_5fhandle_2032',['gbwt_to_handle',['../namespacevg.html#a28c93b1c4a71fadf62fc2582cc8f0ed2',1,'vg']]],
- ['gbwt_5fto_5fpos_2033',['gbwt_to_pos',['../namespacevg.html#ae7b5f995eb3e1e824cc4e7db99c81042',1,'vg']]],
- ['gbwt_5ftrav_5ffinder_2034',['gbwt_trav_finder',['../classvg_1_1Deconstructor.html#a41a7ff33e08c5eee5d2d7088dbc238f4',1,'vg::Deconstructor']]],
- ['gbwtconfig_2035',['GBWTConfig',['../structGBWTConfig.html',1,'GBWTConfig'],['../structGBWTConfig.html#a20a8123e9a054bab77de5e8d9f9c1bd5',1,'GBWTConfig::GBWTConfig()']]],
- ['gbwtgraph_5fhelper_2ecpp_2036',['gbwtgraph_helper.cpp',['../gbwtgraph__helper_8cpp.html',1,'']]],
- ['gbwtgraph_5fhelper_2ehpp_2037',['gbwtgraph_helper.hpp',['../gbwtgraph__helper_8hpp.html',1,'']]],
- ['gbwtgraph_5fname_2038',['gbwtgraph_name',['../structGBWTConfig.html#ac8e90b7bda206414a7055a98f5b55e85',1,'GBWTConfig']]],
- ['gbwthandler_2039',['GBWTHandler',['../structvg_1_1GBWTHandler.html',1,'vg']]],
- ['gbwtscoreprovider_2040',['GBWTScoreProvider',['../classhaplo_1_1GBWTScoreProvider.html',1,'haplo::GBWTScoreProvider< GBWTType >'],['../classhaplo_1_1GBWTScoreProvider.html#abf8bd05e480afa9a2ac2832a13f5b181',1,'haplo::GBWTScoreProvider::GBWTScoreProvider()']]],
- ['gbwttraversalfinder_2041',['GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html',1,'vg::GBWTTraversalFinder'],['../classvg_1_1GBWTTraversalFinder.html#af415423d43372c2770c201a10ace0385',1,'vg::GBWTTraversalFinder::GBWTTraversalFinder()']]],
- ['gbz_2042',['gbz',['../classvg_1_1GBZGraph.html#ac56a91ab9fe591aa7781cd751fe94ed4',1,'vg::GBZGraph::gbz()'],['../classvg_1_1HaplotypePartitioner.html#a533f084057db81844dd0c02f36fb5498',1,'vg::HaplotypePartitioner::gbz()'],['../classvg_1_1Recombinator.html#a977b21bbcc9ea6520dbc97a5014488e6',1,'vg::Recombinator::gbz()']]],
- ['gbz_5fformat_2043',['gbz_format',['../structGBWTConfig.html#a14fe1675f26aa9b74381640c4cffdd47',1,'GBWTConfig']]],
- ['gbz_5foutput_2044',['gbz_output',['../structHaplotypesConfig.html#af71ee285e699443b559375aeac054eb8',1,'HaplotypesConfig']]],
- ['gbzgraph_2045',['GBZGraph',['../classvg_1_1GBZGraph.html',1,'vg']]],
- ['gbzgraph_2ehpp_2046',['gbzgraph.hpp',['../gbzgraph_8hpp.html',1,'']]],
- ['gc_5fcontent_5festimate_2047',['gc_content_estimate',['../classvg_1_1AlignerClient.html#a65428f092aaa5d894b709e247cf0121a',1,'vg::AlignerClient']]],
- ['gcsa_2048',['gcsa',['../classvg_1_1BaseMapper.html#aa41db0eca93c379087c90b602a6ce751',1,'vg::BaseMapper']]],
- ['gcsa_5fdoubling_5fsteps_2049',['gcsa_doubling_steps',['../structvg_1_1IndexingParameters.html#ab480b0e1f6dca30213719734b78904e5',1,'vg::IndexingParameters']]],
- ['gcsa_5fhelper_2ecpp_2050',['gcsa_helper.cpp',['../gcsa__helper_8cpp.html',1,'']]],
- ['gcsa_5fhelper_2ehpp_2051',['gcsa_helper.hpp',['../gcsa__helper_8hpp.html',1,'']]],
- ['gcsa_5find_2052',['gcsa_ind',['../classvg_1_1Filter.html#ae98fe5c85ea704f1ef262b5556bbbbbb',1,'vg::Filter']]],
- ['gcsa_5finitial_5fkmer_5flength_2053',['gcsa_initial_kmer_length',['../structvg_1_1IndexingParameters.html#a890a5822bd592090eaf5b529816ecb32',1,'vg::IndexingParameters']]],
- ['gcsa_5fnodes_5fto_5fpositions_2054',['gcsa_nodes_to_positions',['../namespacevg.html#a3240e7b9bf787fb218d6324389ea234e',1,'vg']]],
- ['gcsa_5fsize_5flimit_2055',['gcsa_size_limit',['../structvg_1_1IndexingParameters.html#a144f6b2b03ccc7ecf4b7d3a504aed1b7',1,'vg::IndexingParameters']]],
- ['gen_5fflat_5fnode_2056',['gen_flat_node',['../structhaplo_1_1haplo__DP__rectangle.html#a87d1fd7ca4ac40321f912724bf5c3f8c',1,'haplo::haplo_DP_rectangle']]],
- ['gen_5frange_5ft_2057',['gen_range_t',['../structhaplo_1_1haplo__DP__rectangle.html#af3fc7fee833ac23bdbc93f73fb5be9d9',1,'haplo::haplo_DP_rectangle']]],
- ['generalizations_2058',['generalizations',['../classvg_1_1IndexRegistry.html#a665cc9431438ef50124b29e518465a05',1,'vg::IndexRegistry']]],
- ['generate_2059',['generate',['../structvg_1_1RecombinatorFragment.html#a411831e7ba9db75f1d14708bb79f7eef',1,'vg::RecombinatorFragment']]],
- ['generate_5fcontinuous_5funiform_2060',['generate_continuous_uniform',['../classvg_1_1MCMCGenotyper.html#a5ebeff817c6548c32c5377ed00c041c6',1,'vg::MCMCGenotyper']]],
- ['generate_5fdiscrete_5funiform_2061',['generate_discrete_uniform',['../classvg_1_1MCMCGenotyper.html#a8b76754fc9611d38463cccd3051c0589',1,'vg::MCMCGenotyper']]],
- ['generate_5ffrom_5fwide_5fgenerator_2062',['generate_from_wide_generator',['../classvg_1_1uniform__int__distribution.html#a6efdc1be7572287df4cfad1acd044d90',1,'vg::uniform_int_distribution']]],
- ['generate_5fhaplotype_2063',['generate_haplotype',['../namespacevg.html#a117021c748aad14cfa190bbd2452405d',1,'vg']]],
- ['generate_5fhaplotypes_2064',['generate_haplotypes',['../classvg_1_1Recombinator.html#a7f803cd4d08d8c699877e274bc3f5ceb',1,'vg::Recombinator::generate_haplotypes(const std::string &kff_file, const Parameters ¶meters) const'],['../classvg_1_1Recombinator.html#a8ac8a32e83455572b44af1da347cd09d',1,'vg::Recombinator::generate_haplotypes(const Haplotypes::TopLevelChain &chain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata, const Parameters ¶meters, double coverage) const']]],
- ['generate_5finitial_5fguess_2065',['generate_initial_guess',['../classvg_1_1MCMCGenotyper.html#aac263c28f16acd3eb17d1f6013b5709e',1,'vg::MCMCGenotyper']]],
- ['generate_5fpaths_2066',['generate_paths',['../classvg_1_1PhaseUnfolder.html#a7a2015207e502ecd4d294af79936bda2',1,'vg::PhaseUnfolder']]],
- ['generate_5fthreads_2067',['generate_threads',['../classvg_1_1PhaseUnfolder.html#abc5cead86bec1446aedd4cb2ec291d3f',1,'vg::PhaseUnfolder']]],
- ['generic_2068',['GENERIC',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cac942dc2a9f958acddc67e11472d3ca0b',1,'handlegraph']]],
- ['genome_2069',['genome',['../classvg_1_1MCMCCaller.html#ad4278b11272792c879ab3463b513ae1e',1,'vg::MCMCCaller']]],
- ['genome_5fstate_2ecpp_2070',['genome_state.cpp',['../genome__state_8cpp.html',1,'']]],
- ['genome_5fstate_2ehpp_2071',['genome_state.hpp',['../genome__state_8hpp.html',1,'']]],
- ['genomestate_2072',['GenomeState',['../classvg_1_1GenomeState.html',1,'vg::GenomeState'],['../classvg_1_1GenomeState.html#ab132518a611296d53c4f59a6b5737374',1,'vg::GenomeState::GenomeState()']]],
- ['genomestatecommand_2073',['GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html',1,'vg']]],
- ['genotype_2074',['Genotype',['../structvg_1_1Genotype.html',1,'vg::Genotype'],['../structvg_1_1Locus.html#a144d9dc0f9d61910db33decca23e4755',1,'vg::Locus::genotype()'],['../classvg_1_1SnarlCaller.html#a3e4d1ad4ece1a1bc1daa4ea6ecfbfa54',1,'vg::SnarlCaller::genotype()'],['../classvg_1_1RatioSupportSnarlCaller.html#afa1d42f1ba7e32ca274e23d0e9795278',1,'vg::RatioSupportSnarlCaller::genotype()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a1be3298970827475c5b96486d58fd833',1,'vg::PoissonSupportSnarlCaller::genotype()']]],
- ['genotype_5fby_5fploidy_2075',['genotype_by_ploidy',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#af331caba29195578f8a48ed527232ed1',1,'vg::NestedFlowCaller::CallRecord']]],
- ['genotype_5flikelihood_2076',['genotype_likelihood',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a555a22f275a83ade8fcd35a1572908',1,'vg::PoissonSupportSnarlCaller']]],
- ['genotype_5fmain_2ecpp_2077',['genotype_main.cpp',['../genotype__main_8cpp.html',1,'']]],
- ['genotype_5fsnarl_2078',['genotype_snarl',['../classvg_1_1Genotyper.html#ae6a3a060adcffc32724498bbfda2c771',1,'vg::Genotyper']]],
- ['genotype_5fsnarls_2079',['genotype_snarls',['../classvg_1_1FlowCaller.html#ae47f36ad1ec53a2381f970d159acbd64',1,'vg::FlowCaller::genotype_snarls()'],['../classvg_1_1NestedFlowCaller.html#a4c00174974936972c989b905a921b154',1,'vg::NestedFlowCaller::genotype_snarls()']]],
- ['genotype_5fsvs_2080',['genotype_svs',['../namespacevg.html#a7d3374c888c7c37f1de8370e151af7f9',1,'vg']]],
- ['genotypekit_2ecpp_2081',['genotypekit.cpp',['../genotypekit_8cpp.html',1,'']]],
- ['genotypekit_2ehpp_2082',['genotypekit.hpp',['../genotypekit_8hpp.html',1,'']]],
- ['genotypelikelihoodcalculator_2083',['GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html',1,'vg']]],
- ['genotypepriorcalculator_2084',['GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html',1,'vg']]],
- ['genotyper_2085',['Genotyper',['../classvg_1_1Genotyper.html',1,'vg']]],
- ['genotyper_2ecpp_2086',['genotyper.cpp',['../genotyper_8cpp.html',1,'']]],
- ['genotyper_2ehpp_2087',['genotyper.hpp',['../genotyper_8hpp.html',1,'']]],
- ['geometric_5fsampling_5fprob_5fln_2088',['geometric_sampling_prob_ln',['../namespacevg.html#ae923ee7bdb53f33511c95f66a9c2773a',1,'vg']]],
- ['get_2089',['get',['../structvg_1_1Annotation.html#a00494075a8d051c16b2485b44c541dce',1,'vg::Annotation::get()'],['../classvg_1_1GBZGraph.html#a69ee920e1aa95a146e8e77f32a717a88',1,'vg::GBZGraph::get()'],['../classvg_1_1GBZGraph.html#a3eb7ff9317143e89c14bd15a682426ac',1,'vg::GBZGraph::get() const'],['../classvg_1_1VcfBuffer.html#ac855a338ea08f2ea75dc73206f9d7520',1,'vg::VcfBuffer::get()'],['../classvg_1_1WindowedVcfBuffer.html#a3c09bb140ab8f8d91f2f67f3dc0e7f0b',1,'vg::WindowedVcfBuffer::get()'],['../classvg_1_1subcommand_1_1Subcommand.html#aa44da5b424f5fcf7133f6a061680693f',1,'vg::subcommand::Subcommand::get()']]],
- ['get_5fadaptive_5fmin_5freseed_5flength_2090',['get_adaptive_min_reseed_length',['../classvg_1_1BaseMapper.html#a7f693887391ddeaebf4a4a609e2ab9b3',1,'vg::BaseMapper']]],
- ['get_5faffinities_2091',['get_affinities',['../classvg_1_1Genotyper.html#abea795c1969c4866c349a07c7f9c7102',1,'vg::Genotyper']]],
- ['get_5faffinities_5ffast_2092',['get_affinities_fast',['../classvg_1_1Genotyper.html#a966eee3f764281271904996546ef205b',1,'vg::Genotyper']]],
- ['get_5faligner_2093',['get_aligner',['../classvg_1_1AlignerClient.html#a683c04ab96b613ea3459738beffe5982',1,'vg::AlignerClient']]],
- ['get_5falignment_5femitter_2094',['get_alignment_emitter',['../namespacevg.html#aa95de659d860fc90fda95df414c89baf',1,'vg']]],
- ['get_5falignment_5fstart_2095',['get_alignment_start',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a5790a8cfd26dd12a19d33fc11cb84933',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['get_5falignments_2096',['get_alignments',['../structvg_1_1AugmentedGraph.html#ad92c283634470f6372777c38a9a70a79',1,'vg::AugmentedGraph::get_alignments(id_t node_id) const'],['../structvg_1_1AugmentedGraph.html#a61465a645ac54c62d4707d570ed56f76',1,'vg::AugmentedGraph::get_alignments(pair< NodeSide, NodeSide >) const'],['../structvg_1_1AugmentedGraph.html#ab3bf8e1a51696ba12329045956b7646a',1,'vg::AugmentedGraph::get_alignments() const']]],
- ['get_5fallele_2097',['get_allele',['../classvg_1_1PhasedGenome.html#a6f89ab856a31dfb7258fd7487c051a5a',1,'vg::PhasedGenome']]],
- ['get_5falleles_2098',['get_alleles',['../classvg_1_1Deconstructor.html#a7977882fef8c75836fede5338925f411',1,'vg::Deconstructor']]],
- ['get_5falt_5fpath_2099',['get_alt_path',['../classvg_1_1VCFTraversalFinder.html#acbbbaa19966bd2a939f9fdc05b414343',1,'vg::VCFTraversalFinder']]],
- ['get_5falt_5ftraversal_2100',['get_alt_traversal',['../classvg_1_1VCFTraversalFinder.html#afd039c87e92906ac02479d8d2df43f13',1,'vg::VCFTraversalFinder']]],
- ['get_5fannotation_2101',['get_annotation',['../classvg_1_1multipath__alignment__t.html#a401b9ef14924b463d54be7a4ced828d6',1,'vg::multipath_alignment_t::get_annotation()'],['../namespacevg.html#a1fda752e24eaed100f6c30904d2ca3e1',1,'vg::get_annotation(const Annotated &annotated, const string &name)'],['../namespacevg.html#a1c9f371af54160a44a44afd80c6cf71a',1,'vg::get_annotation(Annotated *annotated, const string &name)']]],
- ['get_5fany_5fgraph_2102',['get_any_graph',['../structGraphHandler.html#a7155dd41d244081487e79759707f29af',1,'GraphHandler']]],
- ['get_5faverage_5ftraversal_5fsupport_5fswitch_5fthreshold_2103',['get_average_traversal_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a62c1864ae422d93cba4eb248890fd3e4',1,'vg::TraversalSupportFinder']]],
- ['get_5favg_5fbaseq_2104',['get_avg_baseq',['../namespacevg.html#a680a465e72fbddeed584f27a6c3f7b27',1,'vg']]],
- ['get_5favg_5fnode_5fmapq_2105',['get_avg_node_mapq',['../classvg_1_1TraversalSupportFinder.html#a55880f595d8f607a73e8617e7b2aa216',1,'vg::TraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1PackedTraversalSupportFinder.html#a1fd604b1e8eac99954981aca81cafffd',1,'vg::PackedTraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aa3fab4fec47f870d3cc6e2c1fdb46ccb',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_mapq()']]],
- ['get_5favg_5fnode_5fsupport_2106',['get_avg_node_support',['../classvg_1_1TraversalSupportFinder.html#a42cf4393f0ff594d0eaf489b2127cdef',1,'vg::TraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a66cbea99df3ef78364f653a044bec308',1,'vg::PackedTraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#abb0f5d8c3967c099daaf2fb174620f3a',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_support()']]],
- ['get_5fback_5fgraph_5fnode_5fname_2107',['get_back_graph_node_name',['../classvg_1_1FlatFileBackTranslation.html#a816506e29e304f623d790d79271fd344',1,'vg::FlatFileBackTranslation::get_back_graph_node_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a5829e7992e105e0895a81a8aca82e70b',1,'vg::algorithms::GFAIDMapInfo::get_back_graph_node_name()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#acd81ad54c6a6ec680faaae76aaae4397',1,'handlegraph::NamedNodeBackTranslation::get_back_graph_node_name()']]],
- ['get_5fbase_2108',['get_base',['../classvg_1_1IncrementalSubgraph.html#a6ff73a10a56b8116b7d07c32d3f3160a',1,'vg::IncrementalSubgraph::get_base()'],['../classvg_1_1JoinedSpliceGraph.html#a7dcc1d1e3e9c2e1058a5995785b0a224',1,'vg::JoinedSpliceGraph::get_base()'],['../classvg_1_1VG.html#a7cb582e352f75cc9d66e6eff0f4ba659',1,'vg::VG::get_base()'],['../classxg_1_1XG.html#a355dd79f8449b462e7d98916f1a22d9f',1,'xg::XG::get_base()'],['../classhandlegraph_1_1HandleGraph.html#a64d58c3e26e9e7954dd25c3eff7af521',1,'handlegraph::HandleGraph::get_base()']]],
- ['get_5fbase_5fgbwt_5fpath_5fname_2109',['get_base_gbwt_path_name',['../classvg_1_1Transcriptome.html#a1c9af6904f1f282a0782c1e34bc4b9ab',1,'vg::Transcriptome']]],
- ['get_5fbest_5falignment_5fagainst_5fany_5ftree_2110',['get_best_alignment_against_any_tree',['../classvg_1_1MinimizerMapper.html#a12558b08552a22a9a28db3fb0fd3779d',1,'vg::MinimizerMapper']]],
- ['get_5fbest_5fchain_5fstats_2111',['get_best_chain_stats',['../classvg_1_1MinimizerMapper.html#a2f9b9b580ed851b00268f455c2d543cb',1,'vg::MinimizerMapper']]],
- ['get_5fbest_5fgbwtgraph_5fgfa_5fparsing_5fparameters_2112',['get_best_gbwtgraph_gfa_parsing_parameters',['../namespacevg.html#ab35317ee2bc53165662dd776516f341d',1,'vg']]],
- ['get_5fbest_5fsupport_2113',['get_best_support',['../classvg_1_1SupportBasedSnarlCaller.html#a1b5a50373729771229ada685b12627df',1,'vg::SupportBasedSnarlCaller']]],
- ['get_5fbias_2114',['get_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a3f5f06692eeabe27d7c00afc8658cb20',1,'vg::RatioSupportSnarlCaller']]],
- ['get_5fbin_5fsize_2115',['get_bin_size',['../classvg_1_1Packer.html#afef014ad5278ee08959c3ffe2cf15c17',1,'vg::Packer']]],
- ['get_5fbound_2116',['get_bound',['../classhandlegraph_1_1SnarlDecomposition.html#aabee8d2ebb1971ecfd5c4647b84081f2',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fbounds_2117',['get_bounds',['../classvg_1_1Constructor.html#a06078b6af1dc190c74806b30b669daae',1,'vg::Constructor']]],
- ['get_5fbuckets_2118',['get_buckets',['../classvg_1_1OrientedDistanceMeasurer.html#aa21aedba58999e7041483f077720d13b',1,'vg::OrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#aac5383ef03533609d85172e7821a8200',1,'vg::PathOrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#ac885044126300cab4750fd21fd4634fc',1,'vg::SnarlOrientedDistanceMeasurer::get_buckets()']]],
- ['get_5fcategory_2119',['get_category',['../classvg_1_1subcommand_1_1Subcommand.html#a252c8946e450ba4a194b7da6ece5ba2c',1,'vg::subcommand::Subcommand']]],
- ['get_5fcc_5fin_5fwg_2120',['get_cc_in_wg',['../classvg_1_1FlowSort.html#a27df1607587f1f1e1f03ab8369c34ebe',1,'vg::FlowSort']]],
- ['get_5fcenter_2121',['get_center',['../classvg_1_1VariantAdder.html#a2949d0ea5c46f477813df8f5162fe013',1,'vg::VariantAdder']]],
- ['get_5fcenter_5fand_5fradius_2122',['get_center_and_radius',['../classvg_1_1VariantAdder.html#a29a14a6579197519b35653f542d5c1ec',1,'vg::VariantAdder']]],
- ['get_5fchain_5fcode_2123',['get_chain_code',['../classvg_1_1ZipCode.html#aa0f40a265733bd4adfb920006fd9f57a',1,'vg::ZipCode']]],
- ['get_5fchain_5fcomponent_2124',['get_chain_component',['../classvg_1_1ZipCode.html#af85179af0d75add0b10023343c2a407a',1,'vg::ZipCode::get_chain_component()'],['../structvg_1_1ZipCode_1_1node__code__t.html#a52e72d7ff49bcb809cac2f7ab85ad004',1,'vg::ZipCode::node_code_t::get_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5dcd90a391b2382723f3b303687ca1c8',1,'vg::ZipCode::snarl_code_t::get_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#adc51b5f6e09b00eb41964c902d7eb033',1,'vg::ZipCodeForest::sort_value_t::get_chain_component()']]],
- ['get_5fchild_5fcount_2125',['get_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a315c9998b34918303feb08d5143fba7c',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fchild_5fsupport_2126',['get_child_support',['../classvg_1_1TraversalSupportFinder.html#ac46ef820b2a05e8b331677deb80871a9',1,'vg::TraversalSupportFinder::get_child_support()'],['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af112bf57cc9a16c9dc35f6578a3b1c14',1,'vg::NestedCachedPackedTraversalSupportFinder::get_child_support()']]],
- ['get_5fclipped_5fposition_2127',['get_clipped_position',['../classvg_1_1Filter.html#a5cc119894a6baeb450c31dc7c6b75bed',1,'vg::Filter']]],
- ['get_5fclipped_5fref_5fposition_2128',['get_clipped_ref_position',['../classvg_1_1Filter.html#ab1a309b366e677b179772e9bebd9f78f',1,'vg::Filter']]],
- ['get_5fclipped_5fseq_2129',['get_clipped_seq',['../classvg_1_1Filter.html#a4c29ccf736113bb95328467d22f98ad8',1,'vg::Filter']]],
- ['get_5fcluster_5fpairs_2130',['get_cluster_pairs',['../classvg_1_1MultipathMapper.html#a49fdf1a2efedda808c2d3a7bda5a7f98',1,'vg::MultipathMapper']]],
- ['get_5fclusters_2131',['get_clusters',['../classvg_1_1MultipathMapper.html#a0a588e4f282d38add8626debe86c455d',1,'vg::MultipathMapper']]],
- ['get_5fcode_5ftype_2132',['get_code_type',['../classvg_1_1ZipCode.html#ac91d59c7100fefc2011cda07996ed71a',1,'vg::ZipCode::get_code_type()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a0d7f3c9052df0ced4949b909d1ed20b5',1,'vg::ZipCode::snarl_code_t::get_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a9959da3b3a6e98968794073dc049eb0b',1,'vg::ZipCodeForest::sort_value_t::get_code_type()']]],
- ['get_5fcodename_2133',['get_codename',['../classvg_1_1Version.html#a0bab20984ed75b2df12c3ef4a409f922',1,'vg::Version']]],
- ['get_5fconnected_5fcomponents_2134',['get_connected_components',['../classvg_1_1MultipathAlignmentGraph.html#af4fc215d24f20c5ddc3916024c7ab62b',1,'vg::MultipathAlignmentGraph']]],
- ['get_5fconnectivity_2135',['get_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a0b28eb090f0d0f7b1b408a5e772b3105',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fcontained_5forientations_2136',['get_contained_orientations',['../structvg_1_1PathIndex.html#a6a7f7bbcd256a2ed34a58b8abefff712',1,'vg::PathIndex']]],
- ['get_5fcontext_2137',['get_context',['../classvg_1_1Deconstructor.html#a049890802f6b6036a779eb3645bb1307',1,'vg::Deconstructor']]],
- ['get_5fcorrelation_2138',['get_correlation',['../classvg_1_1ZipCodeForest.html#ab939e5ee856a9ac2531d0d8ac14e7cbe',1,'vg::ZipCodeForest']]],
- ['get_5fcount_2139',['get_count',['../classvg_1_1NoAlignmentInBandException.html#a4b5f7f90a2be571131fb12484a9b4c18',1,'vg::NoAlignmentInBandException']]],
- ['get_5fcreate_5fpath_2140',['get_create_path',['../classvg_1_1Paths.html#a4e79d7915cd2f68e55573bcc50c1d417',1,'vg::Paths']]],
- ['get_5fcreated_5fhandle_2141',['get_created_handle',['../classvg_1_1ExtraNodeGraph.html#aac84ee8139e0aa885b87f02ad9ccf8ef',1,'vg::ExtraNodeGraph']]],
- ['get_5fcurrent_5fcolumn_2142',['get_current_column',['../structhaplo_1_1haplo__DP.html#a0061c97ecd2330efdcf0fbabb69d808d',1,'haplo::haplo_DP']]],
- ['get_5fcurrent_5fvmem_5fkb_2143',['get_current_vmem_kb',['../namespacevg.html#a8cd30aaebcab130194ac375f23e6f098',1,'vg']]],
- ['get_5fcut_5fsegments_2144',['get_cut_segments',['../classvg_1_1MultipathAlignmentGraph.html#aaa64dbf4207ebe2fe75044d60be1d07e',1,'vg::MultipathAlignmentGraph']]],
- ['get_5fcyclic_5fsnarl_5fintervals_2145',['get_cyclic_snarl_intervals',['../classvg_1_1ZipCodeForest.html#ad32664318549a51d8727204d665a2bc6',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const interval_state_t &snarl_interval, const interval_state_t &parent_interval, const forward_list< interval_state_t > &child_intervals, forward_list< interval_state_t > &next_intervals) const'],['../classvg_1_1ZipCodeForest.html#a72304772e60e79909b71f8a51e65d6a5',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const ZipCodeForest::interval_state_t &snarl_interval, const ZipCodeForest::interval_state_t &parent_interval, const forward_list< ZipCodeForest::interval_state_t > &child_intervals, forward_list< ZipCodeForest::interval_state_t > &next_intervals) const']]],
- ['get_5fdefault_5flong_5fgiraffe_5findexes_2146',['get_default_long_giraffe_indexes',['../structvg_1_1VGIndexes.html#a8caf19bd7436cd7f9df4f9792aa86483',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fmap_5findexes_2147',['get_default_map_indexes',['../structvg_1_1VGIndexes.html#afcc2119cd690b16f57d4b9d137af58fe',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fmpmap_5findexes_2148',['get_default_mpmap_indexes',['../structvg_1_1VGIndexes.html#a9377b325c6e0f8bbca1368379ad60a0c',1,'vg::VGIndexes']]],
- ['get_5fdefault_5frpvg_5findexes_2149',['get_default_rpvg_indexes',['../structvg_1_1VGIndexes.html#ae56d5009377fed32d392fcff5ac02f7f',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fshort_5fgiraffe_5findexes_2150',['get_default_short_giraffe_indexes',['../structvg_1_1VGIndexes.html#ab0f962c74f9633fe27b0d59f9774358c',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fthreads_2151',['get_default_threads',['../minimizer__main_8cpp.html#a849308cddbd36f5fc06c5e1289112bae',1,'minimizer_main.cpp']]],
- ['get_5fdefault_5fvalue_2152',['get_default_value',['../classvg_1_1OptionInterface.html#ade1ab38610fecb31821e13e5e296454c',1,'vg::OptionInterface::get_default_value()'],['../classvg_1_1BaseOption.html#af13c01c387907bb386b591bff8bbb5e9',1,'vg::BaseOption::get_default_value()']]],
- ['get_5fdegree_2153',['get_degree',['../classvg_1_1ExtraNodeGraph.html#a0cc5cb40e81623b3a3e11bea359e41c5',1,'vg::ExtraNodeGraph::get_degree()'],['../classvg_1_1IncrementalSubgraph.html#ae3365d87d1cd6bfe12d3433197d06a85',1,'vg::IncrementalSubgraph::get_degree()'],['../classvg_1_1SourceSinkOverlay.html#a8bfc476463b487d42c77bda6bdfe2a7d',1,'vg::SourceSinkOverlay::get_degree()'],['../classvg_1_1VG.html#afc0ac00267e00156e04c849a10b1cb74',1,'vg::VG::get_degree()'],['../classhandlegraph_1_1HandleGraph.html#ab259e3aba0da47b0ef1c9b5e43c7d209',1,'handlegraph::HandleGraph::get_degree()']]],
- ['get_5fdepth_5ffrom_5findex_2154',['get_depth_from_index',['../namespacevg_1_1algorithms.html#a4152fa019243d9fd4c41c73fafce2241',1,'vg::algorithms']]],
- ['get_5fdescription_2155',['get_description',['../classvg_1_1OptionInterface.html#aa53deb39285f0045257083eb38d703cd',1,'vg::OptionInterface::get_description()'],['../classvg_1_1BaseOption.html#a4343a02a0967d6f79c0b8ae83c6a0795',1,'vg::BaseOption::get_description()'],['../classvg_1_1subcommand_1_1Subcommand.html#aca3e8621a4002b48b733211c3adc52b5',1,'vg::subcommand::Subcommand::get_description()']]],
- ['get_5fdiagonals_2156',['get_diagonals',['../classvg_1_1WFATree.html#a2bd4732a5815c365d3790b76b9230973',1,'vg::WFATree']]],
- ['get_5fdir_2157',['get_dir',['../namespacevg_1_1temp__file.html#ab1b0884547b4f3403e8cde0ca8b75b7c',1,'vg::temp_file::get_dir()'],['../namespacexg_1_1temp__file.html#a1cef40a1b0f27d1693d827db9773c020',1,'xg::temp_file::get_dir()']]],
- ['get_5fdisjoint_5fsets_2158',['get_disjoint_sets',['../classvg_1_1ContractingGraph.html#acd929119b9b11170f1eb4893a7032fe6',1,'vg::ContractingGraph']]],
- ['get_5fdistance_2159',['get_distance',['../classvg_1_1HaplotypePartitioner.html#a8d98335b0032014b1e033a6610fb644d',1,'vg::HaplotypePartitioner']]],
- ['get_5fdistance_5fend_5fleft_2160',['get_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ad3e98278c0ca79470bc1a58e3fdcf370',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5fend_5fright_2161',['get_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa5d11da32ad7be1dfa88674efd4fa422',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5findex_5faddress_2162',['get_distance_index_address',['../classvg_1_1ZipCode.html#a6cc3964efc186615dab6bdd8bc52fbfb',1,'vg::ZipCode']]],
- ['get_5fdistance_5flimit_2163',['get_distance_limit',['../classvg_1_1MinimizerMapper.html#a27798cd4a1bee171ec38713d402e8793',1,'vg::MinimizerMapper']]],
- ['get_5fdistance_5fmeasurer_2164',['get_distance_measurer',['../classvg_1_1MultipathMapper.html#a56e1c69cfba7c1eebb4cae0af59a018d',1,'vg::MultipathMapper']]],
- ['get_5fdistance_5fstart_5fleft_2165',['get_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a678e476d61bcf781b1461cedb8801c68',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5fstart_5fright_2166',['get_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aedb473ac00ffbd480c09fd04e44fcbb8',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5fto_5fsnarl_5fbound_2167',['get_distance_to_snarl_bound',['../classvg_1_1ZipCode.html#ad39662d894fe714c1d8596b0343557f6',1,'vg::ZipCode']]],
- ['get_5fdistance_5fvalue_2168',['get_distance_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a2a427abecffc91c8f56b715de43a43b3',1,'vg::ZipCodeForest::sort_value_t']]],
- ['get_5fduplicate_5fhandle_2169',['get_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#af51998490e3eac92e0d106b791eebbce',1,'vg::DozeuPinningOverlay']]],
- ['get_5fedge_2170',['get_edge',['../classvg_1_1VG.html#a8668ddc84b9abe4fe9cb5acb3efd877b',1,'vg::VG::get_edge(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a227023072262f46f7c423d30cf8bc443',1,'vg::VG::get_edge(const pair< NodeSide, NodeSide > &sides)'],['../classvg_1_1VG.html#af63d7ba7b69594ee99f3ad99dd394171',1,'vg::VG::get_edge(const NodeTraversal &left, const NodeTraversal &right)']]],
- ['get_5fedge_5fcount_2171',['get_edge_count',['../classvg_1_1IncrementalSubgraph.html#aeab323f77d0363867dc60be6dafe73ce',1,'vg::IncrementalSubgraph::get_edge_count()'],['../classvg_1_1VG.html#ad4577be9213932c313efd3d016b88a31',1,'vg::VG::get_edge_count()'],['../classxg_1_1XG.html#aa624840475fc83351c00ef2728480355',1,'xg::XG::get_edge_count()'],['../classhandlegraph_1_1HandleGraph.html#a20ff62014d7f0f0c01ada8a3d40a278d',1,'handlegraph::HandleGraph::get_edge_count()']]],
- ['get_5fedge_5flength_2172',['get_edge_length',['../classvg_1_1TraversalSupportFinder.html#a4902b9dcdaa53f74f45a394265163311',1,'vg::TraversalSupportFinder']]],
- ['get_5fedge_5fsupport_2173',['get_edge_support',['../classvg_1_1RepresentativeTraversalFinder.html#a452fdd307124349d6b65aa434bab48c7',1,'vg::RepresentativeTraversalFinder::get_edge_support()'],['../classvg_1_1TraversalSupportFinder.html#a8b497d8e282da9696d2ae5df86664069',1,'vg::TraversalSupportFinder::get_edge_support(const edge_t &edge) const =0'],['../classvg_1_1TraversalSupportFinder.html#a958a20d44167e8c29f677e12b950b5fa',1,'vg::TraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const =0'],['../classvg_1_1PackedTraversalSupportFinder.html#a394485c49fb5d8043d9f98385dab1b4a',1,'vg::PackedTraversalSupportFinder::get_edge_support(const edge_t &edge) const'],['../classvg_1_1PackedTraversalSupportFinder.html#a5cfa1254fae043f9920761a533d63480',1,'vg::PackedTraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#a72ae391a14cf1625286d8c3aff3cd7a5',1,'vg::CachedPackedTraversalSupportFinder::get_edge_support()']]],
- ['get_5fedges_2174',['get_edges',['../classvg_1_1ContractingGraph.html#a9faff1ddfb92cfa26ba59803899148e7',1,'vg::ContractingGraph']]],
- ['get_5fend_2175',['get_end',['../classvg_1_1NetGraph.html#acccdda49a6444e96292b90218e273942',1,'vg::NetGraph']]],
- ['get_5fend_5fbound_2176',['get_end_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a4c500f039a8740ff6e771ddf4bf693ad',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fend_5fmatches_2177',['get_end_matches',['../classvg_1_1ReadFilter.html#a3cd3ee44928526e27e42e059b693ba76',1,'vg::ReadFilter::get_end_matches(const Read &read) const'],['../classvg_1_1ReadFilter.html#a1e40faa7aa74f7b17390b06da6ad32e4',1,'vg::ReadFilter::get_end_matches(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#a45116be7bd52bfd9fb40e30f08aee97f',1,'vg::ReadFilter::get_end_matches(const Alignment &read) const']]],
- ['get_5fend_5fof_2178',['get_end_of',['../namespacevg.html#af76e8a5e74f67093a40ed5f2cd15ff28',1,'vg']]],
- ['get_5fendpoints_2179',['get_endpoints',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a9e3d20d5ab60eb99688d6346a788d308',1,'vg::GraphSynchronizer::Lock']]],
- ['get_5fexon_5fhaplotypes_2180',['get_exon_haplotypes',['../classvg_1_1Transcriptome.html#a2753baecefb5f065854fd9fbc1a24dc9',1,'vg::Transcriptome']]],
- ['get_5ffeatures_2181',['get_features',['../classvg_1_1FeatureSet.html#a55b389aa1c68efddb28a188a757568fc',1,'vg::FeatureSet']]],
- ['get_5ffile_5fsize_2182',['get_file_size',['../namespacevg.html#a53098c7c826c3d8d2aab804ba5500fd5',1,'vg']]],
- ['get_5ffilenames_2183',['get_filenames',['../classvg_1_1IndexFile.html#a5833162264de6ce5f2a0d882b4b12839',1,'vg::IndexFile']]],
- ['get_5ffirst_5fnode_5fhandle_2184',['get_first_node_handle',['../structvg_1_1EditedTranscriptPath.html#aec08731a5fd5989db7721a3ecf0859e7',1,'vg::EditedTranscriptPath::get_first_node_handle()'],['../structvg_1_1CompletedTranscriptPath.html#af48eb44f24298e5f3efa4641eb91d813',1,'vg::CompletedTranscriptPath::get_first_node_handle()']]],
- ['get_5ffraction_5fof_5fns_2185',['get_fraction_of_ns',['../namespacevg.html#af8f8da6eb179ba0199fc2fdfe676fde7',1,'vg']]],
- ['get_5ffragment_5flength_5fmean_2186',['get_fragment_length_mean',['../classvg_1_1MinimizerMapper.html#a1e08dfa10f620ef44d102123b38b8fe8',1,'vg::MinimizerMapper']]],
- ['get_5ffragment_5flength_5fsample_5fsize_2187',['get_fragment_length_sample_size',['../classvg_1_1MinimizerMapper.html#ab4c62a806ad7b64072a770c9b4db3417',1,'vg::MinimizerMapper']]],
- ['get_5ffragment_5flength_5fstdev_2188',['get_fragment_length_stdev',['../classvg_1_1MinimizerMapper.html#ae048c4929acb22eabd55f54ac3cc6f18',1,'vg::MinimizerMapper']]],
- ['get_5fg_5fiv_5fsize_2189',['get_g_iv_size',['../classxg_1_1XG.html#a1162be39bbe491975cd47c56fc044489',1,'xg::XG']]],
- ['get_5fgbwt_2190',['get_gbwt',['../classvg_1_1GBWTTraversalFinder.html#a07c5e06ec89e54f2efc2d84974b71ca3',1,'vg::GBWTTraversalFinder::get_gbwt()'],['../namespacevg.html#a571047c58b73b78d02a767c3ab6ec222',1,'vg::get_gbwt()']]],
- ['get_5fgenotype_5flog_5flikelihood_2191',['get_genotype_log_likelihood',['../classvg_1_1Genotyper.html#a9071cdf5ae591b478feaac025b069772',1,'vg::Genotyper']]],
- ['get_5fgenotype_5flog_5fprior_2192',['get_genotype_log_prior',['../classvg_1_1Genotyper.html#a5fc66cb05c4ba80e39d078af9ddce715',1,'vg::Genotyper']]],
- ['get_5fgenotypes_2193',['get_genotypes',['../classvg_1_1Deconstructor.html#abed056375d448eeffebcf1b15633fe79',1,'vg::Deconstructor']]],
- ['get_5fgraph_2194',['get_graph',['../classvg_1_1Packer.html#a19b5aa3c38b65c9e35e2ab7604bdbec4',1,'vg::Packer::get_graph()'],['../classvg_1_1VariantAdder.html#a1271c6d39e6387bac452d9bf80689ed5',1,'vg::VariantAdder::get_graph()'],['../structGraphHandler.html#ab0c19a482787b623d946746f33b2fb80',1,'GraphHandler::get_graph()']]],
- ['get_5fgraph_5fdistance_2195',['get_graph_distance',['../namespacevg_1_1algorithms.html#a0b788763f4e6747ba55e5340de9da855',1,'vg::algorithms']]],
- ['get_5fhandle_2196',['get_handle',['../classvg_1_1DagifiedGraph.html#a57e727b78f3eac1ee34b5dabf08a278f',1,'vg::DagifiedGraph::get_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a78c76b68997b94da8bb714ad87b6ce55',1,'vg::DozeuPinningOverlay::get_handle()'],['../classvg_1_1ExtraNodeGraph.html#a76226cecc78c23a95db06f2765138e6f',1,'vg::ExtraNodeGraph::get_handle()'],['../classvg_1_1GaplessExtender.html#ace7698779da48ed9216169b935b0287c',1,'vg::GaplessExtender::get_handle()'],['../classvg_1_1SnarlGraph.html#a8c06fedda57c3e031d8d3b7fbcb696a8',1,'vg::SnarlGraph::get_handle()'],['../classvg_1_1IdentityOverlay.html#a3fc814950bd9b0b003b82637be9c1d06',1,'vg::IdentityOverlay::get_handle()'],['../classvg_1_1IncrementalSubgraph.html#ac2d018cb5a59b4f43e24a4f30643e0f1',1,'vg::IncrementalSubgraph::get_handle()'],['../classvg_1_1IndexedVG.html#ad9779976b07decd5b593b7a097cac44e',1,'vg::IndexedVG::get_handle()'],['../classvg_1_1MemoizingGraph.html#aa0b891348a82fe4fad7f60ab87fbd4b4',1,'vg::MemoizingGraph::get_handle()'],['../classvg_1_1NullMaskingGraph.html#aea8062f2a253f0397a91005b3924475e',1,'vg::NullMaskingGraph::get_handle()'],['../classvg_1_1PathSubgraph.html#a9d2fc4747e6c86125ba149c90041abcd',1,'vg::PathSubgraph::get_handle()'],['../classvg_1_1ReverseGraph.html#a34a79e8c3f5d5f029d5a1427ca10cfbd',1,'vg::ReverseGraph::get_handle()'],['../classvg_1_1NetGraph.html#a639a1a278626238fe98568320590c64f',1,'vg::NetGraph::get_handle()'],['../classvg_1_1SourceSinkOverlay.html#a7cc144d829750cfb85341d42bd4f7e4a',1,'vg::SourceSinkOverlay::get_handle()'],['../classvg_1_1JoinedSpliceGraph.html#a17636cfa63438f4b5941d54b7632d64b',1,'vg::JoinedSpliceGraph::get_handle()'],['../classvg_1_1StrandSplitGraph.html#a97db8ec5efb4280bfe358b0859e96659',1,'vg::StrandSplitGraph::get_handle()'],['../classvg_1_1SubHandleGraph.html#a4cf66400a93dee8a1e49fcc88ab24eb5',1,'vg::SubHandleGraph::get_handle()'],['../classvg_1_1SubgraphOverlay.html#ab36d552e3882740962729d19069f9ddc',1,'vg::SubgraphOverlay::get_handle()'],['../classvg_1_1SubpathOverlay.html#a3871270e3d47a023f27f9bac6959983b',1,'vg::SubpathOverlay::get_handle()'],['../classvg_1_1TreeSubgraph.html#ab7b56b78b8750cc6453180e7e531d925',1,'vg::TreeSubgraph::get_handle()'],['../classvg_1_1VG.html#a70f50e6766af9262c732de26243658f5',1,'vg::VG::get_handle()'],['../classxg_1_1XG.html#adc5660ffe20948888aeca0c6e6bba90a',1,'xg::XG::get_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0a950e73c94a514de69f95be80f96b7e',1,'handlegraph::algorithms::SubHandleGraph::get_handle()'],['../classhandlegraph_1_1HandleGraph.html#a6dd9d70931835f5c75518b23a780b744',1,'handlegraph::HandleGraph::get_handle()'],['../classhandlegraph_1_1SnarlDecomposition.html#a94e6360cbad97a084d6ec3a6a461e20c',1,'handlegraph::SnarlDecomposition::get_handle()']]],
- ['get_5fhandle_5ffrom_5finward_5fbacking_5fhandle_2197',['get_handle_from_inward_backing_handle',['../classvg_1_1NetGraph.html#a62b87ba5400e8c6d3f6335fc2198cc38',1,'vg::NetGraph']]],
- ['get_5fhandle_5fmemo_2198',['get_handle_memo',['../classvg_1_1MemoizingGraph.html#a522abfb6d16b8e96a77ff6f114275cf8',1,'vg::MemoizingGraph']]],
- ['get_5fhandle_5fof_5fstep_2199',['get_handle_of_step',['../classvg_1_1MemoizingGraph.html#a2b4cd0c4ebef4dcefd5bbafcd1ab3e54',1,'vg::MemoizingGraph::get_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a05ce3d84e3e774a89d4d61a70381cee2',1,'vg::PathSubgraphOverlay::get_handle_of_step()'],['../classvg_1_1VG.html#acb73599cc743a392650a7002c8dc2906',1,'vg::VG::get_handle_of_step()'],['../classxg_1_1XG.html#abbfaa6afca08ec2aca7f2fd550221793',1,'xg::XG::get_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a339e690ce3e2bb8280dd1f3ea45abe42',1,'handlegraph::PathHandleGraph::get_handle_of_step()']]],
- ['get_5fhaplotype_2200',['get_haplotype',['../classhandlegraph_1_1PathMetadata.html#a8ea83e700d11830e7eb695b8a11cb17f',1,'handlegraph::PathMetadata::get_haplotype()'],['../haplotypes__main_8cpp.html#ada326bf02798916f16c46f5d308ebc5b',1,'get_haplotype(): haplotypes_main.cpp']]],
- ['get_5fhaplotype_5falt_5fcontents_2201',['get_haplotype_alt_contents',['../classvg_1_1VCFTraversalFinder.html#a3ce22629a99aae20002c43c7e581c2fb',1,'vg::VCFTraversalFinder']]],
- ['get_5fhaplotype_5fcount_2202',['get_haplotype_count',['../classhaplo_1_1ScoreProvider.html#aac21ae0e24c45170e81b4880f8c21f8d',1,'haplo::ScoreProvider::get_haplotype_count()'],['../classhaplo_1_1GBWTScoreProvider.html#a8aedfce11f295af0fba3ae7f17f20c9b',1,'haplo::GBWTScoreProvider::get_haplotype_count()']]],
- ['get_5fhaplotypes_5fwith_5fsnarl_2203',['get_haplotypes_with_snarl',['../classvg_1_1PhasedGenome.html#a81cff23c8687f759dd464fca51cf306e',1,'vg::PhasedGenome']]],
- ['get_5fhelp_2204',['get_help',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a9880c67cbeb3f5b7ba3bad714844702c',1,'vg::subcommand::BaseOptionGroup::get_help()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a958199095b53020a85a5abc2ae1f0a91',1,'vg::subcommand::OptionGroup::get_help()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a01f89740d89e82cf12c204c28ec01fd2',1,'vg::subcommand::GroupedOptionGroup::get_help()']]],
- ['get_5fid_2205',['get_id',['../classvg_1_1DagifiedGraph.html#ae510cacf154e272f63b37a3207046c96',1,'vg::DagifiedGraph::get_id()'],['../classvg_1_1DozeuPinningOverlay.html#ad84aae5d9cce852e254d5da05da40fa8',1,'vg::DozeuPinningOverlay::get_id()'],['../classvg_1_1ExtraNodeGraph.html#aef3ca5fb2071fdb33a7a8f663473de32',1,'vg::ExtraNodeGraph::get_id()'],['../classvg_1_1SnarlGraph.html#aba421b2e2cd40a7d489c13e0ab81f179',1,'vg::SnarlGraph::get_id()'],['../classvg_1_1IdentityOverlay.html#ab144f5ecbf4a5f49a5ffbea80ebd56ec',1,'vg::IdentityOverlay::get_id()'],['../classvg_1_1IncrementalSubgraph.html#a825edf9eddd3fa6093f2045656ae98f1',1,'vg::IncrementalSubgraph::get_id()'],['../classvg_1_1IndexedVG.html#ad23ba69aad4d8c94f58319bb657e3235',1,'vg::IndexedVG::get_id()'],['../classvg_1_1MemoizingGraph.html#a23b6df961f0e8253fba88423f2bcf128',1,'vg::MemoizingGraph::get_id()'],['../classvg_1_1NullMaskingGraph.html#a541f81de46db62d5e8f37e3cfc51f08e',1,'vg::NullMaskingGraph::get_id()'],['../classvg_1_1PathSubgraph.html#a47ff1fe374dccd07542ed1523327553e',1,'vg::PathSubgraph::get_id()'],['../classvg_1_1ReverseGraph.html#aef09dbb8dd08735bdd123b2a9d0066e0',1,'vg::ReverseGraph::get_id()'],['../classvg_1_1NetGraph.html#a9964476cfff61404eeb9d65cc182aa4a',1,'vg::NetGraph::get_id()'],['../classvg_1_1SourceSinkOverlay.html#a9c10b6562749e62bc1038ef23e8b9b28',1,'vg::SourceSinkOverlay::get_id()'],['../classvg_1_1JoinedSpliceGraph.html#a716f0b44bb48b6148617dc772d66959c',1,'vg::JoinedSpliceGraph::get_id()'],['../classvg_1_1StrandSplitGraph.html#a07bd24e1ed6a14843ddb87108a11c7f8',1,'vg::StrandSplitGraph::get_id()'],['../classvg_1_1SubHandleGraph.html#af40f7f453c71d4e52273479d0b600612',1,'vg::SubHandleGraph::get_id()'],['../classvg_1_1SubgraphOverlay.html#a301c8016ac2769d041c611cebd738c1e',1,'vg::SubgraphOverlay::get_id()'],['../classvg_1_1SubpathOverlay.html#ab58cd06e1330b752ad55e32878e8e64e',1,'vg::SubpathOverlay::get_id()'],['../classvg_1_1TreeSubgraph.html#ae48a59a93737e729ada7660a39fafa50',1,'vg::TreeSubgraph::get_id()'],['../classvg_1_1VG.html#a6f4b9ac16f23eb0420544ce8357736a3',1,'vg::VG::get_id()'],['../classxg_1_1XG.html#a0a9d6bce054a3ebf14807869883e9b98',1,'xg::XG::get_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a8150ada3f96723110a2ec7c1ed16323b',1,'handlegraph::algorithms::SubHandleGraph::get_id()'],['../classhandlegraph_1_1HandleGraph.html#adb7f6e144bf2a59679f7b2eddad934eb',1,'handlegraph::HandleGraph::get_id()'],['../namespacevg.html#ae4370b5cb4b42e8556b0fbc793fbdfc0',1,'vg::get_id()'],['../namespacexg.html#a5aab54915cd81fa71fd2ebc3b9e52fb8',1,'xg::get_id()']]],
- ['get_5fidentifier_2206',['get_identifier',['../classvg_1_1IndexFile.html#a0dde670fabfa3890d26c9e89c8564429',1,'vg::IndexFile::get_identifier()'],['../classvg_1_1ZipCode.html#a9cb3141131af81b42741bc9e7349e58b',1,'vg::ZipCode::get_identifier()']]],
- ['get_5findex_2207',['get_index',['../classvg_1_1RepresentativeTraversalFinder.html#a3e15061afb4437ec04334ed77732fa81',1,'vg::RepresentativeTraversalFinder::get_index()'],['../classvg_1_1IndexRegistry.html#a3738a3916a17ca5a2716e7530b10c434',1,'vg::IndexRegistry::get_index(const IndexName &identifier)'],['../classvg_1_1IndexRegistry.html#a2cde822432825ea731fed5318bd94152',1,'vg::IndexRegistry::get_index(const IndexName &identifier) const']]],
- ['get_5findexes_2208',['get_indexes',['../classvg_1_1RewindPlanException.html#a80a898014c62738052c18e85a0403a24',1,'vg::RewindPlanException']]],
- ['get_5finput_5ffile_2209',['get_input_file',['../namespacevg.html#ab1b8b686ef6eca09515be1abe566c013',1,'vg::get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)'],['../namespacevg.html#a09969fef23098c7729a2f190cecb4694',1,'vg::get_input_file(const string &file_name, function< void(istream &)> callback)']]],
- ['get_5finput_5ffile_5fname_2210',['get_input_file_name',['../namespacevg.html#a5026b599b1094a6c8e157f23b204b09b',1,'vg']]],
- ['get_5finward_5fbacking_5fhandle_2211',['get_inward_backing_handle',['../classvg_1_1NetGraph.html#adc4841db50e7f3073cad16d59426ba5a',1,'vg::NetGraph']]],
- ['get_5firregular_5fsnarl_5fcode_2212',['get_irregular_snarl_code',['../classvg_1_1ZipCode.html#a2057ff4f25f04aa76066c3c5a83239fc',1,'vg::ZipCode']]],
- ['get_5fis_5fcircular_2213',['get_is_circular',['../classvg_1_1MemoizingGraph.html#a2fb48c82bc92aa1fa263a4be92e21891',1,'vg::MemoizingGraph::get_is_circular()'],['../classvg_1_1PathSubgraphOverlay.html#ac33d15bc06e31045d07ecf22e018f0a8',1,'vg::PathSubgraphOverlay::get_is_circular()'],['../classvg_1_1VG.html#a1463f13c63b965a3663932e6fa87537e',1,'vg::VG::get_is_circular()'],['../classxg_1_1XG.html#a841e1c50686d3ea941fb9a01d9639784',1,'xg::XG::get_is_circular()'],['../classhandlegraph_1_1PathHandleGraph.html#a9391c34d9f0c16b21d5bb3bb7ec772e4',1,'handlegraph::PathHandleGraph::get_is_circular()']]],
- ['get_5fis_5flooping_5fchain_2214',['get_is_looping_chain',['../classvg_1_1ZipCode.html#a2c0fa7d7130b57bee9b557750eb97eab',1,'vg::ZipCode::get_is_looping_chain()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#ac917c5b03c10bd9e57b344a708c6b033',1,'vg::ZipCode::chain_code_t::get_is_looping_chain()']]],
- ['get_5fis_5fpaired_2215',['get_is_paired',['../classvg_1_1ReadFilter.html#a8b78c03c1379b1ed5576db5c6772adb3',1,'vg::ReadFilter::get_is_paired(const Read &read) const'],['../classvg_1_1ReadFilter.html#aaf6db93c73e3030a098aa54a21416cd7',1,'vg::ReadFilter::get_is_paired(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#a1aa38e8c41e26d7932caa918cfcfe76e',1,'vg::ReadFilter::get_is_paired(const MultipathAlignment &mp_aln) const']]],
- ['get_5fis_5frev_2216',['get_is_rev',['../namespacevg.html#a1919abd090eae3a01120e0859d434ed9',1,'vg::get_is_rev()'],['../namespacexg.html#aca811d060bb9ddd2ff278e107c882e49',1,'xg::get_is_rev()']]],
- ['get_5fis_5freverse_2217',['get_is_reverse',['../classvg_1_1DagifiedGraph.html#a0a5fa33f94733bb8470ccbc49e608a0d',1,'vg::DagifiedGraph::get_is_reverse()'],['../classvg_1_1DozeuPinningOverlay.html#a02b35f6198096c08f660df1170d556b4',1,'vg::DozeuPinningOverlay::get_is_reverse()'],['../classvg_1_1ExtraNodeGraph.html#ab3b496b4e1d8067cd7ed0e0ae9fb0aa9',1,'vg::ExtraNodeGraph::get_is_reverse()'],['../classvg_1_1SnarlGraph.html#a9deed0e8a0312d6ff12868e86c83cc0f',1,'vg::SnarlGraph::get_is_reverse()'],['../classvg_1_1IdentityOverlay.html#aa7bba299ded8eb2fff2af0adeb52000b',1,'vg::IdentityOverlay::get_is_reverse()'],['../classvg_1_1IncrementalSubgraph.html#ad4282dc0e503dc17e3724a41dbb0462c',1,'vg::IncrementalSubgraph::get_is_reverse()'],['../classvg_1_1IndexedVG.html#acf50f1ad8e40ac18d8a5469d63155a50',1,'vg::IndexedVG::get_is_reverse()'],['../classvg_1_1MemoizingGraph.html#aac8372783c6657f5473b1d33b4495e7c',1,'vg::MemoizingGraph::get_is_reverse()'],['../classvg_1_1NullMaskingGraph.html#ab99a483165208a4aabc1e2275f126a18',1,'vg::NullMaskingGraph::get_is_reverse()'],['../classvg_1_1PathSubgraph.html#a5305f2276ec4eecae4a59a4892cb63ab',1,'vg::PathSubgraph::get_is_reverse()'],['../classvg_1_1ReverseGraph.html#aaa65f6a0677677af70608a0294ec36f5',1,'vg::ReverseGraph::get_is_reverse()'],['../classvg_1_1NetGraph.html#a4581f8ffa5738a409e9e856f15c48a99',1,'vg::NetGraph::get_is_reverse()'],['../classvg_1_1SourceSinkOverlay.html#a274359d605130e8efec7c14791d5044b',1,'vg::SourceSinkOverlay::get_is_reverse()'],['../classvg_1_1JoinedSpliceGraph.html#a7179e1f5120aebb9670120b6cddf51ca',1,'vg::JoinedSpliceGraph::get_is_reverse()'],['../classvg_1_1StrandSplitGraph.html#a2882b925a09ba0ee35cdf8bdac0c4605',1,'vg::StrandSplitGraph::get_is_reverse()'],['../classvg_1_1SubHandleGraph.html#a050d46f68a21d9169d17a6e9580a542f',1,'vg::SubHandleGraph::get_is_reverse()'],['../classvg_1_1SubgraphOverlay.html#a797e1524539c9c96ef96dc5454d35c3a',1,'vg::SubgraphOverlay::get_is_reverse()'],['../classvg_1_1SubpathOverlay.html#ae1560abd95e0a6e64306622a68f7e6ac',1,'vg::SubpathOverlay::get_is_reverse()'],['../classvg_1_1TreeSubgraph.html#aa581eda84f6ae51edb0363b76075fe47',1,'vg::TreeSubgraph::get_is_reverse()'],['../classvg_1_1VG.html#a53e796617804bffe0203e422f2a23148',1,'vg::VG::get_is_reverse()'],['../classxg_1_1XG.html#a7a52d5c8396e40930cfed5f79ea9c201',1,'xg::XG::get_is_reverse()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade72d1d3264d1022227c44edc9329a26',1,'handlegraph::algorithms::SubHandleGraph::get_is_reverse()'],['../classhandlegraph_1_1HandleGraph.html#a92773f90eb58f18adb9418a4440223c1',1,'handlegraph::HandleGraph::get_is_reverse()']]],
- ['get_5fis_5freversed_2218',['get_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#ae65abc62608f0643537bacfa78e0e7aa',1,'vg::ZipCode::node_code_t::get_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae6b247dcfb508636f982df6b3353001e',1,'vg::ZipCode::snarl_code_t::get_is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a79691714f5f3bb06aed0d1a7a4b646ee',1,'vg::ZipCodeTree::tree_item_t::get_is_reversed()']]],
- ['get_5fis_5freversed_5fin_5fparent_2219',['get_is_reversed_in_parent',['../classvg_1_1ZipCode.html#af27a1ca0026e32e588d0bb3b62a5bade',1,'vg::ZipCode']]],
- ['get_5fitem_2220',['get_item',['../classvg_1_1Funnel.html#a5f8f988df65fc91adc7da9dd8d4446ef',1,'vg::Funnel']]],
- ['get_5fitem_5fat_5findex_2221',['get_item_at_index',['../classvg_1_1ZipCodeTree.html#a66ff501bf5fa0044978550b188691068',1,'vg::ZipCodeTree']]],
- ['get_5fiterator_2222',['get_iterator',['../structvg_1_1subcommand_1_1TickChainLink.html#aa21e2c735dba10a3b97c739d66008937',1,'vg::subcommand::TickChainLink']]],
- ['get_5flast_5fchain_5fcomponent_2223',['get_last_chain_component',['../classvg_1_1ZipCode.html#aaf980083db4440866ee59d2a1b89e957',1,'vg::ZipCode']]],
- ['get_5flast_5fcomponent_2224',['get_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa98d04c4d61201facf9e01c189b44f43',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fleaves_2225',['get_leaves',['../classvg_1_1WFATree.html#adea6d9333092f49afcc26f34e4bfc016',1,'vg::WFATree']]],
- ['get_5flength_2226',['get_length',['../classvg_1_1DagifiedGraph.html#a5feaa48467ad288848fb2d1ffcd29fc1',1,'vg::DagifiedGraph::get_length()'],['../classvg_1_1DozeuPinningOverlay.html#a0d9fc0dbb4e18cfe9d7496b72d0f63fb',1,'vg::DozeuPinningOverlay::get_length()'],['../classvg_1_1ExtraNodeGraph.html#ab4385934c980deef266d30118b83a4df',1,'vg::ExtraNodeGraph::get_length()'],['../classvg_1_1SnarlGraph.html#ac521452a597e9159b8c281cc49239ccb',1,'vg::SnarlGraph::get_length()'],['../classvg_1_1IdentityOverlay.html#a659b0f5b71286479ef910bd984c525e6',1,'vg::IdentityOverlay::get_length()'],['../classvg_1_1IncrementalSubgraph.html#a84ee16f64d60195d6ead2a57933af720',1,'vg::IncrementalSubgraph::get_length()'],['../classvg_1_1IndexedVG.html#a235824616974770831a2ce006a954bbe',1,'vg::IndexedVG::get_length()'],['../classvg_1_1MemoizingGraph.html#ab5f66c5dae9ddc74750cb86595fef07e',1,'vg::MemoizingGraph::get_length()'],['../classvg_1_1NullMaskingGraph.html#a2144c791b97d05bf625a50442649def2',1,'vg::NullMaskingGraph::get_length()'],['../classvg_1_1PathSubgraph.html#a777f23f7156addc72dd508d08f069cc7',1,'vg::PathSubgraph::get_length()'],['../classvg_1_1ReadFilter.html#ae2ef22beb751d9415759fc1985da1946',1,'vg::ReadFilter::get_length()'],['../classvg_1_1ReverseGraph.html#a54f7adad266466143efaa59270432d8f',1,'vg::ReverseGraph::get_length()'],['../classvg_1_1NetGraph.html#a8170045aa0032b33628858c0717cc74a',1,'vg::NetGraph::get_length()'],['../classvg_1_1SourceSinkOverlay.html#a03f1de876e4731012b5e7168556d5236',1,'vg::SourceSinkOverlay::get_length()'],['../classvg_1_1JoinedSpliceGraph.html#aafba33cc8aa854fb9dc8d654bb2a3325',1,'vg::JoinedSpliceGraph::get_length()'],['../classvg_1_1StrandSplitGraph.html#a46c7611ab9f71f86e3192a34406860b4',1,'vg::StrandSplitGraph::get_length()'],['../classvg_1_1SubHandleGraph.html#a829ddac36b7fcb67ca87c058fe691a88',1,'vg::SubHandleGraph::get_length()'],['../classvg_1_1SubgraphOverlay.html#a5bc6640c35b21807f14332a51f84a2d9',1,'vg::SubgraphOverlay::get_length()'],['../classvg_1_1SubpathOverlay.html#ae15f1a187d3bf9a590f173fdf4bd8f9b',1,'vg::SubpathOverlay::get_length()'],['../classvg_1_1TreeSubgraph.html#ac6d8e68e5bff645f58f741291a810abe',1,'vg::TreeSubgraph::get_length()'],['../classvg_1_1VG.html#aff75e522e40559f5a5257a5cef776cdc',1,'vg::VG::get_length()'],['../classvg_1_1ZipCode.html#a8a5fd40be34ed83736e027a3ca6d9889',1,'vg::ZipCode::get_length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#ad67b89184b6f5d83cb888b5f14647ae3',1,'vg::ZipCode::node_code_t::get_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a214243244b7e99dfe24df8665860dbb2',1,'vg::ZipCode::chain_code_t::get_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa80045f926e1bfde2fb07e2c2e442732',1,'vg::ZipCode::snarl_code_t::get_length()'],['../classxg_1_1XG.html#aa52bb123eca4dbff84b316a7f56a98cc',1,'xg::XG::get_length()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af858e2c9467b674d836879d39f049a05',1,'handlegraph::algorithms::SubHandleGraph::get_length()'],['../classhandlegraph_1_1HandleGraph.html#a569ff35fb85c725b0b6b6933ed303e49',1,'handlegraph::HandleGraph::get_length()']]],
- ['get_5flocus_5fname_2227',['get_locus_name',['../classhandlegraph_1_1PathMetadata.html#aeea07376b756bc5410dacf86f2c3983d',1,'handlegraph::PathMetadata']]],
- ['get_5flog10_5fprob_5fof_5fdisruption_5fin_5finterval_2228',['get_log10_prob_of_disruption_in_interval',['../classvg_1_1MinimizerMapper.html#a4a680ca76191f68a70d17af1e0548f60',1,'vg::MinimizerMapper']]],
- ['get_5flong_2229',['get_long',['../classvg_1_1Version.html#a5132823f48bf6019f1b94ace3a479de4',1,'vg::Version']]],
- ['get_5flong_5foption_2230',['get_long_option',['../classvg_1_1OptionInterface.html#afba994fe31561a26b7495e78d9423679',1,'vg::OptionInterface::get_long_option()'],['../classvg_1_1BaseOption.html#ad990f7324262866fbc67f6e8adeeecfd',1,'vg::BaseOption::get_long_option()']]],
- ['get_5fmagic_5fnumber_2231',['get_magic_number',['../classvg_1_1ZipCodeCollection.html#a59d0bd8bac747766d3471225e5a6ae05',1,'vg::ZipCodeCollection::get_magic_number()'],['../classxg_1_1XG.html#ac8ed9c987e2693c548ad834b39df7a80',1,'xg::XG::get_magic_number()'],['../classhandlegraph_1_1Serializable.html#a8879f13f2204a80a6c428883187961db',1,'handlegraph::Serializable::get_magic_number()']]],
- ['get_5fmagic_5fnumber_5fas_5fstring_2232',['get_magic_number_as_string',['../classvg_1_1ZipCodeCollection.html#a6ee9653e5766e260ca6c903ca0920265',1,'vg::ZipCodeCollection']]],
- ['get_5fmain_2233',['get_main',['../classvg_1_1subcommand_1_1Subcommand.html#a5a7af092ca69792ed2543bbcc3847ad4',1,'vg::subcommand::Subcommand']]],
- ['get_5fmapping_2234',['get_mapping',['../classvg_1_1PhaseUnfolder.html#aae984d6ac43200dc82e6ef3066e01f15',1,'vg::PhaseUnfolder']]],
- ['get_5fmapq_2235',['get_mapq',['../classvg_1_1ReadFilter.html#a0550e932f7becd1fbccd46787b580216',1,'vg::ReadFilter']]],
- ['get_5fmax_5frss_5fkb_2236',['get_max_rss_kb',['../namespacevg.html#a546b60e87f7fc326074f6dcf2cdd0659',1,'vg']]],
- ['get_5fmax_5fvmem_5fkb_2237',['get_max_vmem_kb',['../namespacevg.html#a917d8892f93a31e2d8c3161de264fea1',1,'vg']]],
- ['get_5fmetavar_2238',['get_metavar',['../namespacevg_1_1subcommand.html#accfa400696eb815cf8c43d0909c0350f',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20bool_20_3e_2239',['get_metavar< bool >',['../namespacevg_1_1subcommand.html#a901fbf8366695921cb7844ee2da2d2a2',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20double_20_3e_2240',['get_metavar< double >',['../namespacevg_1_1subcommand.html#a6ab814763fe6f21091083e68bcf47a92',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20int_20_3e_2241',['get_metavar< int >',['../namespacevg_1_1subcommand.html#ac4cbf20c4fbaa1109469f8a358e1a213',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20int8_5ft_20_3e_2242',['get_metavar< int8_t >',['../namespacevg_1_1subcommand.html#a4945a3300d2d189e4c7fa6ad5d27ddf6',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20size_5ft_20_3e_2243',['get_metavar< size_t >',['../namespacevg_1_1subcommand.html#aebb27d4a98b972c03f63c8715bbd706c',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20std_3a_3astring_20_3e_2244',['get_metavar< std::string >',['../namespacevg_1_1subcommand.html#a1615e3bd0398f56dfcdd1c9dfb864ec9',1,'vg::subcommand']]],
- ['get_5fmin_5fbase_5fqual_5ffraction_2245',['get_min_base_qual_fraction',['../classvg_1_1ReadFilter.html#ad2ca26c062585494f69520f9997d34eb',1,'vg::ReadFilter']]],
- ['get_5fmin_5fnode_5fsupport_2246',['get_min_node_support',['../classvg_1_1TraversalSupportFinder.html#ad166403d1a92690fe10e976d9789c065',1,'vg::TraversalSupportFinder::get_min_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a5a19f9777ecf01f0e8ea86870a993aea',1,'vg::PackedTraversalSupportFinder::get_min_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aeeb7ecc5e9a3fa6f5030d3d41a436c59',1,'vg::CachedPackedTraversalSupportFinder::get_min_node_support()']]],
- ['get_5fmin_5fposition_2247',['get_min_position',['../classvg_1_1StreamSorter.html#a4240a47a167f22d3815de6fe976420b5',1,'vg::StreamSorter']]],
- ['get_5fmin_5ftotal_5fsupport_5ffor_5fcall_2248',['get_min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#ac7e36771ace6cf84d9f4f732cdbc692f',1,'vg::SupportBasedSnarlCaller']]],
- ['get_5fmutable_2249',['get_mutable',['../structvg_1_1Annotation.html#a065db30c6b14ca2938254d603777e5c8',1,'vg::Annotation']]],
- ['get_5fn_5fbins_2250',['get_n_bins',['../classvg_1_1Packer.html#a01716de1dc4501804d81fc38256dd2b5',1,'vg::Packer']]],
- ['get_5fname_2251',['get_name',['../classvg_1_1Configurable.html#aee830d6a5cdcf8e7a2896a443bcc80cc',1,'vg::Configurable::get_name()'],['../structvg_1_1TranscriptPath.html#a0adaddaa3b952ed1f06bd7029673d2aa',1,'vg::TranscriptPath::get_name()'],['../classvg_1_1subcommand_1_1Subcommand.html#ab6c41ce3fe77e286f2caa1672b553293',1,'vg::subcommand::Subcommand::get_name()'],['../haplotypes__main_8cpp.html#a3781abae7c3253f254c4e795863d0c09',1,'get_name(): haplotypes_main.cpp']]],
- ['get_5fnet_2252',['get_net',['../classhandlegraph_1_1SnarlDecomposition.html#a84b4951e1bf931d03539ac6e048fdb98',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fnet_5fgraph_2253',['get_net_graph',['../classvg_1_1GenomeState.html#ad07741efc2a949dd69aee266dbb4500b',1,'vg::GenomeState']]],
- ['get_5fnet_5fhandle_2254',['get_net_handle',['../classvg_1_1ZipCode.html#a051a9144646b660f213fe44d5b123d77',1,'vg::ZipCode']]],
- ['get_5fnet_5fhandle_5fslow_2255',['get_net_handle_slow',['../classvg_1_1ZipCode.html#ad1d40ef72bc5fa0f9e0e933add4265a2',1,'vg::ZipCode']]],
- ['get_5fnext_5falignment_5ffrom_5ffastq_2256',['get_next_alignment_from_fastq',['../namespacevg.html#aca76d8e219f90833fdabe3528c3c6441',1,'vg']]],
- ['get_5fnext_5falignment_5fpair_5ffrom_5ffastqs_2257',['get_next_alignment_pair_from_fastqs',['../namespacevg.html#a3255bd8bf9846a34da799947f7642dc7',1,'vg']]],
- ['get_5fnext_5finterleaved_5falignment_5fpair_5ffrom_5ffastq_2258',['get_next_interleaved_alignment_pair_from_fastq',['../namespacevg.html#ab58cf3da638d7e8833a14ef801c7e2db',1,'vg']]],
- ['get_5fnext_5finterleaved_5frecord_5fpair_5ffrom_5fgaf_2259',['get_next_interleaved_record_pair_from_gaf',['../namespacevg_1_1io.html#a0f27b2a472320e0e45a130b73827d1fd',1,'vg::io']]],
- ['get_5fnext_5fintervals_2260',['get_next_intervals',['../classvg_1_1ZipCodeForest.html#a2c9a60acfcb3f8521eeb7bbf5e36007b',1,'vg::ZipCodeForest']]],
- ['get_5fnext_5fnode_5frecalc_5fdegrees_2261',['get_next_node_recalc_degrees',['../classvg_1_1FlowSort.html#a1fac8545c184446eee5cae0f55567b1f',1,'vg::FlowSort']]],
- ['get_5fnext_5frank_2262',['get_next_rank',['../classvg_1_1Paths.html#aad2977756f0166a341fb488cd5c6a9b0',1,'vg::Paths']]],
- ['get_5fnext_5frecord_5ffrom_5fgaf_2263',['get_next_record_from_gaf',['../namespacevg_1_1io.html#aa357ed5eaa447e495149c7bd7df356b9',1,'vg::io']]],
- ['get_5fnext_5frecord_5fpair_5ffrom_5fgaf_2264',['get_next_record_pair_from_gaf',['../namespacevg_1_1io.html#ab11e877e850b127b8004e7223cc77247',1,'vg::io']]],
- ['get_5fnext_5fstep_2265',['get_next_step',['../classvg_1_1MemoizingGraph.html#a91e5d4f1ce3028d58c162adf8d19e70f',1,'vg::MemoizingGraph::get_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a2e18088c831f6757a4eafa7d862d0329',1,'vg::PathSubgraphOverlay::get_next_step()'],['../classvg_1_1VG.html#a144fb8b69eb2274b8dcea914898919f0',1,'vg::VG::get_next_step()'],['../classxg_1_1XG.html#a6595e2654ee4955763a08ab51780941a',1,'xg::XG::get_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a209786f5c9e2c0210b383f2022ee221f',1,'handlegraph::PathHandleGraph::get_next_step()']]],
- ['get_5fnode_2266',['get_node',['../classvg_1_1VG.html#a95223ec6984efc003e5cac69acd43445',1,'vg::VG::get_node(nid_t id)'],['../classvg_1_1VG.html#aa264e9386b98b57c3549a56870d8e29e',1,'vg::VG::get_node(nid_t id) const']]],
- ['get_5fnode_5fat_5fnucleotide_2267',['get_node_at_nucleotide',['../classvg_1_1VG.html#a07462d3f895e77cb407695e6c8e85727',1,'vg::VG']]],
- ['get_5fnode_5fby_5fid_2268',['get_node_by_id',['../structvg_1_1algorithms_1_1Graph.html#a6113178f0138c18d19ed32a08a4a474e',1,'vg::algorithms::Graph']]],
- ['get_5fnode_5fcode_2269',['get_node_code',['../classvg_1_1ZipCode.html#a1a37e35bfbd8910f64b95906f2930e28',1,'vg::ZipCode']]],
- ['get_5fnode_5fcount_2270',['get_node_count',['../classvg_1_1DagifiedGraph.html#a46afdba1fbffa6ffebce5966a1829918',1,'vg::DagifiedGraph::get_node_count()'],['../classvg_1_1DozeuPinningOverlay.html#ab324121c34fdc2ab5edfaf742f26280d',1,'vg::DozeuPinningOverlay::get_node_count()'],['../classvg_1_1ExtraNodeGraph.html#a0c55bc093996c9148a3b6c4e46634759',1,'vg::ExtraNodeGraph::get_node_count()'],['../classvg_1_1SnarlGraph.html#aa797abb0b6518ca38b557759d074cd33',1,'vg::SnarlGraph::get_node_count()'],['../classvg_1_1IdentityOverlay.html#a9a58eb7938308dad847ded70b1abec56',1,'vg::IdentityOverlay::get_node_count()'],['../classvg_1_1IncrementalSubgraph.html#a076dbda3b4b724157cad61f5f7b76b2b',1,'vg::IncrementalSubgraph::get_node_count()'],['../classvg_1_1IndexedVG.html#aa275aa5b547bf464b95ce162e9a2fcd5',1,'vg::IndexedVG::get_node_count()'],['../classvg_1_1MemoizingGraph.html#a4276a59439fc7edc984fe6e666e3b69e',1,'vg::MemoizingGraph::get_node_count()'],['../classvg_1_1NullMaskingGraph.html#a7a7eeb58c5787789e6b8ae8a9e58101b',1,'vg::NullMaskingGraph::get_node_count()'],['../classvg_1_1PathSubgraph.html#a52f431143ff624475a16629fa46898f0',1,'vg::PathSubgraph::get_node_count()'],['../classvg_1_1ReverseGraph.html#a075661952d5a567b1e09ad9a5624c5a7',1,'vg::ReverseGraph::get_node_count()'],['../classvg_1_1NetGraph.html#a49f4b9958557920e8b81c3f6b6c62de2',1,'vg::NetGraph::get_node_count()'],['../classvg_1_1SourceSinkOverlay.html#ac49954276cde4384262f3501f4ed70ce',1,'vg::SourceSinkOverlay::get_node_count()'],['../classvg_1_1JoinedSpliceGraph.html#a15ac4bff9b6862ec0d7c6cefabb916c9',1,'vg::JoinedSpliceGraph::get_node_count()'],['../classvg_1_1StrandSplitGraph.html#a2a4f01cb39da9b46431a7ea3b46f540f',1,'vg::StrandSplitGraph::get_node_count()'],['../classvg_1_1SubHandleGraph.html#a0ea741c8d98e8c12b9f83b3427bee115',1,'vg::SubHandleGraph::get_node_count()'],['../classvg_1_1SubgraphOverlay.html#a40d036bc03e5bb02b1b0fe657b283b2b',1,'vg::SubgraphOverlay::get_node_count()'],['../classvg_1_1SubpathOverlay.html#a1d0208a9cfe646b6d25741c2bbfbd4b3',1,'vg::SubpathOverlay::get_node_count()'],['../classvg_1_1TreeSubgraph.html#a63dd0c1a1fce7a59a563be0448085246',1,'vg::TreeSubgraph::get_node_count()'],['../classvg_1_1VG.html#a495649c1646b865d6c88b8dc126589b0',1,'vg::VG::get_node_count()'],['../classxg_1_1XG.html#ae7b3b8008c6779aafb72b8e2fc47d4a1',1,'xg::XG::get_node_count()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0c17ba8c59000d2562fb0318a1faaa7c',1,'handlegraph::algorithms::SubHandleGraph::get_node_count()'],['../classhandlegraph_1_1HandleGraph.html#a9f95108e6c3f68f404fa93bd3306e4c6',1,'handlegraph::HandleGraph::get_node_count()']]],
- ['get_5fnode_5fdegree_2271',['get_node_degree',['../classvg_1_1FlowSort.html#a033cbc4da28f5ad6c3be63374eb55ac3',1,'vg::FlowSort']]],
- ['get_5fnode_5fids_2272',['get_node_ids',['../structvg_1_1algorithms_1_1Graph.html#afe478cbb3ccb5f5125b59467db143b59',1,'vg::algorithms::Graph']]],
- ['get_5fnode_5flength_2273',['get_node_length',['../classvg_1_1Mapper.html#a99717b5d61b6db599c177b8bafcb6dd8',1,'vg::Mapper']]],
- ['get_5fnode_5fmapping_2274',['get_node_mapping',['../classvg_1_1Paths.html#a6314d7f8036a65b31d4dfac643bc3598',1,'vg::Paths::get_node_mapping(Node *n)'],['../classvg_1_1Paths.html#a7fa795ccee1427d6cac6e44fafe41e1e',1,'vg::Paths::get_node_mapping(id_t id)'],['../classvg_1_1Paths.html#a99f8491f18c0ccaf1bb7b7bf45500517',1,'vg::Paths::get_node_mapping(id_t id) const']]],
- ['get_5fnode_5fmapping_5fby_5fpath_5fname_2275',['get_node_mapping_by_path_name',['../classvg_1_1Paths.html#a9c9cf2b7f26c788195812e2b8170a6ce',1,'vg::Paths::get_node_mapping_by_path_name(Node *n)'],['../classvg_1_1Paths.html#a72c6a29a41521996fd3454170b1a76f6',1,'vg::Paths::get_node_mapping_by_path_name(id_t id)']]],
- ['get_5fnode_5fmapping_5fcopies_5fby_5frank_2276',['get_node_mapping_copies_by_rank',['../classvg_1_1Paths.html#a36a26abe18d10e17e273fa658be9d5c6',1,'vg::Paths']]],
- ['get_5fnode_5fmappings_5fby_5frank_2277',['get_node_mappings_by_rank',['../classvg_1_1Paths.html#a5a40b701389bcc2c513083b02f17b4f4',1,'vg::Paths']]],
- ['get_5fnode_5fnid_5fto_5fvariant_2278',['get_node_nid_to_variant',['../classvg_1_1VG.html#a52fa15aebd7d190eb743311f31037e55',1,'vg::VG']]],
- ['get_5fnode_5foffset_2279',['get_node_offset',['../classvg_1_1GaplessExtender.html#a12663a32f4bc41137eb372c845f0eafe',1,'vg::GaplessExtender']]],
- ['get_5fnode_5fsupport_2280',['get_node_support',['../classvg_1_1RepresentativeTraversalFinder.html#a40f64596e2e8bb4b78120f351fa3bf79',1,'vg::RepresentativeTraversalFinder']]],
- ['get_5fnodes_2281',['get_nodes',['../classvg_1_1ContractingGraph.html#a9c960fb16e62bc152fcf2f4230eead9c',1,'vg::ContractingGraph::get_nodes()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a932649a134317ad387ee70adc03d4474',1,'vg::SnarlDistanceIndexClusterer::get_nodes()']]],
- ['get_5fnon_5fhts_5falignment_5femitter_2282',['get_non_hts_alignment_emitter',['../namespacevg_1_1io.html#a2f9f4db8b0374c57d2963881784c40d3',1,'vg::io']]],
- ['get_5fnonoverlapping_2283',['get_nonoverlapping',['../classvg_1_1WindowedVcfBuffer.html#a63b89391977d77c5320003d0e0f70469',1,'vg::WindowedVcfBuffer']]],
- ['get_5fnum_5fsamples_2284',['get_num_samples',['../namespacevg.html#afe9d79548464e7842327275008447299',1,'vg']]],
- ['get_5foffset_2285',['get_offset',['../namespacevg.html#af826519a2b2e0cf58394e35d7ab7b84c',1,'vg::get_offset()'],['../namespacexg.html#a6e76d42101c987bf595a807522766cfa',1,'xg::get_offset()']]],
- ['get_5foffset_5fin_5fchain_2286',['get_offset_in_chain',['../classvg_1_1ZipCode.html#a5d8b333ee954fa9a513b6190e1910843',1,'vg::ZipCode']]],
- ['get_5fon_5fstrand_5fdistance_5ftree_2287',['get_on_strand_distance_tree',['../classvg_1_1OrientedDistanceClusterer.html#a736cd908b11ed3a000698291c541bbc0',1,'vg::OrientedDistanceClusterer']]],
- ['get_5foption_5fid_2288',['get_option_id',['../namespacevg_1_1subcommand.html#a7e03678789f1a34608294f43e1047457',1,'vg::subcommand']]],
- ['get_5foption_5fstruct_2289',['get_option_struct',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a58bddced5eb3503314ae1f7ef2bd60d1',1,'vg::subcommand::BaseArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aeeb773f962b7de9459a67f2b74cce151',1,'vg::subcommand::ValueArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a4287432c965cf788c3619aa13634c613',1,'vg::subcommand::FlagArgSpec::get_option_struct()']]],
- ['get_5foption_5fvalue_2290',['get_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#af234d02566c656202396f78df73d35d7',1,'vg::subcommand::BaseOptionGroup']]],
- ['get_5foptions_2291',['get_options',['../classvg_1_1Configurable.html#a553f14c4f4a19bb51d40ffb211945b3a',1,'vg::Configurable']]],
- ['get_5for_5festimate_5fcoverage_2292',['get_or_estimate_coverage',['../namespacevg.html#aba3f6bc9cc27f9c6bb91dc27c7fb28b8',1,'vg']]],
- ['get_5for_5fmake_5fvariant_5fid_2293',['get_or_make_variant_id',['../namespacevg.html#ae9fc5855bb49062ce72e56c805e1545a',1,'vg']]],
- ['get_5foutput_5ffile_5fname_2294',['get_output_file_name',['../namespacevg.html#ae2a0425675c4a85289b230eef2c985b8',1,'vg']]],
- ['get_5foverhang_2295',['get_overhang',['../classvg_1_1ReadFilter.html#a71bb794016b2f59d6495a98b9716e0b5',1,'vg::ReadFilter::get_overhang(const Read &read) const'],['../classvg_1_1ReadFilter.html#a50797c8911ec77ac3a392370a1c91cbe',1,'vg::ReadFilter::get_overhang(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#ab3bff405c9a8994993ea71e0c03b8772',1,'vg::ReadFilter::get_overhang(const MultipathAlignment &mp_aln) const']]],
- ['get_5foverlay_5fhandle_2296',['get_overlay_handle',['../classvg_1_1StrandSplitGraph.html#ab60c1d256ba23abea598861ca7cf7f42',1,'vg::StrandSplitGraph']]],
- ['get_5fparent_2297',['get_parent',['../classhandlegraph_1_1SnarlDecomposition.html#afb665da6af9e2ccfc10e6e667254b91d',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fparent_5fidentifier_2298',['get_parent_identifier',['../classvg_1_1ZipCode.html#a487d7a307e6b728df95581d6d261d526',1,'vg::ZipCode']]],
- ['get_5fparent_5ftraversal_2299',['get_parent_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a2738b92f35c61666df57cd6088f3def1',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fparsed_5fgenotypes_2300',['get_parsed_genotypes',['../classvg_1_1WindowedVcfBuffer.html#a8970a1ba82342645b319a1f7091c6cea',1,'vg::WindowedVcfBuffer']]],
- ['get_5fpath_2301',['get_path',['../classvg_1_1Paths.html#a386fefa3ef22c69bdfa06711ec43ca93',1,'vg::Paths::get_path()'],['../classxg_1_1XG.html#a79017177d025a7608c76a7901da5a463',1,'xg::XG::get_path()'],['../namespacevg.html#a3d972910bf64084a1ee50ca4350c5b59',1,'vg::get_path(const std::vector< handle_t > &first, handle_t second)'],['../namespacevg.html#aa5fc35eee866d216357a5818cd1fb927',1,'vg::get_path(handle_t first, const std::vector< handle_t > &second)'],['../namespacevg.html#a162ed4c8f358ca4c33ab05a27f8349cb',1,'vg::get_path(const std::vector< handle_t > &first, gbwt::node_type second)'],['../namespacevg.html#a66796444cb3b92c35ebeddbb7a9bc6bf',1,'vg::get_path(gbwt::node_type reverse_first, const std::vector< handle_t > &second)']]],
- ['get_5fpath_5fcount_2302',['get_path_count',['../classvg_1_1MemoizingGraph.html#ae0625c7cd87213ce030e03d7373c7216',1,'vg::MemoizingGraph::get_path_count()'],['../classvg_1_1PathSubgraphOverlay.html#a589dea47ddf887c61f88d4ef2f9110a2',1,'vg::PathSubgraphOverlay::get_path_count()'],['../classvg_1_1VG.html#a7b20ecaa6a8a3155b5abb90a3139f6de',1,'vg::VG::get_path_count()'],['../classxg_1_1XG.html#af7b58d4d10af78ac88675a40661967c2',1,'xg::XG::get_path_count()'],['../classhandlegraph_1_1PathHandleGraph.html#acd5df753593ecdfb7aa8c411b98ebad9',1,'handlegraph::PathHandleGraph::get_path_count()']]],
- ['get_5fpath_5fedge_5findex_2303',['get_path_edge_index',['../classvg_1_1PathChunker.html#aef30dd2569597b64d36b19824ebee37f',1,'vg::PathChunker']]],
- ['get_5fpath_5fedges_2304',['get_path_edges',['../classvg_1_1VG.html#a26f160750dfed33c16a257bd5cbecddf',1,'vg::VG']]],
- ['get_5fpath_5fhandle_2305',['get_path_handle',['../classvg_1_1MemoizingGraph.html#ad26dd5209b1364601acf977df6cc52dc',1,'vg::MemoizingGraph::get_path_handle()'],['../classvg_1_1PathSubgraphOverlay.html#a45c63b93ee36ea86ce966aa2f6fc1530',1,'vg::PathSubgraphOverlay::get_path_handle()'],['../classvg_1_1VG.html#a6261550a7c6bbe7eb6ee0976639bc1d7',1,'vg::VG::get_path_handle()'],['../classxg_1_1XG.html#a0cca09a102d01c9f952b857f23f165e1',1,'xg::XG::get_path_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a5d6059d716882a80e3982de17011866e',1,'handlegraph::PathHandleGraph::get_path_handle()']]],
- ['get_5fpath_5fhandle_5fof_5fstep_2306',['get_path_handle_of_step',['../classvg_1_1MemoizingGraph.html#a7a7ec48fc32e5798b58216b3f8fc2624',1,'vg::MemoizingGraph::get_path_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a8a369e743f3f797db333ef04505bb292',1,'vg::PathSubgraphOverlay::get_path_handle_of_step()'],['../classvg_1_1VG.html#aae55721d38d4db3068ca93b4aac8e962',1,'vg::VG::get_path_handle_of_step()'],['../classxg_1_1XG.html#ab12dcc61dc8227d5dfde03b0f6b5ef16',1,'xg::XG::get_path_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a1d1ca9865da585257709f54769f5d6a9',1,'handlegraph::PathHandleGraph::get_path_handle_of_step()'],['../classhandlegraph_1_1PathMetadata.html#a38041ec30b5c66bd94f951f4e61b8bab',1,'handlegraph::PathMetadata::get_path_handle_of_step()']]],
- ['get_5fpath_5fid_2307',['get_path_id',['../classvg_1_1Paths.html#a8fba2fa812589af544a4a0406f78cca7',1,'vg::Paths']]],
- ['get_5fpath_5findex_2308',['get_path_index',['../classvg_1_1GraphSynchronizer.html#aa13b46c21814ff09172452e28a4da71d',1,'vg::GraphSynchronizer']]],
- ['get_5fpath_5flength_2309',['get_path_length',['../classvg_1_1MemoizingGraph.html#a34c10df2b34669fffd3c036636f4f608',1,'vg::MemoizingGraph::get_path_length()'],['../classxg_1_1XG.html#a458bf40b2282e7bd4743781d20f7072b',1,'xg::XG::get_path_length()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#ab71f007638c65db10efbe198f923413b',1,'handlegraph::PathPositionHandleGraph::get_path_length()']]],
- ['get_5fpath_5fname_2310',['get_path_name',['../classvg_1_1MemoizingGraph.html#ad6e5c2da620079ff9fc488a282cb88f9',1,'vg::MemoizingGraph::get_path_name()'],['../classvg_1_1Paths.html#a56b39299430400066796a0332492f7a5',1,'vg::Paths::get_path_name()'],['../classvg_1_1PathSubgraphOverlay.html#a4331971206c3b9cb069b01abad5d965c',1,'vg::PathSubgraphOverlay::get_path_name()'],['../classvg_1_1VG.html#a8ad62c3977b6f38f0b570ea78251dc6d',1,'vg::VG::get_path_name()'],['../classxg_1_1XG.html#acc895561f10e41d82329a45e78bcdbac',1,'xg::XG::get_path_name()'],['../classhandlegraph_1_1PathHandleGraph.html#a565f4312a42dfe77ae14c1ee9ed9f2ba',1,'handlegraph::PathHandleGraph::get_path_name()'],['../classhandlegraph_1_1PathMetadata.html#acf37917fbe8c308de24264854b535018',1,'handlegraph::PathMetadata::get_path_name()']]],
- ['get_5fpath_5fsequence_2311',['get_path_sequence',['../classvg_1_1GraphSynchronizer.html#ac33a770c7ce8206e4649133062333898',1,'vg::GraphSynchronizer']]],
- ['get_5fpayload_5ffrom_5fzip_2312',['get_payload_from_zip',['../classvg_1_1ZipCode.html#a05895f989a23d97b08bd0c1c56bbc3bc',1,'vg::ZipCode']]],
- ['get_5fpayload_5ffrom_5fzipcode_2313',['get_payload_from_zipcode',['../classvg_1_1ZipCode.html#ae9a95e07dd615b3692fe7742990c6c8b',1,'vg::ZipCode']]],
- ['get_5fperipheral_5fattachments_2314',['get_peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#afbd7c2ce70efdcc6c25c20cc7710faa0',1,'vg::GraphSynchronizer::Lock']]],
- ['get_5fphase_5fblock_2315',['get_phase_block',['../classhandlegraph_1_1PathMetadata.html#aadcc53d7a55b54eb2499b66a02500065',1,'handlegraph::PathMetadata']]],
- ['get_5fpos_2316',['get_pos',['../classvg_1_1GaplessExtender.html#a92241e0a9691fc7b06f5258a21d1c9c4',1,'vg::GaplessExtender']]],
- ['get_5fposition_5fof_5fstep_2317',['get_position_of_step',['../classvg_1_1MemoizingGraph.html#ade585496ff8b0d082500a1a76c2b187b',1,'vg::MemoizingGraph::get_position_of_step()'],['../classxg_1_1XG.html#ab6e8ce09a0ed201a56b9f8bd387b4e4d',1,'xg::XG::get_position_of_step()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#a473d58ac35a06551e06ae7f5ad5073be',1,'handlegraph::PathPositionHandleGraph::get_position_of_step()']]],
- ['get_5fpositions_2318',['get_positions',['../classvg_1_1Funnel.html#a617af9590f607720de6a87dfcddbe553',1,'vg::Funnel']]],
- ['get_5fpossible_5ffilenames_2319',['get_possible_filenames',['../classvg_1_1IndexRegistry.html#a6dc3fd500ab65621ad72ae968cedecf0',1,'vg::IndexRegistry']]],
- ['get_5fprefix_2320',['get_prefix',['../classvg_1_1IndexRegistry.html#aa3748affd87c03e3a883ccb9d913eb73',1,'vg::IndexRegistry::get_prefix()'],['../classvg_1_1PhaseUnfolder.html#abae52ee7605f03c82622c63c55463db7',1,'vg::PhaseUnfolder::get_prefix()']]],
- ['get_5fprefix_5fsum_5for_5fidentifier_2321',['get_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#ab2390c393bb641b64ca80183686df54a',1,'vg::ZipCode::node_code_t::get_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34832c0fc381d48cb1424a224f8d9dae',1,'vg::ZipCode::snarl_code_t::get_prefix_sum_or_identifier()']]],
- ['get_5fprevious_5fstep_2322',['get_previous_step',['../classvg_1_1MemoizingGraph.html#a2ceee67be1ab5744fe53de6e1fa5e718',1,'vg::MemoizingGraph::get_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#a5b3b4cb54c2f5fedc9fc4d765c6f8b3a',1,'vg::PathSubgraphOverlay::get_previous_step()'],['../classvg_1_1VG.html#a95d4b19a83f11ac6244855f86555fe76',1,'vg::VG::get_previous_step()'],['../classxg_1_1XG.html#aedec198c2181d7f729c10317e5ca8089',1,'xg::XG::get_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a71040226b29aa5046f4cc04c8c9aa9fb',1,'handlegraph::PathHandleGraph::get_previous_step()']]],
- ['get_5fpriority_2323',['get_priority',['../classvg_1_1subcommand_1_1Subcommand.html#a4dccbaf1dc530dc55b57e1dd9dbc09e1',1,'vg::subcommand::Subcommand']]],
- ['get_5fprob_5fof_5fdisruption_5fin_5fcolumn_2324',['get_prob_of_disruption_in_column',['../classvg_1_1MinimizerMapper.html#a6d4969130b9f7cb75efec316774b8e82',1,'vg::MinimizerMapper']]],
- ['get_5fproc_5fstatus_5fvalue_2325',['get_proc_status_value',['../namespacevg.html#a9fb67697fd1e49bcb389a735ba9fa8f2',1,'vg']]],
- ['get_5fprotobuf_5ftag_2326',['get_protobuf_tag',['../classvg_1_1io_1_1Registry.html#a9ccb7ac94bdb24687992af702d387620',1,'vg::io::Registry']]],
- ['get_5fpruned_5falt_5falleles_2327',['get_pruned_alt_alleles',['../classvg_1_1VCFTraversalFinder.html#a116466101f77d992e54bb3328a42c90b',1,'vg::VCFTraversalFinder']]],
- ['get_5fqual_5fadj_5faligner_2328',['get_qual_adj_aligner',['../classvg_1_1AlignerClient.html#aa84332f52915c20b2f2db1e060736fb5',1,'vg::AlignerClient']]],
- ['get_5fqualities_5fin_5fsnarl_2329',['get_qualities_in_snarl',['../classvg_1_1Genotyper.html#af6518141a6e6f122e5f534c041d16918',1,'vg::Genotyper']]],
- ['get_5fradius_2330',['get_radius',['../classvg_1_1VariantAdder.html#ae974fd5d06287893b0b1f8690624d18f',1,'vg::VariantAdder']]],
- ['get_5frank_5fin_5fsnarl_2331',['get_rank_in_snarl',['../classvg_1_1ZipCode.html#a32750209d049ac9e5fea67c97be1f151',1,'vg::ZipCode']]],
- ['get_5fraw_5fchain_5fcomponent_2332',['get_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a0ab97119fa36e9682bb28118190cb8e4',1,'vg::ZipCode::node_code_t::get_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af202024a5bb84df848c92b06535682c4',1,'vg::ZipCode::snarl_code_t::get_raw_chain_component()']]],
- ['get_5fraw_5fchild_5fcount_2333',['get_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#af740b35df2d7b5cd84b3ab439440e492',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fcode_5ftype_2334',['get_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#abca762bde40792cc01251c5372cd8b61',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fconnectivity_2335',['get_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4f3a37a0ed45286df4f4d3cf254ac376',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fraw_5fdistance_5fend_5fleft_2336',['get_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2619d7eccb0849542a6c8a86bb7937c1',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fdistance_5fend_5fright_2337',['get_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a1fe89643eb1a0f051e5ac71465984a71',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fdistance_5fstart_5fleft_2338',['get_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a39806103fa11d9969668f75045732bec',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fdistance_5fstart_5fright_2339',['get_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a168236545b3436928b1099c1fe572379',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fis_5freversed_2340',['get_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a5009106b8ce3273a9db11d5c177e5760',1,'vg::ZipCode::node_code_t::get_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa00b0cb7326f1fabc61bc7330936f0ee',1,'vg::ZipCode::snarl_code_t::get_raw_is_reversed()']]],
- ['get_5fraw_5flast_5fcomponent_2341',['get_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa3fc8437a85ebad068b816cb2c04d0e3',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fraw_5flength_2342',['get_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ac1eeeb4a44eec49317c89ec69ec5e0',1,'vg::ZipCode::node_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a31621cf955a3423ca4fa85b440597df2',1,'vg::ZipCode::chain_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aabb9e23dfe383bcf8d241675975a80d6',1,'vg::ZipCode::snarl_code_t::get_raw_length()']]],
- ['get_5fraw_5fprefix_5fsum_5for_5fidentifier_2343',['get_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a2382df4c7c2f34b2e538edd9c2c27c66',1,'vg::ZipCode::node_code_t::get_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#adfcdf800c56ed38d46c5d2db8f291e62',1,'vg::ZipCode::snarl_code_t::get_raw_prefix_sum_or_identifier()']]],
- ['get_5fraw_5frecord_5foffset_2344',['get_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04bf6c411365529b20b893c2b30b9f8e',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fsnarl_5frank_5for_5fidentifier_2345',['get_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#af4bfbe05a99156b9cc18446647c88830',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fread_5fcoverage_2346',['get_read_coverage',['../classvg_1_1MinimizerMapper.html#a59563aa4a1d0f00d909edd4cf8b8aa7a',1,'vg::MinimizerMapper']]],
- ['get_5fread_5fdistance_2347',['get_read_distance',['../namespacevg_1_1algorithms.html#a5d8762b533e64039ce1a917b047097d8',1,'vg::algorithms']]],
- ['get_5fread_5ffn_2348',['get_read_fn',['../classvg_1_1io_1_1JSONStreamHelper.html#a549e248d11b13f164c871cbf3ccbf935',1,'vg::io::JSONStreamHelper']]],
- ['get_5fread_5fname_2349',['get_read_name',['../classvg_1_1NGSSimulator.html#a44c1fcd6a665cc7804e561a7c8700a04',1,'vg::NGSSimulator']]],
- ['get_5fread_5foffset_2350',['get_read_offset',['../classvg_1_1GaplessExtender.html#a5c568cad31cb0cc1007ef05183c197ab',1,'vg::GaplessExtender']]],
- ['get_5frecipe_2351',['get_recipe',['../classvg_1_1IndexRegistry.html#a1f378b76124b73c85111a81be74f92b3',1,'vg::IndexRegistry']]],
- ['get_5frecord_5foffset_2352',['get_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae3dde9ebd7b44658b083f4bd372e823f',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fref_5ffollowing_2353',['get_ref_following',['../structhaplo_1_1linear__haplo__structure.html#a2e9ec5540a31571c3daba83abf03d18d',1,'haplo::linear_haplo_structure']]],
- ['get_5fref_5finterval_2354',['get_ref_interval',['../classvg_1_1VCFOutputCaller.html#ab382edfcd67f4f3e73fe032cf8f96b04',1,'vg::VCFOutputCaller']]],
- ['get_5fref_5foffsets_2355',['get_ref_offsets',['../classvg_1_1RatioSupportSnarlCaller.html#a7f838a459153e23e7963a2bd779711de',1,'vg::RatioSupportSnarlCaller::get_ref_offsets()'],['../classvg_1_1TraversalSupportFinder.html#a437e9478fc7551f23246d954af4b0d90',1,'vg::TraversalSupportFinder::get_ref_offsets()']]],
- ['get_5fref_5fposition_2356',['get_ref_position',['../classvg_1_1VCFOutputCaller.html#a9398350530fc4df45918dc1a14eed549',1,'vg::VCFOutputCaller::get_ref_position()'],['../classvg_1_1MCMCCaller.html#a368d2f5dbd85941acceec2a1d7d44d41',1,'vg::MCMCCaller::get_ref_position()']]],
- ['get_5fref_5fpositions_2357',['get_ref_positions',['../classvg_1_1VCFGenotyper.html#a60af53e97463c30ff180d3c1b8356df7',1,'vg::VCFGenotyper']]],
- ['get_5freference_5ftraversal_2358',['get_reference_traversal',['../classvg_1_1LegacyCaller.html#a6d00fa81c7923b88b886f87f28984184',1,'vg::LegacyCaller']]],
- ['get_5fregistry_2359',['get_registry',['../classvg_1_1subcommand_1_1Subcommand.html#a0e3707f1f4e9ce445faea71fddd61a00',1,'vg::subcommand::Subcommand']]],
- ['get_5fregular_5faligner_2360',['get_regular_aligner',['../classvg_1_1AlignerClient.html#a60d4602ba9be4861136af507f8eacaec',1,'vg::AlignerClient']]],
- ['get_5fregular_5fsnarl_5fcode_2361',['get_regular_snarl_code',['../classvg_1_1ZipCode.html#a13c0515e594e7da8c54e29314b1af6a6',1,'vg::ZipCode']]],
- ['get_5frelease_2362',['get_release',['../classvg_1_1Version.html#a3e99ae82ab6bcc07d982012d731e7091',1,'vg::Version']]],
- ['get_5frescue_5fgraph_5ffrom_5fpaths_2363',['get_rescue_graph_from_paths',['../classvg_1_1MultipathMapper.html#a655c6fb1dc987ac5f430007594d7bb42',1,'vg::MultipathMapper']]],
- ['get_5fresolver_2364',['get_resolver',['../classvg_1_1io_1_1Registry.html#a45f5ca692e2d85618f2081e7aa967730',1,'vg::io::Registry']]],
- ['get_5froot_2365',['get_root',['../classvg_1_1TreeSubgraph.html#a16b12e54e0c87d9a84f4d3a809a8171b',1,'vg::TreeSubgraph::get_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#af94fd9c82aaa2742123b25b0ec95311f',1,'handlegraph::SnarlDecomposition::get_root()']]],
- ['get_5frr_5fmemo_2366',['get_rr_memo',['../classvg_1_1MultipathMapper.html#a42169ca0715c4c784584ba3d2a5d34bb',1,'vg::MultipathMapper']]],
- ['get_5fsample_5fname_2367',['get_sample_name',['../classhandlegraph_1_1PathMetadata.html#ada7fda320c3b28c0fb642d7e4a789045',1,'handlegraph::PathMetadata']]],
- ['get_5fscore_2368',['get_score',['../classvg_1_1ReadFilter.html#a3e168659158cf4372fc11b8cda05883d',1,'vg::ReadFilter::get_score()'],['../classvg_1_1Surjector.html#a42d2fa6bd9590a02329f31666fbe0cd5',1,'vg::Surjector::get_score()'],['../classvg_1_1ReadFilter.html#a2144e5b768ebd71768d37265c07deda2',1,'vg::ReadFilter::get_score(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#af800d67aa469136b6318c02e282c5a30',1,'vg::ReadFilter::get_score(const MultipathAlignment &read) const'],['../classvg_1_1Surjector.html#aafe9672e0a82c6540c4d1360070725ec',1,'vg::Surjector::get_score(const Alignment &aln)'],['../classvg_1_1Surjector.html#a4df48f23da07159bb99bc6577d992938',1,'vg::Surjector::get_score(const multipath_alignment_t &mp_aln)']]],
- ['get_5fscores_2369',['get_scores',['../structhaplo_1_1haplo__DP__column.html#a784a7e41856ad01f9bdd88ca59dfb146',1,'haplo::haplo_DP_column']]],
- ['get_5fseed_2370',['get_seed',['../classvg_1_1LazyRNG.html#ac3c6839c2730166a6cb8a10facf8a0c7',1,'vg::LazyRNG']]],
- ['get_5fseed_5fpos_2371',['get_seed_pos',['../classvg_1_1SpliceRegion.html#ab79a29d07732a726cffffea140af98c4',1,'vg::SpliceRegion']]],
- ['get_5fsense_2372',['get_sense',['../classhandlegraph_1_1PathMetadata.html#a6cf06655af059252487f9581cad0dc4a',1,'handlegraph::PathMetadata']]],
- ['get_5fsequence_2373',['get_sequence',['../classvg_1_1DagifiedGraph.html#a5d47d90eeaac4f0a6f1e12f0ed2d197e',1,'vg::DagifiedGraph::get_sequence()'],['../classvg_1_1DozeuPinningOverlay.html#ab7eabd260a4585f04809d8da64b7f2f4',1,'vg::DozeuPinningOverlay::get_sequence()'],['../classvg_1_1ExtraNodeGraph.html#a4b9d7578f0f601b186295d365cf7e487',1,'vg::ExtraNodeGraph::get_sequence()'],['../classvg_1_1SnarlGraph.html#a4a97ed146e23b853fd66a0ad827823e5',1,'vg::SnarlGraph::get_sequence()'],['../classvg_1_1IdentityOverlay.html#ada02cf10738e4fc81c7bb21ecf5d4b56',1,'vg::IdentityOverlay::get_sequence()'],['../classvg_1_1IncrementalSubgraph.html#a61eef0cd10c65efae0cac12816084bb2',1,'vg::IncrementalSubgraph::get_sequence()'],['../classvg_1_1IndexedVG.html#a64c03afcfd0c1c210e8b84a9b78a06dc',1,'vg::IndexedVG::get_sequence()'],['../classvg_1_1MemoizingGraph.html#a841433ccb7c64a657e43130c81c47c39',1,'vg::MemoizingGraph::get_sequence()'],['../classvg_1_1NullMaskingGraph.html#a7a92b5f2747dca58d2fe63368e1294d4',1,'vg::NullMaskingGraph::get_sequence()'],['../classvg_1_1PathSubgraph.html#a1549c36d974dfc4e8bcc54e0e9950646',1,'vg::PathSubgraph::get_sequence()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af008e59ecc555d391149053284ca0cbb',1,'vg::Haplotypes::Subchain::get_sequence()'],['../classvg_1_1ReverseGraph.html#ad815813ebd0d2b33515473bc974c53ad',1,'vg::ReverseGraph::get_sequence()'],['../classvg_1_1NetGraph.html#a4278d3e414d6e5b8e8055d7bdf87c7ac',1,'vg::NetGraph::get_sequence()'],['../classvg_1_1SourceSinkOverlay.html#a4a3eb7401c1b90b33d97672f50a17d39',1,'vg::SourceSinkOverlay::get_sequence()'],['../classvg_1_1JoinedSpliceGraph.html#a6b4f089ed86cdb7ff6ba9177d1187066',1,'vg::JoinedSpliceGraph::get_sequence()'],['../classvg_1_1StrandSplitGraph.html#a878c4be6f6ad6652d3b33f2691bbb570',1,'vg::StrandSplitGraph::get_sequence()'],['../classvg_1_1SubHandleGraph.html#ae9915dd52c55a51616822713509afab0',1,'vg::SubHandleGraph::get_sequence()'],['../classvg_1_1SubgraphOverlay.html#af924de823a9ef5c1a846136eb34637f4',1,'vg::SubgraphOverlay::get_sequence()'],['../classvg_1_1SubpathOverlay.html#a425e89bc05405ef207305c302c18a259',1,'vg::SubpathOverlay::get_sequence()'],['../classvg_1_1TreeSubgraph.html#ae9859d1486d3023b44ab83b3f8c5438c',1,'vg::TreeSubgraph::get_sequence()'],['../classvg_1_1VG.html#a353df9b2449ac859804359632283078b',1,'vg::VG::get_sequence()'],['../classxg_1_1XG.html#ad748df5f6e521774c1d5871ab3519bd8',1,'xg::XG::get_sequence()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4c93978f2d225b926991b34b27528bfd',1,'handlegraph::algorithms::SubHandleGraph::get_sequence()'],['../classhandlegraph_1_1HandleGraph.html#a8cc2ab8a1292e30ba5e167a823f66d92',1,'handlegraph::HandleGraph::get_sequence()']]],
- ['get_5fsequence_5fdictionary_2374',['get_sequence_dictionary',['../namespacevg.html#a2e23f130325e05c894696771e50f2636',1,'vg']]],
- ['get_5fsequence_5fvisits_2375',['get_sequence_visits',['../classvg_1_1HaplotypePartitioner.html#acbe0f7f081cf6db06a894e451d8915b6',1,'vg::HaplotypePartitioner']]],
- ['get_5fsequences_2376',['get_sequences',['../classvg_1_1HaplotypePartitioner.html#a8bdd15927542e95eb536fc9e9bb69aa7',1,'vg::HaplotypePartitioner::get_sequences(handle_t handle) const'],['../classvg_1_1HaplotypePartitioner.html#af88d6e4839d697b5780c453441d3abb0',1,'vg::HaplotypePartitioner::get_sequences(Subchain subchain) const']]],
- ['get_5fshort_2377',['get_short',['../classvg_1_1Version.html#a8105cc0ae9049ca2daf91fbce5efa5e9',1,'vg::Version']]],
- ['get_5fshort_5foptions_2378',['get_short_options',['../classvg_1_1OptionInterface.html#a7c1a8f1f6a3071a502362d9765c94add',1,'vg::OptionInterface::get_short_options()'],['../classvg_1_1BaseOption.html#a5b77fd0a8211f8cabd07b14db491fb64',1,'vg::BaseOption::get_short_options()']]],
- ['get_5fsink_5fhandle_2379',['get_sink_handle',['../classvg_1_1SourceSinkOverlay.html#a71ce03b168ed695659a6ed61a946d089',1,'vg::SourceSinkOverlay']]],
- ['get_5fsize_2380',['get_size',['../structvg_1_1algorithms_1_1Graph.html#ae7a493be0a453a3e82c7c36f0ad70e07',1,'vg::algorithms::Graph']]],
- ['get_5fsizes_2381',['get_sizes',['../structhaplo_1_1haplo__DP__column.html#aa2c307962df62885eaca8caa4723d8a4',1,'haplo::haplo_DP_column']]],
- ['get_5fskip_5fallele_5ffn_2382',['get_skip_allele_fn',['../classvg_1_1SnarlCaller.html#acbc3b71e19fca0c018ff9dd713f2b052',1,'vg::SnarlCaller::get_skip_allele_fn()'],['../classvg_1_1SupportBasedSnarlCaller.html#aa702e223a90771c4090511c23b7c55a7',1,'vg::SupportBasedSnarlCaller::get_skip_allele_fn()']]],
- ['get_5fsnarl_5fchild_5fcount_2383',['get_snarl_child_count',['../classvg_1_1ZipCode.html#ad6d78deca4d723ac8d5ede306abd5578',1,'vg::ZipCode']]],
- ['get_5fsnarl_5frank_5for_5fidentifier_2384',['get_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a078386aa48caae9dda52e73c2975f8b7',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fsnarl_5freference_5fbounds_2385',['get_snarl_reference_bounds',['../classvg_1_1Genotyper.html#a29a6f2fd20161c9313498760578c091a',1,'vg::Genotyper']]],
- ['get_5fsnarl_5ftraversals_2386',['get_snarl_traversals',['../classvg_1_1Genotyper.html#a7a14f1e259fe612b944aadf701ca1585',1,'vg::Genotyper']]],
- ['get_5fsnp_5fref_5fposition_2387',['get_SNP_ref_position',['../structhaplo_1_1linear__haplo__structure.html#a312a7a7a748cc4acd3c4b75717db1fe6',1,'haplo::linear_haplo_structure']]],
- ['get_5fsnv_5fallele_2388',['get_SNV_allele',['../structhaplo_1_1linear__haplo__structure.html#a353eefc81d042a96f98980b7cb2a72aa',1,'haplo::linear_haplo_structure']]],
- ['get_5fsort_5fvalue_2389',['get_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aae5b7a35573e7133c368eb6bf4678aab',1,'vg::ZipCodeForest::sort_value_t']]],
- ['get_5fsource_5fhandle_2390',['get_source_handle',['../classvg_1_1SourceSinkOverlay.html#a4126d6851b442614cb115668eaeeb89f',1,'vg::SourceSinkOverlay']]],
- ['get_5fspanning_5fhaplotypes_2391',['get_spanning_haplotypes',['../classvg_1_1GBWTTraversalFinder.html#a88b35f62878ceab005faf07f7386691c',1,'vg::GBWTTraversalFinder']]],
- ['get_5fstart_2392',['get_start',['../classvg_1_1NetGraph.html#a35e17fbdc2bade4b5b0195d03cb0dc22',1,'vg::NetGraph']]],
- ['get_5fstart_5fbound_2393',['get_start_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a63eea99ca9840f16ef358ee664ecda23',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fstart_5fof_2394',['get_start_of',['../namespacevg.html#afa918cf29c1c8238d88f2bbc94b6abef',1,'vg']]],
- ['get_5fstep_5fat_5fposition_2395',['get_step_at_position',['../classvg_1_1MemoizingGraph.html#acbae8703ecc85597b33e36d5208a4f1e',1,'vg::MemoizingGraph::get_step_at_position()'],['../classxg_1_1XG.html#a087db8dbe184e5a22dda11d61f8fff6a',1,'xg::XG::get_step_at_position()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#aefbae4c3392c32ec13534a44bcc21136',1,'handlegraph::PathPositionHandleGraph::get_step_at_position()']]],
- ['get_5fstep_5fcount_2396',['get_step_count',['../classvg_1_1MemoizingGraph.html#ae0bc7232272e70adab6333dbe3718f46',1,'vg::MemoizingGraph::get_step_count()'],['../classvg_1_1PathSubgraphOverlay.html#ae2df84b76bcec7b4899838a99d3799f5',1,'vg::PathSubgraphOverlay::get_step_count()'],['../classvg_1_1VG.html#a3efe30807d096a6175373bc3f4863dd7',1,'vg::VG::get_step_count()'],['../classxg_1_1XG.html#a0609241ee4795d7c9dd2a2b5cc8ce3a4',1,'xg::XG::get_step_count()'],['../classhandlegraph_1_1PathHandleGraph.html#add91075c3490f8dc5acf667f2b26832c',1,'handlegraph::PathHandleGraph::get_step_count(const path_handle_t &path_handle) const =0'],['../classhandlegraph_1_1PathHandleGraph.html#a6d3a31f0c19054cd2908525119869b80',1,'handlegraph::PathHandleGraph::get_step_count(const handle_t &handle) const']]],
- ['get_5fsteps_2397',['get_steps',['../classvg_1_1IndexingPlan.html#a52c631c507d1cd0f0451ce7de71f2091',1,'vg::IndexingPlan']]],
- ['get_5fstream_5flength_2398',['get_stream_length',['../namespacevg_1_1io.html#aff18a599bd6affc6e2709cb2cff9154c',1,'vg::io']]],
- ['get_5fstream_5fposition_2399',['get_stream_position',['../namespacevg_1_1io.html#aca3b265c558db37b69a837668d2fdf12',1,'vg::io']]],
- ['get_5fsubchains_2400',['get_subchains',['../classvg_1_1HaplotypePartitioner.html#a27be1484d044a8f872083ea6e98d9786',1,'vg::HaplotypePartitioner']]],
- ['get_5fsubgraph_2401',['get_subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a8754c28fbea6df69e6204a9128912a20',1,'vg::GraphSynchronizer::Lock::get_subgraph()'],['../classvg_1_1SpliceRegion.html#ae10fef3784f1d382cb8f3973e1c9ff1b',1,'vg::SpliceRegion::get_subgraph()']]],
- ['get_5fsubrange_2402',['get_subrange',['../classhandlegraph_1_1PathMetadata.html#a80f47deffdb584fa74ea43dad580cce7',1,'handlegraph::PathMetadata']]],
- ['get_5fsubsequence_2403',['get_subsequence',['../classvg_1_1IncrementalSubgraph.html#a258698c76e4d96ecefd38505894f778b',1,'vg::IncrementalSubgraph::get_subsequence()'],['../classvg_1_1JoinedSpliceGraph.html#a2348c9a3357615ce0eea301366344376',1,'vg::JoinedSpliceGraph::get_subsequence()'],['../classvg_1_1VG.html#a45075c22efc7cfb1ed06a8996fec119c',1,'vg::VG::get_subsequence()'],['../classxg_1_1XG.html#a0368861cc6c99d2a1d40c059db62c2a9',1,'xg::XG::get_subsequence()'],['../classhandlegraph_1_1HandleGraph.html#a74c6fcda357516b1160996c63ed40d63',1,'handlegraph::HandleGraph::get_subsequence()']]],
- ['get_5fsuffix_2404',['get_suffix',['../classvg_1_1IndexFile.html#ac81438a82e18b86b443e7d853245d599',1,'vg::IndexFile::get_suffix()'],['../classvg_1_1PhaseUnfolder.html#a97128de268b43c9ccf9dd117829adedf',1,'vg::PhaseUnfolder::get_suffix()']]],
- ['get_5fsupport_2405',['get_support',['../structvg_1_1AugmentedGraph.html#ad239a8516427304ef304e944f7d20c00',1,'vg::AugmentedGraph::get_support(id_t node)'],['../structvg_1_1AugmentedGraph.html#a87c6ed55516068757be3b1ad54a6cfd0',1,'vg::AugmentedGraph::get_support(edge_t edge)'],['../structvg_1_1SupportAugmentedGraph.html#a0ffa85683b46b7f8d6b64da42ba19fbb',1,'vg::SupportAugmentedGraph::get_support(id_t node)'],['../structvg_1_1SupportAugmentedGraph.html#a4c86be41ce8680c5473080c704ddcc10',1,'vg::SupportAugmentedGraph::get_support(edge_t edge)']]],
- ['get_5fsupport_5ffinder_2406',['get_support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a04ebbd23ec0162a72c959351131e17ba',1,'vg::SupportBasedSnarlCaller']]],
- ['get_5fsymbolic_5fbounds_2407',['get_symbolic_bounds',['../classvg_1_1Constructor.html#a31a7837804bd45819ab249687a858fbb',1,'vg::Constructor']]],
- ['get_5fsystem_5fmemory_2408',['get_system_memory',['../classvg_1_1IndexRegistry.html#a1f03f21a783cad871997b03bcd0c8dff',1,'vg::IndexRegistry']]],
- ['get_5ftables_2409',['get_tables',['../classvg_1_1io_1_1Registry.html#aa9f3d682e2b43bfdc3fc30e252a716b9',1,'vg::io::Registry']]],
- ['get_5ftail_5fforest_2410',['get_tail_forest',['../classvg_1_1MinimizerMapper.html#afdbaa5b2938d0050476d078d336286cf',1,'vg::MinimizerMapper']]],
- ['get_5ftarget_5fmemory_5fusage_2411',['get_target_memory_usage',['../classvg_1_1IndexRegistry.html#aa8aae29f234def70dc6de5f1a291cbc0',1,'vg::IndexRegistry']]],
- ['get_5fthread_5fcount_2412',['get_thread_count',['../namespacevg.html#ade988dd38efaa705be15ba17500fe219',1,'vg::get_thread_count()'],['../namespacexg.html#a025cd6958c94d7ce14c1be1425792161',1,'xg::get_thread_count()']]],
- ['get_5fthread_5fstream_2413',['get_thread_stream',['../classvg_1_1io_1_1StreamMultiplexer.html#a749ab082e0364d470d84978c9757ef76',1,'vg::io::StreamMultiplexer']]],
- ['get_5ftop_5flevel_5fchain_5foffset_2414',['get_top_level_chain_offset',['../classvg_1_1ZipCode.html#a304ce8419239ce69dfb69e85e50d3c8c',1,'vg::ZipCode']]],
- ['get_5ftopological_5forder_2415',['get_topological_order',['../classvg_1_1PathSubgraph.html#a591e8f29ef3f356a38aca18e466ae954',1,'vg::PathSubgraph::get_topological_order()'],['../classvg_1_1TreeSubgraph.html#a850f30c11c28ab61148215970b5c6129',1,'vg::TreeSubgraph::get_topological_order()']]],
- ['get_5ftotal_5flength_2416',['get_total_length',['../classxg_1_1XG.html#a4437293fdec75f15a296fb545a6d539d',1,'xg::XG::get_total_length()'],['../classhandlegraph_1_1HandleGraph.html#a4c98da99e0d32ebcc9fd31be4b779e29',1,'handlegraph::HandleGraph::get_total_length()']]],
- ['get_5ftranslation_2417',['get_translation',['../classvg_1_1Translator.html#ac76452dc0c74164d2bcfa25f53ca9828',1,'vg::Translator']]],
- ['get_5ftraversal_5fgenotype_5fsupport_2418',['get_traversal_genotype_support',['../classvg_1_1TraversalSupportFinder.html#a1b818e6111dd2eec62067a562ecc2078',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fmapqs_2419',['get_traversal_mapqs',['../classvg_1_1TraversalSupportFinder.html#a1a7ce9dabeac1835ce0c9765301fcafd',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fof_5fsnarl_2420',['get_traversal_of_snarl',['../namespacevg.html#a871d5cdd29e1806636314021d0b6d451',1,'vg']]],
- ['get_5ftraversal_5forder_2421',['get_traversal_order',['../namespacevg.html#aaa05224d1b8daa421ebfb9320fc1d2d1',1,'vg']]],
- ['get_5ftraversal_5fset_5fsupport_2422',['get_traversal_set_support',['../classvg_1_1TraversalSupportFinder.html#aead4beb53b5148baa538c6481be8700d',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fsizes_2423',['get_traversal_sizes',['../classvg_1_1TraversalSupportFinder.html#a95944f27ca78da63466f5623ad646ee4',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fsupport_2424',['get_traversal_support',['../classvg_1_1TraversalSupportFinder.html#a28c6f9088f6c28d64855d6cac9a65322',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversals_2425',['get_traversals',['../classvg_1_1Deconstructor.html#ad58319907ec3f7bf3e6d130f6469a9a9',1,'vg::Deconstructor']]],
- ['get_5ftree_5fsize_2426',['get_tree_size',['../classvg_1_1ZipCodeTree.html#a1207ebf8f31cd6f17593f100be3c7f00',1,'vg::ZipCodeTree']]],
- ['get_5ftype_2427',['get_type',['../structhaplo_1_1linear__haplo__structure.html#ac0dcdb90717d1585bbc847206746e293',1,'haplo::linear_haplo_structure::get_type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#aef1abc2e62fd2ebcc722e26978bb56b7',1,'vg::ZipCodeTree::tree_item_t::get_type()']]],
- ['get_5funderlying_5fhandle_2428',['get_underlying_handle',['../classvg_1_1DagifiedGraph.html#aea86fce4d0f22943935bad1e5cc17f48',1,'vg::DagifiedGraph::get_underlying_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a5cfe7e76c343f768037c84df85037ace',1,'vg::DozeuPinningOverlay::get_underlying_handle()'],['../classvg_1_1IdentityOverlay.html#a5bfd0bebd074847b5504b9ad3f968836',1,'vg::IdentityOverlay::get_underlying_handle()'],['../classvg_1_1IncrementalSubgraph.html#a6b3e5f09eb2a9edb698eb08c55cc9486',1,'vg::IncrementalSubgraph::get_underlying_handle()'],['../classvg_1_1NullMaskingGraph.html#aa903d2c61cf2ba035aac11a3015c2cab',1,'vg::NullMaskingGraph::get_underlying_handle()'],['../classvg_1_1PathSubgraph.html#aa6c521d9a3770f20483f3f16b0686eeb',1,'vg::PathSubgraph::get_underlying_handle()'],['../classvg_1_1ReverseGraph.html#a246e5d5c82508b512fb4c041bfe38892',1,'vg::ReverseGraph::get_underlying_handle()'],['../classvg_1_1SourceSinkOverlay.html#abe2d0e58471d1ab7840618a02958fc96',1,'vg::SourceSinkOverlay::get_underlying_handle()'],['../classvg_1_1StrandSplitGraph.html#aa6379c95c71b6a6682311733de098d1f',1,'vg::StrandSplitGraph::get_underlying_handle()'],['../classvg_1_1SubHandleGraph.html#a434e6cd60bb278307df255a43681e08a',1,'vg::SubHandleGraph::get_underlying_handle()'],['../classvg_1_1SubpathOverlay.html#a595889f41331fbbc8a049ae56ba29624',1,'vg::SubpathOverlay::get_underlying_handle()'],['../classvg_1_1TreeSubgraph.html#a2d88a6edb6d6d586b6fe26a88e13248f',1,'vg::TreeSubgraph::get_underlying_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ada7dab5b4c9e55607563d1bcf546d401',1,'handlegraph::algorithms::SubHandleGraph::get_underlying_handle()'],['../classhandlegraph_1_1ExpandingOverlayGraph.html#aacfa30b0166f91f1aa80f0fd566d2b65',1,'handlegraph::ExpandingOverlayGraph::get_underlying_handle()']]],
- ['get_5funderlying_5fid_2429',['get_underlying_id',['../classvg_1_1DagifiedGraph.html#ae8707e0886baf125d0c0a25a3cc3a4cc',1,'vg::DagifiedGraph::get_underlying_id()'],['../classvg_1_1DozeuPinningOverlay.html#a45047bf7a55843a4099d9db6b83e2d17',1,'vg::DozeuPinningOverlay::get_underlying_id()']]],
- ['get_5funique_5fhaplotypes_2430',['get_unique_haplotypes',['../classvg_1_1VariantAdder.html#aa9ae7b7fa8ad3ac6bec72ada43a3d4b7',1,'vg::VariantAdder']]],
- ['get_5fvalue_2431',['get_value',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#adf719dd5d99dd4b31952df3af1911ed1',1,'vg::ZipCodeTree::tree_item_t::get_value()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a6d28a735e7c8a6a0cc8b11675fb8d261',1,'vg::subcommand::ArgSpec::get_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#acb802adcf83734cc84ee4745ed4ee505',1,'vg::subcommand::ValueArgSpec::get_value()']]],
- ['get_5fvalue_5fand_5fnext_5findex_2432',['get_value_and_next_index',['../structvg_1_1varint__vector__t.html#afee3663cabce117ecf7b114b0179ae31',1,'vg::varint_vector_t']]],
- ['get_5fvariants_5fin_5fsite_2433',['get_variants_in_site',['../classvg_1_1VCFTraversalFinder.html#ae45b4f713e847be11c4aa07482de3e12',1,'vg::VCFTraversalFinder']]],
- ['get_5fvcf_5fheader_2434',['get_vcf_header',['../classvg_1_1Deconstructor.html#a6c14aa01fabc63b945bc69550335408b',1,'vg::Deconstructor']]],
- ['get_5fversion_2435',['get_version',['../classvg_1_1Version.html#aa6e698d728ebd5e3318511dfde778eaf',1,'vg::Version']]],
- ['get_5fvg_5findex_5fregistry_2436',['get_vg_index_registry',['../structvg_1_1VGIndexes.html#a4291997834048ac385331f19390889c0',1,'vg::VGIndexes']]],
- ['get_5fweight_5fusing_5fother_2437',['get_weight_using_other',['../structvg_1_1algorithms_1_1Graph.html#ad0741db7b09040c706ffaffbb7337098',1,'vg::algorithms::Graph']]],
- ['get_5fwork_5fdir_2438',['get_work_dir',['../classvg_1_1IndexRegistry.html#ac587073860174b6c074d2be7ad53e103',1,'vg::IndexRegistry']]],
- ['getreachablebridges_2439',['getReachableBridges',['../namespacevg.html#af601021f7ec2c0b0d7404030ee7271c9',1,'vg']]],
- ['getreachablebridges2_2440',['getReachableBridges2',['../namespacevg.html#a2dc613a63afb3f23851c96494006630d',1,'vg']]],
- ['gfa_2ecpp_2441',['gfa.cpp',['../gfa_8cpp.html',1,'']]],
- ['gfa_2ehpp_2442',['gfa.hpp',['../gfa_8hpp.html',1,'']]],
- ['gfa_5fhas_5fhaplotypes_2443',['gfa_has_haplotypes',['../classvg_1_1IndexRegistry.html#a019e2efc800d3280acdce7814db8b096',1,'vg::IndexRegistry']]],
- ['gfa_5fid_5fspace_2444',['gfa_id_space',['../classvg_1_1GFAHandleGraph.html#a74dbb782d6ffa6301fc97f7e540ebe40',1,'vg::GFAHandleGraph']]],
- ['gfa_5fparameters_2445',['gfa_parameters',['../structGBWTConfig.html#a07b86c3ec44037b22504eb86d9ebd78d',1,'GBWTConfig']]],
- ['gfa_5fto_5fhandle_2ecpp_2446',['gfa_to_handle.cpp',['../gfa__to__handle_8cpp.html',1,'']]],
- ['gfa_5fto_5fhandle_2ehpp_2447',['gfa_to_handle.hpp',['../gfa__to__handle_8hpp.html',1,'']]],
- ['gfa_5fto_5fhandle_5fgraph_2448',['gfa_to_handle_graph',['../namespacevg_1_1algorithms.html#aedfca626dc003dc3fee77c6bbfcde297',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, GFAIDMapInfo *translation)'],['../namespacevg_1_1algorithms.html#adca14b7dcba0bb21f3fdb0c98d867c72',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, const string &translation_filename)'],['../namespacevg_1_1algorithms.html#a031cb6d0db20a6aaee020c5a6909ba80',1,'vg::algorithms::gfa_to_handle_graph(istream &in, MutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr)']]],
- ['gfa_5fto_5fpath_5fhandle_5fgraph_2449',['gfa_to_path_handle_graph',['../namespacevg_1_1algorithms.html#a9f5c41c06269c778d2c97f39cbc79de8',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a61f2c7006c531ad5dd319ea30ec0087f',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, int64_t max_rgfa_rank, const string &translation_filename, unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a8baa82611439357dc02996ba17ce6aa9',1,'vg::algorithms::gfa_to_path_handle_graph(istream &in, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)']]],
- ['gfaduplicatepatherror_2450',['GFADuplicatePathError',['../structvg_1_1algorithms_1_1GFADuplicatePathError.html',1,'vg::algorithms::GFADuplicatePathError'],['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#aa815b9f84fdf80d9bf29c38d3d68408c',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name)'],['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#a05dd140439b17113dec810a3cdc26bab',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
- ['gfaformaterror_2451',['GFAFormatError',['../structvg_1_1algorithms_1_1GFAFormatError.html',1,'vg::algorithms::GFAFormatError'],['../structvg_1_1algorithms_1_1GFAFormatError.html#add2d72c679e2b69e1c9f9c481228e0fb',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message)'],['../structvg_1_1algorithms_1_1GFAFormatError.html#afdf6dea244cc33a30ae5d9446199bea2',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
- ['gfahandlegraph_2452',['GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html',1,'vg::GFAHandleGraph'],['../classvg_1_1GFAHandleGraph.html#aeffc2278ffcad22cd6950f3fa831f60d',1,'vg::GFAHandleGraph::GFAHandleGraph()']]],
- ['gfaidmapinfo_2453',['GFAIDMapInfo',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html',1,'vg::algorithms']]],
- ['gfaparser_2454',['GFAParser',['../classvg_1_1algorithms_1_1GFAParser.html',1,'vg::algorithms']]],
- ['gff_5ffeature_5fname_2455',['gff_feature_name',['../structvg_1_1IndexingParameters.html#aaeec45d17c4d60468c14debb7fb46709',1,'vg::IndexingParameters']]],
- ['gff_5freader_2ecpp_2456',['gff_reader.cpp',['../gff__reader_8cpp.html',1,'']]],
- ['gff_5freader_2ehpp_2457',['gff_reader.hpp',['../gff__reader_8hpp.html',1,'']]],
- ['gff_5ftranscript_5ftag_2458',['gff_transcript_tag',['../structvg_1_1IndexingParameters.html#aa795ef116d75fdbf71092b831fce2c21',1,'vg::IndexingParameters']]],
- ['gffreader_2459',['GFFReader',['../classvg_1_1GFFReader.html',1,'vg::GFFReader'],['../classvg_1_1GFFReader.html#a886d9cf2d287f8d0f6c87b206c26d893',1,'vg::GFFReader::GFFReader()']]],
- ['gffrecord_2460',['GFFRecord',['../structvg_1_1GFFRecord.html',1,'vg::GFFRecord'],['../structvg_1_1GFFRecord.html#a8fc2a234093eccb6ed958325887e0f08',1,'vg::GFFRecord::GFFRecord()']]],
- ['giraffe_5fgbwt_5fdownsample_2461',['giraffe_gbwt_downsample',['../structvg_1_1IndexingParameters.html#a915eada866d050e347f4b3c00ef5dab9',1,'vg::IndexingParameters']]],
- ['giraffe_5fmain_2ecpp_2462',['giraffe_main.cpp',['../giraffe__main_8cpp.html',1,'']]],
- ['giraffemainoptions_2463',['GiraffeMainOptions',['../structGiraffeMainOptions.html',1,'']]],
- ['globals_2464',['globals',['../classvg_1_1DiagramExplainer.html#ac7ea94549f8c5ecddece74889a88ea88',1,'vg::DiagramExplainer']]],
- ['go_5fleft_2465',['go_left',['../structvg_1_1ChainIterator.html#a785251461ea63262f67548eeadea7684',1,'vg::ChainIterator']]],
- ['golden_5fsection_5fsearch_2466',['golden_section_search',['../namespacevg.html#a314ff925fad534d112e4531617e408fa',1,'vg']]],
- ['google_2467',['google',['../namespacegoogle.html',1,'']]],
- ['gq_2468',['gq',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a021adf386d5306f56c3a330412c13000',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['grandparent_5fnet_5fhandle_2469',['grandparent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6ca403df1dfe6e9554571dba400448f8',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['graph_2470',['Graph',['../structvg_1_1Graph.html',1,'vg::Graph'],['../structvg_1_1algorithms_1_1Graph.html',1,'vg::algorithms::Graph'],['../classvg_1_1BandedGlobalAligner.html#af5168385acfc1ca71f0757269452e5a7',1,'vg::BandedGlobalAligner::graph()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9d4f47628b410f5639f985dae1b1b5e0',1,'vg::BandedGlobalAligner::AltTracebackStack::graph()'],['../classvg_1_1CactusSnarlFinder.html#abb2127506508ae3515f901375b205e2d',1,'vg::CactusSnarlFinder::graph()'],['../classvg_1_1PathChunker.html#afbe0c85ff99dd1134fefcf439b212d4f',1,'vg::PathChunker::graph()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a528e7742b43628c6c93c6542810ffdfd',1,'vg::PathOrientedDistanceMeasurer::graph()'],['../structvg_1_1ConstructedChunk.html#a27e2145253b94e1edecf0f456a12268b',1,'vg::ConstructedChunk::graph()'],['../classvg_1_1ContractingGraph.html#ab79d18f0c2f96761ebdad601ec4ec3d4',1,'vg::ContractingGraph::graph()'],['../classvg_1_1DagifiedGraph.html#a5b2dd0d18c17b2e10aa1b6b6280018ee',1,'vg::DagifiedGraph::graph()'],['../classvg_1_1Deconstructor.html#a74cd5fde9496dcc1865ed74fda2c4ae4',1,'vg::Deconstructor::graph()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a50561ac0fc9bcfd983a71c9fec2b6d2e',1,'vg::DozeuInterface::OrderedGraph::graph()'],['../classvg_1_1DozeuPinningOverlay.html#aff912b269bf3e749ef52c0d86fe12fcf',1,'vg::DozeuPinningOverlay::graph()'],['../classvg_1_1WFATree.html#a313dc78cf7698c0b50b3fb2b0ec28a81',1,'vg::WFATree::graph()'],['../classvg_1_1GaplessExtender.html#a8780650e736d01abf2dd910a3dd235c3',1,'vg::GaplessExtender::graph()'],['../classvg_1_1WFAExtender.html#a7362ec7bfdf80dc2fc343e483bdf0e5d',1,'vg::WFAExtender::graph()'],['../classvg_1_1SnarlState.html#a62e2fb69d55ee9cf1e2653dc4c9c8ead',1,'vg::SnarlState::graph()'],['../structvg_1_1AugmentedGraph.html#afb05832f68a8db43e7a8c510397b8ce3',1,'vg::AugmentedGraph::graph()'],['../classvg_1_1VCFGenotyper.html#ab76cadfc9e7398a693e7a0cb656dc37a',1,'vg::VCFGenotyper::graph()'],['../classvg_1_1LegacyCaller.html#a5065baf9582814e816349b53bc54a4e9',1,'vg::LegacyCaller::graph()'],['../classvg_1_1FlowCaller.html#a5193a03f37a60ed6bdf91157bf02c6dc',1,'vg::FlowCaller::graph()'],['../classvg_1_1NestedFlowCaller.html#af2cc9a536a0a2ca0fd857793f0985d68',1,'vg::NestedFlowCaller::graph()'],['../classvg_1_1GraphSynchronizer.html#ab0856b30a01193d100f9e470ea61a67c',1,'vg::GraphSynchronizer::graph()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a99d071619c6462165528d8428d4bb7fa',1,'haplo::hDP_gbwt_graph_accessor::graph()'],['../structhaplo_1_1linear__haplo__structure.html#acb5692ebbb1a6f91db791d01bb2ab294',1,'haplo::linear_haplo_structure::graph()'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#adf4336380ac7e4944628281010e7057a',1,'vg::SplicedHTSAlignmentEmitter::graph()'],['../classvg_1_1IdentityOverlay.html#aa5f51840702ebb847bc1193bea756960',1,'vg::IdentityOverlay::graph()'],['../classvg_1_1IncrementalSubgraph.html#a45a1fbda6452cbdade4d40bc4dab539c',1,'vg::IncrementalSubgraph::graph()'],['../classvg_1_1AliasGraph.html#a85dd8f136025b7325d9fa19058d2bb4f',1,'vg::AliasGraph::graph()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a932e7e9593e73f7a76a8f1756f4fb1f8',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::graph()'],['../classvg_1_1HandleGraphNodeSet.html#a1d0f4da0abcf0379dfe1672cce88a055',1,'vg::HandleGraphNodeSet::graph()'],['../classvg_1_1Masker.html#a58ab29d84eb1ad7d8d8884927850d674',1,'vg::Masker::graph()'],['../classvg_1_1MCMCGenotyper.html#a63ef4fabc83c478b9ac7933ba16c5adc',1,'vg::MCMCGenotyper::graph()'],['../classvg_1_1MemoizingGraph.html#ae619ad2dfa33c00eced07b7a987e9796',1,'vg::MemoizingGraph::graph()'],['../classvg_1_1MultipathAlignmentEmitter.html#aaaf74750129abc432b73f66d226d35c6',1,'vg::MultipathAlignmentEmitter::graph()'],['../classvg_1_1NullMaskingGraph.html#a691c9aa63e3e20dbba329691b482f311',1,'vg::NullMaskingGraph::graph()'],['../classvg_1_1Packer.html#a52ac5f2ff5549fe1b296efc53204e94f',1,'vg::Packer::graph()'],['../classvg_1_1RareVariantSimplifier.html#ace754988b74595f36762993abead625f',1,'vg::RareVariantSimplifier::graph()'],['../classvg_1_1ReadFilter.html#a73ca67996129403044a23de9544e88fd',1,'vg::ReadFilter::graph()'],['../classvg_1_1RegionExpander.html#af23424b8d8c2f809311afb6b3dceca08',1,'vg::RegionExpander::graph()'],['../classvg_1_1AbstractReadSampler.html#a07bbefa0c0af8f9c4cb5b2c45bcdae53',1,'vg::AbstractReadSampler::graph()'],['../classvg_1_1SmallSnarlSimplifier.html#a54a08fa74dda470c28e2850ded312175',1,'vg::SmallSnarlSimplifier::graph()'],['../classvg_1_1SupportBasedSnarlCaller.html#ab0f5bd05d950be25e87a9f5fbc345a5c',1,'vg::SupportBasedSnarlCaller::graph()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a49cfcfdb9e2c378e973dd8a883e154df',1,'vg::SnarlDistanceIndexClusterer::graph()'],['../classvg_1_1HandleGraphSnarlFinder.html#a377e8778235836602280747eb5813f58',1,'vg::HandleGraphSnarlFinder::graph()'],['../classvg_1_1NetGraph.html#acbae58f3fb38de99ea4a0f0b16ede465',1,'vg::NetGraph::graph()'],['../classvg_1_1StrandSplitGraph.html#a61683c11a40d1881132614159ffc0543',1,'vg::StrandSplitGraph::graph()'],['../classvg_1_1Surjector.html#a118010284d37b604a7bcd7eb8dd13537',1,'vg::Surjector::graph()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a66b0e7a1ac972af0e4d381e4202e1f5e',1,'vg::ExhaustiveTraversalFinder::graph()'],['../classvg_1_1PathRestrictedTraversalFinder.html#aef70365b3b1ee2afb3ac622748923a90',1,'vg::PathRestrictedTraversalFinder::graph()'],['../classvg_1_1PathBasedTraversalFinder.html#a16635d1b5be7de4078a9c2369a1b8073',1,'vg::PathBasedTraversalFinder::graph()'],['../classvg_1_1PathTraversalFinder.html#a7ae6d1d377192e4fab7a9074b83bddbd',1,'vg::PathTraversalFinder::graph()'],['../classvg_1_1TrivialTraversalFinder.html#aeb55a5539b54fd0bf8b4e59db2d4ffca',1,'vg::TrivialTraversalFinder::graph()'],['../classvg_1_1RepresentativeTraversalFinder.html#a66eedfed30f7b436c4eef2b339e356ba',1,'vg::RepresentativeTraversalFinder::graph()'],['../classvg_1_1VCFTraversalFinder.html#ac8e35bbc2e0c34475f13f8d6989fa5b6',1,'vg::VCFTraversalFinder::graph()'],['../classvg_1_1FlowTraversalFinder.html#ad092938a00c2c7c2b046d88fe47c73a8',1,'vg::FlowTraversalFinder::graph()'],['../classvg_1_1GBWTTraversalFinder.html#a1279ffc672ec8ee2fc6e6f1825462e15',1,'vg::GBWTTraversalFinder::graph()'],['../classvg_1_1TraversalSupportFinder.html#a388ac720c48b44f21da264209a25a3b3',1,'vg::TraversalSupportFinder::graph()'],['../classvg_1_1VariantAdder.html#a149b01f65cc10625177011221dfef354',1,'vg::VariantAdder::graph()'],['../classvg_1_1VG.html#a4772c77ed932bfed4d21e247918381a4',1,'vg::VG::graph()'],['../structvg_1_1VG_1_1Plan.html#a06f927768c287c88f81d9761d61da231',1,'vg::VG::Plan::graph()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a0a6667c750efa2c5264c6ffe1c5727aa',1,'handlegraph::PathForEachSocket::iterator::graph()'],['../classhandlegraph_1_1PathForEachSocket.html#a0bdd335f78e28a6a26ab2605c06fa601',1,'handlegraph::PathForEachSocket::graph()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a956c6bef21a026c7426da0650a2927b8',1,'vg::io::GafAlignmentEmitter::graph()'],['../classvg_1_1Transcriptome.html#aee456b8b8e3acaf836914c987d89a16a',1,'vg::Transcriptome::graph()']]],
- ['graph_2ecpp_2471',['graph.cpp',['../graph_8cpp.html',1,'']]],
- ['graph_2ehpp_2472',['graph.hpp',['../graph_8hpp.html',1,'']]],
- ['graph_5fcaller_2ecpp_2473',['graph_caller.cpp',['../graph__caller_8cpp.html',1,'']]],
- ['graph_5fcaller_2ehpp_2474',['graph_caller.hpp',['../graph__caller_8hpp.html',1,'']]],
- ['graph_5fcigar_2475',['graph_cigar',['../classvg_1_1GSSWAligner.html#a429c1cbb1e166acba4e29a8dc172da7d',1,'vg::GSSWAligner']]],
- ['graph_5fend_2476',['graph_end',['../classvg_1_1algorithms_1_1Anchor.html#a3ddb866c3cb925619705602580076942',1,'vg::algorithms::Anchor']]],
- ['graph_5fgbwtgraph_2477',['graph_gbwtgraph',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a91483c9c92517470579d46e605443620',1,'GraphHandler']]],
- ['graph_5fgbz_2478',['graph_gbz',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a759ff53fb7d1c506e3be18f608607ac5',1,'GraphHandler']]],
- ['graph_5finterval_5fto_5fstring_2479',['graph_interval_to_string',['../namespacevg.html#aeade23d997b1899023cfe7f560cc6bc1',1,'vg']]],
- ['graph_5fmixed_5fdistance_5festimate_2480',['graph_mixed_distance_estimate',['../classvg_1_1Mapper.html#a67fb2b4bc540b81be063075ce5593569',1,'vg::Mapper']]],
- ['graph_5fname_2481',['graph_name',['../structGBWTConfig.html#adb800365228cdbb56b99c207e6a342ea',1,'GBWTConfig::graph_name()'],['../structHaplotypesConfig.html#a232a96ba620bbe67e61468c7841bec9d',1,'HaplotypesConfig::graph_name()']]],
- ['graph_5fnone_2482',['graph_none',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50abbfbe5112e8f9046f822fc511ab21631',1,'GraphHandler']]],
- ['graph_5foutput_2483',['graph_output',['../structGBWTConfig.html#adb60e4d83216b0c6b9a4ffd821a54ffb',1,'GBWTConfig']]],
- ['graph_5fpath_2484',['graph_path',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50af316f5a8669d38d1c1801caf9d5671d7',1,'GraphHandler']]],
- ['graph_5fpos_5fat_5fpath_5fposition_2485',['graph_pos_at_path_position',['../classxg_1_1XG.html#a85c47feeb19e96486140c5e1b8184bc7',1,'xg::XG::graph_pos_at_path_position(const path_handle_t &path, size_t path_pos) const'],['../classxg_1_1XG.html#a31c733ed1c2045b1e2a7e9f343dc9296',1,'xg::XG::graph_pos_at_path_position(const std::string &name, size_t path_pos) const']]],
- ['graph_5fpos_5fs_2486',['graph_pos_s',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html',1,'vg::DozeuInterface']]],
- ['graph_5fsource_2487',['graph_source',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a66269d0a2331df8645dfca4cdbc4a2ea',1,'GraphHandler']]],
- ['graph_5fstart_2488',['graph_start',['../classvg_1_1algorithms_1_1Anchor.html#ac7bd5f21e10bae0f6dacb3fcc623752f',1,'vg::algorithms::Anchor']]],
- ['graph_5fsynchronizer_2ecpp_2489',['graph_synchronizer.cpp',['../graph__synchronizer_8cpp.html',1,'']]],
- ['graph_5fsynchronizer_2ehpp_2490',['graph_synchronizer.hpp',['../graph__synchronizer_8hpp.html',1,'']]],
- ['graph_5fto_5fgfa_2491',['graph_to_gfa',['../namespacevg.html#ad8c4a075bb9301c8050d89ed8e6a33b9',1,'vg']]],
- ['graph_5fto_5fxg_5fadjusting_5fpaths_2492',['graph_to_xg_adjusting_paths',['../convert__main_8cpp.html#afe37e7186bce3c6128d32b210f99a9a5',1,'convert_main.cpp']]],
- ['graph_5ftype_2493',['graph_type',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50',1,'GraphHandler']]],
- ['graphcaller_2494',['GraphCaller',['../classvg_1_1GraphCaller.html',1,'vg::GraphCaller'],['../classvg_1_1GraphCaller.html#a621386ff80a0fe3289719c75c282bc5a',1,'vg::GraphCaller::GraphCaller()']]],
- ['graphhandler_2495',['GraphHandler',['../structGraphHandler.html',1,'']]],
- ['graphsynchronizer_2496',['GraphSynchronizer',['../classvg_1_1GraphSynchronizer.html',1,'vg::GraphSynchronizer'],['../classvg_1_1GraphSynchronizer.html#addf1e96558546d4f5e708827b9eb4d67',1,'vg::GraphSynchronizer::GraphSynchronizer()']]],
- ['greater_5fgaffile_2497',['greater_gaffile',['../structgreater__gaffile.html',1,'']]],
- ['greedy_5fmin_5fdist_2498',['greedy_min_dist',['../classvg_1_1MultipathMapper.html#a97d02064d377122ed8cef9e53340ba90',1,'vg::MultipathMapper']]],
- ['greedy_5fpieces_2499',['greedy_pieces',['../classvg_1_1Constructor.html#ac4dce51a25e5f773a0c53e8cd9f07628',1,'vg::Constructor']]],
- ['greedy_5frestart_5fassume_5fsubstitution_2500',['greedy_restart_assume_substitution',['../classvg_1_1BaseMapper.html#a5a3324ff0b1faccb4e976e0d1a369712',1,'vg::BaseMapper']]],
- ['greedy_5frestart_5fmax_5fcount_2501',['greedy_restart_max_count',['../classvg_1_1BaseMapper.html#a5d9a1c8549138e423e1a95a40590fee6',1,'vg::BaseMapper']]],
- ['greedy_5frestart_5fmax_5flcp_2502',['greedy_restart_max_lcp',['../classvg_1_1BaseMapper.html#a4cad1e0b9a03002f35eee233cc34ac54',1,'vg::BaseMapper']]],
- ['greedy_5frestart_5fmin_5flength_2503',['greedy_restart_min_length',['../classvg_1_1BaseMapper.html#abe669bcb3e32a8afb3e71443bbe5076a',1,'vg::BaseMapper']]],
- ['greedymindistanceclusterer_2504',['GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html',1,'vg::GreedyMinDistanceClusterer'],['../classvg_1_1GreedyMinDistanceClusterer.html#a603a74649e16204cace3e714ebe67a74',1,'vg::GreedyMinDistanceClusterer::GreedyMinDistanceClusterer()']]],
- ['groom_5fcomponents_2505',['groom_components',['../classvg_1_1FlowSort.html#a2a52b4d445acf50ebfd8f7dc3a07d044',1,'vg::FlowSort']]],
- ['group_2506',['group',['../classvg_1_1io_1_1MessageEmitter.html#adb0173ebe6170c259448c8dd1d4c0dde',1,'vg::io::MessageEmitter::group()'],['../classvg_1_1SparseUnionFind.html#af91351abb606a1bc16c1cbb5f1b668ab',1,'vg::SparseUnionFind::group()']]],
- ['group_5fcache_2507',['group_cache',['../classvg_1_1IndexedVG.html#a0024489b3eb887d90d18af839722ce66',1,'vg::IndexedVG']]],
- ['group_5fcount_2508',['group_count',['../classvg_1_1io_1_1MessageIterator.html#a34611c431fac53c556d57036cee7e4fe',1,'vg::io::MessageIterator']]],
- ['group_5fhandlers_2509',['group_handlers',['../classvg_1_1io_1_1MessageEmitter.html#a8e586d31762cb47872de4b4723e01696',1,'vg::io::MessageEmitter::group_handlers()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a176d09f4d40ef21965c7a66abc546dbd',1,'vg::io::ProtobufEmitter::group_handlers()']]],
- ['group_5fidx_2510',['group_idx',['../classvg_1_1io_1_1MessageIterator.html#ab2a47479856b6bb8d6fe3c943519d83d',1,'vg::io::MessageIterator']]],
- ['group_5flistener_5ft_2511',['group_listener_t',['../classvg_1_1io_1_1MessageEmitter.html#a4569ac626dfd036074603cc6f05d55e1',1,'vg::io::MessageEmitter::group_listener_t()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a3fdef59aeb9c688e752463a2257ebbfd',1,'vg::io::ProtobufEmitter::group_listener_t()']]],
- ['group_5fmapping_5fquality_5fexact_2512',['group_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#a7e03bd79bceb8a8034ae57ba640069bc',1,'vg::GSSWAligner']]],
- ['group_5fsize_2513',['group_size',['../structvg_1_1Funnel_1_1Item.html#a23706e46f9ebd56acbea3c612358bb79',1,'vg::Funnel::Item::group_size()'],['../classvg_1_1SparseUnionFind.html#aff34e4252e15a68b1e8e79c8cef27a66',1,'vg::SparseUnionFind::group_size()']]],
- ['group_5ftag_2514',['group_tag',['../classvg_1_1io_1_1MessageEmitter.html#ad240e5c3ae379aa3257c498dd4c4e1bf',1,'vg::io::MessageEmitter']]],
- ['group_5fvo_2515',['group_vo',['../classvg_1_1io_1_1MessageIterator.html#ae569fd7dc6129edc5e5dac52b1a67f84',1,'vg::io::MessageIterator']]],
- ['groupedoptiongroup_2516',['GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html',1,'vg::subcommand::GroupedOptionGroup'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a6da6deb7ccf8697e84db1c266dd9180f',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup()=default'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af4f06c1eff0303d1c982b0c2d34c2b55',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(const GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ab1c7b6f34e8d53cf4536625ea6709e80',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(GroupedOptionGroup &&other)=delete']]],
- ['growth_2517',['Growth',['../structvg_1_1FlowSort_1_1Growth.html',1,'vg::FlowSort::Growth'],['../structvg_1_1FlowSort_1_1Growth.html#aa156ae24695e73aee936d00a7ef70d22',1,'vg::FlowSort::Growth::Growth()']]],
- ['gssw_5fmapping_5fto_5falignment_2518',['gssw_mapping_to_alignment',['../classvg_1_1GSSWAligner.html#ab45f7399b68bdc980499d4384515b9b7',1,'vg::GSSWAligner']]],
- ['gsswaligner_2519',['GSSWAligner',['../classvg_1_1GSSWAligner.html',1,'vg::GSSWAligner'],['../classvg_1_1GSSWAligner.html#a02c1c427118eb1a8244274d852684c79',1,'vg::GSSWAligner::GSSWAligner()=default'],['../classvg_1_1GSSWAligner.html#a6c3f1338e6a66850b779e8331a65a61c',1,'vg::GSSWAligner::GSSWAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int8_t _full_length_bonus, double _gc_content)']]],
- ['guess_5fparallel_5fgbwt_5fjobs_2520',['guess_parallel_gbwt_jobs',['../namespacevg.html#a70ebd70e5b26c5fefe30895fa313f3b9',1,'vg']]],
- ['gz_5fsuffix_2521',['GZ_SUFFIX',['../rna__main_8cpp.html#a79e5666abc1e2270209776bd472798e7',1,'rna_main.cpp']]],
- ['protobuf_2522',['protobuf',['../namespacegoogle_1_1protobuf.html',1,'google']]]
+ ['g_5fbv_1967',['g_bv',['../classxg_1_1XG.html#a7fcb333bb6acf85ce76d81de9735b88a',1,'xg::XG']]],
+ ['g_5fbv_5frank_1968',['g_bv_rank',['../classxg_1_1XG.html#abbbc82ab0fe4b0d8abe7e5890a89b952',1,'xg::XG']]],
+ ['g_5fbv_5fselect_1969',['g_bv_select',['../classxg_1_1XG.html#a9eb31aaf28e0ab90154233692bdc0c05',1,'xg::XG']]],
+ ['g_5fiv_1970',['g_iv',['../classxg_1_1XG.html#a7b4b76e9a150ca86d54cee59a3825f4d',1,'xg::XG']]],
+ ['g_5fnode_5fheader_5flength_1971',['G_NODE_HEADER_LENGTH',['../classxg_1_1XG.html#a8a1f38f3430d796f7b2ae452fd80ebbf',1,'xg::XG']]],
+ ['g_5fnode_5fid_5foffset_1972',['G_NODE_ID_OFFSET',['../classxg_1_1XG.html#a841f4db9d178690c836a21b6adc9fafe',1,'xg::XG']]],
+ ['g_5fnode_5fleft_5fcount_5foffset_1973',['G_NODE_LEFT_COUNT_OFFSET',['../classxg_1_1XG.html#a9028d42350d55a928483b76579549145',1,'xg::XG']]],
+ ['g_5fnode_5flength_5foffset_1974',['G_NODE_LENGTH_OFFSET',['../classxg_1_1XG.html#aaf4de09d0f39174f42c793492976acc9',1,'xg::XG']]],
+ ['g_5fnode_5fright_5fcount_5foffset_1975',['G_NODE_RIGHT_COUNT_OFFSET',['../classxg_1_1XG.html#ad4aacfc7ad17ddc586566f8d2a5e92e5',1,'xg::XG']]],
+ ['g_5fnode_5fseq_5fstart_5foffset_1976',['G_NODE_SEQ_START_OFFSET',['../classxg_1_1XG.html#a19673db503954e65456196d791f7db04',1,'xg::XG']]],
+ ['gaf_1977',['GAF',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0bab98a867ffc7b5c1ac2a3e5e171148245',1,'vg::MultipathAlignmentEmitter::GAF()'],['../structGafFile.html#a9dcebeb1a298c34516bdd969dc439560',1,'GafFile::gaf()']]],
+ ['gaf_5foutput_1978',['gaf_output',['../classvg_1_1VCFGenotyper.html#ae00bbce9945411dbab0d14e7cdb4b8c2',1,'vg::VCFGenotyper::gaf_output()'],['../classvg_1_1FlowCaller.html#a93037892a9148b952b186852f77f0fa8',1,'vg::FlowCaller::gaf_output()'],['../classvg_1_1NestedFlowCaller.html#a9114ad05033bc7d50becae55041dfae0',1,'vg::NestedFlowCaller::gaf_output()']]],
+ ['gaf_5fpaired_5finterleaved_5ffor_5feach_1979',['gaf_paired_interleaved_for_each',['../namespacevg_1_1io.html#a1509c614371533861fa7552febf7af92',1,'vg::io::gaf_paired_interleaved_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda)'],['../namespacevg_1_1io.html#ad242e1399847a5c894201b9e32c13a6d',1,'vg::io::gaf_paired_interleaved_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda)']]],
+ ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_1980',['gaf_paired_interleaved_for_each_parallel',['../namespacevg_1_1io.html#a7b473c9f170444107256aa76f522d27a',1,'vg::io::gaf_paired_interleaved_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#a8662ca54b9e1f26e421884a43a4e0e21',1,'vg::io::gaf_paired_interleaved_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)']]],
+ ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_5fafter_5fwait_1981',['gaf_paired_interleaved_for_each_parallel_after_wait',['../namespacevg_1_1io.html#a44d7cb48aae7d9c3621fabc6b31faa6e',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)'],['../namespacevg_1_1io.html#a63b12354bf13d6a19b5addc71fc512c7',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)']]],
+ ['gaf_5fsample_5fname_1982',['gaf_sample_name',['../classvg_1_1GAFOutputCaller.html#a23554330b3cf641645fe7b3070c6d203',1,'vg::GAFOutputCaller']]],
+ ['gaf_5fto_5falignment_1983',['gaf_to_alignment',['../namespacevg_1_1io.html#a44a872a40072dc128fa898a795eeff79',1,'vg::io::gaf_to_alignment(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const gafkluge::GafRecord &gaf, Alignment &aln)'],['../namespacevg_1_1io.html#a363656cc5c1a09f178e3c83785488bad',1,'vg::io::gaf_to_alignment(const HandleGraph &graph, const gafkluge::GafRecord &gaf, Alignment &aln)']]],
+ ['gaf_5funpaired_5ffor_5feach_1984',['gaf_unpaired_for_each',['../namespacevg_1_1io.html#a83d5011d88f6ef27ed8837957505284b',1,'vg::io::gaf_unpaired_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda)'],['../namespacevg_1_1io.html#ada4771a7ea674ee9d986af264ab3c00d',1,'vg::io::gaf_unpaired_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda)']]],
+ ['gaf_5funpaired_5ffor_5feach_5fparallel_1985',['gaf_unpaired_for_each_parallel',['../namespacevg_1_1io.html#a88d2dffc472bbcfded0b1190fc5bc933',1,'vg::io::gaf_unpaired_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#add46b11d285f6b94896c1f5e91a405a7',1,'vg::io::gaf_unpaired_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)']]],
+ ['gafalignmentemitter_1986',['GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html',1,'vg::io::GafAlignmentEmitter'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#ad7b537251b10534375e90a22b795b9cc',1,'vg::io::GafAlignmentEmitter::GafAlignmentEmitter()']]],
+ ['gaffile_1987',['GafFile',['../structGafFile.html',1,'']]],
+ ['gafkluge_1988',['gafkluge',['../namespacegafkluge.html',1,'']]],
+ ['gafkluge_2ehpp_1989',['gafkluge.hpp',['../gafkluge_8hpp.html',1,'']]],
+ ['gafoutputcaller_1990',['GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html',1,'vg::GAFOutputCaller'],['../classvg_1_1GAFOutputCaller.html#a2def7ee0c3eb2f0cbfd139ad0eeeec8b',1,'vg::GAFOutputCaller::GAFOutputCaller()']]],
+ ['gafrecord_1991',['GafRecord',['../structgafkluge_1_1GafRecord.html',1,'gafkluge::GafRecord'],['../structgafkluge_1_1GafRecord.html#a81394a04ad249c56b3f757484a7663bc',1,'gafkluge::GafRecord::GafRecord()']]],
+ ['gafstep_1992',['GafStep',['../structgafkluge_1_1GafStep.html',1,'gafkluge']]],
+ ['gam_1993',['GAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baf8d906e37d32ff64beb1baf4c50958fd',1,'vg::MultipathAlignmentEmitter']]],
+ ['gam_5fformat_1994',['gam_format',['../structGBWTConfig.html#a1fcbf295cfa998c40744359748fda6c7',1,'GBWTConfig']]],
+ ['gamcompare_5fmain_2ecpp_1995',['gamcompare_main.cpp',['../gamcompare__main_8cpp.html',1,'']]],
+ ['gamindex_1996',['GAMIndex',['../namespacevg.html#a9b677be2f409ffcbefd5d9f6149c80c1',1,'vg']]],
+ ['gamma_5fln_1997',['gamma_ln',['../namespacevg.html#a05748ab256c93e2393252aa8ebbdde3d',1,'vg']]],
+ ['gamp_1998',['GAMP',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba00b7d3df4dc1aead7feb32d379bb1a35',1,'vg::MultipathAlignmentEmitter']]],
+ ['gampcompare_5fmain_2ecpp_1999',['gampcompare_main.cpp',['../gampcompare__main_8cpp.html',1,'']]],
+ ['gamsort_5fmain_2ecpp_2000',['gamsort_main.cpp',['../gamsort__main_8cpp.html',1,'']]],
+ ['gamsorter_2001',['GAMSorter',['../namespacevg.html#a6c00bf57d75db83e41ac19a88882c043',1,'vg']]],
+ ['gap_5fdistance_5flimit_2002',['gap_distance_limit',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ad9d07441a40519ff349163eb7d87c916',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['gap_5fextend_2003',['gap_extend',['../classvg_1_1WFATree.html#abe47c55fbdfa81f6b0df6ffdb4c3591e',1,'vg::WFATree::gap_extend()'],['../structScoringOptions.html#a8ae3e44719121535cd43560dddc267aa',1,'ScoringOptions::gap_extend()']]],
+ ['gap_5fextend_5fpenalty_2004',['gap_extend_penalty',['../classvg_1_1WFATree.html#a705cd842a3204b5dbc0c669f3e1c60c7',1,'vg::WFATree']]],
+ ['gap_5fextension_2005',['gap_extension',['../classvg_1_1GSSWAligner.html#afd2379af50d751eee892a10529d64ffb',1,'vg::GSSWAligner::gap_extension()'],['../classvg_1_1DeletionAligner.html#a5fdfc2ac3a633a6e3cd61c2e3beeae97',1,'vg::DeletionAligner::gap_extension()'],['../classvg_1_1SSWAligner.html#a2248e3e561aab8d3b1036d51850b3c2f',1,'vg::SSWAligner::gap_extension()']]],
+ ['gap_5flength_2006',['gap_length',['../structvg_1_1WFAExtender_1_1ErrorModel.html#a9cf62e400ef2e4efb434e8e5a452e7e8',1,'vg::WFAExtender::ErrorModel']]],
+ ['gap_5fmemo_5fmax_5fsize_2007',['gap_memo_max_size',['../classvg_1_1MultipathMapper.html#a864cc168b7061cf1885ef61785e474d3',1,'vg::MultipathMapper']]],
+ ['gap_5fopen_2008',['gap_open',['../classvg_1_1GSSWAligner.html#aa5c0a63b73ad2ff8ec8f05062c768c22',1,'vg::GSSWAligner::gap_open()'],['../classvg_1_1DeletionAligner.html#a7791fe71828711b3208db54db784cf1d',1,'vg::DeletionAligner::gap_open()'],['../classvg_1_1WFATree.html#aec0c57320c07468df3201a106f7e6aa0',1,'vg::WFATree::gap_open()'],['../classvg_1_1SSWAligner.html#a15398a23880418599e81370d485fec0f',1,'vg::SSWAligner::gap_open()'],['../structScoringOptions.html#ab399d0cf09e907906b42d500a54194bc',1,'ScoringOptions::gap_open()']]],
+ ['gap_5fpenalty_2009',['gap_penalty',['../classvg_1_1WFATree.html#a46f357dbdd6957c1c08bb82a275a3bcf',1,'vg::WFATree']]],
+ ['gap_5fscale_2010',['gap_scale',['../classvg_1_1MinimizerMapper.html#a5e6e66b39ed25c3d81f82546231d790a',1,'vg::MinimizerMapper']]],
+ ['gapless_5fextension_5flimit_2011',['gapless_extension_limit',['../classvg_1_1MinimizerMapper.html#af0eb242f1ec9aaaa52e7d03446d09cbf',1,'vg::MinimizerMapper']]],
+ ['gaplessextender_2012',['GaplessExtender',['../classvg_1_1GaplessExtender.html',1,'vg::GaplessExtender'],['../classvg_1_1GaplessExtender.html#a497cc4e85c6433a3e41f04895703f271',1,'vg::GaplessExtender::GaplessExtender()'],['../classvg_1_1GaplessExtender.html#aaebc8d221df2787a68023fce2d99290a',1,'vg::GaplessExtender::GaplessExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner)']]],
+ ['gaplessextension_2013',['GaplessExtension',['../structvg_1_1GaplessExtension.html',1,'vg']]],
+ ['gaps_2014',['gaps',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ac60921b93f505b6731badc2aef7f64f5',1,'vg::WFAExtender::ErrorModel']]],
+ ['gbwt_2015',['gbwt',['../classvg_1_1Deconstructor.html#a52b3fcd3d7357f5dd3624d9caa56539f',1,'vg::Deconstructor::gbwt()'],['../classvg_1_1GBWTTraversalFinder.html#a7827a0ee00890a2d8cf1716017e39db7',1,'vg::GBWTTraversalFinder::gbwt()']]],
+ ['gbwt_5fbuffer_5fsize_2016',['gbwt_buffer_size',['../classvg_1_1HaplotypeIndexer.html#abc8d5ce81546e16ffb7bf652c098bb11',1,'vg::HaplotypeIndexer']]],
+ ['gbwt_5fextender_2ecpp_2017',['gbwt_extender.cpp',['../gbwt__extender_8cpp.html',1,'']]],
+ ['gbwt_5fextender_2ehpp_2018',['gbwt_extender.hpp',['../gbwt__extender_8hpp.html',1,'']]],
+ ['gbwt_5fgraph_2019',['gbwt_graph',['../classvg_1_1MinimizerMapper.html#abb94c27ed347a36fb38f91cf23a582fb',1,'vg::MinimizerMapper::gbwt_graph()'],['../structGraphHandler.html#ad86c0372b075e6e0c5bfbf61801b3222',1,'GraphHandler::gbwt_graph()']]],
+ ['gbwt_5fhelper_2ecpp_2020',['gbwt_helper.cpp',['../gbwt__helper_8cpp.html',1,'']]],
+ ['gbwt_5fhelper_2ehpp_2021',['gbwt_helper.hpp',['../gbwt__helper_8hpp.html',1,'']]],
+ ['gbwt_5findex_2022',['gbwt_index',['../classvg_1_1PhaseUnfolder.html#abe0ad79b8b65bea2a4f871913c83ee65',1,'vg::PhaseUnfolder']]],
+ ['gbwt_5finsert_5fbatch_5fsize_2023',['gbwt_insert_batch_size',['../structvg_1_1IndexingParameters.html#ab408ae73a85875de5dfe376e340f8840',1,'vg::IndexingParameters']]],
+ ['gbwt_5finsert_5fbatch_5fsize_5fincrease_5ffactor_2024',['gbwt_insert_batch_size_increase_factor',['../structvg_1_1IndexingParameters.html#a721125abeca5c4755e875f2e3d8c1d2f',1,'vg::IndexingParameters']]],
+ ['gbwt_5fmain_2ecpp_2025',['gbwt_main.cpp',['../gbwt__main_8cpp.html',1,'']]],
+ ['gbwt_5fname_2026',['gbwt_name',['../structGBWTConfig.html#a5fe3f0a41311811ddf16bcd7dbab4f91',1,'GBWTConfig']]],
+ ['gbwt_5fnode_5fwidth_2027',['gbwt_node_width',['../namespacevg.html#ada6300e45d21f1171c5ff2b71f4d173b',1,'vg']]],
+ ['gbwt_5foutput_2028',['gbwt_output',['../structGBWTConfig.html#a8d9b4d70bb33f75cb147ee91b75c89af',1,'GBWTConfig']]],
+ ['gbwt_5freference_5fsamples_2029',['gbwt_reference_samples',['../classvg_1_1Deconstructor.html#a8f81a59e45aad56aa6edc19756a9eb14',1,'vg::Deconstructor']]],
+ ['gbwt_5fsample_5fto_5fphase_5frange_2030',['gbwt_sample_to_phase_range',['../classvg_1_1Deconstructor.html#a5f58aa9a4d3f29e330a9c9e1c9541884',1,'vg::Deconstructor']]],
+ ['gbwt_5fsampling_5finterval_2031',['gbwt_sampling_interval',['../structvg_1_1IndexingParameters.html#abd33e81c954cb14ed31455a3950abe64',1,'vg::IndexingParameters']]],
+ ['gbwt_5fthread_5ft_2032',['gbwt_thread_t',['../structhaplo_1_1gbwt__thread__t.html',1,'haplo::gbwt_thread_t'],['../structhaplo_1_1gbwt__thread__t.html#a5b148ae0a27b81b4b4af07f200a1255b',1,'haplo::gbwt_thread_t::gbwt_thread_t()'],['../structhaplo_1_1gbwt__thread__t.html#aa52a0e84c11044abd6ce20969629e3a9',1,'haplo::gbwt_thread_t::gbwt_thread_t(const gbwt::vector_type &nodes, const vector< size_t > &node_lengths)']]],
+ ['gbwt_5fto_5fhandle_2033',['gbwt_to_handle',['../namespacevg.html#a28c93b1c4a71fadf62fc2582cc8f0ed2',1,'vg']]],
+ ['gbwt_5fto_5fpos_2034',['gbwt_to_pos',['../namespacevg.html#ae7b5f995eb3e1e824cc4e7db99c81042',1,'vg']]],
+ ['gbwt_5ftrav_5ffinder_2035',['gbwt_trav_finder',['../classvg_1_1Deconstructor.html#a41a7ff33e08c5eee5d2d7088dbc238f4',1,'vg::Deconstructor']]],
+ ['gbwtconfig_2036',['GBWTConfig',['../structGBWTConfig.html',1,'GBWTConfig'],['../structGBWTConfig.html#a20a8123e9a054bab77de5e8d9f9c1bd5',1,'GBWTConfig::GBWTConfig()']]],
+ ['gbwtgraph_5fhelper_2ecpp_2037',['gbwtgraph_helper.cpp',['../gbwtgraph__helper_8cpp.html',1,'']]],
+ ['gbwtgraph_5fhelper_2ehpp_2038',['gbwtgraph_helper.hpp',['../gbwtgraph__helper_8hpp.html',1,'']]],
+ ['gbwtgraph_5fname_2039',['gbwtgraph_name',['../structGBWTConfig.html#ac8e90b7bda206414a7055a98f5b55e85',1,'GBWTConfig']]],
+ ['gbwthandler_2040',['GBWTHandler',['../structvg_1_1GBWTHandler.html',1,'vg']]],
+ ['gbwtscoreprovider_2041',['GBWTScoreProvider',['../classhaplo_1_1GBWTScoreProvider.html',1,'haplo::GBWTScoreProvider< GBWTType >'],['../classhaplo_1_1GBWTScoreProvider.html#abf8bd05e480afa9a2ac2832a13f5b181',1,'haplo::GBWTScoreProvider::GBWTScoreProvider()']]],
+ ['gbwttraversalfinder_2042',['GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html',1,'vg::GBWTTraversalFinder'],['../classvg_1_1GBWTTraversalFinder.html#af415423d43372c2770c201a10ace0385',1,'vg::GBWTTraversalFinder::GBWTTraversalFinder()']]],
+ ['gbz_2043',['gbz',['../classvg_1_1GBZGraph.html#ac56a91ab9fe591aa7781cd751fe94ed4',1,'vg::GBZGraph::gbz()'],['../classvg_1_1HaplotypePartitioner.html#a533f084057db81844dd0c02f36fb5498',1,'vg::HaplotypePartitioner::gbz()'],['../classvg_1_1Recombinator.html#a977b21bbcc9ea6520dbc97a5014488e6',1,'vg::Recombinator::gbz()']]],
+ ['gbz_5fformat_2044',['gbz_format',['../structGBWTConfig.html#a14fe1675f26aa9b74381640c4cffdd47',1,'GBWTConfig']]],
+ ['gbz_5foutput_2045',['gbz_output',['../structHaplotypesConfig.html#af71ee285e699443b559375aeac054eb8',1,'HaplotypesConfig']]],
+ ['gbzgraph_2046',['GBZGraph',['../classvg_1_1GBZGraph.html',1,'vg']]],
+ ['gbzgraph_2ehpp_2047',['gbzgraph.hpp',['../gbzgraph_8hpp.html',1,'']]],
+ ['gc_5fcontent_5festimate_2048',['gc_content_estimate',['../classvg_1_1AlignerClient.html#a65428f092aaa5d894b709e247cf0121a',1,'vg::AlignerClient']]],
+ ['gcsa_2049',['gcsa',['../classvg_1_1BaseMapper.html#aa41db0eca93c379087c90b602a6ce751',1,'vg::BaseMapper']]],
+ ['gcsa_5fdoubling_5fsteps_2050',['gcsa_doubling_steps',['../structvg_1_1IndexingParameters.html#ab480b0e1f6dca30213719734b78904e5',1,'vg::IndexingParameters']]],
+ ['gcsa_5fhelper_2ecpp_2051',['gcsa_helper.cpp',['../gcsa__helper_8cpp.html',1,'']]],
+ ['gcsa_5fhelper_2ehpp_2052',['gcsa_helper.hpp',['../gcsa__helper_8hpp.html',1,'']]],
+ ['gcsa_5find_2053',['gcsa_ind',['../classvg_1_1Filter.html#ae98fe5c85ea704f1ef262b5556bbbbbb',1,'vg::Filter']]],
+ ['gcsa_5finitial_5fkmer_5flength_2054',['gcsa_initial_kmer_length',['../structvg_1_1IndexingParameters.html#a890a5822bd592090eaf5b529816ecb32',1,'vg::IndexingParameters']]],
+ ['gcsa_5fnodes_5fto_5fpositions_2055',['gcsa_nodes_to_positions',['../namespacevg.html#a3240e7b9bf787fb218d6324389ea234e',1,'vg']]],
+ ['gcsa_5fsize_5flimit_2056',['gcsa_size_limit',['../structvg_1_1IndexingParameters.html#a144f6b2b03ccc7ecf4b7d3a504aed1b7',1,'vg::IndexingParameters']]],
+ ['gen_5fflat_5fnode_2057',['gen_flat_node',['../structhaplo_1_1haplo__DP__rectangle.html#a87d1fd7ca4ac40321f912724bf5c3f8c',1,'haplo::haplo_DP_rectangle']]],
+ ['gen_5frange_5ft_2058',['gen_range_t',['../structhaplo_1_1haplo__DP__rectangle.html#af3fc7fee833ac23bdbc93f73fb5be9d9',1,'haplo::haplo_DP_rectangle']]],
+ ['generalizations_2059',['generalizations',['../classvg_1_1IndexRegistry.html#a665cc9431438ef50124b29e518465a05',1,'vg::IndexRegistry']]],
+ ['generate_2060',['generate',['../structvg_1_1RecombinatorFragment.html#a411831e7ba9db75f1d14708bb79f7eef',1,'vg::RecombinatorFragment']]],
+ ['generate_5fcontinuous_5funiform_2061',['generate_continuous_uniform',['../classvg_1_1MCMCGenotyper.html#a5ebeff817c6548c32c5377ed00c041c6',1,'vg::MCMCGenotyper']]],
+ ['generate_5fdiscrete_5funiform_2062',['generate_discrete_uniform',['../classvg_1_1MCMCGenotyper.html#a8b76754fc9611d38463cccd3051c0589',1,'vg::MCMCGenotyper']]],
+ ['generate_5ffrom_5fwide_5fgenerator_2063',['generate_from_wide_generator',['../classvg_1_1uniform__int__distribution.html#a6efdc1be7572287df4cfad1acd044d90',1,'vg::uniform_int_distribution']]],
+ ['generate_5fhaplotype_2064',['generate_haplotype',['../namespacevg.html#a117021c748aad14cfa190bbd2452405d',1,'vg']]],
+ ['generate_5fhaplotypes_2065',['generate_haplotypes',['../classvg_1_1Recombinator.html#a7f803cd4d08d8c699877e274bc3f5ceb',1,'vg::Recombinator::generate_haplotypes(const std::string &kff_file, const Parameters ¶meters) const'],['../classvg_1_1Recombinator.html#a8ac8a32e83455572b44af1da347cd09d',1,'vg::Recombinator::generate_haplotypes(const Haplotypes::TopLevelChain &chain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata, const Parameters ¶meters, double coverage) const']]],
+ ['generate_5finitial_5fguess_2066',['generate_initial_guess',['../classvg_1_1MCMCGenotyper.html#aac263c28f16acd3eb17d1f6013b5709e',1,'vg::MCMCGenotyper']]],
+ ['generate_5fpaths_2067',['generate_paths',['../classvg_1_1PhaseUnfolder.html#a7a2015207e502ecd4d294af79936bda2',1,'vg::PhaseUnfolder']]],
+ ['generate_5fthreads_2068',['generate_threads',['../classvg_1_1PhaseUnfolder.html#abc5cead86bec1446aedd4cb2ec291d3f',1,'vg::PhaseUnfolder']]],
+ ['generic_2069',['GENERIC',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cac942dc2a9f958acddc67e11472d3ca0b',1,'handlegraph']]],
+ ['genome_2070',['genome',['../classvg_1_1MCMCCaller.html#ad4278b11272792c879ab3463b513ae1e',1,'vg::MCMCCaller']]],
+ ['genome_5fstate_2ecpp_2071',['genome_state.cpp',['../genome__state_8cpp.html',1,'']]],
+ ['genome_5fstate_2ehpp_2072',['genome_state.hpp',['../genome__state_8hpp.html',1,'']]],
+ ['genomestate_2073',['GenomeState',['../classvg_1_1GenomeState.html',1,'vg::GenomeState'],['../classvg_1_1GenomeState.html#ab132518a611296d53c4f59a6b5737374',1,'vg::GenomeState::GenomeState()']]],
+ ['genomestatecommand_2074',['GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html',1,'vg']]],
+ ['genotype_2075',['Genotype',['../structvg_1_1Genotype.html',1,'vg::Genotype'],['../structvg_1_1Locus.html#a144d9dc0f9d61910db33decca23e4755',1,'vg::Locus::genotype()'],['../classvg_1_1SnarlCaller.html#a3e4d1ad4ece1a1bc1daa4ea6ecfbfa54',1,'vg::SnarlCaller::genotype()'],['../classvg_1_1RatioSupportSnarlCaller.html#afa1d42f1ba7e32ca274e23d0e9795278',1,'vg::RatioSupportSnarlCaller::genotype()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a1be3298970827475c5b96486d58fd833',1,'vg::PoissonSupportSnarlCaller::genotype()']]],
+ ['genotype_5fby_5fploidy_2076',['genotype_by_ploidy',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#af331caba29195578f8a48ed527232ed1',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['genotype_5flikelihood_2077',['genotype_likelihood',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a555a22f275a83ade8fcd35a1572908',1,'vg::PoissonSupportSnarlCaller']]],
+ ['genotype_5fmain_2ecpp_2078',['genotype_main.cpp',['../genotype__main_8cpp.html',1,'']]],
+ ['genotype_5fsnarl_2079',['genotype_snarl',['../classvg_1_1Genotyper.html#ae6a3a060adcffc32724498bbfda2c771',1,'vg::Genotyper']]],
+ ['genotype_5fsnarls_2080',['genotype_snarls',['../classvg_1_1FlowCaller.html#ae47f36ad1ec53a2381f970d159acbd64',1,'vg::FlowCaller::genotype_snarls()'],['../classvg_1_1NestedFlowCaller.html#a4c00174974936972c989b905a921b154',1,'vg::NestedFlowCaller::genotype_snarls()']]],
+ ['genotype_5fsvs_2081',['genotype_svs',['../namespacevg.html#a7d3374c888c7c37f1de8370e151af7f9',1,'vg']]],
+ ['genotypekit_2ecpp_2082',['genotypekit.cpp',['../genotypekit_8cpp.html',1,'']]],
+ ['genotypekit_2ehpp_2083',['genotypekit.hpp',['../genotypekit_8hpp.html',1,'']]],
+ ['genotypelikelihoodcalculator_2084',['GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html',1,'vg']]],
+ ['genotypepriorcalculator_2085',['GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html',1,'vg']]],
+ ['genotyper_2086',['Genotyper',['../classvg_1_1Genotyper.html',1,'vg']]],
+ ['genotyper_2ecpp_2087',['genotyper.cpp',['../genotyper_8cpp.html',1,'']]],
+ ['genotyper_2ehpp_2088',['genotyper.hpp',['../genotyper_8hpp.html',1,'']]],
+ ['geometric_5fsampling_5fprob_5fln_2089',['geometric_sampling_prob_ln',['../namespacevg.html#ae923ee7bdb53f33511c95f66a9c2773a',1,'vg']]],
+ ['get_2090',['get',['../structvg_1_1Annotation.html#a00494075a8d051c16b2485b44c541dce',1,'vg::Annotation::get()'],['../classvg_1_1GBZGraph.html#a69ee920e1aa95a146e8e77f32a717a88',1,'vg::GBZGraph::get()'],['../classvg_1_1GBZGraph.html#a3eb7ff9317143e89c14bd15a682426ac',1,'vg::GBZGraph::get() const'],['../classvg_1_1VcfBuffer.html#ac855a338ea08f2ea75dc73206f9d7520',1,'vg::VcfBuffer::get()'],['../classvg_1_1WindowedVcfBuffer.html#a3c09bb140ab8f8d91f2f67f3dc0e7f0b',1,'vg::WindowedVcfBuffer::get()'],['../classvg_1_1subcommand_1_1Subcommand.html#aa44da5b424f5fcf7133f6a061680693f',1,'vg::subcommand::Subcommand::get()']]],
+ ['get_5fadaptive_5fmin_5freseed_5flength_2091',['get_adaptive_min_reseed_length',['../classvg_1_1BaseMapper.html#a7f693887391ddeaebf4a4a609e2ab9b3',1,'vg::BaseMapper']]],
+ ['get_5faffinities_2092',['get_affinities',['../classvg_1_1Genotyper.html#abea795c1969c4866c349a07c7f9c7102',1,'vg::Genotyper']]],
+ ['get_5faffinities_5ffast_2093',['get_affinities_fast',['../classvg_1_1Genotyper.html#a966eee3f764281271904996546ef205b',1,'vg::Genotyper']]],
+ ['get_5faligner_2094',['get_aligner',['../classvg_1_1AlignerClient.html#a683c04ab96b613ea3459738beffe5982',1,'vg::AlignerClient']]],
+ ['get_5falignment_5femitter_2095',['get_alignment_emitter',['../namespacevg.html#aa95de659d860fc90fda95df414c89baf',1,'vg']]],
+ ['get_5falignment_5fstart_2096',['get_alignment_start',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a5790a8cfd26dd12a19d33fc11cb84933',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['get_5falignments_2097',['get_alignments',['../structvg_1_1AugmentedGraph.html#ad92c283634470f6372777c38a9a70a79',1,'vg::AugmentedGraph::get_alignments(id_t node_id) const'],['../structvg_1_1AugmentedGraph.html#a61465a645ac54c62d4707d570ed56f76',1,'vg::AugmentedGraph::get_alignments(pair< NodeSide, NodeSide >) const'],['../structvg_1_1AugmentedGraph.html#ab3bf8e1a51696ba12329045956b7646a',1,'vg::AugmentedGraph::get_alignments() const']]],
+ ['get_5fallele_2098',['get_allele',['../classvg_1_1PhasedGenome.html#a6f89ab856a31dfb7258fd7487c051a5a',1,'vg::PhasedGenome']]],
+ ['get_5falleles_2099',['get_alleles',['../classvg_1_1Deconstructor.html#a7977882fef8c75836fede5338925f411',1,'vg::Deconstructor']]],
+ ['get_5falt_5fpath_2100',['get_alt_path',['../classvg_1_1VCFTraversalFinder.html#acbbbaa19966bd2a939f9fdc05b414343',1,'vg::VCFTraversalFinder']]],
+ ['get_5falt_5ftraversal_2101',['get_alt_traversal',['../classvg_1_1VCFTraversalFinder.html#afd039c87e92906ac02479d8d2df43f13',1,'vg::VCFTraversalFinder']]],
+ ['get_5fannotation_2102',['get_annotation',['../classvg_1_1multipath__alignment__t.html#a401b9ef14924b463d54be7a4ced828d6',1,'vg::multipath_alignment_t::get_annotation()'],['../namespacevg.html#a1fda752e24eaed100f6c30904d2ca3e1',1,'vg::get_annotation(const Annotated &annotated, const string &name)'],['../namespacevg.html#a1c9f371af54160a44a44afd80c6cf71a',1,'vg::get_annotation(Annotated *annotated, const string &name)']]],
+ ['get_5fany_5fgraph_2103',['get_any_graph',['../structGraphHandler.html#a7155dd41d244081487e79759707f29af',1,'GraphHandler']]],
+ ['get_5faverage_5ftraversal_5fsupport_5fswitch_5fthreshold_2104',['get_average_traversal_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a62c1864ae422d93cba4eb248890fd3e4',1,'vg::TraversalSupportFinder']]],
+ ['get_5favg_5fbaseq_2105',['get_avg_baseq',['../namespacevg.html#a680a465e72fbddeed584f27a6c3f7b27',1,'vg']]],
+ ['get_5favg_5fnode_5fmapq_2106',['get_avg_node_mapq',['../classvg_1_1TraversalSupportFinder.html#a55880f595d8f607a73e8617e7b2aa216',1,'vg::TraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1PackedTraversalSupportFinder.html#a1fd604b1e8eac99954981aca81cafffd',1,'vg::PackedTraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aa3fab4fec47f870d3cc6e2c1fdb46ccb',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_mapq()']]],
+ ['get_5favg_5fnode_5fsupport_2107',['get_avg_node_support',['../classvg_1_1TraversalSupportFinder.html#a42cf4393f0ff594d0eaf489b2127cdef',1,'vg::TraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a66cbea99df3ef78364f653a044bec308',1,'vg::PackedTraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#abb0f5d8c3967c099daaf2fb174620f3a',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_support()']]],
+ ['get_5fback_5fgraph_5fnode_5fname_2108',['get_back_graph_node_name',['../classvg_1_1FlatFileBackTranslation.html#a816506e29e304f623d790d79271fd344',1,'vg::FlatFileBackTranslation::get_back_graph_node_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a5829e7992e105e0895a81a8aca82e70b',1,'vg::algorithms::GFAIDMapInfo::get_back_graph_node_name()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#acd81ad54c6a6ec680faaae76aaae4397',1,'handlegraph::NamedNodeBackTranslation::get_back_graph_node_name()']]],
+ ['get_5fbase_2109',['get_base',['../classvg_1_1IncrementalSubgraph.html#a6ff73a10a56b8116b7d07c32d3f3160a',1,'vg::IncrementalSubgraph::get_base()'],['../classvg_1_1JoinedSpliceGraph.html#a7dcc1d1e3e9c2e1058a5995785b0a224',1,'vg::JoinedSpliceGraph::get_base()'],['../classvg_1_1VG.html#a7cb582e352f75cc9d66e6eff0f4ba659',1,'vg::VG::get_base()'],['../classxg_1_1XG.html#a355dd79f8449b462e7d98916f1a22d9f',1,'xg::XG::get_base()'],['../classhandlegraph_1_1HandleGraph.html#a64d58c3e26e9e7954dd25c3eff7af521',1,'handlegraph::HandleGraph::get_base()']]],
+ ['get_5fbase_5fgbwt_5fpath_5fname_2110',['get_base_gbwt_path_name',['../classvg_1_1Transcriptome.html#a1c9af6904f1f282a0782c1e34bc4b9ab',1,'vg::Transcriptome']]],
+ ['get_5fbest_5falignment_5fagainst_5fany_5ftree_2111',['get_best_alignment_against_any_tree',['../classvg_1_1MinimizerMapper.html#a12558b08552a22a9a28db3fb0fd3779d',1,'vg::MinimizerMapper']]],
+ ['get_5fbest_5fchain_5fstats_2112',['get_best_chain_stats',['../classvg_1_1MinimizerMapper.html#a2f9b9b580ed851b00268f455c2d543cb',1,'vg::MinimizerMapper']]],
+ ['get_5fbest_5fgbwtgraph_5fgfa_5fparsing_5fparameters_2113',['get_best_gbwtgraph_gfa_parsing_parameters',['../namespacevg.html#ab35317ee2bc53165662dd776516f341d',1,'vg']]],
+ ['get_5fbest_5fsupport_2114',['get_best_support',['../classvg_1_1SupportBasedSnarlCaller.html#a1b5a50373729771229ada685b12627df',1,'vg::SupportBasedSnarlCaller']]],
+ ['get_5fbias_2115',['get_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a3f5f06692eeabe27d7c00afc8658cb20',1,'vg::RatioSupportSnarlCaller']]],
+ ['get_5fbin_5fsize_2116',['get_bin_size',['../classvg_1_1Packer.html#afef014ad5278ee08959c3ffe2cf15c17',1,'vg::Packer']]],
+ ['get_5fbound_2117',['get_bound',['../classhandlegraph_1_1SnarlDecomposition.html#aabee8d2ebb1971ecfd5c4647b84081f2',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fbounds_2118',['get_bounds',['../classvg_1_1Constructor.html#a06078b6af1dc190c74806b30b669daae',1,'vg::Constructor']]],
+ ['get_5fbuckets_2119',['get_buckets',['../classvg_1_1OrientedDistanceMeasurer.html#aa21aedba58999e7041483f077720d13b',1,'vg::OrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#aac5383ef03533609d85172e7821a8200',1,'vg::PathOrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#ac885044126300cab4750fd21fd4634fc',1,'vg::SnarlOrientedDistanceMeasurer::get_buckets()']]],
+ ['get_5fcategory_2120',['get_category',['../classvg_1_1subcommand_1_1Subcommand.html#a252c8946e450ba4a194b7da6ece5ba2c',1,'vg::subcommand::Subcommand']]],
+ ['get_5fcc_5fin_5fwg_2121',['get_cc_in_wg',['../classvg_1_1FlowSort.html#a27df1607587f1f1e1f03ab8369c34ebe',1,'vg::FlowSort']]],
+ ['get_5fcenter_2122',['get_center',['../classvg_1_1VariantAdder.html#a2949d0ea5c46f477813df8f5162fe013',1,'vg::VariantAdder']]],
+ ['get_5fcenter_5fand_5fradius_2123',['get_center_and_radius',['../classvg_1_1VariantAdder.html#a29a14a6579197519b35653f542d5c1ec',1,'vg::VariantAdder']]],
+ ['get_5fchain_5fcode_2124',['get_chain_code',['../classvg_1_1ZipCode.html#aa0f40a265733bd4adfb920006fd9f57a',1,'vg::ZipCode']]],
+ ['get_5fchain_5fcomponent_2125',['get_chain_component',['../classvg_1_1ZipCode.html#af85179af0d75add0b10023343c2a407a',1,'vg::ZipCode::get_chain_component()'],['../structvg_1_1ZipCode_1_1node__code__t.html#a52e72d7ff49bcb809cac2f7ab85ad004',1,'vg::ZipCode::node_code_t::get_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5dcd90a391b2382723f3b303687ca1c8',1,'vg::ZipCode::snarl_code_t::get_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#adc51b5f6e09b00eb41964c902d7eb033',1,'vg::ZipCodeForest::sort_value_t::get_chain_component()']]],
+ ['get_5fchild_5fcount_2126',['get_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a315c9998b34918303feb08d5143fba7c',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fchild_5fsupport_2127',['get_child_support',['../classvg_1_1TraversalSupportFinder.html#ac46ef820b2a05e8b331677deb80871a9',1,'vg::TraversalSupportFinder::get_child_support()'],['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af112bf57cc9a16c9dc35f6578a3b1c14',1,'vg::NestedCachedPackedTraversalSupportFinder::get_child_support()']]],
+ ['get_5fclipped_5fposition_2128',['get_clipped_position',['../classvg_1_1Filter.html#a5cc119894a6baeb450c31dc7c6b75bed',1,'vg::Filter']]],
+ ['get_5fclipped_5fref_5fposition_2129',['get_clipped_ref_position',['../classvg_1_1Filter.html#ab1a309b366e677b179772e9bebd9f78f',1,'vg::Filter']]],
+ ['get_5fclipped_5fseq_2130',['get_clipped_seq',['../classvg_1_1Filter.html#a4c29ccf736113bb95328467d22f98ad8',1,'vg::Filter']]],
+ ['get_5fcluster_5fpairs_2131',['get_cluster_pairs',['../classvg_1_1MultipathMapper.html#a49fdf1a2efedda808c2d3a7bda5a7f98',1,'vg::MultipathMapper']]],
+ ['get_5fclusters_2132',['get_clusters',['../classvg_1_1MultipathMapper.html#a0a588e4f282d38add8626debe86c455d',1,'vg::MultipathMapper']]],
+ ['get_5fcode_5ftype_2133',['get_code_type',['../classvg_1_1ZipCode.html#ac91d59c7100fefc2011cda07996ed71a',1,'vg::ZipCode::get_code_type()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a0d7f3c9052df0ced4949b909d1ed20b5',1,'vg::ZipCode::snarl_code_t::get_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a9959da3b3a6e98968794073dc049eb0b',1,'vg::ZipCodeForest::sort_value_t::get_code_type()']]],
+ ['get_5fcodename_2134',['get_codename',['../classvg_1_1Version.html#a0bab20984ed75b2df12c3ef4a409f922',1,'vg::Version']]],
+ ['get_5fconnected_5fcomponents_2135',['get_connected_components',['../classvg_1_1MultipathAlignmentGraph.html#af4fc215d24f20c5ddc3916024c7ab62b',1,'vg::MultipathAlignmentGraph']]],
+ ['get_5fconnectivity_2136',['get_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a0b28eb090f0d0f7b1b408a5e772b3105',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fcontained_5forientations_2137',['get_contained_orientations',['../structvg_1_1PathIndex.html#a6a7f7bbcd256a2ed34a58b8abefff712',1,'vg::PathIndex']]],
+ ['get_5fcontext_2138',['get_context',['../classvg_1_1Deconstructor.html#a049890802f6b6036a779eb3645bb1307',1,'vg::Deconstructor']]],
+ ['get_5fcorrelation_2139',['get_correlation',['../classvg_1_1ZipCodeForest.html#ab939e5ee856a9ac2531d0d8ac14e7cbe',1,'vg::ZipCodeForest']]],
+ ['get_5fcount_2140',['get_count',['../classvg_1_1NoAlignmentInBandException.html#a4b5f7f90a2be571131fb12484a9b4c18',1,'vg::NoAlignmentInBandException']]],
+ ['get_5fcreate_5fpath_2141',['get_create_path',['../classvg_1_1Paths.html#a4e79d7915cd2f68e55573bcc50c1d417',1,'vg::Paths']]],
+ ['get_5fcreated_5fhandle_2142',['get_created_handle',['../classvg_1_1ExtraNodeGraph.html#aac84ee8139e0aa885b87f02ad9ccf8ef',1,'vg::ExtraNodeGraph']]],
+ ['get_5fcurrent_5fcolumn_2143',['get_current_column',['../structhaplo_1_1haplo__DP.html#a0061c97ecd2330efdcf0fbabb69d808d',1,'haplo::haplo_DP']]],
+ ['get_5fcurrent_5fvmem_5fkb_2144',['get_current_vmem_kb',['../namespacevg.html#a8cd30aaebcab130194ac375f23e6f098',1,'vg']]],
+ ['get_5fcut_5fsegments_2145',['get_cut_segments',['../classvg_1_1MultipathAlignmentGraph.html#aaa64dbf4207ebe2fe75044d60be1d07e',1,'vg::MultipathAlignmentGraph']]],
+ ['get_5fcyclic_5fsnarl_5fintervals_2146',['get_cyclic_snarl_intervals',['../classvg_1_1ZipCodeForest.html#ad32664318549a51d8727204d665a2bc6',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const interval_state_t &snarl_interval, const interval_state_t &parent_interval, const forward_list< interval_state_t > &child_intervals, forward_list< interval_state_t > &next_intervals) const'],['../classvg_1_1ZipCodeForest.html#a72304772e60e79909b71f8a51e65d6a5',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const ZipCodeForest::interval_state_t &snarl_interval, const ZipCodeForest::interval_state_t &parent_interval, const forward_list< ZipCodeForest::interval_state_t > &child_intervals, forward_list< ZipCodeForest::interval_state_t > &next_intervals) const']]],
+ ['get_5fdefault_5flong_5fgiraffe_5findexes_2147',['get_default_long_giraffe_indexes',['../structvg_1_1VGIndexes.html#a8caf19bd7436cd7f9df4f9792aa86483',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fmap_5findexes_2148',['get_default_map_indexes',['../structvg_1_1VGIndexes.html#afcc2119cd690b16f57d4b9d137af58fe',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fmpmap_5findexes_2149',['get_default_mpmap_indexes',['../structvg_1_1VGIndexes.html#a9377b325c6e0f8bbca1368379ad60a0c',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5frpvg_5findexes_2150',['get_default_rpvg_indexes',['../structvg_1_1VGIndexes.html#ae56d5009377fed32d392fcff5ac02f7f',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fshort_5fgiraffe_5findexes_2151',['get_default_short_giraffe_indexes',['../structvg_1_1VGIndexes.html#ab0f962c74f9633fe27b0d59f9774358c',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fthreads_2152',['get_default_threads',['../minimizer__main_8cpp.html#a849308cddbd36f5fc06c5e1289112bae',1,'minimizer_main.cpp']]],
+ ['get_5fdefault_5fvalue_2153',['get_default_value',['../classvg_1_1OptionInterface.html#ade1ab38610fecb31821e13e5e296454c',1,'vg::OptionInterface::get_default_value()'],['../classvg_1_1BaseOption.html#af13c01c387907bb386b591bff8bbb5e9',1,'vg::BaseOption::get_default_value()']]],
+ ['get_5fdegree_2154',['get_degree',['../classvg_1_1ExtraNodeGraph.html#a0cc5cb40e81623b3a3e11bea359e41c5',1,'vg::ExtraNodeGraph::get_degree()'],['../classvg_1_1IncrementalSubgraph.html#ae3365d87d1cd6bfe12d3433197d06a85',1,'vg::IncrementalSubgraph::get_degree()'],['../classvg_1_1SourceSinkOverlay.html#a8bfc476463b487d42c77bda6bdfe2a7d',1,'vg::SourceSinkOverlay::get_degree()'],['../classvg_1_1VG.html#afc0ac00267e00156e04c849a10b1cb74',1,'vg::VG::get_degree()'],['../classhandlegraph_1_1HandleGraph.html#ab259e3aba0da47b0ef1c9b5e43c7d209',1,'handlegraph::HandleGraph::get_degree()']]],
+ ['get_5fdepth_5ffrom_5findex_2155',['get_depth_from_index',['../namespacevg_1_1algorithms.html#a4152fa019243d9fd4c41c73fafce2241',1,'vg::algorithms']]],
+ ['get_5fdescription_2156',['get_description',['../classvg_1_1OptionInterface.html#aa53deb39285f0045257083eb38d703cd',1,'vg::OptionInterface::get_description()'],['../classvg_1_1BaseOption.html#a4343a02a0967d6f79c0b8ae83c6a0795',1,'vg::BaseOption::get_description()'],['../classvg_1_1subcommand_1_1Subcommand.html#aca3e8621a4002b48b733211c3adc52b5',1,'vg::subcommand::Subcommand::get_description()']]],
+ ['get_5fdiagonals_2157',['get_diagonals',['../classvg_1_1WFATree.html#a2bd4732a5815c365d3790b76b9230973',1,'vg::WFATree']]],
+ ['get_5fdir_2158',['get_dir',['../namespacevg_1_1temp__file.html#ab1b0884547b4f3403e8cde0ca8b75b7c',1,'vg::temp_file::get_dir()'],['../namespacexg_1_1temp__file.html#a1cef40a1b0f27d1693d827db9773c020',1,'xg::temp_file::get_dir()']]],
+ ['get_5fdisjoint_5fsets_2159',['get_disjoint_sets',['../classvg_1_1ContractingGraph.html#acd929119b9b11170f1eb4893a7032fe6',1,'vg::ContractingGraph']]],
+ ['get_5fdistance_2160',['get_distance',['../classvg_1_1HaplotypePartitioner.html#a8d98335b0032014b1e033a6610fb644d',1,'vg::HaplotypePartitioner']]],
+ ['get_5fdistance_5fend_5fleft_2161',['get_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ad3e98278c0ca79470bc1a58e3fdcf370',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5fend_5fright_2162',['get_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa5d11da32ad7be1dfa88674efd4fa422',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5findex_5faddress_2163',['get_distance_index_address',['../classvg_1_1ZipCode.html#a6cc3964efc186615dab6bdd8bc52fbfb',1,'vg::ZipCode']]],
+ ['get_5fdistance_5flimit_2164',['get_distance_limit',['../classvg_1_1MinimizerMapper.html#a27798cd4a1bee171ec38713d402e8793',1,'vg::MinimizerMapper']]],
+ ['get_5fdistance_5fmeasurer_2165',['get_distance_measurer',['../classvg_1_1MultipathMapper.html#a56e1c69cfba7c1eebb4cae0af59a018d',1,'vg::MultipathMapper']]],
+ ['get_5fdistance_5fstart_5fleft_2166',['get_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a678e476d61bcf781b1461cedb8801c68',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5fstart_5fright_2167',['get_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aedb473ac00ffbd480c09fd04e44fcbb8',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5fto_5fsnarl_5fbound_2168',['get_distance_to_snarl_bound',['../classvg_1_1ZipCode.html#ad39662d894fe714c1d8596b0343557f6',1,'vg::ZipCode']]],
+ ['get_5fdistance_5fvalue_2169',['get_distance_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a2a427abecffc91c8f56b715de43a43b3',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['get_5fduplicate_5fhandle_2170',['get_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#af51998490e3eac92e0d106b791eebbce',1,'vg::DozeuPinningOverlay']]],
+ ['get_5fedge_2171',['get_edge',['../classvg_1_1VG.html#a8668ddc84b9abe4fe9cb5acb3efd877b',1,'vg::VG::get_edge(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a227023072262f46f7c423d30cf8bc443',1,'vg::VG::get_edge(const pair< NodeSide, NodeSide > &sides)'],['../classvg_1_1VG.html#af63d7ba7b69594ee99f3ad99dd394171',1,'vg::VG::get_edge(const NodeTraversal &left, const NodeTraversal &right)']]],
+ ['get_5fedge_5fcount_2172',['get_edge_count',['../classvg_1_1IncrementalSubgraph.html#aeab323f77d0363867dc60be6dafe73ce',1,'vg::IncrementalSubgraph::get_edge_count()'],['../classvg_1_1VG.html#ad4577be9213932c313efd3d016b88a31',1,'vg::VG::get_edge_count()'],['../classxg_1_1XG.html#aa624840475fc83351c00ef2728480355',1,'xg::XG::get_edge_count()'],['../classhandlegraph_1_1HandleGraph.html#a20ff62014d7f0f0c01ada8a3d40a278d',1,'handlegraph::HandleGraph::get_edge_count()']]],
+ ['get_5fedge_5flength_2173',['get_edge_length',['../classvg_1_1TraversalSupportFinder.html#a4902b9dcdaa53f74f45a394265163311',1,'vg::TraversalSupportFinder']]],
+ ['get_5fedge_5fsupport_2174',['get_edge_support',['../classvg_1_1RepresentativeTraversalFinder.html#a452fdd307124349d6b65aa434bab48c7',1,'vg::RepresentativeTraversalFinder::get_edge_support()'],['../classvg_1_1TraversalSupportFinder.html#a8b497d8e282da9696d2ae5df86664069',1,'vg::TraversalSupportFinder::get_edge_support(const edge_t &edge) const =0'],['../classvg_1_1TraversalSupportFinder.html#a958a20d44167e8c29f677e12b950b5fa',1,'vg::TraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const =0'],['../classvg_1_1PackedTraversalSupportFinder.html#a394485c49fb5d8043d9f98385dab1b4a',1,'vg::PackedTraversalSupportFinder::get_edge_support(const edge_t &edge) const'],['../classvg_1_1PackedTraversalSupportFinder.html#a5cfa1254fae043f9920761a533d63480',1,'vg::PackedTraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#a72ae391a14cf1625286d8c3aff3cd7a5',1,'vg::CachedPackedTraversalSupportFinder::get_edge_support()']]],
+ ['get_5fedges_2175',['get_edges',['../classvg_1_1ContractingGraph.html#a9faff1ddfb92cfa26ba59803899148e7',1,'vg::ContractingGraph']]],
+ ['get_5fend_2176',['get_end',['../classvg_1_1NetGraph.html#acccdda49a6444e96292b90218e273942',1,'vg::NetGraph']]],
+ ['get_5fend_5fbound_2177',['get_end_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a4c500f039a8740ff6e771ddf4bf693ad',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fend_5fmatches_2178',['get_end_matches',['../classvg_1_1ReadFilter.html#a3cd3ee44928526e27e42e059b693ba76',1,'vg::ReadFilter::get_end_matches(const Read &read) const'],['../classvg_1_1ReadFilter.html#a1e40faa7aa74f7b17390b06da6ad32e4',1,'vg::ReadFilter::get_end_matches(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#a45116be7bd52bfd9fb40e30f08aee97f',1,'vg::ReadFilter::get_end_matches(const Alignment &read) const']]],
+ ['get_5fend_5fof_2179',['get_end_of',['../namespacevg.html#af76e8a5e74f67093a40ed5f2cd15ff28',1,'vg']]],
+ ['get_5fendpoints_2180',['get_endpoints',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a9e3d20d5ab60eb99688d6346a788d308',1,'vg::GraphSynchronizer::Lock']]],
+ ['get_5fexon_5fhaplotypes_2181',['get_exon_haplotypes',['../classvg_1_1Transcriptome.html#a2753baecefb5f065854fd9fbc1a24dc9',1,'vg::Transcriptome']]],
+ ['get_5ffeatures_2182',['get_features',['../classvg_1_1FeatureSet.html#a55b389aa1c68efddb28a188a757568fc',1,'vg::FeatureSet']]],
+ ['get_5ffile_5fsize_2183',['get_file_size',['../namespacevg.html#a53098c7c826c3d8d2aab804ba5500fd5',1,'vg']]],
+ ['get_5ffilenames_2184',['get_filenames',['../classvg_1_1IndexFile.html#a5833162264de6ce5f2a0d882b4b12839',1,'vg::IndexFile']]],
+ ['get_5ffirst_5fnode_5fhandle_2185',['get_first_node_handle',['../structvg_1_1EditedTranscriptPath.html#aec08731a5fd5989db7721a3ecf0859e7',1,'vg::EditedTranscriptPath::get_first_node_handle()'],['../structvg_1_1CompletedTranscriptPath.html#af48eb44f24298e5f3efa4641eb91d813',1,'vg::CompletedTranscriptPath::get_first_node_handle()']]],
+ ['get_5ffraction_5fof_5fns_2186',['get_fraction_of_ns',['../namespacevg.html#af8f8da6eb179ba0199fc2fdfe676fde7',1,'vg']]],
+ ['get_5ffragment_5flength_5fmean_2187',['get_fragment_length_mean',['../classvg_1_1MinimizerMapper.html#a1e08dfa10f620ef44d102123b38b8fe8',1,'vg::MinimizerMapper']]],
+ ['get_5ffragment_5flength_5fsample_5fsize_2188',['get_fragment_length_sample_size',['../classvg_1_1MinimizerMapper.html#ab4c62a806ad7b64072a770c9b4db3417',1,'vg::MinimizerMapper']]],
+ ['get_5ffragment_5flength_5fstdev_2189',['get_fragment_length_stdev',['../classvg_1_1MinimizerMapper.html#ae048c4929acb22eabd55f54ac3cc6f18',1,'vg::MinimizerMapper']]],
+ ['get_5fg_5fiv_5fsize_2190',['get_g_iv_size',['../classxg_1_1XG.html#a1162be39bbe491975cd47c56fc044489',1,'xg::XG']]],
+ ['get_5fgbwt_2191',['get_gbwt',['../classvg_1_1GBWTTraversalFinder.html#a07c5e06ec89e54f2efc2d84974b71ca3',1,'vg::GBWTTraversalFinder::get_gbwt()'],['../namespacevg.html#a571047c58b73b78d02a767c3ab6ec222',1,'vg::get_gbwt()']]],
+ ['get_5fgenotype_5flog_5flikelihood_2192',['get_genotype_log_likelihood',['../classvg_1_1Genotyper.html#a9071cdf5ae591b478feaac025b069772',1,'vg::Genotyper']]],
+ ['get_5fgenotype_5flog_5fprior_2193',['get_genotype_log_prior',['../classvg_1_1Genotyper.html#a5fc66cb05c4ba80e39d078af9ddce715',1,'vg::Genotyper']]],
+ ['get_5fgenotypes_2194',['get_genotypes',['../classvg_1_1Deconstructor.html#abed056375d448eeffebcf1b15633fe79',1,'vg::Deconstructor']]],
+ ['get_5fgraph_2195',['get_graph',['../classvg_1_1Packer.html#a19b5aa3c38b65c9e35e2ab7604bdbec4',1,'vg::Packer::get_graph()'],['../classvg_1_1VariantAdder.html#a1271c6d39e6387bac452d9bf80689ed5',1,'vg::VariantAdder::get_graph()'],['../structGraphHandler.html#ab0c19a482787b623d946746f33b2fb80',1,'GraphHandler::get_graph()']]],
+ ['get_5fgraph_5fdistance_2196',['get_graph_distance',['../namespacevg_1_1algorithms.html#a0b788763f4e6747ba55e5340de9da855',1,'vg::algorithms']]],
+ ['get_5fhandle_2197',['get_handle',['../classvg_1_1DagifiedGraph.html#a57e727b78f3eac1ee34b5dabf08a278f',1,'vg::DagifiedGraph::get_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a78c76b68997b94da8bb714ad87b6ce55',1,'vg::DozeuPinningOverlay::get_handle()'],['../classvg_1_1ExtraNodeGraph.html#a76226cecc78c23a95db06f2765138e6f',1,'vg::ExtraNodeGraph::get_handle()'],['../classvg_1_1GaplessExtender.html#ace7698779da48ed9216169b935b0287c',1,'vg::GaplessExtender::get_handle()'],['../classvg_1_1SnarlGraph.html#a8c06fedda57c3e031d8d3b7fbcb696a8',1,'vg::SnarlGraph::get_handle()'],['../classvg_1_1IdentityOverlay.html#a3fc814950bd9b0b003b82637be9c1d06',1,'vg::IdentityOverlay::get_handle()'],['../classvg_1_1IncrementalSubgraph.html#ac2d018cb5a59b4f43e24a4f30643e0f1',1,'vg::IncrementalSubgraph::get_handle()'],['../classvg_1_1IndexedVG.html#ad9779976b07decd5b593b7a097cac44e',1,'vg::IndexedVG::get_handle()'],['../classvg_1_1MemoizingGraph.html#aa0b891348a82fe4fad7f60ab87fbd4b4',1,'vg::MemoizingGraph::get_handle()'],['../classvg_1_1NullMaskingGraph.html#aea8062f2a253f0397a91005b3924475e',1,'vg::NullMaskingGraph::get_handle()'],['../classvg_1_1PathSubgraph.html#a9d2fc4747e6c86125ba149c90041abcd',1,'vg::PathSubgraph::get_handle()'],['../classvg_1_1ReverseGraph.html#a34a79e8c3f5d5f029d5a1427ca10cfbd',1,'vg::ReverseGraph::get_handle()'],['../classvg_1_1NetGraph.html#a639a1a278626238fe98568320590c64f',1,'vg::NetGraph::get_handle()'],['../classvg_1_1SourceSinkOverlay.html#a7cc144d829750cfb85341d42bd4f7e4a',1,'vg::SourceSinkOverlay::get_handle()'],['../classvg_1_1JoinedSpliceGraph.html#a17636cfa63438f4b5941d54b7632d64b',1,'vg::JoinedSpliceGraph::get_handle()'],['../classvg_1_1StrandSplitGraph.html#a97db8ec5efb4280bfe358b0859e96659',1,'vg::StrandSplitGraph::get_handle()'],['../classvg_1_1SubHandleGraph.html#a4cf66400a93dee8a1e49fcc88ab24eb5',1,'vg::SubHandleGraph::get_handle()'],['../classvg_1_1SubgraphOverlay.html#ab36d552e3882740962729d19069f9ddc',1,'vg::SubgraphOverlay::get_handle()'],['../classvg_1_1SubpathOverlay.html#a3871270e3d47a023f27f9bac6959983b',1,'vg::SubpathOverlay::get_handle()'],['../classvg_1_1TreeSubgraph.html#ab7b56b78b8750cc6453180e7e531d925',1,'vg::TreeSubgraph::get_handle()'],['../classvg_1_1VG.html#a70f50e6766af9262c732de26243658f5',1,'vg::VG::get_handle()'],['../classxg_1_1XG.html#adc5660ffe20948888aeca0c6e6bba90a',1,'xg::XG::get_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0a950e73c94a514de69f95be80f96b7e',1,'handlegraph::algorithms::SubHandleGraph::get_handle()'],['../classhandlegraph_1_1HandleGraph.html#a6dd9d70931835f5c75518b23a780b744',1,'handlegraph::HandleGraph::get_handle()'],['../classhandlegraph_1_1SnarlDecomposition.html#a94e6360cbad97a084d6ec3a6a461e20c',1,'handlegraph::SnarlDecomposition::get_handle()']]],
+ ['get_5fhandle_5ffrom_5finward_5fbacking_5fhandle_2198',['get_handle_from_inward_backing_handle',['../classvg_1_1NetGraph.html#a62b87ba5400e8c6d3f6335fc2198cc38',1,'vg::NetGraph']]],
+ ['get_5fhandle_5fmemo_2199',['get_handle_memo',['../classvg_1_1MemoizingGraph.html#a522abfb6d16b8e96a77ff6f114275cf8',1,'vg::MemoizingGraph']]],
+ ['get_5fhandle_5fof_5fstep_2200',['get_handle_of_step',['../classvg_1_1MemoizingGraph.html#a2b4cd0c4ebef4dcefd5bbafcd1ab3e54',1,'vg::MemoizingGraph::get_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a05ce3d84e3e774a89d4d61a70381cee2',1,'vg::PathSubgraphOverlay::get_handle_of_step()'],['../classvg_1_1VG.html#acb73599cc743a392650a7002c8dc2906',1,'vg::VG::get_handle_of_step()'],['../classxg_1_1XG.html#abbfaa6afca08ec2aca7f2fd550221793',1,'xg::XG::get_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a339e690ce3e2bb8280dd1f3ea45abe42',1,'handlegraph::PathHandleGraph::get_handle_of_step()']]],
+ ['get_5fhaplotype_2201',['get_haplotype',['../classhandlegraph_1_1PathMetadata.html#a8ea83e700d11830e7eb695b8a11cb17f',1,'handlegraph::PathMetadata::get_haplotype()'],['../haplotypes__main_8cpp.html#ada326bf02798916f16c46f5d308ebc5b',1,'get_haplotype(): haplotypes_main.cpp']]],
+ ['get_5fhaplotype_5falt_5fcontents_2202',['get_haplotype_alt_contents',['../classvg_1_1VCFTraversalFinder.html#a3ce22629a99aae20002c43c7e581c2fb',1,'vg::VCFTraversalFinder']]],
+ ['get_5fhaplotype_5fcount_2203',['get_haplotype_count',['../classhaplo_1_1ScoreProvider.html#aac21ae0e24c45170e81b4880f8c21f8d',1,'haplo::ScoreProvider::get_haplotype_count()'],['../classhaplo_1_1GBWTScoreProvider.html#a8aedfce11f295af0fba3ae7f17f20c9b',1,'haplo::GBWTScoreProvider::get_haplotype_count()']]],
+ ['get_5fhaplotypes_5fwith_5fsnarl_2204',['get_haplotypes_with_snarl',['../classvg_1_1PhasedGenome.html#a81cff23c8687f759dd464fca51cf306e',1,'vg::PhasedGenome']]],
+ ['get_5fhelp_2205',['get_help',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a9880c67cbeb3f5b7ba3bad714844702c',1,'vg::subcommand::BaseOptionGroup::get_help()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a958199095b53020a85a5abc2ae1f0a91',1,'vg::subcommand::OptionGroup::get_help()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a01f89740d89e82cf12c204c28ec01fd2',1,'vg::subcommand::GroupedOptionGroup::get_help()']]],
+ ['get_5fid_2206',['get_id',['../classvg_1_1DagifiedGraph.html#ae510cacf154e272f63b37a3207046c96',1,'vg::DagifiedGraph::get_id()'],['../classvg_1_1DozeuPinningOverlay.html#ad84aae5d9cce852e254d5da05da40fa8',1,'vg::DozeuPinningOverlay::get_id()'],['../classvg_1_1ExtraNodeGraph.html#aef3ca5fb2071fdb33a7a8f663473de32',1,'vg::ExtraNodeGraph::get_id()'],['../classvg_1_1SnarlGraph.html#aba421b2e2cd40a7d489c13e0ab81f179',1,'vg::SnarlGraph::get_id()'],['../classvg_1_1IdentityOverlay.html#ab144f5ecbf4a5f49a5ffbea80ebd56ec',1,'vg::IdentityOverlay::get_id()'],['../classvg_1_1IncrementalSubgraph.html#a825edf9eddd3fa6093f2045656ae98f1',1,'vg::IncrementalSubgraph::get_id()'],['../classvg_1_1IndexedVG.html#ad23ba69aad4d8c94f58319bb657e3235',1,'vg::IndexedVG::get_id()'],['../classvg_1_1MemoizingGraph.html#a23b6df961f0e8253fba88423f2bcf128',1,'vg::MemoizingGraph::get_id()'],['../classvg_1_1NullMaskingGraph.html#a541f81de46db62d5e8f37e3cfc51f08e',1,'vg::NullMaskingGraph::get_id()'],['../classvg_1_1PathSubgraph.html#a47ff1fe374dccd07542ed1523327553e',1,'vg::PathSubgraph::get_id()'],['../classvg_1_1ReverseGraph.html#aef09dbb8dd08735bdd123b2a9d0066e0',1,'vg::ReverseGraph::get_id()'],['../classvg_1_1NetGraph.html#a9964476cfff61404eeb9d65cc182aa4a',1,'vg::NetGraph::get_id()'],['../classvg_1_1SourceSinkOverlay.html#a9c10b6562749e62bc1038ef23e8b9b28',1,'vg::SourceSinkOverlay::get_id()'],['../classvg_1_1JoinedSpliceGraph.html#a716f0b44bb48b6148617dc772d66959c',1,'vg::JoinedSpliceGraph::get_id()'],['../classvg_1_1StrandSplitGraph.html#a07bd24e1ed6a14843ddb87108a11c7f8',1,'vg::StrandSplitGraph::get_id()'],['../classvg_1_1SubHandleGraph.html#af40f7f453c71d4e52273479d0b600612',1,'vg::SubHandleGraph::get_id()'],['../classvg_1_1SubgraphOverlay.html#a301c8016ac2769d041c611cebd738c1e',1,'vg::SubgraphOverlay::get_id()'],['../classvg_1_1SubpathOverlay.html#ab58cd06e1330b752ad55e32878e8e64e',1,'vg::SubpathOverlay::get_id()'],['../classvg_1_1TreeSubgraph.html#ae48a59a93737e729ada7660a39fafa50',1,'vg::TreeSubgraph::get_id()'],['../classvg_1_1VG.html#a6f4b9ac16f23eb0420544ce8357736a3',1,'vg::VG::get_id()'],['../classxg_1_1XG.html#a0a9d6bce054a3ebf14807869883e9b98',1,'xg::XG::get_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a8150ada3f96723110a2ec7c1ed16323b',1,'handlegraph::algorithms::SubHandleGraph::get_id()'],['../classhandlegraph_1_1HandleGraph.html#adb7f6e144bf2a59679f7b2eddad934eb',1,'handlegraph::HandleGraph::get_id()'],['../namespacevg.html#ae4370b5cb4b42e8556b0fbc793fbdfc0',1,'vg::get_id()'],['../namespacexg.html#a5aab54915cd81fa71fd2ebc3b9e52fb8',1,'xg::get_id()']]],
+ ['get_5fidentifier_2207',['get_identifier',['../classvg_1_1IndexFile.html#a0dde670fabfa3890d26c9e89c8564429',1,'vg::IndexFile::get_identifier()'],['../classvg_1_1ZipCode.html#a9cb3141131af81b42741bc9e7349e58b',1,'vg::ZipCode::get_identifier()']]],
+ ['get_5findex_2208',['get_index',['../classvg_1_1RepresentativeTraversalFinder.html#a3e15061afb4437ec04334ed77732fa81',1,'vg::RepresentativeTraversalFinder::get_index()'],['../classvg_1_1IndexRegistry.html#a3738a3916a17ca5a2716e7530b10c434',1,'vg::IndexRegistry::get_index(const IndexName &identifier)'],['../classvg_1_1IndexRegistry.html#a2cde822432825ea731fed5318bd94152',1,'vg::IndexRegistry::get_index(const IndexName &identifier) const']]],
+ ['get_5findexes_2209',['get_indexes',['../classvg_1_1RewindPlanException.html#a80a898014c62738052c18e85a0403a24',1,'vg::RewindPlanException']]],
+ ['get_5finput_5ffile_2210',['get_input_file',['../namespacevg.html#ab1b8b686ef6eca09515be1abe566c013',1,'vg::get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)'],['../namespacevg.html#a09969fef23098c7729a2f190cecb4694',1,'vg::get_input_file(const string &file_name, function< void(istream &)> callback)']]],
+ ['get_5finput_5ffile_5fname_2211',['get_input_file_name',['../namespacevg.html#a5026b599b1094a6c8e157f23b204b09b',1,'vg']]],
+ ['get_5finward_5fbacking_5fhandle_2212',['get_inward_backing_handle',['../classvg_1_1NetGraph.html#adc4841db50e7f3073cad16d59426ba5a',1,'vg::NetGraph']]],
+ ['get_5firregular_5fsnarl_5fcode_2213',['get_irregular_snarl_code',['../classvg_1_1ZipCode.html#a2057ff4f25f04aa76066c3c5a83239fc',1,'vg::ZipCode']]],
+ ['get_5fis_5fcircular_2214',['get_is_circular',['../classvg_1_1MemoizingGraph.html#a2fb48c82bc92aa1fa263a4be92e21891',1,'vg::MemoizingGraph::get_is_circular()'],['../classvg_1_1PathSubgraphOverlay.html#ac33d15bc06e31045d07ecf22e018f0a8',1,'vg::PathSubgraphOverlay::get_is_circular()'],['../classvg_1_1VG.html#a1463f13c63b965a3663932e6fa87537e',1,'vg::VG::get_is_circular()'],['../classxg_1_1XG.html#a841e1c50686d3ea941fb9a01d9639784',1,'xg::XG::get_is_circular()'],['../classhandlegraph_1_1PathHandleGraph.html#a9391c34d9f0c16b21d5bb3bb7ec772e4',1,'handlegraph::PathHandleGraph::get_is_circular()']]],
+ ['get_5fis_5flooping_5fchain_2215',['get_is_looping_chain',['../classvg_1_1ZipCode.html#a2c0fa7d7130b57bee9b557750eb97eab',1,'vg::ZipCode::get_is_looping_chain()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#ac917c5b03c10bd9e57b344a708c6b033',1,'vg::ZipCode::chain_code_t::get_is_looping_chain()']]],
+ ['get_5fis_5fpaired_2216',['get_is_paired',['../classvg_1_1ReadFilter.html#a8b78c03c1379b1ed5576db5c6772adb3',1,'vg::ReadFilter::get_is_paired(const Read &read) const'],['../classvg_1_1ReadFilter.html#aaf6db93c73e3030a098aa54a21416cd7',1,'vg::ReadFilter::get_is_paired(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#a1aa38e8c41e26d7932caa918cfcfe76e',1,'vg::ReadFilter::get_is_paired(const MultipathAlignment &mp_aln) const']]],
+ ['get_5fis_5frev_2217',['get_is_rev',['../namespacevg.html#a1919abd090eae3a01120e0859d434ed9',1,'vg::get_is_rev()'],['../namespacexg.html#aca811d060bb9ddd2ff278e107c882e49',1,'xg::get_is_rev()']]],
+ ['get_5fis_5freverse_2218',['get_is_reverse',['../classvg_1_1DagifiedGraph.html#a0a5fa33f94733bb8470ccbc49e608a0d',1,'vg::DagifiedGraph::get_is_reverse()'],['../classvg_1_1DozeuPinningOverlay.html#a02b35f6198096c08f660df1170d556b4',1,'vg::DozeuPinningOverlay::get_is_reverse()'],['../classvg_1_1ExtraNodeGraph.html#ab3b496b4e1d8067cd7ed0e0ae9fb0aa9',1,'vg::ExtraNodeGraph::get_is_reverse()'],['../classvg_1_1SnarlGraph.html#a9deed0e8a0312d6ff12868e86c83cc0f',1,'vg::SnarlGraph::get_is_reverse()'],['../classvg_1_1IdentityOverlay.html#aa7bba299ded8eb2fff2af0adeb52000b',1,'vg::IdentityOverlay::get_is_reverse()'],['../classvg_1_1IncrementalSubgraph.html#ad4282dc0e503dc17e3724a41dbb0462c',1,'vg::IncrementalSubgraph::get_is_reverse()'],['../classvg_1_1IndexedVG.html#acf50f1ad8e40ac18d8a5469d63155a50',1,'vg::IndexedVG::get_is_reverse()'],['../classvg_1_1MemoizingGraph.html#aac8372783c6657f5473b1d33b4495e7c',1,'vg::MemoizingGraph::get_is_reverse()'],['../classvg_1_1NullMaskingGraph.html#ab99a483165208a4aabc1e2275f126a18',1,'vg::NullMaskingGraph::get_is_reverse()'],['../classvg_1_1PathSubgraph.html#a5305f2276ec4eecae4a59a4892cb63ab',1,'vg::PathSubgraph::get_is_reverse()'],['../classvg_1_1ReverseGraph.html#aaa65f6a0677677af70608a0294ec36f5',1,'vg::ReverseGraph::get_is_reverse()'],['../classvg_1_1NetGraph.html#a4581f8ffa5738a409e9e856f15c48a99',1,'vg::NetGraph::get_is_reverse()'],['../classvg_1_1SourceSinkOverlay.html#a274359d605130e8efec7c14791d5044b',1,'vg::SourceSinkOverlay::get_is_reverse()'],['../classvg_1_1JoinedSpliceGraph.html#a7179e1f5120aebb9670120b6cddf51ca',1,'vg::JoinedSpliceGraph::get_is_reverse()'],['../classvg_1_1StrandSplitGraph.html#a2882b925a09ba0ee35cdf8bdac0c4605',1,'vg::StrandSplitGraph::get_is_reverse()'],['../classvg_1_1SubHandleGraph.html#a050d46f68a21d9169d17a6e9580a542f',1,'vg::SubHandleGraph::get_is_reverse()'],['../classvg_1_1SubgraphOverlay.html#a797e1524539c9c96ef96dc5454d35c3a',1,'vg::SubgraphOverlay::get_is_reverse()'],['../classvg_1_1SubpathOverlay.html#ae1560abd95e0a6e64306622a68f7e6ac',1,'vg::SubpathOverlay::get_is_reverse()'],['../classvg_1_1TreeSubgraph.html#aa581eda84f6ae51edb0363b76075fe47',1,'vg::TreeSubgraph::get_is_reverse()'],['../classvg_1_1VG.html#a53e796617804bffe0203e422f2a23148',1,'vg::VG::get_is_reverse()'],['../classxg_1_1XG.html#a7a52d5c8396e40930cfed5f79ea9c201',1,'xg::XG::get_is_reverse()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade72d1d3264d1022227c44edc9329a26',1,'handlegraph::algorithms::SubHandleGraph::get_is_reverse()'],['../classhandlegraph_1_1HandleGraph.html#a92773f90eb58f18adb9418a4440223c1',1,'handlegraph::HandleGraph::get_is_reverse()']]],
+ ['get_5fis_5freversed_2219',['get_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#ae65abc62608f0643537bacfa78e0e7aa',1,'vg::ZipCode::node_code_t::get_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae6b247dcfb508636f982df6b3353001e',1,'vg::ZipCode::snarl_code_t::get_is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a79691714f5f3bb06aed0d1a7a4b646ee',1,'vg::ZipCodeTree::tree_item_t::get_is_reversed()']]],
+ ['get_5fis_5freversed_5fin_5fparent_2220',['get_is_reversed_in_parent',['../classvg_1_1ZipCode.html#af27a1ca0026e32e588d0bb3b62a5bade',1,'vg::ZipCode']]],
+ ['get_5fitem_2221',['get_item',['../classvg_1_1Funnel.html#a5f8f988df65fc91adc7da9dd8d4446ef',1,'vg::Funnel']]],
+ ['get_5fitem_5fat_5findex_2222',['get_item_at_index',['../classvg_1_1ZipCodeTree.html#a66ff501bf5fa0044978550b188691068',1,'vg::ZipCodeTree']]],
+ ['get_5fiterator_2223',['get_iterator',['../structvg_1_1subcommand_1_1TickChainLink.html#aa21e2c735dba10a3b97c739d66008937',1,'vg::subcommand::TickChainLink']]],
+ ['get_5flast_5fchain_5fcomponent_2224',['get_last_chain_component',['../classvg_1_1ZipCode.html#aaf980083db4440866ee59d2a1b89e957',1,'vg::ZipCode']]],
+ ['get_5flast_5fcomponent_2225',['get_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa98d04c4d61201facf9e01c189b44f43',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fleaves_2226',['get_leaves',['../classvg_1_1WFATree.html#adea6d9333092f49afcc26f34e4bfc016',1,'vg::WFATree']]],
+ ['get_5flength_2227',['get_length',['../classvg_1_1DagifiedGraph.html#a5feaa48467ad288848fb2d1ffcd29fc1',1,'vg::DagifiedGraph::get_length()'],['../classvg_1_1DozeuPinningOverlay.html#a0d9fc0dbb4e18cfe9d7496b72d0f63fb',1,'vg::DozeuPinningOverlay::get_length()'],['../classvg_1_1ExtraNodeGraph.html#ab4385934c980deef266d30118b83a4df',1,'vg::ExtraNodeGraph::get_length()'],['../classvg_1_1SnarlGraph.html#ac521452a597e9159b8c281cc49239ccb',1,'vg::SnarlGraph::get_length()'],['../classvg_1_1IdentityOverlay.html#a659b0f5b71286479ef910bd984c525e6',1,'vg::IdentityOverlay::get_length()'],['../classvg_1_1IncrementalSubgraph.html#a84ee16f64d60195d6ead2a57933af720',1,'vg::IncrementalSubgraph::get_length()'],['../classvg_1_1IndexedVG.html#a235824616974770831a2ce006a954bbe',1,'vg::IndexedVG::get_length()'],['../classvg_1_1MemoizingGraph.html#ab5f66c5dae9ddc74750cb86595fef07e',1,'vg::MemoizingGraph::get_length()'],['../classvg_1_1NullMaskingGraph.html#a2144c791b97d05bf625a50442649def2',1,'vg::NullMaskingGraph::get_length()'],['../classvg_1_1PathSubgraph.html#a777f23f7156addc72dd508d08f069cc7',1,'vg::PathSubgraph::get_length()'],['../classvg_1_1ReadFilter.html#ae2ef22beb751d9415759fc1985da1946',1,'vg::ReadFilter::get_length()'],['../classvg_1_1ReverseGraph.html#a54f7adad266466143efaa59270432d8f',1,'vg::ReverseGraph::get_length()'],['../classvg_1_1NetGraph.html#a8170045aa0032b33628858c0717cc74a',1,'vg::NetGraph::get_length()'],['../classvg_1_1SourceSinkOverlay.html#a03f1de876e4731012b5e7168556d5236',1,'vg::SourceSinkOverlay::get_length()'],['../classvg_1_1JoinedSpliceGraph.html#aafba33cc8aa854fb9dc8d654bb2a3325',1,'vg::JoinedSpliceGraph::get_length()'],['../classvg_1_1StrandSplitGraph.html#a46c7611ab9f71f86e3192a34406860b4',1,'vg::StrandSplitGraph::get_length()'],['../classvg_1_1SubHandleGraph.html#a829ddac36b7fcb67ca87c058fe691a88',1,'vg::SubHandleGraph::get_length()'],['../classvg_1_1SubgraphOverlay.html#a5bc6640c35b21807f14332a51f84a2d9',1,'vg::SubgraphOverlay::get_length()'],['../classvg_1_1SubpathOverlay.html#ae15f1a187d3bf9a590f173fdf4bd8f9b',1,'vg::SubpathOverlay::get_length()'],['../classvg_1_1TreeSubgraph.html#ac6d8e68e5bff645f58f741291a810abe',1,'vg::TreeSubgraph::get_length()'],['../classvg_1_1VG.html#aff75e522e40559f5a5257a5cef776cdc',1,'vg::VG::get_length()'],['../classvg_1_1ZipCode.html#a8a5fd40be34ed83736e027a3ca6d9889',1,'vg::ZipCode::get_length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#ad67b89184b6f5d83cb888b5f14647ae3',1,'vg::ZipCode::node_code_t::get_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a214243244b7e99dfe24df8665860dbb2',1,'vg::ZipCode::chain_code_t::get_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa80045f926e1bfde2fb07e2c2e442732',1,'vg::ZipCode::snarl_code_t::get_length()'],['../classxg_1_1XG.html#aa52bb123eca4dbff84b316a7f56a98cc',1,'xg::XG::get_length()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af858e2c9467b674d836879d39f049a05',1,'handlegraph::algorithms::SubHandleGraph::get_length()'],['../classhandlegraph_1_1HandleGraph.html#a569ff35fb85c725b0b6b6933ed303e49',1,'handlegraph::HandleGraph::get_length()']]],
+ ['get_5flocus_5fname_2228',['get_locus_name',['../classhandlegraph_1_1PathMetadata.html#aeea07376b756bc5410dacf86f2c3983d',1,'handlegraph::PathMetadata']]],
+ ['get_5flog10_5fprob_5fof_5fdisruption_5fin_5finterval_2229',['get_log10_prob_of_disruption_in_interval',['../classvg_1_1MinimizerMapper.html#a4a680ca76191f68a70d17af1e0548f60',1,'vg::MinimizerMapper']]],
+ ['get_5flong_2230',['get_long',['../classvg_1_1Version.html#a5132823f48bf6019f1b94ace3a479de4',1,'vg::Version']]],
+ ['get_5flong_5foption_2231',['get_long_option',['../classvg_1_1OptionInterface.html#afba994fe31561a26b7495e78d9423679',1,'vg::OptionInterface::get_long_option()'],['../classvg_1_1BaseOption.html#ad990f7324262866fbc67f6e8adeeecfd',1,'vg::BaseOption::get_long_option()']]],
+ ['get_5fmagic_5fnumber_2232',['get_magic_number',['../classvg_1_1ZipCodeCollection.html#a59d0bd8bac747766d3471225e5a6ae05',1,'vg::ZipCodeCollection::get_magic_number()'],['../classxg_1_1XG.html#ac8ed9c987e2693c548ad834b39df7a80',1,'xg::XG::get_magic_number()'],['../classhandlegraph_1_1Serializable.html#a8879f13f2204a80a6c428883187961db',1,'handlegraph::Serializable::get_magic_number()']]],
+ ['get_5fmagic_5fnumber_5fas_5fstring_2233',['get_magic_number_as_string',['../classvg_1_1ZipCodeCollection.html#a6ee9653e5766e260ca6c903ca0920265',1,'vg::ZipCodeCollection']]],
+ ['get_5fmain_2234',['get_main',['../classvg_1_1subcommand_1_1Subcommand.html#a5a7af092ca69792ed2543bbcc3847ad4',1,'vg::subcommand::Subcommand']]],
+ ['get_5fmapping_2235',['get_mapping',['../classvg_1_1PhaseUnfolder.html#aae984d6ac43200dc82e6ef3066e01f15',1,'vg::PhaseUnfolder']]],
+ ['get_5fmapq_2236',['get_mapq',['../classvg_1_1ReadFilter.html#a0550e932f7becd1fbccd46787b580216',1,'vg::ReadFilter']]],
+ ['get_5fmax_5frss_5fkb_2237',['get_max_rss_kb',['../namespacevg.html#a546b60e87f7fc326074f6dcf2cdd0659',1,'vg']]],
+ ['get_5fmax_5fvmem_5fkb_2238',['get_max_vmem_kb',['../namespacevg.html#a917d8892f93a31e2d8c3161de264fea1',1,'vg']]],
+ ['get_5fmetavar_2239',['get_metavar',['../namespacevg_1_1subcommand.html#accfa400696eb815cf8c43d0909c0350f',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20bool_20_3e_2240',['get_metavar< bool >',['../namespacevg_1_1subcommand.html#a901fbf8366695921cb7844ee2da2d2a2',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20double_20_3e_2241',['get_metavar< double >',['../namespacevg_1_1subcommand.html#a6ab814763fe6f21091083e68bcf47a92',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20int_20_3e_2242',['get_metavar< int >',['../namespacevg_1_1subcommand.html#ac4cbf20c4fbaa1109469f8a358e1a213',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20int8_5ft_20_3e_2243',['get_metavar< int8_t >',['../namespacevg_1_1subcommand.html#a4945a3300d2d189e4c7fa6ad5d27ddf6',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20size_5ft_20_3e_2244',['get_metavar< size_t >',['../namespacevg_1_1subcommand.html#aebb27d4a98b972c03f63c8715bbd706c',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20std_3a_3astring_20_3e_2245',['get_metavar< std::string >',['../namespacevg_1_1subcommand.html#a1615e3bd0398f56dfcdd1c9dfb864ec9',1,'vg::subcommand']]],
+ ['get_5fmin_5fbase_5fqual_5ffraction_2246',['get_min_base_qual_fraction',['../classvg_1_1ReadFilter.html#ad2ca26c062585494f69520f9997d34eb',1,'vg::ReadFilter']]],
+ ['get_5fmin_5fnode_5fsupport_2247',['get_min_node_support',['../classvg_1_1TraversalSupportFinder.html#ad166403d1a92690fe10e976d9789c065',1,'vg::TraversalSupportFinder::get_min_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a5a19f9777ecf01f0e8ea86870a993aea',1,'vg::PackedTraversalSupportFinder::get_min_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aeeb7ecc5e9a3fa6f5030d3d41a436c59',1,'vg::CachedPackedTraversalSupportFinder::get_min_node_support()']]],
+ ['get_5fmin_5fposition_2248',['get_min_position',['../classvg_1_1StreamSorter.html#a4240a47a167f22d3815de6fe976420b5',1,'vg::StreamSorter']]],
+ ['get_5fmin_5ftotal_5fsupport_5ffor_5fcall_2249',['get_min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#ac7e36771ace6cf84d9f4f732cdbc692f',1,'vg::SupportBasedSnarlCaller']]],
+ ['get_5fmutable_2250',['get_mutable',['../structvg_1_1Annotation.html#a065db30c6b14ca2938254d603777e5c8',1,'vg::Annotation']]],
+ ['get_5fn_5fbins_2251',['get_n_bins',['../classvg_1_1Packer.html#a01716de1dc4501804d81fc38256dd2b5',1,'vg::Packer']]],
+ ['get_5fname_2252',['get_name',['../classvg_1_1Configurable.html#aee830d6a5cdcf8e7a2896a443bcc80cc',1,'vg::Configurable::get_name()'],['../structvg_1_1TranscriptPath.html#a0adaddaa3b952ed1f06bd7029673d2aa',1,'vg::TranscriptPath::get_name()'],['../classvg_1_1subcommand_1_1Subcommand.html#ab6c41ce3fe77e286f2caa1672b553293',1,'vg::subcommand::Subcommand::get_name()'],['../haplotypes__main_8cpp.html#a3781abae7c3253f254c4e795863d0c09',1,'get_name(): haplotypes_main.cpp']]],
+ ['get_5fnet_2253',['get_net',['../classhandlegraph_1_1SnarlDecomposition.html#a84b4951e1bf931d03539ac6e048fdb98',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fnet_5fgraph_2254',['get_net_graph',['../classvg_1_1GenomeState.html#ad07741efc2a949dd69aee266dbb4500b',1,'vg::GenomeState']]],
+ ['get_5fnet_5fhandle_2255',['get_net_handle',['../classvg_1_1ZipCode.html#a051a9144646b660f213fe44d5b123d77',1,'vg::ZipCode']]],
+ ['get_5fnet_5fhandle_5fslow_2256',['get_net_handle_slow',['../classvg_1_1ZipCode.html#ad1d40ef72bc5fa0f9e0e933add4265a2',1,'vg::ZipCode']]],
+ ['get_5fnext_5falignment_5ffrom_5ffastq_2257',['get_next_alignment_from_fastq',['../namespacevg.html#aca76d8e219f90833fdabe3528c3c6441',1,'vg']]],
+ ['get_5fnext_5falignment_5fpair_5ffrom_5ffastqs_2258',['get_next_alignment_pair_from_fastqs',['../namespacevg.html#a3255bd8bf9846a34da799947f7642dc7',1,'vg']]],
+ ['get_5fnext_5finterleaved_5falignment_5fpair_5ffrom_5ffastq_2259',['get_next_interleaved_alignment_pair_from_fastq',['../namespacevg.html#ab58cf3da638d7e8833a14ef801c7e2db',1,'vg']]],
+ ['get_5fnext_5finterleaved_5frecord_5fpair_5ffrom_5fgaf_2260',['get_next_interleaved_record_pair_from_gaf',['../namespacevg_1_1io.html#a0f27b2a472320e0e45a130b73827d1fd',1,'vg::io']]],
+ ['get_5fnext_5fintervals_2261',['get_next_intervals',['../classvg_1_1ZipCodeForest.html#a2c9a60acfcb3f8521eeb7bbf5e36007b',1,'vg::ZipCodeForest']]],
+ ['get_5fnext_5fnode_5frecalc_5fdegrees_2262',['get_next_node_recalc_degrees',['../classvg_1_1FlowSort.html#a1fac8545c184446eee5cae0f55567b1f',1,'vg::FlowSort']]],
+ ['get_5fnext_5frank_2263',['get_next_rank',['../classvg_1_1Paths.html#aad2977756f0166a341fb488cd5c6a9b0',1,'vg::Paths']]],
+ ['get_5fnext_5frecord_5ffrom_5fgaf_2264',['get_next_record_from_gaf',['../namespacevg_1_1io.html#aa357ed5eaa447e495149c7bd7df356b9',1,'vg::io']]],
+ ['get_5fnext_5frecord_5fpair_5ffrom_5fgaf_2265',['get_next_record_pair_from_gaf',['../namespacevg_1_1io.html#ab11e877e850b127b8004e7223cc77247',1,'vg::io']]],
+ ['get_5fnext_5fstep_2266',['get_next_step',['../classvg_1_1MemoizingGraph.html#a91e5d4f1ce3028d58c162adf8d19e70f',1,'vg::MemoizingGraph::get_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a2e18088c831f6757a4eafa7d862d0329',1,'vg::PathSubgraphOverlay::get_next_step()'],['../classvg_1_1VG.html#a144fb8b69eb2274b8dcea914898919f0',1,'vg::VG::get_next_step()'],['../classxg_1_1XG.html#a6595e2654ee4955763a08ab51780941a',1,'xg::XG::get_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a209786f5c9e2c0210b383f2022ee221f',1,'handlegraph::PathHandleGraph::get_next_step()']]],
+ ['get_5fnode_2267',['get_node',['../classvg_1_1VG.html#a95223ec6984efc003e5cac69acd43445',1,'vg::VG::get_node(nid_t id)'],['../classvg_1_1VG.html#aa264e9386b98b57c3549a56870d8e29e',1,'vg::VG::get_node(nid_t id) const']]],
+ ['get_5fnode_5fat_5fnucleotide_2268',['get_node_at_nucleotide',['../classvg_1_1VG.html#a07462d3f895e77cb407695e6c8e85727',1,'vg::VG']]],
+ ['get_5fnode_5fby_5fid_2269',['get_node_by_id',['../structvg_1_1algorithms_1_1Graph.html#a6113178f0138c18d19ed32a08a4a474e',1,'vg::algorithms::Graph']]],
+ ['get_5fnode_5fcode_2270',['get_node_code',['../classvg_1_1ZipCode.html#a1a37e35bfbd8910f64b95906f2930e28',1,'vg::ZipCode']]],
+ ['get_5fnode_5fcount_2271',['get_node_count',['../classvg_1_1DagifiedGraph.html#a46afdba1fbffa6ffebce5966a1829918',1,'vg::DagifiedGraph::get_node_count()'],['../classvg_1_1DozeuPinningOverlay.html#ab324121c34fdc2ab5edfaf742f26280d',1,'vg::DozeuPinningOverlay::get_node_count()'],['../classvg_1_1ExtraNodeGraph.html#a0c55bc093996c9148a3b6c4e46634759',1,'vg::ExtraNodeGraph::get_node_count()'],['../classvg_1_1SnarlGraph.html#aa797abb0b6518ca38b557759d074cd33',1,'vg::SnarlGraph::get_node_count()'],['../classvg_1_1IdentityOverlay.html#a9a58eb7938308dad847ded70b1abec56',1,'vg::IdentityOverlay::get_node_count()'],['../classvg_1_1IncrementalSubgraph.html#a076dbda3b4b724157cad61f5f7b76b2b',1,'vg::IncrementalSubgraph::get_node_count()'],['../classvg_1_1IndexedVG.html#aa275aa5b547bf464b95ce162e9a2fcd5',1,'vg::IndexedVG::get_node_count()'],['../classvg_1_1MemoizingGraph.html#a4276a59439fc7edc984fe6e666e3b69e',1,'vg::MemoizingGraph::get_node_count()'],['../classvg_1_1NullMaskingGraph.html#a7a7eeb58c5787789e6b8ae8a9e58101b',1,'vg::NullMaskingGraph::get_node_count()'],['../classvg_1_1PathSubgraph.html#a52f431143ff624475a16629fa46898f0',1,'vg::PathSubgraph::get_node_count()'],['../classvg_1_1ReverseGraph.html#a075661952d5a567b1e09ad9a5624c5a7',1,'vg::ReverseGraph::get_node_count()'],['../classvg_1_1NetGraph.html#a49f4b9958557920e8b81c3f6b6c62de2',1,'vg::NetGraph::get_node_count()'],['../classvg_1_1SourceSinkOverlay.html#ac49954276cde4384262f3501f4ed70ce',1,'vg::SourceSinkOverlay::get_node_count()'],['../classvg_1_1JoinedSpliceGraph.html#a15ac4bff9b6862ec0d7c6cefabb916c9',1,'vg::JoinedSpliceGraph::get_node_count()'],['../classvg_1_1StrandSplitGraph.html#a2a4f01cb39da9b46431a7ea3b46f540f',1,'vg::StrandSplitGraph::get_node_count()'],['../classvg_1_1SubHandleGraph.html#a0ea741c8d98e8c12b9f83b3427bee115',1,'vg::SubHandleGraph::get_node_count()'],['../classvg_1_1SubgraphOverlay.html#a40d036bc03e5bb02b1b0fe657b283b2b',1,'vg::SubgraphOverlay::get_node_count()'],['../classvg_1_1SubpathOverlay.html#a1d0208a9cfe646b6d25741c2bbfbd4b3',1,'vg::SubpathOverlay::get_node_count()'],['../classvg_1_1TreeSubgraph.html#a63dd0c1a1fce7a59a563be0448085246',1,'vg::TreeSubgraph::get_node_count()'],['../classvg_1_1VG.html#a495649c1646b865d6c88b8dc126589b0',1,'vg::VG::get_node_count()'],['../classxg_1_1XG.html#ae7b3b8008c6779aafb72b8e2fc47d4a1',1,'xg::XG::get_node_count()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0c17ba8c59000d2562fb0318a1faaa7c',1,'handlegraph::algorithms::SubHandleGraph::get_node_count()'],['../classhandlegraph_1_1HandleGraph.html#a9f95108e6c3f68f404fa93bd3306e4c6',1,'handlegraph::HandleGraph::get_node_count()']]],
+ ['get_5fnode_5fdegree_2272',['get_node_degree',['../classvg_1_1FlowSort.html#a033cbc4da28f5ad6c3be63374eb55ac3',1,'vg::FlowSort']]],
+ ['get_5fnode_5fids_2273',['get_node_ids',['../structvg_1_1algorithms_1_1Graph.html#afe478cbb3ccb5f5125b59467db143b59',1,'vg::algorithms::Graph']]],
+ ['get_5fnode_5flength_2274',['get_node_length',['../classvg_1_1Mapper.html#a99717b5d61b6db599c177b8bafcb6dd8',1,'vg::Mapper']]],
+ ['get_5fnode_5fmapping_2275',['get_node_mapping',['../classvg_1_1Paths.html#a6314d7f8036a65b31d4dfac643bc3598',1,'vg::Paths::get_node_mapping(Node *n)'],['../classvg_1_1Paths.html#a7fa795ccee1427d6cac6e44fafe41e1e',1,'vg::Paths::get_node_mapping(id_t id)'],['../classvg_1_1Paths.html#a99f8491f18c0ccaf1bb7b7bf45500517',1,'vg::Paths::get_node_mapping(id_t id) const']]],
+ ['get_5fnode_5fmapping_5fby_5fpath_5fname_2276',['get_node_mapping_by_path_name',['../classvg_1_1Paths.html#a9c9cf2b7f26c788195812e2b8170a6ce',1,'vg::Paths::get_node_mapping_by_path_name(Node *n)'],['../classvg_1_1Paths.html#a72c6a29a41521996fd3454170b1a76f6',1,'vg::Paths::get_node_mapping_by_path_name(id_t id)']]],
+ ['get_5fnode_5fmapping_5fcopies_5fby_5frank_2277',['get_node_mapping_copies_by_rank',['../classvg_1_1Paths.html#a36a26abe18d10e17e273fa658be9d5c6',1,'vg::Paths']]],
+ ['get_5fnode_5fmappings_5fby_5frank_2278',['get_node_mappings_by_rank',['../classvg_1_1Paths.html#a5a40b701389bcc2c513083b02f17b4f4',1,'vg::Paths']]],
+ ['get_5fnode_5fnid_5fto_5fvariant_2279',['get_node_nid_to_variant',['../classvg_1_1VG.html#a52fa15aebd7d190eb743311f31037e55',1,'vg::VG']]],
+ ['get_5fnode_5foffset_2280',['get_node_offset',['../classvg_1_1GaplessExtender.html#a12663a32f4bc41137eb372c845f0eafe',1,'vg::GaplessExtender']]],
+ ['get_5fnode_5fsupport_2281',['get_node_support',['../classvg_1_1RepresentativeTraversalFinder.html#a40f64596e2e8bb4b78120f351fa3bf79',1,'vg::RepresentativeTraversalFinder']]],
+ ['get_5fnodes_2282',['get_nodes',['../classvg_1_1ContractingGraph.html#a9c960fb16e62bc152fcf2f4230eead9c',1,'vg::ContractingGraph::get_nodes()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a932649a134317ad387ee70adc03d4474',1,'vg::SnarlDistanceIndexClusterer::get_nodes()']]],
+ ['get_5fnon_5fhts_5falignment_5femitter_2283',['get_non_hts_alignment_emitter',['../namespacevg_1_1io.html#a2f9f4db8b0374c57d2963881784c40d3',1,'vg::io']]],
+ ['get_5fnonoverlapping_2284',['get_nonoverlapping',['../classvg_1_1WindowedVcfBuffer.html#a63b89391977d77c5320003d0e0f70469',1,'vg::WindowedVcfBuffer']]],
+ ['get_5fnum_5fsamples_2285',['get_num_samples',['../namespacevg.html#afe9d79548464e7842327275008447299',1,'vg']]],
+ ['get_5foffset_2286',['get_offset',['../namespacevg.html#af826519a2b2e0cf58394e35d7ab7b84c',1,'vg::get_offset()'],['../namespacexg.html#a6e76d42101c987bf595a807522766cfa',1,'xg::get_offset()']]],
+ ['get_5foffset_5fin_5fchain_2287',['get_offset_in_chain',['../classvg_1_1ZipCode.html#a5d8b333ee954fa9a513b6190e1910843',1,'vg::ZipCode']]],
+ ['get_5fon_5fstrand_5fdistance_5ftree_2288',['get_on_strand_distance_tree',['../classvg_1_1OrientedDistanceClusterer.html#a736cd908b11ed3a000698291c541bbc0',1,'vg::OrientedDistanceClusterer']]],
+ ['get_5foption_5fid_2289',['get_option_id',['../namespacevg_1_1subcommand.html#a7e03678789f1a34608294f43e1047457',1,'vg::subcommand']]],
+ ['get_5foption_5fstruct_2290',['get_option_struct',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a58bddced5eb3503314ae1f7ef2bd60d1',1,'vg::subcommand::BaseArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aeeb773f962b7de9459a67f2b74cce151',1,'vg::subcommand::ValueArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a4287432c965cf788c3619aa13634c613',1,'vg::subcommand::FlagArgSpec::get_option_struct()']]],
+ ['get_5foption_5fvalue_2291',['get_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#af234d02566c656202396f78df73d35d7',1,'vg::subcommand::BaseOptionGroup']]],
+ ['get_5foptions_2292',['get_options',['../classvg_1_1Configurable.html#a553f14c4f4a19bb51d40ffb211945b3a',1,'vg::Configurable']]],
+ ['get_5for_5festimate_5fcoverage_2293',['get_or_estimate_coverage',['../namespacevg.html#aba3f6bc9cc27f9c6bb91dc27c7fb28b8',1,'vg']]],
+ ['get_5for_5fmake_5fvariant_5fid_2294',['get_or_make_variant_id',['../namespacevg.html#ae9fc5855bb49062ce72e56c805e1545a',1,'vg']]],
+ ['get_5foutput_5ffile_5fname_2295',['get_output_file_name',['../namespacevg.html#ae2a0425675c4a85289b230eef2c985b8',1,'vg']]],
+ ['get_5foverhang_2296',['get_overhang',['../classvg_1_1ReadFilter.html#a71bb794016b2f59d6495a98b9716e0b5',1,'vg::ReadFilter::get_overhang(const Read &read) const'],['../classvg_1_1ReadFilter.html#a50797c8911ec77ac3a392370a1c91cbe',1,'vg::ReadFilter::get_overhang(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#ab3bff405c9a8994993ea71e0c03b8772',1,'vg::ReadFilter::get_overhang(const MultipathAlignment &mp_aln) const']]],
+ ['get_5foverlay_5fhandle_2297',['get_overlay_handle',['../classvg_1_1StrandSplitGraph.html#ab60c1d256ba23abea598861ca7cf7f42',1,'vg::StrandSplitGraph']]],
+ ['get_5fparent_2298',['get_parent',['../classhandlegraph_1_1SnarlDecomposition.html#afb665da6af9e2ccfc10e6e667254b91d',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fparent_5fidentifier_2299',['get_parent_identifier',['../classvg_1_1ZipCode.html#a487d7a307e6b728df95581d6d261d526',1,'vg::ZipCode']]],
+ ['get_5fparent_5ftraversal_2300',['get_parent_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a2738b92f35c61666df57cd6088f3def1',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fparsed_5fgenotypes_2301',['get_parsed_genotypes',['../classvg_1_1WindowedVcfBuffer.html#a8970a1ba82342645b319a1f7091c6cea',1,'vg::WindowedVcfBuffer']]],
+ ['get_5fpath_2302',['get_path',['../classvg_1_1Paths.html#a386fefa3ef22c69bdfa06711ec43ca93',1,'vg::Paths::get_path()'],['../classxg_1_1XG.html#a79017177d025a7608c76a7901da5a463',1,'xg::XG::get_path()'],['../namespacevg.html#a3d972910bf64084a1ee50ca4350c5b59',1,'vg::get_path(const std::vector< handle_t > &first, handle_t second)'],['../namespacevg.html#aa5fc35eee866d216357a5818cd1fb927',1,'vg::get_path(handle_t first, const std::vector< handle_t > &second)'],['../namespacevg.html#a162ed4c8f358ca4c33ab05a27f8349cb',1,'vg::get_path(const std::vector< handle_t > &first, gbwt::node_type second)'],['../namespacevg.html#a66796444cb3b92c35ebeddbb7a9bc6bf',1,'vg::get_path(gbwt::node_type reverse_first, const std::vector< handle_t > &second)']]],
+ ['get_5fpath_5fbase_5fname_2303',['get_path_base_name',['../namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65',1,'vg']]],
+ ['get_5fpath_5fcount_2304',['get_path_count',['../classvg_1_1MemoizingGraph.html#ae0625c7cd87213ce030e03d7373c7216',1,'vg::MemoizingGraph::get_path_count()'],['../classvg_1_1PathSubgraphOverlay.html#a589dea47ddf887c61f88d4ef2f9110a2',1,'vg::PathSubgraphOverlay::get_path_count()'],['../classvg_1_1VG.html#a7b20ecaa6a8a3155b5abb90a3139f6de',1,'vg::VG::get_path_count()'],['../classxg_1_1XG.html#af7b58d4d10af78ac88675a40661967c2',1,'xg::XG::get_path_count()'],['../classhandlegraph_1_1PathHandleGraph.html#acd5df753593ecdfb7aa8c411b98ebad9',1,'handlegraph::PathHandleGraph::get_path_count()']]],
+ ['get_5fpath_5fedge_5findex_2305',['get_path_edge_index',['../classvg_1_1PathChunker.html#aef30dd2569597b64d36b19824ebee37f',1,'vg::PathChunker']]],
+ ['get_5fpath_5fedges_2306',['get_path_edges',['../classvg_1_1VG.html#a26f160750dfed33c16a257bd5cbecddf',1,'vg::VG']]],
+ ['get_5fpath_5fhandle_2307',['get_path_handle',['../classvg_1_1MemoizingGraph.html#ad26dd5209b1364601acf977df6cc52dc',1,'vg::MemoizingGraph::get_path_handle()'],['../classvg_1_1PathSubgraphOverlay.html#a45c63b93ee36ea86ce966aa2f6fc1530',1,'vg::PathSubgraphOverlay::get_path_handle()'],['../classvg_1_1VG.html#a6261550a7c6bbe7eb6ee0976639bc1d7',1,'vg::VG::get_path_handle()'],['../classxg_1_1XG.html#a0cca09a102d01c9f952b857f23f165e1',1,'xg::XG::get_path_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a5d6059d716882a80e3982de17011866e',1,'handlegraph::PathHandleGraph::get_path_handle()']]],
+ ['get_5fpath_5fhandle_5fof_5fstep_2308',['get_path_handle_of_step',['../classvg_1_1MemoizingGraph.html#a7a7ec48fc32e5798b58216b3f8fc2624',1,'vg::MemoizingGraph::get_path_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a8a369e743f3f797db333ef04505bb292',1,'vg::PathSubgraphOverlay::get_path_handle_of_step()'],['../classvg_1_1VG.html#aae55721d38d4db3068ca93b4aac8e962',1,'vg::VG::get_path_handle_of_step()'],['../classxg_1_1XG.html#ab12dcc61dc8227d5dfde03b0f6b5ef16',1,'xg::XG::get_path_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a1d1ca9865da585257709f54769f5d6a9',1,'handlegraph::PathHandleGraph::get_path_handle_of_step()'],['../classhandlegraph_1_1PathMetadata.html#a38041ec30b5c66bd94f951f4e61b8bab',1,'handlegraph::PathMetadata::get_path_handle_of_step()']]],
+ ['get_5fpath_5fid_2309',['get_path_id',['../classvg_1_1Paths.html#a8fba2fa812589af544a4a0406f78cca7',1,'vg::Paths']]],
+ ['get_5fpath_5findex_2310',['get_path_index',['../classvg_1_1GraphSynchronizer.html#aa13b46c21814ff09172452e28a4da71d',1,'vg::GraphSynchronizer']]],
+ ['get_5fpath_5flength_2311',['get_path_length',['../classvg_1_1MemoizingGraph.html#a34c10df2b34669fffd3c036636f4f608',1,'vg::MemoizingGraph::get_path_length()'],['../classxg_1_1XG.html#a458bf40b2282e7bd4743781d20f7072b',1,'xg::XG::get_path_length()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#ab71f007638c65db10efbe198f923413b',1,'handlegraph::PathPositionHandleGraph::get_path_length()']]],
+ ['get_5fpath_5fname_2312',['get_path_name',['../classvg_1_1MemoizingGraph.html#ad6e5c2da620079ff9fc488a282cb88f9',1,'vg::MemoizingGraph::get_path_name()'],['../classvg_1_1Paths.html#a56b39299430400066796a0332492f7a5',1,'vg::Paths::get_path_name()'],['../classvg_1_1PathSubgraphOverlay.html#a4331971206c3b9cb069b01abad5d965c',1,'vg::PathSubgraphOverlay::get_path_name()'],['../classvg_1_1VG.html#a8ad62c3977b6f38f0b570ea78251dc6d',1,'vg::VG::get_path_name()'],['../classxg_1_1XG.html#acc895561f10e41d82329a45e78bcdbac',1,'xg::XG::get_path_name()'],['../classhandlegraph_1_1PathHandleGraph.html#a565f4312a42dfe77ae14c1ee9ed9f2ba',1,'handlegraph::PathHandleGraph::get_path_name()'],['../classhandlegraph_1_1PathMetadata.html#acf37917fbe8c308de24264854b535018',1,'handlegraph::PathMetadata::get_path_name()']]],
+ ['get_5fpath_5fsequence_2313',['get_path_sequence',['../classvg_1_1GraphSynchronizer.html#ac33a770c7ce8206e4649133062333898',1,'vg::GraphSynchronizer']]],
+ ['get_5fpayload_5ffrom_5fzip_2314',['get_payload_from_zip',['../classvg_1_1ZipCode.html#a05895f989a23d97b08bd0c1c56bbc3bc',1,'vg::ZipCode']]],
+ ['get_5fpayload_5ffrom_5fzipcode_2315',['get_payload_from_zipcode',['../classvg_1_1ZipCode.html#ae9a95e07dd615b3692fe7742990c6c8b',1,'vg::ZipCode']]],
+ ['get_5fperipheral_5fattachments_2316',['get_peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#afbd7c2ce70efdcc6c25c20cc7710faa0',1,'vg::GraphSynchronizer::Lock']]],
+ ['get_5fphase_5fblock_2317',['get_phase_block',['../classhandlegraph_1_1PathMetadata.html#aadcc53d7a55b54eb2499b66a02500065',1,'handlegraph::PathMetadata']]],
+ ['get_5fpos_2318',['get_pos',['../classvg_1_1GaplessExtender.html#a92241e0a9691fc7b06f5258a21d1c9c4',1,'vg::GaplessExtender']]],
+ ['get_5fposition_5fof_5fstep_2319',['get_position_of_step',['../classvg_1_1MemoizingGraph.html#ade585496ff8b0d082500a1a76c2b187b',1,'vg::MemoizingGraph::get_position_of_step()'],['../classxg_1_1XG.html#ab6e8ce09a0ed201a56b9f8bd387b4e4d',1,'xg::XG::get_position_of_step()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#a473d58ac35a06551e06ae7f5ad5073be',1,'handlegraph::PathPositionHandleGraph::get_position_of_step()']]],
+ ['get_5fpositions_2320',['get_positions',['../classvg_1_1Funnel.html#a617af9590f607720de6a87dfcddbe553',1,'vg::Funnel']]],
+ ['get_5fpossible_5ffilenames_2321',['get_possible_filenames',['../classvg_1_1IndexRegistry.html#a6dc3fd500ab65621ad72ae968cedecf0',1,'vg::IndexRegistry']]],
+ ['get_5fprefix_2322',['get_prefix',['../classvg_1_1IndexRegistry.html#aa3748affd87c03e3a883ccb9d913eb73',1,'vg::IndexRegistry::get_prefix()'],['../classvg_1_1PhaseUnfolder.html#abae52ee7605f03c82622c63c55463db7',1,'vg::PhaseUnfolder::get_prefix()']]],
+ ['get_5fprefix_5fsum_5for_5fidentifier_2323',['get_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#ab2390c393bb641b64ca80183686df54a',1,'vg::ZipCode::node_code_t::get_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34832c0fc381d48cb1424a224f8d9dae',1,'vg::ZipCode::snarl_code_t::get_prefix_sum_or_identifier()']]],
+ ['get_5fprevious_5fstep_2324',['get_previous_step',['../classvg_1_1MemoizingGraph.html#a2ceee67be1ab5744fe53de6e1fa5e718',1,'vg::MemoizingGraph::get_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#a5b3b4cb54c2f5fedc9fc4d765c6f8b3a',1,'vg::PathSubgraphOverlay::get_previous_step()'],['../classvg_1_1VG.html#a95d4b19a83f11ac6244855f86555fe76',1,'vg::VG::get_previous_step()'],['../classxg_1_1XG.html#aedec198c2181d7f729c10317e5ca8089',1,'xg::XG::get_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a71040226b29aa5046f4cc04c8c9aa9fb',1,'handlegraph::PathHandleGraph::get_previous_step()']]],
+ ['get_5fpriority_2325',['get_priority',['../classvg_1_1subcommand_1_1Subcommand.html#a4dccbaf1dc530dc55b57e1dd9dbc09e1',1,'vg::subcommand::Subcommand']]],
+ ['get_5fprob_5fof_5fdisruption_5fin_5fcolumn_2326',['get_prob_of_disruption_in_column',['../classvg_1_1MinimizerMapper.html#a6d4969130b9f7cb75efec316774b8e82',1,'vg::MinimizerMapper']]],
+ ['get_5fproc_5fstatus_5fvalue_2327',['get_proc_status_value',['../namespacevg.html#a9fb67697fd1e49bcb389a735ba9fa8f2',1,'vg']]],
+ ['get_5fprotobuf_5ftag_2328',['get_protobuf_tag',['../classvg_1_1io_1_1Registry.html#a9ccb7ac94bdb24687992af702d387620',1,'vg::io::Registry']]],
+ ['get_5fpruned_5falt_5falleles_2329',['get_pruned_alt_alleles',['../classvg_1_1VCFTraversalFinder.html#a116466101f77d992e54bb3328a42c90b',1,'vg::VCFTraversalFinder']]],
+ ['get_5fqual_5fadj_5faligner_2330',['get_qual_adj_aligner',['../classvg_1_1AlignerClient.html#aa84332f52915c20b2f2db1e060736fb5',1,'vg::AlignerClient']]],
+ ['get_5fqualities_5fin_5fsnarl_2331',['get_qualities_in_snarl',['../classvg_1_1Genotyper.html#af6518141a6e6f122e5f534c041d16918',1,'vg::Genotyper']]],
+ ['get_5fradius_2332',['get_radius',['../classvg_1_1VariantAdder.html#ae974fd5d06287893b0b1f8690624d18f',1,'vg::VariantAdder']]],
+ ['get_5frank_5fin_5fsnarl_2333',['get_rank_in_snarl',['../classvg_1_1ZipCode.html#a32750209d049ac9e5fea67c97be1f151',1,'vg::ZipCode']]],
+ ['get_5fraw_5fchain_5fcomponent_2334',['get_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a0ab97119fa36e9682bb28118190cb8e4',1,'vg::ZipCode::node_code_t::get_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af202024a5bb84df848c92b06535682c4',1,'vg::ZipCode::snarl_code_t::get_raw_chain_component()']]],
+ ['get_5fraw_5fchild_5fcount_2335',['get_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#af740b35df2d7b5cd84b3ab439440e492',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fcode_5ftype_2336',['get_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#abca762bde40792cc01251c5372cd8b61',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fconnectivity_2337',['get_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4f3a37a0ed45286df4f4d3cf254ac376',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fraw_5fdistance_5fend_5fleft_2338',['get_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2619d7eccb0849542a6c8a86bb7937c1',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fdistance_5fend_5fright_2339',['get_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a1fe89643eb1a0f051e5ac71465984a71',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fdistance_5fstart_5fleft_2340',['get_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a39806103fa11d9969668f75045732bec',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fdistance_5fstart_5fright_2341',['get_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a168236545b3436928b1099c1fe572379',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fis_5freversed_2342',['get_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a5009106b8ce3273a9db11d5c177e5760',1,'vg::ZipCode::node_code_t::get_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa00b0cb7326f1fabc61bc7330936f0ee',1,'vg::ZipCode::snarl_code_t::get_raw_is_reversed()']]],
+ ['get_5fraw_5flast_5fcomponent_2343',['get_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa3fc8437a85ebad068b816cb2c04d0e3',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fraw_5flength_2344',['get_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ac1eeeb4a44eec49317c89ec69ec5e0',1,'vg::ZipCode::node_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a31621cf955a3423ca4fa85b440597df2',1,'vg::ZipCode::chain_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aabb9e23dfe383bcf8d241675975a80d6',1,'vg::ZipCode::snarl_code_t::get_raw_length()']]],
+ ['get_5fraw_5fprefix_5fsum_5for_5fidentifier_2345',['get_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a2382df4c7c2f34b2e538edd9c2c27c66',1,'vg::ZipCode::node_code_t::get_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#adfcdf800c56ed38d46c5d2db8f291e62',1,'vg::ZipCode::snarl_code_t::get_raw_prefix_sum_or_identifier()']]],
+ ['get_5fraw_5frecord_5foffset_2346',['get_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04bf6c411365529b20b893c2b30b9f8e',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fsnarl_5frank_5for_5fidentifier_2347',['get_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#af4bfbe05a99156b9cc18446647c88830',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fread_5fcoverage_2348',['get_read_coverage',['../classvg_1_1MinimizerMapper.html#a59563aa4a1d0f00d909edd4cf8b8aa7a',1,'vg::MinimizerMapper']]],
+ ['get_5fread_5fdistance_2349',['get_read_distance',['../namespacevg_1_1algorithms.html#a5d8762b533e64039ce1a917b047097d8',1,'vg::algorithms']]],
+ ['get_5fread_5ffn_2350',['get_read_fn',['../classvg_1_1io_1_1JSONStreamHelper.html#a549e248d11b13f164c871cbf3ccbf935',1,'vg::io::JSONStreamHelper']]],
+ ['get_5fread_5fname_2351',['get_read_name',['../classvg_1_1NGSSimulator.html#a44c1fcd6a665cc7804e561a7c8700a04',1,'vg::NGSSimulator']]],
+ ['get_5fread_5foffset_2352',['get_read_offset',['../classvg_1_1GaplessExtender.html#a5c568cad31cb0cc1007ef05183c197ab',1,'vg::GaplessExtender']]],
+ ['get_5frecipe_2353',['get_recipe',['../classvg_1_1IndexRegistry.html#a1f378b76124b73c85111a81be74f92b3',1,'vg::IndexRegistry']]],
+ ['get_5frecord_5foffset_2354',['get_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae3dde9ebd7b44658b083f4bd372e823f',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fref_5ffollowing_2355',['get_ref_following',['../structhaplo_1_1linear__haplo__structure.html#a2e9ec5540a31571c3daba83abf03d18d',1,'haplo::linear_haplo_structure']]],
+ ['get_5fref_5finterval_2356',['get_ref_interval',['../classvg_1_1VCFOutputCaller.html#ab382edfcd67f4f3e73fe032cf8f96b04',1,'vg::VCFOutputCaller']]],
+ ['get_5fref_5foffsets_2357',['get_ref_offsets',['../classvg_1_1RatioSupportSnarlCaller.html#a7f838a459153e23e7963a2bd779711de',1,'vg::RatioSupportSnarlCaller::get_ref_offsets()'],['../classvg_1_1TraversalSupportFinder.html#a437e9478fc7551f23246d954af4b0d90',1,'vg::TraversalSupportFinder::get_ref_offsets()']]],
+ ['get_5fref_5fposition_2358',['get_ref_position',['../classvg_1_1VCFOutputCaller.html#a9398350530fc4df45918dc1a14eed549',1,'vg::VCFOutputCaller::get_ref_position()'],['../classvg_1_1MCMCCaller.html#a368d2f5dbd85941acceec2a1d7d44d41',1,'vg::MCMCCaller::get_ref_position()']]],
+ ['get_5fref_5fpositions_2359',['get_ref_positions',['../classvg_1_1VCFGenotyper.html#a60af53e97463c30ff180d3c1b8356df7',1,'vg::VCFGenotyper']]],
+ ['get_5freference_5ftraversal_2360',['get_reference_traversal',['../classvg_1_1LegacyCaller.html#a6d00fa81c7923b88b886f87f28984184',1,'vg::LegacyCaller']]],
+ ['get_5fregistry_2361',['get_registry',['../classvg_1_1subcommand_1_1Subcommand.html#a0e3707f1f4e9ce445faea71fddd61a00',1,'vg::subcommand::Subcommand']]],
+ ['get_5fregular_5faligner_2362',['get_regular_aligner',['../classvg_1_1AlignerClient.html#a60d4602ba9be4861136af507f8eacaec',1,'vg::AlignerClient']]],
+ ['get_5fregular_5fsnarl_5fcode_2363',['get_regular_snarl_code',['../classvg_1_1ZipCode.html#a13c0515e594e7da8c54e29314b1af6a6',1,'vg::ZipCode']]],
+ ['get_5frelease_2364',['get_release',['../classvg_1_1Version.html#a3e99ae82ab6bcc07d982012d731e7091',1,'vg::Version']]],
+ ['get_5frescue_5fgraph_5ffrom_5fpaths_2365',['get_rescue_graph_from_paths',['../classvg_1_1MultipathMapper.html#a655c6fb1dc987ac5f430007594d7bb42',1,'vg::MultipathMapper']]],
+ ['get_5fresolver_2366',['get_resolver',['../classvg_1_1io_1_1Registry.html#a45f5ca692e2d85618f2081e7aa967730',1,'vg::io::Registry']]],
+ ['get_5froot_2367',['get_root',['../classvg_1_1TreeSubgraph.html#a16b12e54e0c87d9a84f4d3a809a8171b',1,'vg::TreeSubgraph::get_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#af94fd9c82aaa2742123b25b0ec95311f',1,'handlegraph::SnarlDecomposition::get_root()']]],
+ ['get_5frr_5fmemo_2368',['get_rr_memo',['../classvg_1_1MultipathMapper.html#a42169ca0715c4c784584ba3d2a5d34bb',1,'vg::MultipathMapper']]],
+ ['get_5fsample_5fname_2369',['get_sample_name',['../classhandlegraph_1_1PathMetadata.html#ada7fda320c3b28c0fb642d7e4a789045',1,'handlegraph::PathMetadata']]],
+ ['get_5fscore_2370',['get_score',['../classvg_1_1ReadFilter.html#a3e168659158cf4372fc11b8cda05883d',1,'vg::ReadFilter::get_score()'],['../classvg_1_1Surjector.html#a42d2fa6bd9590a02329f31666fbe0cd5',1,'vg::Surjector::get_score()'],['../classvg_1_1ReadFilter.html#a2144e5b768ebd71768d37265c07deda2',1,'vg::ReadFilter::get_score(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#af800d67aa469136b6318c02e282c5a30',1,'vg::ReadFilter::get_score(const MultipathAlignment &read) const'],['../classvg_1_1Surjector.html#aafe9672e0a82c6540c4d1360070725ec',1,'vg::Surjector::get_score(const Alignment &aln)'],['../classvg_1_1Surjector.html#a4df48f23da07159bb99bc6577d992938',1,'vg::Surjector::get_score(const multipath_alignment_t &mp_aln)']]],
+ ['get_5fscores_2371',['get_scores',['../structhaplo_1_1haplo__DP__column.html#a784a7e41856ad01f9bdd88ca59dfb146',1,'haplo::haplo_DP_column']]],
+ ['get_5fseed_2372',['get_seed',['../classvg_1_1LazyRNG.html#ac3c6839c2730166a6cb8a10facf8a0c7',1,'vg::LazyRNG']]],
+ ['get_5fseed_5fpos_2373',['get_seed_pos',['../classvg_1_1SpliceRegion.html#ab79a29d07732a726cffffea140af98c4',1,'vg::SpliceRegion']]],
+ ['get_5fsense_2374',['get_sense',['../classhandlegraph_1_1PathMetadata.html#a6cf06655af059252487f9581cad0dc4a',1,'handlegraph::PathMetadata']]],
+ ['get_5fsequence_2375',['get_sequence',['../classvg_1_1DagifiedGraph.html#a5d47d90eeaac4f0a6f1e12f0ed2d197e',1,'vg::DagifiedGraph::get_sequence()'],['../classvg_1_1DozeuPinningOverlay.html#ab7eabd260a4585f04809d8da64b7f2f4',1,'vg::DozeuPinningOverlay::get_sequence()'],['../classvg_1_1ExtraNodeGraph.html#a4b9d7578f0f601b186295d365cf7e487',1,'vg::ExtraNodeGraph::get_sequence()'],['../classvg_1_1SnarlGraph.html#a4a97ed146e23b853fd66a0ad827823e5',1,'vg::SnarlGraph::get_sequence()'],['../classvg_1_1IdentityOverlay.html#ada02cf10738e4fc81c7bb21ecf5d4b56',1,'vg::IdentityOverlay::get_sequence()'],['../classvg_1_1IncrementalSubgraph.html#a61eef0cd10c65efae0cac12816084bb2',1,'vg::IncrementalSubgraph::get_sequence()'],['../classvg_1_1IndexedVG.html#a64c03afcfd0c1c210e8b84a9b78a06dc',1,'vg::IndexedVG::get_sequence()'],['../classvg_1_1MemoizingGraph.html#a841433ccb7c64a657e43130c81c47c39',1,'vg::MemoizingGraph::get_sequence()'],['../classvg_1_1NullMaskingGraph.html#a7a92b5f2747dca58d2fe63368e1294d4',1,'vg::NullMaskingGraph::get_sequence()'],['../classvg_1_1PathSubgraph.html#a1549c36d974dfc4e8bcc54e0e9950646',1,'vg::PathSubgraph::get_sequence()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af008e59ecc555d391149053284ca0cbb',1,'vg::Haplotypes::Subchain::get_sequence()'],['../classvg_1_1ReverseGraph.html#ad815813ebd0d2b33515473bc974c53ad',1,'vg::ReverseGraph::get_sequence()'],['../classvg_1_1NetGraph.html#a4278d3e414d6e5b8e8055d7bdf87c7ac',1,'vg::NetGraph::get_sequence()'],['../classvg_1_1SourceSinkOverlay.html#a4a3eb7401c1b90b33d97672f50a17d39',1,'vg::SourceSinkOverlay::get_sequence()'],['../classvg_1_1JoinedSpliceGraph.html#a6b4f089ed86cdb7ff6ba9177d1187066',1,'vg::JoinedSpliceGraph::get_sequence()'],['../classvg_1_1StrandSplitGraph.html#a878c4be6f6ad6652d3b33f2691bbb570',1,'vg::StrandSplitGraph::get_sequence()'],['../classvg_1_1SubHandleGraph.html#ae9915dd52c55a51616822713509afab0',1,'vg::SubHandleGraph::get_sequence()'],['../classvg_1_1SubgraphOverlay.html#af924de823a9ef5c1a846136eb34637f4',1,'vg::SubgraphOverlay::get_sequence()'],['../classvg_1_1SubpathOverlay.html#a425e89bc05405ef207305c302c18a259',1,'vg::SubpathOverlay::get_sequence()'],['../classvg_1_1TreeSubgraph.html#ae9859d1486d3023b44ab83b3f8c5438c',1,'vg::TreeSubgraph::get_sequence()'],['../classvg_1_1VG.html#a353df9b2449ac859804359632283078b',1,'vg::VG::get_sequence()'],['../classxg_1_1XG.html#ad748df5f6e521774c1d5871ab3519bd8',1,'xg::XG::get_sequence()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4c93978f2d225b926991b34b27528bfd',1,'handlegraph::algorithms::SubHandleGraph::get_sequence()'],['../classhandlegraph_1_1HandleGraph.html#a8cc2ab8a1292e30ba5e167a823f66d92',1,'handlegraph::HandleGraph::get_sequence()']]],
+ ['get_5fsequence_5fdictionary_2376',['get_sequence_dictionary',['../namespacevg.html#a2e23f130325e05c894696771e50f2636',1,'vg']]],
+ ['get_5fsequence_5fvisits_2377',['get_sequence_visits',['../classvg_1_1HaplotypePartitioner.html#acbe0f7f081cf6db06a894e451d8915b6',1,'vg::HaplotypePartitioner']]],
+ ['get_5fsequences_2378',['get_sequences',['../classvg_1_1HaplotypePartitioner.html#a8bdd15927542e95eb536fc9e9bb69aa7',1,'vg::HaplotypePartitioner::get_sequences(handle_t handle) const'],['../classvg_1_1HaplotypePartitioner.html#af88d6e4839d697b5780c453441d3abb0',1,'vg::HaplotypePartitioner::get_sequences(Subchain subchain) const']]],
+ ['get_5fshort_2379',['get_short',['../classvg_1_1Version.html#a8105cc0ae9049ca2daf91fbce5efa5e9',1,'vg::Version']]],
+ ['get_5fshort_5foptions_2380',['get_short_options',['../classvg_1_1OptionInterface.html#a7c1a8f1f6a3071a502362d9765c94add',1,'vg::OptionInterface::get_short_options()'],['../classvg_1_1BaseOption.html#a5b77fd0a8211f8cabd07b14db491fb64',1,'vg::BaseOption::get_short_options()']]],
+ ['get_5fsink_5fhandle_2381',['get_sink_handle',['../classvg_1_1SourceSinkOverlay.html#a71ce03b168ed695659a6ed61a946d089',1,'vg::SourceSinkOverlay']]],
+ ['get_5fsize_2382',['get_size',['../structvg_1_1algorithms_1_1Graph.html#ae7a493be0a453a3e82c7c36f0ad70e07',1,'vg::algorithms::Graph']]],
+ ['get_5fsizes_2383',['get_sizes',['../structhaplo_1_1haplo__DP__column.html#aa2c307962df62885eaca8caa4723d8a4',1,'haplo::haplo_DP_column']]],
+ ['get_5fskip_5fallele_5ffn_2384',['get_skip_allele_fn',['../classvg_1_1SnarlCaller.html#acbc3b71e19fca0c018ff9dd713f2b052',1,'vg::SnarlCaller::get_skip_allele_fn()'],['../classvg_1_1SupportBasedSnarlCaller.html#aa702e223a90771c4090511c23b7c55a7',1,'vg::SupportBasedSnarlCaller::get_skip_allele_fn()']]],
+ ['get_5fsnarl_5fchild_5fcount_2385',['get_snarl_child_count',['../classvg_1_1ZipCode.html#ad6d78deca4d723ac8d5ede306abd5578',1,'vg::ZipCode']]],
+ ['get_5fsnarl_5frank_5for_5fidentifier_2386',['get_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a078386aa48caae9dda52e73c2975f8b7',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fsnarl_5freference_5fbounds_2387',['get_snarl_reference_bounds',['../classvg_1_1Genotyper.html#a29a6f2fd20161c9313498760578c091a',1,'vg::Genotyper']]],
+ ['get_5fsnarl_5ftraversals_2388',['get_snarl_traversals',['../classvg_1_1Genotyper.html#a7a14f1e259fe612b944aadf701ca1585',1,'vg::Genotyper']]],
+ ['get_5fsnp_5fref_5fposition_2389',['get_SNP_ref_position',['../structhaplo_1_1linear__haplo__structure.html#a312a7a7a748cc4acd3c4b75717db1fe6',1,'haplo::linear_haplo_structure']]],
+ ['get_5fsnv_5fallele_2390',['get_SNV_allele',['../structhaplo_1_1linear__haplo__structure.html#a353eefc81d042a96f98980b7cb2a72aa',1,'haplo::linear_haplo_structure']]],
+ ['get_5fsort_5fvalue_2391',['get_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aae5b7a35573e7133c368eb6bf4678aab',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['get_5fsource_5fhandle_2392',['get_source_handle',['../classvg_1_1SourceSinkOverlay.html#a4126d6851b442614cb115668eaeeb89f',1,'vg::SourceSinkOverlay']]],
+ ['get_5fspanning_5fhaplotypes_2393',['get_spanning_haplotypes',['../classvg_1_1GBWTTraversalFinder.html#a88b35f62878ceab005faf07f7386691c',1,'vg::GBWTTraversalFinder']]],
+ ['get_5fstart_2394',['get_start',['../classvg_1_1NetGraph.html#a35e17fbdc2bade4b5b0195d03cb0dc22',1,'vg::NetGraph']]],
+ ['get_5fstart_5fbound_2395',['get_start_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a63eea99ca9840f16ef358ee664ecda23',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fstart_5fof_2396',['get_start_of',['../namespacevg.html#afa918cf29c1c8238d88f2bbc94b6abef',1,'vg']]],
+ ['get_5fstep_5fat_5fposition_2397',['get_step_at_position',['../classvg_1_1MemoizingGraph.html#acbae8703ecc85597b33e36d5208a4f1e',1,'vg::MemoizingGraph::get_step_at_position()'],['../classxg_1_1XG.html#a087db8dbe184e5a22dda11d61f8fff6a',1,'xg::XG::get_step_at_position()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#aefbae4c3392c32ec13534a44bcc21136',1,'handlegraph::PathPositionHandleGraph::get_step_at_position()']]],
+ ['get_5fstep_5fcount_2398',['get_step_count',['../classvg_1_1MemoizingGraph.html#ae0bc7232272e70adab6333dbe3718f46',1,'vg::MemoizingGraph::get_step_count()'],['../classvg_1_1PathSubgraphOverlay.html#ae2df84b76bcec7b4899838a99d3799f5',1,'vg::PathSubgraphOverlay::get_step_count()'],['../classvg_1_1VG.html#a3efe30807d096a6175373bc3f4863dd7',1,'vg::VG::get_step_count()'],['../classxg_1_1XG.html#a0609241ee4795d7c9dd2a2b5cc8ce3a4',1,'xg::XG::get_step_count()'],['../classhandlegraph_1_1PathHandleGraph.html#add91075c3490f8dc5acf667f2b26832c',1,'handlegraph::PathHandleGraph::get_step_count(const path_handle_t &path_handle) const =0'],['../classhandlegraph_1_1PathHandleGraph.html#a6d3a31f0c19054cd2908525119869b80',1,'handlegraph::PathHandleGraph::get_step_count(const handle_t &handle) const']]],
+ ['get_5fsteps_2399',['get_steps',['../classvg_1_1IndexingPlan.html#a52c631c507d1cd0f0451ce7de71f2091',1,'vg::IndexingPlan']]],
+ ['get_5fstream_5flength_2400',['get_stream_length',['../namespacevg_1_1io.html#aff18a599bd6affc6e2709cb2cff9154c',1,'vg::io']]],
+ ['get_5fstream_5fposition_2401',['get_stream_position',['../namespacevg_1_1io.html#aca3b265c558db37b69a837668d2fdf12',1,'vg::io']]],
+ ['get_5fsubchains_2402',['get_subchains',['../classvg_1_1HaplotypePartitioner.html#a27be1484d044a8f872083ea6e98d9786',1,'vg::HaplotypePartitioner']]],
+ ['get_5fsubgraph_2403',['get_subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a8754c28fbea6df69e6204a9128912a20',1,'vg::GraphSynchronizer::Lock::get_subgraph()'],['../classvg_1_1SpliceRegion.html#ae10fef3784f1d382cb8f3973e1c9ff1b',1,'vg::SpliceRegion::get_subgraph()']]],
+ ['get_5fsubrange_2404',['get_subrange',['../classhandlegraph_1_1PathMetadata.html#a80f47deffdb584fa74ea43dad580cce7',1,'handlegraph::PathMetadata']]],
+ ['get_5fsubsequence_2405',['get_subsequence',['../classvg_1_1IncrementalSubgraph.html#a258698c76e4d96ecefd38505894f778b',1,'vg::IncrementalSubgraph::get_subsequence()'],['../classvg_1_1JoinedSpliceGraph.html#a2348c9a3357615ce0eea301366344376',1,'vg::JoinedSpliceGraph::get_subsequence()'],['../classvg_1_1VG.html#a45075c22efc7cfb1ed06a8996fec119c',1,'vg::VG::get_subsequence()'],['../classxg_1_1XG.html#a0368861cc6c99d2a1d40c059db62c2a9',1,'xg::XG::get_subsequence()'],['../classhandlegraph_1_1HandleGraph.html#a74c6fcda357516b1160996c63ed40d63',1,'handlegraph::HandleGraph::get_subsequence()']]],
+ ['get_5fsuffix_2406',['get_suffix',['../classvg_1_1IndexFile.html#ac81438a82e18b86b443e7d853245d599',1,'vg::IndexFile::get_suffix()'],['../classvg_1_1PhaseUnfolder.html#a97128de268b43c9ccf9dd117829adedf',1,'vg::PhaseUnfolder::get_suffix()']]],
+ ['get_5fsupport_2407',['get_support',['../structvg_1_1AugmentedGraph.html#ad239a8516427304ef304e944f7d20c00',1,'vg::AugmentedGraph::get_support(id_t node)'],['../structvg_1_1AugmentedGraph.html#a87c6ed55516068757be3b1ad54a6cfd0',1,'vg::AugmentedGraph::get_support(edge_t edge)'],['../structvg_1_1SupportAugmentedGraph.html#a0ffa85683b46b7f8d6b64da42ba19fbb',1,'vg::SupportAugmentedGraph::get_support(id_t node)'],['../structvg_1_1SupportAugmentedGraph.html#a4c86be41ce8680c5473080c704ddcc10',1,'vg::SupportAugmentedGraph::get_support(edge_t edge)']]],
+ ['get_5fsupport_5ffinder_2408',['get_support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a04ebbd23ec0162a72c959351131e17ba',1,'vg::SupportBasedSnarlCaller']]],
+ ['get_5fsymbolic_5fbounds_2409',['get_symbolic_bounds',['../classvg_1_1Constructor.html#a31a7837804bd45819ab249687a858fbb',1,'vg::Constructor']]],
+ ['get_5fsystem_5fmemory_2410',['get_system_memory',['../classvg_1_1IndexRegistry.html#a1f03f21a783cad871997b03bcd0c8dff',1,'vg::IndexRegistry']]],
+ ['get_5ftables_2411',['get_tables',['../classvg_1_1io_1_1Registry.html#aa9f3d682e2b43bfdc3fc30e252a716b9',1,'vg::io::Registry']]],
+ ['get_5ftail_5fforest_2412',['get_tail_forest',['../classvg_1_1MinimizerMapper.html#afdbaa5b2938d0050476d078d336286cf',1,'vg::MinimizerMapper']]],
+ ['get_5ftarget_5fmemory_5fusage_2413',['get_target_memory_usage',['../classvg_1_1IndexRegistry.html#aa8aae29f234def70dc6de5f1a291cbc0',1,'vg::IndexRegistry']]],
+ ['get_5fthread_5fcount_2414',['get_thread_count',['../namespacevg.html#ade988dd38efaa705be15ba17500fe219',1,'vg::get_thread_count()'],['../namespacexg.html#a025cd6958c94d7ce14c1be1425792161',1,'xg::get_thread_count()']]],
+ ['get_5fthread_5fstream_2415',['get_thread_stream',['../classvg_1_1io_1_1StreamMultiplexer.html#a749ab082e0364d470d84978c9757ef76',1,'vg::io::StreamMultiplexer']]],
+ ['get_5ftop_5flevel_5fchain_5foffset_2416',['get_top_level_chain_offset',['../classvg_1_1ZipCode.html#a304ce8419239ce69dfb69e85e50d3c8c',1,'vg::ZipCode']]],
+ ['get_5ftopological_5forder_2417',['get_topological_order',['../classvg_1_1PathSubgraph.html#a591e8f29ef3f356a38aca18e466ae954',1,'vg::PathSubgraph::get_topological_order()'],['../classvg_1_1TreeSubgraph.html#a850f30c11c28ab61148215970b5c6129',1,'vg::TreeSubgraph::get_topological_order()']]],
+ ['get_5ftotal_5flength_2418',['get_total_length',['../classxg_1_1XG.html#a4437293fdec75f15a296fb545a6d539d',1,'xg::XG::get_total_length()'],['../classhandlegraph_1_1HandleGraph.html#a4c98da99e0d32ebcc9fd31be4b779e29',1,'handlegraph::HandleGraph::get_total_length()']]],
+ ['get_5ftranslation_2419',['get_translation',['../classvg_1_1Translator.html#ac76452dc0c74164d2bcfa25f53ca9828',1,'vg::Translator']]],
+ ['get_5ftraversal_5fgenotype_5fsupport_2420',['get_traversal_genotype_support',['../classvg_1_1TraversalSupportFinder.html#a1b818e6111dd2eec62067a562ecc2078',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fmapqs_2421',['get_traversal_mapqs',['../classvg_1_1TraversalSupportFinder.html#a1a7ce9dabeac1835ce0c9765301fcafd',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fof_5fsnarl_2422',['get_traversal_of_snarl',['../namespacevg.html#a871d5cdd29e1806636314021d0b6d451',1,'vg']]],
+ ['get_5ftraversal_5forder_2423',['get_traversal_order',['../namespacevg.html#aaa05224d1b8daa421ebfb9320fc1d2d1',1,'vg']]],
+ ['get_5ftraversal_5fset_5fsupport_2424',['get_traversal_set_support',['../classvg_1_1TraversalSupportFinder.html#aead4beb53b5148baa538c6481be8700d',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fsizes_2425',['get_traversal_sizes',['../classvg_1_1TraversalSupportFinder.html#a95944f27ca78da63466f5623ad646ee4',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fsupport_2426',['get_traversal_support',['../classvg_1_1TraversalSupportFinder.html#a28c6f9088f6c28d64855d6cac9a65322',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversals_2427',['get_traversals',['../classvg_1_1Deconstructor.html#ad58319907ec3f7bf3e6d130f6469a9a9',1,'vg::Deconstructor']]],
+ ['get_5ftree_5fsize_2428',['get_tree_size',['../classvg_1_1ZipCodeTree.html#a1207ebf8f31cd6f17593f100be3c7f00',1,'vg::ZipCodeTree']]],
+ ['get_5ftype_2429',['get_type',['../structhaplo_1_1linear__haplo__structure.html#ac0dcdb90717d1585bbc847206746e293',1,'haplo::linear_haplo_structure::get_type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#aef1abc2e62fd2ebcc722e26978bb56b7',1,'vg::ZipCodeTree::tree_item_t::get_type()']]],
+ ['get_5funderlying_5fhandle_2430',['get_underlying_handle',['../classvg_1_1DagifiedGraph.html#aea86fce4d0f22943935bad1e5cc17f48',1,'vg::DagifiedGraph::get_underlying_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a5cfe7e76c343f768037c84df85037ace',1,'vg::DozeuPinningOverlay::get_underlying_handle()'],['../classvg_1_1IdentityOverlay.html#a5bfd0bebd074847b5504b9ad3f968836',1,'vg::IdentityOverlay::get_underlying_handle()'],['../classvg_1_1IncrementalSubgraph.html#a6b3e5f09eb2a9edb698eb08c55cc9486',1,'vg::IncrementalSubgraph::get_underlying_handle()'],['../classvg_1_1NullMaskingGraph.html#aa903d2c61cf2ba035aac11a3015c2cab',1,'vg::NullMaskingGraph::get_underlying_handle()'],['../classvg_1_1PathSubgraph.html#aa6c521d9a3770f20483f3f16b0686eeb',1,'vg::PathSubgraph::get_underlying_handle()'],['../classvg_1_1ReverseGraph.html#a246e5d5c82508b512fb4c041bfe38892',1,'vg::ReverseGraph::get_underlying_handle()'],['../classvg_1_1SourceSinkOverlay.html#abe2d0e58471d1ab7840618a02958fc96',1,'vg::SourceSinkOverlay::get_underlying_handle()'],['../classvg_1_1StrandSplitGraph.html#aa6379c95c71b6a6682311733de098d1f',1,'vg::StrandSplitGraph::get_underlying_handle()'],['../classvg_1_1SubHandleGraph.html#a434e6cd60bb278307df255a43681e08a',1,'vg::SubHandleGraph::get_underlying_handle()'],['../classvg_1_1SubpathOverlay.html#a595889f41331fbbc8a049ae56ba29624',1,'vg::SubpathOverlay::get_underlying_handle()'],['../classvg_1_1TreeSubgraph.html#a2d88a6edb6d6d586b6fe26a88e13248f',1,'vg::TreeSubgraph::get_underlying_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ada7dab5b4c9e55607563d1bcf546d401',1,'handlegraph::algorithms::SubHandleGraph::get_underlying_handle()'],['../classhandlegraph_1_1ExpandingOverlayGraph.html#aacfa30b0166f91f1aa80f0fd566d2b65',1,'handlegraph::ExpandingOverlayGraph::get_underlying_handle()']]],
+ ['get_5funderlying_5fid_2431',['get_underlying_id',['../classvg_1_1DagifiedGraph.html#ae8707e0886baf125d0c0a25a3cc3a4cc',1,'vg::DagifiedGraph::get_underlying_id()'],['../classvg_1_1DozeuPinningOverlay.html#a45047bf7a55843a4099d9db6b83e2d17',1,'vg::DozeuPinningOverlay::get_underlying_id()']]],
+ ['get_5funique_5fhaplotypes_2432',['get_unique_haplotypes',['../classvg_1_1VariantAdder.html#aa9ae7b7fa8ad3ac6bec72ada43a3d4b7',1,'vg::VariantAdder']]],
+ ['get_5fvalue_2433',['get_value',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#adf719dd5d99dd4b31952df3af1911ed1',1,'vg::ZipCodeTree::tree_item_t::get_value()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a6d28a735e7c8a6a0cc8b11675fb8d261',1,'vg::subcommand::ArgSpec::get_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#acb802adcf83734cc84ee4745ed4ee505',1,'vg::subcommand::ValueArgSpec::get_value()']]],
+ ['get_5fvalue_5fand_5fnext_5findex_2434',['get_value_and_next_index',['../structvg_1_1varint__vector__t.html#afee3663cabce117ecf7b114b0179ae31',1,'vg::varint_vector_t']]],
+ ['get_5fvariants_5fin_5fsite_2435',['get_variants_in_site',['../classvg_1_1VCFTraversalFinder.html#ae45b4f713e847be11c4aa07482de3e12',1,'vg::VCFTraversalFinder']]],
+ ['get_5fvcf_5fheader_2436',['get_vcf_header',['../classvg_1_1Deconstructor.html#a6c14aa01fabc63b945bc69550335408b',1,'vg::Deconstructor']]],
+ ['get_5fversion_2437',['get_version',['../classvg_1_1Version.html#aa6e698d728ebd5e3318511dfde778eaf',1,'vg::Version']]],
+ ['get_5fvg_5findex_5fregistry_2438',['get_vg_index_registry',['../structvg_1_1VGIndexes.html#a4291997834048ac385331f19390889c0',1,'vg::VGIndexes']]],
+ ['get_5fweight_5fusing_5fother_2439',['get_weight_using_other',['../structvg_1_1algorithms_1_1Graph.html#ad0741db7b09040c706ffaffbb7337098',1,'vg::algorithms::Graph']]],
+ ['get_5fwork_5fdir_2440',['get_work_dir',['../classvg_1_1IndexRegistry.html#ac587073860174b6c074d2be7ad53e103',1,'vg::IndexRegistry']]],
+ ['getreachablebridges_2441',['getReachableBridges',['../namespacevg.html#af601021f7ec2c0b0d7404030ee7271c9',1,'vg']]],
+ ['getreachablebridges2_2442',['getReachableBridges2',['../namespacevg.html#a2dc613a63afb3f23851c96494006630d',1,'vg']]],
+ ['gfa_2ecpp_2443',['gfa.cpp',['../gfa_8cpp.html',1,'']]],
+ ['gfa_2ehpp_2444',['gfa.hpp',['../gfa_8hpp.html',1,'']]],
+ ['gfa_5fhas_5fhaplotypes_2445',['gfa_has_haplotypes',['../classvg_1_1IndexRegistry.html#a019e2efc800d3280acdce7814db8b096',1,'vg::IndexRegistry']]],
+ ['gfa_5fid_5fspace_2446',['gfa_id_space',['../classvg_1_1GFAHandleGraph.html#a74dbb782d6ffa6301fc97f7e540ebe40',1,'vg::GFAHandleGraph']]],
+ ['gfa_5fparameters_2447',['gfa_parameters',['../structGBWTConfig.html#a07b86c3ec44037b22504eb86d9ebd78d',1,'GBWTConfig']]],
+ ['gfa_5fto_5fhandle_2ecpp_2448',['gfa_to_handle.cpp',['../gfa__to__handle_8cpp.html',1,'']]],
+ ['gfa_5fto_5fhandle_2ehpp_2449',['gfa_to_handle.hpp',['../gfa__to__handle_8hpp.html',1,'']]],
+ ['gfa_5fto_5fhandle_5fgraph_2450',['gfa_to_handle_graph',['../namespacevg_1_1algorithms.html#aedfca626dc003dc3fee77c6bbfcde297',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, GFAIDMapInfo *translation)'],['../namespacevg_1_1algorithms.html#adca14b7dcba0bb21f3fdb0c98d867c72',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, const string &translation_filename)'],['../namespacevg_1_1algorithms.html#a031cb6d0db20a6aaee020c5a6909ba80',1,'vg::algorithms::gfa_to_handle_graph(istream &in, MutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr)']]],
+ ['gfa_5fto_5fpath_5fhandle_5fgraph_2451',['gfa_to_path_handle_graph',['../namespacevg_1_1algorithms.html#a9f5c41c06269c778d2c97f39cbc79de8',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a61f2c7006c531ad5dd319ea30ec0087f',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, int64_t max_rgfa_rank, const string &translation_filename, unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a8baa82611439357dc02996ba17ce6aa9',1,'vg::algorithms::gfa_to_path_handle_graph(istream &in, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)']]],
+ ['gfaduplicatepatherror_2452',['GFADuplicatePathError',['../structvg_1_1algorithms_1_1GFADuplicatePathError.html',1,'vg::algorithms::GFADuplicatePathError'],['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#aa815b9f84fdf80d9bf29c38d3d68408c',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name)'],['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#a05dd140439b17113dec810a3cdc26bab',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
+ ['gfaformaterror_2453',['GFAFormatError',['../structvg_1_1algorithms_1_1GFAFormatError.html',1,'vg::algorithms::GFAFormatError'],['../structvg_1_1algorithms_1_1GFAFormatError.html#add2d72c679e2b69e1c9f9c481228e0fb',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message)'],['../structvg_1_1algorithms_1_1GFAFormatError.html#afdf6dea244cc33a30ae5d9446199bea2',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
+ ['gfahandlegraph_2454',['GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html',1,'vg::GFAHandleGraph'],['../classvg_1_1GFAHandleGraph.html#aeffc2278ffcad22cd6950f3fa831f60d',1,'vg::GFAHandleGraph::GFAHandleGraph()']]],
+ ['gfaidmapinfo_2455',['GFAIDMapInfo',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html',1,'vg::algorithms']]],
+ ['gfaparser_2456',['GFAParser',['../classvg_1_1algorithms_1_1GFAParser.html',1,'vg::algorithms']]],
+ ['gff_5ffeature_5fname_2457',['gff_feature_name',['../structvg_1_1IndexingParameters.html#aaeec45d17c4d60468c14debb7fb46709',1,'vg::IndexingParameters']]],
+ ['gff_5freader_2ecpp_2458',['gff_reader.cpp',['../gff__reader_8cpp.html',1,'']]],
+ ['gff_5freader_2ehpp_2459',['gff_reader.hpp',['../gff__reader_8hpp.html',1,'']]],
+ ['gff_5ftranscript_5ftag_2460',['gff_transcript_tag',['../structvg_1_1IndexingParameters.html#aa795ef116d75fdbf71092b831fce2c21',1,'vg::IndexingParameters']]],
+ ['gffreader_2461',['GFFReader',['../classvg_1_1GFFReader.html',1,'vg::GFFReader'],['../classvg_1_1GFFReader.html#a886d9cf2d287f8d0f6c87b206c26d893',1,'vg::GFFReader::GFFReader()']]],
+ ['gffrecord_2462',['GFFRecord',['../structvg_1_1GFFRecord.html',1,'vg::GFFRecord'],['../structvg_1_1GFFRecord.html#a8fc2a234093eccb6ed958325887e0f08',1,'vg::GFFRecord::GFFRecord()']]],
+ ['giraffe_5fgbwt_5fdownsample_2463',['giraffe_gbwt_downsample',['../structvg_1_1IndexingParameters.html#a915eada866d050e347f4b3c00ef5dab9',1,'vg::IndexingParameters']]],
+ ['giraffe_5fmain_2ecpp_2464',['giraffe_main.cpp',['../giraffe__main_8cpp.html',1,'']]],
+ ['giraffemainoptions_2465',['GiraffeMainOptions',['../structGiraffeMainOptions.html',1,'']]],
+ ['globals_2466',['globals',['../classvg_1_1DiagramExplainer.html#ac7ea94549f8c5ecddece74889a88ea88',1,'vg::DiagramExplainer']]],
+ ['go_5fleft_2467',['go_left',['../structvg_1_1ChainIterator.html#a785251461ea63262f67548eeadea7684',1,'vg::ChainIterator']]],
+ ['golden_5fsection_5fsearch_2468',['golden_section_search',['../namespacevg.html#a314ff925fad534d112e4531617e408fa',1,'vg']]],
+ ['google_2469',['google',['../namespacegoogle.html',1,'']]],
+ ['gq_2470',['gq',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a021adf386d5306f56c3a330412c13000',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['grandparent_5fnet_5fhandle_2471',['grandparent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6ca403df1dfe6e9554571dba400448f8',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['graph_2472',['Graph',['../structvg_1_1Graph.html',1,'vg::Graph'],['../structvg_1_1algorithms_1_1Graph.html',1,'vg::algorithms::Graph'],['../classvg_1_1BandedGlobalAligner.html#af5168385acfc1ca71f0757269452e5a7',1,'vg::BandedGlobalAligner::graph()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9d4f47628b410f5639f985dae1b1b5e0',1,'vg::BandedGlobalAligner::AltTracebackStack::graph()'],['../classvg_1_1CactusSnarlFinder.html#abb2127506508ae3515f901375b205e2d',1,'vg::CactusSnarlFinder::graph()'],['../classvg_1_1PathChunker.html#afbe0c85ff99dd1134fefcf439b212d4f',1,'vg::PathChunker::graph()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a528e7742b43628c6c93c6542810ffdfd',1,'vg::PathOrientedDistanceMeasurer::graph()'],['../structvg_1_1ConstructedChunk.html#a27e2145253b94e1edecf0f456a12268b',1,'vg::ConstructedChunk::graph()'],['../classvg_1_1ContractingGraph.html#ab79d18f0c2f96761ebdad601ec4ec3d4',1,'vg::ContractingGraph::graph()'],['../classvg_1_1DagifiedGraph.html#a5b2dd0d18c17b2e10aa1b6b6280018ee',1,'vg::DagifiedGraph::graph()'],['../classvg_1_1Deconstructor.html#a74cd5fde9496dcc1865ed74fda2c4ae4',1,'vg::Deconstructor::graph()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a50561ac0fc9bcfd983a71c9fec2b6d2e',1,'vg::DozeuInterface::OrderedGraph::graph()'],['../classvg_1_1DozeuPinningOverlay.html#aff912b269bf3e749ef52c0d86fe12fcf',1,'vg::DozeuPinningOverlay::graph()'],['../classvg_1_1WFATree.html#a313dc78cf7698c0b50b3fb2b0ec28a81',1,'vg::WFATree::graph()'],['../classvg_1_1GaplessExtender.html#a8780650e736d01abf2dd910a3dd235c3',1,'vg::GaplessExtender::graph()'],['../classvg_1_1WFAExtender.html#a7362ec7bfdf80dc2fc343e483bdf0e5d',1,'vg::WFAExtender::graph()'],['../classvg_1_1SnarlState.html#a62e2fb69d55ee9cf1e2653dc4c9c8ead',1,'vg::SnarlState::graph()'],['../structvg_1_1AugmentedGraph.html#afb05832f68a8db43e7a8c510397b8ce3',1,'vg::AugmentedGraph::graph()'],['../classvg_1_1VCFGenotyper.html#ab76cadfc9e7398a693e7a0cb656dc37a',1,'vg::VCFGenotyper::graph()'],['../classvg_1_1LegacyCaller.html#a5065baf9582814e816349b53bc54a4e9',1,'vg::LegacyCaller::graph()'],['../classvg_1_1FlowCaller.html#a5193a03f37a60ed6bdf91157bf02c6dc',1,'vg::FlowCaller::graph()'],['../classvg_1_1NestedFlowCaller.html#af2cc9a536a0a2ca0fd857793f0985d68',1,'vg::NestedFlowCaller::graph()'],['../classvg_1_1GraphSynchronizer.html#ab0856b30a01193d100f9e470ea61a67c',1,'vg::GraphSynchronizer::graph()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a99d071619c6462165528d8428d4bb7fa',1,'haplo::hDP_gbwt_graph_accessor::graph()'],['../structhaplo_1_1linear__haplo__structure.html#acb5692ebbb1a6f91db791d01bb2ab294',1,'haplo::linear_haplo_structure::graph()'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#adf4336380ac7e4944628281010e7057a',1,'vg::SplicedHTSAlignmentEmitter::graph()'],['../classvg_1_1IdentityOverlay.html#aa5f51840702ebb847bc1193bea756960',1,'vg::IdentityOverlay::graph()'],['../classvg_1_1IncrementalSubgraph.html#a45a1fbda6452cbdade4d40bc4dab539c',1,'vg::IncrementalSubgraph::graph()'],['../classvg_1_1AliasGraph.html#a85dd8f136025b7325d9fa19058d2bb4f',1,'vg::AliasGraph::graph()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a932e7e9593e73f7a76a8f1756f4fb1f8',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::graph()'],['../classvg_1_1HandleGraphNodeSet.html#a1d0f4da0abcf0379dfe1672cce88a055',1,'vg::HandleGraphNodeSet::graph()'],['../classvg_1_1Masker.html#a58ab29d84eb1ad7d8d8884927850d674',1,'vg::Masker::graph()'],['../classvg_1_1MCMCGenotyper.html#a63ef4fabc83c478b9ac7933ba16c5adc',1,'vg::MCMCGenotyper::graph()'],['../classvg_1_1MemoizingGraph.html#ae619ad2dfa33c00eced07b7a987e9796',1,'vg::MemoizingGraph::graph()'],['../classvg_1_1MultipathAlignmentEmitter.html#aaaf74750129abc432b73f66d226d35c6',1,'vg::MultipathAlignmentEmitter::graph()'],['../classvg_1_1NullMaskingGraph.html#a691c9aa63e3e20dbba329691b482f311',1,'vg::NullMaskingGraph::graph()'],['../classvg_1_1Packer.html#a52ac5f2ff5549fe1b296efc53204e94f',1,'vg::Packer::graph()'],['../classvg_1_1RareVariantSimplifier.html#ace754988b74595f36762993abead625f',1,'vg::RareVariantSimplifier::graph()'],['../classvg_1_1ReadFilter.html#a73ca67996129403044a23de9544e88fd',1,'vg::ReadFilter::graph()'],['../classvg_1_1RegionExpander.html#af23424b8d8c2f809311afb6b3dceca08',1,'vg::RegionExpander::graph()'],['../classvg_1_1AbstractReadSampler.html#a07bbefa0c0af8f9c4cb5b2c45bcdae53',1,'vg::AbstractReadSampler::graph()'],['../classvg_1_1SmallSnarlSimplifier.html#a54a08fa74dda470c28e2850ded312175',1,'vg::SmallSnarlSimplifier::graph()'],['../classvg_1_1SupportBasedSnarlCaller.html#ab0f5bd05d950be25e87a9f5fbc345a5c',1,'vg::SupportBasedSnarlCaller::graph()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a49cfcfdb9e2c378e973dd8a883e154df',1,'vg::SnarlDistanceIndexClusterer::graph()'],['../classvg_1_1HandleGraphSnarlFinder.html#a377e8778235836602280747eb5813f58',1,'vg::HandleGraphSnarlFinder::graph()'],['../classvg_1_1NetGraph.html#acbae58f3fb38de99ea4a0f0b16ede465',1,'vg::NetGraph::graph()'],['../classvg_1_1StrandSplitGraph.html#a61683c11a40d1881132614159ffc0543',1,'vg::StrandSplitGraph::graph()'],['../classvg_1_1Surjector.html#a118010284d37b604a7bcd7eb8dd13537',1,'vg::Surjector::graph()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a66b0e7a1ac972af0e4d381e4202e1f5e',1,'vg::ExhaustiveTraversalFinder::graph()'],['../classvg_1_1PathRestrictedTraversalFinder.html#aef70365b3b1ee2afb3ac622748923a90',1,'vg::PathRestrictedTraversalFinder::graph()'],['../classvg_1_1PathBasedTraversalFinder.html#a16635d1b5be7de4078a9c2369a1b8073',1,'vg::PathBasedTraversalFinder::graph()'],['../classvg_1_1PathTraversalFinder.html#a7ae6d1d377192e4fab7a9074b83bddbd',1,'vg::PathTraversalFinder::graph()'],['../classvg_1_1TrivialTraversalFinder.html#aeb55a5539b54fd0bf8b4e59db2d4ffca',1,'vg::TrivialTraversalFinder::graph()'],['../classvg_1_1RepresentativeTraversalFinder.html#a66eedfed30f7b436c4eef2b339e356ba',1,'vg::RepresentativeTraversalFinder::graph()'],['../classvg_1_1VCFTraversalFinder.html#ac8e35bbc2e0c34475f13f8d6989fa5b6',1,'vg::VCFTraversalFinder::graph()'],['../classvg_1_1FlowTraversalFinder.html#ad092938a00c2c7c2b046d88fe47c73a8',1,'vg::FlowTraversalFinder::graph()'],['../classvg_1_1GBWTTraversalFinder.html#a1279ffc672ec8ee2fc6e6f1825462e15',1,'vg::GBWTTraversalFinder::graph()'],['../classvg_1_1TraversalSupportFinder.html#a388ac720c48b44f21da264209a25a3b3',1,'vg::TraversalSupportFinder::graph()'],['../classvg_1_1VariantAdder.html#a149b01f65cc10625177011221dfef354',1,'vg::VariantAdder::graph()'],['../classvg_1_1VG.html#a4772c77ed932bfed4d21e247918381a4',1,'vg::VG::graph()'],['../structvg_1_1VG_1_1Plan.html#a06f927768c287c88f81d9761d61da231',1,'vg::VG::Plan::graph()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a0a6667c750efa2c5264c6ffe1c5727aa',1,'handlegraph::PathForEachSocket::iterator::graph()'],['../classhandlegraph_1_1PathForEachSocket.html#a0bdd335f78e28a6a26ab2605c06fa601',1,'handlegraph::PathForEachSocket::graph()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a956c6bef21a026c7426da0650a2927b8',1,'vg::io::GafAlignmentEmitter::graph()'],['../classvg_1_1Transcriptome.html#aee456b8b8e3acaf836914c987d89a16a',1,'vg::Transcriptome::graph()']]],
+ ['graph_2ecpp_2473',['graph.cpp',['../graph_8cpp.html',1,'']]],
+ ['graph_2ehpp_2474',['graph.hpp',['../graph_8hpp.html',1,'']]],
+ ['graph_5fcaller_2ecpp_2475',['graph_caller.cpp',['../graph__caller_8cpp.html',1,'']]],
+ ['graph_5fcaller_2ehpp_2476',['graph_caller.hpp',['../graph__caller_8hpp.html',1,'']]],
+ ['graph_5fcigar_2477',['graph_cigar',['../classvg_1_1GSSWAligner.html#a429c1cbb1e166acba4e29a8dc172da7d',1,'vg::GSSWAligner']]],
+ ['graph_5fend_2478',['graph_end',['../classvg_1_1algorithms_1_1Anchor.html#a3ddb866c3cb925619705602580076942',1,'vg::algorithms::Anchor']]],
+ ['graph_5fgbwtgraph_2479',['graph_gbwtgraph',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a91483c9c92517470579d46e605443620',1,'GraphHandler']]],
+ ['graph_5fgbz_2480',['graph_gbz',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a759ff53fb7d1c506e3be18f608607ac5',1,'GraphHandler']]],
+ ['graph_5finterval_5fto_5fstring_2481',['graph_interval_to_string',['../namespacevg.html#aeade23d997b1899023cfe7f560cc6bc1',1,'vg']]],
+ ['graph_5fmixed_5fdistance_5festimate_2482',['graph_mixed_distance_estimate',['../classvg_1_1Mapper.html#a67fb2b4bc540b81be063075ce5593569',1,'vg::Mapper']]],
+ ['graph_5fname_2483',['graph_name',['../structGBWTConfig.html#adb800365228cdbb56b99c207e6a342ea',1,'GBWTConfig::graph_name()'],['../structHaplotypesConfig.html#a232a96ba620bbe67e61468c7841bec9d',1,'HaplotypesConfig::graph_name()']]],
+ ['graph_5fnone_2484',['graph_none',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50abbfbe5112e8f9046f822fc511ab21631',1,'GraphHandler']]],
+ ['graph_5foutput_2485',['graph_output',['../structGBWTConfig.html#adb60e4d83216b0c6b9a4ffd821a54ffb',1,'GBWTConfig']]],
+ ['graph_5fpath_2486',['graph_path',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50af316f5a8669d38d1c1801caf9d5671d7',1,'GraphHandler']]],
+ ['graph_5fpos_5fat_5fpath_5fposition_2487',['graph_pos_at_path_position',['../classxg_1_1XG.html#a85c47feeb19e96486140c5e1b8184bc7',1,'xg::XG::graph_pos_at_path_position(const path_handle_t &path, size_t path_pos) const'],['../classxg_1_1XG.html#a31c733ed1c2045b1e2a7e9f343dc9296',1,'xg::XG::graph_pos_at_path_position(const std::string &name, size_t path_pos) const']]],
+ ['graph_5fpos_5fs_2488',['graph_pos_s',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html',1,'vg::DozeuInterface']]],
+ ['graph_5fsource_2489',['graph_source',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a66269d0a2331df8645dfca4cdbc4a2ea',1,'GraphHandler']]],
+ ['graph_5fstart_2490',['graph_start',['../classvg_1_1algorithms_1_1Anchor.html#ac7bd5f21e10bae0f6dacb3fcc623752f',1,'vg::algorithms::Anchor']]],
+ ['graph_5fsynchronizer_2ecpp_2491',['graph_synchronizer.cpp',['../graph__synchronizer_8cpp.html',1,'']]],
+ ['graph_5fsynchronizer_2ehpp_2492',['graph_synchronizer.hpp',['../graph__synchronizer_8hpp.html',1,'']]],
+ ['graph_5fto_5fgfa_2493',['graph_to_gfa',['../namespacevg.html#ad8c4a075bb9301c8050d89ed8e6a33b9',1,'vg']]],
+ ['graph_5fto_5fxg_5fadjusting_5fpaths_2494',['graph_to_xg_adjusting_paths',['../convert__main_8cpp.html#afe37e7186bce3c6128d32b210f99a9a5',1,'convert_main.cpp']]],
+ ['graph_5ftype_2495',['graph_type',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50',1,'GraphHandler']]],
+ ['graphcaller_2496',['GraphCaller',['../classvg_1_1GraphCaller.html',1,'vg::GraphCaller'],['../classvg_1_1GraphCaller.html#a621386ff80a0fe3289719c75c282bc5a',1,'vg::GraphCaller::GraphCaller()']]],
+ ['graphhandler_2497',['GraphHandler',['../structGraphHandler.html',1,'']]],
+ ['graphsynchronizer_2498',['GraphSynchronizer',['../classvg_1_1GraphSynchronizer.html',1,'vg::GraphSynchronizer'],['../classvg_1_1GraphSynchronizer.html#addf1e96558546d4f5e708827b9eb4d67',1,'vg::GraphSynchronizer::GraphSynchronizer()']]],
+ ['greater_5fgaffile_2499',['greater_gaffile',['../structgreater__gaffile.html',1,'']]],
+ ['greedy_5fmin_5fdist_2500',['greedy_min_dist',['../classvg_1_1MultipathMapper.html#a97d02064d377122ed8cef9e53340ba90',1,'vg::MultipathMapper']]],
+ ['greedy_5fpieces_2501',['greedy_pieces',['../classvg_1_1Constructor.html#ac4dce51a25e5f773a0c53e8cd9f07628',1,'vg::Constructor']]],
+ ['greedy_5frestart_5fassume_5fsubstitution_2502',['greedy_restart_assume_substitution',['../classvg_1_1BaseMapper.html#a5a3324ff0b1faccb4e976e0d1a369712',1,'vg::BaseMapper']]],
+ ['greedy_5frestart_5fmax_5fcount_2503',['greedy_restart_max_count',['../classvg_1_1BaseMapper.html#a5d9a1c8549138e423e1a95a40590fee6',1,'vg::BaseMapper']]],
+ ['greedy_5frestart_5fmax_5flcp_2504',['greedy_restart_max_lcp',['../classvg_1_1BaseMapper.html#a4cad1e0b9a03002f35eee233cc34ac54',1,'vg::BaseMapper']]],
+ ['greedy_5frestart_5fmin_5flength_2505',['greedy_restart_min_length',['../classvg_1_1BaseMapper.html#abe669bcb3e32a8afb3e71443bbe5076a',1,'vg::BaseMapper']]],
+ ['greedymindistanceclusterer_2506',['GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html',1,'vg::GreedyMinDistanceClusterer'],['../classvg_1_1GreedyMinDistanceClusterer.html#a603a74649e16204cace3e714ebe67a74',1,'vg::GreedyMinDistanceClusterer::GreedyMinDistanceClusterer()']]],
+ ['groom_5fcomponents_2507',['groom_components',['../classvg_1_1FlowSort.html#a2a52b4d445acf50ebfd8f7dc3a07d044',1,'vg::FlowSort']]],
+ ['group_2508',['group',['../classvg_1_1io_1_1MessageEmitter.html#adb0173ebe6170c259448c8dd1d4c0dde',1,'vg::io::MessageEmitter::group()'],['../classvg_1_1SparseUnionFind.html#af91351abb606a1bc16c1cbb5f1b668ab',1,'vg::SparseUnionFind::group()']]],
+ ['group_5fcache_2509',['group_cache',['../classvg_1_1IndexedVG.html#a0024489b3eb887d90d18af839722ce66',1,'vg::IndexedVG']]],
+ ['group_5fcount_2510',['group_count',['../classvg_1_1io_1_1MessageIterator.html#a34611c431fac53c556d57036cee7e4fe',1,'vg::io::MessageIterator']]],
+ ['group_5fhandlers_2511',['group_handlers',['../classvg_1_1io_1_1MessageEmitter.html#a8e586d31762cb47872de4b4723e01696',1,'vg::io::MessageEmitter::group_handlers()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a176d09f4d40ef21965c7a66abc546dbd',1,'vg::io::ProtobufEmitter::group_handlers()']]],
+ ['group_5fidx_2512',['group_idx',['../classvg_1_1io_1_1MessageIterator.html#ab2a47479856b6bb8d6fe3c943519d83d',1,'vg::io::MessageIterator']]],
+ ['group_5flistener_5ft_2513',['group_listener_t',['../classvg_1_1io_1_1MessageEmitter.html#a4569ac626dfd036074603cc6f05d55e1',1,'vg::io::MessageEmitter::group_listener_t()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a3fdef59aeb9c688e752463a2257ebbfd',1,'vg::io::ProtobufEmitter::group_listener_t()']]],
+ ['group_5fmapping_5fquality_5fexact_2514',['group_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#a7e03bd79bceb8a8034ae57ba640069bc',1,'vg::GSSWAligner']]],
+ ['group_5fsize_2515',['group_size',['../structvg_1_1Funnel_1_1Item.html#a23706e46f9ebd56acbea3c612358bb79',1,'vg::Funnel::Item::group_size()'],['../classvg_1_1SparseUnionFind.html#aff34e4252e15a68b1e8e79c8cef27a66',1,'vg::SparseUnionFind::group_size()']]],
+ ['group_5ftag_2516',['group_tag',['../classvg_1_1io_1_1MessageEmitter.html#ad240e5c3ae379aa3257c498dd4c4e1bf',1,'vg::io::MessageEmitter']]],
+ ['group_5fvo_2517',['group_vo',['../classvg_1_1io_1_1MessageIterator.html#ae569fd7dc6129edc5e5dac52b1a67f84',1,'vg::io::MessageIterator']]],
+ ['groupedoptiongroup_2518',['GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html',1,'vg::subcommand::GroupedOptionGroup'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a6da6deb7ccf8697e84db1c266dd9180f',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup()=default'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af4f06c1eff0303d1c982b0c2d34c2b55',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(const GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ab1c7b6f34e8d53cf4536625ea6709e80',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(GroupedOptionGroup &&other)=delete']]],
+ ['growth_2519',['Growth',['../structvg_1_1FlowSort_1_1Growth.html',1,'vg::FlowSort::Growth'],['../structvg_1_1FlowSort_1_1Growth.html#aa156ae24695e73aee936d00a7ef70d22',1,'vg::FlowSort::Growth::Growth()']]],
+ ['gssw_5fmapping_5fto_5falignment_2520',['gssw_mapping_to_alignment',['../classvg_1_1GSSWAligner.html#ab45f7399b68bdc980499d4384515b9b7',1,'vg::GSSWAligner']]],
+ ['gsswaligner_2521',['GSSWAligner',['../classvg_1_1GSSWAligner.html',1,'vg::GSSWAligner'],['../classvg_1_1GSSWAligner.html#a02c1c427118eb1a8244274d852684c79',1,'vg::GSSWAligner::GSSWAligner()=default'],['../classvg_1_1GSSWAligner.html#a6c3f1338e6a66850b779e8331a65a61c',1,'vg::GSSWAligner::GSSWAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int8_t _full_length_bonus, double _gc_content)']]],
+ ['guess_5fparallel_5fgbwt_5fjobs_2522',['guess_parallel_gbwt_jobs',['../namespacevg.html#a70ebd70e5b26c5fefe30895fa313f3b9',1,'vg']]],
+ ['gz_5fsuffix_2523',['GZ_SUFFIX',['../rna__main_8cpp.html#a79e5666abc1e2270209776bd472798e7',1,'rna_main.cpp']]],
+ ['protobuf_2524',['protobuf',['../namespacegoogle_1_1protobuf.html',1,'google']]]
];
diff --git a/search/all_8.js b/search/all_8.js
index f3822f0de1..28afa0a3fe 100644
--- a/search/all_8.js
+++ b/search/all_8.js
@@ -1,251 +1,251 @@
var searchData=
[
- ['algorithms_2523',['algorithms',['../namespacehandlegraph_1_1algorithms.html',1,'handlegraph']]],
- ['halt_2524',['halt',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aeabcba66f2745dd0e6a4793e954aa23d',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['handle_2525',['handle',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a2d575dc899c6ef50c6ffe7c374573fb9',1,'vg::io::BlockedGzipInputStream::handle()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a726e457d2e98e4ca6ffa742a4378949f',1,'vg::io::BlockedGzipOutputStream::handle()'],['../classxg_1_1XGPath.html#a93ab3c3284afd4d780368ab03d51ee43',1,'xg::XGPath::handle()'],['../classvg_1_1io_1_1MessageIterator.html#a4b3ba16717c1900a0638518bd33a4a59',1,'vg::io::MessageIterator::handle()'],['../classvg_1_1io_1_1ProtobufEmitter.html#afb457287f96e5ed57d53f91fd5247ec7',1,'vg::io::ProtobufEmitter::handle()']]],
- ['handle_2ehpp_2526',['handle.hpp',['../handle_8hpp.html',1,'']]],
- ['handle2component_2527',['Handle2Component',['../namespacevg.html#a7143bc6d4008d03bc4a0ac4d4ba26948',1,'vg']]],
- ['handle_5fat_5forder_2528',['handle_at_order',['../classvg_1_1IncrementalSubgraph.html#a8c2059a01cfda921bd8c5f91bd3763c7',1,'vg::IncrementalSubgraph']]],
- ['handle_5fat_5fpath_5fposition_2529',['handle_at_path_position',['../classxg_1_1XG.html#a63e8b7be4676a9fb4c77e16f0c76b5a8',1,'xg::XG']]],
- ['handle_5fat_5fposition_2530',['handle_at_position',['../classxg_1_1XGPath.html#ac3dac0fefe450c561f44dadd3ac00487',1,'xg::XGPath']]],
- ['handle_5fbase_5foption_2531',['handle_base_option',['../classvg_1_1ConfigurableParser.html#a0c39f36cf64d91a336afaac0604ff9f0',1,'vg::ConfigurableParser']]],
- ['handle_5fbuffer_2532',['handle_buffer',['../classvg_1_1VcfBuffer.html#a1d8968beb2952113ea8a724dad1e1752',1,'vg::VcfBuffer']]],
- ['handle_5ffull_5flength_2533',['handle_full_length',['../namespacevg.html#a536dfd4326c17ad4d072d2c9021e4b7c',1,'vg']]],
- ['handle_5fgraph_2534',['handle_graph',['../classvg_1_1TargetValueSearch.html#a99dd4b74b5894a228a6d31174ca322de',1,'vg::TargetValueSearch::handle_graph()'],['../classvg_1_1MinDistanceClusterer.html#a6bc0aa3fb6df2824a2fe88f941312f09',1,'vg::MinDistanceClusterer::handle_graph()']]],
- ['handle_5fgraph_2ecpp_2535',['handle_graph.cpp',['../handle__graph_8cpp.html',1,'']]],
- ['handle_5fgraph_2ehpp_2536',['handle_graph.hpp',['../handle__graph_8hpp.html',1,'']]],
- ['handle_5fgraph_5fto_5fcactus_2537',['handle_graph_to_cactus',['../namespacevg.html#a3d4e7ee3d7394e2318e874dc98dd8320',1,'vg']]],
- ['handle_5fidxs_2538',['handle_idxs',['../classvg_1_1JoinedSpliceGraph.html#af3e4ce836a5ba9b208bde5bfe245a97e',1,'vg::JoinedSpliceGraph']]],
- ['handle_5frank_2539',['handle_rank',['../classxg_1_1XG.html#a2e8f51499dd0ba67d52100bf380b0936',1,'xg::XG']]],
- ['handle_5fstart_2540',['handle_start',['../classxg_1_1XGPath.html#a5a62bf71a4a85c9617402504a2be01a4',1,'xg::XGPath']]],
- ['handle_5ft_2541',['handle_t',['../structhandlegraph_1_1handle__t.html',1,'handlegraph::handle_t'],['../namespacevg.html#aaed4a2b7bc668cf2e076733ee26e036a',1,'vg::handle_t()'],['../namespacevg_1_1io.html#a3943ae5818e3556e216014f0df531502',1,'vg::io::handle_t()']]],
- ['handle_5fto_5fgbwt_2542',['handle_to_gbwt',['../namespacevg.html#a1fa5cc80bff735a8803aa9f564c29994',1,'vg']]],
- ['handle_5fto_5frank_2543',['handle_to_rank',['../classhandlegraph_1_1RankedHandleGraph.html#a6a21763bef01676efd4dd10767681bfc',1,'handlegraph::RankedHandleGraph']]],
- ['handle_5fval_5frange_2544',['handle_val_range',['../classvg_1_1DagifiedGraph.html#a3cbeb57dc989a7f0963553041c156252',1,'vg::DagifiedGraph::handle_val_range()'],['../classvg_1_1DozeuPinningOverlay.html#a55cd7c6586c7da513046ed232fe95440',1,'vg::DozeuPinningOverlay::handle_val_range()']]],
- ['handlegraph_2545',['HandleGraph',['../classhandlegraph_1_1HandleGraph.html',1,'handlegraph::HandleGraph'],['../namespacehandlegraph.html',1,'handlegraph'],['../namespacevg.html#ad5781c55c25f1446e1fc74c72c051c62',1,'vg::HandleGraph()'],['../namespacevg_1_1io.html#a172e1fe036e09c51c5a60918463de08f',1,'vg::io::HandleGraph()']]],
- ['handlegraphnodeset_2546',['HandleGraphNodeSet',['../classvg_1_1HandleGraphNodeSet.html',1,'vg::HandleGraphNodeSet'],['../classvg_1_1HandleGraphNodeSet.html#af257f6c350350577cc2bef059a133837',1,'vg::HandleGraphNodeSet::HandleGraphNodeSet()']]],
- ['handlegraphsnarlfinder_2547',['HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html',1,'vg::HandleGraphSnarlFinder'],['../classvg_1_1HandleGraphSnarlFinder.html#a8fb53057585d8e64313485c02a15cec5',1,'vg::HandleGraphSnarlFinder::HandleGraphSnarlFinder()']]],
- ['handler_2548',['Handler',['../structvg_1_1temp__file_1_1Handler.html',1,'vg::temp_file::Handler'],['../structxg_1_1temp__file_1_1Handler.html',1,'xg::temp_file::Handler']]],
- ['handles_2549',['handles',['../classxg_1_1XGPath.html#a2363dd10eb299ca6cc52655e517ad9e1',1,'xg::XGPath']]],
- ['handleset_2550',['HandleSet',['../namespacevg.html#a0942a662fe36dad76d2d0e310ec66e3f',1,'vg']]],
- ['haplo_2551',['haplo',['../namespacehaplo.html',1,'']]],
- ['haplo_5fdp_2552',['haplo_DP',['../structhaplo_1_1haplo__DP.html',1,'haplo::haplo_DP'],['../structhaplo_1_1haplo__DP.html#a35035e7b00f8d5503ae3582afebbac50',1,'haplo::haplo_DP::haplo_DP()']]],
- ['haplo_5fdp_5fcolumn_2553',['haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html',1,'haplo::haplo_DP_column'],['../structhaplo_1_1haplo__DP__column.html#a15c9d8c26ba9eba47510eaac32b49eb8',1,'haplo::haplo_DP_column::haplo_DP_column()']]],
- ['haplo_5fdp_5frectangle_2554',['haplo_DP_rectangle',['../structhaplo_1_1haplo__DP__rectangle.html',1,'haplo::haplo_DP_rectangle'],['../structhaplo_1_1haplo__DP__rectangle.html#a54e3de46211170326d89ee11f9d61fab',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle()'],['../structhaplo_1_1haplo__DP__rectangle.html#a5e2a880c7d8974ac08021256994a51e2',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle(bool inclusive_interval)']]],
- ['haplo_5fnode_2555',['haplo_node',['../classvg_1_1PhasedGenome_1_1iterator.html#a1ae0c6a2bdb23511f58dc2986b36117e',1,'vg::PhasedGenome::iterator']]],
- ['haplo_5fscore_5fprovider_2556',['haplo_score_provider',['../classvg_1_1BaseMapper.html#af69ce88df203124121b71bdfdc6f3694',1,'vg::BaseMapper']]],
- ['haplo_5fscore_5ftype_2557',['haplo_score_type',['../namespacehaplo.html#aa35eb194ac0f5a70dae8d2283c170736',1,'haplo']]],
- ['haploid_5fprior_5flogprob_2558',['haploid_prior_logprob',['../classvg_1_1Genotyper.html#a76e36b8cc1f5a8a5522c5ae3f57b5464',1,'vg::Genotyper']]],
- ['haploid_5fscoring_2559',['haploid_scoring',['../structvg_1_1Recombinator_1_1Parameters.html#a500ad8a5fa909da483c0d84121b80dbd',1,'vg::Recombinator::Parameters']]],
- ['haplomath_2560',['haploMath',['../namespacehaplo_1_1haploMath.html',1,'haplo']]],
- ['haplotype_2561',['Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html',1,'vg::PhasedGenome::Haplotype'],['../classvg_1_1PhasedGenome_1_1iterator.html#a2a8d7bc98747d6a54dbeef69cc966afc',1,'vg::PhasedGenome::iterator::Haplotype()'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#aba98c5b032e48cf1a83b21cae31966a0',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversal node_traversal)'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a61d6bf4127d5e607eccca43b730b8d74',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversalIterator first, NodeTraversalIterator last)'],['../structvg_1_1AppendHaplotypeCommand.html#a5dcde06b8eb329a38ae49f612218ad90',1,'vg::AppendHaplotypeCommand::haplotype()'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a096fd6e4d5329e8242d4d1a69e95314b',1,'vg::ReplaceSnarlHaplotypeCommand::haplotype()'],['../structvg_1_1RecombinatorFragment.html#a566d752b9670dbf52d1e3998758c1754',1,'vg::RecombinatorFragment::haplotype()'],['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271ca00c31e80a8b69bfe7bd279f2bfa4b3ba',1,'handlegraph::HAPLOTYPE()']]],
- ['haplotype_5fconsistency_5fexponent_2562',['haplotype_consistency_exponent',['../classvg_1_1BaseMapper.html#a33465e76a17e2580a6e095f3373239c5',1,'vg::BaseMapper']]],
- ['haplotype_5fconsistent_5falignments_2563',['haplotype_consistent_alignments',['../namespacevg.html#ab5a2adbf9370dc37be337d927341f9db',1,'vg']]],
- ['haplotype_5fextracter_2ecpp_2564',['haplotype_extracter.cpp',['../haplotype__extracter_8cpp.html',1,'']]],
- ['haplotype_5fextracter_2ehpp_2565',['haplotype_extracter.hpp',['../haplotype__extracter_8hpp.html',1,'']]],
- ['haplotype_5fgbwt_5fids_2566',['haplotype_gbwt_ids',['../structvg_1_1TranscriptPath.html#aafc713083bff5a107e2eb70e4d131541',1,'vg::TranscriptPath']]],
- ['haplotype_5findexer_2567',['haplotype_indexer',['../structGBWTConfig.html#a29a942d7e187971aa7821a5aacb65acd',1,'GBWTConfig']]],
- ['haplotype_5findexer_2ecpp_2568',['haplotype_indexer.cpp',['../haplotype__indexer_8cpp.html',1,'']]],
- ['haplotype_5findexer_2ehpp_2569',['haplotype_indexer.hpp',['../haplotype__indexer_8hpp.html',1,'']]],
- ['haplotype_5finput_2570',['haplotype_input',['../structHaplotypesConfig.html#a9bca6d317d27daae42a19413e3e336b2',1,'HaplotypesConfig']]],
- ['haplotype_5fmatch_2571',['HAPLOTYPE_MATCH',['../classhandlegraph_1_1PathMetadata.html#a3f78e2ed41434be9b84823f5724734e9',1,'handlegraph::PathMetadata']]],
- ['haplotype_5fnumber_2572',['haplotype_number',['../classvg_1_1PhasedGenome_1_1iterator.html#a3d0bbf671bf2801e44d23fea4da0e397',1,'vg::PhasedGenome::iterator']]],
- ['haplotype_5foutput_2573',['haplotype_output',['../structHaplotypesConfig.html#a75dc83e4850abb0e9d8542285a844574',1,'HaplotypesConfig']]],
- ['haplotype_5fto_5fstring_2574',['haplotype_to_string',['../classvg_1_1VariantAdder.html#a86108ed47c5e85a23d31fe380ae2670d',1,'vg::VariantAdder']]],
- ['haplotype_5ftranscript_5fpaths_2575',['haplotype_transcript_paths',['../classvg_1_1Transcriptome.html#a8103dfe99f0bb36e806cab44d2e21d54',1,'vg::Transcriptome']]],
- ['haplotypeindexer_2576',['HaplotypeIndexer',['../classvg_1_1HaplotypeIndexer.html',1,'vg::HaplotypeIndexer'],['../classvg_1_1HaplotypeIndexer.html#ae0b8cbfe64f32152ceefa57daf9ece72',1,'vg::HaplotypeIndexer::HaplotypeIndexer()']]],
- ['haplotypenode_2577',['HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html',1,'vg::PhasedGenome::HaplotypeNode'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a4f0160b2daeebec5d984b4fe1921887a',1,'vg::PhasedGenome::Haplotype::HaplotypeNode()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a584a6b469c7f9709ea7da34f867f49aa',1,'vg::PhasedGenome::HaplotypeNode::HaplotypeNode()']]],
- ['haplotypepartitioner_2578',['HaplotypePartitioner',['../classvg_1_1HaplotypePartitioner.html',1,'vg::HaplotypePartitioner'],['../classvg_1_1HaplotypePartitioner.html#a6faa6da8cc4a62f7cabc8d66e19e9ac1',1,'vg::HaplotypePartitioner::HaplotypePartitioner()']]],
- ['haplotypes_2579',['Haplotypes',['../classvg_1_1Haplotypes.html',1,'vg::Haplotypes'],['../classvg_1_1SnarlState.html#a98f04166481311709d9a8d3b05b0245e',1,'vg::SnarlState::haplotypes()'],['../classvg_1_1PhasedGenome.html#aa7b2bebc28cc37da09216fca8361c75c',1,'vg::PhasedGenome::haplotypes()'],['../structvg_1_1Recombinator_1_1Statistics.html#a1541408a463fbbcea0e4a3ac08bac9df',1,'vg::Recombinator::Statistics::haplotypes()'],['../classvg_1_1Recombinator.html#a536bca6a31d76be8d90571b24b8ff0e8',1,'vg::Recombinator::haplotypes()'],['../structGBWTConfig.html#a1b5f59745e1b75e70af68ef9e8cd0378',1,'GBWTConfig::haplotypes()']]],
- ['haplotypes_2ecpp_2580',['haplotypes.cpp',['../haplotypes_8cpp.html',1,'']]],
- ['haplotypes_2ehpp_2581',['haplotypes.hpp',['../haplotypes_8hpp.html',1,'']]],
- ['haplotypes_5fdefaults_2582',['haplotypes_defaults',['../namespacehaplotypes__defaults.html',1,'']]],
- ['haplotypes_5fmain_2ecpp_2583',['haplotypes_main.cpp',['../haplotypes__main_8cpp.html',1,'']]],
- ['haplotypesconfig_2584',['HaplotypesConfig',['../structHaplotypesConfig.html',1,'HaplotypesConfig'],['../structHaplotypesConfig.html#a45bef8cdfe50758d06d6d078b5a6a13f',1,'HaplotypesConfig::HaplotypesConfig()']]],
- ['hard_5fhit_5fcap_2585',['hard_hit_cap',['../classvg_1_1MinimizerMapper.html#aaf577b72776f431ec4dc5faac505322e',1,'vg::MinimizerMapper']]],
- ['hard_5fhit_5fmax_2586',['hard_hit_max',['../classvg_1_1BaseMapper.html#a4e6260be560a0bf2a10cfb409e611e65',1,'vg::BaseMapper']]],
- ['has_5fannotation_2587',['has_annotation',['../classvg_1_1multipath__alignment__t.html#a6b60350a3dada734b919bdf15f41bf82',1,'vg::multipath_alignment_t::has_annotation()'],['../namespacevg.html#a34f4e73b242fa5b34d30ecc4da496835',1,'vg::has_annotation()']]],
- ['has_5fargument_2588',['has_argument',['../classvg_1_1OptionInterface.html#a29383428b6a6e40109fb4949286f07f7',1,'vg::OptionInterface::has_argument()'],['../classvg_1_1OptionValueParser.html#af8d6268a6cec527dd0e117aef58cbd63',1,'vg::OptionValueParser::has_argument()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a104c6803a28a2528b33759ac8ad69175',1,'vg::OptionValueParser< vector< Item > >::has_argument()'],['../classvg_1_1BaseOption.html#a3aa53d25627ae95383edce8f6e001caa',1,'vg::BaseOption::has_argument()'],['../classvg_1_1OptionValueParser.html#aabf09c8e0e807fb19debad284331387d',1,'vg::OptionValueParser::has_argument()']]],
- ['has_5fbase_5fgraph_2589',['has_base_graph',['../structvg_1_1AugmentedGraph.html#ae1b8b8c8246ccfe1f2d56250a3361177',1,'vg::AugmentedGraph']]],
- ['has_5fbuffer_2590',['has_buffer',['../classvg_1_1VcfBuffer.html#a13f0fa2e0b50cd133c117bd1f34715c3',1,'vg::VcfBuffer']]],
- ['has_5fchain_5fvalues_2591',['has_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab62e9f2483533263e5df33fd9c5ad882',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['has_5fconnection_2592',['has_connection',['../classvg_1_1subpath__t.html#a972d307d386a636cc2dc1fc170f56df3',1,'vg::subpath_t']]],
- ['has_5fcontent_2593',['has_content',['../structvg_1_1BitStringTree_1_1TreeNode.html#ac222ba76d226ad0f457be10e8c8a8b30',1,'vg::BitStringTree::TreeNode']]],
- ['has_5fcurrent_2594',['has_current',['../classvg_1_1io_1_1MessageIterator.html#abcbec4e2b7376ae5ca8bbd4e05d9103a',1,'vg::io::MessageIterator::has_current()'],['../classvg_1_1io_1_1ProtobufIterator.html#a59294f819b65352528da9224ea39d973',1,'vg::io::ProtobufIterator::has_current()']]],
- ['has_5fedge_2595',['has_edge',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a6fd765d7a5623bef825effc7fdf46b87',1,'haplo::hDP_gbwt_graph_accessor::has_edge()'],['../classvg_1_1VG.html#a501886a0c593ac3231cfcc6989911ced',1,'vg::VG::has_edge(const handle_t &left, const handle_t &right) const'],['../classvg_1_1VG.html#a447d717e83131c526d26e6d2f0a091a6',1,'vg::VG::has_edge(const NodeSide &side1, const NodeSide &side2) const'],['../classvg_1_1VG.html#a1c7ff3b6f9cfca2c21e1a8d1c848fc01',1,'vg::VG::has_edge(const pair< NodeSide, NodeSide > &sides) const'],['../classvg_1_1VG.html#aa69701fcb4bf9e8b593681ba1d818571',1,'vg::VG::has_edge(Edge *edge) const'],['../classvg_1_1VG.html#ab2c85fad61f57260c913bc565a549832',1,'vg::VG::has_edge(const Edge &edge) const'],['../classhandlegraph_1_1HandleGraph.html#a069448fbe58665b9ff531ad0b8c5af57',1,'handlegraph::HandleGraph::has_edge(const handle_t &left, const handle_t &right) const'],['../classhandlegraph_1_1HandleGraph.html#a6171cdd6036c73623c96656f8b44fe9d',1,'handlegraph::HandleGraph::has_edge(const edge_t &edge) const']]],
- ['has_5fend_2596',['has_end',['../structvg_1_1Haplotypes_1_1Subchain.html#ae9fbddda11e52d6e9b98156a50224a73',1,'vg::Haplotypes::Subchain::has_end()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a0aa037691bcf20d78faad42eea3c8f57',1,'vg::HaplotypePartitioner::Subchain::has_end()']]],
- ['has_5fexcluded_5frefpos_2597',['has_excluded_refpos',['../classvg_1_1ReadFilter.html#ac772c0651477027191108e64ab7c53cb',1,'vg::ReadFilter::has_excluded_refpos(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab609cc20f1e49dc1001e71fe82c5ead4',1,'vg::ReadFilter::has_excluded_refpos(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#aca79c3eda85a8f4fafcd25a243b7efd4',1,'vg::ReadFilter::has_excluded_refpos(const Alignment &aln) const']]],
- ['has_5fexcuded_5ffeature_2598',['has_excuded_feature',['../classvg_1_1ReadFilter.html#a2d30291c0c609d58670f40e2eb9661e4',1,'vg::ReadFilter']]],
- ['has_5ffixed_5ffragment_5flength_5fdistr_2599',['has_fixed_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ad0a2d836cfcaddae8569bf1a024aa56b',1,'vg::PairedEndMapper']]],
- ['has_5fgrandparent_5fhandle_2600',['has_grandparent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d823f95b1440029399ae07f5d5ce0ec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['has_5fincorrect_5forder_5fexons_2601',['has_incorrect_order_exons',['../classvg_1_1Transcriptome.html#a4cba921dae9fe3eae2361b0b7391b7b3',1,'vg::Transcriptome']]],
- ['has_5fincremental_5fsearch_2602',['has_incremental_search',['../classhaplo_1_1ScoreProvider.html#a1455c3ccb6a9d03e5d79636e79be301a',1,'haplo::ScoreProvider::has_incremental_search()'],['../classhaplo_1_1GBWTScoreProvider.html#abe35e78c1d11af952b27dc8c36c1909f',1,'haplo::GBWTScoreProvider::has_incremental_search()']]],
- ['has_5finversion_2603',['has_inversion',['../namespacevg.html#a1b545f6474c6e528176031149a8bc570',1,'vg']]],
- ['has_5finverting_5fedge_2604',['has_inverting_edge',['../classvg_1_1VG.html#a49fb4de3494407b800c3efda254851cf',1,'vg::VG']]],
- ['has_5finverting_5fedge_5ffrom_2605',['has_inverting_edge_from',['../classvg_1_1VG.html#a7b7bbf066c6608211e7527ba50b23e48',1,'vg::VG']]],
- ['has_5finverting_5fedge_5fto_2606',['has_inverting_edge_to',['../classvg_1_1VG.html#a63088ee0039a8e1f5cf6b5a3b23f745a',1,'vg::VG']]],
- ['has_5finverting_5fedges_2607',['has_inverting_edges',['../classvg_1_1VG.html#a8d1dbb49df52e016746829776ca0f952',1,'vg::VG']]],
- ['has_5fmapping_2608',['has_mapping',['../classvg_1_1Paths.html#a32ecf6382d9fa9c9826cb59f8e79349e',1,'vg::Paths']]],
- ['has_5fnext_2609',['has_next',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a376e3ac5d3d820bd4b5ac55f1ad0d69b',1,'vg::BandedGlobalAligner::AltTracebackStack::has_next()'],['../classvg_1_1subpath__t.html#acb3834a6661d55a407a58cff5cd539c3',1,'vg::subpath_t::has_next()']]],
- ['has_5fnext_5fstep_2610',['has_next_step',['../classvg_1_1MemoizingGraph.html#a3c6e172a85dd0c03a290bf4b5b04792e',1,'vg::MemoizingGraph::has_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a56d9a8eb9dfbbac174ed677e4f22f14d',1,'vg::PathSubgraphOverlay::has_next_step()'],['../classvg_1_1VG.html#add23d09d2925d505f793979f7fe35921',1,'vg::VG::has_next_step()'],['../classxg_1_1XG.html#ad193420b3ab85a6d2b47f305779d6b5c',1,'xg::XG::has_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a81bf54cb4d07a0d47c84862ecebc349d',1,'handlegraph::PathHandleGraph::has_next_step()']]],
- ['has_5fnode_2611',['has_node',['../classvg_1_1DagifiedGraph.html#ad6c8a0d0a6c21fee9c10065927d4ba97',1,'vg::DagifiedGraph::has_node()'],['../classvg_1_1DozeuPinningOverlay.html#a696d9ff9c1731e98d7235a637d794174',1,'vg::DozeuPinningOverlay::has_node()'],['../classvg_1_1ExtraNodeGraph.html#a89299bba0acddf6e2bb2a8d6cb561b86',1,'vg::ExtraNodeGraph::has_node()'],['../classvg_1_1SnarlGraph.html#a43e8f719e0d3b9814e3328d14c28c85e',1,'vg::SnarlGraph::has_node()'],['../classvg_1_1IdentityOverlay.html#a56aabb0a049d7bbf9079733d7824e0db',1,'vg::IdentityOverlay::has_node()'],['../classvg_1_1IncrementalSubgraph.html#a29fe9b69774ab975e3b6fe15900d1c9e',1,'vg::IncrementalSubgraph::has_node()'],['../classvg_1_1IndexedVG.html#a184b4de54cd807fc818091c56bac41a8',1,'vg::IndexedVG::has_node()'],['../classvg_1_1MemoizingGraph.html#a5e5fea73aaa5c9b403b7e63318e15702',1,'vg::MemoizingGraph::has_node()'],['../classvg_1_1NullMaskingGraph.html#a550edf96fd717710f5051804d0d1bafe',1,'vg::NullMaskingGraph::has_node()'],['../classvg_1_1PathSubgraph.html#ad13f4f28e024ac0d43991cb9d162420f',1,'vg::PathSubgraph::has_node()'],['../classvg_1_1ReverseGraph.html#a98c0e584e6cb8246c9b2deb65d92e370',1,'vg::ReverseGraph::has_node()'],['../classvg_1_1NetGraph.html#a99ddd8990ab25cd314618321a5837ff9',1,'vg::NetGraph::has_node()'],['../classvg_1_1SourceSinkOverlay.html#ad2e4740b5a84271e053840e6b60fc53c',1,'vg::SourceSinkOverlay::has_node()'],['../classvg_1_1JoinedSpliceGraph.html#af167d082a5c148792ae9a533eac068f0',1,'vg::JoinedSpliceGraph::has_node()'],['../classvg_1_1StrandSplitGraph.html#aad17d3113bdc3f8ec03327a16ccfadd9',1,'vg::StrandSplitGraph::has_node()'],['../classvg_1_1SubHandleGraph.html#a66e144a38ed8437cbf71a186a6e8afa0',1,'vg::SubHandleGraph::has_node()'],['../classvg_1_1SubgraphOverlay.html#aaa8aca387ac5ba4f962d03da956979a2',1,'vg::SubgraphOverlay::has_node()'],['../classvg_1_1SubpathOverlay.html#a7c9a83697a1f3041e3dfbcb10f3a831b',1,'vg::SubpathOverlay::has_node()'],['../classvg_1_1TreeSubgraph.html#a84c11ffd899e018587d6ccb25dd1211b',1,'vg::TreeSubgraph::has_node()'],['../classvg_1_1VG.html#ac9339913ecff654569a9c81ae091ebfe',1,'vg::VG::has_node(nid_t id) const'],['../classvg_1_1VG.html#a049bd863e2ac7e93aec79404d56b4a34',1,'vg::VG::has_node(const Node *node) const'],['../classvg_1_1VG.html#ab000649761c7201555284390dd8a4fa0',1,'vg::VG::has_node(const Node &node) const'],['../classxg_1_1XG.html#a60dd1cf3ec755863aabc99e6948011e0',1,'xg::XG::has_node()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a29475639dafe548f44b4c0e995005083',1,'handlegraph::algorithms::SubHandleGraph::has_node()'],['../classhandlegraph_1_1HandleGraph.html#a6e58a79001cd7d839ac1f1adaff34dfb',1,'handlegraph::HandleGraph::has_node()']]],
- ['has_5fnode_5fmapping_2612',['has_node_mapping',['../classvg_1_1Paths.html#a4f744ed09e266781a366dd11a73993b8',1,'vg::Paths::has_node_mapping(id_t id) const'],['../classvg_1_1Paths.html#a48f74571d94bdd9845ff761d51701034',1,'vg::Paths::has_node_mapping(Node *n) const']]],
- ['has_5fnovel_5fexon_5fboundaries_2613',['has_novel_exon_boundaries',['../classvg_1_1Transcriptome.html#aaf34b6da5110fa44f787994be4ea2791',1,'vg::Transcriptome']]],
- ['has_5foverlapping_5fexons_2614',['has_overlapping_exons',['../classvg_1_1Transcriptome.html#a405f6a2b87ab7d919d0cb8780b1362a5',1,'vg::Transcriptome']]],
- ['has_5foverlay_5fnode_5ffor_2615',['has_overlay_node_for',['../classvg_1_1StrandSplitGraph.html#a66d77e125b056b19273bb037fef6012c',1,'vg::StrandSplitGraph']]],
- ['has_5fparent_5fhandle_2616',['has_parent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a67fd7b54bbaafc48baee628bc60efad2',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['has_5fpath_2617',['has_path',['../classvg_1_1MemoizingGraph.html#a62559a9038db86f33b149616dd6c5d27',1,'vg::MemoizingGraph::has_path()'],['../classvg_1_1subpath__t.html#a55a56773ae505e410262b8954d34fc3c',1,'vg::subpath_t::has_path()'],['../classvg_1_1Paths.html#a38cd0087925c24ea1bf8a22755c30cbf',1,'vg::Paths::has_path()'],['../classvg_1_1PathSubgraphOverlay.html#a284e49aa618e321cc8402f4b98c9b41b',1,'vg::PathSubgraphOverlay::has_path()'],['../classvg_1_1VG.html#a0328316df2438f0006349c71206810e6',1,'vg::VG::has_path()'],['../classxg_1_1XG.html#a243d2c25b54008f0f79c480b5ff9429c',1,'xg::XG::has_path()'],['../classhandlegraph_1_1PathHandleGraph.html#ab7de11c1e994bc104378c4b798013430',1,'handlegraph::PathHandleGraph::has_path()']]],
- ['has_5fposition_2618',['has_position',['../structvg_1_1algorithms_1_1GFAFormatError.html#adb7cfa3f30ee5710575bee189251b473',1,'vg::algorithms::GFAFormatError']]],
- ['has_5fprevious_5fstep_2619',['has_previous_step',['../classvg_1_1MemoizingGraph.html#aed383459047e290a94817d010361a24f',1,'vg::MemoizingGraph::has_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#aa21af9591c2d1e457c32aaa703cda785',1,'vg::PathSubgraphOverlay::has_previous_step()'],['../classvg_1_1VG.html#ac5f9ec61fe7a32e3756e4b7fc77939ba',1,'vg::VG::has_previous_step()'],['../classxg_1_1XG.html#af833a0ffe45757002869b5802c8d3747',1,'xg::XG::has_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a93a1ee451e750cb82f1711fd6c3db8cc',1,'handlegraph::PathHandleGraph::has_previous_step()']]],
- ['has_5fqualities_2620',['has_qualities',['../classvg_1_1Packer.html#ae00e614a5cb879210690e3b94e2dcc6e',1,'vg::Packer']]],
- ['has_5freachability_5fedges_2621',['has_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#a77a113d4c5b6b5ca1d7748c1b812e8d3',1,'vg::MultipathAlignmentGraph']]],
- ['has_5fref_2622',['has_ref',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a27de160925943418d3af61d2e3c753dc',1,'vg::Deconstructor::NestingInfo']]],
- ['has_5frepeat_2623',['has_repeat',['../classvg_1_1ReadFilter.html#a9aecb91c19bb44bb9be32c4f30c44538',1,'vg::ReadFilter']]],
- ['has_5fstart_2624',['has_start',['../classvg_1_1multipath__alignment__t.html#af56553f4ec379201916081cba150781b',1,'vg::multipath_alignment_t::has_start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#ac1b3268f8305395fc8e35530d900b230',1,'vg::Haplotypes::Subchain::has_start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#ab13d2b1ae3f525cea9be92630f32c3e9',1,'vg::HaplotypePartitioner::Subchain::has_start()']]],
- ['has_5fsupports_2625',['has_supports',['../classvg_1_1RepresentativeTraversalFinder.html#a7010e7fc85d3b2454bc5e09a504aee23',1,'vg::RepresentativeTraversalFinder::has_supports()'],['../structvg_1_1AugmentedGraph.html#a5519dec3147cb54da3e32cdb2f6c1428',1,'vg::AugmentedGraph::has_supports()'],['../structvg_1_1SupportAugmentedGraph.html#a32dc8f5559a750e393b8cedfb42cbf83',1,'vg::SupportAugmentedGraph::has_supports()']]],
- ['has_5ftabix_2626',['has_tabix',['../classvg_1_1VcfBuffer.html#ae0a4db2dd14b0a00545ef726879a0951',1,'vg::VcfBuffer::has_tabix()'],['../classvg_1_1WindowedVcfBuffer.html#a84bbabd4f6b5b948ce6d2d0aa5fa7ff4',1,'vg::WindowedVcfBuffer::has_tabix()']]],
- ['has_5ftranslation_2627',['has_translation',['../classvg_1_1Translator.html#ae6ccab957bfb3f7eba512f7021a4052b',1,'vg::Translator']]],
- ['hash_2628',['hash',['../classvg_1_1VG.html#a2b75ca400f858be77b0716ab7c68dfcb',1,'vg::VG']]],
- ['hash_3c_20const_20vg_3a_3asnarl_20_3e_2629',['hash< const vg::Snarl >',['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3aedge_5ft_20_3e_2630',['hash< handlegraph::edge_t >',['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3ahandle_5ft_20_3e_2631',['hash< handlegraph::handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_2632',['hash< handlegraph::net_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3apath_5fhandle_5ft_20_3e_2633',['hash< handlegraph::path_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3astep_5fhandle_5ft_20_3e_2634',['hash< handlegraph::step_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html',1,'std']]],
- ['hash_3c_20pair_3c_20a_2c_20b_20_3e_20_3e_2635',['hash< pair< A, B > >',['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html',1,'std']]],
- ['hash_3c_20std_3a_3atuple_3c_20tt_2e_2e_2e_20_3e_20_3e_2636',['hash< std::tuple< TT... > >',['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3anodeside_20_3e_2637',['hash< vg::NodeSide >',['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3anodetraversal_20_3e_2638',['hash< vg::NodeTraversal >',['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3azipcodetree_3a_3aoriented_5fseed_5ft_20_3e_2639',['hash< vg::ZipCodeTree::oriented_seed_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3azipcodetree_3a_3aseed_5fresult_5ft_20_3e_2640',['hash< vg::ZipCodeTree::seed_result_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html',1,'std']]],
- ['hash_5falignment_2641',['hash_alignment',['../namespacevg.html#a94f469aebb2be5b0028c337108d253fb',1,'vg']]],
- ['hash_5fambiguous_5fallele_5fset_2642',['hash_ambiguous_allele_set',['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html',1,'vg::Genotyper']]],
- ['hash_5fmap_2643',['hash_map',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_2ehpp_2644',['hash_map.hpp',['../hash__map_8hpp.html',1,'']]],
- ['hash_5fmap_3c_20const_20vg_3a_3amapping_5ft_20_2a_2c_20pair_3c_20list_3c_20vg_3a_3amapping_5ft_20_3e_3a_3aiterator_2c_20int64_5ft_20_3e_20_3e_2645',['hash_map< const vg::mapping_t *, pair< list< vg::mapping_t >::iterator, int64_t > >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20handlegraph_3a_3anet_5fhandle_5ft_2c_20size_5ft_20_3e_2646',['hash_map< handlegraph::net_handle_t, size_t >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20id_5ft_2c_20map_3c_20int64_5ft_2c_20set_3c_20vg_3a_3amapping_5ft_20_2a_20_3e_20_3e_20_3e_2647',['hash_map< id_t, map< int64_t, set< vg::mapping_t * > > >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20k_20_2a_2c_20v_20_3e_2648',['hash_map< K *, V >',['../classvg_1_1hash__map_3_01K_01_5_00_01V_01_4.html',1,'vg']]],
- ['hash_5fmap_3c_20nid_5ft_2c_20vector_3c_20pair_3c_20nid_5ft_2c_20bool_20_3e_20_3e_20_3e_2649',['hash_map< nid_t, vector< pair< nid_t, bool > > >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20nid_5ft_2c_20vg_3a_3anode_20_2a_20_3e_2650',['hash_map< nid_t, vg::Node * >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20vg_3a_3aedge_20_2a_2c_20int_20_3e_2651',['hash_map< vg::Edge *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20vg_3a_3anode_20_2a_2c_20int_20_3e_2652',['hash_map< vg::Node *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fnode_5ftraversal_2653',['hash_node_traversal',['../structvg_1_1Genotyper_1_1hash__node__traversal.html',1,'vg::Genotyper']]],
- ['hash_5foriented_5fedge_2654',['hash_oriented_edge',['../structvg_1_1Genotyper_1_1hash__oriented__edge.html',1,'vg::Genotyper']]],
- ['hash_5fset_2655',['hash_set',['../classvg_1_1hash__set.html',1,'vg']]],
- ['hash_5fset_3c_20k_20_2a_20_3e_2656',['hash_set< K * >',['../classvg_1_1hash__set_3_01K_01_5_01_4.html',1,'vg']]],
- ['hash_5fset_3c_20pair_3c_20size_5ft_2c_20size_5ft_20_3e_20_3e_2657',['hash_set< pair< size_t, size_t > >',['../classvg_1_1hash__set.html',1,'vg']]],
- ['hash_5fset_3c_20vg_3a_3aid_5ft_20_3e_2658',['hash_set< vg::id_t >',['../classvg_1_1hash__set.html',1,'vg']]],
- ['hash_5ftable_5fmax_5fwidth_2659',['HASH_TABLE_MAX_WIDTH',['../minimizer__main_8cpp.html#a6eb56e166572ca736f815a988e170c68',1,'minimizer_main.cpp']]],
- ['hash_5ftable_5fmin_5fwidth_2660',['HASH_TABLE_MIN_WIDTH',['../minimizer__main_8cpp.html#ab0b28c6a5c118414fc8ca717901f2054',1,'minimizer_main.cpp']]],
- ['hash_5fto_5frgb_2661',['hash_to_rgb',['../namespacevg.html#a8bc1d89bbcee041956e59895ed605ca3',1,'vg']]],
- ['hashed_2662',['hashed',['../classvg_1_1Colors.html#a9c14e90e97e7fd193b25461a40ff6235',1,'vg::Colors::hashed()'],['../classvg_1_1Pictographs.html#a42c157819fffed93d2bfa730c5517e56',1,'vg::Pictographs::hashed()']]],
- ['hashed_5fchar_2663',['hashed_char',['../classvg_1_1Pictographs.html#a91309563adbfaaf7eab19a51623d66c2',1,'vg::Pictographs']]],
- ['hashgraph_2664',['HashGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a88fe737c0668785017687666e0aa74a8',1,'vg::IndexingParameters']]],
- ['have_5finput_5ffile_2665',['have_input_file',['../namespacevg.html#a7c950dca7cd25a5ce9846be2a6b93e13',1,'vg']]],
- ['hdp_5fgbwt_5fgraph_5faccessor_2666',['hDP_gbwt_graph_accessor',['../classhaplo_1_1hDP__gbwt__graph__accessor.html',1,'haplo::hDP_gbwt_graph_accessor< GBWTType >'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a63ed5e1c48904968ae61ff21f411c0db',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type old_node, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a7a8d1f9ad8428fe0ff0b6071dc6f47ef',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)']]],
- ['head_5fnodes_2667',['head_nodes',['../classvg_1_1VG.html#a7eecc0bd555c31d1c541c3ce44b421c3',1,'vg::VG::head_nodes(vector< Node * > &nodes)'],['../classvg_1_1VG.html#a3a44c415fb5882c184e2f35bb3999700',1,'vg::VG::head_nodes(void)'],['../namespacehandlegraph_1_1algorithms.html#a3d26728fa655f872ccac738a2bcb6166',1,'handlegraph::algorithms::head_nodes()']]],
- ['head_5ftail_5fnodes_2668',['head_tail_nodes',['../classvg_1_1Paths.html#a3fd42adbd3d58aee08370f043dc1643d',1,'vg::Paths']]],
- ['header_2669',['Header',['../structvg_1_1Haplotypes_1_1Header.html',1,'vg::Haplotypes::Header'],['../classvg_1_1Haplotypes.html#ac2671cb0e5d0cdf19a8aa849ec9a2577',1,'vg::Haplotypes::header()']]],
- ['header_5flisteners_2670',['header_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aeedc94c6fcd57b9da7e627c2136eab45',1,'vg::algorithms::GFAParser']]],
- ['header_5fmutex_2671',['header_mutex',['../classvg_1_1HTSWriter.html#af9d539c1312350395949b75010134032',1,'vg::HTSWriter']]],
- ['heading_2672',['heading',['../structvg_1_1subcommand_1_1OptionGroup.html#a93bdf7b70e92b0a05ec270a4fa1495df',1,'vg::subcommand::OptionGroup']]],
- ['help_2673',['help',['../structvg_1_1subcommand_1_1BaseArgSpec.html#abf8444c205dd6aa3c900d111ffdccac0',1,'vg::subcommand::BaseArgSpec']]],
- ['help_5fadd_2674',['help_add',['../add__main_8cpp.html#ad49fa30ce6a9b619ad5df1cfa8621d9a',1,'add_main.cpp']]],
- ['help_5falign_2675',['help_align',['../align__main_8cpp.html#ac749b2692aaca8eeaa6b48d7b44e167d',1,'align_main.cpp']]],
- ['help_5fannotate_2676',['help_annotate',['../annotate__main_8cpp.html#a6957d47b527eacd587f20f9d11ccd333',1,'annotate_main.cpp']]],
- ['help_5faugment_2677',['help_augment',['../augment__main_8cpp.html#a7cf03aa52fd6e8d75e480d4d0632b71c',1,'augment_main.cpp']]],
- ['help_5fautoindex_2678',['help_autoindex',['../autoindex__main_8cpp.html#a4a3c7ba0d785194a42444bdedac4db50',1,'autoindex_main.cpp']]],
- ['help_5fbenchmark_2679',['help_benchmark',['../benchmark__main_8cpp.html#a1e3da44e3dcc6fea154d15a1986ade1b',1,'benchmark_main.cpp']]],
- ['help_5fcall_2680',['help_call',['../call__main_8cpp.html#ab92ccd67b3c20b7be7c46281c4cabfb3',1,'call_main.cpp']]],
- ['help_5fchain_2681',['help_chain',['../chain__main_8cpp.html#a88894e89fc3e50d33042f88c993a0e0c',1,'chain_main.cpp']]],
- ['help_5fchunk_2682',['help_chunk',['../chunk__main_8cpp.html#a502600dcc3e4e15a338642fe554fbf8d',1,'chunk_main.cpp']]],
- ['help_5fcircularize_2683',['help_circularize',['../circularize__main_8cpp.html#a0613e20e02d0fbb56d7270a7b268ffb3',1,'circularize_main.cpp']]],
- ['help_5fclip_2684',['help_clip',['../clip__main_8cpp.html#a451b2ddc17b7d65f1bac0fcd7cac810c',1,'clip_main.cpp']]],
- ['help_5fcluster_2685',['help_cluster',['../cluster__main_8cpp.html#a4099bc0f1cb9fecb87c903e578ff2a17',1,'cluster_main.cpp']]],
- ['help_5fcombine_2686',['help_combine',['../combine__main_8cpp.html#a14fa4eb501b75ae37a166fb633cda8dd',1,'combine_main.cpp']]],
- ['help_5fconcat_2687',['help_concat',['../concat__main_8cpp.html#a795aaef3bab6d86036c1362ba5b76ac0',1,'concat_main.cpp']]],
- ['help_5fconstruct_2688',['help_construct',['../construct__main_8cpp.html#a0c8b1d02948ee021399fef93344a9def',1,'construct_main.cpp']]],
- ['help_5fconvert_2689',['help_convert',['../convert__main_8cpp.html#a61c2208fb6645c58f794c57e1851a194',1,'convert_main.cpp']]],
- ['help_5fdeconstruct_2690',['help_deconstruct',['../deconstruct__main_8cpp.html#a32554f3b30e86c414a7c6940beb660e3',1,'deconstruct_main.cpp']]],
- ['help_5fdepth_2691',['help_depth',['../depth__main_8cpp.html#aa182528e1e692b2b6ea79e3ed6a36661',1,'depth_main.cpp']]],
- ['help_5fdotplot_2692',['help_dotplot',['../dotplot__main_8cpp.html#a628ebfce6d823f9dca7722f0721a5a3b',1,'dotplot_main.cpp']]],
- ['help_5fexplode_2693',['help_explode',['../explode__main_8cpp.html#a5ed55d49ef3d15ac39e1e275e6792907',1,'explode_main.cpp']]],
- ['help_5ffilter_2694',['help_filter',['../filter__main_8cpp.html#a9072d5dfad52adc43da1d2a700be313b',1,'filter_main.cpp']]],
- ['help_5ffind_2695',['help_find',['../find__main_8cpp.html#a61f46a85b426fbf3e48cdffc07d107f8',1,'find_main.cpp']]],
- ['help_5fgamcompare_2696',['help_gamcompare',['../gamcompare__main_8cpp.html#a33c9728d9a784c1ae54baae635b6e56d',1,'gamcompare_main.cpp']]],
- ['help_5fgampcompare_2697',['help_gampcompare',['../gampcompare__main_8cpp.html#a4eb570f78fda3fc79752c40fccb794d9',1,'gampcompare_main.cpp']]],
- ['help_5fgamsort_2698',['help_gamsort',['../gamsort__main_8cpp.html#ab37435867b2e79dc2fd17af9f6b3667b',1,'gamsort_main.cpp']]],
- ['help_5fgbwt_2699',['help_gbwt',['../gbwt__main_8cpp.html#a73013ddacba7ab20beed9e8022b2b57b',1,'gbwt_main.cpp']]],
- ['help_5fgenotype_2700',['help_genotype',['../genotype__main_8cpp.html#a7d9960cb294ff9984b99ed7816f06323',1,'genotype_main.cpp']]],
- ['help_5fgiraffe_2701',['help_giraffe',['../giraffe__main_8cpp.html#aa6d5c2140d259252f3cad8b7bf6b4b1a',1,'giraffe_main.cpp']]],
- ['help_5fhaplotypes_2702',['help_haplotypes',['../haplotypes__main_8cpp.html#a06899318e624a0766060720e2403f380',1,'haplotypes_main.cpp']]],
- ['help_5fhelp_2703',['help_help',['../help__main_8cpp.html#abbe09b0c0e2e4abc339997cd4b8c1bf7',1,'help_main.cpp']]],
- ['help_5fids_2704',['help_ids',['../ids__main_8cpp.html#ae3e40ed9a49e6e00fe241abf728c11ea',1,'ids_main.cpp']]],
- ['help_5findex_2705',['help_index',['../index__main_8cpp.html#a24afe767ac485cebbc2f2b47ef515274',1,'index_main.cpp']]],
- ['help_5finject_2706',['help_inject',['../inject__main_8cpp.html#a10c867b9f97d3e0d6a1396bad277880a',1,'inject_main.cpp']]],
- ['help_5fjoin_2707',['help_join',['../join__main_8cpp.html#af6a676c62773f02853c583961fe3a59d',1,'join_main.cpp']]],
- ['help_5fkmers_2708',['help_kmers',['../kmers__main_8cpp.html#ab5e392cd094049b8b9a863d2ce1acdb4',1,'kmers_main.cpp']]],
- ['help_5fmain_2ecpp_2709',['help_main.cpp',['../help__main_8cpp.html',1,'']]],
- ['help_5fmap_2710',['help_map',['../map__main_8cpp.html#afec224c846352e16703d590d52bad501',1,'map_main.cpp']]],
- ['help_5fmask_2711',['help_mask',['../mask__main_8cpp.html#a0502efe715f6be3e9b8abd1514c3faae',1,'mask_main.cpp']]],
- ['help_5fmcmc_2712',['help_mcmc',['../mcmc__main_8cpp.html#a2d01e9b5436c54c18299e579f8f850e9',1,'mcmc_main.cpp']]],
- ['help_5fminimizer_2713',['help_minimizer',['../minimizer__main_8cpp.html#a45dc67f0fe9ce978202fda58585b6b52',1,'minimizer_main.cpp']]],
- ['help_5fmod_2714',['help_mod',['../mod__main_8cpp.html#a7ff398c2ef9439dc08f0d318693c9b0b',1,'mod_main.cpp']]],
- ['help_5fmpmap_2715',['help_mpmap',['../mpmap__main_8cpp.html#ad68f4a7fc19b061a16fe9d7fb2810133',1,'mpmap_main.cpp']]],
- ['help_5fmsga_2716',['help_msga',['../msga__main_8cpp.html#a75ed90adae627c02a0d46998bb73ee99',1,'msga_main.cpp']]],
- ['help_5fpack_2717',['help_pack',['../pack__main_8cpp.html#aadaeba7e32c73f9093b262830bd2541e',1,'pack_main.cpp']]],
- ['help_5fpaths_2718',['help_paths',['../paths__main_8cpp.html#a290bac84a159c7e6ab2a9abca73f7000',1,'paths_main.cpp']]],
- ['help_5fprune_2719',['help_prune',['../prune__main_8cpp.html#a4da6cb650889066af17a6223ba1bfa81',1,'prune_main.cpp']]],
- ['help_5frna_2720',['help_rna',['../rna__main_8cpp.html#a703e9ebf973bfcd363ce619ccaff160b',1,'rna_main.cpp']]],
- ['help_5fsift_2721',['help_sift',['../sift__main_8cpp.html#ad82567fc886ab61b4c209226f45b0d8f',1,'sift_main.cpp']]],
- ['help_5fsim_2722',['help_sim',['../sim__main_8cpp.html#ab2368d74cf2fb693982eeb4676e6b534',1,'sim_main.cpp']]],
- ['help_5fsimplify_2723',['help_simplify',['../simplify__main_8cpp.html#a6fbde48f0c083d661e2e8e8b2b0a17e7',1,'simplify_main.cpp']]],
- ['help_5fsnarl_2724',['help_snarl',['../snarls__main_8cpp.html#a4f8c80c7a187ae51a198f3ec42d85f26',1,'snarls_main.cpp']]],
- ['help_5fsort_2725',['help_sort',['../sort__main_8cpp.html#aa2e0a3c74cb1ee9a7278b5399da39a1b',1,'sort_main.cpp']]],
- ['help_5fstats_2726',['help_stats',['../stats__main_8cpp.html#a8a996696d6e2c9ecca6dffd6fbc8bf26',1,'stats_main.cpp']]],
- ['help_5fsurject_2727',['help_surject',['../surject__main_8cpp.html#a9d8217a048300f2a321bfe032e31c769',1,'surject_main.cpp']]],
- ['help_5ftrace_2728',['help_trace',['../trace__main_8cpp.html#a1e6c8dca8a2b0b1ba628313be3a56fe8',1,'trace_main.cpp']]],
- ['help_5ftranslate_2729',['help_translate',['../translate__main_8cpp.html#ad94d99f9e08a28731eb6f4d42d64b553',1,'translate_main.cpp']]],
- ['help_5fvalidate_2730',['help_validate',['../validate__main_8cpp.html#ab89c45aa2e33410d5c76183fd5148cff',1,'validate_main.cpp']]],
- ['help_5fvectorize_2731',['help_vectorize',['../vectorize__main_8cpp.html#a66888bb2b18d743f2ada4c879d2999da',1,'vectorize_main.cpp']]],
- ['help_5fversion_2732',['help_version',['../version__main_8cpp.html#a5c4af51f2cb117ca875b8b1c6be39639',1,'version_main.cpp']]],
- ['help_5fview_2733',['help_view',['../view__main_8cpp.html#a764409d4876e90847c2d8635194f0a3e',1,'view_main.cpp']]],
- ['help_5fviz_2734',['help_viz',['../viz__main_8cpp.html#a81fc7d050b03830c81c731e0ceb98bd1',1,'viz_main.cpp']]],
- ['help_5fzipcode_2735',['help_zipcode',['../zipcode__main_8cpp.html#abc97cba8ea07b911b9c5da9defcc81d8',1,'zipcode_main.cpp']]],
- ['here_2736',['here',['../structvg_1_1Range.html#a518913f6703568c7e704a2723d81e483',1,'vg::Range']]],
- ['het_5fadjustment_2737',['HET_ADJUSTMENT',['../classvg_1_1Recombinator.html#acfb904a0f73882a7d9140efe4e78108e',1,'vg::Recombinator::HET_ADJUSTMENT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a652df2520fd051ebb03fd8494a6e0b11',1,'vg::Recombinator::Parameters::het_adjustment()']]],
- ['het_5fprior_5flogprob_2738',['het_prior_logprob',['../classvg_1_1Genotyper.html#a21799af8d6da86a3bbcfffb1060d27cf',1,'vg::Genotyper']]],
- ['heterozygous_2739',['heterozygous',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa3f649a400509ec3cc8b778d14ce2dd26',1,'vg::Recombinator']]],
- ['heterozygous_5fprior_5fln_2740',['heterozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ac5782c89f874dd212631d6451ef4b842',1,'vg::FixedGenotypePriorCalculator']]],
- ['hex2bin_2741',['hex2bin',['../bin2ascii_8h.html#a63db266c863090d6b7c179df1ea160f1',1,'bin2ascii.h']]],
- ['hfile_5fbackend_2742',['hFILE_backend',['../structhFILE__backend.html',1,'']]],
- ['hfile_5fcppstream_2743',['hFILE_cppstream',['../structvg_1_1io_1_1hFILE__cppstream.html',1,'vg::io']]],
- ['hfile_5fcppstream_2ecpp_2744',['hfile_cppstream.cpp',['../hfile__cppstream_8cpp.html',1,'']]],
- ['hfile_5fcppstream_2ehpp_2745',['hfile_cppstream.hpp',['../hfile__cppstream_8hpp.html',1,'']]],
- ['hfile_5finit_2746',['hfile_init',['../hfile__internal_8hpp.html#abf020a8f3a695c1848cb3671855383b8',1,'hfile_internal.hpp']]],
- ['hfile_5finternal_2ehpp_2747',['hfile_internal.hpp',['../hfile__internal_8hpp.html',1,'']]],
- ['hfile_5fwrap_2748',['hfile_wrap',['../namespacevg_1_1io.html#a62b10a042ea08faa5da35ff07183d49b',1,'vg::io::hfile_wrap(std::istream &input)'],['../namespacevg_1_1io.html#a4fa9b57a79b55cf4eeb10806be649ede',1,'vg::io::hfile_wrap(std::ostream &output)']]],
- ['hint_5fpaths_2749',['hint_paths',['../classvg_1_1CactusSnarlFinder.html#a380a95f5119b76793da6ba19320a1750',1,'vg::CactusSnarlFinder']]],
- ['hit_5fcap_2750',['hit_cap',['../classvg_1_1MinimizerMapper.html#a1097206776713f059fca80f221b8478c',1,'vg::MinimizerMapper']]],
- ['hit_5fmax_2751',['hit_max',['../classvg_1_1BaseMapper.html#a29b8cec81cc68e9d90405c42fbc8ef64',1,'vg::BaseMapper']]],
- ['hit_5ft_2752',['hit_t',['../classvg_1_1MEMClusterer.html#a679c48e684ac52020fb363aa946037c7',1,'vg::MEMClusterer']]],
- ['hitedge_2753',['HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html',1,'vg::MEMClusterer::HitEdge'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#adfc12ed7c93d550e05882555d0004235',1,'vg::MEMClusterer::HitEdge::HitEdge(size_t to_idx, int32_t weight, int64_t distance)'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a16766cbf34e0ec89d8bbdcd7f9d42988',1,'vg::MEMClusterer::HitEdge::HitEdge()=default']]],
- ['hitgraph_2754',['HitGraph',['../classvg_1_1MEMClusterer_1_1HitGraph.html',1,'vg::MEMClusterer::HitGraph'],['../classvg_1_1MEMClusterer_1_1HitGraph.html#a9895e95cdaa1b95876c79c07d29fe852',1,'vg::MEMClusterer::HitGraph::HitGraph()']]],
- ['hitnode_2755',['HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html',1,'vg::MEMClusterer::HitNode'],['../classvg_1_1MEMClusterer_1_1HitNode.html#a3156b62ac2208fdac8d0b12475011472',1,'vg::MEMClusterer::HitNode::HitNode(const MaximalExactMatch &mem, pos_t start_pos, int32_t score)'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aaeb6e6e2bb1c2ce2cda76adce19a40d6',1,'vg::MEMClusterer::HitNode::HitNode()=default']]],
- ['hits_2756',['hits',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aa60067efaa8910104760c8d910471a29',1,'vg::MinimizerMapper::Minimizer']]],
- ['holder_2757',['Holder',['../structvg_1_1subcommand_1_1RangeArgSpec.html#ad4fcbe28c637e8a88821368d02ec7621',1,'vg::subcommand::RangeArgSpec::Holder()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ad6398c9b83de015bcad49cf70c0e572f',1,'vg::subcommand::FlagArgSpec::Holder()']]],
- ['homozygous_5fprior_5fln_2758',['homozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ade32a0216586eb9467d476e2880c188b',1,'vg::FixedGenotypePriorCalculator']]],
- ['hts_5falignment_5femitter_2ecpp_2759',['hts_alignment_emitter.cpp',['../hts__alignment__emitter_8cpp.html',1,'']]],
- ['hts_5falignment_5femitter_2ehpp_2760',['hts_alignment_emitter.hpp',['../hts__alignment__emitter_8hpp.html',1,'']]],
- ['hts_5ffile_5fheader_2761',['hts_file_header',['../namespacevg.html#a0676eec9e08d9589fe286cabdd16ffb3',1,'vg']]],
- ['hts_5ffor_5feach_2762',['hts_for_each',['../namespacevg.html#a1f1e53242cb6ccf3d567c73c0895c4ca',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#ad7abb14966c1c20cff85c5744a47de0e',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda)']]],
- ['hts_5ffor_5feach_5fparallel_2763',['hts_for_each_parallel',['../namespacevg.html#a7c0d37c85747f2bce6ba3356a813524a',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#a59c6c494c2e7663fb14e40c978b4f9e5',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda)']]],
- ['hts_5fmode_2764',['hts_mode',['../classvg_1_1HTSWriter.html#ab2151e3837dd1503111bf7d1daa1fa56',1,'vg::HTSWriter']]],
- ['hts_5fstring_5fheader_2765',['hts_string_header',['../namespacevg.html#abc01af3a6e386a06a2971c17a0e6d1b1',1,'vg::hts_string_header(string &header, const map< string, int64_t > &path_length, const map< string, string > &rg_sample)'],['../namespacevg.html#aeb8cd62602cb90541b2270a79aed7595',1,'vg::hts_string_header(string &header, const vector< pair< string, int64_t >> &path_order_and_length, const map< string, string > &rg_sample)']]],
- ['htsalignmentemitter_2766',['HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html',1,'vg::HTSAlignmentEmitter'],['../classvg_1_1HTSAlignmentEmitter.html#acc9b5714c55e4b644216066eda386dbd',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSAlignmentEmitter.html#a0c76946bf064ecac88e21a2467ea2410',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a780156f43d54cf16906948ad8286c20f',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(HTSAlignmentEmitter &&other)=delete']]],
- ['htslib_5fheaders_2767',['HTSLIB_HEADERS',['../classvg_1_1Version.html#a73127428a2f929f7e52e2a1e811cf688',1,'vg::Version']]],
- ['htslib_5flibrary_2768',['HTSLIB_LIBRARY',['../classvg_1_1Version.html#a75639877908fb90dcd272674544f3c4e',1,'vg::Version']]],
- ['htswriter_2769',['HTSWriter',['../classvg_1_1HTSWriter.html',1,'vg::HTSWriter'],['../classvg_1_1HTSWriter.html#a8257b1e35ac5abf92b43b8a823c66aa5',1,'vg::HTSWriter::HTSWriter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSWriter.html#ae2fc6b2a60e3bc9441956faf87ff6a07',1,'vg::HTSWriter::HTSWriter(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a0a23221d8449a4b4e0b1278995ad0207',1,'vg::HTSWriter::HTSWriter(HTSWriter &&other)=delete']]],
- ['internal_2770',['internal',['../namespacehandlegraph_1_1algorithms_1_1internal.html',1,'handlegraph::algorithms']]]
+ ['algorithms_2525',['algorithms',['../namespacehandlegraph_1_1algorithms.html',1,'handlegraph']]],
+ ['halt_2526',['halt',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aeabcba66f2745dd0e6a4793e954aa23d',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['handle_2527',['handle',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a2d575dc899c6ef50c6ffe7c374573fb9',1,'vg::io::BlockedGzipInputStream::handle()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a726e457d2e98e4ca6ffa742a4378949f',1,'vg::io::BlockedGzipOutputStream::handle()'],['../classxg_1_1XGPath.html#a93ab3c3284afd4d780368ab03d51ee43',1,'xg::XGPath::handle()'],['../classvg_1_1io_1_1MessageIterator.html#a4b3ba16717c1900a0638518bd33a4a59',1,'vg::io::MessageIterator::handle()'],['../classvg_1_1io_1_1ProtobufEmitter.html#afb457287f96e5ed57d53f91fd5247ec7',1,'vg::io::ProtobufEmitter::handle()']]],
+ ['handle_2ehpp_2528',['handle.hpp',['../handle_8hpp.html',1,'']]],
+ ['handle2component_2529',['Handle2Component',['../namespacevg.html#a7143bc6d4008d03bc4a0ac4d4ba26948',1,'vg']]],
+ ['handle_5fat_5forder_2530',['handle_at_order',['../classvg_1_1IncrementalSubgraph.html#a8c2059a01cfda921bd8c5f91bd3763c7',1,'vg::IncrementalSubgraph']]],
+ ['handle_5fat_5fpath_5fposition_2531',['handle_at_path_position',['../classxg_1_1XG.html#a63e8b7be4676a9fb4c77e16f0c76b5a8',1,'xg::XG']]],
+ ['handle_5fat_5fposition_2532',['handle_at_position',['../classxg_1_1XGPath.html#ac3dac0fefe450c561f44dadd3ac00487',1,'xg::XGPath']]],
+ ['handle_5fbase_5foption_2533',['handle_base_option',['../classvg_1_1ConfigurableParser.html#a0c39f36cf64d91a336afaac0604ff9f0',1,'vg::ConfigurableParser']]],
+ ['handle_5fbuffer_2534',['handle_buffer',['../classvg_1_1VcfBuffer.html#a1d8968beb2952113ea8a724dad1e1752',1,'vg::VcfBuffer']]],
+ ['handle_5ffull_5flength_2535',['handle_full_length',['../namespacevg.html#a536dfd4326c17ad4d072d2c9021e4b7c',1,'vg']]],
+ ['handle_5fgraph_2536',['handle_graph',['../classvg_1_1TargetValueSearch.html#a99dd4b74b5894a228a6d31174ca322de',1,'vg::TargetValueSearch::handle_graph()'],['../classvg_1_1MinDistanceClusterer.html#a6bc0aa3fb6df2824a2fe88f941312f09',1,'vg::MinDistanceClusterer::handle_graph()']]],
+ ['handle_5fgraph_2ecpp_2537',['handle_graph.cpp',['../handle__graph_8cpp.html',1,'']]],
+ ['handle_5fgraph_2ehpp_2538',['handle_graph.hpp',['../handle__graph_8hpp.html',1,'']]],
+ ['handle_5fgraph_5fto_5fcactus_2539',['handle_graph_to_cactus',['../namespacevg.html#a3d4e7ee3d7394e2318e874dc98dd8320',1,'vg']]],
+ ['handle_5fidxs_2540',['handle_idxs',['../classvg_1_1JoinedSpliceGraph.html#af3e4ce836a5ba9b208bde5bfe245a97e',1,'vg::JoinedSpliceGraph']]],
+ ['handle_5frank_2541',['handle_rank',['../classxg_1_1XG.html#a2e8f51499dd0ba67d52100bf380b0936',1,'xg::XG']]],
+ ['handle_5fstart_2542',['handle_start',['../classxg_1_1XGPath.html#a5a62bf71a4a85c9617402504a2be01a4',1,'xg::XGPath']]],
+ ['handle_5ft_2543',['handle_t',['../structhandlegraph_1_1handle__t.html',1,'handlegraph::handle_t'],['../namespacevg.html#aaed4a2b7bc668cf2e076733ee26e036a',1,'vg::handle_t()'],['../namespacevg_1_1io.html#a3943ae5818e3556e216014f0df531502',1,'vg::io::handle_t()']]],
+ ['handle_5fto_5fgbwt_2544',['handle_to_gbwt',['../namespacevg.html#a1fa5cc80bff735a8803aa9f564c29994',1,'vg']]],
+ ['handle_5fto_5frank_2545',['handle_to_rank',['../classhandlegraph_1_1RankedHandleGraph.html#a6a21763bef01676efd4dd10767681bfc',1,'handlegraph::RankedHandleGraph']]],
+ ['handle_5fval_5frange_2546',['handle_val_range',['../classvg_1_1DagifiedGraph.html#a3cbeb57dc989a7f0963553041c156252',1,'vg::DagifiedGraph::handle_val_range()'],['../classvg_1_1DozeuPinningOverlay.html#a55cd7c6586c7da513046ed232fe95440',1,'vg::DozeuPinningOverlay::handle_val_range()']]],
+ ['handlegraph_2547',['HandleGraph',['../classhandlegraph_1_1HandleGraph.html',1,'handlegraph::HandleGraph'],['../namespacehandlegraph.html',1,'handlegraph'],['../namespacevg.html#ad5781c55c25f1446e1fc74c72c051c62',1,'vg::HandleGraph()'],['../namespacevg_1_1io.html#a172e1fe036e09c51c5a60918463de08f',1,'vg::io::HandleGraph()']]],
+ ['handlegraphnodeset_2548',['HandleGraphNodeSet',['../classvg_1_1HandleGraphNodeSet.html',1,'vg::HandleGraphNodeSet'],['../classvg_1_1HandleGraphNodeSet.html#af257f6c350350577cc2bef059a133837',1,'vg::HandleGraphNodeSet::HandleGraphNodeSet()']]],
+ ['handlegraphsnarlfinder_2549',['HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html',1,'vg::HandleGraphSnarlFinder'],['../classvg_1_1HandleGraphSnarlFinder.html#a8fb53057585d8e64313485c02a15cec5',1,'vg::HandleGraphSnarlFinder::HandleGraphSnarlFinder()']]],
+ ['handler_2550',['Handler',['../structvg_1_1temp__file_1_1Handler.html',1,'vg::temp_file::Handler'],['../structxg_1_1temp__file_1_1Handler.html',1,'xg::temp_file::Handler']]],
+ ['handles_2551',['handles',['../classxg_1_1XGPath.html#a2363dd10eb299ca6cc52655e517ad9e1',1,'xg::XGPath']]],
+ ['handleset_2552',['HandleSet',['../namespacevg.html#a0942a662fe36dad76d2d0e310ec66e3f',1,'vg']]],
+ ['haplo_2553',['haplo',['../namespacehaplo.html',1,'']]],
+ ['haplo_5fdp_2554',['haplo_DP',['../structhaplo_1_1haplo__DP.html',1,'haplo::haplo_DP'],['../structhaplo_1_1haplo__DP.html#a35035e7b00f8d5503ae3582afebbac50',1,'haplo::haplo_DP::haplo_DP()']]],
+ ['haplo_5fdp_5fcolumn_2555',['haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html',1,'haplo::haplo_DP_column'],['../structhaplo_1_1haplo__DP__column.html#a15c9d8c26ba9eba47510eaac32b49eb8',1,'haplo::haplo_DP_column::haplo_DP_column()']]],
+ ['haplo_5fdp_5frectangle_2556',['haplo_DP_rectangle',['../structhaplo_1_1haplo__DP__rectangle.html',1,'haplo::haplo_DP_rectangle'],['../structhaplo_1_1haplo__DP__rectangle.html#a54e3de46211170326d89ee11f9d61fab',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle()'],['../structhaplo_1_1haplo__DP__rectangle.html#a5e2a880c7d8974ac08021256994a51e2',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle(bool inclusive_interval)']]],
+ ['haplo_5fnode_2557',['haplo_node',['../classvg_1_1PhasedGenome_1_1iterator.html#a1ae0c6a2bdb23511f58dc2986b36117e',1,'vg::PhasedGenome::iterator']]],
+ ['haplo_5fscore_5fprovider_2558',['haplo_score_provider',['../classvg_1_1BaseMapper.html#af69ce88df203124121b71bdfdc6f3694',1,'vg::BaseMapper']]],
+ ['haplo_5fscore_5ftype_2559',['haplo_score_type',['../namespacehaplo.html#aa35eb194ac0f5a70dae8d2283c170736',1,'haplo']]],
+ ['haploid_5fprior_5flogprob_2560',['haploid_prior_logprob',['../classvg_1_1Genotyper.html#a76e36b8cc1f5a8a5522c5ae3f57b5464',1,'vg::Genotyper']]],
+ ['haploid_5fscoring_2561',['haploid_scoring',['../structvg_1_1Recombinator_1_1Parameters.html#a500ad8a5fa909da483c0d84121b80dbd',1,'vg::Recombinator::Parameters']]],
+ ['haplomath_2562',['haploMath',['../namespacehaplo_1_1haploMath.html',1,'haplo']]],
+ ['haplotype_2563',['Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html',1,'vg::PhasedGenome::Haplotype'],['../classvg_1_1PhasedGenome_1_1iterator.html#a2a8d7bc98747d6a54dbeef69cc966afc',1,'vg::PhasedGenome::iterator::Haplotype()'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#aba98c5b032e48cf1a83b21cae31966a0',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversal node_traversal)'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a61d6bf4127d5e607eccca43b730b8d74',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversalIterator first, NodeTraversalIterator last)'],['../structvg_1_1AppendHaplotypeCommand.html#a5dcde06b8eb329a38ae49f612218ad90',1,'vg::AppendHaplotypeCommand::haplotype()'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a096fd6e4d5329e8242d4d1a69e95314b',1,'vg::ReplaceSnarlHaplotypeCommand::haplotype()'],['../structvg_1_1RecombinatorFragment.html#a566d752b9670dbf52d1e3998758c1754',1,'vg::RecombinatorFragment::haplotype()'],['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271ca00c31e80a8b69bfe7bd279f2bfa4b3ba',1,'handlegraph::HAPLOTYPE()']]],
+ ['haplotype_5fconsistency_5fexponent_2564',['haplotype_consistency_exponent',['../classvg_1_1BaseMapper.html#a33465e76a17e2580a6e095f3373239c5',1,'vg::BaseMapper']]],
+ ['haplotype_5fconsistent_5falignments_2565',['haplotype_consistent_alignments',['../namespacevg.html#ab5a2adbf9370dc37be337d927341f9db',1,'vg']]],
+ ['haplotype_5fextracter_2ecpp_2566',['haplotype_extracter.cpp',['../haplotype__extracter_8cpp.html',1,'']]],
+ ['haplotype_5fextracter_2ehpp_2567',['haplotype_extracter.hpp',['../haplotype__extracter_8hpp.html',1,'']]],
+ ['haplotype_5fgbwt_5fids_2568',['haplotype_gbwt_ids',['../structvg_1_1TranscriptPath.html#aafc713083bff5a107e2eb70e4d131541',1,'vg::TranscriptPath']]],
+ ['haplotype_5findexer_2569',['haplotype_indexer',['../structGBWTConfig.html#a29a942d7e187971aa7821a5aacb65acd',1,'GBWTConfig']]],
+ ['haplotype_5findexer_2ecpp_2570',['haplotype_indexer.cpp',['../haplotype__indexer_8cpp.html',1,'']]],
+ ['haplotype_5findexer_2ehpp_2571',['haplotype_indexer.hpp',['../haplotype__indexer_8hpp.html',1,'']]],
+ ['haplotype_5finput_2572',['haplotype_input',['../structHaplotypesConfig.html#a9bca6d317d27daae42a19413e3e336b2',1,'HaplotypesConfig']]],
+ ['haplotype_5fmatch_2573',['HAPLOTYPE_MATCH',['../classhandlegraph_1_1PathMetadata.html#a3f78e2ed41434be9b84823f5724734e9',1,'handlegraph::PathMetadata']]],
+ ['haplotype_5fnumber_2574',['haplotype_number',['../classvg_1_1PhasedGenome_1_1iterator.html#a3d0bbf671bf2801e44d23fea4da0e397',1,'vg::PhasedGenome::iterator']]],
+ ['haplotype_5foutput_2575',['haplotype_output',['../structHaplotypesConfig.html#a75dc83e4850abb0e9d8542285a844574',1,'HaplotypesConfig']]],
+ ['haplotype_5fto_5fstring_2576',['haplotype_to_string',['../classvg_1_1VariantAdder.html#a86108ed47c5e85a23d31fe380ae2670d',1,'vg::VariantAdder']]],
+ ['haplotype_5ftranscript_5fpaths_2577',['haplotype_transcript_paths',['../classvg_1_1Transcriptome.html#a8103dfe99f0bb36e806cab44d2e21d54',1,'vg::Transcriptome']]],
+ ['haplotypeindexer_2578',['HaplotypeIndexer',['../classvg_1_1HaplotypeIndexer.html',1,'vg::HaplotypeIndexer'],['../classvg_1_1HaplotypeIndexer.html#ae0b8cbfe64f32152ceefa57daf9ece72',1,'vg::HaplotypeIndexer::HaplotypeIndexer()']]],
+ ['haplotypenode_2579',['HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html',1,'vg::PhasedGenome::HaplotypeNode'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a4f0160b2daeebec5d984b4fe1921887a',1,'vg::PhasedGenome::Haplotype::HaplotypeNode()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a584a6b469c7f9709ea7da34f867f49aa',1,'vg::PhasedGenome::HaplotypeNode::HaplotypeNode()']]],
+ ['haplotypepartitioner_2580',['HaplotypePartitioner',['../classvg_1_1HaplotypePartitioner.html',1,'vg::HaplotypePartitioner'],['../classvg_1_1HaplotypePartitioner.html#a6faa6da8cc4a62f7cabc8d66e19e9ac1',1,'vg::HaplotypePartitioner::HaplotypePartitioner()']]],
+ ['haplotypes_2581',['Haplotypes',['../classvg_1_1Haplotypes.html',1,'vg::Haplotypes'],['../classvg_1_1SnarlState.html#a98f04166481311709d9a8d3b05b0245e',1,'vg::SnarlState::haplotypes()'],['../classvg_1_1PhasedGenome.html#aa7b2bebc28cc37da09216fca8361c75c',1,'vg::PhasedGenome::haplotypes()'],['../structvg_1_1Recombinator_1_1Statistics.html#a1541408a463fbbcea0e4a3ac08bac9df',1,'vg::Recombinator::Statistics::haplotypes()'],['../classvg_1_1Recombinator.html#a536bca6a31d76be8d90571b24b8ff0e8',1,'vg::Recombinator::haplotypes()'],['../structGBWTConfig.html#a1b5f59745e1b75e70af68ef9e8cd0378',1,'GBWTConfig::haplotypes()']]],
+ ['haplotypes_2ecpp_2582',['haplotypes.cpp',['../haplotypes_8cpp.html',1,'']]],
+ ['haplotypes_2ehpp_2583',['haplotypes.hpp',['../haplotypes_8hpp.html',1,'']]],
+ ['haplotypes_5fdefaults_2584',['haplotypes_defaults',['../namespacehaplotypes__defaults.html',1,'']]],
+ ['haplotypes_5fmain_2ecpp_2585',['haplotypes_main.cpp',['../haplotypes__main_8cpp.html',1,'']]],
+ ['haplotypesconfig_2586',['HaplotypesConfig',['../structHaplotypesConfig.html',1,'HaplotypesConfig'],['../structHaplotypesConfig.html#a45bef8cdfe50758d06d6d078b5a6a13f',1,'HaplotypesConfig::HaplotypesConfig()']]],
+ ['hard_5fhit_5fcap_2587',['hard_hit_cap',['../classvg_1_1MinimizerMapper.html#aaf577b72776f431ec4dc5faac505322e',1,'vg::MinimizerMapper']]],
+ ['hard_5fhit_5fmax_2588',['hard_hit_max',['../classvg_1_1BaseMapper.html#a4e6260be560a0bf2a10cfb409e611e65',1,'vg::BaseMapper']]],
+ ['has_5fannotation_2589',['has_annotation',['../classvg_1_1multipath__alignment__t.html#a6b60350a3dada734b919bdf15f41bf82',1,'vg::multipath_alignment_t::has_annotation()'],['../namespacevg.html#a34f4e73b242fa5b34d30ecc4da496835',1,'vg::has_annotation()']]],
+ ['has_5fargument_2590',['has_argument',['../classvg_1_1OptionInterface.html#a29383428b6a6e40109fb4949286f07f7',1,'vg::OptionInterface::has_argument()'],['../classvg_1_1OptionValueParser.html#af8d6268a6cec527dd0e117aef58cbd63',1,'vg::OptionValueParser::has_argument()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a104c6803a28a2528b33759ac8ad69175',1,'vg::OptionValueParser< vector< Item > >::has_argument()'],['../classvg_1_1BaseOption.html#a3aa53d25627ae95383edce8f6e001caa',1,'vg::BaseOption::has_argument()'],['../classvg_1_1OptionValueParser.html#aabf09c8e0e807fb19debad284331387d',1,'vg::OptionValueParser::has_argument()']]],
+ ['has_5fbase_5fgraph_2591',['has_base_graph',['../structvg_1_1AugmentedGraph.html#ae1b8b8c8246ccfe1f2d56250a3361177',1,'vg::AugmentedGraph']]],
+ ['has_5fbuffer_2592',['has_buffer',['../classvg_1_1VcfBuffer.html#a13f0fa2e0b50cd133c117bd1f34715c3',1,'vg::VcfBuffer']]],
+ ['has_5fchain_5fvalues_2593',['has_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab62e9f2483533263e5df33fd9c5ad882',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['has_5fconnection_2594',['has_connection',['../classvg_1_1subpath__t.html#a972d307d386a636cc2dc1fc170f56df3',1,'vg::subpath_t']]],
+ ['has_5fcontent_2595',['has_content',['../structvg_1_1BitStringTree_1_1TreeNode.html#ac222ba76d226ad0f457be10e8c8a8b30',1,'vg::BitStringTree::TreeNode']]],
+ ['has_5fcurrent_2596',['has_current',['../classvg_1_1io_1_1MessageIterator.html#abcbec4e2b7376ae5ca8bbd4e05d9103a',1,'vg::io::MessageIterator::has_current()'],['../classvg_1_1io_1_1ProtobufIterator.html#a59294f819b65352528da9224ea39d973',1,'vg::io::ProtobufIterator::has_current()']]],
+ ['has_5fedge_2597',['has_edge',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a6fd765d7a5623bef825effc7fdf46b87',1,'haplo::hDP_gbwt_graph_accessor::has_edge()'],['../classvg_1_1VG.html#a501886a0c593ac3231cfcc6989911ced',1,'vg::VG::has_edge(const handle_t &left, const handle_t &right) const'],['../classvg_1_1VG.html#a447d717e83131c526d26e6d2f0a091a6',1,'vg::VG::has_edge(const NodeSide &side1, const NodeSide &side2) const'],['../classvg_1_1VG.html#a1c7ff3b6f9cfca2c21e1a8d1c848fc01',1,'vg::VG::has_edge(const pair< NodeSide, NodeSide > &sides) const'],['../classvg_1_1VG.html#aa69701fcb4bf9e8b593681ba1d818571',1,'vg::VG::has_edge(Edge *edge) const'],['../classvg_1_1VG.html#ab2c85fad61f57260c913bc565a549832',1,'vg::VG::has_edge(const Edge &edge) const'],['../classhandlegraph_1_1HandleGraph.html#a069448fbe58665b9ff531ad0b8c5af57',1,'handlegraph::HandleGraph::has_edge(const handle_t &left, const handle_t &right) const'],['../classhandlegraph_1_1HandleGraph.html#a6171cdd6036c73623c96656f8b44fe9d',1,'handlegraph::HandleGraph::has_edge(const edge_t &edge) const']]],
+ ['has_5fend_2598',['has_end',['../structvg_1_1Haplotypes_1_1Subchain.html#ae9fbddda11e52d6e9b98156a50224a73',1,'vg::Haplotypes::Subchain::has_end()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a0aa037691bcf20d78faad42eea3c8f57',1,'vg::HaplotypePartitioner::Subchain::has_end()']]],
+ ['has_5fexcluded_5frefpos_2599',['has_excluded_refpos',['../classvg_1_1ReadFilter.html#ac772c0651477027191108e64ab7c53cb',1,'vg::ReadFilter::has_excluded_refpos(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab609cc20f1e49dc1001e71fe82c5ead4',1,'vg::ReadFilter::has_excluded_refpos(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#aca79c3eda85a8f4fafcd25a243b7efd4',1,'vg::ReadFilter::has_excluded_refpos(const Alignment &aln) const']]],
+ ['has_5fexcuded_5ffeature_2600',['has_excuded_feature',['../classvg_1_1ReadFilter.html#a2d30291c0c609d58670f40e2eb9661e4',1,'vg::ReadFilter']]],
+ ['has_5ffixed_5ffragment_5flength_5fdistr_2601',['has_fixed_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ad0a2d836cfcaddae8569bf1a024aa56b',1,'vg::PairedEndMapper']]],
+ ['has_5fgrandparent_5fhandle_2602',['has_grandparent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d823f95b1440029399ae07f5d5ce0ec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['has_5fincorrect_5forder_5fexons_2603',['has_incorrect_order_exons',['../classvg_1_1Transcriptome.html#a4cba921dae9fe3eae2361b0b7391b7b3',1,'vg::Transcriptome']]],
+ ['has_5fincremental_5fsearch_2604',['has_incremental_search',['../classhaplo_1_1ScoreProvider.html#a1455c3ccb6a9d03e5d79636e79be301a',1,'haplo::ScoreProvider::has_incremental_search()'],['../classhaplo_1_1GBWTScoreProvider.html#abe35e78c1d11af952b27dc8c36c1909f',1,'haplo::GBWTScoreProvider::has_incremental_search()']]],
+ ['has_5finversion_2605',['has_inversion',['../namespacevg.html#a1b545f6474c6e528176031149a8bc570',1,'vg']]],
+ ['has_5finverting_5fedge_2606',['has_inverting_edge',['../classvg_1_1VG.html#a49fb4de3494407b800c3efda254851cf',1,'vg::VG']]],
+ ['has_5finverting_5fedge_5ffrom_2607',['has_inverting_edge_from',['../classvg_1_1VG.html#a7b7bbf066c6608211e7527ba50b23e48',1,'vg::VG']]],
+ ['has_5finverting_5fedge_5fto_2608',['has_inverting_edge_to',['../classvg_1_1VG.html#a63088ee0039a8e1f5cf6b5a3b23f745a',1,'vg::VG']]],
+ ['has_5finverting_5fedges_2609',['has_inverting_edges',['../classvg_1_1VG.html#a8d1dbb49df52e016746829776ca0f952',1,'vg::VG']]],
+ ['has_5fmapping_2610',['has_mapping',['../classvg_1_1Paths.html#a32ecf6382d9fa9c9826cb59f8e79349e',1,'vg::Paths']]],
+ ['has_5fnext_2611',['has_next',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a376e3ac5d3d820bd4b5ac55f1ad0d69b',1,'vg::BandedGlobalAligner::AltTracebackStack::has_next()'],['../classvg_1_1subpath__t.html#acb3834a6661d55a407a58cff5cd539c3',1,'vg::subpath_t::has_next()']]],
+ ['has_5fnext_5fstep_2612',['has_next_step',['../classvg_1_1MemoizingGraph.html#a3c6e172a85dd0c03a290bf4b5b04792e',1,'vg::MemoizingGraph::has_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a56d9a8eb9dfbbac174ed677e4f22f14d',1,'vg::PathSubgraphOverlay::has_next_step()'],['../classvg_1_1VG.html#add23d09d2925d505f793979f7fe35921',1,'vg::VG::has_next_step()'],['../classxg_1_1XG.html#ad193420b3ab85a6d2b47f305779d6b5c',1,'xg::XG::has_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a81bf54cb4d07a0d47c84862ecebc349d',1,'handlegraph::PathHandleGraph::has_next_step()']]],
+ ['has_5fnode_2613',['has_node',['../classvg_1_1DagifiedGraph.html#ad6c8a0d0a6c21fee9c10065927d4ba97',1,'vg::DagifiedGraph::has_node()'],['../classvg_1_1DozeuPinningOverlay.html#a696d9ff9c1731e98d7235a637d794174',1,'vg::DozeuPinningOverlay::has_node()'],['../classvg_1_1ExtraNodeGraph.html#a89299bba0acddf6e2bb2a8d6cb561b86',1,'vg::ExtraNodeGraph::has_node()'],['../classvg_1_1SnarlGraph.html#a43e8f719e0d3b9814e3328d14c28c85e',1,'vg::SnarlGraph::has_node()'],['../classvg_1_1IdentityOverlay.html#a56aabb0a049d7bbf9079733d7824e0db',1,'vg::IdentityOverlay::has_node()'],['../classvg_1_1IncrementalSubgraph.html#a29fe9b69774ab975e3b6fe15900d1c9e',1,'vg::IncrementalSubgraph::has_node()'],['../classvg_1_1IndexedVG.html#a184b4de54cd807fc818091c56bac41a8',1,'vg::IndexedVG::has_node()'],['../classvg_1_1MemoizingGraph.html#a5e5fea73aaa5c9b403b7e63318e15702',1,'vg::MemoizingGraph::has_node()'],['../classvg_1_1NullMaskingGraph.html#a550edf96fd717710f5051804d0d1bafe',1,'vg::NullMaskingGraph::has_node()'],['../classvg_1_1PathSubgraph.html#ad13f4f28e024ac0d43991cb9d162420f',1,'vg::PathSubgraph::has_node()'],['../classvg_1_1ReverseGraph.html#a98c0e584e6cb8246c9b2deb65d92e370',1,'vg::ReverseGraph::has_node()'],['../classvg_1_1NetGraph.html#a99ddd8990ab25cd314618321a5837ff9',1,'vg::NetGraph::has_node()'],['../classvg_1_1SourceSinkOverlay.html#ad2e4740b5a84271e053840e6b60fc53c',1,'vg::SourceSinkOverlay::has_node()'],['../classvg_1_1JoinedSpliceGraph.html#af167d082a5c148792ae9a533eac068f0',1,'vg::JoinedSpliceGraph::has_node()'],['../classvg_1_1StrandSplitGraph.html#aad17d3113bdc3f8ec03327a16ccfadd9',1,'vg::StrandSplitGraph::has_node()'],['../classvg_1_1SubHandleGraph.html#a66e144a38ed8437cbf71a186a6e8afa0',1,'vg::SubHandleGraph::has_node()'],['../classvg_1_1SubgraphOverlay.html#aaa8aca387ac5ba4f962d03da956979a2',1,'vg::SubgraphOverlay::has_node()'],['../classvg_1_1SubpathOverlay.html#a7c9a83697a1f3041e3dfbcb10f3a831b',1,'vg::SubpathOverlay::has_node()'],['../classvg_1_1TreeSubgraph.html#a84c11ffd899e018587d6ccb25dd1211b',1,'vg::TreeSubgraph::has_node()'],['../classvg_1_1VG.html#ac9339913ecff654569a9c81ae091ebfe',1,'vg::VG::has_node(nid_t id) const'],['../classvg_1_1VG.html#a049bd863e2ac7e93aec79404d56b4a34',1,'vg::VG::has_node(const Node *node) const'],['../classvg_1_1VG.html#ab000649761c7201555284390dd8a4fa0',1,'vg::VG::has_node(const Node &node) const'],['../classxg_1_1XG.html#a60dd1cf3ec755863aabc99e6948011e0',1,'xg::XG::has_node()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a29475639dafe548f44b4c0e995005083',1,'handlegraph::algorithms::SubHandleGraph::has_node()'],['../classhandlegraph_1_1HandleGraph.html#a6e58a79001cd7d839ac1f1adaff34dfb',1,'handlegraph::HandleGraph::has_node()']]],
+ ['has_5fnode_5fmapping_2614',['has_node_mapping',['../classvg_1_1Paths.html#a4f744ed09e266781a366dd11a73993b8',1,'vg::Paths::has_node_mapping(id_t id) const'],['../classvg_1_1Paths.html#a48f74571d94bdd9845ff761d51701034',1,'vg::Paths::has_node_mapping(Node *n) const']]],
+ ['has_5fnovel_5fexon_5fboundaries_2615',['has_novel_exon_boundaries',['../classvg_1_1Transcriptome.html#aaf34b6da5110fa44f787994be4ea2791',1,'vg::Transcriptome']]],
+ ['has_5foverlapping_5fexons_2616',['has_overlapping_exons',['../classvg_1_1Transcriptome.html#a405f6a2b87ab7d919d0cb8780b1362a5',1,'vg::Transcriptome']]],
+ ['has_5foverlay_5fnode_5ffor_2617',['has_overlay_node_for',['../classvg_1_1StrandSplitGraph.html#a66d77e125b056b19273bb037fef6012c',1,'vg::StrandSplitGraph']]],
+ ['has_5fparent_5fhandle_2618',['has_parent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a67fd7b54bbaafc48baee628bc60efad2',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['has_5fpath_2619',['has_path',['../classvg_1_1MemoizingGraph.html#a62559a9038db86f33b149616dd6c5d27',1,'vg::MemoizingGraph::has_path()'],['../classvg_1_1subpath__t.html#a55a56773ae505e410262b8954d34fc3c',1,'vg::subpath_t::has_path()'],['../classvg_1_1Paths.html#a38cd0087925c24ea1bf8a22755c30cbf',1,'vg::Paths::has_path()'],['../classvg_1_1PathSubgraphOverlay.html#a284e49aa618e321cc8402f4b98c9b41b',1,'vg::PathSubgraphOverlay::has_path()'],['../classvg_1_1VG.html#a0328316df2438f0006349c71206810e6',1,'vg::VG::has_path()'],['../classxg_1_1XG.html#a243d2c25b54008f0f79c480b5ff9429c',1,'xg::XG::has_path()'],['../classhandlegraph_1_1PathHandleGraph.html#ab7de11c1e994bc104378c4b798013430',1,'handlegraph::PathHandleGraph::has_path()']]],
+ ['has_5fposition_2620',['has_position',['../structvg_1_1algorithms_1_1GFAFormatError.html#adb7cfa3f30ee5710575bee189251b473',1,'vg::algorithms::GFAFormatError']]],
+ ['has_5fprevious_5fstep_2621',['has_previous_step',['../classvg_1_1MemoizingGraph.html#aed383459047e290a94817d010361a24f',1,'vg::MemoizingGraph::has_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#aa21af9591c2d1e457c32aaa703cda785',1,'vg::PathSubgraphOverlay::has_previous_step()'],['../classvg_1_1VG.html#ac5f9ec61fe7a32e3756e4b7fc77939ba',1,'vg::VG::has_previous_step()'],['../classxg_1_1XG.html#af833a0ffe45757002869b5802c8d3747',1,'xg::XG::has_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a93a1ee451e750cb82f1711fd6c3db8cc',1,'handlegraph::PathHandleGraph::has_previous_step()']]],
+ ['has_5fqualities_2622',['has_qualities',['../classvg_1_1Packer.html#ae00e614a5cb879210690e3b94e2dcc6e',1,'vg::Packer']]],
+ ['has_5freachability_5fedges_2623',['has_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#a77a113d4c5b6b5ca1d7748c1b812e8d3',1,'vg::MultipathAlignmentGraph']]],
+ ['has_5fref_2624',['has_ref',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a27de160925943418d3af61d2e3c753dc',1,'vg::Deconstructor::NestingInfo']]],
+ ['has_5frepeat_2625',['has_repeat',['../classvg_1_1ReadFilter.html#a9aecb91c19bb44bb9be32c4f30c44538',1,'vg::ReadFilter']]],
+ ['has_5fstart_2626',['has_start',['../classvg_1_1multipath__alignment__t.html#af56553f4ec379201916081cba150781b',1,'vg::multipath_alignment_t::has_start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#ac1b3268f8305395fc8e35530d900b230',1,'vg::Haplotypes::Subchain::has_start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#ab13d2b1ae3f525cea9be92630f32c3e9',1,'vg::HaplotypePartitioner::Subchain::has_start()']]],
+ ['has_5fsupports_2627',['has_supports',['../classvg_1_1RepresentativeTraversalFinder.html#a7010e7fc85d3b2454bc5e09a504aee23',1,'vg::RepresentativeTraversalFinder::has_supports()'],['../structvg_1_1AugmentedGraph.html#a5519dec3147cb54da3e32cdb2f6c1428',1,'vg::AugmentedGraph::has_supports()'],['../structvg_1_1SupportAugmentedGraph.html#a32dc8f5559a750e393b8cedfb42cbf83',1,'vg::SupportAugmentedGraph::has_supports()']]],
+ ['has_5ftabix_2628',['has_tabix',['../classvg_1_1VcfBuffer.html#ae0a4db2dd14b0a00545ef726879a0951',1,'vg::VcfBuffer::has_tabix()'],['../classvg_1_1WindowedVcfBuffer.html#a84bbabd4f6b5b948ce6d2d0aa5fa7ff4',1,'vg::WindowedVcfBuffer::has_tabix()']]],
+ ['has_5ftranslation_2629',['has_translation',['../classvg_1_1Translator.html#ae6ccab957bfb3f7eba512f7021a4052b',1,'vg::Translator']]],
+ ['hash_2630',['hash',['../classvg_1_1VG.html#a2b75ca400f858be77b0716ab7c68dfcb',1,'vg::VG']]],
+ ['hash_3c_20const_20vg_3a_3asnarl_20_3e_2631',['hash< const vg::Snarl >',['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3aedge_5ft_20_3e_2632',['hash< handlegraph::edge_t >',['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3ahandle_5ft_20_3e_2633',['hash< handlegraph::handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_2634',['hash< handlegraph::net_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3apath_5fhandle_5ft_20_3e_2635',['hash< handlegraph::path_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3astep_5fhandle_5ft_20_3e_2636',['hash< handlegraph::step_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20pair_3c_20a_2c_20b_20_3e_20_3e_2637',['hash< pair< A, B > >',['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html',1,'std']]],
+ ['hash_3c_20std_3a_3atuple_3c_20tt_2e_2e_2e_20_3e_20_3e_2638',['hash< std::tuple< TT... > >',['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3anodeside_20_3e_2639',['hash< vg::NodeSide >',['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3anodetraversal_20_3e_2640',['hash< vg::NodeTraversal >',['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3azipcodetree_3a_3aoriented_5fseed_5ft_20_3e_2641',['hash< vg::ZipCodeTree::oriented_seed_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3azipcodetree_3a_3aseed_5fresult_5ft_20_3e_2642',['hash< vg::ZipCodeTree::seed_result_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html',1,'std']]],
+ ['hash_5falignment_2643',['hash_alignment',['../namespacevg.html#a94f469aebb2be5b0028c337108d253fb',1,'vg']]],
+ ['hash_5fambiguous_5fallele_5fset_2644',['hash_ambiguous_allele_set',['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html',1,'vg::Genotyper']]],
+ ['hash_5fmap_2645',['hash_map',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_2ehpp_2646',['hash_map.hpp',['../hash__map_8hpp.html',1,'']]],
+ ['hash_5fmap_3c_20const_20vg_3a_3amapping_5ft_20_2a_2c_20pair_3c_20list_3c_20vg_3a_3amapping_5ft_20_3e_3a_3aiterator_2c_20int64_5ft_20_3e_20_3e_2647',['hash_map< const vg::mapping_t *, pair< list< vg::mapping_t >::iterator, int64_t > >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20handlegraph_3a_3anet_5fhandle_5ft_2c_20size_5ft_20_3e_2648',['hash_map< handlegraph::net_handle_t, size_t >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20id_5ft_2c_20map_3c_20int64_5ft_2c_20set_3c_20vg_3a_3amapping_5ft_20_2a_20_3e_20_3e_20_3e_2649',['hash_map< id_t, map< int64_t, set< vg::mapping_t * > > >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20k_20_2a_2c_20v_20_3e_2650',['hash_map< K *, V >',['../classvg_1_1hash__map_3_01K_01_5_00_01V_01_4.html',1,'vg']]],
+ ['hash_5fmap_3c_20nid_5ft_2c_20vector_3c_20pair_3c_20nid_5ft_2c_20bool_20_3e_20_3e_20_3e_2651',['hash_map< nid_t, vector< pair< nid_t, bool > > >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20nid_5ft_2c_20vg_3a_3anode_20_2a_20_3e_2652',['hash_map< nid_t, vg::Node * >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20vg_3a_3aedge_20_2a_2c_20int_20_3e_2653',['hash_map< vg::Edge *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20vg_3a_3anode_20_2a_2c_20int_20_3e_2654',['hash_map< vg::Node *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fnode_5ftraversal_2655',['hash_node_traversal',['../structvg_1_1Genotyper_1_1hash__node__traversal.html',1,'vg::Genotyper']]],
+ ['hash_5foriented_5fedge_2656',['hash_oriented_edge',['../structvg_1_1Genotyper_1_1hash__oriented__edge.html',1,'vg::Genotyper']]],
+ ['hash_5fset_2657',['hash_set',['../classvg_1_1hash__set.html',1,'vg']]],
+ ['hash_5fset_3c_20k_20_2a_20_3e_2658',['hash_set< K * >',['../classvg_1_1hash__set_3_01K_01_5_01_4.html',1,'vg']]],
+ ['hash_5fset_3c_20pair_3c_20size_5ft_2c_20size_5ft_20_3e_20_3e_2659',['hash_set< pair< size_t, size_t > >',['../classvg_1_1hash__set.html',1,'vg']]],
+ ['hash_5fset_3c_20vg_3a_3aid_5ft_20_3e_2660',['hash_set< vg::id_t >',['../classvg_1_1hash__set.html',1,'vg']]],
+ ['hash_5ftable_5fmax_5fwidth_2661',['HASH_TABLE_MAX_WIDTH',['../minimizer__main_8cpp.html#a6eb56e166572ca736f815a988e170c68',1,'minimizer_main.cpp']]],
+ ['hash_5ftable_5fmin_5fwidth_2662',['HASH_TABLE_MIN_WIDTH',['../minimizer__main_8cpp.html#ab0b28c6a5c118414fc8ca717901f2054',1,'minimizer_main.cpp']]],
+ ['hash_5fto_5frgb_2663',['hash_to_rgb',['../namespacevg.html#a8bc1d89bbcee041956e59895ed605ca3',1,'vg']]],
+ ['hashed_2664',['hashed',['../classvg_1_1Colors.html#a9c14e90e97e7fd193b25461a40ff6235',1,'vg::Colors::hashed()'],['../classvg_1_1Pictographs.html#a42c157819fffed93d2bfa730c5517e56',1,'vg::Pictographs::hashed()']]],
+ ['hashed_5fchar_2665',['hashed_char',['../classvg_1_1Pictographs.html#a91309563adbfaaf7eab19a51623d66c2',1,'vg::Pictographs']]],
+ ['hashgraph_2666',['HashGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a88fe737c0668785017687666e0aa74a8',1,'vg::IndexingParameters']]],
+ ['have_5finput_5ffile_2667',['have_input_file',['../namespacevg.html#a7c950dca7cd25a5ce9846be2a6b93e13',1,'vg']]],
+ ['hdp_5fgbwt_5fgraph_5faccessor_2668',['hDP_gbwt_graph_accessor',['../classhaplo_1_1hDP__gbwt__graph__accessor.html',1,'haplo::hDP_gbwt_graph_accessor< GBWTType >'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a63ed5e1c48904968ae61ff21f411c0db',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type old_node, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a7a8d1f9ad8428fe0ff0b6071dc6f47ef',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)']]],
+ ['head_5fnodes_2669',['head_nodes',['../classvg_1_1VG.html#a7eecc0bd555c31d1c541c3ce44b421c3',1,'vg::VG::head_nodes(vector< Node * > &nodes)'],['../classvg_1_1VG.html#a3a44c415fb5882c184e2f35bb3999700',1,'vg::VG::head_nodes(void)'],['../namespacehandlegraph_1_1algorithms.html#a3d26728fa655f872ccac738a2bcb6166',1,'handlegraph::algorithms::head_nodes()']]],
+ ['head_5ftail_5fnodes_2670',['head_tail_nodes',['../classvg_1_1Paths.html#a3fd42adbd3d58aee08370f043dc1643d',1,'vg::Paths']]],
+ ['header_2671',['Header',['../structvg_1_1Haplotypes_1_1Header.html',1,'vg::Haplotypes::Header'],['../classvg_1_1Haplotypes.html#ac2671cb0e5d0cdf19a8aa849ec9a2577',1,'vg::Haplotypes::header()']]],
+ ['header_5flisteners_2672',['header_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aeedc94c6fcd57b9da7e627c2136eab45',1,'vg::algorithms::GFAParser']]],
+ ['header_5fmutex_2673',['header_mutex',['../classvg_1_1HTSWriter.html#af9d539c1312350395949b75010134032',1,'vg::HTSWriter']]],
+ ['heading_2674',['heading',['../structvg_1_1subcommand_1_1OptionGroup.html#a93bdf7b70e92b0a05ec270a4fa1495df',1,'vg::subcommand::OptionGroup']]],
+ ['help_2675',['help',['../structvg_1_1subcommand_1_1BaseArgSpec.html#abf8444c205dd6aa3c900d111ffdccac0',1,'vg::subcommand::BaseArgSpec']]],
+ ['help_5fadd_2676',['help_add',['../add__main_8cpp.html#ad49fa30ce6a9b619ad5df1cfa8621d9a',1,'add_main.cpp']]],
+ ['help_5falign_2677',['help_align',['../align__main_8cpp.html#ac749b2692aaca8eeaa6b48d7b44e167d',1,'align_main.cpp']]],
+ ['help_5fannotate_2678',['help_annotate',['../annotate__main_8cpp.html#a6957d47b527eacd587f20f9d11ccd333',1,'annotate_main.cpp']]],
+ ['help_5faugment_2679',['help_augment',['../augment__main_8cpp.html#a7cf03aa52fd6e8d75e480d4d0632b71c',1,'augment_main.cpp']]],
+ ['help_5fautoindex_2680',['help_autoindex',['../autoindex__main_8cpp.html#a4a3c7ba0d785194a42444bdedac4db50',1,'autoindex_main.cpp']]],
+ ['help_5fbenchmark_2681',['help_benchmark',['../benchmark__main_8cpp.html#a1e3da44e3dcc6fea154d15a1986ade1b',1,'benchmark_main.cpp']]],
+ ['help_5fcall_2682',['help_call',['../call__main_8cpp.html#ab92ccd67b3c20b7be7c46281c4cabfb3',1,'call_main.cpp']]],
+ ['help_5fchain_2683',['help_chain',['../chain__main_8cpp.html#a88894e89fc3e50d33042f88c993a0e0c',1,'chain_main.cpp']]],
+ ['help_5fchunk_2684',['help_chunk',['../chunk__main_8cpp.html#a502600dcc3e4e15a338642fe554fbf8d',1,'chunk_main.cpp']]],
+ ['help_5fcircularize_2685',['help_circularize',['../circularize__main_8cpp.html#a0613e20e02d0fbb56d7270a7b268ffb3',1,'circularize_main.cpp']]],
+ ['help_5fclip_2686',['help_clip',['../clip__main_8cpp.html#a451b2ddc17b7d65f1bac0fcd7cac810c',1,'clip_main.cpp']]],
+ ['help_5fcluster_2687',['help_cluster',['../cluster__main_8cpp.html#a4099bc0f1cb9fecb87c903e578ff2a17',1,'cluster_main.cpp']]],
+ ['help_5fcombine_2688',['help_combine',['../combine__main_8cpp.html#a14fa4eb501b75ae37a166fb633cda8dd',1,'combine_main.cpp']]],
+ ['help_5fconcat_2689',['help_concat',['../concat__main_8cpp.html#a795aaef3bab6d86036c1362ba5b76ac0',1,'concat_main.cpp']]],
+ ['help_5fconstruct_2690',['help_construct',['../construct__main_8cpp.html#a0c8b1d02948ee021399fef93344a9def',1,'construct_main.cpp']]],
+ ['help_5fconvert_2691',['help_convert',['../convert__main_8cpp.html#a61c2208fb6645c58f794c57e1851a194',1,'convert_main.cpp']]],
+ ['help_5fdeconstruct_2692',['help_deconstruct',['../deconstruct__main_8cpp.html#a32554f3b30e86c414a7c6940beb660e3',1,'deconstruct_main.cpp']]],
+ ['help_5fdepth_2693',['help_depth',['../depth__main_8cpp.html#aa182528e1e692b2b6ea79e3ed6a36661',1,'depth_main.cpp']]],
+ ['help_5fdotplot_2694',['help_dotplot',['../dotplot__main_8cpp.html#a628ebfce6d823f9dca7722f0721a5a3b',1,'dotplot_main.cpp']]],
+ ['help_5fexplode_2695',['help_explode',['../explode__main_8cpp.html#a5ed55d49ef3d15ac39e1e275e6792907',1,'explode_main.cpp']]],
+ ['help_5ffilter_2696',['help_filter',['../filter__main_8cpp.html#a9072d5dfad52adc43da1d2a700be313b',1,'filter_main.cpp']]],
+ ['help_5ffind_2697',['help_find',['../find__main_8cpp.html#a61f46a85b426fbf3e48cdffc07d107f8',1,'find_main.cpp']]],
+ ['help_5fgamcompare_2698',['help_gamcompare',['../gamcompare__main_8cpp.html#a33c9728d9a784c1ae54baae635b6e56d',1,'gamcompare_main.cpp']]],
+ ['help_5fgampcompare_2699',['help_gampcompare',['../gampcompare__main_8cpp.html#a4eb570f78fda3fc79752c40fccb794d9',1,'gampcompare_main.cpp']]],
+ ['help_5fgamsort_2700',['help_gamsort',['../gamsort__main_8cpp.html#ab37435867b2e79dc2fd17af9f6b3667b',1,'gamsort_main.cpp']]],
+ ['help_5fgbwt_2701',['help_gbwt',['../gbwt__main_8cpp.html#a73013ddacba7ab20beed9e8022b2b57b',1,'gbwt_main.cpp']]],
+ ['help_5fgenotype_2702',['help_genotype',['../genotype__main_8cpp.html#a7d9960cb294ff9984b99ed7816f06323',1,'genotype_main.cpp']]],
+ ['help_5fgiraffe_2703',['help_giraffe',['../giraffe__main_8cpp.html#aa6d5c2140d259252f3cad8b7bf6b4b1a',1,'giraffe_main.cpp']]],
+ ['help_5fhaplotypes_2704',['help_haplotypes',['../haplotypes__main_8cpp.html#a06899318e624a0766060720e2403f380',1,'haplotypes_main.cpp']]],
+ ['help_5fhelp_2705',['help_help',['../help__main_8cpp.html#abbe09b0c0e2e4abc339997cd4b8c1bf7',1,'help_main.cpp']]],
+ ['help_5fids_2706',['help_ids',['../ids__main_8cpp.html#ae3e40ed9a49e6e00fe241abf728c11ea',1,'ids_main.cpp']]],
+ ['help_5findex_2707',['help_index',['../index__main_8cpp.html#a24afe767ac485cebbc2f2b47ef515274',1,'index_main.cpp']]],
+ ['help_5finject_2708',['help_inject',['../inject__main_8cpp.html#a10c867b9f97d3e0d6a1396bad277880a',1,'inject_main.cpp']]],
+ ['help_5fjoin_2709',['help_join',['../join__main_8cpp.html#af6a676c62773f02853c583961fe3a59d',1,'join_main.cpp']]],
+ ['help_5fkmers_2710',['help_kmers',['../kmers__main_8cpp.html#ab5e392cd094049b8b9a863d2ce1acdb4',1,'kmers_main.cpp']]],
+ ['help_5fmain_2ecpp_2711',['help_main.cpp',['../help__main_8cpp.html',1,'']]],
+ ['help_5fmap_2712',['help_map',['../map__main_8cpp.html#afec224c846352e16703d590d52bad501',1,'map_main.cpp']]],
+ ['help_5fmask_2713',['help_mask',['../mask__main_8cpp.html#a0502efe715f6be3e9b8abd1514c3faae',1,'mask_main.cpp']]],
+ ['help_5fmcmc_2714',['help_mcmc',['../mcmc__main_8cpp.html#a2d01e9b5436c54c18299e579f8f850e9',1,'mcmc_main.cpp']]],
+ ['help_5fminimizer_2715',['help_minimizer',['../minimizer__main_8cpp.html#a45dc67f0fe9ce978202fda58585b6b52',1,'minimizer_main.cpp']]],
+ ['help_5fmod_2716',['help_mod',['../mod__main_8cpp.html#a7ff398c2ef9439dc08f0d318693c9b0b',1,'mod_main.cpp']]],
+ ['help_5fmpmap_2717',['help_mpmap',['../mpmap__main_8cpp.html#ad68f4a7fc19b061a16fe9d7fb2810133',1,'mpmap_main.cpp']]],
+ ['help_5fmsga_2718',['help_msga',['../msga__main_8cpp.html#a75ed90adae627c02a0d46998bb73ee99',1,'msga_main.cpp']]],
+ ['help_5fpack_2719',['help_pack',['../pack__main_8cpp.html#aadaeba7e32c73f9093b262830bd2541e',1,'pack_main.cpp']]],
+ ['help_5fpaths_2720',['help_paths',['../paths__main_8cpp.html#a290bac84a159c7e6ab2a9abca73f7000',1,'paths_main.cpp']]],
+ ['help_5fprune_2721',['help_prune',['../prune__main_8cpp.html#a4da6cb650889066af17a6223ba1bfa81',1,'prune_main.cpp']]],
+ ['help_5frna_2722',['help_rna',['../rna__main_8cpp.html#a703e9ebf973bfcd363ce619ccaff160b',1,'rna_main.cpp']]],
+ ['help_5fsift_2723',['help_sift',['../sift__main_8cpp.html#ad82567fc886ab61b4c209226f45b0d8f',1,'sift_main.cpp']]],
+ ['help_5fsim_2724',['help_sim',['../sim__main_8cpp.html#ab2368d74cf2fb693982eeb4676e6b534',1,'sim_main.cpp']]],
+ ['help_5fsimplify_2725',['help_simplify',['../simplify__main_8cpp.html#a6fbde48f0c083d661e2e8e8b2b0a17e7',1,'simplify_main.cpp']]],
+ ['help_5fsnarl_2726',['help_snarl',['../snarls__main_8cpp.html#a4f8c80c7a187ae51a198f3ec42d85f26',1,'snarls_main.cpp']]],
+ ['help_5fsort_2727',['help_sort',['../sort__main_8cpp.html#aa2e0a3c74cb1ee9a7278b5399da39a1b',1,'sort_main.cpp']]],
+ ['help_5fstats_2728',['help_stats',['../stats__main_8cpp.html#a8a996696d6e2c9ecca6dffd6fbc8bf26',1,'stats_main.cpp']]],
+ ['help_5fsurject_2729',['help_surject',['../surject__main_8cpp.html#a9d8217a048300f2a321bfe032e31c769',1,'surject_main.cpp']]],
+ ['help_5ftrace_2730',['help_trace',['../trace__main_8cpp.html#a1e6c8dca8a2b0b1ba628313be3a56fe8',1,'trace_main.cpp']]],
+ ['help_5ftranslate_2731',['help_translate',['../translate__main_8cpp.html#ad94d99f9e08a28731eb6f4d42d64b553',1,'translate_main.cpp']]],
+ ['help_5fvalidate_2732',['help_validate',['../validate__main_8cpp.html#ab89c45aa2e33410d5c76183fd5148cff',1,'validate_main.cpp']]],
+ ['help_5fvectorize_2733',['help_vectorize',['../vectorize__main_8cpp.html#a66888bb2b18d743f2ada4c879d2999da',1,'vectorize_main.cpp']]],
+ ['help_5fversion_2734',['help_version',['../version__main_8cpp.html#a5c4af51f2cb117ca875b8b1c6be39639',1,'version_main.cpp']]],
+ ['help_5fview_2735',['help_view',['../view__main_8cpp.html#a764409d4876e90847c2d8635194f0a3e',1,'view_main.cpp']]],
+ ['help_5fviz_2736',['help_viz',['../viz__main_8cpp.html#a81fc7d050b03830c81c731e0ceb98bd1',1,'viz_main.cpp']]],
+ ['help_5fzipcode_2737',['help_zipcode',['../zipcode__main_8cpp.html#abc97cba8ea07b911b9c5da9defcc81d8',1,'zipcode_main.cpp']]],
+ ['here_2738',['here',['../structvg_1_1Range.html#a518913f6703568c7e704a2723d81e483',1,'vg::Range']]],
+ ['het_5fadjustment_2739',['HET_ADJUSTMENT',['../classvg_1_1Recombinator.html#acfb904a0f73882a7d9140efe4e78108e',1,'vg::Recombinator::HET_ADJUSTMENT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a652df2520fd051ebb03fd8494a6e0b11',1,'vg::Recombinator::Parameters::het_adjustment()']]],
+ ['het_5fprior_5flogprob_2740',['het_prior_logprob',['../classvg_1_1Genotyper.html#a21799af8d6da86a3bbcfffb1060d27cf',1,'vg::Genotyper']]],
+ ['heterozygous_2741',['heterozygous',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa3f649a400509ec3cc8b778d14ce2dd26',1,'vg::Recombinator']]],
+ ['heterozygous_5fprior_5fln_2742',['heterozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ac5782c89f874dd212631d6451ef4b842',1,'vg::FixedGenotypePriorCalculator']]],
+ ['hex2bin_2743',['hex2bin',['../bin2ascii_8h.html#a63db266c863090d6b7c179df1ea160f1',1,'bin2ascii.h']]],
+ ['hfile_5fbackend_2744',['hFILE_backend',['../structhFILE__backend.html',1,'']]],
+ ['hfile_5fcppstream_2745',['hFILE_cppstream',['../structvg_1_1io_1_1hFILE__cppstream.html',1,'vg::io']]],
+ ['hfile_5fcppstream_2ecpp_2746',['hfile_cppstream.cpp',['../hfile__cppstream_8cpp.html',1,'']]],
+ ['hfile_5fcppstream_2ehpp_2747',['hfile_cppstream.hpp',['../hfile__cppstream_8hpp.html',1,'']]],
+ ['hfile_5finit_2748',['hfile_init',['../hfile__internal_8hpp.html#abf020a8f3a695c1848cb3671855383b8',1,'hfile_internal.hpp']]],
+ ['hfile_5finternal_2ehpp_2749',['hfile_internal.hpp',['../hfile__internal_8hpp.html',1,'']]],
+ ['hfile_5fwrap_2750',['hfile_wrap',['../namespacevg_1_1io.html#a62b10a042ea08faa5da35ff07183d49b',1,'vg::io::hfile_wrap(std::istream &input)'],['../namespacevg_1_1io.html#a4fa9b57a79b55cf4eeb10806be649ede',1,'vg::io::hfile_wrap(std::ostream &output)']]],
+ ['hint_5fpaths_2751',['hint_paths',['../classvg_1_1CactusSnarlFinder.html#a380a95f5119b76793da6ba19320a1750',1,'vg::CactusSnarlFinder']]],
+ ['hit_5fcap_2752',['hit_cap',['../classvg_1_1MinimizerMapper.html#a1097206776713f059fca80f221b8478c',1,'vg::MinimizerMapper']]],
+ ['hit_5fmax_2753',['hit_max',['../classvg_1_1BaseMapper.html#a29b8cec81cc68e9d90405c42fbc8ef64',1,'vg::BaseMapper']]],
+ ['hit_5ft_2754',['hit_t',['../classvg_1_1MEMClusterer.html#a679c48e684ac52020fb363aa946037c7',1,'vg::MEMClusterer']]],
+ ['hitedge_2755',['HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html',1,'vg::MEMClusterer::HitEdge'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#adfc12ed7c93d550e05882555d0004235',1,'vg::MEMClusterer::HitEdge::HitEdge(size_t to_idx, int32_t weight, int64_t distance)'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a16766cbf34e0ec89d8bbdcd7f9d42988',1,'vg::MEMClusterer::HitEdge::HitEdge()=default']]],
+ ['hitgraph_2756',['HitGraph',['../classvg_1_1MEMClusterer_1_1HitGraph.html',1,'vg::MEMClusterer::HitGraph'],['../classvg_1_1MEMClusterer_1_1HitGraph.html#a9895e95cdaa1b95876c79c07d29fe852',1,'vg::MEMClusterer::HitGraph::HitGraph()']]],
+ ['hitnode_2757',['HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html',1,'vg::MEMClusterer::HitNode'],['../classvg_1_1MEMClusterer_1_1HitNode.html#a3156b62ac2208fdac8d0b12475011472',1,'vg::MEMClusterer::HitNode::HitNode(const MaximalExactMatch &mem, pos_t start_pos, int32_t score)'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aaeb6e6e2bb1c2ce2cda76adce19a40d6',1,'vg::MEMClusterer::HitNode::HitNode()=default']]],
+ ['hits_2758',['hits',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aa60067efaa8910104760c8d910471a29',1,'vg::MinimizerMapper::Minimizer']]],
+ ['holder_2759',['Holder',['../structvg_1_1subcommand_1_1RangeArgSpec.html#ad4fcbe28c637e8a88821368d02ec7621',1,'vg::subcommand::RangeArgSpec::Holder()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ad6398c9b83de015bcad49cf70c0e572f',1,'vg::subcommand::FlagArgSpec::Holder()']]],
+ ['homozygous_5fprior_5fln_2760',['homozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ade32a0216586eb9467d476e2880c188b',1,'vg::FixedGenotypePriorCalculator']]],
+ ['hts_5falignment_5femitter_2ecpp_2761',['hts_alignment_emitter.cpp',['../hts__alignment__emitter_8cpp.html',1,'']]],
+ ['hts_5falignment_5femitter_2ehpp_2762',['hts_alignment_emitter.hpp',['../hts__alignment__emitter_8hpp.html',1,'']]],
+ ['hts_5ffile_5fheader_2763',['hts_file_header',['../namespacevg.html#a0676eec9e08d9589fe286cabdd16ffb3',1,'vg']]],
+ ['hts_5ffor_5feach_2764',['hts_for_each',['../namespacevg.html#a1f1e53242cb6ccf3d567c73c0895c4ca',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#ad7abb14966c1c20cff85c5744a47de0e',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda)']]],
+ ['hts_5ffor_5feach_5fparallel_2765',['hts_for_each_parallel',['../namespacevg.html#a7c0d37c85747f2bce6ba3356a813524a',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#a59c6c494c2e7663fb14e40c978b4f9e5',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda)']]],
+ ['hts_5fmode_2766',['hts_mode',['../classvg_1_1HTSWriter.html#ab2151e3837dd1503111bf7d1daa1fa56',1,'vg::HTSWriter']]],
+ ['hts_5fstring_5fheader_2767',['hts_string_header',['../namespacevg.html#abc01af3a6e386a06a2971c17a0e6d1b1',1,'vg::hts_string_header(string &header, const map< string, int64_t > &path_length, const map< string, string > &rg_sample)'],['../namespacevg.html#aeb8cd62602cb90541b2270a79aed7595',1,'vg::hts_string_header(string &header, const vector< pair< string, int64_t >> &path_order_and_length, const map< string, string > &rg_sample)']]],
+ ['htsalignmentemitter_2768',['HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html',1,'vg::HTSAlignmentEmitter'],['../classvg_1_1HTSAlignmentEmitter.html#acc9b5714c55e4b644216066eda386dbd',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSAlignmentEmitter.html#a0c76946bf064ecac88e21a2467ea2410',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a780156f43d54cf16906948ad8286c20f',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(HTSAlignmentEmitter &&other)=delete']]],
+ ['htslib_5fheaders_2769',['HTSLIB_HEADERS',['../classvg_1_1Version.html#a73127428a2f929f7e52e2a1e811cf688',1,'vg::Version']]],
+ ['htslib_5flibrary_2770',['HTSLIB_LIBRARY',['../classvg_1_1Version.html#a75639877908fb90dcd272674544f3c4e',1,'vg::Version']]],
+ ['htswriter_2771',['HTSWriter',['../classvg_1_1HTSWriter.html',1,'vg::HTSWriter'],['../classvg_1_1HTSWriter.html#a8257b1e35ac5abf92b43b8a823c66aa5',1,'vg::HTSWriter::HTSWriter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSWriter.html#ae2fc6b2a60e3bc9441956faf87ff6a07',1,'vg::HTSWriter::HTSWriter(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a0a23221d8449a4b4e0b1278995ad0207',1,'vg::HTSWriter::HTSWriter(HTSWriter &&other)=delete']]],
+ ['internal_2772',['internal',['../namespacehandlegraph_1_1algorithms_1_1internal.html',1,'handlegraph::algorithms']]]
];
diff --git a/search/all_9.js b/search/all_9.js
index 2cd0eba078..7fba31eb35 100644
--- a/search/all_9.js
+++ b/search/all_9.js
@@ -1,294 +1,294 @@
var searchData=
[
- ['i_2771',['I',['../structhaplo_1_1haplo__DP__rectangle.html#ad961ad4ab25e6d0358b58dc44b3c0319',1,'haplo::haplo_DP_rectangle']]],
- ['id_2772',['id',['../structvg_1_1RecombinatorHaplotype.html#a6b099beac53df44fd9ec1d2c88aa8303',1,'vg::RecombinatorHaplotype::id()'],['../structReferenceInterval.html#a197a86ed0f4a316bd59ea19ba28bee0a',1,'ReferenceInterval::id()'],['../structvg_1_1Node.html#af886497fd0ba196f651b5d8f9678b52d',1,'vg::Node::id()'],['../namespacevg.html#a9f6602b7e7a46c19819c8f362147b315',1,'vg::id()'],['../namespacexg.html#a7bfa373a28253072de64785adc9b1188',1,'xg::id()']]],
- ['id_5finterval_2773',['id_interval',['../classvg_1_1HaplotypeIndexer.html#af71885cc768549e78097e76e77e90ea8',1,'vg::HaplotypeIndexer']]],
- ['id_5fmap_2774',['id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a22e20a6a984b3dd5def4ad22836b15b9',1,'vg::algorithms::GFAParser']]],
- ['id_5forder_2775',['id_order',['../namespacevg_1_1algorithms.html#a54730e9452c2609633da201ba85a8bca',1,'vg::algorithms']]],
- ['id_5frank_5fmap_2776',['id_rank_map',['../classvg_1_1Viz.html#a5caef0a1bce287d9a5012d36fc1de043',1,'vg::Viz']]],
- ['id_5fsort_2777',['id_sort',['../classvg_1_1VG.html#ab1aecdffe7759a1e14248e00f2866b84',1,'vg::VG']]],
- ['id_5fsort_2ecpp_2778',['id_sort.cpp',['../id__sort_8cpp.html',1,'']]],
- ['id_5fsort_2ehpp_2779',['id_sort.hpp',['../id__sort_8hpp.html',1,'']]],
- ['id_5ft_2780',['id_t',['../namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821',1,'vg::id_t()'],['../namespacehandlegraph.html#a9d001e7b9d625e6b4ef53430e6a0c180',1,'handlegraph::id_t()']]],
- ['id_5fto_5fedge_5findices_2781',['id_to_edge_indices',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75ad6266609d35ec42e64abb2a29c7c8',1,'vg::IndexedVG::CacheEntry']]],
- ['id_5fto_5findex_2782',['id_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a1bef2cbc66c4d3d005cab5f79d5cf76e',1,'vg::subcommand::OptionGroup']]],
- ['id_5fto_5fname_2783',['id_to_name',['../classvg_1_1Paths.html#a75a67b0c836eb9a21ae0eee3a213d62c',1,'vg::Paths::id_to_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a0ef46eac291cd354dc89e90d31e87777',1,'vg::algorithms::GFAIDMapInfo::id_to_name()']]],
- ['id_5fto_5fnode_5findex_2784',['id_to_node_index',['../structvg_1_1IndexedVG_1_1CacheEntry.html#aa83d17938b7e420d9c592707721eed35',1,'vg::IndexedVG::CacheEntry']]],
- ['id_5fto_5fprefix_2785',['id_to_prefix',['../classvg_1_1StreamIndexBase.html#a4b0e44b8cb40b33c5ef4db47a8a89272',1,'vg::StreamIndexBase']]],
- ['id_5fto_5frank_2786',['id_to_rank',['../classVectorizer.html#aae03497d2de713a68c6d453d32f9cf4a',1,'Vectorizer::id_to_rank()'],['../classvg_1_1Viz.html#a2474cd8505ed561cd414648438fedb5e',1,'vg::Viz::id_to_rank()'],['../classxg_1_1XG.html#a39172dc94153da745dd765f3c45ceeea',1,'xg::XG::id_to_rank()'],['../classhandlegraph_1_1RankedHandleGraph.html#a4c919e31efff422d9a29fa264290836c',1,'handlegraph::RankedHandleGraph::id_to_rank()']]],
- ['identifier_2787',['identifier',['../classvg_1_1IndexFile.html#a0b5a76c50d22d7325f10fa7b881338b9',1,'vg::IndexFile']]],
- ['identify_5faligned_5fsplice_5fcandidates_2788',['identify_aligned_splice_candidates',['../classvg_1_1MultipathMapper.html#aa97ce2f7dcd38916169b78483b7c21ec',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< multipath_alignment_t > &multipath_alns, const vector< size_t > &cluster_idxs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const'],['../classvg_1_1MultipathMapper.html#a63fc3e0fac9b46faf4c28fe47c88c784',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool read_1, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, const vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const']]],
- ['identify_5fpinning_5fpoints_2789',['identify_pinning_points',['../classvg_1_1GSSWAligner.html#a4cd705824a3926a510fea64f883cab66',1,'vg::GSSWAligner']]],
- ['identify_5fsources_5fand_5fsinks_2790',['identify_sources_and_sinks',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aff810bb5affe3201fccf437be3290fde',1,'vg::MEMClusterer::HitGraph']]],
- ['identify_5fstart_5fsubpaths_2791',['identify_start_subpaths',['../namespacevg.html#a0844cc3c2da56dfed0e9436d7f0dd7de',1,'vg']]],
- ['identify_5funaligned_5fsplice_5fcandidates_2792',['identify_unaligned_splice_candidates',['../classvg_1_1MultipathMapper.html#a50f4e1e71c3fb6272009297f1e012493',1,'vg::MultipathMapper']]],
- ['identity_2793',['identity',['../structvg_1_1Alignment.html#a06341663199b9893a9f2b288a768cfe3',1,'vg::Alignment::identity()'],['../namespacevg.html#ab3c5c7a407962a8c735c1d533cc0b186',1,'vg::identity()']]],
- ['identity_5foverlay_2ecpp_2794',['identity_overlay.cpp',['../identity__overlay_8cpp.html',1,'']]],
- ['identity_5foverlay_2ehpp_2795',['identity_overlay.hpp',['../identity__overlay_8hpp.html',1,'']]],
- ['identity_5ftranslation_2796',['identity_translation',['../classvg_1_1VG.html#ab015755dc8b427f4e226f920eb26c428',1,'vg::VG']]],
- ['identity_5fweight_2797',['identity_weight',['../classvg_1_1Mapper.html#aabc9f9048a56b9b52fdf8d5271f7f60d',1,'vg::Mapper']]],
- ['identityoverlay_2798',['IdentityOverlay',['../classvg_1_1IdentityOverlay.html',1,'vg::IdentityOverlay'],['../classvg_1_1IdentityOverlay.html#ab287d9dd0b6b6c0832dc725a2cdb6740',1,'vg::IdentityOverlay::IdentityOverlay(const HandleGraph *graph)'],['../classvg_1_1IdentityOverlay.html#a8a699d8689c9d93e72a7e78023cc3413',1,'vg::IdentityOverlay::IdentityOverlay()=default']]],
- ['ids_5fmain_2ecpp_2799',['ids_main.cpp',['../ids__main_8cpp.html',1,'']]],
- ['idscanner_2800',['IDScanner',['../structvg_1_1IDScanner.html',1,'vg']]],
- ['ignore_5fmissing_5fcontigs_2801',['ignore_missing_contigs',['../classvg_1_1VariantAdder.html#a7a8bd35e29cbd240fd0f2a7156630943',1,'vg::VariantAdder']]],
- ['image_5fheight_2802',['image_height',['../classvg_1_1Viz.html#ab34e44856e2c4d64ddf4d11aac46e5f6',1,'vg::Viz']]],
- ['image_5fwidth_2803',['image_width',['../classvg_1_1Viz.html#a5dfce1ae146aff9f2aead08e304833bd',1,'vg::Viz']]],
- ['immutable_5fpath_5ffrom_5flength_2804',['immutable_path_from_length',['../classvg_1_1MinimizerMapper.html#ab3008803e2ce57d5bbcd6a077f9dcde6',1,'vg::MinimizerMapper']]],
- ['immutablepath_2805',['ImmutablePath',['../classvg_1_1MinimizerMapper.html#af12f40d8ae25f153fba1dc122fda29f0',1,'vg::MinimizerMapper']]],
- ['imperfect_5fpairs_5fto_5fretry_2806',['imperfect_pairs_to_retry',['../classvg_1_1Mapper.html#a05444e0f52bddbe50304289a34d0b551',1,'vg::Mapper']]],
- ['in_2807',['in',['../classvg_1_1GFFReader.html#a349dc0d2a38d966c4c4c265ac056346f',1,'vg::GFFReader']]],
- ['in_5ffrom_2808',['in_from',['../classvg_1_1ExtraNodeGraph.html#a4b2d9d6b68d55c26d367ad717b13da15',1,'vg::ExtraNodeGraph']]],
- ['in_5fnontrivial_5fchain_2809',['in_nontrivial_chain',['../classvg_1_1SnarlManager.html#a92c63ede9881ce261258540ceb40fddb',1,'vg::SnarlManager']]],
- ['in_5fplace_5fsubvector_2810',['in_place_subvector',['../namespacevg.html#a62239efefb85e451fcec6519644186d1',1,'vg']]],
- ['in_5fuse_2811',['in_use',['../structvg_1_1GBWTHandler.html#a1fb3dbca40a78ec37d8e04eef008bd70',1,'vg::GBWTHandler::in_use()'],['../structGraphHandler.html#a44741d974047430e73a3589c74659939',1,'GraphHandler::in_use()']]],
- ['include_2812',['include',['../classvg_1_1VG.html#a66e4dac76edcf0218f9749352c19acae',1,'vg::VG']]],
- ['include_5fchildren_2813',['include_children',['../classvg_1_1SparseUnionFind.html#acf3b218b8e2fee9fa73df6d4071eb0da',1,'vg::SparseUnionFind']]],
- ['include_5fendpoints_2814',['include_endpoints',['../classvg_1_1VCFTraversalFinder.html#a27189437955d4b5f8b8ca92433c8fac2',1,'vg::VCFTraversalFinder']]],
- ['include_5ffull_5flength_5fbonuses_2815',['include_full_length_bonuses',['../classvg_1_1Mapper.html#a9472c75cceb3382b70bbd27bfbc4a894',1,'vg::Mapper']]],
- ['include_5fnamed_5fpaths_2816',['include_named_paths',['../structGBWTConfig.html#aedd88b893790abdf53541629fdfdbcd0',1,'GBWTConfig']]],
- ['include_5fnested_2817',['include_nested',['../classvg_1_1VCFOutputCaller.html#afb5fc9a52eb170a49d6f77aad30e13f7',1,'vg::VCFOutputCaller']]],
- ['include_5freference_2818',['include_reference',['../structvg_1_1Recombinator_1_1Parameters.html#a0f3128635c9d1c82a996e4ae060b0072',1,'vg::Recombinator::Parameters']]],
- ['include_5freversing_5ftraversals_2819',['include_reversing_traversals',['../classvg_1_1ExhaustiveTraversalFinder.html#a1904edecc299fc004b02ce44ea9301f8',1,'vg::ExhaustiveTraversalFinder']]],
- ['inclusive_5finterval_2820',['inclusive_interval',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af66a44ac51fe4a01ce0b24e0490b657b',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['incorrectly_5fmapped_2821',['incorrectly_mapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac1473f460d502f5988365b86acaa27ea',1,'vg::Counts']]],
- ['increment_5fcoverage_2822',['increment_coverage',['../classvg_1_1Packer.html#ab97f6f0bb52c3641aceb5ffe4359492d',1,'vg::Packer::increment_coverage(size_t i)'],['../classvg_1_1Packer.html#a4da9199584ad1279a1e0a54aea12c6c1',1,'vg::Packer::increment_coverage(size_t i, size_t v)']]],
- ['increment_5fedge_5fcoverage_2823',['increment_edge_coverage',['../classvg_1_1Packer.html#a7e2313be4468ea83a3e8b6a75b00cd7c',1,'vg::Packer::increment_edge_coverage(size_t i)'],['../classvg_1_1Packer.html#abdc73870b8a141908a21eb7ff7c31d4f',1,'vg::Packer::increment_edge_coverage(size_t i, size_t v)']]],
- ['increment_5fnode_5fids_2824',['increment_node_ids',['../classvg_1_1Paths.html#a8a9b275a5979218a784105364248b5ba',1,'vg::Paths::increment_node_ids()'],['../classvg_1_1VG.html#a86b3ecdf29d100a8d43f6aaccd6f2e0e',1,'vg::VG::increment_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a902b211a1f86645818b3da1cb64af0be',1,'handlegraph::MutableHandleGraph::increment_node_ids(nid_t increment)'],['../classhandlegraph_1_1MutableHandleGraph.html#a877dc8c0ae9a584907d45328512720cc',1,'handlegraph::MutableHandleGraph::increment_node_ids(long increment)']]],
- ['increment_5fnode_5fmapping_5fids_2825',['increment_node_mapping_ids',['../namespacevg.html#a9fa6175557c33cd572b8726222cf6547',1,'vg']]],
- ['increment_5fnode_5fquality_2826',['increment_node_quality',['../classvg_1_1Packer.html#a0195e9186f8162fc4fab673fbd65b0a8',1,'vg::Packer']]],
- ['increment_5fprogress_2827',['increment_progress',['../classvg_1_1Progressive.html#ab1de11917caf25974a02e2f5c3946280',1,'vg::Progressive']]],
- ['incremental_5fextend_2828',['incremental_extend',['../classhaplo_1_1ScoreProvider.html#a834b5b57b025ae27cc2c668869ee9b13',1,'haplo::ScoreProvider::incremental_extend()'],['../classhaplo_1_1GBWTScoreProvider.html#af52bee39ffe97d84ba020c49f7fbf7a6',1,'haplo::GBWTScoreProvider::incremental_extend()']]],
- ['incremental_5ffind_2829',['incremental_find',['../classhaplo_1_1ScoreProvider.html#a6272d9bca95e7846807ef2e71d616a9c',1,'haplo::ScoreProvider::incremental_find()'],['../classhaplo_1_1GBWTScoreProvider.html#a540105f41d66c4b536fda44fce248680',1,'haplo::GBWTScoreProvider::incremental_find()']]],
- ['incremental_5fsubgraph_2ecpp_2830',['incremental_subgraph.cpp',['../incremental__subgraph_8cpp.html',1,'']]],
- ['incremental_5fsubgraph_2ehpp_2831',['incremental_subgraph.hpp',['../incremental__subgraph_8hpp.html',1,'']]],
- ['incrementalsearchstate_2832',['IncrementalSearchState',['../namespacehaplo.html#ae3347fe51140216cb836936c306c97bf',1,'haplo']]],
- ['incrementalsubgraph_2833',['IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html',1,'vg::IncrementalSubgraph'],['../classvg_1_1IncrementalSubgraph.html#ab942f4d62b91144afce73896b8004609',1,'vg::IncrementalSubgraph::IncrementalSubgraph(const HandleGraph &graph, const pos_t &starting_position, bool extract_left, int64_t max_distance=numeric_limits< int64_t >::max(), size_t frontier_copy_limit=numeric_limits< size_t >::max(), size_t max_num_nodes=numeric_limits< size_t >::max())'],['../classvg_1_1IncrementalSubgraph.html#a4c8f5a87dfcf68630d645a9469e75837',1,'vg::IncrementalSubgraph::IncrementalSubgraph()=default']]],
- ['incrementiter_2834',['IncrementIter',['../structvg_1_1IncrementIter.html',1,'vg::IncrementIter'],['../structvg_1_1IncrementIter.html#a1231b6b6c0fde0c7ae6cf69b9cfe9a6b',1,'vg::IncrementIter::IncrementIter()']]],
- ['indel_5ferror_5fprop_2835',['indel_error_prop',['../classvg_1_1NGSSimulator.html#ae16494345e539020ebd09b0998500559',1,'vg::NGSSimulator']]],
- ['indel_5fpoly_5frate_2836',['indel_poly_rate',['../classvg_1_1NGSSimulator.html#af84310145f8991c92d48684a0664ba8e',1,'vg::NGSSimulator']]],
- ['index_2837',['index',['../structhaplo_1_1linear__haplo__structure.html#a79e51544898895192d319f95e95cf2f1',1,'haplo::linear_haplo_structure::index()'],['../classhaplo_1_1GBWTScoreProvider.html#ae24f0ba2be7fdc64cb0d0a33123e41ad',1,'haplo::GBWTScoreProvider::index()'],['../classhaplo_1_1LinearScoreProvider.html#a1ceb289752fb8e83c13e52e82bea393b',1,'haplo::LinearScoreProvider::index()'],['../classvg_1_1IndexedVG.html#a4f618ecb46d596aa053450a4de13e990',1,'vg::IndexedVG::index()'],['../classvg_1_1StreamIndex.html#a8ee1930510b5d02e9a00ba1a246ba146',1,'vg::StreamIndex::index()']]],
- ['index_5fcompressed_2838',['index_compressed',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a8733ef08a80d49962c42b2f3286f9dff',1,'vg::GBWTHandler']]],
- ['index_5fdynamic_2839',['index_dynamic',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a79071bcf44e60960f566a4fe9590d63d',1,'vg::GBWTHandler']]],
- ['index_5fedge_5fby_5fnode_5fsides_2840',['index_edge_by_node_sides',['../classvg_1_1VG.html#a53ff7033966852f5fb3852716cab21a9',1,'vg::VG']]],
- ['index_5fmain_2ecpp_2841',['index_main.cpp',['../index__main_8cpp.html',1,'']]],
- ['index_5fnode_5fto_5fpath_2842',['index_node_to_path',['../classxg_1_1XG.html#a4599310a72acd2ccfbe9d6041cc51dd1',1,'xg::XG']]],
- ['index_5fnone_2843',['index_none',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a1dc536bf1ea474d215a9a7e0c7663924',1,'vg::GBWTHandler']]],
- ['index_5fof_2844',['index_of',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a622e1fefb7e7aa8977623b183ea9b457',1,'vg::DozeuInterface::OrderedGraph']]],
- ['index_5fpath_5fnames_2845',['index_path_names',['../classxg_1_1XG.html#aff97dc01cda8460ebeb98a4b789e3485',1,'xg::XG']]],
- ['index_5fregistry_2846',['index_registry',['../classvg_1_1IndexRegistry.html#a866b81f28ca2fba68aff7de143f35b9b',1,'vg::IndexRegistry']]],
- ['index_5fregistry_2ecpp_2847',['index_registry.cpp',['../index__registry_8cpp.html',1,'']]],
- ['index_5fregistry_2ehpp_2848',['index_registry.hpp',['../index__registry_8hpp.html',1,'']]],
- ['index_5fto_5fnode_2849',['index_to_node',['../classvg_1_1Packer.html#a967dcbe2cbcb6df4c7e2d938f7cd11fa',1,'vg::Packer']]],
- ['index_5ftype_2850',['index_type',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033',1,'vg::GBWTHandler']]],
- ['indexed_5fvg_2ecpp_2851',['indexed_vg.cpp',['../indexed__vg_8cpp.html',1,'']]],
- ['indexed_5fvg_2ehpp_2852',['indexed_vg.hpp',['../indexed__vg_8hpp.html',1,'']]],
- ['indexedvg_2853',['IndexedVG',['../classvg_1_1IndexedVG.html',1,'vg::IndexedVG'],['../classvg_1_1IndexedVG.html#a89030b52047b0e005a5c86b7f9a206f6',1,'vg::IndexedVG::IndexedVG(string graph_filename)'],['../classvg_1_1IndexedVG.html#a0972bd3bf8d93bfa8b41aff828aab070',1,'vg::IndexedVG::IndexedVG(const IndexedVG &other)=delete']]],
- ['indexes_2854',['indexes',['../classvg_1_1GraphSynchronizer.html#a1127fed39b1d4775bf03ada4f87b23b4',1,'vg::GraphSynchronizer::indexes()'],['../classvg_1_1RewindPlanException.html#abf38371b59f5d1ebc55806967bc3b12b',1,'vg::RewindPlanException::indexes()'],['../structvg_1_1VectorView.html#a54433c9bb742729c00a4d48adaa88015',1,'vg::VectorView::indexes()']]],
- ['indexfile_2855',['IndexFile',['../classvg_1_1IndexFile.html',1,'vg::IndexFile'],['../classvg_1_1IndexFile.html#ae22fd6ea5fd4419ca8ed2070410638ca',1,'vg::IndexFile::IndexFile()']]],
- ['indexgroup_2856',['IndexGroup',['../namespacevg.html#a96bc10f0ba77bc672e88a9f7d6e126b6',1,'vg']]],
- ['indexingparameters_2857',['IndexingParameters',['../structvg_1_1IndexingParameters.html',1,'vg']]],
- ['indexingplan_2858',['IndexingPlan',['../classvg_1_1IndexingPlan.html',1,'vg::IndexingPlan'],['../classvg_1_1IndexRegistry.html#a490f2f891225b54cb14e32d593f30f5c',1,'vg::IndexRegistry::IndexingPlan()'],['../classvg_1_1IndexingPlan.html#a5e6231a7a515964589ea8e55e8e2d5fe',1,'vg::IndexingPlan::IndexingPlan()']]],
- ['indexname_2859',['IndexName',['../namespacevg.html#a7027e98a84fa4b0fa42f72bf4a1d862f',1,'vg']]],
- ['indexrecipe_2860',['IndexRecipe',['../structvg_1_1IndexRecipe.html',1,'vg::IndexRecipe'],['../structvg_1_1IndexRecipe.html#a11948f5026c5aff21e22775446e419b6',1,'vg::IndexRecipe::IndexRecipe()']]],
- ['indexregistry_2861',['IndexRegistry',['../classvg_1_1IndexRegistry.html',1,'vg::IndexRegistry'],['../classvg_1_1IndexingPlan.html#a77ea72c93e5f6c8a5e65279ae52aec32',1,'vg::IndexingPlan::IndexRegistry()'],['../classvg_1_1IndexRegistry.html#a0a0debbd6d61db053403e7cbca69d4c2',1,'vg::IndexRegistry::IndexRegistry()=default'],['../classvg_1_1IndexRegistry.html#aec3008292713502924fcf3cc51253e4f',1,'vg::IndexRegistry::IndexRegistry(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#aa4f9837b4beb749a06b3dcb3150475b0',1,'vg::IndexRegistry::IndexRegistry(IndexRegistry &&other)']]],
- ['init_2862',['init',['../classvg_1_1SpliceStats.html#afd5923a5cd636a140697cad2605fc415',1,'vg::SpliceStats::init()'],['../classvg_1_1VG.html#aafd0f191fe33bd4590f15f309d0fd89c',1,'vg::VG::init()'],['../classvg_1_1Viz.html#aad7ceb7896288f2d4444b10cceb946d8',1,'vg::Viz::init()']]],
- ['init_5fcoverage_5fbin_2863',['init_coverage_bin',['../classvg_1_1Packer.html#abdd9bd13b38dced4c61d78e5baf3c0fb',1,'vg::Packer']]],
- ['init_5fedge_5fcoverage_5fbin_2864',['init_edge_coverage_bin',['../classvg_1_1Packer.html#a693598b3d8227598075e02fbc8124789',1,'vg::Packer']]],
- ['init_5fmapper_2865',['init_mapper',['../classvg_1_1Filter.html#abd9fa5045b867b20e1b20e3d74d77e4b',1,'vg::Filter']]],
- ['init_5fnode_5fquality_5fbin_2866',['init_node_quality_bin',['../classvg_1_1Packer.html#aff44bf5abf4eacda46958eeb436eb2e4',1,'vg::Packer']]],
- ['init_5fsnarls_2867',['init_snarls',['../classvg_1_1Masker.html#a28b4317d6319672c9b9fa02b0e515335',1,'vg::Masker']]],
- ['init_5fstate_2868',['init_state',['../classvg_1_1DinucleotideMachine.html#a35193673a88abc7f0933d2f65fd7f2ea',1,'vg::DinucleotideMachine']]],
- ['init_5ftraceback_5findexes_2869',['init_traceback_indexes',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ab251d4ff6f6b7f351f29c5dd29ead002',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['initial_5fposition_2870',['initial_position',['../namespacevg.html#acd31d3a8dc67801f147d0ba1b0059c3f',1,'vg::initial_position(const Path &path)'],['../namespacevg.html#a5273bbd5e5d0f9bbf639c19c962a58dd',1,'vg::initial_position(const path_t &path)']]],
- ['initialize_5fsam_5ffile_2871',['initialize_sam_file',['../classvg_1_1HTSWriter.html#a3063999c0e6b467c7717edfb53040166',1,'vg::HTSWriter']]],
- ['inject_5fmain_2ecpp_2872',['inject_main.cpp',['../inject__main_8cpp.html',1,'']]],
- ['inline_5fitems_2873',['inline_items',['../structvg_1_1MatchPos_1_1PathList.html#abffe04434a41c9f8dfcb85ef8d3d26f9',1,'vg::MatchPos::PathList']]],
- ['inner_5fvalue_2874',['inner_value',['../structhaplo_1_1haplo__DP__rectangle.html#a68817623682eb451f4a5a42a8ae8ef8a',1,'haplo::haplo_DP_rectangle']]],
- ['input_2875',['input',['../structvg_1_1io_1_1hFILE__cppstream.html#a301bcdddd00f4d40033b4ca94691f9a6',1,'vg::io::hFILE_cppstream']]],
- ['input_5fdefault_2876',['INPUT_DEFAULT',['../convert__main_8cpp.html#a9427417f4ca764d74efec8fcaf9e2ca8',1,'convert_main.cpp']]],
- ['input_5ffilenames_2877',['input_filenames',['../structGBWTConfig.html#a106dff4206c7414bf053f9c2405a0739',1,'GBWTConfig']]],
- ['input_5fgaf_2878',['input_gaf',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa68ce48b22e2cb1ea6edb3f351cff52ed',1,'convert_main.cpp']]],
- ['input_5fgam_2879',['input_gam',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaa45b4c6e90a30a90deb1183ec3b127a6',1,'convert_main.cpp']]],
- ['input_5fgbwtgraph_2880',['input_gbwtgraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa2cdb682495850f7e3a5dea532a556eb2',1,'convert_main.cpp']]],
- ['input_5fgfa_2881',['input_gfa',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaf3349e3c8dbf0909922809cb8776aebd',1,'convert_main.cpp']]],
- ['input_5fgroup_2882',['input_group',['../structvg_1_1IndexRecipe.html#aa22beac92907ecf99b821ee6bfed4e33',1,'vg::IndexRecipe']]],
- ['input_5fhandlegraph_2883',['input_handlegraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa6c28171b952beaf1784c655853a0e66c',1,'convert_main.cpp']]],
- ['input_5fin_5fprogress_2884',['input_in_progress',['../classvg_1_1Funnel.html#a755941e4c7988487e539256c16b507bb',1,'vg::Funnel']]],
- ['input_5ftype_2885',['input_type',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8ef',1,'convert_main.cpp']]],
- ['input_5fvcf_2886',['input_vcf',['../classvg_1_1VCFGenotyper.html#a3fea7ea6e20998a5de5e95776e7f67bb',1,'vg::VCFGenotyper']]],
- ['inputs_2887',['inputs',['../structvg_1_1IndexRecipe.html#aa23088153a85cc207ab3901afcd1ff5b',1,'vg::IndexRecipe::inputs()'],['../classvg_1_1InsufficientInputException.html#a8798c889fb558ee1c9042e10e7f136e2',1,'vg::InsufficientInputException::inputs()']]],
- ['inputs_5fas_5fjobs_2888',['inputs_as_jobs',['../structGBWTConfig.html#ac12bbd2e3c10bdaf3ee07de4191c88d6',1,'GBWTConfig']]],
- ['inputstream_2889',['inputStream',['../namespacevg_1_1io.html#a857cf3810d138ef43e25aa37f147ac25',1,'vg::io']]],
- ['ins_2890',['INS',['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): xdrop_aligner.cpp']]],
- ['ins_5fpredecessor_2891',['ins_predecessor',['../classvg_1_1WFATree.html#a8ab38ec2797b5119eb9ffd213bdb957e',1,'vg::WFATree']]],
- ['insert_2892',['insert',['../classvg_1_1SnarlState.html#a428e616c3ef0bab94325edbd728819e3',1,'vg::SnarlState::insert(const vector< pair< handle_t, size_t >> &haplotype)'],['../classvg_1_1SnarlState.html#a8489b6496d77d037d0ee2f0367119a3a',1,'vg::SnarlState::insert(size_t overall_lane, const vector< handle_t > &haplotype, bool backward=false)'],['../classvg_1_1HandleGraphNodeSet.html#a2c8d82e307853b75c099422d8e5e717c',1,'vg::HandleGraphNodeSet::insert()'],['../structvg_1_1RecombinatorHaplotype.html#a370a97d18bca8d1448eb359eee91be6e',1,'vg::RecombinatorHaplotype::insert()'],['../classvg_1_1SmallBitset.html#a9336d107ad4a8f98005ecfcf313e1334',1,'vg::SmallBitset::insert()'],['../classvg_1_1BitStringTree.html#ac323a5f006f9ad739facc0f306b1b6ed',1,'vg::BitStringTree::insert()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#a1658df8b5e184e15cce3b5e70bc2769c',1,'vg::BitStringTree::TreeNode::insert()'],['../structjob__type.html#a28737e853741fb1798c718e3637070b0',1,'job_type::insert()']]],
- ['insert_5fcol_2893',['insert_col',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a9a17e99af8ce2b7992fddef79c4e8b18',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['insert_5fgbwt_5fpath_2894',['insert_gbwt_path',['../namespacevg.html#a9bf4a7dd2a81bb5b873127156a2dfb33',1,'vg']]],
- ['insert_5fhandles_2895',['insert_handles',['../classvg_1_1GenomeState.html#aa85289ade641db44976ac969c5fb6750',1,'vg::GenomeState']]],
- ['insert_5fhaplotype_2896',['insert_haplotype',['../classvg_1_1GenomeState.html#a371e13f6d644e9979fa0e5177ffaadba',1,'vg::GenomeState']]],
- ['insert_5fleft_2897',['insert_left',['../classvg_1_1PhasedGenome.html#a02e624546cf3f5675fbfa128c080c75d',1,'vg::PhasedGenome']]],
- ['insert_5fmapping_2898',['insert_mapping',['../classvg_1_1Paths.html#aa6e0eb5748713837711612e5e347f8cb',1,'vg::Paths']]],
- ['insert_5fmean_2899',['insert_mean',['../classvg_1_1Filter.html#ab8a36803dfa97e61678756f7b7a3a31c',1,'vg::Filter']]],
- ['insert_5fpath_2900',['insert_path',['../classvg_1_1PhaseUnfolder.html#a28e7cee8d0922cf0aac91dba0d86f1c3',1,'vg::PhaseUnfolder']]],
- ['insert_5fright_2901',['insert_right',['../classvg_1_1PhasedGenome.html#adfbd6242bff1445e5210f4046150fc85',1,'vg::PhasedGenome']]],
- ['insert_5frow_2902',['insert_row',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ade4c512c3713ac162359ed6d9207537d',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['insert_5fsd_2903',['insert_sd',['../classvg_1_1Filter.html#ac302d7b67d23285ad615d864197a9e1b',1,'vg::Filter']]],
- ['insert_5fsize_5ffilter_2904',['insert_size_filter',['../classvg_1_1Filter.html#a198243f4ffebc1b1442ca4521542ac99',1,'vg::Filter']]],
- ['insert_5ftraceback_2905',['insert_traceback',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#aa6db44fa8e957169e11fd1a7853d2a19',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['insertcol_2906',['InsertCol',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faa0a1ece7d481572fa684460331afbfa4',1,'vg::BandedGlobalAligner']]],
- ['inserthaplotypecommand_2907',['InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html',1,'vg']]],
- ['insertion_2908',['insertion',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebaf8105fdf086223fa49c6b63a3097a645',1,'vg::WFAAlignment']]],
- ['insertion_5fbias_5flarge_2909',['insertion_bias_large',['../classvg_1_1PoissonSupportSnarlCaller.html#a82d1c5780e74107618f3e50d7085f38e',1,'vg::PoissonSupportSnarlCaller']]],
- ['insertion_5fbias_5fsmall_2910',['insertion_bias_small',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a5120550fa398555a1a414717469664',1,'vg::PoissonSupportSnarlCaller']]],
- ['insertion_5ffilter_2911',['insertion_filter',['../classvg_1_1Filter.html#a02bb368759eef77f7f7aa3753b23469e',1,'vg::Filter']]],
- ['insertion_5fthreshold_2912',['insertion_threshold',['../classvg_1_1PoissonSupportSnarlCaller.html#a7787ef040764a33043fdbf3ba2f80509',1,'vg::PoissonSupportSnarlCaller']]],
- ['insertions_2913',['INSERTIONS',['../structvg_1_1WFANode.html#a99807b74ee148f30fae2549a8aa54339',1,'vg::WFANode::INSERTIONS()'],['../structvg_1_1InsertHaplotypeCommand.html#a5dfd52deff7c8c3fc76fa7b4dee45032',1,'vg::InsertHaplotypeCommand::insertions()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a44ad82bbfa6098c648bc1a6fcd61d102',1,'vg::ReplaceLocalHaplotypeCommand::insertions()']]],
- ['insertrow_2914',['InsertRow',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2fac7adaac601fdfa40491cb7906ca9e989',1,'vg::BandedGlobalAligner']]],
- ['insufficientinputexception_2915',['InsufficientInputException',['../classvg_1_1InsufficientInputException.html',1,'vg::InsufficientInputException'],['../classvg_1_1InsufficientInputException.html#a2361f9743d9c5f2af8bb170a6240b891',1,'vg::InsufficientInputException::InsufficientInputException()=delete'],['../classvg_1_1InsufficientInputException.html#af9014e0e82772828f66dc699e2eb8734',1,'vg::InsufficientInputException::InsufficientInputException(const IndexName &target, const IndexRegistry ®istry) noexcept']]],
- ['int_5fis_5finc_2916',['int_is_inc',['../structhaplo_1_1haplo__DP__rectangle.html#a45856786beeaa7213275fcaf3eaa6878',1,'haplo::haplo_DP_rectangle']]],
- ['int_5fis_5fnonnegative_2917',['int_is_nonnegative',['../namespacevg_1_1subcommand.html#aafa3ba89747f1886e118e7d6421078e3',1,'vg::subcommand']]],
- ['int_5fitvl_5ft_2918',['int_itvl_t',['../structhaplo_1_1int__itvl__t.html',1,'haplo']]],
- ['int_5fto_5fstring_2919',['int_to_string',['../namespacegafkluge.html#ad9c7bb306be39ddca425533a3583d71e',1,'gafkluge']]],
- ['int_5fweighted_5fsum_2920',['int_weighted_sum',['../namespacehaplo_1_1haploMath.html#a5bc2868874173d377a55c788f21796ef',1,'haplo::haploMath::int_weighted_sum(double *values, int64_t *counts, size_t n_values)'],['../namespacehaplo_1_1haploMath.html#ab17ccf8a6fa509f269bdaf1c69e4f6bc',1,'haplo::haploMath::int_weighted_sum(vector< double > values, vector< int64_t > counts)']]],
- ['integer_5fpower_2921',['integer_power',['../namespacevg.html#aca4239af1a9e3eb1283f78bf5cc1411a',1,'vg::integer_power(uint64_t base, uint64_t exponent)'],['../namespacevg.html#aa7c32d1e90ec006624a7ee03655f3c35',1,'vg::integer_power(size_t x, size_t power)']]],
- ['integrated_5fsnarl_5ffinder_2ecpp_2922',['integrated_snarl_finder.cpp',['../integrated__snarl__finder_8cpp.html',1,'']]],
- ['integrated_5fsnarl_5ffinder_2ehpp_2923',['integrated_snarl_finder.hpp',['../integrated__snarl__finder_8hpp.html',1,'']]],
- ['integratedsnarlfinder_2924',['IntegratedSnarlFinder',['../classvg_1_1IntegratedSnarlFinder.html',1,'vg::IntegratedSnarlFinder'],['../classvg_1_1IntegratedSnarlFinder.html#a888085d87664c7e58ad4f988091c62f5',1,'vg::IntegratedSnarlFinder::IntegratedSnarlFinder()']]],
- ['interchromosomal_5ffilter_2925',['interchromosomal_filter',['../classvg_1_1Filter.html#a1f1daa97b40d6ca6b2a3f37950f4f117',1,'vg::Filter']]],
- ['interleaved_2926',['interleaved',['../classvg_1_1ReadFilter.html#a3d7c97fa34473eb5b1e3bce2dd64d6eb',1,'vg::ReadFilter']]],
- ['internal_5fid_5fmap_2927',['internal_id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a5bdb46afdb654469e3dc42fdfbe048ab',1,'vg::algorithms::GFAParser']]],
- ['internal_5fscore_2928',['internal_score',['../structvg_1_1GaplessExtension.html#a0045e76ebc1c911201d6744d6c20e50a',1,'vg::GaplessExtension']]],
- ['intersect_5fpath_5foffsets_2929',['intersect_path_offsets',['../namespacevg_1_1algorithms.html#a9ce4dabb6661657c7d72593afc3f41df',1,'vg::algorithms']]],
- ['intersect_5fpath_5foffsets_2ecpp_2930',['intersect_path_offsets.cpp',['../intersect__path__offsets_8cpp.html',1,'']]],
- ['intersect_5fpath_5foffsets_2ehpp_2931',['intersect_path_offsets.hpp',['../intersect__path__offsets_8hpp.html',1,'']]],
- ['intersection_2932',['intersection',['../structhaplo_1_1int__itvl__t.html#ade4051b750fcce428be13a69663ec035',1,'haplo::int_itvl_t']]],
- ['interval_5fend_2933',['interval_end',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#af58f43315b7386134bf8a034c0c39694',1,'vg::ZipCodeForest::interval_state_t']]],
- ['interval_5flength_2934',['interval_length',['../namespacevg.html#a9467900ec651b93d47190413208cdf6f',1,'vg']]],
- ['interval_5fsize_2935',['interval_size',['../structhaplo_1_1haplo__DP__rectangle.html#a751f03ab1d68636c47340dbd376b66a8',1,'haplo::haplo_DP_rectangle']]],
- ['interval_5fstart_2936',['interval_start',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a7a2843b5a5a25b77f55ddb80998028bd',1,'vg::ZipCodeForest::interval_state_t']]],
- ['interval_5fstate_5ft_2937',['interval_state_t',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html',1,'vg::ZipCodeForest::interval_state_t'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#aa86bab20d96ef26dc66afadf5dd22195',1,'vg::ZipCodeForest::interval_state_t::interval_state_t()']]],
- ['intervals_5fto_5fprocess_2938',['intervals_to_process',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#aafe37939d028547b7ae3ee68fda10ed1',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['into_5fcutting_5fsnarl_2939',['into_cutting_snarl',['../classvg_1_1MultipathAlignmentGraph.html#a44bd7328dd8ea140223226ae4da8afff',1,'vg::MultipathAlignmentGraph']]],
- ['into_5fwhich_5fsnarl_2940',['into_which_snarl',['../classvg_1_1SnarlManager.html#ac08074e3073ecd2ef72a57116b459577',1,'vg::SnarlManager::into_which_snarl(int64_t id, bool reverse) const'],['../classvg_1_1SnarlManager.html#a852f930d4e68e9bbd664ebe5a73a4669',1,'vg::SnarlManager::into_which_snarl(const Visit &visit) const']]],
- ['introduce_2941',['introduce',['../classvg_1_1Funnel.html#adfe8a13519ae236c400f3ad68980e16c',1,'vg::Funnel']]],
- ['intron_5flength_5flog_5flikelihood_2942',['intron_length_log_likelihood',['../classvg_1_1SpliceStats.html#ad61aebd450e01500b86d1fec55b8ccd9',1,'vg::SpliceStats']]],
- ['intron_5flength_5fscore_2943',['intron_length_score',['../classvg_1_1SpliceStats.html#aedf26f015ecfb06f71aadbca66c81935',1,'vg::SpliceStats']]],
- ['invalid_2944',['invalid',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a26ab26b5bf5a066a0902a79defda6b5d',1,'haplo::linear_haplo_structure']]],
- ['inverse_2945',['inverse',['../classvg_1_1Filter.html#a05e7274611008cdd5b89d1fa81605882',1,'vg::Filter::inverse()'],['../classvg_1_1VectorViewInverse.html#a54a9cc36f21c2562f2f0836e5a040773',1,'vg::VectorViewInverse::inverse()']]],
- ['inversion_5ffilter_2946',['inversion_filter',['../classvg_1_1Filter.html#a5503147c786a4d9bfb18fc081630b5f6',1,'vg::Filter']]],
- ['invert_2947',['invert',['../structvg_1_1Counts.html#a3a4cf08069fb263d89a96b86313a04a2',1,'vg::Counts']]],
- ['invert_5ftranslation_2948',['invert_translation',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#abeffeb079b7f3997db8cfbb9a701f63c',1,'vg::algorithms::GFAIDMapInfo']]],
- ['invocations_2949',['invocations',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af75c21b33a10d3ddc7f36f7567cc1aae',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['irregular_5fsnarl_2950',['IRREGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a96d1de8b0fd352dc3449d17eab32f6f4',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fdistance_5fleft_5fend_5foffset_2951',['IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET',['../classvg_1_1ZipCode.html#a0c43ecf172f0ddde09366b3facdad4f9',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fdistance_5fleft_5fstart_5foffset_2952',['IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET',['../classvg_1_1ZipCode.html#a81836246de1e66c3febd653cd0525988',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fdistance_5fright_5fend_5foffset_2953',['IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET',['../classvg_1_1ZipCode.html#a2cccc444095b38bd7e73ff6e55f930be',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fdistance_5fright_5fstart_5foffset_2954',['IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET',['../classvg_1_1ZipCode.html#acdcb0967e1dd6d01833a7fc66f6ef64b',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5frecord_5foffset_2955',['IRREGULAR_SNARL_RECORD_OFFSET',['../classvg_1_1ZipCode.html#a8f5228bda68297b861a839396970f5bc',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fsize_2956',['IRREGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a8ec98e693ea6d5c1972479f9066ef405',1,'vg::ZipCode']]],
- ['is_5fa_5fduplicate_5fhandle_2957',['is_a_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#a3089cf35214f919d15030e029df3f6eb',1,'vg::DozeuPinningOverlay']]],
- ['is_5fa_5fduplicate_5fid_2958',['is_a_duplicate_id',['../classvg_1_1DozeuPinningOverlay.html#ab549aa4693c8425cd1df8d04a04a178f',1,'vg::DozeuPinningOverlay']]],
- ['is_5facyclic_2959',['is_acyclic',['../namespacehandlegraph_1_1algorithms.html#a03c1bfbc47b88a0bd18ca2cc93a1b0b3',1,'handlegraph::algorithms']]],
- ['is_5facyclic_2ecpp_2960',['is_acyclic.cpp',['../is__acyclic_8cpp.html',1,'']]],
- ['is_5fall_5fn_2961',['is_all_n',['../namespacevg.html#abe6f7955b97d8537da2133a47f37f462',1,'vg']]],
- ['is_5falt_2962',['is_alt',['../classvg_1_1Paths.html#a3e8fd05a0a584cbae2f2919b5ab98e4d',1,'vg::Paths']]],
- ['is_5fancestor_5fnext_2963',['is_ancestor_next',['../classvg_1_1VG.html#a7903acd7a977a85fdd78d306f2063252',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ab919097a72a96dada04310b2aaf019f8',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
- ['is_5fancestor_5fprev_2964',['is_ancestor_prev',['../classvg_1_1VG.html#a25215a67c3eac7570e2ab62e825ae169',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ae6699fe9d747f761f6efae39c3c0501c',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
- ['is_5fany_5fpainted_2965',['is_any_painted',['../structvg_1_1Funnel_1_1PaintableSpace.html#ab42e113d364cfa7da4e7b0c76ba448f1',1,'vg::Funnel::PaintableSpace']]],
- ['is_5fchain_2966',['is_chain',['../structvg_1_1ZipCode_1_1decoder__t.html#abcbad7044eb813105e2cadefbf5a05ff',1,'vg::ZipCode::decoder_t::is_chain()'],['../classhandlegraph_1_1SnarlDecomposition.html#ad383774992bf6a3acc5fd34dc8cd9770',1,'handlegraph::SnarlDecomposition::is_chain()']]],
- ['is_5fchecked_5fin_2967',['is_checked_in',['../structvg_1_1Watchdog_1_1thread__state__t.html#aae7887d9b7548a028a6b7271aabd44eb',1,'vg::Watchdog::thread_state_t']]],
- ['is_5fchild_2968',['is_child',['../classvg_1_1NetGraph.html#a25dbff454e5c9aa081c354f05523a512',1,'vg::NetGraph']]],
- ['is_5fcircular_2969',['is_circular',['../classxg_1_1XGPath.html#a4cc65b6cfdbd12f6220dde5a716fd345',1,'xg::XGPath::is_circular()'],['../structvg_1_1Path.html#ad04d3a1745f479f32b4a4358bec17c8f',1,'vg::Path::is_circular()']]],
- ['is_5fcompacted_2970',['is_compacted',['../classvg_1_1Packer.html#aa7f90bbde45e8487029a424392b653ad',1,'vg::Packer']]],
- ['is_5fconsistent_2971',['is_consistent',['../classvg_1_1MultipathMapper.html#a76742066028c14330177d74d9cd0286c',1,'vg::MultipathMapper']]],
- ['is_5fcorrect_2972',['is_correct',['../classvg_1_1Funnel.html#a4296184811926cf97a42d52aaf3fc6f6',1,'vg::Funnel']]],
- ['is_5fcorrectly_5fmapped_2973',['is_correctly_mapped',['../classvg_1_1ReadFilter.html#ac5da32515034e6669d9e14de3c748122',1,'vg::ReadFilter::is_correctly_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab76d4dc77becdaf866f724d5b88dcdb5',1,'vg::ReadFilter::is_correctly_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a053397b20bc378d11f11b365e6d68032',1,'vg::ReadFilter::is_correctly_mapped(const MultipathAlignment &alignment) const']]],
- ['is_5fdirected_5facyclic_2974',['is_directed_acyclic',['../namespacehandlegraph_1_1algorithms.html#afe81ab458644253f1064ffa3c73783a3',1,'handlegraph::algorithms']]],
- ['is_5fdynamic_2975',['is_dynamic',['../classvg_1_1Packer.html#a370e8ef56ffd369c6a498aa36ed9c570',1,'vg::Packer']]],
- ['is_5fempty_2976',['is_empty',['../structhaplo_1_1haplo__DP__column.html#af8bc221754159aa83d44d9373359939c',1,'haplo::haplo_DP_column::is_empty()'],['../classvg_1_1MemoizingGraph.html#a4596372ebc27c5e849127f4f09d9ae6b',1,'vg::MemoizingGraph::is_empty()'],['../classhandlegraph_1_1PathHandleGraph.html#aef3f2c04d1e315e485460dcd902467cb',1,'handlegraph::PathHandleGraph::is_empty()'],['../namespacevg.html#a3620df68e5af61a8eb660e4a4838ea06',1,'vg::is_empty()'],['../namespacexg.html#a9ef9c7147d5ae7c20d60ec17581d81bb',1,'xg::is_empty()']]],
- ['is_5fend_2977',['is_end',['../structvg_1_1CactusSide.html#a960c0e9a2c2dc004aac017030f6ad805',1,'vg::CactusSide::is_end()'],['../classvg_1_1NodeSide.html#a1493cac020ed0c9b1cbd37e2a99eb9b5',1,'vg::NodeSide::is_end()']]],
- ['is_5fequal_2978',['is_equal',['../classvg_1_1ZipCode.html#a38f2c794e04f2ad21447358fd7b93665',1,'vg::ZipCode']]],
- ['is_5fextendable_2979',['is_extendable',['../classvg_1_1IncrementalSubgraph.html#ada07715a97931d98157e8fc5aba697a9',1,'vg::IncrementalSubgraph']]],
- ['is_5fexternally_5fend_5fend_5fconnected_2980',['is_externally_end_end_connected',['../classvg_1_1ZipCode.html#ac59bc5911574a1fa356cac4f90471324',1,'vg::ZipCode']]],
- ['is_5fexternally_5fstart_5fend_5fconnected_2981',['is_externally_start_end_connected',['../classvg_1_1ZipCode.html#a28d318606661f6e99b2374b5a87f370f',1,'vg::ZipCode']]],
- ['is_5fexternally_5fstart_5fstart_5fconnected_2982',['is_externally_start_start_connected',['../classvg_1_1ZipCode.html#a842b8118dd218d6451199c1fd5f2e04b',1,'vg::ZipCode']]],
- ['is_5ffarther_5fthan_2983',['is_farther_than',['../classvg_1_1ZipCode.html#a967a3c40a7c49674c6d14883b6b02e71',1,'vg::ZipCode']]],
- ['is_5ffinalized_2984',['is_finalized',['../classvg_1_1FragmentLengthDistribution.html#a4f1fa1f539e504fdd0f92467b81e9172',1,'vg::FragmentLengthDistribution']]],
- ['is_5ffinished_2985',['is_finished',['../classvg_1_1IndexFile.html#a80f432755770a31c2c1fa4c41d404f8b',1,'vg::IndexFile']]],
- ['is_5ffixed_2986',['is_fixed',['../classvg_1_1FragmentLengthDistribution.html#adcfca733e40d173dcbaf2e8c617c74ec',1,'vg::FragmentLengthDistribution']]],
- ['is_5fgzipped_2987',['is_gzipped',['../namespacevg.html#a8f065676bdbe54b44e45961d7d40d8a5',1,'vg']]],
- ['is_5fhaplotype_2988',['is_haplotype',['../structvg_1_1TranscriptPath.html#ac4cca688d7aa76da99a285b769b2cab8',1,'vg::TranscriptPath']]],
- ['is_5fhead_5fnode_2989',['is_head_node',['../classvg_1_1VG.html#a80438f4ab98e10b68caab27fdece09ab',1,'vg::VG::is_head_node(nid_t id)'],['../classvg_1_1VG.html#a1bc3866468d5eb941fa6ba010ccce2ec',1,'vg::VG::is_head_node(Node *node)'],['../namespacevg_1_1algorithms.html#aa4cb6665721af1f7c749ca8f73472d6c',1,'vg::algorithms::is_head_node()']]],
- ['is_5fhead_5for_5ftail_5fnode_2990',['is_head_or_tail_node',['../classvg_1_1Paths.html#afec902ce6a22b7aa3aeee25f20eb1386',1,'vg::Paths']]],
- ['is_5fid_5fsortable_2991',['is_id_sortable',['../namespacevg.html#a5570a5685bef6eee6ac2697920ebc6c0',1,'vg']]],
- ['is_5fin_5frange_2992',['is_in_range',['../classvg_1_1StreamIndexBase.html#ab2b832d8cca9dee3c38d452dc47da0e3',1,'vg::StreamIndexBase']]],
- ['is_5finstantiation_5fof_2993',['is_instantiation_of',['../structvg_1_1is__instantiation__of.html',1,'vg']]],
- ['is_5finstantiation_5fof_3c_20predicate_3c_20predicateargs_2e_2e_2e_20_3e_2c_20predicate_20_3e_2994',['is_instantiation_of< Predicate< PredicateArgs... >, Predicate >',['../structvg_1_1is__instantiation__of_3_01Predicate_3_01PredicateArgs_8_8_8_01_4_00_01Predicate_01_4.html',1,'vg']]],
- ['is_5fintermediate_2995',['is_intermediate',['../classvg_1_1IndexingPlan.html#ae04def089761ea2ef65532fabd909794',1,'vg::IndexingPlan']]],
- ['is_5finterval_2996',['is_interval',['../structgafkluge_1_1GafStep.html#a681b0a984c816cf87468a4143b740a90',1,'gafkluge::GafStep']]],
- ['is_5fleaf_2997',['is_leaf',['../structvg_1_1WFANode.html#af75c62d0086aaa47baa79808601cf4f0',1,'vg::WFANode::is_leaf()'],['../classvg_1_1SnarlManager.html#aef63882ba4ef5e098890b1eeb3bbb985',1,'vg::SnarlManager::is_leaf()']]],
- ['is_5fleft_5fclipped_2998',['is_left_clipped',['../classvg_1_1Filter.html#a08ace85cd60850045415e5e6640b0038',1,'vg::Filter']]],
- ['is_5flooping_5fchain_2999',['is_looping_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#afbb04850e68908d3802cb5164563577b',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['is_5fmapped_3000',['is_mapped',['../classvg_1_1ReadFilter.html#a1acad05129d0a6146416f596903216a8',1,'vg::ReadFilter::is_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#acf05b0ded409cd19894c24b6fe9412bf',1,'vg::ReadFilter::is_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#ad1fe573ba370f839adb1cd28350cac81',1,'vg::ReadFilter::is_mapped(const MultipathAlignment &mp_alignment) const']]],
- ['is_5fmatch_3001',['is_match',['../namespacevg.html#a52292dfd3869a811170f7c5c0d9da564',1,'vg']]],
- ['is_5fmissing_3002',['is_missing',['../namespacegafkluge.html#a190e58cca553fe5b7b67dac6f7aad7d4',1,'gafkluge::is_missing(const std::string &s)'],['../namespacegafkluge.html#ae093534cbdd3fda37e3a75ea91a0f6b2',1,'gafkluge::is_missing(int64_t i)']]],
- ['is_5fnew_3003',['is_new',['../structhaplo_1_1haplo__DP__rectangle.html#a509976d09905bfe9312bc855641a7a59',1,'haplo::haplo_DP_rectangle']]],
- ['is_5fnode_3004',['is_node',['../classhandlegraph_1_1SnarlDecomposition.html#a6f410ac594c7ed44a7cc9b6e44077900',1,'handlegraph::SnarlDecomposition']]],
- ['is_5fnovel_5fedge_3005',['is_novel_edge',['../structvg_1_1AugmentedGraph.html#ab0dd61392dacbee763cea6297d95f876',1,'vg::AugmentedGraph']]],
- ['is_5fnovel_5fnode_3006',['is_novel_node',['../structvg_1_1AugmentedGraph.html#ac6f4df5e0f80b0509ff3ec26b685d5c9',1,'vg::AugmentedGraph']]],
- ['is_5fnumber_3007',['is_number',['../namespacevg.html#af051490e6e94b4c476695610472cdf5b',1,'vg::is_number(const std::string &s)'],['../namespacevg.html#a97c44463adc7ddcc77ac9664692a62b8',1,'vg::is_number(const string &s)']]],
- ['is_5fordered_3008',['is_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a313e2b7266bdfbe3ee864d80a5e7b67c',1,'vg::ZipCodeForest::interval_state_t']]],
- ['is_5fours_3009',['is_ours',['../classvg_1_1ExtraNodeGraph.html#a16421769feafbfb95e2466391a6fa97c',1,'vg::ExtraNodeGraph::is_ours()'],['../classvg_1_1SourceSinkOverlay.html#abe7c1c7dcdf76a6116f500654e73fb89',1,'vg::SourceSinkOverlay::is_ours()']]],
- ['is_5fphased_3010',['is_phased',['../structvg_1_1Genotype.html#a7aceacf9d5e3def3d6e675ef34906aab',1,'vg::Genotype']]],
- ['is_5fproper_5fpair_3011',['is_proper_pair',['../classvg_1_1ReadFilter.html#ad5ebb80a71eaf7c765f33b306ab230d8',1,'vg::ReadFilter']]],
- ['is_5freference_3012',['is_reference',['../structvg_1_1TranscriptPath.html#a61efb7a65128254f6039323ca0507e95',1,'vg::TranscriptPath']]],
- ['is_5frend_3013',['is_rend',['../structvg_1_1ChainIterator.html#adb9db0a0ea4cac8bca359c97d293aaa9',1,'vg::ChainIterator']]],
- ['is_5frepetitive_3014',['is_repetitive',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a4ad3bbc4813727c0af8fa25f18d02512',1,'vg::MinimizerMapper::Minimizer']]],
- ['is_5frev_3015',['is_rev',['../namespacevg.html#aac725dd44bc5a8f540554d4b1882c1fe',1,'vg::is_rev()'],['../namespacexg.html#a92c2e7f37dfa3b8b8dbb07d80e5482be',1,'xg::is_rev()']]],
- ['is_5freverse_3016',['is_reverse',['../structvg_1_1Genotyper_1_1Affinity.html#ae1707128484386f3a20eb8c6a8f9ec95',1,'vg::Genotyper::Affinity::is_reverse()'],['../structvg_1_1Transcript.html#ab7c8b040643b29e7213839f95390625f',1,'vg::Transcript::is_reverse()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a54539368bfd495fe1ab7cbcd60f6d528',1,'vg::ZipCodeTree::oriented_seed_t::is_reverse()'],['../structgafkluge_1_1GafStep.html#a18b7374dcc0b3a2386dd6090fbb7d8fe',1,'gafkluge::GafStep::is_reverse()'],['../structvg_1_1Position.html#aeb715b329bd7371ca380a2f2abdcbd13',1,'vg::Position::is_reverse()'],['../classvg_1_1mapping__t.html#a26eda6f4c9bc3da9376c2e0f5569aa62',1,'vg::mapping_t::is_reverse()'],['../classvg_1_1position__t.html#a7028d95b6cc9c55db816e9500949283b',1,'vg::position_t::is_reverse()'],['../classxg_1_1XGPath.html#a89bfa5d4417fea7455c520e6817108e7',1,'xg::XGPath::is_reverse()']]],
- ['is_5freverse_5fordered_3017',['is_reverse_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae6d743daadce96f680039a166503bee9',1,'vg::ZipCodeForest::interval_state_t']]],
- ['is_5freversed_3018',['is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a781979f7c9ed42859087a19c07be8898',1,'vg::ZipCode::node_code_t::is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8c08c6dddaf7f3d1e75964c6bf701c3d',1,'vg::ZipCode::snarl_code_t::is_reversed()'],['../structvg_1_1MIPayload.html#a391d9d5e1cd44eccb39a6a31f56a6890',1,'vg::MIPayload::is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ab491085e63a9027e460098d5bc3f98ca',1,'vg::ZipCodeTree::tree_item_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af4a9de3c328470293caa0d958094201e',1,'vg::ZipCodeForest::child_info_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae0f46b456027c5360dad34c0480c8ebb',1,'vg::ZipCodeForest::interval_state_t::is_reversed()']]],
- ['is_5freversed_5fin_5fparent_3019',['is_reversed_in_parent',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a81a6e5692e0b2100e9204bdb48454dd6',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['is_5froot_3020',['is_root',['../classvg_1_1WFATree.html#af1ad9e8285b7a9414d8af9ec257add49',1,'vg::WFATree::is_root()'],['../classvg_1_1SnarlManager.html#a294ce522d34dadb5288d6115c88dfa89',1,'vg::SnarlManager::is_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#afef6c85a6564d6d3ec65bfb245e1f38c',1,'handlegraph::SnarlDecomposition::is_root()']]],
- ['is_5fsecondary_3021',['is_secondary',['../structvg_1_1Alignment.html#a59a4b8c7367fb468e46bcf6ae292888f',1,'vg::Alignment::is_secondary()'],['../classvg_1_1ReadFilter.html#a947155b6ed467a8ea83ac80db6e11a63',1,'vg::ReadFilter::is_secondary(const Read &read) const'],['../classvg_1_1ReadFilter.html#a44451e4c12ff1a923221d019c31c610c',1,'vg::ReadFilter::is_secondary(const MultipathAlignment &mp_aln) const'],['../classvg_1_1ReadFilter.html#ab4ae201744c8abc543d60afb24b294eb',1,'vg::ReadFilter::is_secondary(const Alignment &aln) const']]],
- ['is_5fseed_3022',['is_seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab29219e6df18063f714a379f5d769cf7',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['is_5fself_5flooping_3023',['is_self_looping',['../classvg_1_1VG.html#ad09549b6cfab8e1097dd207e01e57812',1,'vg::VG']]],
- ['is_5fsentinel_3024',['is_sentinel',['../classhandlegraph_1_1SnarlDecomposition.html#af3ce2079f249448a8c8a829daedd1678',1,'handlegraph::SnarlDecomposition']]],
- ['is_5fsingle_5fstranded_3025',['is_single_stranded',['../namespacehandlegraph_1_1algorithms.html#afbca1e7b54575bfce7f0844dbda83c6f',1,'handlegraph::algorithms']]],
- ['is_5fsingle_5fstranded_2ecpp_3026',['is_single_stranded.cpp',['../is__single__stranded_8cpp.html',1,'']]],
- ['is_5fskippable_3027',['is_skippable',['../classvg_1_1algorithms_1_1Anchor.html#a002732eac1459215244c89710a4ef2e3',1,'vg::algorithms::Anchor']]],
- ['is_5fsnarl_3028',['is_snarl',['../classhandlegraph_1_1SnarlDecomposition.html#a32b29fc153b3a355cae8b15008ec8c1b',1,'handlegraph::SnarlDecomposition']]],
- ['is_5fsnarl_5fsmaller_5fthan_5freads_3029',['is_snarl_smaller_than_reads',['../classvg_1_1Genotyper.html#a7c7f091482612f6b0cd2baf0c19c45fb',1,'vg::Genotyper']]],
- ['is_5fsnv_3030',['is_snv',['../structhaplo_1_1linear__haplo__structure.html#aa95f64d55f6bf7b1239396ba4a722a05',1,'haplo::linear_haplo_structure']]],
- ['is_5fsolitary_5fref_3031',['is_solitary_ref',['../structhaplo_1_1linear__haplo__structure.html#a5909bdd11b10437a4d70af1fda222a85',1,'haplo::linear_haplo_structure']]],
- ['is_5fsplit_3032',['is_split',['../classvg_1_1ReadFilter.html#a34d313741dcfe8c009dfcc380d1293ad',1,'vg::ReadFilter::is_split(const Read &read) const'],['../classvg_1_1ReadFilter.html#a956bc9e366bb25f9544dbb3d8573b5b5',1,'vg::ReadFilter::is_split(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a3fcb1771035304240c7a0401d84ef60b',1,'vg::ReadFilter::is_split(const MultipathAlignment &mp_aln) const']]],
- ['is_5fstable_3033',['is_stable',['../structgafkluge_1_1GafStep.html#ad41f5cafc50a114daeec6b0cf08101eb',1,'gafkluge::GafStep']]],
- ['is_5fstatic_3034',['is_static',['../structvg_1_1subcommand_1_1TickChainLink.html#aae7e5f61e0f577ae29fd404c6f0a9482',1,'vg::subcommand::TickChainLink::is_static()'],['../structvg_1_1Range.html#a07b020e2621ac7d0a6cc636384242c73',1,'vg::Range::is_static()'],['../structvg_1_1subcommand_1_1RangeArgSpec.html#a20410637df207e212fee01c268624d85',1,'vg::subcommand::RangeArgSpec::is_static()']]],
- ['is_5ftail_5fnode_3035',['is_tail_node',['../classvg_1_1VG.html#a660692b8769618259f69be25bfed0bc3',1,'vg::VG::is_tail_node(nid_t id)'],['../classvg_1_1VG.html#af58b227f21324d30be531088ed49b0f1',1,'vg::VG::is_tail_node(Node *node)'],['../namespacevg_1_1algorithms.html#ac8e4eb795d14d441c4b2944c070a1d78',1,'vg::algorithms::is_tail_node()']]],
- ['is_5ftraversable_3036',['is_traversable',['../classvg_1_1LegacyCaller.html#a369827412ee13857083444776aa240c7',1,'vg::LegacyCaller::is_traversable()'],['../classvg_1_1MCMCCaller.html#a1e632e1f6e31cd559ec0a6c3cff1db7c',1,'vg::MCMCCaller::is_traversable()']]],
- ['is_5ftrivial_3037',['is_trivial',['../classvg_1_1SnarlManager.html#a5fdc8b210fa5339485b1e0a8ab1683b6',1,'vg::SnarlManager']]],
- ['is_5ftrivial_5fchain_3038',['is_trivial_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a8e92509271514f3510eabdfbe7da9e1d',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::is_trivial_chain()'],['../structvg_1_1MIPayload.html#a9a1ab910b382a0ec41e12036f9b8ae04',1,'vg::MIPayload::is_trivial_chain()']]],
- ['is_5fvalid_3039',['is_valid',['../classvg_1_1Sampler.html#a6f979036816c6f3657c98193b9b1e22d',1,'vg::Sampler::is_valid()'],['../classvg_1_1VG.html#aa77d93fdf76698460ce509ea5dcde954',1,'vg::VG::is_valid()'],['../structvg_1_1Range.html#a15b962d68b5743aa9ba5f8a487007a83',1,'vg::Range::is_valid()']]],
- ['is_5fvalid_5ftag_3040',['is_valid_tag',['../classvg_1_1io_1_1Registry.html#a4985634eed56438635dfbe0999103305',1,'vg::io::Registry']]],
- ['is_5fvg_3041',['is_vg',['../classvg_1_1LegacyCaller.html#a80d266e926310b4def5ac48e3211029f',1,'vg::LegacyCaller']]],
- ['is_5fweakly_5fconnected_3042',['is_weakly_connected',['../namespacehandlegraph_1_1algorithms.html#a99bd1e8b398ce2df3530cc47baef8818',1,'handlegraph::algorithms']]],
- ['isatgc_3043',['isATGC',['../namespacevg.html#a92c923774a6526b7bfc7f06ae4ae7a18',1,'vg']]],
- ['isbgzf_3044',['IsBGZF',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a1eb2633e42ca1b50ab167497e581e6bd',1,'vg::io::BlockedGzipInputStream']]],
- ['isforward_3045',['isForward',['../structvg_1_1BREAKPOINT.html#a3179531d48993e05d802907b730e1631',1,'vg::BREAKPOINT']]],
- ['issue_5furl_3046',['ISSUE_URL',['../namespacevg.html#ae77436235694e5e661c74799ab326d0b',1,'vg']]],
- ['it_3047',['it',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1bc7243523f7c66a5d86bbe6b28176af',1,'vg::ZipCodeTree::iterator::it()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3ab48e9f50bb0651c4eef055721366ea',1,'vg::ZipCodeTree::reverse_iterator::it()']]],
- ['item_3048',['Item',['../structvg_1_1Funnel_1_1Item.html',1,'vg::Funnel']]],
- ['item_5fbonus_3049',['item_bonus',['../classvg_1_1MinimizerMapper.html#a7646fc428d4eb41fb022dd9c61afa687',1,'vg::MinimizerMapper']]],
- ['item_5fcount_3050',['item_count',['../structvg_1_1MatchPos_1_1PathList.html#ad3ebb006eb120b2934d64cece179d0e8',1,'vg::MatchPos::PathList']]],
- ['item_5fscale_3051',['item_scale',['../classvg_1_1MinimizerMapper.html#af637ac92b12ecfebb815cedb5d56f58e',1,'vg::MinimizerMapper']]],
- ['item_5fvo_3052',['item_vo',['../classvg_1_1io_1_1MessageIterator.html#a1f58abce5de3c8f71a82e689c0170c49',1,'vg::io::MessageIterator']]],
- ['items_3053',['items',['../structvg_1_1Funnel_1_1Stage.html#a787bab13fd8bd1bccb1ac8e7821688c6',1,'vg::Funnel::Stage::items()'],['../structvg_1_1VectorView.html#a1d1194d5eac47211eda065d3dc6312ef',1,'vg::VectorView::items()']]],
- ['iteratee_3054',['iteratee',['../classvg_1_1ShuffledPairs_1_1iterator.html#a09d41523db4b9b9c6cebb02ecf7bfa3c',1,'vg::ShuffledPairs::iterator']]],
- ['iteratee_2ehpp_3055',['iteratee.hpp',['../iteratee_8hpp.html',1,'']]],
- ['iterator_3056',['iterator',['../classvg_1_1ShuffledPairs_1_1iterator.html',1,'vg::ShuffledPairs::iterator'],['../classvg_1_1ZipCodeTree_1_1iterator.html',1,'vg::ZipCodeTree::iterator'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html',1,'handlegraph::PathForEachSocket::iterator'],['../classvg_1_1PhasedGenome_1_1iterator.html',1,'vg::PhasedGenome::iterator'],['../structvg_1_1PathIndex.html#a0a0f36c0f57cc92dfb70f05eb4e5c482',1,'vg::PathIndex::iterator()'],['../classvg_1_1ShuffledPairs_1_1iterator.html#ade5cfb8f4e824c4d02c51df5ca396096',1,'vg::ShuffledPairs::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ShuffledPairs_1_1iterator.html#a3b52dd39c46e409ef1bfd67ab8ee76e4',1,'vg::ShuffledPairs::iterator::iterator(const ShuffledPairs &iteratee, size_t start_at)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0f330d79400d74c3da0c81e4af73d441',1,'vg::PhasedGenome::iterator::iterator(size_t rank, int haplotype_number, HaplotypeNode *haplo_node)'],['../classvg_1_1PhasedGenome_1_1iterator.html#ac8ddc9db361c6f07887fdc36b5484bcf',1,'vg::PhasedGenome::iterator::iterator()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a03bdcb94d8ed8b6e895ff003412185e4',1,'vg::PhasedGenome::iterator::iterator(const iterator &other)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aba25925d1c05e690d672b69ff66a3beb',1,'vg::ZipCodeTree::iterator::iterator(vector< tree_item_t >::const_iterator begin, vector< tree_item_t >::const_iterator end)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a51bef2f0839b26694742584b8a6dbedd',1,'vg::ZipCodeTree::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a171cb654dcd53b1bf78670b4002ba988',1,'vg::ZipCodeTree::iterator::iterator(iterator &&other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac02b7134a97591fcd4a821093a0a4ab4',1,'handlegraph::PathForEachSocket::iterator::iterator(const iterator &other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aed3d6dd2502cf236a6a55ed29e8c41dc',1,'handlegraph::PathForEachSocket::iterator::iterator()=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#af854ca3bd6cdbcfc8af01f7879f85106',1,'handlegraph::PathForEachSocket::iterator::iterator(const step_handle_t &step, bool force_unequal, const PathHandleGraph *graph)']]],
- ['iterator_5fcategory_3057',['iterator_category',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#afe1f2a02d394f83c867bdca78ac9fc50',1,'std::iterator_traits< vg::PhasedGenome::iterator >::iterator_category()'],['../classvg_1_1count__back__inserter.html#a21cffdfe58f87b579e5f71c16390e39d',1,'vg::count_back_inserter::iterator_category()'],['../structvg_1_1VectorView_1_1const__iterator.html#a3e5943959256e2400b3ab9b486cad7a9',1,'vg::VectorView::const_iterator::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#a11520b7b8d397962dd529faebccde56a',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a01b368cc72243f1d414e88999b856b34',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::iterator_category()']]],
- ['iterator_5ftraits_3c_20vg_3a_3aphasedgenome_3a_3aiterator_20_3e_3058',['iterator_traits< vg::PhasedGenome::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html',1,'std']]],
- ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3aiterator_20_3e_3059',['iterator_traits< vg::ZipCodeTree::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html',1,'std']]],
- ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3areverse_5fiterator_20_3e_3060',['iterator_traits< vg::ZipCodeTree::reverse_iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html',1,'std']]],
- ['iterfcmp_3061',['IterFCmp',['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html',1,'vg::IncrementalSubgraph']]]
+ ['i_2773',['I',['../structhaplo_1_1haplo__DP__rectangle.html#ad961ad4ab25e6d0358b58dc44b3c0319',1,'haplo::haplo_DP_rectangle']]],
+ ['id_2774',['id',['../structvg_1_1RecombinatorHaplotype.html#a6b099beac53df44fd9ec1d2c88aa8303',1,'vg::RecombinatorHaplotype::id()'],['../structReferenceInterval.html#a197a86ed0f4a316bd59ea19ba28bee0a',1,'ReferenceInterval::id()'],['../structvg_1_1Node.html#af886497fd0ba196f651b5d8f9678b52d',1,'vg::Node::id()'],['../namespacevg.html#a9f6602b7e7a46c19819c8f362147b315',1,'vg::id()'],['../namespacexg.html#a7bfa373a28253072de64785adc9b1188',1,'xg::id()']]],
+ ['id_5finterval_2775',['id_interval',['../classvg_1_1HaplotypeIndexer.html#af71885cc768549e78097e76e77e90ea8',1,'vg::HaplotypeIndexer']]],
+ ['id_5fmap_2776',['id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a22e20a6a984b3dd5def4ad22836b15b9',1,'vg::algorithms::GFAParser']]],
+ ['id_5forder_2777',['id_order',['../namespacevg_1_1algorithms.html#a54730e9452c2609633da201ba85a8bca',1,'vg::algorithms']]],
+ ['id_5frank_5fmap_2778',['id_rank_map',['../classvg_1_1Viz.html#a5caef0a1bce287d9a5012d36fc1de043',1,'vg::Viz']]],
+ ['id_5fsort_2779',['id_sort',['../classvg_1_1VG.html#ab1aecdffe7759a1e14248e00f2866b84',1,'vg::VG']]],
+ ['id_5fsort_2ecpp_2780',['id_sort.cpp',['../id__sort_8cpp.html',1,'']]],
+ ['id_5fsort_2ehpp_2781',['id_sort.hpp',['../id__sort_8hpp.html',1,'']]],
+ ['id_5ft_2782',['id_t',['../namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821',1,'vg::id_t()'],['../namespacehandlegraph.html#a9d001e7b9d625e6b4ef53430e6a0c180',1,'handlegraph::id_t()']]],
+ ['id_5fto_5fedge_5findices_2783',['id_to_edge_indices',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75ad6266609d35ec42e64abb2a29c7c8',1,'vg::IndexedVG::CacheEntry']]],
+ ['id_5fto_5findex_2784',['id_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a1bef2cbc66c4d3d005cab5f79d5cf76e',1,'vg::subcommand::OptionGroup']]],
+ ['id_5fto_5fname_2785',['id_to_name',['../classvg_1_1Paths.html#a75a67b0c836eb9a21ae0eee3a213d62c',1,'vg::Paths::id_to_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a0ef46eac291cd354dc89e90d31e87777',1,'vg::algorithms::GFAIDMapInfo::id_to_name()']]],
+ ['id_5fto_5fnode_5findex_2786',['id_to_node_index',['../structvg_1_1IndexedVG_1_1CacheEntry.html#aa83d17938b7e420d9c592707721eed35',1,'vg::IndexedVG::CacheEntry']]],
+ ['id_5fto_5fprefix_2787',['id_to_prefix',['../classvg_1_1StreamIndexBase.html#a4b0e44b8cb40b33c5ef4db47a8a89272',1,'vg::StreamIndexBase']]],
+ ['id_5fto_5frank_2788',['id_to_rank',['../classVectorizer.html#aae03497d2de713a68c6d453d32f9cf4a',1,'Vectorizer::id_to_rank()'],['../classvg_1_1Viz.html#a2474cd8505ed561cd414648438fedb5e',1,'vg::Viz::id_to_rank()'],['../classxg_1_1XG.html#a39172dc94153da745dd765f3c45ceeea',1,'xg::XG::id_to_rank()'],['../classhandlegraph_1_1RankedHandleGraph.html#a4c919e31efff422d9a29fa264290836c',1,'handlegraph::RankedHandleGraph::id_to_rank()']]],
+ ['identifier_2789',['identifier',['../classvg_1_1IndexFile.html#a0b5a76c50d22d7325f10fa7b881338b9',1,'vg::IndexFile']]],
+ ['identify_5faligned_5fsplice_5fcandidates_2790',['identify_aligned_splice_candidates',['../classvg_1_1MultipathMapper.html#aa97ce2f7dcd38916169b78483b7c21ec',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< multipath_alignment_t > &multipath_alns, const vector< size_t > &cluster_idxs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const'],['../classvg_1_1MultipathMapper.html#a63fc3e0fac9b46faf4c28fe47c88c784',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool read_1, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, const vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const']]],
+ ['identify_5fpinning_5fpoints_2791',['identify_pinning_points',['../classvg_1_1GSSWAligner.html#a4cd705824a3926a510fea64f883cab66',1,'vg::GSSWAligner']]],
+ ['identify_5fsources_5fand_5fsinks_2792',['identify_sources_and_sinks',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aff810bb5affe3201fccf437be3290fde',1,'vg::MEMClusterer::HitGraph']]],
+ ['identify_5fstart_5fsubpaths_2793',['identify_start_subpaths',['../namespacevg.html#a0844cc3c2da56dfed0e9436d7f0dd7de',1,'vg']]],
+ ['identify_5funaligned_5fsplice_5fcandidates_2794',['identify_unaligned_splice_candidates',['../classvg_1_1MultipathMapper.html#a50f4e1e71c3fb6272009297f1e012493',1,'vg::MultipathMapper']]],
+ ['identity_2795',['identity',['../structvg_1_1Alignment.html#a06341663199b9893a9f2b288a768cfe3',1,'vg::Alignment::identity()'],['../namespacevg.html#ab3c5c7a407962a8c735c1d533cc0b186',1,'vg::identity()']]],
+ ['identity_5foverlay_2ecpp_2796',['identity_overlay.cpp',['../identity__overlay_8cpp.html',1,'']]],
+ ['identity_5foverlay_2ehpp_2797',['identity_overlay.hpp',['../identity__overlay_8hpp.html',1,'']]],
+ ['identity_5ftranslation_2798',['identity_translation',['../classvg_1_1VG.html#ab015755dc8b427f4e226f920eb26c428',1,'vg::VG']]],
+ ['identity_5fweight_2799',['identity_weight',['../classvg_1_1Mapper.html#aabc9f9048a56b9b52fdf8d5271f7f60d',1,'vg::Mapper']]],
+ ['identityoverlay_2800',['IdentityOverlay',['../classvg_1_1IdentityOverlay.html',1,'vg::IdentityOverlay'],['../classvg_1_1IdentityOverlay.html#ab287d9dd0b6b6c0832dc725a2cdb6740',1,'vg::IdentityOverlay::IdentityOverlay(const HandleGraph *graph)'],['../classvg_1_1IdentityOverlay.html#a8a699d8689c9d93e72a7e78023cc3413',1,'vg::IdentityOverlay::IdentityOverlay()=default']]],
+ ['ids_5fmain_2ecpp_2801',['ids_main.cpp',['../ids__main_8cpp.html',1,'']]],
+ ['idscanner_2802',['IDScanner',['../structvg_1_1IDScanner.html',1,'vg']]],
+ ['ignore_5fmissing_5fcontigs_2803',['ignore_missing_contigs',['../classvg_1_1VariantAdder.html#a7a8bd35e29cbd240fd0f2a7156630943',1,'vg::VariantAdder']]],
+ ['image_5fheight_2804',['image_height',['../classvg_1_1Viz.html#ab34e44856e2c4d64ddf4d11aac46e5f6',1,'vg::Viz']]],
+ ['image_5fwidth_2805',['image_width',['../classvg_1_1Viz.html#a5dfce1ae146aff9f2aead08e304833bd',1,'vg::Viz']]],
+ ['immutable_5fpath_5ffrom_5flength_2806',['immutable_path_from_length',['../classvg_1_1MinimizerMapper.html#ab3008803e2ce57d5bbcd6a077f9dcde6',1,'vg::MinimizerMapper']]],
+ ['immutablepath_2807',['ImmutablePath',['../classvg_1_1MinimizerMapper.html#af12f40d8ae25f153fba1dc122fda29f0',1,'vg::MinimizerMapper']]],
+ ['imperfect_5fpairs_5fto_5fretry_2808',['imperfect_pairs_to_retry',['../classvg_1_1Mapper.html#a05444e0f52bddbe50304289a34d0b551',1,'vg::Mapper']]],
+ ['in_2809',['in',['../classvg_1_1GFFReader.html#a349dc0d2a38d966c4c4c265ac056346f',1,'vg::GFFReader']]],
+ ['in_5ffrom_2810',['in_from',['../classvg_1_1ExtraNodeGraph.html#a4b2d9d6b68d55c26d367ad717b13da15',1,'vg::ExtraNodeGraph']]],
+ ['in_5fnontrivial_5fchain_2811',['in_nontrivial_chain',['../classvg_1_1SnarlManager.html#a92c63ede9881ce261258540ceb40fddb',1,'vg::SnarlManager']]],
+ ['in_5fplace_5fsubvector_2812',['in_place_subvector',['../namespacevg.html#a62239efefb85e451fcec6519644186d1',1,'vg']]],
+ ['in_5fuse_2813',['in_use',['../structvg_1_1GBWTHandler.html#a1fb3dbca40a78ec37d8e04eef008bd70',1,'vg::GBWTHandler::in_use()'],['../structGraphHandler.html#a44741d974047430e73a3589c74659939',1,'GraphHandler::in_use()']]],
+ ['include_2814',['include',['../classvg_1_1VG.html#a66e4dac76edcf0218f9749352c19acae',1,'vg::VG']]],
+ ['include_5fchildren_2815',['include_children',['../classvg_1_1SparseUnionFind.html#acf3b218b8e2fee9fa73df6d4071eb0da',1,'vg::SparseUnionFind']]],
+ ['include_5fendpoints_2816',['include_endpoints',['../classvg_1_1VCFTraversalFinder.html#a27189437955d4b5f8b8ca92433c8fac2',1,'vg::VCFTraversalFinder']]],
+ ['include_5ffull_5flength_5fbonuses_2817',['include_full_length_bonuses',['../classvg_1_1Mapper.html#a9472c75cceb3382b70bbd27bfbc4a894',1,'vg::Mapper']]],
+ ['include_5fnamed_5fpaths_2818',['include_named_paths',['../structGBWTConfig.html#aedd88b893790abdf53541629fdfdbcd0',1,'GBWTConfig']]],
+ ['include_5fnested_2819',['include_nested',['../classvg_1_1VCFOutputCaller.html#afb5fc9a52eb170a49d6f77aad30e13f7',1,'vg::VCFOutputCaller']]],
+ ['include_5freference_2820',['include_reference',['../structvg_1_1Recombinator_1_1Parameters.html#a0f3128635c9d1c82a996e4ae060b0072',1,'vg::Recombinator::Parameters']]],
+ ['include_5freversing_5ftraversals_2821',['include_reversing_traversals',['../classvg_1_1ExhaustiveTraversalFinder.html#a1904edecc299fc004b02ce44ea9301f8',1,'vg::ExhaustiveTraversalFinder']]],
+ ['inclusive_5finterval_2822',['inclusive_interval',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af66a44ac51fe4a01ce0b24e0490b657b',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['incorrectly_5fmapped_2823',['incorrectly_mapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac1473f460d502f5988365b86acaa27ea',1,'vg::Counts']]],
+ ['increment_5fcoverage_2824',['increment_coverage',['../classvg_1_1Packer.html#ab97f6f0bb52c3641aceb5ffe4359492d',1,'vg::Packer::increment_coverage(size_t i)'],['../classvg_1_1Packer.html#a4da9199584ad1279a1e0a54aea12c6c1',1,'vg::Packer::increment_coverage(size_t i, size_t v)']]],
+ ['increment_5fedge_5fcoverage_2825',['increment_edge_coverage',['../classvg_1_1Packer.html#a7e2313be4468ea83a3e8b6a75b00cd7c',1,'vg::Packer::increment_edge_coverage(size_t i)'],['../classvg_1_1Packer.html#abdc73870b8a141908a21eb7ff7c31d4f',1,'vg::Packer::increment_edge_coverage(size_t i, size_t v)']]],
+ ['increment_5fnode_5fids_2826',['increment_node_ids',['../classvg_1_1Paths.html#a8a9b275a5979218a784105364248b5ba',1,'vg::Paths::increment_node_ids()'],['../classvg_1_1VG.html#a86b3ecdf29d100a8d43f6aaccd6f2e0e',1,'vg::VG::increment_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a902b211a1f86645818b3da1cb64af0be',1,'handlegraph::MutableHandleGraph::increment_node_ids(nid_t increment)'],['../classhandlegraph_1_1MutableHandleGraph.html#a877dc8c0ae9a584907d45328512720cc',1,'handlegraph::MutableHandleGraph::increment_node_ids(long increment)']]],
+ ['increment_5fnode_5fmapping_5fids_2827',['increment_node_mapping_ids',['../namespacevg.html#a9fa6175557c33cd572b8726222cf6547',1,'vg']]],
+ ['increment_5fnode_5fquality_2828',['increment_node_quality',['../classvg_1_1Packer.html#a0195e9186f8162fc4fab673fbd65b0a8',1,'vg::Packer']]],
+ ['increment_5fprogress_2829',['increment_progress',['../classvg_1_1Progressive.html#ab1de11917caf25974a02e2f5c3946280',1,'vg::Progressive']]],
+ ['incremental_5fextend_2830',['incremental_extend',['../classhaplo_1_1ScoreProvider.html#a834b5b57b025ae27cc2c668869ee9b13',1,'haplo::ScoreProvider::incremental_extend()'],['../classhaplo_1_1GBWTScoreProvider.html#af52bee39ffe97d84ba020c49f7fbf7a6',1,'haplo::GBWTScoreProvider::incremental_extend()']]],
+ ['incremental_5ffind_2831',['incremental_find',['../classhaplo_1_1ScoreProvider.html#a6272d9bca95e7846807ef2e71d616a9c',1,'haplo::ScoreProvider::incremental_find()'],['../classhaplo_1_1GBWTScoreProvider.html#a540105f41d66c4b536fda44fce248680',1,'haplo::GBWTScoreProvider::incremental_find()']]],
+ ['incremental_5fsubgraph_2ecpp_2832',['incremental_subgraph.cpp',['../incremental__subgraph_8cpp.html',1,'']]],
+ ['incremental_5fsubgraph_2ehpp_2833',['incremental_subgraph.hpp',['../incremental__subgraph_8hpp.html',1,'']]],
+ ['incrementalsearchstate_2834',['IncrementalSearchState',['../namespacehaplo.html#ae3347fe51140216cb836936c306c97bf',1,'haplo']]],
+ ['incrementalsubgraph_2835',['IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html',1,'vg::IncrementalSubgraph'],['../classvg_1_1IncrementalSubgraph.html#ab942f4d62b91144afce73896b8004609',1,'vg::IncrementalSubgraph::IncrementalSubgraph(const HandleGraph &graph, const pos_t &starting_position, bool extract_left, int64_t max_distance=numeric_limits< int64_t >::max(), size_t frontier_copy_limit=numeric_limits< size_t >::max(), size_t max_num_nodes=numeric_limits< size_t >::max())'],['../classvg_1_1IncrementalSubgraph.html#a4c8f5a87dfcf68630d645a9469e75837',1,'vg::IncrementalSubgraph::IncrementalSubgraph()=default']]],
+ ['incrementiter_2836',['IncrementIter',['../structvg_1_1IncrementIter.html',1,'vg::IncrementIter'],['../structvg_1_1IncrementIter.html#a1231b6b6c0fde0c7ae6cf69b9cfe9a6b',1,'vg::IncrementIter::IncrementIter()']]],
+ ['indel_5ferror_5fprop_2837',['indel_error_prop',['../classvg_1_1NGSSimulator.html#ae16494345e539020ebd09b0998500559',1,'vg::NGSSimulator']]],
+ ['indel_5fpoly_5frate_2838',['indel_poly_rate',['../classvg_1_1NGSSimulator.html#af84310145f8991c92d48684a0664ba8e',1,'vg::NGSSimulator']]],
+ ['index_2839',['index',['../structhaplo_1_1linear__haplo__structure.html#a79e51544898895192d319f95e95cf2f1',1,'haplo::linear_haplo_structure::index()'],['../classhaplo_1_1GBWTScoreProvider.html#ae24f0ba2be7fdc64cb0d0a33123e41ad',1,'haplo::GBWTScoreProvider::index()'],['../classhaplo_1_1LinearScoreProvider.html#a1ceb289752fb8e83c13e52e82bea393b',1,'haplo::LinearScoreProvider::index()'],['../classvg_1_1IndexedVG.html#a4f618ecb46d596aa053450a4de13e990',1,'vg::IndexedVG::index()'],['../classvg_1_1StreamIndex.html#a8ee1930510b5d02e9a00ba1a246ba146',1,'vg::StreamIndex::index()']]],
+ ['index_5fcompressed_2840',['index_compressed',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a8733ef08a80d49962c42b2f3286f9dff',1,'vg::GBWTHandler']]],
+ ['index_5fdynamic_2841',['index_dynamic',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a79071bcf44e60960f566a4fe9590d63d',1,'vg::GBWTHandler']]],
+ ['index_5fedge_5fby_5fnode_5fsides_2842',['index_edge_by_node_sides',['../classvg_1_1VG.html#a53ff7033966852f5fb3852716cab21a9',1,'vg::VG']]],
+ ['index_5fmain_2ecpp_2843',['index_main.cpp',['../index__main_8cpp.html',1,'']]],
+ ['index_5fnode_5fto_5fpath_2844',['index_node_to_path',['../classxg_1_1XG.html#a4599310a72acd2ccfbe9d6041cc51dd1',1,'xg::XG']]],
+ ['index_5fnone_2845',['index_none',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a1dc536bf1ea474d215a9a7e0c7663924',1,'vg::GBWTHandler']]],
+ ['index_5fof_2846',['index_of',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a622e1fefb7e7aa8977623b183ea9b457',1,'vg::DozeuInterface::OrderedGraph']]],
+ ['index_5fpath_5fnames_2847',['index_path_names',['../classxg_1_1XG.html#aff97dc01cda8460ebeb98a4b789e3485',1,'xg::XG']]],
+ ['index_5fregistry_2848',['index_registry',['../classvg_1_1IndexRegistry.html#a866b81f28ca2fba68aff7de143f35b9b',1,'vg::IndexRegistry']]],
+ ['index_5fregistry_2ecpp_2849',['index_registry.cpp',['../index__registry_8cpp.html',1,'']]],
+ ['index_5fregistry_2ehpp_2850',['index_registry.hpp',['../index__registry_8hpp.html',1,'']]],
+ ['index_5fto_5fnode_2851',['index_to_node',['../classvg_1_1Packer.html#a967dcbe2cbcb6df4c7e2d938f7cd11fa',1,'vg::Packer']]],
+ ['index_5ftype_2852',['index_type',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033',1,'vg::GBWTHandler']]],
+ ['indexed_5fvg_2ecpp_2853',['indexed_vg.cpp',['../indexed__vg_8cpp.html',1,'']]],
+ ['indexed_5fvg_2ehpp_2854',['indexed_vg.hpp',['../indexed__vg_8hpp.html',1,'']]],
+ ['indexedvg_2855',['IndexedVG',['../classvg_1_1IndexedVG.html',1,'vg::IndexedVG'],['../classvg_1_1IndexedVG.html#a89030b52047b0e005a5c86b7f9a206f6',1,'vg::IndexedVG::IndexedVG(string graph_filename)'],['../classvg_1_1IndexedVG.html#a0972bd3bf8d93bfa8b41aff828aab070',1,'vg::IndexedVG::IndexedVG(const IndexedVG &other)=delete']]],
+ ['indexes_2856',['indexes',['../classvg_1_1GraphSynchronizer.html#a1127fed39b1d4775bf03ada4f87b23b4',1,'vg::GraphSynchronizer::indexes()'],['../classvg_1_1RewindPlanException.html#abf38371b59f5d1ebc55806967bc3b12b',1,'vg::RewindPlanException::indexes()'],['../structvg_1_1VectorView.html#a54433c9bb742729c00a4d48adaa88015',1,'vg::VectorView::indexes()']]],
+ ['indexfile_2857',['IndexFile',['../classvg_1_1IndexFile.html',1,'vg::IndexFile'],['../classvg_1_1IndexFile.html#ae22fd6ea5fd4419ca8ed2070410638ca',1,'vg::IndexFile::IndexFile()']]],
+ ['indexgroup_2858',['IndexGroup',['../namespacevg.html#a96bc10f0ba77bc672e88a9f7d6e126b6',1,'vg']]],
+ ['indexingparameters_2859',['IndexingParameters',['../structvg_1_1IndexingParameters.html',1,'vg']]],
+ ['indexingplan_2860',['IndexingPlan',['../classvg_1_1IndexingPlan.html',1,'vg::IndexingPlan'],['../classvg_1_1IndexRegistry.html#a490f2f891225b54cb14e32d593f30f5c',1,'vg::IndexRegistry::IndexingPlan()'],['../classvg_1_1IndexingPlan.html#a5e6231a7a515964589ea8e55e8e2d5fe',1,'vg::IndexingPlan::IndexingPlan()']]],
+ ['indexname_2861',['IndexName',['../namespacevg.html#a7027e98a84fa4b0fa42f72bf4a1d862f',1,'vg']]],
+ ['indexrecipe_2862',['IndexRecipe',['../structvg_1_1IndexRecipe.html',1,'vg::IndexRecipe'],['../structvg_1_1IndexRecipe.html#a11948f5026c5aff21e22775446e419b6',1,'vg::IndexRecipe::IndexRecipe()']]],
+ ['indexregistry_2863',['IndexRegistry',['../classvg_1_1IndexRegistry.html',1,'vg::IndexRegistry'],['../classvg_1_1IndexingPlan.html#a77ea72c93e5f6c8a5e65279ae52aec32',1,'vg::IndexingPlan::IndexRegistry()'],['../classvg_1_1IndexRegistry.html#a0a0debbd6d61db053403e7cbca69d4c2',1,'vg::IndexRegistry::IndexRegistry()=default'],['../classvg_1_1IndexRegistry.html#aec3008292713502924fcf3cc51253e4f',1,'vg::IndexRegistry::IndexRegistry(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#aa4f9837b4beb749a06b3dcb3150475b0',1,'vg::IndexRegistry::IndexRegistry(IndexRegistry &&other)']]],
+ ['init_2864',['init',['../classvg_1_1SpliceStats.html#afd5923a5cd636a140697cad2605fc415',1,'vg::SpliceStats::init()'],['../classvg_1_1VG.html#aafd0f191fe33bd4590f15f309d0fd89c',1,'vg::VG::init()'],['../classvg_1_1Viz.html#aad7ceb7896288f2d4444b10cceb946d8',1,'vg::Viz::init()']]],
+ ['init_5fcoverage_5fbin_2865',['init_coverage_bin',['../classvg_1_1Packer.html#abdd9bd13b38dced4c61d78e5baf3c0fb',1,'vg::Packer']]],
+ ['init_5fedge_5fcoverage_5fbin_2866',['init_edge_coverage_bin',['../classvg_1_1Packer.html#a693598b3d8227598075e02fbc8124789',1,'vg::Packer']]],
+ ['init_5fmapper_2867',['init_mapper',['../classvg_1_1Filter.html#abd9fa5045b867b20e1b20e3d74d77e4b',1,'vg::Filter']]],
+ ['init_5fnode_5fquality_5fbin_2868',['init_node_quality_bin',['../classvg_1_1Packer.html#aff44bf5abf4eacda46958eeb436eb2e4',1,'vg::Packer']]],
+ ['init_5fsnarls_2869',['init_snarls',['../classvg_1_1Masker.html#a28b4317d6319672c9b9fa02b0e515335',1,'vg::Masker']]],
+ ['init_5fstate_2870',['init_state',['../classvg_1_1DinucleotideMachine.html#a35193673a88abc7f0933d2f65fd7f2ea',1,'vg::DinucleotideMachine']]],
+ ['init_5ftraceback_5findexes_2871',['init_traceback_indexes',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ab251d4ff6f6b7f351f29c5dd29ead002',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['initial_5fposition_2872',['initial_position',['../namespacevg.html#acd31d3a8dc67801f147d0ba1b0059c3f',1,'vg::initial_position(const Path &path)'],['../namespacevg.html#a5273bbd5e5d0f9bbf639c19c962a58dd',1,'vg::initial_position(const path_t &path)']]],
+ ['initialize_5fsam_5ffile_2873',['initialize_sam_file',['../classvg_1_1HTSWriter.html#a3063999c0e6b467c7717edfb53040166',1,'vg::HTSWriter']]],
+ ['inject_5fmain_2ecpp_2874',['inject_main.cpp',['../inject__main_8cpp.html',1,'']]],
+ ['inline_5fitems_2875',['inline_items',['../structvg_1_1MatchPos_1_1PathList.html#abffe04434a41c9f8dfcb85ef8d3d26f9',1,'vg::MatchPos::PathList']]],
+ ['inner_5fvalue_2876',['inner_value',['../structhaplo_1_1haplo__DP__rectangle.html#a68817623682eb451f4a5a42a8ae8ef8a',1,'haplo::haplo_DP_rectangle']]],
+ ['input_2877',['input',['../structvg_1_1io_1_1hFILE__cppstream.html#a301bcdddd00f4d40033b4ca94691f9a6',1,'vg::io::hFILE_cppstream']]],
+ ['input_5fdefault_2878',['INPUT_DEFAULT',['../convert__main_8cpp.html#a9427417f4ca764d74efec8fcaf9e2ca8',1,'convert_main.cpp']]],
+ ['input_5ffilenames_2879',['input_filenames',['../structGBWTConfig.html#a106dff4206c7414bf053f9c2405a0739',1,'GBWTConfig']]],
+ ['input_5fgaf_2880',['input_gaf',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa68ce48b22e2cb1ea6edb3f351cff52ed',1,'convert_main.cpp']]],
+ ['input_5fgam_2881',['input_gam',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaa45b4c6e90a30a90deb1183ec3b127a6',1,'convert_main.cpp']]],
+ ['input_5fgbwtgraph_2882',['input_gbwtgraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa2cdb682495850f7e3a5dea532a556eb2',1,'convert_main.cpp']]],
+ ['input_5fgfa_2883',['input_gfa',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaf3349e3c8dbf0909922809cb8776aebd',1,'convert_main.cpp']]],
+ ['input_5fgroup_2884',['input_group',['../structvg_1_1IndexRecipe.html#aa22beac92907ecf99b821ee6bfed4e33',1,'vg::IndexRecipe']]],
+ ['input_5fhandlegraph_2885',['input_handlegraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa6c28171b952beaf1784c655853a0e66c',1,'convert_main.cpp']]],
+ ['input_5fin_5fprogress_2886',['input_in_progress',['../classvg_1_1Funnel.html#a755941e4c7988487e539256c16b507bb',1,'vg::Funnel']]],
+ ['input_5ftype_2887',['input_type',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8ef',1,'convert_main.cpp']]],
+ ['input_5fvcf_2888',['input_vcf',['../classvg_1_1VCFGenotyper.html#a3fea7ea6e20998a5de5e95776e7f67bb',1,'vg::VCFGenotyper']]],
+ ['inputs_2889',['inputs',['../structvg_1_1IndexRecipe.html#aa23088153a85cc207ab3901afcd1ff5b',1,'vg::IndexRecipe::inputs()'],['../classvg_1_1InsufficientInputException.html#a8798c889fb558ee1c9042e10e7f136e2',1,'vg::InsufficientInputException::inputs()']]],
+ ['inputs_5fas_5fjobs_2890',['inputs_as_jobs',['../structGBWTConfig.html#ac12bbd2e3c10bdaf3ee07de4191c88d6',1,'GBWTConfig']]],
+ ['inputstream_2891',['inputStream',['../namespacevg_1_1io.html#a857cf3810d138ef43e25aa37f147ac25',1,'vg::io']]],
+ ['ins_2892',['INS',['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): xdrop_aligner.cpp']]],
+ ['ins_5fpredecessor_2893',['ins_predecessor',['../classvg_1_1WFATree.html#a8ab38ec2797b5119eb9ffd213bdb957e',1,'vg::WFATree']]],
+ ['insert_2894',['insert',['../classvg_1_1SnarlState.html#a428e616c3ef0bab94325edbd728819e3',1,'vg::SnarlState::insert(const vector< pair< handle_t, size_t >> &haplotype)'],['../classvg_1_1SnarlState.html#a8489b6496d77d037d0ee2f0367119a3a',1,'vg::SnarlState::insert(size_t overall_lane, const vector< handle_t > &haplotype, bool backward=false)'],['../classvg_1_1HandleGraphNodeSet.html#a2c8d82e307853b75c099422d8e5e717c',1,'vg::HandleGraphNodeSet::insert()'],['../structvg_1_1RecombinatorHaplotype.html#a370a97d18bca8d1448eb359eee91be6e',1,'vg::RecombinatorHaplotype::insert()'],['../classvg_1_1SmallBitset.html#a9336d107ad4a8f98005ecfcf313e1334',1,'vg::SmallBitset::insert()'],['../classvg_1_1BitStringTree.html#ac323a5f006f9ad739facc0f306b1b6ed',1,'vg::BitStringTree::insert()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#a1658df8b5e184e15cce3b5e70bc2769c',1,'vg::BitStringTree::TreeNode::insert()'],['../structjob__type.html#a28737e853741fb1798c718e3637070b0',1,'job_type::insert()']]],
+ ['insert_5fcol_2895',['insert_col',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a9a17e99af8ce2b7992fddef79c4e8b18',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['insert_5fgbwt_5fpath_2896',['insert_gbwt_path',['../namespacevg.html#a9bf4a7dd2a81bb5b873127156a2dfb33',1,'vg']]],
+ ['insert_5fhandles_2897',['insert_handles',['../classvg_1_1GenomeState.html#aa85289ade641db44976ac969c5fb6750',1,'vg::GenomeState']]],
+ ['insert_5fhaplotype_2898',['insert_haplotype',['../classvg_1_1GenomeState.html#a371e13f6d644e9979fa0e5177ffaadba',1,'vg::GenomeState']]],
+ ['insert_5fleft_2899',['insert_left',['../classvg_1_1PhasedGenome.html#a02e624546cf3f5675fbfa128c080c75d',1,'vg::PhasedGenome']]],
+ ['insert_5fmapping_2900',['insert_mapping',['../classvg_1_1Paths.html#aa6e0eb5748713837711612e5e347f8cb',1,'vg::Paths']]],
+ ['insert_5fmean_2901',['insert_mean',['../classvg_1_1Filter.html#ab8a36803dfa97e61678756f7b7a3a31c',1,'vg::Filter']]],
+ ['insert_5fpath_2902',['insert_path',['../classvg_1_1PhaseUnfolder.html#a28e7cee8d0922cf0aac91dba0d86f1c3',1,'vg::PhaseUnfolder']]],
+ ['insert_5fright_2903',['insert_right',['../classvg_1_1PhasedGenome.html#adfbd6242bff1445e5210f4046150fc85',1,'vg::PhasedGenome']]],
+ ['insert_5frow_2904',['insert_row',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ade4c512c3713ac162359ed6d9207537d',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['insert_5fsd_2905',['insert_sd',['../classvg_1_1Filter.html#ac302d7b67d23285ad615d864197a9e1b',1,'vg::Filter']]],
+ ['insert_5fsize_5ffilter_2906',['insert_size_filter',['../classvg_1_1Filter.html#a198243f4ffebc1b1442ca4521542ac99',1,'vg::Filter']]],
+ ['insert_5ftraceback_2907',['insert_traceback',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#aa6db44fa8e957169e11fd1a7853d2a19',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['insertcol_2908',['InsertCol',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faa0a1ece7d481572fa684460331afbfa4',1,'vg::BandedGlobalAligner']]],
+ ['inserthaplotypecommand_2909',['InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html',1,'vg']]],
+ ['insertion_2910',['insertion',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebaf8105fdf086223fa49c6b63a3097a645',1,'vg::WFAAlignment']]],
+ ['insertion_5fbias_5flarge_2911',['insertion_bias_large',['../classvg_1_1PoissonSupportSnarlCaller.html#a82d1c5780e74107618f3e50d7085f38e',1,'vg::PoissonSupportSnarlCaller']]],
+ ['insertion_5fbias_5fsmall_2912',['insertion_bias_small',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a5120550fa398555a1a414717469664',1,'vg::PoissonSupportSnarlCaller']]],
+ ['insertion_5ffilter_2913',['insertion_filter',['../classvg_1_1Filter.html#a02bb368759eef77f7f7aa3753b23469e',1,'vg::Filter']]],
+ ['insertion_5fthreshold_2914',['insertion_threshold',['../classvg_1_1PoissonSupportSnarlCaller.html#a7787ef040764a33043fdbf3ba2f80509',1,'vg::PoissonSupportSnarlCaller']]],
+ ['insertions_2915',['INSERTIONS',['../structvg_1_1WFANode.html#a99807b74ee148f30fae2549a8aa54339',1,'vg::WFANode::INSERTIONS()'],['../structvg_1_1InsertHaplotypeCommand.html#a5dfd52deff7c8c3fc76fa7b4dee45032',1,'vg::InsertHaplotypeCommand::insertions()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a44ad82bbfa6098c648bc1a6fcd61d102',1,'vg::ReplaceLocalHaplotypeCommand::insertions()']]],
+ ['insertrow_2916',['InsertRow',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2fac7adaac601fdfa40491cb7906ca9e989',1,'vg::BandedGlobalAligner']]],
+ ['insufficientinputexception_2917',['InsufficientInputException',['../classvg_1_1InsufficientInputException.html',1,'vg::InsufficientInputException'],['../classvg_1_1InsufficientInputException.html#a2361f9743d9c5f2af8bb170a6240b891',1,'vg::InsufficientInputException::InsufficientInputException()=delete'],['../classvg_1_1InsufficientInputException.html#af9014e0e82772828f66dc699e2eb8734',1,'vg::InsufficientInputException::InsufficientInputException(const IndexName &target, const IndexRegistry ®istry) noexcept']]],
+ ['int_5fis_5finc_2918',['int_is_inc',['../structhaplo_1_1haplo__DP__rectangle.html#a45856786beeaa7213275fcaf3eaa6878',1,'haplo::haplo_DP_rectangle']]],
+ ['int_5fis_5fnonnegative_2919',['int_is_nonnegative',['../namespacevg_1_1subcommand.html#aafa3ba89747f1886e118e7d6421078e3',1,'vg::subcommand']]],
+ ['int_5fitvl_5ft_2920',['int_itvl_t',['../structhaplo_1_1int__itvl__t.html',1,'haplo']]],
+ ['int_5fto_5fstring_2921',['int_to_string',['../namespacegafkluge.html#ad9c7bb306be39ddca425533a3583d71e',1,'gafkluge']]],
+ ['int_5fweighted_5fsum_2922',['int_weighted_sum',['../namespacehaplo_1_1haploMath.html#a5bc2868874173d377a55c788f21796ef',1,'haplo::haploMath::int_weighted_sum(double *values, int64_t *counts, size_t n_values)'],['../namespacehaplo_1_1haploMath.html#ab17ccf8a6fa509f269bdaf1c69e4f6bc',1,'haplo::haploMath::int_weighted_sum(vector< double > values, vector< int64_t > counts)']]],
+ ['integer_5fpower_2923',['integer_power',['../namespacevg.html#aca4239af1a9e3eb1283f78bf5cc1411a',1,'vg::integer_power(uint64_t base, uint64_t exponent)'],['../namespacevg.html#aa7c32d1e90ec006624a7ee03655f3c35',1,'vg::integer_power(size_t x, size_t power)']]],
+ ['integrated_5fsnarl_5ffinder_2ecpp_2924',['integrated_snarl_finder.cpp',['../integrated__snarl__finder_8cpp.html',1,'']]],
+ ['integrated_5fsnarl_5ffinder_2ehpp_2925',['integrated_snarl_finder.hpp',['../integrated__snarl__finder_8hpp.html',1,'']]],
+ ['integratedsnarlfinder_2926',['IntegratedSnarlFinder',['../classvg_1_1IntegratedSnarlFinder.html',1,'vg::IntegratedSnarlFinder'],['../classvg_1_1IntegratedSnarlFinder.html#a888085d87664c7e58ad4f988091c62f5',1,'vg::IntegratedSnarlFinder::IntegratedSnarlFinder()']]],
+ ['interchromosomal_5ffilter_2927',['interchromosomal_filter',['../classvg_1_1Filter.html#a1f1daa97b40d6ca6b2a3f37950f4f117',1,'vg::Filter']]],
+ ['interleaved_2928',['interleaved',['../classvg_1_1ReadFilter.html#a3d7c97fa34473eb5b1e3bce2dd64d6eb',1,'vg::ReadFilter']]],
+ ['internal_5fid_5fmap_2929',['internal_id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a5bdb46afdb654469e3dc42fdfbe048ab',1,'vg::algorithms::GFAParser']]],
+ ['internal_5fscore_2930',['internal_score',['../structvg_1_1GaplessExtension.html#a0045e76ebc1c911201d6744d6c20e50a',1,'vg::GaplessExtension']]],
+ ['intersect_5fpath_5foffsets_2931',['intersect_path_offsets',['../namespacevg_1_1algorithms.html#a9ce4dabb6661657c7d72593afc3f41df',1,'vg::algorithms']]],
+ ['intersect_5fpath_5foffsets_2ecpp_2932',['intersect_path_offsets.cpp',['../intersect__path__offsets_8cpp.html',1,'']]],
+ ['intersect_5fpath_5foffsets_2ehpp_2933',['intersect_path_offsets.hpp',['../intersect__path__offsets_8hpp.html',1,'']]],
+ ['intersection_2934',['intersection',['../structhaplo_1_1int__itvl__t.html#ade4051b750fcce428be13a69663ec035',1,'haplo::int_itvl_t']]],
+ ['interval_5fend_2935',['interval_end',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#af58f43315b7386134bf8a034c0c39694',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['interval_5flength_2936',['interval_length',['../namespacevg.html#a9467900ec651b93d47190413208cdf6f',1,'vg']]],
+ ['interval_5fsize_2937',['interval_size',['../structhaplo_1_1haplo__DP__rectangle.html#a751f03ab1d68636c47340dbd376b66a8',1,'haplo::haplo_DP_rectangle']]],
+ ['interval_5fstart_2938',['interval_start',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a7a2843b5a5a25b77f55ddb80998028bd',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['interval_5fstate_5ft_2939',['interval_state_t',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html',1,'vg::ZipCodeForest::interval_state_t'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#aa86bab20d96ef26dc66afadf5dd22195',1,'vg::ZipCodeForest::interval_state_t::interval_state_t()']]],
+ ['intervals_5fto_5fprocess_2940',['intervals_to_process',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#aafe37939d028547b7ae3ee68fda10ed1',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['into_5fcutting_5fsnarl_2941',['into_cutting_snarl',['../classvg_1_1MultipathAlignmentGraph.html#a44bd7328dd8ea140223226ae4da8afff',1,'vg::MultipathAlignmentGraph']]],
+ ['into_5fwhich_5fsnarl_2942',['into_which_snarl',['../classvg_1_1SnarlManager.html#ac08074e3073ecd2ef72a57116b459577',1,'vg::SnarlManager::into_which_snarl(int64_t id, bool reverse) const'],['../classvg_1_1SnarlManager.html#a852f930d4e68e9bbd664ebe5a73a4669',1,'vg::SnarlManager::into_which_snarl(const Visit &visit) const']]],
+ ['introduce_2943',['introduce',['../classvg_1_1Funnel.html#adfe8a13519ae236c400f3ad68980e16c',1,'vg::Funnel']]],
+ ['intron_5flength_5flog_5flikelihood_2944',['intron_length_log_likelihood',['../classvg_1_1SpliceStats.html#ad61aebd450e01500b86d1fec55b8ccd9',1,'vg::SpliceStats']]],
+ ['intron_5flength_5fscore_2945',['intron_length_score',['../classvg_1_1SpliceStats.html#aedf26f015ecfb06f71aadbca66c81935',1,'vg::SpliceStats']]],
+ ['invalid_2946',['invalid',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a26ab26b5bf5a066a0902a79defda6b5d',1,'haplo::linear_haplo_structure']]],
+ ['inverse_2947',['inverse',['../classvg_1_1Filter.html#a05e7274611008cdd5b89d1fa81605882',1,'vg::Filter::inverse()'],['../classvg_1_1VectorViewInverse.html#a54a9cc36f21c2562f2f0836e5a040773',1,'vg::VectorViewInverse::inverse()']]],
+ ['inversion_5ffilter_2948',['inversion_filter',['../classvg_1_1Filter.html#a5503147c786a4d9bfb18fc081630b5f6',1,'vg::Filter']]],
+ ['invert_2949',['invert',['../structvg_1_1Counts.html#a3a4cf08069fb263d89a96b86313a04a2',1,'vg::Counts']]],
+ ['invert_5ftranslation_2950',['invert_translation',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#abeffeb079b7f3997db8cfbb9a701f63c',1,'vg::algorithms::GFAIDMapInfo']]],
+ ['invocations_2951',['invocations',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af75c21b33a10d3ddc7f36f7567cc1aae',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['irregular_5fsnarl_2952',['IRREGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a96d1de8b0fd352dc3449d17eab32f6f4',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fdistance_5fleft_5fend_5foffset_2953',['IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET',['../classvg_1_1ZipCode.html#a0c43ecf172f0ddde09366b3facdad4f9',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fdistance_5fleft_5fstart_5foffset_2954',['IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET',['../classvg_1_1ZipCode.html#a81836246de1e66c3febd653cd0525988',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fdistance_5fright_5fend_5foffset_2955',['IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET',['../classvg_1_1ZipCode.html#a2cccc444095b38bd7e73ff6e55f930be',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fdistance_5fright_5fstart_5foffset_2956',['IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET',['../classvg_1_1ZipCode.html#acdcb0967e1dd6d01833a7fc66f6ef64b',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5frecord_5foffset_2957',['IRREGULAR_SNARL_RECORD_OFFSET',['../classvg_1_1ZipCode.html#a8f5228bda68297b861a839396970f5bc',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fsize_2958',['IRREGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a8ec98e693ea6d5c1972479f9066ef405',1,'vg::ZipCode']]],
+ ['is_5fa_5fduplicate_5fhandle_2959',['is_a_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#a3089cf35214f919d15030e029df3f6eb',1,'vg::DozeuPinningOverlay']]],
+ ['is_5fa_5fduplicate_5fid_2960',['is_a_duplicate_id',['../classvg_1_1DozeuPinningOverlay.html#ab549aa4693c8425cd1df8d04a04a178f',1,'vg::DozeuPinningOverlay']]],
+ ['is_5facyclic_2961',['is_acyclic',['../namespacehandlegraph_1_1algorithms.html#a03c1bfbc47b88a0bd18ca2cc93a1b0b3',1,'handlegraph::algorithms']]],
+ ['is_5facyclic_2ecpp_2962',['is_acyclic.cpp',['../is__acyclic_8cpp.html',1,'']]],
+ ['is_5fall_5fn_2963',['is_all_n',['../namespacevg.html#abe6f7955b97d8537da2133a47f37f462',1,'vg']]],
+ ['is_5falt_2964',['is_alt',['../classvg_1_1Paths.html#a3e8fd05a0a584cbae2f2919b5ab98e4d',1,'vg::Paths']]],
+ ['is_5fancestor_5fnext_2965',['is_ancestor_next',['../classvg_1_1VG.html#a7903acd7a977a85fdd78d306f2063252',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ab919097a72a96dada04310b2aaf019f8',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
+ ['is_5fancestor_5fprev_2966',['is_ancestor_prev',['../classvg_1_1VG.html#a25215a67c3eac7570e2ab62e825ae169',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ae6699fe9d747f761f6efae39c3c0501c',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
+ ['is_5fany_5fpainted_2967',['is_any_painted',['../structvg_1_1Funnel_1_1PaintableSpace.html#ab42e113d364cfa7da4e7b0c76ba448f1',1,'vg::Funnel::PaintableSpace']]],
+ ['is_5fchain_2968',['is_chain',['../structvg_1_1ZipCode_1_1decoder__t.html#abcbad7044eb813105e2cadefbf5a05ff',1,'vg::ZipCode::decoder_t::is_chain()'],['../classhandlegraph_1_1SnarlDecomposition.html#ad383774992bf6a3acc5fd34dc8cd9770',1,'handlegraph::SnarlDecomposition::is_chain()']]],
+ ['is_5fchecked_5fin_2969',['is_checked_in',['../structvg_1_1Watchdog_1_1thread__state__t.html#aae7887d9b7548a028a6b7271aabd44eb',1,'vg::Watchdog::thread_state_t']]],
+ ['is_5fchild_2970',['is_child',['../classvg_1_1NetGraph.html#a25dbff454e5c9aa081c354f05523a512',1,'vg::NetGraph']]],
+ ['is_5fcircular_2971',['is_circular',['../classxg_1_1XGPath.html#a4cc65b6cfdbd12f6220dde5a716fd345',1,'xg::XGPath::is_circular()'],['../structvg_1_1Path.html#ad04d3a1745f479f32b4a4358bec17c8f',1,'vg::Path::is_circular()']]],
+ ['is_5fcompacted_2972',['is_compacted',['../classvg_1_1Packer.html#aa7f90bbde45e8487029a424392b653ad',1,'vg::Packer']]],
+ ['is_5fconsistent_2973',['is_consistent',['../classvg_1_1MultipathMapper.html#a76742066028c14330177d74d9cd0286c',1,'vg::MultipathMapper']]],
+ ['is_5fcorrect_2974',['is_correct',['../classvg_1_1Funnel.html#a4296184811926cf97a42d52aaf3fc6f6',1,'vg::Funnel']]],
+ ['is_5fcorrectly_5fmapped_2975',['is_correctly_mapped',['../classvg_1_1ReadFilter.html#ac5da32515034e6669d9e14de3c748122',1,'vg::ReadFilter::is_correctly_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab76d4dc77becdaf866f724d5b88dcdb5',1,'vg::ReadFilter::is_correctly_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a053397b20bc378d11f11b365e6d68032',1,'vg::ReadFilter::is_correctly_mapped(const MultipathAlignment &alignment) const']]],
+ ['is_5fdirected_5facyclic_2976',['is_directed_acyclic',['../namespacehandlegraph_1_1algorithms.html#afe81ab458644253f1064ffa3c73783a3',1,'handlegraph::algorithms']]],
+ ['is_5fdynamic_2977',['is_dynamic',['../classvg_1_1Packer.html#a370e8ef56ffd369c6a498aa36ed9c570',1,'vg::Packer']]],
+ ['is_5fempty_2978',['is_empty',['../structhaplo_1_1haplo__DP__column.html#af8bc221754159aa83d44d9373359939c',1,'haplo::haplo_DP_column::is_empty()'],['../classvg_1_1MemoizingGraph.html#a4596372ebc27c5e849127f4f09d9ae6b',1,'vg::MemoizingGraph::is_empty()'],['../classhandlegraph_1_1PathHandleGraph.html#aef3f2c04d1e315e485460dcd902467cb',1,'handlegraph::PathHandleGraph::is_empty()'],['../namespacevg.html#a3620df68e5af61a8eb660e4a4838ea06',1,'vg::is_empty()'],['../namespacexg.html#a9ef9c7147d5ae7c20d60ec17581d81bb',1,'xg::is_empty()']]],
+ ['is_5fend_2979',['is_end',['../structvg_1_1CactusSide.html#a960c0e9a2c2dc004aac017030f6ad805',1,'vg::CactusSide::is_end()'],['../classvg_1_1NodeSide.html#a1493cac020ed0c9b1cbd37e2a99eb9b5',1,'vg::NodeSide::is_end()']]],
+ ['is_5fequal_2980',['is_equal',['../classvg_1_1ZipCode.html#a38f2c794e04f2ad21447358fd7b93665',1,'vg::ZipCode']]],
+ ['is_5fextendable_2981',['is_extendable',['../classvg_1_1IncrementalSubgraph.html#ada07715a97931d98157e8fc5aba697a9',1,'vg::IncrementalSubgraph']]],
+ ['is_5fexternally_5fend_5fend_5fconnected_2982',['is_externally_end_end_connected',['../classvg_1_1ZipCode.html#ac59bc5911574a1fa356cac4f90471324',1,'vg::ZipCode']]],
+ ['is_5fexternally_5fstart_5fend_5fconnected_2983',['is_externally_start_end_connected',['../classvg_1_1ZipCode.html#a28d318606661f6e99b2374b5a87f370f',1,'vg::ZipCode']]],
+ ['is_5fexternally_5fstart_5fstart_5fconnected_2984',['is_externally_start_start_connected',['../classvg_1_1ZipCode.html#a842b8118dd218d6451199c1fd5f2e04b',1,'vg::ZipCode']]],
+ ['is_5ffarther_5fthan_2985',['is_farther_than',['../classvg_1_1ZipCode.html#a967a3c40a7c49674c6d14883b6b02e71',1,'vg::ZipCode']]],
+ ['is_5ffinalized_2986',['is_finalized',['../classvg_1_1FragmentLengthDistribution.html#a4f1fa1f539e504fdd0f92467b81e9172',1,'vg::FragmentLengthDistribution']]],
+ ['is_5ffinished_2987',['is_finished',['../classvg_1_1IndexFile.html#a80f432755770a31c2c1fa4c41d404f8b',1,'vg::IndexFile']]],
+ ['is_5ffixed_2988',['is_fixed',['../classvg_1_1FragmentLengthDistribution.html#adcfca733e40d173dcbaf2e8c617c74ec',1,'vg::FragmentLengthDistribution']]],
+ ['is_5fgzipped_2989',['is_gzipped',['../namespacevg.html#a8f065676bdbe54b44e45961d7d40d8a5',1,'vg']]],
+ ['is_5fhaplotype_2990',['is_haplotype',['../structvg_1_1TranscriptPath.html#ac4cca688d7aa76da99a285b769b2cab8',1,'vg::TranscriptPath']]],
+ ['is_5fhead_5fnode_2991',['is_head_node',['../classvg_1_1VG.html#a80438f4ab98e10b68caab27fdece09ab',1,'vg::VG::is_head_node(nid_t id)'],['../classvg_1_1VG.html#a1bc3866468d5eb941fa6ba010ccce2ec',1,'vg::VG::is_head_node(Node *node)'],['../namespacevg_1_1algorithms.html#aa4cb6665721af1f7c749ca8f73472d6c',1,'vg::algorithms::is_head_node()']]],
+ ['is_5fhead_5for_5ftail_5fnode_2992',['is_head_or_tail_node',['../classvg_1_1Paths.html#afec902ce6a22b7aa3aeee25f20eb1386',1,'vg::Paths']]],
+ ['is_5fid_5fsortable_2993',['is_id_sortable',['../namespacevg.html#a5570a5685bef6eee6ac2697920ebc6c0',1,'vg']]],
+ ['is_5fin_5frange_2994',['is_in_range',['../classvg_1_1StreamIndexBase.html#ab2b832d8cca9dee3c38d452dc47da0e3',1,'vg::StreamIndexBase']]],
+ ['is_5finstantiation_5fof_2995',['is_instantiation_of',['../structvg_1_1is__instantiation__of.html',1,'vg']]],
+ ['is_5finstantiation_5fof_3c_20predicate_3c_20predicateargs_2e_2e_2e_20_3e_2c_20predicate_20_3e_2996',['is_instantiation_of< Predicate< PredicateArgs... >, Predicate >',['../structvg_1_1is__instantiation__of_3_01Predicate_3_01PredicateArgs_8_8_8_01_4_00_01Predicate_01_4.html',1,'vg']]],
+ ['is_5fintermediate_2997',['is_intermediate',['../classvg_1_1IndexingPlan.html#ae04def089761ea2ef65532fabd909794',1,'vg::IndexingPlan']]],
+ ['is_5finterval_2998',['is_interval',['../structgafkluge_1_1GafStep.html#a681b0a984c816cf87468a4143b740a90',1,'gafkluge::GafStep']]],
+ ['is_5fleaf_2999',['is_leaf',['../structvg_1_1WFANode.html#af75c62d0086aaa47baa79808601cf4f0',1,'vg::WFANode::is_leaf()'],['../classvg_1_1SnarlManager.html#aef63882ba4ef5e098890b1eeb3bbb985',1,'vg::SnarlManager::is_leaf()']]],
+ ['is_5fleft_5fclipped_3000',['is_left_clipped',['../classvg_1_1Filter.html#a08ace85cd60850045415e5e6640b0038',1,'vg::Filter']]],
+ ['is_5flooping_5fchain_3001',['is_looping_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#afbb04850e68908d3802cb5164563577b',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['is_5fmapped_3002',['is_mapped',['../classvg_1_1ReadFilter.html#a1acad05129d0a6146416f596903216a8',1,'vg::ReadFilter::is_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#acf05b0ded409cd19894c24b6fe9412bf',1,'vg::ReadFilter::is_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#ad1fe573ba370f839adb1cd28350cac81',1,'vg::ReadFilter::is_mapped(const MultipathAlignment &mp_alignment) const']]],
+ ['is_5fmatch_3003',['is_match',['../namespacevg.html#a52292dfd3869a811170f7c5c0d9da564',1,'vg']]],
+ ['is_5fmissing_3004',['is_missing',['../namespacegafkluge.html#a190e58cca553fe5b7b67dac6f7aad7d4',1,'gafkluge::is_missing(const std::string &s)'],['../namespacegafkluge.html#ae093534cbdd3fda37e3a75ea91a0f6b2',1,'gafkluge::is_missing(int64_t i)']]],
+ ['is_5fnew_3005',['is_new',['../structhaplo_1_1haplo__DP__rectangle.html#a509976d09905bfe9312bc855641a7a59',1,'haplo::haplo_DP_rectangle']]],
+ ['is_5fnode_3006',['is_node',['../classhandlegraph_1_1SnarlDecomposition.html#a6f410ac594c7ed44a7cc9b6e44077900',1,'handlegraph::SnarlDecomposition']]],
+ ['is_5fnovel_5fedge_3007',['is_novel_edge',['../structvg_1_1AugmentedGraph.html#ab0dd61392dacbee763cea6297d95f876',1,'vg::AugmentedGraph']]],
+ ['is_5fnovel_5fnode_3008',['is_novel_node',['../structvg_1_1AugmentedGraph.html#ac6f4df5e0f80b0509ff3ec26b685d5c9',1,'vg::AugmentedGraph']]],
+ ['is_5fnumber_3009',['is_number',['../namespacevg.html#af051490e6e94b4c476695610472cdf5b',1,'vg::is_number(const std::string &s)'],['../namespacevg.html#a97c44463adc7ddcc77ac9664692a62b8',1,'vg::is_number(const string &s)']]],
+ ['is_5fordered_3010',['is_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a313e2b7266bdfbe3ee864d80a5e7b67c',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['is_5fours_3011',['is_ours',['../classvg_1_1ExtraNodeGraph.html#a16421769feafbfb95e2466391a6fa97c',1,'vg::ExtraNodeGraph::is_ours()'],['../classvg_1_1SourceSinkOverlay.html#abe7c1c7dcdf76a6116f500654e73fb89',1,'vg::SourceSinkOverlay::is_ours()']]],
+ ['is_5fphased_3012',['is_phased',['../structvg_1_1Genotype.html#a7aceacf9d5e3def3d6e675ef34906aab',1,'vg::Genotype']]],
+ ['is_5fproper_5fpair_3013',['is_proper_pair',['../classvg_1_1ReadFilter.html#ad5ebb80a71eaf7c765f33b306ab230d8',1,'vg::ReadFilter']]],
+ ['is_5freference_3014',['is_reference',['../structvg_1_1TranscriptPath.html#a61efb7a65128254f6039323ca0507e95',1,'vg::TranscriptPath']]],
+ ['is_5frend_3015',['is_rend',['../structvg_1_1ChainIterator.html#adb9db0a0ea4cac8bca359c97d293aaa9',1,'vg::ChainIterator']]],
+ ['is_5frepetitive_3016',['is_repetitive',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a4ad3bbc4813727c0af8fa25f18d02512',1,'vg::MinimizerMapper::Minimizer']]],
+ ['is_5frev_3017',['is_rev',['../namespacevg.html#aac725dd44bc5a8f540554d4b1882c1fe',1,'vg::is_rev()'],['../namespacexg.html#a92c2e7f37dfa3b8b8dbb07d80e5482be',1,'xg::is_rev()']]],
+ ['is_5freverse_3018',['is_reverse',['../structvg_1_1Genotyper_1_1Affinity.html#ae1707128484386f3a20eb8c6a8f9ec95',1,'vg::Genotyper::Affinity::is_reverse()'],['../structvg_1_1Transcript.html#ab7c8b040643b29e7213839f95390625f',1,'vg::Transcript::is_reverse()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a54539368bfd495fe1ab7cbcd60f6d528',1,'vg::ZipCodeTree::oriented_seed_t::is_reverse()'],['../structgafkluge_1_1GafStep.html#a18b7374dcc0b3a2386dd6090fbb7d8fe',1,'gafkluge::GafStep::is_reverse()'],['../structvg_1_1Position.html#aeb715b329bd7371ca380a2f2abdcbd13',1,'vg::Position::is_reverse()'],['../classvg_1_1mapping__t.html#a26eda6f4c9bc3da9376c2e0f5569aa62',1,'vg::mapping_t::is_reverse()'],['../classvg_1_1position__t.html#a7028d95b6cc9c55db816e9500949283b',1,'vg::position_t::is_reverse()'],['../classxg_1_1XGPath.html#a89bfa5d4417fea7455c520e6817108e7',1,'xg::XGPath::is_reverse()']]],
+ ['is_5freverse_5fordered_3019',['is_reverse_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae6d743daadce96f680039a166503bee9',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['is_5freversed_3020',['is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a781979f7c9ed42859087a19c07be8898',1,'vg::ZipCode::node_code_t::is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8c08c6dddaf7f3d1e75964c6bf701c3d',1,'vg::ZipCode::snarl_code_t::is_reversed()'],['../structvg_1_1MIPayload.html#a391d9d5e1cd44eccb39a6a31f56a6890',1,'vg::MIPayload::is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ab491085e63a9027e460098d5bc3f98ca',1,'vg::ZipCodeTree::tree_item_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af4a9de3c328470293caa0d958094201e',1,'vg::ZipCodeForest::child_info_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae0f46b456027c5360dad34c0480c8ebb',1,'vg::ZipCodeForest::interval_state_t::is_reversed()']]],
+ ['is_5freversed_5fin_5fparent_3021',['is_reversed_in_parent',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a81a6e5692e0b2100e9204bdb48454dd6',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['is_5froot_3022',['is_root',['../classvg_1_1WFATree.html#af1ad9e8285b7a9414d8af9ec257add49',1,'vg::WFATree::is_root()'],['../classvg_1_1SnarlManager.html#a294ce522d34dadb5288d6115c88dfa89',1,'vg::SnarlManager::is_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#afef6c85a6564d6d3ec65bfb245e1f38c',1,'handlegraph::SnarlDecomposition::is_root()']]],
+ ['is_5fsecondary_3023',['is_secondary',['../structvg_1_1Alignment.html#a59a4b8c7367fb468e46bcf6ae292888f',1,'vg::Alignment::is_secondary()'],['../classvg_1_1ReadFilter.html#a947155b6ed467a8ea83ac80db6e11a63',1,'vg::ReadFilter::is_secondary(const Read &read) const'],['../classvg_1_1ReadFilter.html#a44451e4c12ff1a923221d019c31c610c',1,'vg::ReadFilter::is_secondary(const MultipathAlignment &mp_aln) const'],['../classvg_1_1ReadFilter.html#ab4ae201744c8abc543d60afb24b294eb',1,'vg::ReadFilter::is_secondary(const Alignment &aln) const']]],
+ ['is_5fseed_3024',['is_seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab29219e6df18063f714a379f5d769cf7',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['is_5fself_5flooping_3025',['is_self_looping',['../classvg_1_1VG.html#ad09549b6cfab8e1097dd207e01e57812',1,'vg::VG']]],
+ ['is_5fsentinel_3026',['is_sentinel',['../classhandlegraph_1_1SnarlDecomposition.html#af3ce2079f249448a8c8a829daedd1678',1,'handlegraph::SnarlDecomposition']]],
+ ['is_5fsingle_5fstranded_3027',['is_single_stranded',['../namespacehandlegraph_1_1algorithms.html#afbca1e7b54575bfce7f0844dbda83c6f',1,'handlegraph::algorithms']]],
+ ['is_5fsingle_5fstranded_2ecpp_3028',['is_single_stranded.cpp',['../is__single__stranded_8cpp.html',1,'']]],
+ ['is_5fskippable_3029',['is_skippable',['../classvg_1_1algorithms_1_1Anchor.html#a002732eac1459215244c89710a4ef2e3',1,'vg::algorithms::Anchor']]],
+ ['is_5fsnarl_3030',['is_snarl',['../classhandlegraph_1_1SnarlDecomposition.html#a32b29fc153b3a355cae8b15008ec8c1b',1,'handlegraph::SnarlDecomposition']]],
+ ['is_5fsnarl_5fsmaller_5fthan_5freads_3031',['is_snarl_smaller_than_reads',['../classvg_1_1Genotyper.html#a7c7f091482612f6b0cd2baf0c19c45fb',1,'vg::Genotyper']]],
+ ['is_5fsnv_3032',['is_snv',['../structhaplo_1_1linear__haplo__structure.html#aa95f64d55f6bf7b1239396ba4a722a05',1,'haplo::linear_haplo_structure']]],
+ ['is_5fsolitary_5fref_3033',['is_solitary_ref',['../structhaplo_1_1linear__haplo__structure.html#a5909bdd11b10437a4d70af1fda222a85',1,'haplo::linear_haplo_structure']]],
+ ['is_5fsplit_3034',['is_split',['../classvg_1_1ReadFilter.html#a34d313741dcfe8c009dfcc380d1293ad',1,'vg::ReadFilter::is_split(const Read &read) const'],['../classvg_1_1ReadFilter.html#a956bc9e366bb25f9544dbb3d8573b5b5',1,'vg::ReadFilter::is_split(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a3fcb1771035304240c7a0401d84ef60b',1,'vg::ReadFilter::is_split(const MultipathAlignment &mp_aln) const']]],
+ ['is_5fstable_3035',['is_stable',['../structgafkluge_1_1GafStep.html#ad41f5cafc50a114daeec6b0cf08101eb',1,'gafkluge::GafStep']]],
+ ['is_5fstatic_3036',['is_static',['../structvg_1_1subcommand_1_1TickChainLink.html#aae7e5f61e0f577ae29fd404c6f0a9482',1,'vg::subcommand::TickChainLink::is_static()'],['../structvg_1_1Range.html#a07b020e2621ac7d0a6cc636384242c73',1,'vg::Range::is_static()'],['../structvg_1_1subcommand_1_1RangeArgSpec.html#a20410637df207e212fee01c268624d85',1,'vg::subcommand::RangeArgSpec::is_static()']]],
+ ['is_5ftail_5fnode_3037',['is_tail_node',['../classvg_1_1VG.html#a660692b8769618259f69be25bfed0bc3',1,'vg::VG::is_tail_node(nid_t id)'],['../classvg_1_1VG.html#af58b227f21324d30be531088ed49b0f1',1,'vg::VG::is_tail_node(Node *node)'],['../namespacevg_1_1algorithms.html#ac8e4eb795d14d441c4b2944c070a1d78',1,'vg::algorithms::is_tail_node()']]],
+ ['is_5ftraversable_3038',['is_traversable',['../classvg_1_1LegacyCaller.html#a369827412ee13857083444776aa240c7',1,'vg::LegacyCaller::is_traversable()'],['../classvg_1_1MCMCCaller.html#a1e632e1f6e31cd559ec0a6c3cff1db7c',1,'vg::MCMCCaller::is_traversable()']]],
+ ['is_5ftrivial_3039',['is_trivial',['../classvg_1_1SnarlManager.html#a5fdc8b210fa5339485b1e0a8ab1683b6',1,'vg::SnarlManager']]],
+ ['is_5ftrivial_5fchain_3040',['is_trivial_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a8e92509271514f3510eabdfbe7da9e1d',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::is_trivial_chain()'],['../structvg_1_1MIPayload.html#a9a1ab910b382a0ec41e12036f9b8ae04',1,'vg::MIPayload::is_trivial_chain()']]],
+ ['is_5fvalid_3041',['is_valid',['../classvg_1_1Sampler.html#a6f979036816c6f3657c98193b9b1e22d',1,'vg::Sampler::is_valid()'],['../classvg_1_1VG.html#aa77d93fdf76698460ce509ea5dcde954',1,'vg::VG::is_valid()'],['../structvg_1_1Range.html#a15b962d68b5743aa9ba5f8a487007a83',1,'vg::Range::is_valid()']]],
+ ['is_5fvalid_5ftag_3042',['is_valid_tag',['../classvg_1_1io_1_1Registry.html#a4985634eed56438635dfbe0999103305',1,'vg::io::Registry']]],
+ ['is_5fvg_3043',['is_vg',['../classvg_1_1LegacyCaller.html#a80d266e926310b4def5ac48e3211029f',1,'vg::LegacyCaller']]],
+ ['is_5fweakly_5fconnected_3044',['is_weakly_connected',['../namespacehandlegraph_1_1algorithms.html#a99bd1e8b398ce2df3530cc47baef8818',1,'handlegraph::algorithms']]],
+ ['isatgc_3045',['isATGC',['../namespacevg.html#a92c923774a6526b7bfc7f06ae4ae7a18',1,'vg']]],
+ ['isbgzf_3046',['IsBGZF',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a1eb2633e42ca1b50ab167497e581e6bd',1,'vg::io::BlockedGzipInputStream']]],
+ ['isforward_3047',['isForward',['../structvg_1_1BREAKPOINT.html#a3179531d48993e05d802907b730e1631',1,'vg::BREAKPOINT']]],
+ ['issue_5furl_3048',['ISSUE_URL',['../namespacevg.html#ae77436235694e5e661c74799ab326d0b',1,'vg']]],
+ ['it_3049',['it',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1bc7243523f7c66a5d86bbe6b28176af',1,'vg::ZipCodeTree::iterator::it()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3ab48e9f50bb0651c4eef055721366ea',1,'vg::ZipCodeTree::reverse_iterator::it()']]],
+ ['item_3050',['Item',['../structvg_1_1Funnel_1_1Item.html',1,'vg::Funnel']]],
+ ['item_5fbonus_3051',['item_bonus',['../classvg_1_1MinimizerMapper.html#a7646fc428d4eb41fb022dd9c61afa687',1,'vg::MinimizerMapper']]],
+ ['item_5fcount_3052',['item_count',['../structvg_1_1MatchPos_1_1PathList.html#ad3ebb006eb120b2934d64cece179d0e8',1,'vg::MatchPos::PathList']]],
+ ['item_5fscale_3053',['item_scale',['../classvg_1_1MinimizerMapper.html#af637ac92b12ecfebb815cedb5d56f58e',1,'vg::MinimizerMapper']]],
+ ['item_5fvo_3054',['item_vo',['../classvg_1_1io_1_1MessageIterator.html#a1f58abce5de3c8f71a82e689c0170c49',1,'vg::io::MessageIterator']]],
+ ['items_3055',['items',['../structvg_1_1Funnel_1_1Stage.html#a787bab13fd8bd1bccb1ac8e7821688c6',1,'vg::Funnel::Stage::items()'],['../structvg_1_1VectorView.html#a1d1194d5eac47211eda065d3dc6312ef',1,'vg::VectorView::items()']]],
+ ['iteratee_3056',['iteratee',['../classvg_1_1ShuffledPairs_1_1iterator.html#a09d41523db4b9b9c6cebb02ecf7bfa3c',1,'vg::ShuffledPairs::iterator']]],
+ ['iteratee_2ehpp_3057',['iteratee.hpp',['../iteratee_8hpp.html',1,'']]],
+ ['iterator_3058',['iterator',['../classvg_1_1ShuffledPairs_1_1iterator.html',1,'vg::ShuffledPairs::iterator'],['../classvg_1_1ZipCodeTree_1_1iterator.html',1,'vg::ZipCodeTree::iterator'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html',1,'handlegraph::PathForEachSocket::iterator'],['../classvg_1_1PhasedGenome_1_1iterator.html',1,'vg::PhasedGenome::iterator'],['../structvg_1_1PathIndex.html#a0a0f36c0f57cc92dfb70f05eb4e5c482',1,'vg::PathIndex::iterator()'],['../classvg_1_1ShuffledPairs_1_1iterator.html#ade5cfb8f4e824c4d02c51df5ca396096',1,'vg::ShuffledPairs::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ShuffledPairs_1_1iterator.html#a3b52dd39c46e409ef1bfd67ab8ee76e4',1,'vg::ShuffledPairs::iterator::iterator(const ShuffledPairs &iteratee, size_t start_at)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0f330d79400d74c3da0c81e4af73d441',1,'vg::PhasedGenome::iterator::iterator(size_t rank, int haplotype_number, HaplotypeNode *haplo_node)'],['../classvg_1_1PhasedGenome_1_1iterator.html#ac8ddc9db361c6f07887fdc36b5484bcf',1,'vg::PhasedGenome::iterator::iterator()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a03bdcb94d8ed8b6e895ff003412185e4',1,'vg::PhasedGenome::iterator::iterator(const iterator &other)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aba25925d1c05e690d672b69ff66a3beb',1,'vg::ZipCodeTree::iterator::iterator(vector< tree_item_t >::const_iterator begin, vector< tree_item_t >::const_iterator end)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a51bef2f0839b26694742584b8a6dbedd',1,'vg::ZipCodeTree::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a171cb654dcd53b1bf78670b4002ba988',1,'vg::ZipCodeTree::iterator::iterator(iterator &&other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac02b7134a97591fcd4a821093a0a4ab4',1,'handlegraph::PathForEachSocket::iterator::iterator(const iterator &other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aed3d6dd2502cf236a6a55ed29e8c41dc',1,'handlegraph::PathForEachSocket::iterator::iterator()=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#af854ca3bd6cdbcfc8af01f7879f85106',1,'handlegraph::PathForEachSocket::iterator::iterator(const step_handle_t &step, bool force_unequal, const PathHandleGraph *graph)']]],
+ ['iterator_5fcategory_3059',['iterator_category',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#afe1f2a02d394f83c867bdca78ac9fc50',1,'std::iterator_traits< vg::PhasedGenome::iterator >::iterator_category()'],['../classvg_1_1count__back__inserter.html#a21cffdfe58f87b579e5f71c16390e39d',1,'vg::count_back_inserter::iterator_category()'],['../structvg_1_1VectorView_1_1const__iterator.html#a3e5943959256e2400b3ab9b486cad7a9',1,'vg::VectorView::const_iterator::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#a11520b7b8d397962dd529faebccde56a',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a01b368cc72243f1d414e88999b856b34',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::iterator_category()']]],
+ ['iterator_5ftraits_3c_20vg_3a_3aphasedgenome_3a_3aiterator_20_3e_3060',['iterator_traits< vg::PhasedGenome::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html',1,'std']]],
+ ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3aiterator_20_3e_3061',['iterator_traits< vg::ZipCodeTree::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html',1,'std']]],
+ ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3areverse_5fiterator_20_3e_3062',['iterator_traits< vg::ZipCodeTree::reverse_iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html',1,'std']]],
+ ['iterfcmp_3063',['IterFCmp',['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html',1,'vg::IncrementalSubgraph']]]
];
diff --git a/search/all_a.js b/search/all_a.js
index bd1c009eb6..e4c8efb234 100644
--- a/search/all_a.js
+++ b/search/all_a.js
@@ -1,33 +1,33 @@
var searchData=
[
- ['j2pb_5ferror_3062',['j2pb_error',['../classj2pb__error.html',1,'j2pb_error'],['../classj2pb__error.html#af314b5998280a0298ef786b0d3e50765',1,'j2pb_error::j2pb_error(const std::string &e)'],['../classj2pb__error.html#a8276d8df905431fe862af63d9e2eb09a',1,'j2pb_error::j2pb_error(const FieldDescriptor *field, const std::string &e)']]],
- ['jaccard_5fcoefficient_3063',['jaccard_coefficient',['../namespacevg.html#aff10785a6df2466c851785b406172e89',1,'vg']]],
- ['jitter_5fhomopolymer_5fends_3064',['jitter_homopolymer_ends',['../classvg_1_1MultipathAlignmentGraph.html#a406e1b266f46b28d5d7b4e2041a9210d',1,'vg::MultipathAlignmentGraph']]],
- ['job_5ffunc_3065',['job_func',['../classvg_1_1JobSchedule.html#a801f56bdc606a6ef0c3c26ac2a27ec24',1,'vg::JobSchedule']]],
- ['job_5fid_3066',['job_id',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a0f28a2f70f5f09a423d0f97a8e4343c4',1,'vg::Haplotypes::TopLevelChain']]],
- ['job_5fschedule_2ecpp_3067',['job_schedule.cpp',['../job__schedule_8cpp.html',1,'']]],
- ['job_5fschedule_2ehpp_3068',['job_schedule.hpp',['../job__schedule_8hpp.html',1,'']]],
- ['job_5ftype_3069',['job_type',['../structjob__type.html',1,'']]],
- ['jobs_3070',['jobs',['../classvg_1_1Haplotypes.html#af1b40bc51ea14870df84ab86ca71c0ce',1,'vg::Haplotypes']]],
- ['jobs_5ffor_5fcached_5fpaths_3071',['jobs_for_cached_paths',['../classvg_1_1Haplotypes.html#a5974594af8a92b2e030163a5359a7265',1,'vg::Haplotypes']]],
- ['jobschedule_3072',['JobSchedule',['../classvg_1_1JobSchedule.html',1,'vg::JobSchedule'],['../classvg_1_1JobSchedule.html#a3a959781a3d2b43dba66483468b27401',1,'vg::JobSchedule::JobSchedule()']]],
- ['join_3073',['join',['../structvg_1_1WFAAlignment.html#af2ab05c29ced20c7ad917e83a8b8c71a',1,'vg::WFAAlignment']]],
- ['join_5fheads_3074',['join_heads',['../classvg_1_1VG.html#a817384b8d147371448ad60e1db097b52',1,'vg::VG::join_heads(void)'],['../classvg_1_1VG.html#adc40377520118436b729cd68be16d0ba',1,'vg::VG::join_heads(Node *node, bool from_start=false)']]],
- ['join_5fmain_2ecpp_3075',['join_main.cpp',['../join__main_8cpp.html',1,'']]],
- ['join_5ftails_3076',['join_tails',['../classvg_1_1VG.html#a33e3f7942afd3ca82bfb78083c245146',1,'vg::VG']]],
- ['joinedsplicegraph_3077',['JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html',1,'vg::JoinedSpliceGraph'],['../classvg_1_1JoinedSpliceGraph.html#ac9f9c336a88b2c291c348cff4c30d563',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph(const HandleGraph &parent_graph, const IncrementalSubgraph &left_subgraph, handle_t left_splice_node, size_t left_splice_offset, const IncrementalSubgraph &right_subgraph, handle_t right_splice_node, size_t right_splice_offset)'],['../classvg_1_1JoinedSpliceGraph.html#a994fd7ad86bf77793da9a6ee2612cabc',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph()=default']]],
- ['joint_5finitial_5fdistr_3078',['joint_initial_distr',['../classvg_1_1NGSSimulator.html#a147d596d664076c94b468230d78290c4',1,'vg::NGSSimulator']]],
- ['json_3079',['JSON',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa0ecd11c1d7a287401d148a23bbd7a2f8',1,'vg::subcommand']]],
- ['json2graph_3080',['json2graph',['../namespacevg_1_1io.html#a550ead63070ee82e14eb16659099755b',1,'vg::io']]],
- ['json2graph_2ehpp_3081',['json2graph.hpp',['../json2graph_8hpp.html',1,'']]],
- ['json2pb_3082',['json2pb',['../json2pb_8cpp.html#a2eb37967f22b379b956fe97f7c974203',1,'json2pb(Message &msg, const char *buf, size_t size): json2pb.cpp'],['../json2pb_8cpp.html#a947740c497c7efcc20241ca8dcd890c5',1,'json2pb(Message &msg, FILE *fp): json2pb.cpp'],['../json2pb_8cpp.html#a3b3ae0b9e33187a31a408a4e4e82898b',1,'json2pb(Message &msg, const std::string &data): json2pb.cpp'],['../json2pb_8h.html#aee640ab0597802043d3778f2f8d251ab',1,'json2pb(google::protobuf::Message &msg, const char *buf, size_t size): json2pb.h'],['../json2pb_8h.html#ad3edc7550a299bb85558377c35581364',1,'json2pb(google::protobuf::Message &msg, FILE *fp): json2pb.h'],['../json2pb_8h.html#ae83324c05726c12f6a3602a6aa7b2182',1,'json2pb(google::protobuf::Message &msg, const std::string &data): json2pb.h']]],
- ['json2pb_2ecpp_3083',['json2pb.cpp',['../json2pb_8cpp.html',1,'']]],
- ['json2pb_2eh_3084',['json2pb.h',['../json2pb_8h.html',1,'']]],
- ['json_5fautoptr_3085',['json_autoptr',['../structjson__autoptr.html',1,'json_autoptr'],['../structjson__autoptr.html#a3879742fd5ef3183006f93ebc6e57678',1,'json_autoptr::json_autoptr()']]],
- ['json_5fboolean_3086',['json_boolean',['../json2pb_8cpp.html#a250fb410df685e30b6cac97ff6e76982',1,'json2pb.cpp']]],
- ['json_5fstream_5fhelper_2ehpp_3087',['json_stream_helper.hpp',['../json__stream__helper_8hpp.html',1,'']]],
- ['jsonstreamhelper_3088',['JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html',1,'vg::io::JSONStreamHelper< T >'],['../classvg_1_1io_1_1JSONStreamHelper.html#ad795787bc270c5cfe737535f2e242aa6',1,'vg::io::JSONStreamHelper::JSONStreamHelper()']]],
- ['jump_5falong_5fclosest_5fpath_3089',['jump_along_closest_path',['../namespacevg_1_1algorithms.html#a633a1600c6a7e447c040fefb1432e508',1,'vg::algorithms']]],
- ['jump_5falong_5fpath_2ecpp_3090',['jump_along_path.cpp',['../jump__along__path_8cpp.html',1,'']]],
- ['jump_5falong_5fpath_2ehpp_3091',['jump_along_path.hpp',['../jump__along__path_8hpp.html',1,'']]]
+ ['j2pb_5ferror_3064',['j2pb_error',['../classj2pb__error.html',1,'j2pb_error'],['../classj2pb__error.html#af314b5998280a0298ef786b0d3e50765',1,'j2pb_error::j2pb_error(const std::string &e)'],['../classj2pb__error.html#a8276d8df905431fe862af63d9e2eb09a',1,'j2pb_error::j2pb_error(const FieldDescriptor *field, const std::string &e)']]],
+ ['jaccard_5fcoefficient_3065',['jaccard_coefficient',['../namespacevg.html#aff10785a6df2466c851785b406172e89',1,'vg']]],
+ ['jitter_5fhomopolymer_5fends_3066',['jitter_homopolymer_ends',['../classvg_1_1MultipathAlignmentGraph.html#a406e1b266f46b28d5d7b4e2041a9210d',1,'vg::MultipathAlignmentGraph']]],
+ ['job_5ffunc_3067',['job_func',['../classvg_1_1JobSchedule.html#a801f56bdc606a6ef0c3c26ac2a27ec24',1,'vg::JobSchedule']]],
+ ['job_5fid_3068',['job_id',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a0f28a2f70f5f09a423d0f97a8e4343c4',1,'vg::Haplotypes::TopLevelChain']]],
+ ['job_5fschedule_2ecpp_3069',['job_schedule.cpp',['../job__schedule_8cpp.html',1,'']]],
+ ['job_5fschedule_2ehpp_3070',['job_schedule.hpp',['../job__schedule_8hpp.html',1,'']]],
+ ['job_5ftype_3071',['job_type',['../structjob__type.html',1,'']]],
+ ['jobs_3072',['jobs',['../classvg_1_1Haplotypes.html#af1b40bc51ea14870df84ab86ca71c0ce',1,'vg::Haplotypes']]],
+ ['jobs_5ffor_5fcached_5fpaths_3073',['jobs_for_cached_paths',['../classvg_1_1Haplotypes.html#a5974594af8a92b2e030163a5359a7265',1,'vg::Haplotypes']]],
+ ['jobschedule_3074',['JobSchedule',['../classvg_1_1JobSchedule.html',1,'vg::JobSchedule'],['../classvg_1_1JobSchedule.html#a3a959781a3d2b43dba66483468b27401',1,'vg::JobSchedule::JobSchedule()']]],
+ ['join_3075',['join',['../structvg_1_1WFAAlignment.html#af2ab05c29ced20c7ad917e83a8b8c71a',1,'vg::WFAAlignment']]],
+ ['join_5fheads_3076',['join_heads',['../classvg_1_1VG.html#a817384b8d147371448ad60e1db097b52',1,'vg::VG::join_heads(void)'],['../classvg_1_1VG.html#adc40377520118436b729cd68be16d0ba',1,'vg::VG::join_heads(Node *node, bool from_start=false)']]],
+ ['join_5fmain_2ecpp_3077',['join_main.cpp',['../join__main_8cpp.html',1,'']]],
+ ['join_5ftails_3078',['join_tails',['../classvg_1_1VG.html#a33e3f7942afd3ca82bfb78083c245146',1,'vg::VG']]],
+ ['joinedsplicegraph_3079',['JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html',1,'vg::JoinedSpliceGraph'],['../classvg_1_1JoinedSpliceGraph.html#ac9f9c336a88b2c291c348cff4c30d563',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph(const HandleGraph &parent_graph, const IncrementalSubgraph &left_subgraph, handle_t left_splice_node, size_t left_splice_offset, const IncrementalSubgraph &right_subgraph, handle_t right_splice_node, size_t right_splice_offset)'],['../classvg_1_1JoinedSpliceGraph.html#a994fd7ad86bf77793da9a6ee2612cabc',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph()=default']]],
+ ['joint_5finitial_5fdistr_3080',['joint_initial_distr',['../classvg_1_1NGSSimulator.html#a147d596d664076c94b468230d78290c4',1,'vg::NGSSimulator']]],
+ ['json_3081',['JSON',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa0ecd11c1d7a287401d148a23bbd7a2f8',1,'vg::subcommand']]],
+ ['json2graph_3082',['json2graph',['../namespacevg_1_1io.html#a550ead63070ee82e14eb16659099755b',1,'vg::io']]],
+ ['json2graph_2ehpp_3083',['json2graph.hpp',['../json2graph_8hpp.html',1,'']]],
+ ['json2pb_3084',['json2pb',['../json2pb_8cpp.html#a2eb37967f22b379b956fe97f7c974203',1,'json2pb(Message &msg, const char *buf, size_t size): json2pb.cpp'],['../json2pb_8cpp.html#a947740c497c7efcc20241ca8dcd890c5',1,'json2pb(Message &msg, FILE *fp): json2pb.cpp'],['../json2pb_8cpp.html#a3b3ae0b9e33187a31a408a4e4e82898b',1,'json2pb(Message &msg, const std::string &data): json2pb.cpp'],['../json2pb_8h.html#aee640ab0597802043d3778f2f8d251ab',1,'json2pb(google::protobuf::Message &msg, const char *buf, size_t size): json2pb.h'],['../json2pb_8h.html#ad3edc7550a299bb85558377c35581364',1,'json2pb(google::protobuf::Message &msg, FILE *fp): json2pb.h'],['../json2pb_8h.html#ae83324c05726c12f6a3602a6aa7b2182',1,'json2pb(google::protobuf::Message &msg, const std::string &data): json2pb.h']]],
+ ['json2pb_2ecpp_3085',['json2pb.cpp',['../json2pb_8cpp.html',1,'']]],
+ ['json2pb_2eh_3086',['json2pb.h',['../json2pb_8h.html',1,'']]],
+ ['json_5fautoptr_3087',['json_autoptr',['../structjson__autoptr.html',1,'json_autoptr'],['../structjson__autoptr.html#a3879742fd5ef3183006f93ebc6e57678',1,'json_autoptr::json_autoptr()']]],
+ ['json_5fboolean_3088',['json_boolean',['../json2pb_8cpp.html#a250fb410df685e30b6cac97ff6e76982',1,'json2pb.cpp']]],
+ ['json_5fstream_5fhelper_2ehpp_3089',['json_stream_helper.hpp',['../json__stream__helper_8hpp.html',1,'']]],
+ ['jsonstreamhelper_3090',['JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html',1,'vg::io::JSONStreamHelper< T >'],['../classvg_1_1io_1_1JSONStreamHelper.html#ad795787bc270c5cfe737535f2e242aa6',1,'vg::io::JSONStreamHelper::JSONStreamHelper()']]],
+ ['jump_5falong_5fclosest_5fpath_3091',['jump_along_closest_path',['../namespacevg_1_1algorithms.html#a633a1600c6a7e447c040fefb1432e508',1,'vg::algorithms']]],
+ ['jump_5falong_5fpath_2ecpp_3092',['jump_along_path.cpp',['../jump__along__path_8cpp.html',1,'']]],
+ ['jump_5falong_5fpath_2ehpp_3093',['jump_along_path.hpp',['../jump__along__path_8hpp.html',1,'']]]
];
diff --git a/search/all_b.js b/search/all_b.js
index 602579ee99..635573b4f0 100644
--- a/search/all_b.js
+++ b/search/all_b.js
@@ -1,52 +1,52 @@
var searchData=
[
- ['k_3092',['k',['../classvg_1_1ParallelKFFReader.html#a8060dbef6faaf286f33f3af5be8d32c6',1,'vg::ParallelKFFReader::k()'],['../classvg_1_1MEMAccelerator.html#ab01dc4463ca21d56a9059e38f7e6a2fe',1,'vg::MEMAccelerator::k()'],['../structvg_1_1Haplotypes_1_1Header.html#ab0357bc5db25d4ff1590fc540f4f1ffe',1,'vg::Haplotypes::Header::k()'],['../structHaplotypesConfig.html#aaa9163a17295c26ec249d47205be0177',1,'HaplotypesConfig::k()'],['../classvg_1_1Haplotypes.html#af081161e7b2e1867d83aef6427082cd5',1,'vg::Haplotypes::k()'],['../classvg_1_1FlowTraversalFinder.html#a6f3d138926abc87592571c2182faf31e',1,'vg::FlowTraversalFinder::K()'],['../namespacehaplotypes__defaults.html#a53866dde2f0b53eb6e41923c4e3eb9ff',1,'haplotypes_defaults::k()']]],
- ['k_5fwidest_5fpaths_2ecpp_3093',['k_widest_paths.cpp',['../k__widest__paths_8cpp.html',1,'']]],
- ['k_5fwidest_5fpaths_2ehpp_3094',['k_widest_paths.hpp',['../k__widest__paths_8hpp.html',1,'']]],
- ['karger_5fstein_3095',['karger_stein',['../classvg_1_1MCMCGenotyper.html#ae04571da16e2129ef7d56aea9cc899b5',1,'vg::MCMCGenotyper']]],
- ['kargers_5fmin_5fcut_3096',['kargers_min_cut',['../namespacevg_1_1algorithms.html#a0820d23864c46dc1bc71ec68aee4e55e',1,'vg::algorithms']]],
- ['keep_3097',['keep',['../structvg_1_1Counts.html#a4ffc0e936d50a5bce649cc973f8cbe98',1,'vg::Counts']]],
- ['keep_5fconflicted_5fgenotypes_3098',['keep_conflicted_genotypes',['../classvg_1_1Deconstructor.html#af67896b3d980c332c69159fecafb2ae2',1,'vg::Deconstructor']]],
- ['keep_5fintermediates_3099',['keep_intermediates',['../classvg_1_1IndexRegistry.html#a1b0ad4bff3fc2a7d514c6e1b46d3ca23',1,'vg::IndexRegistry']]],
- ['keep_5fpath_3100',['keep_path',['../classvg_1_1VG.html#a65cc16f52f478a25e84c6f1fc2805915',1,'vg::VG']]],
- ['keep_5fpaths_3101',['keep_paths',['../classvg_1_1Paths.html#a4ed60968ce4b7d6e4bd7f3d24c895f94',1,'vg::Paths::keep_paths()'],['../classvg_1_1VG.html#ac2aa9d438bcec4d7facbfcc44abea8fd',1,'vg::VG::keep_paths()']]],
- ['key_3102',['key',['../classvg_1_1ProblemDumpExplainer.html#a40a9715e80632f9e2e70b4d54f749579',1,'vg::ProblemDumpExplainer::key()'],['../structvg_1_1WFAPoint.html#ae19b5b586bb269c2e465d6a8e87c0041',1,'vg::WFAPoint::key()']]],
- ['key_5ftype_3103',['key_type',['../structvg_1_1WFAPoint.html#a7f118f60c7b8ac46926e6627afaa4d23',1,'vg::WFAPoint']]],
- ['kff_2ecpp_3104',['kff.cpp',['../kff_8cpp.html',1,'']]],
- ['kff_2ehpp_3105',['kff.hpp',['../kff_8hpp.html',1,'']]],
- ['kff_5fblock_5fsize_3106',['KFF_BLOCK_SIZE',['../classvg_1_1Recombinator.html#aae3d85fd81e178aedb975015652a6cc4',1,'vg::Recombinator']]],
- ['kff_5fbytes_3107',['kff_bytes',['../namespacevg.html#ae8290bb0f46f4410bd8d19a9214f42d9',1,'vg']]],
- ['kff_5fdecode_3108',['kff_decode',['../namespacevg.html#adbd931ab5e8c6d8549262292b5fd1bdb',1,'vg::kff_decode(uint8_t byte, size_t chars, const std::string &decoding, std::string &output)'],['../namespacevg.html#a508b66314d777de73b671860cc1ba66f',1,'vg::kff_decode(const uint8_t *kmer, size_t k, const std::string &decoding)']]],
- ['kff_5fencode_3109',['kff_encode',['../namespacevg.html#a703f0e894fc3faab71d1f56963a1b1f2',1,'vg::kff_encode(const std::string &kmer, size_t start, size_t limit, const uint8_t *encoding)'],['../namespacevg.html#ad8ec52a5e105f9ff5dc0ee6a882f11ef',1,'vg::kff_encode(const std::string &kmer, const uint8_t *encoding)']]],
- ['kff_5fget_3110',['kff_get',['../namespacevg.html#a971fa4f581aa13c4d3a29728485a496a',1,'vg']]],
- ['kff_5finvert_3111',['kff_invert',['../namespacevg.html#afff8c68e07248aa6b304c3b9f45f8e4b',1,'vg']]],
- ['kff_5fis_5ftrivial_3112',['kff_is_trivial',['../namespacevg.html#ab293dcf09c223de43976346c70763cd8',1,'vg']]],
- ['kff_5fparse_3113',['kff_parse',['../namespacevg.html#ac3021a605be981221a7454ed41329abb',1,'vg']]],
- ['kff_5frecode_3114',['kff_recode',['../namespacevg.html#a1d573b735cb520c77d373fe1231fb94d',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, size_t chars, const uint8_t *encoding)'],['../namespacevg.html#acc31374a96e3cd653324ab57eb9714ff',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, const uint8_t *encoding)'],['../namespacevg.html#ab6b770ea79c9b74e89ecff6f5e347bf6',1,'vg::kff_recode(const uint8_t *kmer, size_t k, kff_recoding_t recoding)'],['../namespacevg.html#a92ba361b3ec6a01bac17e71af08d2223',1,'vg::kff_recode(const uint8_t *kmers, size_t n, size_t k, kff_recoding_t recoding)']]],
- ['kff_5frecode_5ftrivial_3115',['kff_recode_trivial',['../namespacevg.html#ad52eac0801905a9d5f2ba805f1387213',1,'vg']]],
- ['kff_5frecoding_3116',['kff_recoding',['../namespacevg.html#a1429f1c00018d575e753609329896f31',1,'vg']]],
- ['kff_5frecoding_5ft_3117',['kff_recoding_t',['../structvg_1_1kff__recoding__t.html',1,'vg']]],
- ['kff_5freverse_5fcomplement_3118',['kff_reverse_complement',['../namespacevg.html#a213d22fbc9d8056efb8082e529ab0f22',1,'vg']]],
- ['kff_5fset_3119',['kff_set',['../namespacevg.html#ad78d3175e64e6a9c019275b5b3e17fe5',1,'vg']]],
- ['kmer_3120',['kmer',['../structvg_1_1KmerPosition.html#a79c4fa6766d55a1fea8fdc00adab02b3',1,'vg::KmerPosition']]],
- ['kmer_2ecpp_3121',['kmer.cpp',['../kmer_8cpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8cpp.html',1,'(Global Namespace)']]],
- ['kmer_2ehpp_3122',['kmer.hpp',['../kmer_8hpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8hpp.html',1,'(Global Namespace)']]],
- ['kmer_5fcounts_3123',['kmer_counts',['../structvg_1_1Haplotypes_1_1Subchain.html#a68ff855e7047ec8154df21ad2a817c10',1,'vg::Haplotypes::Subchain::kmer_counts()'],['../classvg_1_1Haplotypes.html#a48ed72eff81d77df7a4159afd0c6d20e',1,'vg::Haplotypes::kmer_counts()']]],
- ['kmer_5finput_3124',['kmer_input',['../structHaplotypesConfig.html#adfb31d19cd310ad8ec89e29fe0dd5e28',1,'HaplotypesConfig']]],
- ['kmer_5flength_3125',['kmer_length',['../structPruningParameters.html#ae3cd0ffe16bbdd3d2d5092ef57f4219a',1,'PruningParameters']]],
- ['kmer_5foutput_3126',['kmer_output',['../structHaplotypesConfig.html#ac2857225a416e464c728691eb28d8a2e',1,'HaplotypesConfig']]],
- ['kmer_5fpresence_3127',['kmer_presence',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5f',1,'vg::Recombinator']]],
- ['kmer_5fsize_3128',['kmer_size',['../classvg_1_1VariantAdder.html#acda70938d1a3eb2eb5da18dd2805ae26',1,'vg::VariantAdder']]],
- ['kmer_5ft_3129',['kmer_t',['../structvg_1_1kmer__t.html',1,'vg::kmer_t'],['../structvg_1_1algorithms_1_1kmer__t.html',1,'vg::algorithms::kmer_t'],['../structvg_1_1kmer__t.html#a83d1946c92dcdc9c6adbc03b4da30312',1,'vg::kmer_t::kmer_t()'],['../structvg_1_1algorithms_1_1kmer__t.html#ae029bc309fbd34a7dd7391f9a74f79f5',1,'vg::algorithms::kmer_t::kmer_t()']]],
- ['kmer_5fto_5fgcsa_5fkmers_3130',['kmer_to_gcsa_kmers',['../namespacevg.html#a661fc17618ee9ff7bd9d469c74c63369',1,'vg']]],
- ['kmer_5ftype_3131',['kmer_type',['../classvg_1_1ParallelKFFReader.html#a2691b5fdcfab5c9b5187fdf3a979e2e1',1,'vg::ParallelKFFReader::kmer_type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a13b4b76384742f4ee127b52faff37aa6',1,'vg::Haplotypes::Subchain::kmer_type()'],['../classvg_1_1HaplotypePartitioner.html#a2780337120cfec8463356829af22aa97',1,'vg::HaplotypePartitioner::kmer_type()']]],
- ['kmermatch_3132',['KmerMatch',['../structvg_1_1KmerMatch.html',1,'vg']]],
- ['kmerposition_3133',['KmerPosition',['../structvg_1_1KmerPosition.html',1,'vg']]],
- ['kmers_3134',['kmers',['../structvg_1_1Haplotypes_1_1Subchain.html#a57018e7275a6afc9ba8548391b670c3a',1,'vg::Haplotypes::Subchain::kmers()'],['../structvg_1_1Recombinator_1_1Statistics.html#a5a5878a01bd909e752eb99795da76a1f',1,'vg::Recombinator::Statistics::kmers()'],['../classvg_1_1Haplotypes.html#a85b9a6d31a3485f0ccf925023543414b',1,'vg::Haplotypes::kmers()']]],
- ['kmers_5fmain_2ecpp_3135',['kmers_main.cpp',['../kmers__main_8cpp.html',1,'']]],
- ['kmers_5fpresent_3136',['kmers_present',['../structvg_1_1Haplotypes_1_1Subchain.html#ae50f824b6f2d2e9a33b16613c01a7096',1,'vg::Haplotypes::Subchain']]],
- ['kmp_2ecpp_3137',['kmp.cpp',['../kmp_8cpp.html',1,'']]],
- ['kmp_2ehpp_3138',['kmp.hpp',['../kmp_8hpp.html',1,'']]],
- ['kmp_5fsearch_3139',['kmp_search',['../namespacevg.html#a4f32c345e847a3627afcee659116730c',1,'vg']]],
- ['know_5foffset_3140',['know_offset',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a62a78fd952dc7239a74fd042eae0e562',1,'vg::io::BlockedGzipInputStream::know_offset()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae88df3ee23df1392e53453f82b1859e2',1,'vg::io::BlockedGzipOutputStream::know_offset()']]]
+ ['k_3094',['k',['../classvg_1_1ParallelKFFReader.html#a8060dbef6faaf286f33f3af5be8d32c6',1,'vg::ParallelKFFReader::k()'],['../classvg_1_1MEMAccelerator.html#ab01dc4463ca21d56a9059e38f7e6a2fe',1,'vg::MEMAccelerator::k()'],['../structvg_1_1Haplotypes_1_1Header.html#ab0357bc5db25d4ff1590fc540f4f1ffe',1,'vg::Haplotypes::Header::k()'],['../structHaplotypesConfig.html#aaa9163a17295c26ec249d47205be0177',1,'HaplotypesConfig::k()'],['../classvg_1_1Haplotypes.html#af081161e7b2e1867d83aef6427082cd5',1,'vg::Haplotypes::k()'],['../classvg_1_1FlowTraversalFinder.html#a6f3d138926abc87592571c2182faf31e',1,'vg::FlowTraversalFinder::K()'],['../namespacehaplotypes__defaults.html#a53866dde2f0b53eb6e41923c4e3eb9ff',1,'haplotypes_defaults::k()']]],
+ ['k_5fwidest_5fpaths_2ecpp_3095',['k_widest_paths.cpp',['../k__widest__paths_8cpp.html',1,'']]],
+ ['k_5fwidest_5fpaths_2ehpp_3096',['k_widest_paths.hpp',['../k__widest__paths_8hpp.html',1,'']]],
+ ['karger_5fstein_3097',['karger_stein',['../classvg_1_1MCMCGenotyper.html#ae04571da16e2129ef7d56aea9cc899b5',1,'vg::MCMCGenotyper']]],
+ ['kargers_5fmin_5fcut_3098',['kargers_min_cut',['../namespacevg_1_1algorithms.html#a0820d23864c46dc1bc71ec68aee4e55e',1,'vg::algorithms']]],
+ ['keep_3099',['keep',['../structvg_1_1Counts.html#a4ffc0e936d50a5bce649cc973f8cbe98',1,'vg::Counts']]],
+ ['keep_5fconflicted_5fgenotypes_3100',['keep_conflicted_genotypes',['../classvg_1_1Deconstructor.html#af67896b3d980c332c69159fecafb2ae2',1,'vg::Deconstructor']]],
+ ['keep_5fintermediates_3101',['keep_intermediates',['../classvg_1_1IndexRegistry.html#a1b0ad4bff3fc2a7d514c6e1b46d3ca23',1,'vg::IndexRegistry']]],
+ ['keep_5fpath_3102',['keep_path',['../classvg_1_1VG.html#a65cc16f52f478a25e84c6f1fc2805915',1,'vg::VG']]],
+ ['keep_5fpaths_3103',['keep_paths',['../classvg_1_1Paths.html#a4ed60968ce4b7d6e4bd7f3d24c895f94',1,'vg::Paths::keep_paths()'],['../classvg_1_1VG.html#ac2aa9d438bcec4d7facbfcc44abea8fd',1,'vg::VG::keep_paths()']]],
+ ['key_3104',['key',['../classvg_1_1ProblemDumpExplainer.html#a40a9715e80632f9e2e70b4d54f749579',1,'vg::ProblemDumpExplainer::key()'],['../structvg_1_1WFAPoint.html#ae19b5b586bb269c2e465d6a8e87c0041',1,'vg::WFAPoint::key()']]],
+ ['key_5ftype_3105',['key_type',['../structvg_1_1WFAPoint.html#a7f118f60c7b8ac46926e6627afaa4d23',1,'vg::WFAPoint']]],
+ ['kff_2ecpp_3106',['kff.cpp',['../kff_8cpp.html',1,'']]],
+ ['kff_2ehpp_3107',['kff.hpp',['../kff_8hpp.html',1,'']]],
+ ['kff_5fblock_5fsize_3108',['KFF_BLOCK_SIZE',['../classvg_1_1Recombinator.html#aae3d85fd81e178aedb975015652a6cc4',1,'vg::Recombinator']]],
+ ['kff_5fbytes_3109',['kff_bytes',['../namespacevg.html#ae8290bb0f46f4410bd8d19a9214f42d9',1,'vg']]],
+ ['kff_5fdecode_3110',['kff_decode',['../namespacevg.html#adbd931ab5e8c6d8549262292b5fd1bdb',1,'vg::kff_decode(uint8_t byte, size_t chars, const std::string &decoding, std::string &output)'],['../namespacevg.html#a508b66314d777de73b671860cc1ba66f',1,'vg::kff_decode(const uint8_t *kmer, size_t k, const std::string &decoding)']]],
+ ['kff_5fencode_3111',['kff_encode',['../namespacevg.html#a703f0e894fc3faab71d1f56963a1b1f2',1,'vg::kff_encode(const std::string &kmer, size_t start, size_t limit, const uint8_t *encoding)'],['../namespacevg.html#ad8ec52a5e105f9ff5dc0ee6a882f11ef',1,'vg::kff_encode(const std::string &kmer, const uint8_t *encoding)']]],
+ ['kff_5fget_3112',['kff_get',['../namespacevg.html#a971fa4f581aa13c4d3a29728485a496a',1,'vg']]],
+ ['kff_5finvert_3113',['kff_invert',['../namespacevg.html#afff8c68e07248aa6b304c3b9f45f8e4b',1,'vg']]],
+ ['kff_5fis_5ftrivial_3114',['kff_is_trivial',['../namespacevg.html#ab293dcf09c223de43976346c70763cd8',1,'vg']]],
+ ['kff_5fparse_3115',['kff_parse',['../namespacevg.html#ac3021a605be981221a7454ed41329abb',1,'vg']]],
+ ['kff_5frecode_3116',['kff_recode',['../namespacevg.html#a1d573b735cb520c77d373fe1231fb94d',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, size_t chars, const uint8_t *encoding)'],['../namespacevg.html#acc31374a96e3cd653324ab57eb9714ff',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, const uint8_t *encoding)'],['../namespacevg.html#ab6b770ea79c9b74e89ecff6f5e347bf6',1,'vg::kff_recode(const uint8_t *kmer, size_t k, kff_recoding_t recoding)'],['../namespacevg.html#a92ba361b3ec6a01bac17e71af08d2223',1,'vg::kff_recode(const uint8_t *kmers, size_t n, size_t k, kff_recoding_t recoding)']]],
+ ['kff_5frecode_5ftrivial_3117',['kff_recode_trivial',['../namespacevg.html#ad52eac0801905a9d5f2ba805f1387213',1,'vg']]],
+ ['kff_5frecoding_3118',['kff_recoding',['../namespacevg.html#a1429f1c00018d575e753609329896f31',1,'vg']]],
+ ['kff_5frecoding_5ft_3119',['kff_recoding_t',['../structvg_1_1kff__recoding__t.html',1,'vg']]],
+ ['kff_5freverse_5fcomplement_3120',['kff_reverse_complement',['../namespacevg.html#a213d22fbc9d8056efb8082e529ab0f22',1,'vg']]],
+ ['kff_5fset_3121',['kff_set',['../namespacevg.html#ad78d3175e64e6a9c019275b5b3e17fe5',1,'vg']]],
+ ['kmer_3122',['kmer',['../structvg_1_1KmerPosition.html#a79c4fa6766d55a1fea8fdc00adab02b3',1,'vg::KmerPosition']]],
+ ['kmer_2ecpp_3123',['kmer.cpp',['../kmer_8cpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8cpp.html',1,'(Global Namespace)']]],
+ ['kmer_2ehpp_3124',['kmer.hpp',['../kmer_8hpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8hpp.html',1,'(Global Namespace)']]],
+ ['kmer_5fcounts_3125',['kmer_counts',['../structvg_1_1Haplotypes_1_1Subchain.html#a68ff855e7047ec8154df21ad2a817c10',1,'vg::Haplotypes::Subchain::kmer_counts()'],['../classvg_1_1Haplotypes.html#a48ed72eff81d77df7a4159afd0c6d20e',1,'vg::Haplotypes::kmer_counts()']]],
+ ['kmer_5finput_3126',['kmer_input',['../structHaplotypesConfig.html#adfb31d19cd310ad8ec89e29fe0dd5e28',1,'HaplotypesConfig']]],
+ ['kmer_5flength_3127',['kmer_length',['../structPruningParameters.html#ae3cd0ffe16bbdd3d2d5092ef57f4219a',1,'PruningParameters']]],
+ ['kmer_5foutput_3128',['kmer_output',['../structHaplotypesConfig.html#ac2857225a416e464c728691eb28d8a2e',1,'HaplotypesConfig']]],
+ ['kmer_5fpresence_3129',['kmer_presence',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5f',1,'vg::Recombinator']]],
+ ['kmer_5fsize_3130',['kmer_size',['../classvg_1_1VariantAdder.html#acda70938d1a3eb2eb5da18dd2805ae26',1,'vg::VariantAdder']]],
+ ['kmer_5ft_3131',['kmer_t',['../structvg_1_1kmer__t.html',1,'vg::kmer_t'],['../structvg_1_1algorithms_1_1kmer__t.html',1,'vg::algorithms::kmer_t'],['../structvg_1_1kmer__t.html#a83d1946c92dcdc9c6adbc03b4da30312',1,'vg::kmer_t::kmer_t()'],['../structvg_1_1algorithms_1_1kmer__t.html#ae029bc309fbd34a7dd7391f9a74f79f5',1,'vg::algorithms::kmer_t::kmer_t()']]],
+ ['kmer_5fto_5fgcsa_5fkmers_3132',['kmer_to_gcsa_kmers',['../namespacevg.html#a661fc17618ee9ff7bd9d469c74c63369',1,'vg']]],
+ ['kmer_5ftype_3133',['kmer_type',['../classvg_1_1ParallelKFFReader.html#a2691b5fdcfab5c9b5187fdf3a979e2e1',1,'vg::ParallelKFFReader::kmer_type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a13b4b76384742f4ee127b52faff37aa6',1,'vg::Haplotypes::Subchain::kmer_type()'],['../classvg_1_1HaplotypePartitioner.html#a2780337120cfec8463356829af22aa97',1,'vg::HaplotypePartitioner::kmer_type()']]],
+ ['kmermatch_3134',['KmerMatch',['../structvg_1_1KmerMatch.html',1,'vg']]],
+ ['kmerposition_3135',['KmerPosition',['../structvg_1_1KmerPosition.html',1,'vg']]],
+ ['kmers_3136',['kmers',['../structvg_1_1Haplotypes_1_1Subchain.html#a57018e7275a6afc9ba8548391b670c3a',1,'vg::Haplotypes::Subchain::kmers()'],['../structvg_1_1Recombinator_1_1Statistics.html#a5a5878a01bd909e752eb99795da76a1f',1,'vg::Recombinator::Statistics::kmers()'],['../classvg_1_1Haplotypes.html#a85b9a6d31a3485f0ccf925023543414b',1,'vg::Haplotypes::kmers()']]],
+ ['kmers_5fmain_2ecpp_3137',['kmers_main.cpp',['../kmers__main_8cpp.html',1,'']]],
+ ['kmers_5fpresent_3138',['kmers_present',['../structvg_1_1Haplotypes_1_1Subchain.html#ae50f824b6f2d2e9a33b16613c01a7096',1,'vg::Haplotypes::Subchain']]],
+ ['kmp_2ecpp_3139',['kmp.cpp',['../kmp_8cpp.html',1,'']]],
+ ['kmp_2ehpp_3140',['kmp.hpp',['../kmp_8hpp.html',1,'']]],
+ ['kmp_5fsearch_3141',['kmp_search',['../namespacevg.html#a4f32c345e847a3627afcee659116730c',1,'vg']]],
+ ['know_5foffset_3142',['know_offset',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a62a78fd952dc7239a74fd042eae0e562',1,'vg::io::BlockedGzipInputStream::know_offset()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae88df3ee23df1392e53453f82b1859e2',1,'vg::io::BlockedGzipOutputStream::know_offset()']]]
];
diff --git a/search/all_c.js b/search/all_c.js
index 2d592cdba9..146f1a48fd 100644
--- a/search/all_c.js
+++ b/search/all_c.js
@@ -1,154 +1,154 @@
var searchData=
[
- ['lane_3141',['lane',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a197d4920d6cbdfabac08f0de992a425a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
- ['large_5falignment_5fband_5fpadding_3142',['large_alignment_band_padding',['../classvg_1_1VariantAdder.html#aefe81cd7c81a7f3ba54c73e25c24ba3f',1,'vg::VariantAdder']]],
- ['larger_5fprime_3143',['larger_prime',['../classvg_1_1ShuffledPairs.html#a20b31eca7b0fc0185246c560fd8e266d',1,'vg::ShuffledPairs']]],
- ['last_3144',['last',['../structvg_1_1FeatureSet_1_1Feature.html#a9fb23b0b9affcc51a2610bb287b2082b',1,'vg::FeatureSet::Feature::last()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a1f9f68c932a97214ed914c8ba2c882f2',1,'vg::Counts::last()']]],
- ['last_5fcheckin_3145',['last_checkin',['../structvg_1_1Watchdog_1_1thread__state__t.html#ad54ba05d09be7a40b4e9504b8d020ea6',1,'vg::Watchdog::thread_state_t']]],
- ['last_5fcomponent_3146',['last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac65c35c84d5c173dc46077e3f0a831e5',1,'vg::ZipCode::chain_code_t']]],
- ['last_5fcorrect_5fstage_3147',['last_correct_stage',['../classvg_1_1Funnel.html#a996005ebe76091bbba404bf4a2a9a405',1,'vg::Funnel']]],
- ['last_5fgroup_5fmin_5fid_3148',['last_group_min_id',['../classvg_1_1StreamIndexBase.html#aef3a7bd46aeb49185a8cd6a9a261e883',1,'vg::StreamIndexBase']]],
- ['last_5fnode_5flength_3149',['last_node_length',['../structvg_1_1PathIndex.html#ac64a3532df12093eeccf3201184ea4d9',1,'vg::PathIndex']]],
- ['last_5fpath_5fposition_3150',['last_path_position',['../namespacevg.html#aa1c1e5b8ce9f9607976913317102d6dc',1,'vg']]],
- ['last_5fprogress_3151',['last_progress',['../classvg_1_1Progressive.html#a4984481e2b887e5fb78ea40728f1b97f',1,'vg::Progressive']]],
- ['last_5ftagged_5fstage_3152',['last_tagged_stage',['../classvg_1_1Funnel.html#ab53e816bd740407417b0bd8d14d5237c',1,'vg::Funnel']]],
- ['latest_3153',['latest',['../classvg_1_1Funnel.html#a933c8a296c5a680aa96b0b913c465250',1,'vg::Funnel']]],
- ['layout_5forder_3154',['layout_order',['../classvg_1_1DagifiedGraph.html#a50789da1e0a8c4ede5e2c1b73c7980a0',1,'vg::DagifiedGraph']]],
- ['layout_5forder_5fof_5fhandle_3155',['layout_order_of_handle',['../classvg_1_1DagifiedGraph.html#af364d952c459117f871368bcc9d33573',1,'vg::DagifiedGraph']]],
- ['lazier_5ftopological_5forder_3156',['lazier_topological_order',['../namespacehandlegraph_1_1algorithms.html#a26e0547c886eede7d3c0766907f39645',1,'handlegraph::algorithms']]],
- ['lazy_5ftopological_5forder_3157',['lazy_topological_order',['../namespacehandlegraph_1_1algorithms.html#ac9c0542f382080d1af3914714a62b9b6',1,'handlegraph::algorithms']]],
- ['lazy_5ftopological_5forder_5finternal_3158',['lazy_topological_order_internal',['../namespacehandlegraph_1_1algorithms.html#a53c98a2b062e6b5e92757945788b2e91',1,'handlegraph::algorithms']]],
- ['lazyrng_3159',['LazyRNG',['../classvg_1_1LazyRNG.html',1,'vg::LazyRNG'],['../classvg_1_1LazyRNG.html#a34ef87c442913becab5f596f50bd850e',1,'vg::LazyRNG::LazyRNG()']]],
- ['lcp_3160',['lcp',['../classvg_1_1BaseMapper.html#a4046b98185c00ff397089435d5b2b8d8',1,'vg::BaseMapper']]],
- ['lcp_5find_3161',['lcp_ind',['../classvg_1_1Filter.html#ab65e7196a6b891a266d16838e5d870d4',1,'vg::Filter']]],
- ['left_3162',['left',['../structvg_1_1Support.html#a31d59f62a09c71915856740c5450ecf5',1,'vg::Support']]],
- ['left_5fborder_3163',['left_border',['../classvg_1_1Viz.html#a4c472c524f9bdfc37d9073f9257ca529',1,'vg::Viz']]],
- ['left_5fdegree_3164',['left_degree',['../classvg_1_1VG.html#af9ac6e61dfa9350459dbb9586088c4a5',1,'vg::VG']]],
- ['left_5fends_3165',['left_ends',['../structvg_1_1ConstructedChunk.html#a0d6c6d4304190097a7a832d11a31bf3d',1,'vg::ConstructedChunk']]],
- ['left_5ffull_3166',['left_full',['../structvg_1_1GaplessExtension.html#a6b4301b3f1f75362d7904402fadde5a6',1,'vg::GaplessExtension']]],
- ['left_5fhandle_5ftrans_3167',['left_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#a03cd96a5b62b5a1450587032017a18bf',1,'vg::JoinedSpliceGraph']]],
- ['left_5fmaximal_3168',['left_maximal',['../structvg_1_1GaplessExtension.html#a3b8b053fc8800c5453b002cbc2aad173',1,'vg::GaplessExtension']]],
- ['left_5fseed_5fnode_3169',['left_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a8152492345122b0db73d6242b2958b45',1,'vg::JoinedSpliceGraph']]],
- ['left_5fsplice_5fnode_3170',['left_splice_node',['../classvg_1_1JoinedSpliceGraph.html#a37860d9de2993abb60cdf2fecce96c22',1,'vg::JoinedSpliceGraph']]],
- ['left_5fsplice_5foffset_3171',['left_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a7b502013abbbbad97b3edbaa24023612',1,'vg::JoinedSpliceGraph']]],
- ['left_5fsubgraph_3172',['left_subgraph',['../classvg_1_1JoinedSpliceGraph.html#ac59cd1a60d45bb3bad8241cadc53c56e',1,'vg::JoinedSpliceGraph']]],
- ['left_5ftelomere_5fnode_3173',['left_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#ac4abe06cebb2edac649930a7597cc126',1,'vg::PhasedGenome::Haplotype']]],
- ['legacycaller_3174',['LegacyCaller',['../classvg_1_1LegacyCaller.html',1,'vg::LegacyCaller'],['../classvg_1_1LegacyCaller.html#a7c9d6aa80ac330f844aedc80d267c6dc',1,'vg::LegacyCaller::LegacyCaller()']]],
- ['len_3175',['len',['../structvg_1_1SeqComplexity.html#abafe41d418fc2e9c14681e87f994dc0c',1,'vg::SeqComplexity']]],
- ['length_3176',['length',['../structvg_1_1WFAAlignment.html#a742372d503ae6c788b263ec474507b68',1,'vg::WFAAlignment::length()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac06d9b8444018d7490500c9dfa97a03b',1,'haplo::hDP_gbwt_graph_accessor::length()'],['../structhaplo_1_1haplo__DP__column.html#a43833a8ca83be7d6c2daa13b7707f32f',1,'haplo::haplo_DP_column::length()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#afd3e1c8befad3a1911504cfbd3f54ccd',1,'vg::MinimizerMapper::Minimizer::length()'],['../classvg_1_1mapping__t.html#ac2e746a37c551e0ecc8a4549135b8440',1,'vg::mapping_t::length()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#af210cde60043f4b87fa1bbd51487695d',1,'vg::HaplotypePartitioner::Subchain::length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#af7223d49a43bb2863961ab3e4113d2e2',1,'vg::ZipCode::node_code_t::length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a794a822da9c5425158d1ed42da500c03',1,'vg::ZipCode::chain_code_t::length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab0d97bad1f0171c35e784ff6d0c79c2c',1,'vg::ZipCode::snarl_code_t::length()'],['../structvg_1_1algorithms_1_1walk__t.html#a4be6edd3b92c2b9670ea09ec82aa3846',1,'vg::algorithms::walk_t::length()'],['../structMappingRun.html#af5b291d6db781206833956c21d74c94f',1,'MappingRun::length()'],['../structvg_1_1Path.html#ac512f92c7b82e38265062cd3fdc90acf',1,'vg::Path::length()'],['../structvg_1_1WFANode.html#a9f70c59baed78d97644100b45cf865cd',1,'vg::WFANode::length()'],['../structvg_1_1GaplessExtension.html#a9c16f9e41fdfafb22a6a64c1e852bb9c',1,'vg::GaplessExtension::length()'],['../classvg_1_1MaximalExactMatch.html#a8f70425ec532b9c43694efbd40d2d587',1,'vg::MaximalExactMatch::length()'],['../classvg_1_1MEMAccelerator.html#a32cb183aeee38c64432c8ea66ff167d6',1,'vg::MEMAccelerator::length()'],['../classvg_1_1BitString.html#a07225c6d00ba670f2dd0b3d6dd83bf70',1,'vg::BitString::length()'],['../classvg_1_1VG.html#a23641dedefa2b6d573939515fcf5974c',1,'vg::VG::length()'],['../classvg_1_1algorithms_1_1Anchor.html#a2fbd6d0440d796d4feb855488bab5b24',1,'vg::algorithms::Anchor::length()'],['../classvg_1_1algorithms_1_1GFAParser.html#aea0cfcb22ae0987ea37f64c5cd547322',1,'vg::algorithms::GFAParser::length()'],['../structReferenceInterval.html#ae74cc528a4962e5049a5028f3d2fd416',1,'ReferenceInterval::length()']]],
- ['lengths_3177',['lengths',['../classvg_1_1FragmentLengthDistribution.html#a368340de267064b485b898da2331dc97',1,'vg::FragmentLengthDistribution']]],
- ['less_5fthan_3178',['less_than',['../classvg_1_1StreamSorter.html#a4ebd8489bcf1ea8c3155c1aa202ab2e2',1,'vg::StreamSorter::less_than(const Message &a, const Message &b) const'],['../classvg_1_1StreamSorter.html#a243723f25750130a537550ac111be9ed',1,'vg::StreamSorter::less_than(const Position &a, const Position &b) const']]],
- ['likelihood_3179',['likelihood',['../structvg_1_1Genotype.html#afac9953bdbfbc0e3991e1b8a6e7e8c36',1,'vg::Genotype']]],
- ['likelihood_5fln_3180',['likelihood_ln',['../structvg_1_1Genotyper_1_1Affinity.html#ad1c0431bc83746580740d35e43fd2a46',1,'vg::Genotyper::Affinity']]],
- ['likelihoods_3181',['likelihoods',['../classvg_1_1VG.html#ada5821862279a350885f5368a54a5cba',1,'vg::VG']]],
- ['likely_5fmate_5fpositions_3182',['likely_mate_positions',['../classvg_1_1Mapper.html#a77e11337e9d2aed7a7ffdbb01e1ddd01',1,'vg::Mapper']]],
- ['likely_5fmismapping_3183',['likely_mismapping',['../classvg_1_1MultipathMapper.html#a30d9d4d69c937777d844baf2d60aed45',1,'vg::MultipathMapper']]],
- ['likely_5fmisrescue_3184',['likely_misrescue',['../classvg_1_1MultipathMapper.html#af0f679cfdca87e7a4d150c4f4c2b329a',1,'vg::MultipathMapper']]],
- ['limit_3185',['limit',['../structMappingRun.html#a3000c865dac9811ac82dc54c8073f553',1,'MappingRun']]],
- ['line_3186',['line',['../classvg_1_1TSVExplainer.html#a4d5e63408088dcb1185b613fb57bab04',1,'vg::TSVExplainer']]],
- ['line_5fnumber_3187',['line_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#aa460a34b2f085a161a113d4b83cbd1b4',1,'vg::algorithms::GFAFormatError']]],
- ['linear_5fhaplo_5fstructure_3188',['linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html',1,'haplo::linear_haplo_structure'],['../structhaplo_1_1linear__haplo__structure.html#abde17ce1452b109275975bf0e4f2d51c',1,'haplo::linear_haplo_structure::linear_haplo_structure()']]],
- ['linear_5fstructure_3189',['linear_structure',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a236e15ad7f30e98b2f6b1e9720b5d922',1,'vg::HaplotypePartitioner::Parameters']]],
- ['linearscoreprovider_3190',['LinearScoreProvider',['../classhaplo_1_1LinearScoreProvider.html',1,'haplo::LinearScoreProvider'],['../classhaplo_1_1LinearScoreProvider.html#a096c19ba7e847bdeb344e79d487ba675',1,'haplo::LinearScoreProvider::LinearScoreProvider()']]],
- ['linearunrepresentable_3191',['linearUnrepresentable',['../classhaplo_1_1linear__haplo__structure_1_1linearUnrepresentable.html',1,'haplo::linear_haplo_structure']]],
- ['list_5fhaplotypes_3192',['list_haplotypes',['../namespacevg.html#abe3c447c811f77c28669a36c4d3376b9',1,'vg']]],
- ['list_5fnames_3193',['list_names',['../structGBWTConfig.html#ac775ff572f553bd1dae5a7ee81c14078',1,'GBWTConfig']]],
- ['literal_5ftarget_5fmemory_5fusage_3194',['literal_target_memory_usage',['../classvg_1_1IndexingPlan.html#a93541f9db06d755f91d420072fe733e4',1,'vg::IndexingPlan']]],
- ['ln_5fto_5flog10_3195',['ln_to_log10',['../namespacevg.html#a664ec3301c226596ad971b97a8e1fa65',1,'vg']]],
- ['load_3196',['load',['../classvg_1_1Packer.html#aa85311440b3cd054439b59d64581a58a',1,'vg::Packer::load()'],['../classvg_1_1Packers.html#a66b45adedcd2fb5da8cd8aaf8bd43abc',1,'vg::Packers::load()'],['../classvg_1_1Paths.html#ab8a32e29f758ec6b62e0dc87e7f8018d',1,'vg::Paths::load()'],['../classvg_1_1StreamIndexBase.html#af30b1923f99ff4946103625f90ea1d9c',1,'vg::StreamIndexBase::load()'],['../classvg_1_1Translator.html#aec046a08186a8235a9dec5e844e30536',1,'vg::Translator::load()'],['../classxg_1_1XGPath.html#aeeb9f00d9af56f7f4aae8981f9dafe35',1,'xg::XGPath::load()']]],
- ['load_5falignments_3197',['load_alignments',['../classvg_1_1MSAConverter.html#aa03dea64fc16011eb69d212deb115446',1,'vg::MSAConverter']]],
- ['load_5fbed_3198',['load_bed',['../classvg_1_1FeatureSet.html#a373be59592f7f4f8c98f6d76563051ef',1,'vg::FeatureSet']]],
- ['load_5ffrom_5ffile_3199',['load_from_file',['../classvg_1_1Packer.html#a55b21208921e13f2399f4475d4d02b32',1,'vg::Packer']]],
- ['load_5ffrom_5fold_5fversion_3200',['load_from_old_version',['../classxg_1_1XGPath.html#ac67bde23d92b8720ece6d1176e09a103',1,'xg::XGPath']]],
- ['load_5ffunction_5ft_3201',['load_function_t',['../namespacevg_1_1io.html#a645533291ad3ae31bd8db73e51b3ac31',1,'vg::io']]],
- ['load_5fgbwt_3202',['load_gbwt',['../namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e',1,'vg::load_gbwt(gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a5197b188ae631a5adcd9689a18138042',1,'vg::load_gbwt(gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
- ['load_5fgbwtgraph_3203',['load_gbwtgraph',['../structGraphHandler.html#aa04b99afe3ef6c536a14f0aa371d4f4b',1,'GraphHandler::load_gbwtgraph()'],['../namespacevg.html#af83417b41cb483c6cad692b718c2bc02',1,'vg::load_gbwtgraph()']]],
- ['load_5fgbz_3204',['load_gbz',['../structGraphHandler.html#a74c5a92b327a6cfef23afac62eb413a5',1,'GraphHandler::load_gbz()'],['../namespacevg.html#a7f775d6f61207052e3c157e5ad6cfcf0',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a142177e721683d3e4d428f6cb8f22981',1,'vg::load_gbz(gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a1bd12c27c337a889da2db07d54d2e1d6',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
- ['load_5fgcsa_3205',['load_gcsa',['../namespacevg.html#afb0e46d1a71de77dddab10d147ac0538',1,'vg']]],
- ['load_5flcp_3206',['load_lcp',['../namespacevg.html#a0679feb8bafbf4be20c4bffa633223c6',1,'vg']]],
- ['load_5fminimizer_3207',['load_minimizer',['../namespacevg.html#a649b144d7ce85a247af73055577c4d91',1,'vg']]],
- ['load_5fone_3208',['load_one',['../classvg_1_1io_1_1VPKG.html#affd67a72df658a50228c6cae7efe7753',1,'vg::io::VPKG::load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a60cacf98de761eab29ed168ee56e8e39',1,'vg::io::VPKG::load_one(const string &filename)']]],
- ['load_5fpack_5fas_5fsupports_3209',['load_pack_as_supports',['../structvg_1_1SupportAugmentedGraph.html#ac7374e695e572eb9eace645005992ec9',1,'vg::SupportAugmentedGraph']]],
- ['load_5fproto_5fto_5fgraph_3210',['load_proto_to_graph',['../namespacevg_1_1io.html#aeef1360dbaeba693008f3ee0d39dde30',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const vg::io::message_sender_function_t &for_each_message)'],['../namespacevg_1_1io.html#ad96a1414b35d7f181ddbb3194d6dcf6c',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const function< void(const function< void(Graph &)> &)> &chunk_sender)']]],
- ['load_5fproto_5fto_5fgraph_2ecpp_3211',['load_proto_to_graph.cpp',['../load__proto__to__graph_8cpp.html',1,'']]],
- ['load_5fproto_5fto_5fgraph_2ehpp_3212',['load_proto_to_graph.hpp',['../load__proto__to__graph_8hpp.html',1,'']]],
- ['load_5fr_5findex_3213',['load_r_index',['../namespacevg.html#a4ab05fd111751cbf31c3a6a5189a76ff',1,'vg']]],
- ['load_5fsubchain_5fheader_3214',['load_subchain_header',['../namespacevg.html#a4d9b75e74f770318a088011e478c5400',1,'vg']]],
- ['load_5fsubchain_5fkmers_5fpresent_3215',['load_subchain_kmers_present',['../namespacevg.html#a76469b7556e38a779309eeaf9e92ba75',1,'vg']]],
- ['load_5fsupports_3216',['load_supports',['../structvg_1_1SupportAugmentedGraph.html#a1aef5debe026648525732be7bc6cc4b1',1,'vg::SupportAugmentedGraph']]],
- ['load_5ftranslation_5fback_5fmap_3217',['load_translation_back_map',['../namespacevg.html#a3cde90cbb8b1fc46d2b830bf87dba997',1,'vg::load_translation_back_map(HandleGraph &graph, ifstream &input_stream)'],['../namespacevg.html#a0b717077a15106d70c8ce4cc035ca890',1,'vg::load_translation_back_map(const gbwtgraph::GBWTGraph &graph)']]],
- ['load_5ftranslation_5fmap_3218',['load_translation_map',['../namespacevg.html#a11a634196a7420547646dc30d2c57b18',1,'vg::load_translation_map(ifstream &input_stream)'],['../namespacevg.html#a709e93bb1c0dbdcdbc928960e42688ec',1,'vg::load_translation_map(const gbwtgraph::GBWTGraph &graph)']]],
- ['load_5ftranslations_3219',['load_translations',['../structvg_1_1AugmentedGraph.html#af86dc51d58ee0cfa4513602dccc373cd',1,'vg::AugmentedGraph']]],
- ['load_5fv1_3220',['load_v1',['../structvg_1_1Haplotypes_1_1Subchain.html#aacfeb074e57aa98d8ab342114af74e56',1,'vg::Haplotypes::Subchain::load_v1()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a1ace0bf2f790aec2cc6be94bd751009f',1,'vg::Haplotypes::TopLevelChain::load_v1()']]],
- ['load_5fv2_3221',['load_v2',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ab6639ac2e85e25e7e5a4e854e0960708',1,'vg::Haplotypes::TopLevelChain']]],
- ['loader_2ehpp_3222',['loader.hpp',['../loader_8hpp.html',1,'']]],
- ['local_5fhandle_3223',['local_handle',['../classxg_1_1XGPath.html#a6a9566f974aebd3c74fc00ee9dc0c5f0',1,'xg::XGPath']]],
- ['localhaplotype_3224',['LocalHaplotype',['../structvg_1_1Recombinator_1_1LocalHaplotype.html',1,'vg::Recombinator']]],
- ['locally_5fexpand_5fgraph_3225',['locally_expand_graph',['../namespacevg_1_1algorithms.html#aa015cfde6842fff0d0dcd81f7130c659',1,'vg::algorithms']]],
- ['locally_5fexpand_5fgraph_2ecpp_3226',['locally_expand_graph.cpp',['../locally__expand__graph_8cpp.html',1,'']]],
- ['locally_5fexpand_5fgraph_2ehpp_3227',['locally_expand_graph.hpp',['../locally__expand__graph_8hpp.html',1,'']]],
- ['locationsupport_3228',['LocationSupport',['../structvg_1_1LocationSupport.html',1,'vg']]],
- ['lock_3229',['Lock',['../classvg_1_1GraphSynchronizer_1_1Lock.html',1,'vg::GraphSynchronizer::Lock'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a62805a6582a0280c58509f232079b416',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t path_offset, size_t context_bases, bool reflect)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a64972da675bb40fbbaec55470aeebdc4',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t start, size_t past_end)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1a6ed95994cc497481d3338986a30e49',1,'vg::GraphSynchronizer::Lock::lock()']]],
- ['locked_5fnodes_3230',['locked_nodes',['../classvg_1_1GraphSynchronizer_1_1Lock.html#acfb5bf6caa6040ec1028250324296355',1,'vg::GraphSynchronizer::Lock::locked_nodes()'],['../classvg_1_1GraphSynchronizer.html#a275e3112ec47229a197e3ecc118771c4',1,'vg::GraphSynchronizer::locked_nodes()']]],
- ['locus_3231',['Locus',['../structvg_1_1Locus.html',1,'vg::Locus'],['../structvg_1_1Alignment.html#afe47b70cd7b78e97a9cf18e9c60ef4f0',1,'vg::Alignment::locus()']]],
- ['locus_5fmatch_5fany_3232',['LOCUS_MATCH_ANY',['../classhandlegraph_1_1PathMetadata.html#a613e59743ad6e1df8e9682fdf087e715',1,'handlegraph::PathMetadata']]],
- ['locus_5fmatch_5fnumerical_5fwithout_5fhaplotype_3233',['LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#ab26b62f4dc1863aeae2798e008b38c80',1,'handlegraph::PathMetadata']]],
- ['locus_5fto_5fvariant_3234',['locus_to_variant',['../classvg_1_1Genotyper.html#a55c456d612728331007f2f6c4307195f',1,'vg::Genotyper']]],
- ['log10_5fadd_5fone_3235',['log10_add_one',['../namespacevg.html#a16b2b6e110a2f72a871c309b888b013c',1,'vg']]],
- ['log10_5fto_5fln_3236',['log10_to_ln',['../namespacevg.html#a48d9ec9295afc7457506af4ddaf44217',1,'vg']]],
- ['log_5falignment_3237',['log_alignment',['../classvg_1_1MinimizerMapper.html#ab02245901b7ec1710512eab20aec3a48',1,'vg::MinimizerMapper::log_alignment(const Alignment &aln)'],['../classvg_1_1MinimizerMapper.html#aed8f32c63a79281d8693c19f6d6d5521',1,'vg::MinimizerMapper::log_alignment(const Path &path, bool force_condensed=false)']]],
- ['log_5fbase_3238',['log_base',['../classvg_1_1GSSWAligner.html#a5a1a7e6edc3764ff32f7815999d6345f',1,'vg::GSSWAligner::log_base()'],['../classvg_1_1SpliceStats.html#ae01c237b5e011851147a342b8e7aa3ad',1,'vg::SpliceStats::log_base()']]],
- ['log_5fbits_3239',['log_bits',['../classvg_1_1MinimizerMapper.html#a8d6f418b719d4a4671562c9eeb998601',1,'vg::MinimizerMapper']]],
- ['log_5fcontinue_5ffactor_3240',['log_continue_factor',['../structhaplo_1_1haploMath_1_1RRMemo.html#a4a3dacc819f40fd7e5063821b133028d',1,'haplo::haploMath::RRMemo']]],
- ['log_5fcontinue_5fprobability_3241',['log_continue_probability',['../structhaplo_1_1haploMath_1_1RRMemo.html#afd6af2944e0a42df7f251fe008ba3e90',1,'haplo::haploMath::RRMemo']]],
- ['log_5flikelihood_3242',['log_likelihood',['../structvg_1_1Genotype.html#ad14f6fc449e1086ccd2de2bc4ad419a4',1,'vg::Genotype']]],
- ['log_5flikelihood_5fapprox_5ffactor_3243',['log_likelihood_approx_factor',['../classvg_1_1MultipathMapper.html#a28e3e0b047b5d3c195431982f76084c1',1,'vg::MultipathMapper']]],
- ['log_5fname_3244',['log_name',['../classvg_1_1MinimizerMapper.html#ad49858579fbcd962383387351e2b0183',1,'vg::MinimizerMapper']]],
- ['log_5fpopulation_5fsize_3245',['log_population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#a27a02a4732a9e50c9a1cb9f0b7d7ac3b',1,'haplo::haploMath::RRMemo']]],
- ['log_5fposterior_3246',['log_posterior',['../structvg_1_1Genotype.html#a743da1ba7239bddcd6316a60f66bd307',1,'vg::Genotype']]],
- ['log_5fprior_3247',['log_prior',['../structvg_1_1Genotype.html#a94b836b6384c02e11478b2ec18ab0ad7',1,'vg::Genotype']]],
- ['log_5freads_3248',['log_reads',['../structGiraffeMainOptions.html#a2b54df0c377a105e57c67c93b1b98ce9',1,'GiraffeMainOptions']]],
- ['log_5frecombination_5fpenalty_3249',['log_recombination_penalty',['../structhaplo_1_1haploMath_1_1RRMemo.html#aa33b509ee804234be1fb33061b3a9f76',1,'haplo::haploMath::RRMemo']]],
- ['log_5ftarget_3250',['log_target',['../classvg_1_1MCMCGenotyper.html#a4622c5efee68d8f148b961a92a1abc62',1,'vg::MCMCGenotyper']]],
- ['logdiff_3251',['logdiff',['../namespacehaplo_1_1haploMath.html#af0182b1e73c64ac6ef0be9d621cce576',1,'haplo::haploMath']]],
- ['lognormal_5fpdf_3252',['lognormal_pdf',['../namespacevg.html#afe6b7d44806f0d50d79f7de39800495d',1,'vg']]],
- ['logprob_5fadd_3253',['logprob_add',['../namespacevg.html#a64b25a99232585c5e76baf01d1ef5520',1,'vg']]],
- ['logprob_5fgeometric_5fmean_3254',['logprob_geometric_mean',['../namespacevg.html#a0f8a1a81a5402187152a97ca6293b4f1',1,'vg']]],
- ['logprob_5finvert_3255',['logprob_invert',['../namespacevg.html#a1056422cd0697f2bbdcf8a085486793a',1,'vg']]],
- ['logprob_5fsum_3256',['logprob_sum',['../namespacevg.html#a93d81b5193ecfc9600990bd427337adf',1,'vg']]],
- ['logprob_5fto_5fphred_3257',['logprob_to_phred',['../namespacevg.html#a66d295b4b0f83393ce621b44d88680a6',1,'vg']]],
- ['logprob_5fto_5fprob_3258',['logprob_to_prob',['../namespacevg.html#aea77a4ed92d78c48a08fce58cf319c4d',1,'vg']]],
- ['logrrdiff_3259',['logRRDiff',['../structhaplo_1_1haploMath_1_1RRMemo.html#a770235503ce0b9bc84f8ec5585f7d328',1,'haplo::haploMath::RRMemo']]],
- ['logs_3260',['logS',['../structhaplo_1_1haploMath_1_1RRMemo.html#a3c54d778760482c2bc80935ceefb0f61',1,'haplo::haploMath::RRMemo']]],
- ['logs_5fbases_3261',['logS_bases',['../structhaplo_1_1haploMath_1_1RRMemo.html#a00657f76fd1b56312b031ef79728c9c7',1,'haplo::haploMath::RRMemo']]],
- ['logsum_3262',['logsum',['../namespacehaplo_1_1haploMath.html#a5bc510bf3fca2eeaba726ababf32678f',1,'haplo::haploMath']]],
- ['logt_3263',['logT',['../structhaplo_1_1haploMath_1_1RRMemo.html#ac74af8f5adda75809d2995a37ca79317',1,'haplo::haploMath::RRMemo']]],
- ['logt_5fbase_3264',['logT_base',['../structhaplo_1_1haploMath_1_1RRMemo.html#a8e9b242f45b301e58dbe4e67f6added1',1,'haplo::haploMath::RRMemo']]],
- ['long_5flimit_3265',['LONG_LIMIT',['../classvg_1_1MinimizerMapper.html#a1d68225843da9cfb161b838be3017e58',1,'vg::MinimizerMapper']]],
- ['long_5fopt_3266',['long_opt',['../classvg_1_1BaseOption.html#a580b1cd4960ac113db781935d89cb7b1',1,'vg::BaseOption']]],
- ['long_5foptions_3267',['long_options',['../classvg_1_1ConfigurableParser.html#a25d7c47bbc3c439235fb751722d027c8',1,'vg::ConfigurableParser']]],
- ['long_5foptions_5fused_3268',['long_options_used',['../classvg_1_1ConfigurableParser.html#a60395eaf832c2acfa46fe0763749614f',1,'vg::ConfigurableParser']]],
- ['long_5fread_5fminimizer_5fk_3269',['long_read_minimizer_k',['../structvg_1_1IndexingParameters.html#ac8e9a153245b64380d773561d8534c51',1,'vg::IndexingParameters']]],
- ['long_5fread_5fminimizer_5fw_3270',['long_read_minimizer_w',['../structvg_1_1IndexingParameters.html#a7cf3ea634d6c4b3f45bf2d11867ab70c',1,'vg::IndexingParameters::long_read_minimizer_w()'],['../structvg_1_1IndexingParameters.html#aca76950e194d8a550b71ffcee55aa8df',1,'vg::IndexingParameters::long_read_minimizer_W()']]],
- ['long_5fref_5fcontig_3271',['long_ref_contig',['../classvg_1_1Deconstructor.html#a6341c9416e41420f60f9faf7ea942d07',1,'vg::Deconstructor']]],
- ['longest_5fcommon_5fprefix_3272',['longest_common_prefix',['../namespacevg.html#a2d872af86508016fe8b78d61a190e90a',1,'vg']]],
- ['longest_5fdetectable_5fgap_3273',['longest_detectable_gap',['../classvg_1_1GSSWAligner.html#a9a0d0245bdab8420b4f760d818a3d9cc',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment, const string::const_iterator &read_pos) const'],['../classvg_1_1GSSWAligner.html#a6c803e19e479e8310fda8976ac30eb3a',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length, size_t read_pos) const'],['../classvg_1_1GSSWAligner.html#a00852660c55c381bdcc3546bdb2b1a93',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment) const'],['../classvg_1_1GSSWAligner.html#a6f2bbbc1b2c955874ad531cab3bf4879',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length) const']]],
- ['longest_5fdetectable_5fgap_5fin_5frange_3274',['longest_detectable_gap_in_range',['../classvg_1_1MinimizerMapper.html#aa0f917b2d622c95d9f8bc65186cb898f',1,'vg::MinimizerMapper']]],
- ['longest_5fpaths_5fin_5fforest_3275',['longest_paths_in_forest',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a98105712f44db6c5fadc3b9bd64f97f0',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['look_5fback_3276',['look_back',['../classvg_1_1ZipCodeTree.html#aefac261dda914b102fa57dd504af15d5',1,'vg::ZipCodeTree']]],
- ['lookback_5ftransition_5fiterator_3277',['lookback_transition_iterator',['../namespacevg_1_1algorithms.html#ac8e2917f0a06c55852e4ef044548f2bb',1,'vg::algorithms']]],
- ['lookup_5ffor_5fread_5fin_3278',['lookup_for_read_in',['../structvg_1_1read__alignment__index__t.html#add622e2d97706e4ad842ed27d2a93726',1,'vg::read_alignment_index_t']]],
- ['lookup_5fin_3279',['lookup_in',['../structvg_1_1alignment__index__t.html#a96d88d8fc53918a02c51b6ba811e88be',1,'vg::alignment_index_t']]],
- ['loop_5fleft_3280',['loop_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3374b357e0bc3bc98bd131d7dc0a3209',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['loop_5fright_3281',['loop_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae793bc31b5603ef670a83187fde8616c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['low_5fcomplexity_5fp_5fvalue_3282',['low_complexity_p_value',['../classvg_1_1Surjector.html#a1df336db06fea7951c960f71265d513d',1,'vg::Surjector']]],
- ['lower_5fbound_3283',['lower_bound',['../structvg_1_1BREAKPOINT.html#a1b854b285738913830671a54ce0857f5',1,'vg::BREAKPOINT']]],
- ['lower_5fbound_5fheuristic_3284',['lower_bound_heuristic',['../classvg_1_1TargetValueSearch.html#a93c1f2cb35452719dc87fb4ec8cf714e',1,'vg::TargetValueSearch']]],
- ['lowercase_5fwarned_5falt_3285',['lowercase_warned_alt',['../classvg_1_1Constructor.html#af296f5e32632a4fee39ac4bc11589c09',1,'vg::Constructor']]],
- ['lowercase_5fwarned_5fsequences_3286',['lowercase_warned_sequences',['../classvg_1_1Constructor.html#a4a5f08f7d9c8e7bc821a7618e019289d',1,'vg::Constructor']]],
- ['lru_5fcache_5fsize_3287',['lru_cache_size',['../classvg_1_1Packer.html#a32572a24fe3c3b372e1ff24ec9720da0',1,'vg::Packer']]],
- ['lv0_5falt_5flen_3288',['lv0_alt_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a64a400033d2ff787c487d78feee21a7d',1,'vg::Deconstructor::NestingInfo']]],
- ['lv0_5fref_5flen_3289',['lv0_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ab628cbae94feb0e11bd46e09fc1900f4',1,'vg::Deconstructor::NestingInfo']]],
- ['lv0_5fref_5fname_3290',['lv0_ref_name',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2eda67779fb6821700d9c89d8b9671f7',1,'vg::Deconstructor::NestingInfo']]],
- ['lv0_5fref_5fstart_3291',['lv0_ref_start',['../structvg_1_1Deconstructor_1_1NestingInfo.html#af6bb1c0f6383981be4bfea3ce0fe565f',1,'vg::Deconstructor::NestingInfo']]]
+ ['lane_3143',['lane',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a197d4920d6cbdfabac08f0de992a425a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
+ ['large_5falignment_5fband_5fpadding_3144',['large_alignment_band_padding',['../classvg_1_1VariantAdder.html#aefe81cd7c81a7f3ba54c73e25c24ba3f',1,'vg::VariantAdder']]],
+ ['larger_5fprime_3145',['larger_prime',['../classvg_1_1ShuffledPairs.html#a20b31eca7b0fc0185246c560fd8e266d',1,'vg::ShuffledPairs']]],
+ ['last_3146',['last',['../structvg_1_1FeatureSet_1_1Feature.html#a9fb23b0b9affcc51a2610bb287b2082b',1,'vg::FeatureSet::Feature::last()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a1f9f68c932a97214ed914c8ba2c882f2',1,'vg::Counts::last()']]],
+ ['last_5fcheckin_3147',['last_checkin',['../structvg_1_1Watchdog_1_1thread__state__t.html#ad54ba05d09be7a40b4e9504b8d020ea6',1,'vg::Watchdog::thread_state_t']]],
+ ['last_5fcomponent_3148',['last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac65c35c84d5c173dc46077e3f0a831e5',1,'vg::ZipCode::chain_code_t']]],
+ ['last_5fcorrect_5fstage_3149',['last_correct_stage',['../classvg_1_1Funnel.html#a996005ebe76091bbba404bf4a2a9a405',1,'vg::Funnel']]],
+ ['last_5fgroup_5fmin_5fid_3150',['last_group_min_id',['../classvg_1_1StreamIndexBase.html#aef3a7bd46aeb49185a8cd6a9a261e883',1,'vg::StreamIndexBase']]],
+ ['last_5fnode_5flength_3151',['last_node_length',['../structvg_1_1PathIndex.html#ac64a3532df12093eeccf3201184ea4d9',1,'vg::PathIndex']]],
+ ['last_5fpath_5fposition_3152',['last_path_position',['../namespacevg.html#aa1c1e5b8ce9f9607976913317102d6dc',1,'vg']]],
+ ['last_5fprogress_3153',['last_progress',['../classvg_1_1Progressive.html#a4984481e2b887e5fb78ea40728f1b97f',1,'vg::Progressive']]],
+ ['last_5ftagged_5fstage_3154',['last_tagged_stage',['../classvg_1_1Funnel.html#ab53e816bd740407417b0bd8d14d5237c',1,'vg::Funnel']]],
+ ['latest_3155',['latest',['../classvg_1_1Funnel.html#a933c8a296c5a680aa96b0b913c465250',1,'vg::Funnel']]],
+ ['layout_5forder_3156',['layout_order',['../classvg_1_1DagifiedGraph.html#a50789da1e0a8c4ede5e2c1b73c7980a0',1,'vg::DagifiedGraph']]],
+ ['layout_5forder_5fof_5fhandle_3157',['layout_order_of_handle',['../classvg_1_1DagifiedGraph.html#af364d952c459117f871368bcc9d33573',1,'vg::DagifiedGraph']]],
+ ['lazier_5ftopological_5forder_3158',['lazier_topological_order',['../namespacehandlegraph_1_1algorithms.html#a26e0547c886eede7d3c0766907f39645',1,'handlegraph::algorithms']]],
+ ['lazy_5ftopological_5forder_3159',['lazy_topological_order',['../namespacehandlegraph_1_1algorithms.html#ac9c0542f382080d1af3914714a62b9b6',1,'handlegraph::algorithms']]],
+ ['lazy_5ftopological_5forder_5finternal_3160',['lazy_topological_order_internal',['../namespacehandlegraph_1_1algorithms.html#a53c98a2b062e6b5e92757945788b2e91',1,'handlegraph::algorithms']]],
+ ['lazyrng_3161',['LazyRNG',['../classvg_1_1LazyRNG.html',1,'vg::LazyRNG'],['../classvg_1_1LazyRNG.html#a34ef87c442913becab5f596f50bd850e',1,'vg::LazyRNG::LazyRNG()']]],
+ ['lcp_3162',['lcp',['../classvg_1_1BaseMapper.html#a4046b98185c00ff397089435d5b2b8d8',1,'vg::BaseMapper']]],
+ ['lcp_5find_3163',['lcp_ind',['../classvg_1_1Filter.html#ab65e7196a6b891a266d16838e5d870d4',1,'vg::Filter']]],
+ ['left_3164',['left',['../structvg_1_1Support.html#a31d59f62a09c71915856740c5450ecf5',1,'vg::Support']]],
+ ['left_5fborder_3165',['left_border',['../classvg_1_1Viz.html#a4c472c524f9bdfc37d9073f9257ca529',1,'vg::Viz']]],
+ ['left_5fdegree_3166',['left_degree',['../classvg_1_1VG.html#af9ac6e61dfa9350459dbb9586088c4a5',1,'vg::VG']]],
+ ['left_5fends_3167',['left_ends',['../structvg_1_1ConstructedChunk.html#a0d6c6d4304190097a7a832d11a31bf3d',1,'vg::ConstructedChunk']]],
+ ['left_5ffull_3168',['left_full',['../structvg_1_1GaplessExtension.html#a6b4301b3f1f75362d7904402fadde5a6',1,'vg::GaplessExtension']]],
+ ['left_5fhandle_5ftrans_3169',['left_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#a03cd96a5b62b5a1450587032017a18bf',1,'vg::JoinedSpliceGraph']]],
+ ['left_5fmaximal_3170',['left_maximal',['../structvg_1_1GaplessExtension.html#a3b8b053fc8800c5453b002cbc2aad173',1,'vg::GaplessExtension']]],
+ ['left_5fseed_5fnode_3171',['left_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a8152492345122b0db73d6242b2958b45',1,'vg::JoinedSpliceGraph']]],
+ ['left_5fsplice_5fnode_3172',['left_splice_node',['../classvg_1_1JoinedSpliceGraph.html#a37860d9de2993abb60cdf2fecce96c22',1,'vg::JoinedSpliceGraph']]],
+ ['left_5fsplice_5foffset_3173',['left_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a7b502013abbbbad97b3edbaa24023612',1,'vg::JoinedSpliceGraph']]],
+ ['left_5fsubgraph_3174',['left_subgraph',['../classvg_1_1JoinedSpliceGraph.html#ac59cd1a60d45bb3bad8241cadc53c56e',1,'vg::JoinedSpliceGraph']]],
+ ['left_5ftelomere_5fnode_3175',['left_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#ac4abe06cebb2edac649930a7597cc126',1,'vg::PhasedGenome::Haplotype']]],
+ ['legacycaller_3176',['LegacyCaller',['../classvg_1_1LegacyCaller.html',1,'vg::LegacyCaller'],['../classvg_1_1LegacyCaller.html#a7c9d6aa80ac330f844aedc80d267c6dc',1,'vg::LegacyCaller::LegacyCaller()']]],
+ ['len_3177',['len',['../structvg_1_1SeqComplexity.html#abafe41d418fc2e9c14681e87f994dc0c',1,'vg::SeqComplexity']]],
+ ['length_3178',['length',['../structvg_1_1WFAAlignment.html#a742372d503ae6c788b263ec474507b68',1,'vg::WFAAlignment::length()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac06d9b8444018d7490500c9dfa97a03b',1,'haplo::hDP_gbwt_graph_accessor::length()'],['../structhaplo_1_1haplo__DP__column.html#a43833a8ca83be7d6c2daa13b7707f32f',1,'haplo::haplo_DP_column::length()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#afd3e1c8befad3a1911504cfbd3f54ccd',1,'vg::MinimizerMapper::Minimizer::length()'],['../classvg_1_1mapping__t.html#ac2e746a37c551e0ecc8a4549135b8440',1,'vg::mapping_t::length()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#af210cde60043f4b87fa1bbd51487695d',1,'vg::HaplotypePartitioner::Subchain::length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#af7223d49a43bb2863961ab3e4113d2e2',1,'vg::ZipCode::node_code_t::length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a794a822da9c5425158d1ed42da500c03',1,'vg::ZipCode::chain_code_t::length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab0d97bad1f0171c35e784ff6d0c79c2c',1,'vg::ZipCode::snarl_code_t::length()'],['../structvg_1_1algorithms_1_1walk__t.html#a4be6edd3b92c2b9670ea09ec82aa3846',1,'vg::algorithms::walk_t::length()'],['../structMappingRun.html#af5b291d6db781206833956c21d74c94f',1,'MappingRun::length()'],['../structvg_1_1Path.html#ac512f92c7b82e38265062cd3fdc90acf',1,'vg::Path::length()'],['../structvg_1_1WFANode.html#a9f70c59baed78d97644100b45cf865cd',1,'vg::WFANode::length()'],['../structvg_1_1GaplessExtension.html#a9c16f9e41fdfafb22a6a64c1e852bb9c',1,'vg::GaplessExtension::length()'],['../classvg_1_1MaximalExactMatch.html#a8f70425ec532b9c43694efbd40d2d587',1,'vg::MaximalExactMatch::length()'],['../classvg_1_1MEMAccelerator.html#a32cb183aeee38c64432c8ea66ff167d6',1,'vg::MEMAccelerator::length()'],['../classvg_1_1BitString.html#a07225c6d00ba670f2dd0b3d6dd83bf70',1,'vg::BitString::length()'],['../classvg_1_1VG.html#a23641dedefa2b6d573939515fcf5974c',1,'vg::VG::length()'],['../classvg_1_1algorithms_1_1Anchor.html#a2fbd6d0440d796d4feb855488bab5b24',1,'vg::algorithms::Anchor::length()'],['../classvg_1_1algorithms_1_1GFAParser.html#aea0cfcb22ae0987ea37f64c5cd547322',1,'vg::algorithms::GFAParser::length()'],['../structReferenceInterval.html#ae74cc528a4962e5049a5028f3d2fd416',1,'ReferenceInterval::length()']]],
+ ['lengths_3179',['lengths',['../classvg_1_1FragmentLengthDistribution.html#a368340de267064b485b898da2331dc97',1,'vg::FragmentLengthDistribution']]],
+ ['less_5fthan_3180',['less_than',['../classvg_1_1StreamSorter.html#a4ebd8489bcf1ea8c3155c1aa202ab2e2',1,'vg::StreamSorter::less_than(const Message &a, const Message &b) const'],['../classvg_1_1StreamSorter.html#a243723f25750130a537550ac111be9ed',1,'vg::StreamSorter::less_than(const Position &a, const Position &b) const']]],
+ ['likelihood_3181',['likelihood',['../structvg_1_1Genotype.html#afac9953bdbfbc0e3991e1b8a6e7e8c36',1,'vg::Genotype']]],
+ ['likelihood_5fln_3182',['likelihood_ln',['../structvg_1_1Genotyper_1_1Affinity.html#ad1c0431bc83746580740d35e43fd2a46',1,'vg::Genotyper::Affinity']]],
+ ['likelihoods_3183',['likelihoods',['../classvg_1_1VG.html#ada5821862279a350885f5368a54a5cba',1,'vg::VG']]],
+ ['likely_5fmate_5fpositions_3184',['likely_mate_positions',['../classvg_1_1Mapper.html#a77e11337e9d2aed7a7ffdbb01e1ddd01',1,'vg::Mapper']]],
+ ['likely_5fmismapping_3185',['likely_mismapping',['../classvg_1_1MultipathMapper.html#a30d9d4d69c937777d844baf2d60aed45',1,'vg::MultipathMapper']]],
+ ['likely_5fmisrescue_3186',['likely_misrescue',['../classvg_1_1MultipathMapper.html#af0f679cfdca87e7a4d150c4f4c2b329a',1,'vg::MultipathMapper']]],
+ ['limit_3187',['limit',['../structMappingRun.html#a3000c865dac9811ac82dc54c8073f553',1,'MappingRun']]],
+ ['line_3188',['line',['../classvg_1_1TSVExplainer.html#a4d5e63408088dcb1185b613fb57bab04',1,'vg::TSVExplainer']]],
+ ['line_5fnumber_3189',['line_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#aa460a34b2f085a161a113d4b83cbd1b4',1,'vg::algorithms::GFAFormatError']]],
+ ['linear_5fhaplo_5fstructure_3190',['linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html',1,'haplo::linear_haplo_structure'],['../structhaplo_1_1linear__haplo__structure.html#abde17ce1452b109275975bf0e4f2d51c',1,'haplo::linear_haplo_structure::linear_haplo_structure()']]],
+ ['linear_5fstructure_3191',['linear_structure',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a236e15ad7f30e98b2f6b1e9720b5d922',1,'vg::HaplotypePartitioner::Parameters']]],
+ ['linearscoreprovider_3192',['LinearScoreProvider',['../classhaplo_1_1LinearScoreProvider.html',1,'haplo::LinearScoreProvider'],['../classhaplo_1_1LinearScoreProvider.html#a096c19ba7e847bdeb344e79d487ba675',1,'haplo::LinearScoreProvider::LinearScoreProvider()']]],
+ ['linearunrepresentable_3193',['linearUnrepresentable',['../classhaplo_1_1linear__haplo__structure_1_1linearUnrepresentable.html',1,'haplo::linear_haplo_structure']]],
+ ['list_5fhaplotypes_3194',['list_haplotypes',['../namespacevg.html#abe3c447c811f77c28669a36c4d3376b9',1,'vg']]],
+ ['list_5fnames_3195',['list_names',['../structGBWTConfig.html#ac775ff572f553bd1dae5a7ee81c14078',1,'GBWTConfig']]],
+ ['literal_5ftarget_5fmemory_5fusage_3196',['literal_target_memory_usage',['../classvg_1_1IndexingPlan.html#a93541f9db06d755f91d420072fe733e4',1,'vg::IndexingPlan']]],
+ ['ln_5fto_5flog10_3197',['ln_to_log10',['../namespacevg.html#a664ec3301c226596ad971b97a8e1fa65',1,'vg']]],
+ ['load_3198',['load',['../classvg_1_1Packer.html#aa85311440b3cd054439b59d64581a58a',1,'vg::Packer::load()'],['../classvg_1_1Packers.html#a66b45adedcd2fb5da8cd8aaf8bd43abc',1,'vg::Packers::load()'],['../classvg_1_1Paths.html#ab8a32e29f758ec6b62e0dc87e7f8018d',1,'vg::Paths::load()'],['../classvg_1_1StreamIndexBase.html#af30b1923f99ff4946103625f90ea1d9c',1,'vg::StreamIndexBase::load()'],['../classvg_1_1Translator.html#aec046a08186a8235a9dec5e844e30536',1,'vg::Translator::load()'],['../classxg_1_1XGPath.html#aeeb9f00d9af56f7f4aae8981f9dafe35',1,'xg::XGPath::load()']]],
+ ['load_5falignments_3199',['load_alignments',['../classvg_1_1MSAConverter.html#aa03dea64fc16011eb69d212deb115446',1,'vg::MSAConverter']]],
+ ['load_5fbed_3200',['load_bed',['../classvg_1_1FeatureSet.html#a373be59592f7f4f8c98f6d76563051ef',1,'vg::FeatureSet']]],
+ ['load_5ffrom_5ffile_3201',['load_from_file',['../classvg_1_1Packer.html#a55b21208921e13f2399f4475d4d02b32',1,'vg::Packer']]],
+ ['load_5ffrom_5fold_5fversion_3202',['load_from_old_version',['../classxg_1_1XGPath.html#ac67bde23d92b8720ece6d1176e09a103',1,'xg::XGPath']]],
+ ['load_5ffunction_5ft_3203',['load_function_t',['../namespacevg_1_1io.html#a645533291ad3ae31bd8db73e51b3ac31',1,'vg::io']]],
+ ['load_5fgbwt_3204',['load_gbwt',['../namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e',1,'vg::load_gbwt(gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a5197b188ae631a5adcd9689a18138042',1,'vg::load_gbwt(gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
+ ['load_5fgbwtgraph_3205',['load_gbwtgraph',['../structGraphHandler.html#aa04b99afe3ef6c536a14f0aa371d4f4b',1,'GraphHandler::load_gbwtgraph()'],['../namespacevg.html#af83417b41cb483c6cad692b718c2bc02',1,'vg::load_gbwtgraph()']]],
+ ['load_5fgbz_3206',['load_gbz',['../structGraphHandler.html#a74c5a92b327a6cfef23afac62eb413a5',1,'GraphHandler::load_gbz()'],['../namespacevg.html#a7f775d6f61207052e3c157e5ad6cfcf0',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a142177e721683d3e4d428f6cb8f22981',1,'vg::load_gbz(gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a1bd12c27c337a889da2db07d54d2e1d6',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
+ ['load_5fgcsa_3207',['load_gcsa',['../namespacevg.html#afb0e46d1a71de77dddab10d147ac0538',1,'vg']]],
+ ['load_5flcp_3208',['load_lcp',['../namespacevg.html#a0679feb8bafbf4be20c4bffa633223c6',1,'vg']]],
+ ['load_5fminimizer_3209',['load_minimizer',['../namespacevg.html#a649b144d7ce85a247af73055577c4d91',1,'vg']]],
+ ['load_5fone_3210',['load_one',['../classvg_1_1io_1_1VPKG.html#affd67a72df658a50228c6cae7efe7753',1,'vg::io::VPKG::load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a60cacf98de761eab29ed168ee56e8e39',1,'vg::io::VPKG::load_one(const string &filename)']]],
+ ['load_5fpack_5fas_5fsupports_3211',['load_pack_as_supports',['../structvg_1_1SupportAugmentedGraph.html#ac7374e695e572eb9eace645005992ec9',1,'vg::SupportAugmentedGraph']]],
+ ['load_5fproto_5fto_5fgraph_3212',['load_proto_to_graph',['../namespacevg_1_1io.html#aeef1360dbaeba693008f3ee0d39dde30',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const vg::io::message_sender_function_t &for_each_message)'],['../namespacevg_1_1io.html#ad96a1414b35d7f181ddbb3194d6dcf6c',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const function< void(const function< void(Graph &)> &)> &chunk_sender)']]],
+ ['load_5fproto_5fto_5fgraph_2ecpp_3213',['load_proto_to_graph.cpp',['../load__proto__to__graph_8cpp.html',1,'']]],
+ ['load_5fproto_5fto_5fgraph_2ehpp_3214',['load_proto_to_graph.hpp',['../load__proto__to__graph_8hpp.html',1,'']]],
+ ['load_5fr_5findex_3215',['load_r_index',['../namespacevg.html#a4ab05fd111751cbf31c3a6a5189a76ff',1,'vg']]],
+ ['load_5fsubchain_5fheader_3216',['load_subchain_header',['../namespacevg.html#a4d9b75e74f770318a088011e478c5400',1,'vg']]],
+ ['load_5fsubchain_5fkmers_5fpresent_3217',['load_subchain_kmers_present',['../namespacevg.html#a76469b7556e38a779309eeaf9e92ba75',1,'vg']]],
+ ['load_5fsupports_3218',['load_supports',['../structvg_1_1SupportAugmentedGraph.html#a1aef5debe026648525732be7bc6cc4b1',1,'vg::SupportAugmentedGraph']]],
+ ['load_5ftranslation_5fback_5fmap_3219',['load_translation_back_map',['../namespacevg.html#a3cde90cbb8b1fc46d2b830bf87dba997',1,'vg::load_translation_back_map(HandleGraph &graph, ifstream &input_stream)'],['../namespacevg.html#a0b717077a15106d70c8ce4cc035ca890',1,'vg::load_translation_back_map(const gbwtgraph::GBWTGraph &graph)']]],
+ ['load_5ftranslation_5fmap_3220',['load_translation_map',['../namespacevg.html#a11a634196a7420547646dc30d2c57b18',1,'vg::load_translation_map(ifstream &input_stream)'],['../namespacevg.html#a709e93bb1c0dbdcdbc928960e42688ec',1,'vg::load_translation_map(const gbwtgraph::GBWTGraph &graph)']]],
+ ['load_5ftranslations_3221',['load_translations',['../structvg_1_1AugmentedGraph.html#af86dc51d58ee0cfa4513602dccc373cd',1,'vg::AugmentedGraph']]],
+ ['load_5fv1_3222',['load_v1',['../structvg_1_1Haplotypes_1_1Subchain.html#aacfeb074e57aa98d8ab342114af74e56',1,'vg::Haplotypes::Subchain::load_v1()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a1ace0bf2f790aec2cc6be94bd751009f',1,'vg::Haplotypes::TopLevelChain::load_v1()']]],
+ ['load_5fv2_3223',['load_v2',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ab6639ac2e85e25e7e5a4e854e0960708',1,'vg::Haplotypes::TopLevelChain']]],
+ ['loader_2ehpp_3224',['loader.hpp',['../loader_8hpp.html',1,'']]],
+ ['local_5fhandle_3225',['local_handle',['../classxg_1_1XGPath.html#a6a9566f974aebd3c74fc00ee9dc0c5f0',1,'xg::XGPath']]],
+ ['localhaplotype_3226',['LocalHaplotype',['../structvg_1_1Recombinator_1_1LocalHaplotype.html',1,'vg::Recombinator']]],
+ ['locally_5fexpand_5fgraph_3227',['locally_expand_graph',['../namespacevg_1_1algorithms.html#aa015cfde6842fff0d0dcd81f7130c659',1,'vg::algorithms']]],
+ ['locally_5fexpand_5fgraph_2ecpp_3228',['locally_expand_graph.cpp',['../locally__expand__graph_8cpp.html',1,'']]],
+ ['locally_5fexpand_5fgraph_2ehpp_3229',['locally_expand_graph.hpp',['../locally__expand__graph_8hpp.html',1,'']]],
+ ['locationsupport_3230',['LocationSupport',['../structvg_1_1LocationSupport.html',1,'vg']]],
+ ['lock_3231',['Lock',['../classvg_1_1GraphSynchronizer_1_1Lock.html',1,'vg::GraphSynchronizer::Lock'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a62805a6582a0280c58509f232079b416',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t path_offset, size_t context_bases, bool reflect)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a64972da675bb40fbbaec55470aeebdc4',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t start, size_t past_end)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1a6ed95994cc497481d3338986a30e49',1,'vg::GraphSynchronizer::Lock::lock()']]],
+ ['locked_5fnodes_3232',['locked_nodes',['../classvg_1_1GraphSynchronizer_1_1Lock.html#acfb5bf6caa6040ec1028250324296355',1,'vg::GraphSynchronizer::Lock::locked_nodes()'],['../classvg_1_1GraphSynchronizer.html#a275e3112ec47229a197e3ecc118771c4',1,'vg::GraphSynchronizer::locked_nodes()']]],
+ ['locus_3233',['Locus',['../structvg_1_1Locus.html',1,'vg::Locus'],['../structvg_1_1Alignment.html#afe47b70cd7b78e97a9cf18e9c60ef4f0',1,'vg::Alignment::locus()']]],
+ ['locus_5fmatch_5fany_3234',['LOCUS_MATCH_ANY',['../classhandlegraph_1_1PathMetadata.html#a613e59743ad6e1df8e9682fdf087e715',1,'handlegraph::PathMetadata']]],
+ ['locus_5fmatch_5fnumerical_5fwithout_5fhaplotype_3235',['LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#ab26b62f4dc1863aeae2798e008b38c80',1,'handlegraph::PathMetadata']]],
+ ['locus_5fto_5fvariant_3236',['locus_to_variant',['../classvg_1_1Genotyper.html#a55c456d612728331007f2f6c4307195f',1,'vg::Genotyper']]],
+ ['log10_5fadd_5fone_3237',['log10_add_one',['../namespacevg.html#a16b2b6e110a2f72a871c309b888b013c',1,'vg']]],
+ ['log10_5fto_5fln_3238',['log10_to_ln',['../namespacevg.html#a48d9ec9295afc7457506af4ddaf44217',1,'vg']]],
+ ['log_5falignment_3239',['log_alignment',['../classvg_1_1MinimizerMapper.html#ab02245901b7ec1710512eab20aec3a48',1,'vg::MinimizerMapper::log_alignment(const Alignment &aln)'],['../classvg_1_1MinimizerMapper.html#aed8f32c63a79281d8693c19f6d6d5521',1,'vg::MinimizerMapper::log_alignment(const Path &path, bool force_condensed=false)']]],
+ ['log_5fbase_3240',['log_base',['../classvg_1_1GSSWAligner.html#a5a1a7e6edc3764ff32f7815999d6345f',1,'vg::GSSWAligner::log_base()'],['../classvg_1_1SpliceStats.html#ae01c237b5e011851147a342b8e7aa3ad',1,'vg::SpliceStats::log_base()']]],
+ ['log_5fbits_3241',['log_bits',['../classvg_1_1MinimizerMapper.html#a8d6f418b719d4a4671562c9eeb998601',1,'vg::MinimizerMapper']]],
+ ['log_5fcontinue_5ffactor_3242',['log_continue_factor',['../structhaplo_1_1haploMath_1_1RRMemo.html#a4a3dacc819f40fd7e5063821b133028d',1,'haplo::haploMath::RRMemo']]],
+ ['log_5fcontinue_5fprobability_3243',['log_continue_probability',['../structhaplo_1_1haploMath_1_1RRMemo.html#afd6af2944e0a42df7f251fe008ba3e90',1,'haplo::haploMath::RRMemo']]],
+ ['log_5flikelihood_3244',['log_likelihood',['../structvg_1_1Genotype.html#ad14f6fc449e1086ccd2de2bc4ad419a4',1,'vg::Genotype']]],
+ ['log_5flikelihood_5fapprox_5ffactor_3245',['log_likelihood_approx_factor',['../classvg_1_1MultipathMapper.html#a28e3e0b047b5d3c195431982f76084c1',1,'vg::MultipathMapper']]],
+ ['log_5fname_3246',['log_name',['../classvg_1_1MinimizerMapper.html#ad49858579fbcd962383387351e2b0183',1,'vg::MinimizerMapper']]],
+ ['log_5fpopulation_5fsize_3247',['log_population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#a27a02a4732a9e50c9a1cb9f0b7d7ac3b',1,'haplo::haploMath::RRMemo']]],
+ ['log_5fposterior_3248',['log_posterior',['../structvg_1_1Genotype.html#a743da1ba7239bddcd6316a60f66bd307',1,'vg::Genotype']]],
+ ['log_5fprior_3249',['log_prior',['../structvg_1_1Genotype.html#a94b836b6384c02e11478b2ec18ab0ad7',1,'vg::Genotype']]],
+ ['log_5freads_3250',['log_reads',['../structGiraffeMainOptions.html#a2b54df0c377a105e57c67c93b1b98ce9',1,'GiraffeMainOptions']]],
+ ['log_5frecombination_5fpenalty_3251',['log_recombination_penalty',['../structhaplo_1_1haploMath_1_1RRMemo.html#aa33b509ee804234be1fb33061b3a9f76',1,'haplo::haploMath::RRMemo']]],
+ ['log_5ftarget_3252',['log_target',['../classvg_1_1MCMCGenotyper.html#a4622c5efee68d8f148b961a92a1abc62',1,'vg::MCMCGenotyper']]],
+ ['logdiff_3253',['logdiff',['../namespacehaplo_1_1haploMath.html#af0182b1e73c64ac6ef0be9d621cce576',1,'haplo::haploMath']]],
+ ['lognormal_5fpdf_3254',['lognormal_pdf',['../namespacevg.html#afe6b7d44806f0d50d79f7de39800495d',1,'vg']]],
+ ['logprob_5fadd_3255',['logprob_add',['../namespacevg.html#a64b25a99232585c5e76baf01d1ef5520',1,'vg']]],
+ ['logprob_5fgeometric_5fmean_3256',['logprob_geometric_mean',['../namespacevg.html#a0f8a1a81a5402187152a97ca6293b4f1',1,'vg']]],
+ ['logprob_5finvert_3257',['logprob_invert',['../namespacevg.html#a1056422cd0697f2bbdcf8a085486793a',1,'vg']]],
+ ['logprob_5fsum_3258',['logprob_sum',['../namespacevg.html#a93d81b5193ecfc9600990bd427337adf',1,'vg']]],
+ ['logprob_5fto_5fphred_3259',['logprob_to_phred',['../namespacevg.html#a66d295b4b0f83393ce621b44d88680a6',1,'vg']]],
+ ['logprob_5fto_5fprob_3260',['logprob_to_prob',['../namespacevg.html#aea77a4ed92d78c48a08fce58cf319c4d',1,'vg']]],
+ ['logrrdiff_3261',['logRRDiff',['../structhaplo_1_1haploMath_1_1RRMemo.html#a770235503ce0b9bc84f8ec5585f7d328',1,'haplo::haploMath::RRMemo']]],
+ ['logs_3262',['logS',['../structhaplo_1_1haploMath_1_1RRMemo.html#a3c54d778760482c2bc80935ceefb0f61',1,'haplo::haploMath::RRMemo']]],
+ ['logs_5fbases_3263',['logS_bases',['../structhaplo_1_1haploMath_1_1RRMemo.html#a00657f76fd1b56312b031ef79728c9c7',1,'haplo::haploMath::RRMemo']]],
+ ['logsum_3264',['logsum',['../namespacehaplo_1_1haploMath.html#a5bc510bf3fca2eeaba726ababf32678f',1,'haplo::haploMath']]],
+ ['logt_3265',['logT',['../structhaplo_1_1haploMath_1_1RRMemo.html#ac74af8f5adda75809d2995a37ca79317',1,'haplo::haploMath::RRMemo']]],
+ ['logt_5fbase_3266',['logT_base',['../structhaplo_1_1haploMath_1_1RRMemo.html#a8e9b242f45b301e58dbe4e67f6added1',1,'haplo::haploMath::RRMemo']]],
+ ['long_5flimit_3267',['LONG_LIMIT',['../classvg_1_1MinimizerMapper.html#a1d68225843da9cfb161b838be3017e58',1,'vg::MinimizerMapper']]],
+ ['long_5fopt_3268',['long_opt',['../classvg_1_1BaseOption.html#a580b1cd4960ac113db781935d89cb7b1',1,'vg::BaseOption']]],
+ ['long_5foptions_3269',['long_options',['../classvg_1_1ConfigurableParser.html#a25d7c47bbc3c439235fb751722d027c8',1,'vg::ConfigurableParser']]],
+ ['long_5foptions_5fused_3270',['long_options_used',['../classvg_1_1ConfigurableParser.html#a60395eaf832c2acfa46fe0763749614f',1,'vg::ConfigurableParser']]],
+ ['long_5fread_5fminimizer_5fk_3271',['long_read_minimizer_k',['../structvg_1_1IndexingParameters.html#ac8e9a153245b64380d773561d8534c51',1,'vg::IndexingParameters']]],
+ ['long_5fread_5fminimizer_5fw_3272',['long_read_minimizer_w',['../structvg_1_1IndexingParameters.html#a7cf3ea634d6c4b3f45bf2d11867ab70c',1,'vg::IndexingParameters::long_read_minimizer_w()'],['../structvg_1_1IndexingParameters.html#aca76950e194d8a550b71ffcee55aa8df',1,'vg::IndexingParameters::long_read_minimizer_W()']]],
+ ['long_5fref_5fcontig_3273',['long_ref_contig',['../classvg_1_1Deconstructor.html#a6341c9416e41420f60f9faf7ea942d07',1,'vg::Deconstructor']]],
+ ['longest_5fcommon_5fprefix_3274',['longest_common_prefix',['../namespacevg.html#a2d872af86508016fe8b78d61a190e90a',1,'vg']]],
+ ['longest_5fdetectable_5fgap_3275',['longest_detectable_gap',['../classvg_1_1GSSWAligner.html#a9a0d0245bdab8420b4f760d818a3d9cc',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment, const string::const_iterator &read_pos) const'],['../classvg_1_1GSSWAligner.html#a6c803e19e479e8310fda8976ac30eb3a',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length, size_t read_pos) const'],['../classvg_1_1GSSWAligner.html#a00852660c55c381bdcc3546bdb2b1a93',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment) const'],['../classvg_1_1GSSWAligner.html#a6f2bbbc1b2c955874ad531cab3bf4879',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length) const']]],
+ ['longest_5fdetectable_5fgap_5fin_5frange_3276',['longest_detectable_gap_in_range',['../classvg_1_1MinimizerMapper.html#aa0f917b2d622c95d9f8bc65186cb898f',1,'vg::MinimizerMapper']]],
+ ['longest_5fpaths_5fin_5fforest_3277',['longest_paths_in_forest',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a98105712f44db6c5fadc3b9bd64f97f0',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['look_5fback_3278',['look_back',['../classvg_1_1ZipCodeTree.html#aefac261dda914b102fa57dd504af15d5',1,'vg::ZipCodeTree']]],
+ ['lookback_5ftransition_5fiterator_3279',['lookback_transition_iterator',['../namespacevg_1_1algorithms.html#ac8e2917f0a06c55852e4ef044548f2bb',1,'vg::algorithms']]],
+ ['lookup_5ffor_5fread_5fin_3280',['lookup_for_read_in',['../structvg_1_1read__alignment__index__t.html#add622e2d97706e4ad842ed27d2a93726',1,'vg::read_alignment_index_t']]],
+ ['lookup_5fin_3281',['lookup_in',['../structvg_1_1alignment__index__t.html#a96d88d8fc53918a02c51b6ba811e88be',1,'vg::alignment_index_t']]],
+ ['loop_5fleft_3282',['loop_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3374b357e0bc3bc98bd131d7dc0a3209',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['loop_5fright_3283',['loop_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae793bc31b5603ef670a83187fde8616c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['low_5fcomplexity_5fp_5fvalue_3284',['low_complexity_p_value',['../classvg_1_1Surjector.html#a1df336db06fea7951c960f71265d513d',1,'vg::Surjector']]],
+ ['lower_5fbound_3285',['lower_bound',['../structvg_1_1BREAKPOINT.html#a1b854b285738913830671a54ce0857f5',1,'vg::BREAKPOINT']]],
+ ['lower_5fbound_5fheuristic_3286',['lower_bound_heuristic',['../classvg_1_1TargetValueSearch.html#a93c1f2cb35452719dc87fb4ec8cf714e',1,'vg::TargetValueSearch']]],
+ ['lowercase_5fwarned_5falt_3287',['lowercase_warned_alt',['../classvg_1_1Constructor.html#af296f5e32632a4fee39ac4bc11589c09',1,'vg::Constructor']]],
+ ['lowercase_5fwarned_5fsequences_3288',['lowercase_warned_sequences',['../classvg_1_1Constructor.html#a4a5f08f7d9c8e7bc821a7618e019289d',1,'vg::Constructor']]],
+ ['lru_5fcache_5fsize_3289',['lru_cache_size',['../classvg_1_1Packer.html#a32572a24fe3c3b372e1ff24ec9720da0',1,'vg::Packer']]],
+ ['lv0_5falt_5flen_3290',['lv0_alt_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a64a400033d2ff787c487d78feee21a7d',1,'vg::Deconstructor::NestingInfo']]],
+ ['lv0_5fref_5flen_3291',['lv0_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ab628cbae94feb0e11bd46e09fc1900f4',1,'vg::Deconstructor::NestingInfo']]],
+ ['lv0_5fref_5fname_3292',['lv0_ref_name',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2eda67779fb6821700d9c89d8b9671f7',1,'vg::Deconstructor::NestingInfo']]],
+ ['lv0_5fref_5fstart_3293',['lv0_ref_start',['../structvg_1_1Deconstructor_1_1NestingInfo.html#af6bb1c0f6383981be4bfea3ce0fe565f',1,'vg::Deconstructor::NestingInfo']]]
];
diff --git a/search/all_d.js b/search/all_d.js
index 539569ace7..7db10d699b 100644
--- a/search/all_d.js
+++ b/search/all_d.js
@@ -1,626 +1,626 @@
var searchData=
[
- ['m_5fa_3292',['m_a',['../classvg_1_1uniform__real__distribution.html#a7504f90f6d4dea77942a9ca0c0cc3f57',1,'vg::uniform_real_distribution::m_a()'],['../classvg_1_1uniform__int__distribution.html#a2d084a9d58cbc2f4a202d7ba640207ac',1,'vg::uniform_int_distribution::m_a()']]],
- ['m_5falpha_3293',['m_alpha',['../classvg_1_1truncated__normal__distribution.html#a103e91e1a5b135b61ef12bb1396b073d',1,'vg::truncated_normal_distribution']]],
- ['m_5fb_3294',['m_b',['../classvg_1_1uniform__real__distribution.html#a736effb600abacbb4ad5dbd9960449b7',1,'vg::uniform_real_distribution::m_b()'],['../classvg_1_1uniform__int__distribution.html#a8fcf808d445c2826852f79c4bac7f594',1,'vg::uniform_int_distribution::m_b()']]],
- ['m_5fbeta_3295',['m_beta',['../classvg_1_1truncated__normal__distribution.html#ab4ba11d217ace97234dbc707180a388a',1,'vg::truncated_normal_distribution']]],
- ['m_5fdistu1_3296',['m_distU1',['../classvg_1_1normal__distribution.html#a88845be3c45acd203b683f83a658b3bd',1,'vg::normal_distribution::m_distU1()'],['../classvg_1_1truncated__normal__distribution.html#a0020a9172587312e5342375bb0730ec5',1,'vg::truncated_normal_distribution::m_distU1()']]],
- ['m_5fmean_3297',['m_mean',['../classvg_1_1normal__distribution.html#ac215210d6799c86403804a8700f8870f',1,'vg::normal_distribution']]],
- ['m_5fmu_3298',['m_mu',['../classvg_1_1truncated__normal__distribution.html#a16eb85a95c575485c51f3915c27fb206',1,'vg::truncated_normal_distribution']]],
- ['m_5fsigma_3299',['m_sigma',['../classvg_1_1truncated__normal__distribution.html#acc168175a443e25b3b7a49ddbd2d0d65',1,'vg::truncated_normal_distribution']]],
- ['m_5fstddev_3300',['m_stddev',['../classvg_1_1normal__distribution.html#a4940854c4f61e99e8c62acb754619bed',1,'vg::normal_distribution']]],
- ['m_5fsums_3301',['m_sums',['../classvg_1_1discrete__distribution.html#a175dbe373664d84a0a354f1d2febb1b1',1,'vg::discrete_distribution']]],
- ['m_5fweights_3302',['m_weights',['../classvg_1_1discrete__distribution.html#aae17bac88e7ee1c979e4c44287f9a2fe',1,'vg::discrete_distribution']]],
- ['magic_5fbytes_3303',['MAGIC_BYTES',['../classvg_1_1StreamIndexBase.html#a9bbb2b0134f0e831fc2ec5db056b7397',1,'vg::StreamIndexBase']]],
- ['magic_5fnumber_3304',['MAGIC_NUMBER',['../structvg_1_1Haplotypes_1_1Header.html#a08c60e1b376c1a451b42810f5131758b',1,'vg::Haplotypes::Header::MAGIC_NUMBER()'],['../structvg_1_1Haplotypes_1_1Header.html#ae84cdbdc1d89ebf53496eed304acafd3',1,'vg::Haplotypes::Header::magic_number()'],['../classvg_1_1ZipCodeCollection.html#a27434270b2b8b6e6a66f783efb8150c2',1,'vg::ZipCodeCollection::magic_number()']]],
- ['main_3305',['main',['../main_8cpp.html#a813f1942a22b88bf4ff8686af6c643bd',1,'main(int argc, char *argv[]) VG_PREFLIGHT_EVERYWHERE: main.cpp'],['../main_8cpp.html#a3c04138a5bfe5d72780bb7e82a18e627',1,'main(int argc, char **argv): main.cpp']]],
- ['main_2ecpp_3306',['main.cpp',['../main_8cpp.html',1,'']]],
- ['main_5fadd_3307',['main_add',['../add__main_8cpp.html#a70f2a72c5f1d86661c78534083fbe668',1,'add_main.cpp']]],
- ['main_5falign_3308',['main_align',['../align__main_8cpp.html#acc3c08d6346e0538c36aa20a0af338f2',1,'align_main.cpp']]],
- ['main_5fannotate_3309',['main_annotate',['../annotate__main_8cpp.html#ae4b460c351b8e163410fbacf4244f7f2',1,'annotate_main.cpp']]],
- ['main_5faugment_3310',['main_augment',['../augment__main_8cpp.html#a39b28115682b22f672ec0f6932d0f259',1,'augment_main.cpp']]],
- ['main_5fautoindex_3311',['main_autoindex',['../autoindex__main_8cpp.html#a0c5af200c1937f0b3c5723ce0220a7bf',1,'autoindex_main.cpp']]],
- ['main_5fbenchmark_3312',['main_benchmark',['../benchmark__main_8cpp.html#add0702a6210234f5e42ee9c301265d6a',1,'benchmark_main.cpp']]],
- ['main_5fcall_3313',['main_call',['../call__main_8cpp.html#ac255329e18ef1a778298cd5fdc5d3050',1,'call_main.cpp']]],
- ['main_5fchain_3314',['main_chain',['../chain__main_8cpp.html#af61d7259730b08c0c8ff61629e51d78a',1,'chain_main.cpp']]],
- ['main_5fchunk_3315',['main_chunk',['../chunk__main_8cpp.html#aa34cae934dcb31ac7653f079d0d4bf93',1,'chunk_main.cpp']]],
- ['main_5fcircularize_3316',['main_circularize',['../circularize__main_8cpp.html#a1d21512b4c5eb417fa6a1b20a72c1195',1,'circularize_main.cpp']]],
- ['main_5fclip_3317',['main_clip',['../clip__main_8cpp.html#af09a429b96343cf918b8fdea5ebf1a4b',1,'clip_main.cpp']]],
- ['main_5fcluster_3318',['main_cluster',['../cluster__main_8cpp.html#a88693148489c263b15047d96976b9b94',1,'cluster_main.cpp']]],
- ['main_5fcombine_3319',['main_combine',['../combine__main_8cpp.html#a7f4bcb1d0c551b46ed39797df9d0da60',1,'combine_main.cpp']]],
- ['main_5fconcat_3320',['main_concat',['../concat__main_8cpp.html#a22a9b545fc267c18654f312d4fa8d701',1,'concat_main.cpp']]],
- ['main_5fconstruct_3321',['main_construct',['../construct__main_8cpp.html#a385574d21007babb8ef7fa73c9b39cee',1,'construct_main.cpp']]],
- ['main_5fconvert_3322',['main_convert',['../convert__main_8cpp.html#abd9dc3a752930342a8096088f2d4b742',1,'convert_main.cpp']]],
- ['main_5fdeconstruct_3323',['main_deconstruct',['../deconstruct__main_8cpp.html#a80a32834c987861cb4c90d124e0aba12',1,'deconstruct_main.cpp']]],
- ['main_5fdepth_3324',['main_depth',['../depth__main_8cpp.html#a7db982076303bea19c79ee8df88e086f',1,'depth_main.cpp']]],
- ['main_5fdotplot_3325',['main_dotplot',['../dotplot__main_8cpp.html#a74751264f7ead208e151be5408766053',1,'dotplot_main.cpp']]],
- ['main_5fexplode_3326',['main_explode',['../explode__main_8cpp.html#a0448cf7f521dde683e09f6c57df48d67',1,'explode_main.cpp']]],
- ['main_5ffilter_3327',['main_filter',['../filter__main_8cpp.html#af14726647fef6f08e5f916f8a1b4ae0e',1,'filter_main.cpp']]],
- ['main_5ffind_3328',['main_find',['../find__main_8cpp.html#a35569e011de224c166556ea563a4861e',1,'find_main.cpp']]],
- ['main_5ffunction_3329',['main_function',['../classvg_1_1subcommand_1_1Subcommand.html#a8c500a86e1c9c51cea715508a19c75fa',1,'vg::subcommand::Subcommand']]],
- ['main_5fgamcompare_3330',['main_gamcompare',['../gamcompare__main_8cpp.html#a0685b1cc8cff4ca811a199eb1746ddf7',1,'gamcompare_main.cpp']]],
- ['main_5fgampcompare_3331',['main_gampcompare',['../gampcompare__main_8cpp.html#a4b081154219461589d0978c7d993d547',1,'gampcompare_main.cpp']]],
- ['main_5fgamsort_3332',['main_gamsort',['../gamsort__main_8cpp.html#a0aa266bac1f77e7c3625c293f1050108',1,'gamsort_main.cpp']]],
- ['main_5fgbwt_3333',['main_gbwt',['../gbwt__main_8cpp.html#a2018904e4679a19c52921f97afab4592',1,'gbwt_main.cpp']]],
- ['main_5fgenotype_3334',['main_genotype',['../genotype__main_8cpp.html#a04819bc8264065b3aadb2b7bf3a923fa',1,'genotype_main.cpp']]],
- ['main_5fgiraffe_3335',['main_giraffe',['../giraffe__main_8cpp.html#a03a19bdd804f12c23f77bb885e91df4a',1,'giraffe_main.cpp']]],
- ['main_5fhaplotypes_3336',['main_haplotypes',['../haplotypes__main_8cpp.html#ae8ab8ef2233eb016b7b7f0c2bd5c9411',1,'haplotypes_main.cpp']]],
- ['main_5fhelp_3337',['main_help',['../help__main_8cpp.html#ad13a4a4aadfb1314983f35c8cca2e5c7',1,'help_main.cpp']]],
- ['main_5fids_3338',['main_ids',['../ids__main_8cpp.html#aaefd32fe84e813daa1089df0d0bd955f',1,'ids_main.cpp']]],
- ['main_5findex_3339',['main_index',['../index__main_8cpp.html#a7a9da678374c285546cdf243a185b15e',1,'index_main.cpp']]],
- ['main_5finject_3340',['main_inject',['../inject__main_8cpp.html#a214bda0795dc475a91ffd32752b2ee8e',1,'inject_main.cpp']]],
- ['main_5fjoin_3341',['main_join',['../join__main_8cpp.html#a904b50e94b5426c0bb0a39523aada064',1,'join_main.cpp']]],
- ['main_5fkmers_3342',['main_kmers',['../kmers__main_8cpp.html#af32e430824ef93e29253ec42f2edb21e',1,'kmers_main.cpp']]],
- ['main_5fmap_3343',['main_map',['../map__main_8cpp.html#ac963a6cd2cd103405e86f088d5c8358a',1,'map_main.cpp']]],
- ['main_5fmask_3344',['main_mask',['../mask__main_8cpp.html#a66e6db9d20d50a757d7ab70d7ca458f8',1,'mask_main.cpp']]],
- ['main_5fmcmc_3345',['main_mcmc',['../mcmc__main_8cpp.html#a7a702ad991c4285feaeee55461c95a63',1,'mcmc_main.cpp']]],
- ['main_5fminimizer_3346',['main_minimizer',['../minimizer__main_8cpp.html#a5a43d1ef287159cce46f07df1b8b088d',1,'minimizer_main.cpp']]],
- ['main_5fmod_3347',['main_mod',['../mod__main_8cpp.html#ab561b57168cf02964d1a14e024108f2e',1,'mod_main.cpp']]],
- ['main_5fmpmap_3348',['main_mpmap',['../mpmap__main_8cpp.html#a8deece908ee37e2d38e61b2c921e508f',1,'mpmap_main.cpp']]],
- ['main_5fmsga_3349',['main_msga',['../msga__main_8cpp.html#a60a999194e7689bb509442f1caa2354e',1,'msga_main.cpp']]],
- ['main_5fpack_3350',['main_pack',['../pack__main_8cpp.html#a0b3d5bb3cabcd119b839dded9853de23',1,'pack_main.cpp']]],
- ['main_5fpaths_3351',['main_paths',['../paths__main_8cpp.html#a6357ea987a573514a31781145d74cd61',1,'paths_main.cpp']]],
- ['main_5fprune_3352',['main_prune',['../prune__main_8cpp.html#a5b6c70447534213ea13f56ad785d881b',1,'prune_main.cpp']]],
- ['main_5frna_3353',['main_rna',['../rna__main_8cpp.html#a6d06f637eb10cfbb38bb55619ceb3c00',1,'rna_main.cpp']]],
- ['main_5fsift_3354',['main_sift',['../sift__main_8cpp.html#a5c78b9bf77f34696d562b5abffb7a1ef',1,'sift_main.cpp']]],
- ['main_5fsim_3355',['main_sim',['../sim__main_8cpp.html#a1926f81c841475ca54d3100d6340d468',1,'sim_main.cpp']]],
- ['main_5fsimplify_3356',['main_simplify',['../simplify__main_8cpp.html#a16ebf24b0dce88509b5e97fc2fc777b8',1,'simplify_main.cpp']]],
- ['main_5fsnarl_3357',['main_snarl',['../snarls__main_8cpp.html#a4bda7d45d00c828d1e8555573c1c3caf',1,'snarls_main.cpp']]],
- ['main_5fsort_3358',['main_sort',['../sort__main_8cpp.html#a40dc673c2ce8bc4c8ae1496857641885',1,'sort_main.cpp']]],
- ['main_5fstats_3359',['main_stats',['../stats__main_8cpp.html#a6e64cedc2b30a69dea5b727edded704d',1,'stats_main.cpp']]],
- ['main_5fsurject_3360',['main_surject',['../surject__main_8cpp.html#a51d014c6923a46c0f34ca4deb59d11b0',1,'surject_main.cpp']]],
- ['main_5ftest_3361',['main_test',['../test__main_8cpp.html#abd8de8d504f1b1aa53207643a7b553b4',1,'test_main.cpp']]],
- ['main_5ftrace_3362',['main_trace',['../trace__main_8cpp.html#a7bc03098058581a46cba55a13de823e9',1,'trace_main.cpp']]],
- ['main_5ftranslate_3363',['main_translate',['../translate__main_8cpp.html#a2578e3814e52126bf55e62054a01ec7d',1,'translate_main.cpp']]],
- ['main_5fvalidate_3364',['main_validate',['../validate__main_8cpp.html#a8249f1e29a84af534ef5116f778267fb',1,'validate_main.cpp']]],
- ['main_5fvectorize_3365',['main_vectorize',['../vectorize__main_8cpp.html#a8e4da879b5896dd1e13ee84e310870ea',1,'vectorize_main.cpp']]],
- ['main_5fversion_3366',['main_version',['../version__main_8cpp.html#a972dc6662988df17dcc0b4cc0abf6e54',1,'version_main.cpp']]],
- ['main_5fview_3367',['main_view',['../view__main_8cpp.html#a868d2fd8e59794e18a2ecee28f838143',1,'view_main.cpp']]],
- ['main_5fviz_3368',['main_viz',['../viz__main_8cpp.html#a9e415066b5a221e559f9a402b85f386d',1,'viz_main.cpp']]],
- ['main_5fzipcode_3369',['main_zipcode',['../zipcode__main_8cpp.html#a8b81469e01a40dbf9eefbdf90e0c0427',1,'zipcode_main.cpp']]],
- ['make_5fbands_3370',['make_bands',['../classvg_1_1Mapper.html#aafecbaf352024b2847928860fe6c1168',1,'vg::Mapper']]],
- ['make_5fcircular_3371',['make_circular',['../classvg_1_1Paths.html#a1e8760e2c86dd64141c2d0df35926430',1,'vg::Paths']]],
- ['make_5fcompact_3372',['make_compact',['../classvg_1_1Packer.html#a66e266fca00d4e74b7bda1ddbcf384e3',1,'vg::Packer']]],
- ['make_5fdynamic_3373',['make_dynamic',['../classvg_1_1Packer.html#ac3ab6cab2e0cf0ae4e65663db73184e8',1,'vg::Packer']]],
- ['make_5fedge_3374',['make_edge',['../classvg_1_1PhaseUnfolder.html#a82b0a653c98ead9bc4c31d283583d102',1,'vg::PhaseUnfolder']]],
- ['make_5fempty_3375',['make_empty',['../structvg_1_1WFAAlignment.html#ae54f9060454a45ea9a2131a9b5b81c38',1,'vg::WFAAlignment']]],
- ['make_5fgraph_3376',['make_graph',['../classvg_1_1MSAConverter.html#aa4556065637b908e37d2cbf7534b930a',1,'vg::MSAConverter']]],
- ['make_5fhit_5fgraph_3377',['make_hit_graph',['../classvg_1_1MEMClusterer.html#ac65c43448463ef346199437b073c1467',1,'vg::MEMClusterer::make_hit_graph()'],['../classvg_1_1NullClusterer.html#a4e7540aadd3d1eb3d4616cf0d268b3f0',1,'vg::NullClusterer::make_hit_graph()'],['../classvg_1_1OrientedDistanceClusterer.html#af520fdf27e87d46d3a7a5976ec6179c2',1,'vg::OrientedDistanceClusterer::make_hit_graph()'],['../classvg_1_1TVSClusterer.html#a33dff32277c63fa9dc42969c01094900',1,'vg::TVSClusterer::make_hit_graph()'],['../classvg_1_1MinDistanceClusterer.html#a8f3bd899d336e3a30f77e2985eaceb81',1,'vg::MinDistanceClusterer::make_hit_graph()'],['../classvg_1_1GreedyMinDistanceClusterer.html#ad5a3eda064089d19eec2338ccc82e515',1,'vg::GreedyMinDistanceClusterer::make_hit_graph()'],['../classvg_1_1ComponentMinDistanceClusterer.html#afe8b8bc133b5ef94999264dabb3452b8',1,'vg::ComponentMinDistanceClusterer::make_hit_graph()']]],
- ['make_5findexes_3378',['make_indexes',['../classvg_1_1IndexRegistry.html#a4c954dbadbab6cdcd3e81b438864668d',1,'vg::IndexRegistry']]],
- ['make_5flinear_3379',['make_linear',['../classvg_1_1Paths.html#aa82bcbd02b83a9f0781c3696ef46d371',1,'vg::Paths']]],
- ['make_5flong_5foptions_3380',['make_long_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aec2fb8fe7d2b574993b33658440227e0',1,'vg::subcommand::BaseOptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8db74c059e0822c3b25ea7d05bcce340',1,'vg::subcommand::OptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af521b678294674ffcd04b670b5cde737',1,'vg::subcommand::GroupedOptionGroup::make_long_options()']]],
- ['make_5fnontrivial_5fmultipath_5falignment_3381',['make_nontrivial_multipath_alignment',['../classvg_1_1MultipathMapper.html#a4e4be08a92493e0e3b865783b4701cd7',1,'vg::MultipathMapper']]],
- ['make_5fnull_5falignment_3382',['make_null_alignment',['../classvg_1_1Surjector.html#a139ffe849fc1164217e45ea5755fc518',1,'vg::Surjector']]],
- ['make_5fnull_5fmp_5falignment_3383',['make_null_mp_alignment',['../classvg_1_1Surjector.html#a7db137631f3315ede2f6887334a161b4',1,'vg::Surjector']]],
- ['make_5fplan_3384',['make_plan',['../classvg_1_1IndexRegistry.html#ab31ecdcf8f9d50a1310667d23c6410e2',1,'vg::IndexRegistry']]],
- ['make_5fpos_5ft_3385',['make_pos_t',['../namespacevg.html#a2d9f0a2379194fb00d706e90d373b378',1,'vg::make_pos_t(const Position &pos)'],['../namespacevg.html#a1b348dcfac955a7030a3721f436e7d5d',1,'vg::make_pos_t(const position_t &pos)'],['../namespacevg.html#afc066dab7543192bf782959ef160f2d4',1,'vg::make_pos_t(gcsa::node_type node)'],['../namespacevg.html#a1d85d380ba4b936ac8a715a72062866c',1,'vg::make_pos_t(id_t id, bool is_rev, offset_t off)'],['../namespacexg.html#aace66781c520f719a1f8f64ab24f2589',1,'xg::make_pos_t()']]],
- ['make_5fposition_3386',['make_position',['../namespacevg.html#a6247de8deb27aaabf2bc0d6fc755f693',1,'vg::make_position(const pos_t &pos)'],['../namespacevg.html#ac6af3d55800703f7534ca07a84450580',1,'vg::make_position(id_t id, bool is_rev, offset_t off)'],['../namespacevg.html#a4cdd9b08b7b6d6e15d00536554f3ca56',1,'vg::make_position(gcsa::node_type node)']]],
- ['make_5fprefix_5fsuffix_5ftable_3387',['make_prefix_suffix_table',['../namespacevg.html#a3ff1638bd636bb4b9746545dc261aea1',1,'vg']]],
- ['make_5fshort_5foptions_3388',['make_short_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a0a5933555ce227565029122dfd6f15e9',1,'vg::subcommand::BaseOptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8ef56a59e757ab9cd808cf9112e1f64b',1,'vg::subcommand::OptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3f2f2249f4edee37552c77bce6c4a42c',1,'vg::subcommand::GroupedOptionGroup::make_short_options()']]],
- ['make_5fshuffle_5fseed_3389',['make_shuffle_seed',['../namespacevg.html#aeca2b8e2d5730b1d5b94c1d3861757d7',1,'vg::make_shuffle_seed(const multipath_alignment_t &aln)'],['../namespacevg.html#acc312d814d6a06a4a5159c7943675bbe',1,'vg::make_shuffle_seed(const Alignment &aln)'],['../namespacevg.html#a2ec8fc79a1f84c6ef4a02c9d7c7a2850',1,'vg::make_shuffle_seed(const T *ptr)'],['../namespacevg.html#a04ebc20fd2965b1932e27958dd0c602c',1,'vg::make_shuffle_seed(const pair< T1, T2 > &p)']]],
- ['make_5fsingle_5fstranded_3390',['make_single_stranded',['../namespacehandlegraph_1_1algorithms.html#a8cac1e5f4dc0c5e0e501ebb9fc58fca3',1,'handlegraph::algorithms']]],
- ['make_5fsnarl_5fgraph_3391',['make_snarl_graph',['../classvg_1_1MCMCGenotyper.html#abbbf0c2625e4039f5a79b8b360515b41',1,'vg::MCMCGenotyper']]],
- ['make_5fsnarl_5fmap_3392',['make_snarl_map',['../classvg_1_1MCMCGenotyper.html#a5e31dd64fad5dfb14d38be487fc14e59',1,'vg::MCMCGenotyper']]],
- ['make_5fsubset_5fgraph_3393',['make_subset_graph',['../classvg_1_1Genotyper.html#ab11a87f5f21d3a7122ec85f6d853f336',1,'vg::Genotyper']]],
- ['make_5fsupport_3394',['make_support',['../namespacevg.html#a1c0ae5cc687e77bb7cee28e975a005b3',1,'vg']]],
- ['make_5ftemporary_5fdistance_5findex_3395',['make_temporary_distance_index',['../namespacevg.html#ae55954f00a00c8b34d20966f7d9fe72a',1,'vg']]],
- ['make_5ftranslation_3396',['make_translation',['../namespacevg.html#a028aa842a68b6993a37a82c7645e0633',1,'vg']]],
- ['make_5funlocalized_5finsertion_3397',['make_unlocalized_insertion',['../structvg_1_1WFAAlignment.html#aee475e8a07f1e06f61411f581813252e',1,'vg::WFAAlignment']]],
- ['make_5fvariant_5fid_3398',['make_variant_id',['../namespacevg.html#aa74ef603900cf05ce35dbab813d21deb',1,'vg']]],
- ['manage_3399',['manage',['../classvg_1_1SnarlManager.html#adb68da18eef20aa324c498444a9ed77f',1,'vg::SnarlManager']]],
- ['manager_3400',['manager',['../classvg_1_1GenomeState.html#a6c9277391547084f77ff1dbfbe481310',1,'vg::GenomeState']]],
- ['many_5flimit_3401',['MANY_LIMIT',['../classvg_1_1MinimizerMapper.html#aecc1f538f9a05a7f3fd29b5a425ec522',1,'vg::MinimizerMapper']]],
- ['map_3402',['map',['../classvg_1_1MinimizerMapper.html#a4c955e7607a1c07d2ca2b22a065e8b91',1,'vg::MinimizerMapper::map(Alignment &aln, AlignmentEmitter &alignment_emitter)'],['../classvg_1_1MinimizerMapper.html#a182c026fcc4e3a8dea5de373d1a79bbb',1,'vg::MinimizerMapper::map(Alignment &aln)']]],
- ['map_5fentry_5ftype_3403',['map_entry_type',['../structvg_1_1WFAPoint.html#ac125c09256ece943d40cf65152a9837a',1,'vg::WFAPoint']]],
- ['map_5ffrom_5fchains_3404',['map_from_chains',['../classvg_1_1MinimizerMapper.html#af098e417ff3df9ff70d18cd4cd12555b',1,'vg::MinimizerMapper']]],
- ['map_5ffrom_5fextensions_3405',['map_from_extensions',['../classvg_1_1MinimizerMapper.html#aaaaff0f62d2003bd8814c3fd90dd8226',1,'vg::MinimizerMapper']]],
- ['map_5fkeys_5fto_5fset_3406',['map_keys_to_set',['../namespacevg.html#ace99283a6b34f0891dc0b49f0cd60eea',1,'vg']]],
- ['map_5fmain_2ecpp_3407',['map_main.cpp',['../map__main_8cpp.html',1,'']]],
- ['map_5forder_5fto_5foriginal_3408',['map_order_to_original',['../classvg_1_1WindowedVcfBuffer.html#ab62203851ffc243bd9183f9174739bbd',1,'vg::WindowedVcfBuffer']]],
- ['map_5fover_3409',['map_over',['../namespacevg.html#a4833086451a8b97af4709aa6c7385177',1,'vg']]],
- ['map_5fpaired_3410',['map_paired',['../classvg_1_1MinimizerMapper.html#a5c90ef4f961998cc7904e78225b36f50',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer)'],['../classvg_1_1MinimizerMapper.html#ab5f4c707ec44ba8f742c79bb0153c157',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2)']]],
- ['map_5fstage_5fresults_5fto_5fprevious_5fstage_3411',['map_stage_results_to_previous_stage',['../classvg_1_1Funnel.html#aeca18258bb42790609df5f17d2394135',1,'vg::Funnel']]],
- ['map_5fvariants_3412',['map_variants',['../haplotypes__main_8cpp.html#a1e43abd4f18210a8a4e131afbc8d182d',1,'haplotypes_main.cpp']]],
- ['mapper_3413',['Mapper',['../classvg_1_1Mapper.html',1,'vg::Mapper'],['../classvg_1_1Mapper.html#a1d808071bd518202414fba56f5ec333e',1,'vg::Mapper::Mapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr)'],['../classvg_1_1Mapper.html#ae47e4e50adf1a5132656e9dd9a227628',1,'vg::Mapper::Mapper(void)']]],
- ['mapper_2ecpp_3414',['mapper.cpp',['../mapper_8cpp.html',1,'']]],
- ['mapper_2ehpp_3415',['mapper.hpp',['../mapper_8hpp.html',1,'']]],
- ['mapper_5falignment_5fcutoff_3416',['mapper_alignment_cutoff',['../classvg_1_1VariantAdder.html#aa4281d59699cd880523cb47a146e5462',1,'vg::VariantAdder']]],
- ['mapping_3417',['Mapping',['../structvg_1_1Mapping.html',1,'vg::Mapping'],['../classvg_1_1PhaseUnfolder.html#ae30c8d79f4461cae38e4ec2268a22022',1,'vg::PhaseUnfolder::mapping()'],['../structvg_1_1Path.html#a5d91e68bc4c6f7a5915cb4a42cc21caf',1,'vg::Path::mapping()'],['../classvg_1_1path__t.html#ab7f2f4df754fec9f8631c8388cbe4aad',1,'vg::path_t::mapping() const'],['../classvg_1_1path__t.html#a07af6243d1650ddef63ed19804da8071',1,'vg::path_t::mapping(size_t i) const']]],
- ['mapping_5fagainst_5fpath_3418',['mapping_against_path',['../namespacevg.html#ad2e7730a993652e18d80ca77dac73713',1,'vg']]],
- ['mapping_5fcigar_3419',['mapping_cigar',['../namespacevg.html#a5a0bb992cac134b2eed1e7b84eaecc2c',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char >> &cigar, char mismatch_operation)'],['../namespacevg.html#a642736d2f652e5ab522e1f26b874e097',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char > > &cigar, char mismatch_operation='M')']]],
- ['mapping_5fedits_3420',['mapping_edits',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a9eb8dcec1e61b69092af38a89e82917a',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['mapping_5fends_5fin_5fdeletion_3421',['mapping_ends_in_deletion',['../namespacevg.html#afeef6a4c023183ead5725398b14d443c',1,'vg']]],
- ['mapping_5fenters_5fside_3422',['mapping_enters_side',['../classvg_1_1Genotyper.html#aa2b4d94f59265c107895c48a26b107a6',1,'vg::Genotyper']]],
- ['mapping_5fexits_5fside_3423',['mapping_exits_side',['../classvg_1_1Genotyper.html#a8b054a94fb2ceb4c65731188227b0cf8',1,'vg::Genotyper']]],
- ['mapping_5ffrom_5flength_3424',['mapping_from_length',['../namespacevg.html#aa2aa77c6d4db628d13488c0bd82538ed',1,'vg::mapping_from_length(const Mapping &m)'],['../namespacevg.html#a151a868062bd12ac34b9aea68dc8d4f0',1,'vg::mapping_from_length(const path_mapping_t &mapping)']]],
- ['mapping_5fis_5fmatch_3425',['mapping_is_match',['../namespacevg.html#a78ea8a2cf04759a3cfecbe4bf3e926c2',1,'vg']]],
- ['mapping_5fis_5fsimple_5fmatch_3426',['mapping_is_simple_match',['../namespacevg.html#ae8ba5042b838f859a078cf014f1a0871',1,'vg']]],
- ['mapping_5fis_5ftotal_5fdeletion_3427',['mapping_is_total_deletion',['../namespacevg.html#a6d10b5bc5677fdb0ae164f79848bb1bb',1,'vg']]],
- ['mapping_5fis_5ftotal_5finsertion_3428',['mapping_is_total_insertion',['../namespacevg.html#a54cdb9b97e741de6ced9fefbc2bf48f3',1,'vg']]],
- ['mapping_5fis_5ftotal_5fmatch_3429',['mapping_is_total_match',['../classvg_1_1VG.html#acd555e66c8fa99984c8cb24aef0ab6f9',1,'vg::VG']]],
- ['mapping_5fitr_3430',['mapping_itr',['../classvg_1_1Paths.html#ae2bd0d7232fb84776841ac7c4bfea0d2',1,'vg::Paths']]],
- ['mapping_5flikelihoods_3431',['mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a9c55acfb3c1116daeba543b42303ce7d',1,'vg::MultipathMapper']]],
- ['mapping_5fpath_5fid_3432',['mapping_path_id',['../classvg_1_1Paths.html#abb58996e669d1b9271772a929f6bebe2',1,'vg::Paths']]],
- ['mapping_5fpath_5fname_3433',['mapping_path_name',['../classvg_1_1Paths.html#ab520f6e02a5a9b2e11f10a6455be5bdd',1,'vg::Paths']]],
- ['mapping_5fpositions_3434',['mapping_positions',['../structvg_1_1PathIndex.html#acc0b1da5ad0b4f428ceb623a4d3f806f',1,'vg::PathIndex']]],
- ['mapping_5fquality_3435',['mapping_quality',['../structvg_1_1Alignment.html#a78851a70cc8a3e8f3e71409693130230',1,'vg::Alignment::mapping_quality()'],['../structvg_1_1MultipathAlignment.html#add653bff58eeb96872463fdc21b3dfd5',1,'vg::MultipathAlignment::mapping_quality()'],['../classvg_1_1multipath__alignment__t.html#a7a9fd028a082d666d19522d27ea5aa2c',1,'vg::multipath_alignment_t::mapping_quality()']]],
- ['mapping_5fquality_5fmethod_3436',['mapping_quality_method',['../classvg_1_1BaseMapper.html#a0b1fe81d11d92332f613d8a29dcadb37',1,'vg::BaseMapper']]],
- ['mapping_5fquality_5fscore_5fdiff_3437',['mapping_quality_score_diff',['../classvg_1_1GSSWAligner.html#a1c341fd9f6dd51131b714d580f5ccfea',1,'vg::GSSWAligner']]],
- ['mapping_5fsequence_3438',['mapping_sequence',['../namespacevg.html#a2b648cd1a51584623d6618565d3ca9c6',1,'vg::mapping_sequence(const Mapping &mp, const string &node_seq)'],['../namespacevg.html#ac23702705b681eacdfd1b3bcbc5254b5',1,'vg::mapping_sequence(const Mapping &mp, const Node &n)']]],
- ['mapping_5fsize_3439',['mapping_size',['../classvg_1_1path__t.html#aa3e09b61e5f2b803461ac3e20df6117c',1,'vg::path_t']]],
- ['mapping_5fstarts_5fin_5fdeletion_3440',['mapping_starts_in_deletion',['../namespacevg.html#aa377b3e776e312c717aedec842216f48',1,'vg']]],
- ['mapping_5fstring_3441',['mapping_string',['../namespacevg.html#ad993b1f289a57f3413b85840984b459c',1,'vg']]],
- ['mapping_5ft_3442',['mapping_t',['../classvg_1_1mapping__t.html',1,'vg::mapping_t'],['../classvg_1_1mapping__t.html#aa47429bfca4c4120a2e5c116d6d54450',1,'vg::mapping_t::mapping_t(void)'],['../classvg_1_1mapping__t.html#a6c9be43df27053b2bc5599faad299513',1,'vg::mapping_t::mapping_t(const Mapping &m)']]],
- ['mapping_5fto_5fgbwt_3443',['mapping_to_gbwt',['../namespacevg.html#ace1a7180fda8bb98abba24fb19183e9d',1,'vg']]],
- ['mapping_5fto_5fhandle_3444',['mapping_to_handle',['../namespacevg.html#acdaa29c218d5d55e76fe4ab168f7a14b',1,'vg']]],
- ['mapping_5fto_5flength_3445',['mapping_to_length',['../namespacevg.html#a9ef1ccef545dfc30f9123eba61267b4a',1,'vg::mapping_to_length(const Mapping &m)'],['../namespacevg.html#a3f709a91987a7d669b3974fa00aa8ecd',1,'vg::mapping_to_length(const path_mapping_t &mapping)']]],
- ['mapping_5ftype_3446',['mapping_type',['../structvg_1_1RebuildJob.html#afdbb259fb3fc369a7824f6420b2043c0',1,'vg::RebuildJob']]],
- ['mappinghash_3447',['MappingHash',['../structvg_1_1MappingHash.html',1,'vg']]],
- ['mappingqualitymethod_3448',['MappingQualityMethod',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39',1,'vg']]],
- ['mappingrun_3449',['MappingRun',['../structMappingRun.html',1,'']]],
- ['mappings_3450',['mappings',['../structvg_1_1RebuildJob.html#a82f413afdbd0c9f3c697ab84774542bf',1,'vg::RebuildJob']]],
- ['mappings_5fby_5frank_3451',['mappings_by_rank',['../classvg_1_1Paths.html#a27d349c3f4795f1389d3824e1c1e3e8f',1,'vg::Paths']]],
- ['mappings_5fequivalent_3452',['mappings_equivalent',['../namespacevg.html#af26a23818c9426d77ef25b07bbaaf605',1,'vg']]],
- ['mapq_3453',['mapq',['../structgafkluge_1_1GafRecord.html#a09ffb165e71177223d73e2fea5ed1399',1,'gafkluge::GafRecord']]],
- ['mapq_5fscaling_5ffactor_3454',['mapq_scaling_factor',['../classvg_1_1MultipathMapper.html#aadbb94f74824864d7bed5c63cb85687e',1,'vg::MultipathMapper']]],
- ['mapq_5fscore_5fscale_3455',['mapq_score_scale',['../classvg_1_1MinimizerMapper.html#a0e13799b9b7e3f64d06d10bde825924c',1,'vg::MinimizerMapper']]],
- ['mapq_5fscore_5fwindow_3456',['mapq_score_window',['../classvg_1_1MinimizerMapper.html#ace4a8ce19de89dd8f42f807b71c66dd3',1,'vg::MinimizerMapper']]],
- ['maps_5fto_5fnode_3457',['maps_to_node',['../namespacevg.html#a242b97c26d74e9fc05ad16c31b21dcca',1,'vg']]],
- ['margin_5fafter_3458',['margin_after',['../classvg_1_1algorithms_1_1Anchor.html#ade738d4df1585fa0dc6fc935da262ee0',1,'vg::algorithms::Anchor']]],
- ['margin_5fbefore_3459',['margin_before',['../classvg_1_1algorithms_1_1Anchor.html#a545c9c26a24e8d37459944c5632c79e2',1,'vg::algorithms::Anchor']]],
- ['mark_5fdfs_3460',['mark_dfs',['../classvg_1_1FlowSort.html#a498b6d9f0a37f2588e4ad08b6c35a0ff',1,'vg::FlowSort']]],
- ['mark_5fsmallvariant_5falignments_3461',['mark_smallVariant_alignments',['../classvg_1_1Filter.html#a2ab59f83f673047f5c2106456c4426c3',1,'vg::Filter']]],
- ['mark_5fsv_5falignments_3462',['mark_sv_alignments',['../classvg_1_1Filter.html#a267d55220fcf5239f12dcc852586bc71',1,'vg::Filter']]],
- ['markovdistribution_3463',['MarkovDistribution',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator::MarkovDistribution< From, To >'],['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#aef78cda42fffdef670a3ceb7e4877ee9',1,'vg::NGSSimulator::MarkovDistribution::MarkovDistribution()']]],
- ['markovdistribution_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_20_3e_20_3e_3464',['MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > >',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator']]],
- ['mask_3465',['mask',['../classvg_1_1ReadMasker.html#ad6d292712ead5b6f89940f020fd8fcc2',1,'vg::ReadMasker::mask()'],['../classvg_1_1GaplessExtender.html#a9824f8144fd4f3515c7333fbeb6e2afd',1,'vg::GaplessExtender::mask()'],['../classvg_1_1WFAExtender.html#a1af2acef8bd391f46798288e9322019b',1,'vg::WFAExtender::mask()']]],
- ['mask_5fmain_2ecpp_3466',['mask_main.cpp',['../mask__main_8cpp.html',1,'']]],
- ['mask_5fsequences_3467',['mask_sequences',['../classvg_1_1Masker.html#a18d454c702ded8fdb3436f90135631ed',1,'vg::Masker']]],
- ['masker_3468',['Masker',['../classvg_1_1Masker.html',1,'vg::Masker'],['../classvg_1_1Masker.html#a0c3817b4839ee4b2dd6d38d193cd61e8',1,'vg::Masker::Masker(gbwtgraph::GBWTGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#ab302923c0d437d4e997e1c11d35125ac',1,'vg::Masker::Masker(MutablePathDeletableHandleGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#a5398d6fdb929425966c9b71c0c9dc2fd',1,'vg::Masker::Masker()=default'],['../classvg_1_1Masker.html#aae42512f78c75af240e164d16a3445e1',1,'vg::Masker::Masker(Masker &&other)=default']]],
- ['masker_2ecpp_3469',['masker.cpp',['../masker_8cpp.html',1,'']]],
- ['masker_2ehpp_3470',['masker.hpp',['../masker_8hpp.html',1,'']]],
- ['match_3471',['match',['../classvg_1_1GSSWAligner.html#a7323efd4ef078ab5866b8c2b9fea87a8',1,'vg::GSSWAligner::match()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a4fdc2b0adb79d04c4e928a61e891aa84',1,'vg::BandedGlobalAligner::BAMatrix::match()'],['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebae6fe3d73bbbc5c70e386589f9732e9af',1,'vg::WFAAlignment::match()'],['../classvg_1_1SSWAligner.html#a8ec16a3583a2d8347ee9eaf1853b8cc8',1,'vg::SSWAligner::match()'],['../structScoringOptions.html#a3a450e63987f79011a51819efd5420a4',1,'ScoringOptions::match()'],['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faac03946390169c005fafc9a38b114e6a',1,'vg::BandedGlobalAligner::Match()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): xdrop_aligner.cpp']]],
- ['match_5fbackward_3472',['match_backward',['../namespacevg.html#a3495eb8e73ceeece9957079280edc921',1,'vg']]],
- ['match_5fcount_3473',['match_count',['../classvg_1_1MaximalExactMatch.html#ab7a9c66468635a1498efdeb394c1fad6',1,'vg::MaximalExactMatch']]],
- ['match_5ffanouts_5ft_3474',['match_fanouts_t',['../classvg_1_1MEMClusterer.html#a3127930f2b575bed2937c21382924480',1,'vg::MEMClusterer::match_fanouts_t()'],['../classvg_1_1MultipathMapper.html#a165e5c0531ff4337ce6542da263d3fbd',1,'vg::MultipathMapper::match_fanouts_t()']]],
- ['match_5fforward_3475',['match_forward',['../structvg_1_1WFANode.html#a368dbe3b756f08e21718cbfac97978fd',1,'vg::WFANode::match_forward()'],['../namespacevg.html#abcb300141666ec86856482f6a59cec4c',1,'vg::match_forward()']]],
- ['match_5finitial_3476',['match_initial',['../namespacevg.html#a4b1defb1ef0b163389ff84745294d1d0',1,'vg']]],
- ['match_5fpredecessor_3477',['match_predecessor',['../classvg_1_1WFATree.html#a4242e9739a9f789386354f4582dea547',1,'vg::WFATree']]],
- ['matches_3478',['MATCHES',['../structvg_1_1WFANode.html#a0188bfd686597181c42f2384c21e9e19',1,'vg::WFANode::MATCHES()'],['../structvg_1_1SeqComplexity.html#a03e3682e2a96bbf0595d38694d3818ad',1,'vg::SeqComplexity::matches()'],['../structgafkluge_1_1GafRecord.html#a0cac64f74ee1a099fafc4148d08a630c',1,'gafkluge::GafRecord::matches()'],['../classvg_1_1DinucleotideMachine.html#a2250f97747bf0e9390ed7326d357c557',1,'vg::DinucleotideMachine::matches(uint32_t state, const char *dinucleotide) const'],['../classvg_1_1DinucleotideMachine.html#aa30db9eff5e43b78cd23094f3d7edce5',1,'vg::DinucleotideMachine::matches(uint32_t state, const string &dinucleotide) const']]],
- ['matches_5fannotation_3479',['matches_annotation',['../classvg_1_1ReadFilter.html#a95d1165f7c3901772a70ba863d1fc983',1,'vg::ReadFilter']]],
- ['matches_5fname_3480',['matches_name',['../classvg_1_1ReadFilter.html#ab72c4fd96eedcb4bcd6aa565e97dfe4d',1,'vg::ReadFilter']]],
- ['matching_3481',['matching',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a6bb2874bc8c41f0606f8f142a465e469',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['matchpos_3482',['MatchPos',['../structvg_1_1MatchPos.html',1,'vg::MatchPos'],['../structvg_1_1MatchPos.html#ab44cfadd41dfc2ec79266e4fe204458f',1,'vg::MatchPos::MatchPos()'],['../structvg_1_1MatchPos.html#a167922796c04609cdf6a129c7135f869',1,'vg::MatchPos::MatchPos(uint32_t seq_offset, uint32_t node_offset, const PathList &path)']]],
- ['mate_5fmapped_5fto_5fdisjoint_5fsubgraph_3483',['mate_mapped_to_disjoint_subgraph',['../structvg_1_1Alignment.html#a95ed4d8c7a57e34a96871b74ff851821',1,'vg::Alignment']]],
- ['mate_5fon_5freverse_5fstrand_3484',['mate_on_reverse_strand',['../structvg_1_1Alignment.html#aef312ed490cb8adf8b89eb36b46ee7d6',1,'vg::Alignment']]],
- ['mate_5frescues_3485',['mate_rescues',['../classvg_1_1Mapper.html#a56cec2a0bdc2a2398bd494cf0acb80a2',1,'vg::Mapper']]],
- ['mate_5funmapped_3486',['mate_unmapped',['../structvg_1_1Alignment.html#a061bf4ec65ccf7ff88e73e9e4ff268b7',1,'vg::Alignment']]],
- ['mates_3487',['mates',['../structvg_1_1BREAKPOINT.html#a7469d5658b49020a71529d1704b962f9',1,'vg::BREAKPOINT']]],
- ['matrix_5finvert_3488',['matrix_invert',['../namespacevg.html#a7effc13e3f877e676d65d9164a44b4a6',1,'vg']]],
- ['matrix_5fmultiply_3489',['matrix_multiply',['../namespacevg.html#a02d66ca193142fb4825a62b300d60697',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< vector< double >> &B)'],['../namespacevg.html#a9a1927488f1b7b82758828d5a53ca845',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< double > &b)']]],
- ['matrix_5fstate_3490',['matrix_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a5b8b44e10a1bc42b694728459e4b4271',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['matrix_5ft_3491',['matrix_t',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2f',1,'vg::BandedGlobalAligner']]],
- ['max_3492',['max',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a45c40bccc3fd5b000987f633c8ec8df4',1,'vg::WFAExtender::ErrorModel::Event::max()'],['../classvg_1_1WideningPRNG.html#a3083db737b68cc80dacad05c9e1ae1ee',1,'vg::WideningPRNG::max()'],['../namespacestd.html#a032e2e35689ce96dfb488db853f83334',1,'std::max()']]],
- ['max_5falignment_5fgap_3493',['max_alignment_gap',['../classvg_1_1MultipathMapper.html#aaf8af884f81cfd5ed869f26a8b8403d4',1,'vg::MultipathMapper']]],
- ['max_5falignments_3494',['max_alignments',['../classvg_1_1MinimizerMapper.html#a6062b78a7f795cb2a585eb6695bde675',1,'vg::MinimizerMapper']]],
- ['max_5falt_5fmappings_3495',['max_alt_mappings',['../classvg_1_1MultipathMapper.html#a87223306ba0d983104e48d4ded4e685d',1,'vg::MultipathMapper']]],
- ['max_5fanchors_3496',['max_anchors',['../classvg_1_1Surjector.html#a5a735901a421d305e6cbf13a016fdc9d',1,'vg::Surjector']]],
- ['max_5fattempts_3497',['max_attempts',['../classvg_1_1Mapper.html#ac9973fcf3d75d4396f6b6bdec58156a6',1,'vg::Mapper']]],
- ['max_5fband_5fcells_3498',['max_band_cells',['../classvg_1_1Surjector.html#a0e22a6f6da976c0b505caa6c1ad10ed8',1,'vg::Surjector']]],
- ['max_5fband_5fjump_3499',['max_band_jump',['../classvg_1_1Mapper.html#a916fd22fce2ebf7953863590c45f5150',1,'vg::Mapper']]],
- ['max_5fbranch_5ftrim_5flength_3500',['max_branch_trim_length',['../classvg_1_1MultipathMapper.html#a9e260c61a4b39d27286957c4f012a26a',1,'vg::MultipathMapper']]],
- ['max_5fbubble_5fpaths_3501',['max_bubble_paths',['../classvg_1_1LegacyCaller.html#a807ba6e24d16bac14c24fdc973cb837b',1,'vg::LegacyCaller::max_bubble_paths()'],['../classvg_1_1RepresentativeTraversalFinder.html#ad2de8e0f74e29d2338d0e9f99a764e23',1,'vg::RepresentativeTraversalFinder::max_bubble_paths()']]],
- ['max_5fbuf_5fsize_3502',['max_buf_size',['../classvg_1_1StreamSorter.html#a192491eeef2fa2c99522f2ad23f12035',1,'vg::StreamSorter']]],
- ['max_5fchain_5fconnection_3503',['max_chain_connection',['../classvg_1_1MinimizerMapper.html#a4d54618686eb23ac6a4a2c3579f3fec9',1,'vg::MinimizerMapper']]],
- ['max_5fchaining_5fproblems_3504',['max_chaining_problems',['../classvg_1_1MinimizerMapper.html#a034098134b882ab3e4c8dc0542763f97',1,'vg::MinimizerMapper']]],
- ['max_5fchains_5fper_5ftree_3505',['max_chains_per_tree',['../classvg_1_1MinimizerMapper.html#ada8578ed33c349fa8f9e5ff7562ac71f',1,'vg::MinimizerMapper']]],
- ['max_5fcluster_5fmapping_5fquality_3506',['max_cluster_mapping_quality',['../classvg_1_1Mapper.html#a92ea8476aae3d65f0b46f6c7353c21be',1,'vg::Mapper']]],
- ['max_5fcontext_5fradius_3507',['max_context_radius',['../classvg_1_1VariantAdder.html#a943bba24f9a1a7197744e74ee5465e5d',1,'vg::VariantAdder']]],
- ['max_5fdagify_5fduplications_3508',['max_dagify_duplications',['../classvg_1_1MultipathMapper.html#a10c136d72e6f32ff28cd608efc1f31db',1,'vg::MultipathMapper']]],
- ['max_5fdegree_3509',['max_degree',['../structPruningParameters.html#a58d4dca5e0623280f669e386a5eadd2f',1,'PruningParameters']]],
- ['max_5fdeletion_5fscan_5fnodes_3510',['max_deletion_scan_nodes',['../classvg_1_1VCFTraversalFinder.html#a3e61ffdb1cf6733311b444df38928137',1,'vg::VCFTraversalFinder']]],
- ['max_5fdepth_3511',['max_depth',['../classvg_1_1RepresentativeTraversalFinder.html#a79339337af609bc33f77cf4696962492',1,'vg::RepresentativeTraversalFinder::max_depth()'],['../classvg_1_1ZipCode.html#aa9b8e3ee702697e3692a83e2307d9084',1,'vg::ZipCode::max_depth()']]],
- ['max_5fdiagonal_3512',['max_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#abde71e96e8aac83b5233fa782b514290',1,'vg::WFATree::ScoreProperties']]],
- ['max_5fdirect_5fto_5fchain_3513',['max_direct_to_chain',['../classvg_1_1MinimizerMapper.html#adfe5996aca0f60eace262a8c06f76f30',1,'vg::MinimizerMapper']]],
- ['max_5fdisplayed_5fsuggestions_5fper_5fcategory_3514',['MAX_DISPLAYED_SUGGESTIONS_PER_CATEGORY',['../classvg_1_1DiagramExplainer.html#abb72da5ad3b5613b80c4a39c7e4b8f18',1,'vg::DiagramExplainer']]],
- ['max_5fdistance_3515',['max_distance',['../classvg_1_1WFATree.html#a761ae97d39a69d470cae27ef7cfb28a9',1,'vg::WFATree::max_distance()'],['../classvg_1_1IncrementalSubgraph.html#a06d0598eae084de70fa40ed859ce9704',1,'vg::IncrementalSubgraph::max_distance()']]],
- ['max_5fdistance_5ffrom_5fstart_3516',['max_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#a0d573babd81fa2d0c209c75afec6c91d',1,'vg::IncrementalSubgraph']]],
- ['max_5fdozeu_5fcells_3517',['max_dozeu_cells',['../classvg_1_1MinimizerMapper.html#aa462df061307b0b35996a6ecd33091f7',1,'vg::MinimizerMapper']]],
- ['max_5fdp_5fcells_3518',['max_dp_cells',['../classvg_1_1MinimizerMapper.html#af673f62cfdb402e93acaf2eb81680772',1,'vg::MinimizerMapper']]],
- ['max_5fexpected_5fdist_5fapprox_5ferror_3519',['max_expected_dist_approx_error',['../classvg_1_1OrientedDistanceClusterer.html#a74174c834516a6b4116ff6b9972ae10c',1,'vg::OrientedDistanceClusterer::max_expected_dist_approx_error()'],['../classvg_1_1MultipathMapper.html#a23d02e5f180a337a4b9eff178fc0b65d',1,'vg::MultipathMapper::max_expected_dist_approx_error()']]],
- ['max_5fexponential_5fcdf_3520',['max_exponential_cdf',['../namespacevg.html#a82dc203eaecb442a26d8f1a3db773dda',1,'vg']]],
- ['max_5fexponential_5flog_5flikelihood_3521',['max_exponential_log_likelihood',['../namespacevg.html#a617472d242ff7aad1126a6b70e70a7a8',1,'vg']]],
- ['max_5fexponential_5frate_5fintercept_3522',['max_exponential_rate_intercept',['../classvg_1_1MultipathMapper.html#a3b9f8d9eb806a7dd7e05a0b1c4851bc8',1,'vg::MultipathMapper']]],
- ['max_5fexponential_5frate_5fslope_3523',['max_exponential_rate_slope',['../classvg_1_1MultipathMapper.html#a0c2252c568582797db9b65756694eaff',1,'vg::MultipathMapper']]],
- ['max_5fexponential_5fshape_5fintercept_3524',['max_exponential_shape_intercept',['../classvg_1_1MultipathMapper.html#a2e7f7551674fa412abd1333c0baf6672',1,'vg::MultipathMapper']]],
- ['max_5fexponential_5fshape_5fslope_3525',['max_exponential_shape_slope',['../classvg_1_1MultipathMapper.html#a8ea8f5c8ad1906ccf0b878a6821a16e2',1,'vg::MultipathMapper']]],
- ['max_5fextension_5fmismatches_3526',['max_extension_mismatches',['../classvg_1_1MinimizerMapper.html#a30fd35c63e316b4a1fcdeca3752ea667',1,'vg::MinimizerMapper']]],
- ['max_5fextensions_3527',['max_extensions',['../classvg_1_1MinimizerMapper.html#a5d03747a37700e9a3f73c308709f70d1',1,'vg::MinimizerMapper']]],
- ['max_5ffan_5fin_3528',['max_fan_in',['../classvg_1_1StreamSorter.html#a673ce446e1ba8b9917f9475b9003364d',1,'vg::StreamSorter']]],
- ['max_5ffanout_5fbase_5fquality_3529',['max_fanout_base_quality',['../classvg_1_1MultipathMapper.html#a63f9b0403dceed8c8055ce5c423dd8fe',1,'vg::MultipathMapper']]],
- ['max_5ffans_5fout_3530',['max_fans_out',['../classvg_1_1MultipathMapper.html#a46f2835eebe0c9ab495e697c975534b6',1,'vg::MultipathMapper']]],
- ['max_5fflow_5fsort_3531',['max_flow_sort',['../classvg_1_1FlowSort.html#a8a5d0ba61635331b2107ad3df4972ff1',1,'vg::FlowSort']]],
- ['max_5ffragment_5flength_3532',['max_fragment_length',['../classvg_1_1MinimizerMapper.html#a4575d140e45d04d3d36e6a99bf7b0241',1,'vg::MinimizerMapper']]],
- ['max_5ffragments_3533',['max_fragments',['../classvg_1_1MinimizerMapper.html#a50848190e760fb1f3c45fd785f57c8a3',1,'vg::MinimizerMapper']]],
- ['max_5fgap_3534',['max_gap',['../classvg_1_1MEMClusterer.html#a9b8459888ec7b51e739c3be04825b4fd',1,'vg::MEMClusterer']]],
- ['max_5fgroup_5fsize_3535',['max_group_size',['../classvg_1_1io_1_1MessageEmitter.html#a4bcef07ec2af1cb44f4cd3abfe58f29c',1,'vg::io::MessageEmitter']]],
- ['max_5fhandle_3536',['max_handle',['../classvg_1_1DozeuPinningOverlay.html#a63162330a1caec7a81abf6b5f747da32',1,'vg::DozeuPinningOverlay']]],
- ['max_5fhandle_5fmemo_5fsize_3537',['max_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a478ef9dbdebaccadc78679868baa350d',1,'vg::MemoizingGraph']]],
- ['max_5fhet_5fbias_3538',['max_het_bias',['../classvg_1_1Genotyper.html#a96285d96b960d50199ad3167c20ddf91',1,'vg::Genotyper::max_het_bias()'],['../classvg_1_1RatioSupportSnarlCaller.html#a78f0c7800c9c27021c66d68cbd0335b7',1,'vg::RatioSupportSnarlCaller::max_het_bias()']]],
- ['max_5fid_3539',['max_id',['../structvg_1_1ConstructedChunk.html#aca49ac5cc43f6390443ab02496fdfd74',1,'vg::ConstructedChunk::max_id()'],['../classvg_1_1Constructor.html#a8466741ece82babe9e892a50bd06a1d9',1,'vg::Constructor::max_id()'],['../classvg_1_1DagifiedGraph.html#a154919be0eb8719eb2fa0181584a9c66',1,'vg::DagifiedGraph::max_id()'],['../classvg_1_1SubHandleGraph.html#ad0090894570f0c53d4c3011472a01d37',1,'vg::SubHandleGraph::max_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a90afa5abb895d5bb6800cd99759de14a',1,'vg::algorithms::GFAIDMapInfo::max_id()'],['../classxg_1_1XG.html#a2cf5a51e7056900fd3872792ef5fa2a5',1,'xg::XG::max_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade12e1983845ebfbf47782b8867c708c',1,'handlegraph::algorithms::SubHandleGraph::max_id()']]],
- ['max_5fin_3540',['max_in',['../classvg_1_1algorithms_1_1TracedScore.html#a8d01a37cedeb1e7e7667f05bdb8f67e9',1,'vg::algorithms::TracedScore']]],
- ['max_5findel_5fbases_3541',['max_indel_bases',['../classvg_1_1MinimizerMapper.html#a05b1280ff66b9ad01015c490f35fc005',1,'vg::MinimizerMapper']]],
- ['max_5findel_5fbases_5fper_5fbase_3542',['max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a82da9f52e8af8e9dde669c903d441adc',1,'vg::MinimizerMapper']]],
- ['max_5findel_5fhet_5fbias_3543',['max_indel_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a9298ec62feb5ab8f593fdf2c6cd2b620',1,'vg::RatioSupportSnarlCaller']]],
- ['max_5finput_5fversion_3544',['MAX_INPUT_VERSION',['../classvg_1_1StreamIndexBase.html#aa497c1ad37621af86f5f40d45e0f30b2',1,'vg::StreamIndexBase']]],
- ['max_5fintron_5flength_3545',['max_intron_length',['../classvg_1_1MultipathMapper.html#a51be0d0325abe9a3afa023477d9c2ab0',1,'vg::MultipathMapper']]],
- ['max_5fiterations_3546',['max_iterations',['../classvg_1_1SmallSnarlSimplifier.html#a212bd3bc07ab19cb42edef936ee62f7a',1,'vg::SmallSnarlSimplifier::max_iterations()'],['../minimizer__main_8cpp.html#a932fcab549241f3cf9efead93803fabc',1,'MAX_ITERATIONS(): minimizer_main.cpp']]],
- ['max_5fkmers_5fper_5fblock_3547',['max_kmers_per_block',['../classvg_1_1ParallelKFFReader.html#a0179377c78c5e599f903b70c954ffd12',1,'vg::ParallelKFFReader']]],
- ['max_5flength_3548',['max_length',['../classvg_1_1ReadFilter.html#a2afae0acb031354f67f95f20dda1c4b8',1,'vg::ReadFilter::max_length()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9abd4efb2ac344eea5ff58477c7014a769',1,'vg::Counts::max_length()']]],
- ['max_5flink_5flength_3549',['max_link_length',['../classvg_1_1JoinedSpliceGraph.html#a25612fe4db491aa5cbcc06f5816bd5bd',1,'vg::JoinedSpliceGraph']]],
- ['max_5flocal_5fextensions_3550',['max_local_extensions',['../classvg_1_1MinimizerMapper.html#a4e6142c1ccdde28230769e5a8b629d9f',1,'vg::MinimizerMapper']]],
- ['max_5flookback_5fbases_3551',['max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ae94869146878dba80c980d4e35830abe',1,'vg::MinimizerMapper']]],
- ['max_5flookback_5fbases_5fper_5fbase_3552',['max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a48ec2ca2886d6f069546d6a424becb61',1,'vg::MinimizerMapper']]],
- ['max_5flow_5fcomplexity_5fanchor_5fprune_3553',['max_low_complexity_anchor_prune',['../classvg_1_1Surjector.html#a0f304005022b214c309ff60a1f186b1f',1,'vg::Surjector']]],
- ['max_5flow_5fcomplexity_5fanchor_5ftrim_3554',['max_low_complexity_anchor_trim',['../classvg_1_1Surjector.html#a9c0cf333d85aef40eda8354075dfa01e',1,'vg::Surjector']]],
- ['max_5fma_5fbias_3555',['max_ma_bias',['../classvg_1_1RatioSupportSnarlCaller.html#ac6d48f0372786d80db440fa67523af9e',1,'vg::RatioSupportSnarlCaller']]],
- ['max_5fmapping_5fp_5fvalue_3556',['max_mapping_p_value',['../classvg_1_1MultipathMapper.html#aa7656b2372ae8450e48a9db512ce309d',1,'vg::MultipathMapper']]],
- ['max_5fmapping_5fquality_3557',['max_mapping_quality',['../classvg_1_1BaseMapper.html#a467884235c316072a1ed7136faa14be3',1,'vg::BaseMapper']]],
- ['max_5fmemory_5fproportion_3558',['max_memory_proportion',['../structvg_1_1IndexingParameters.html#a28aa7110447f9ba3a74e1e3326959751',1,'vg::IndexingParameters']]],
- ['max_5fmessage_5fsize_3559',['MAX_MESSAGE_SIZE',['../classvg_1_1io_1_1MessageEmitter.html#a67ece9e5b7c411ccb40169b650e1f5ae',1,'vg::io::MessageEmitter::MAX_MESSAGE_SIZE()'],['../classvg_1_1io_1_1MessageIterator.html#a5b2b881e4032fb2ecfa8da35ad13e602',1,'vg::io::MessageIterator::MAX_MESSAGE_SIZE()']]],
- ['max_5fmiddle_5fdp_5flength_3560',['max_middle_dp_length',['../classvg_1_1MinimizerMapper.html#aa8bdbd3ae354863aaa50bcd0fdfb340f',1,'vg::MinimizerMapper']]],
- ['max_5fmiddle_5fgap_3561',['max_middle_gap',['../classvg_1_1MinimizerMapper.html#a9e0bcb7de51be992126d051cf343a9c5',1,'vg::MinimizerMapper']]],
- ['max_5fmin_5fchain_5fscore_3562',['max_min_chain_score',['../classvg_1_1MinimizerMapper.html#a5dc73dddd111a8a64b5285a2e75e3ba5',1,'vg::MinimizerMapper']]],
- ['max_5fmismatches_3563',['MAX_MISMATCHES',['../classvg_1_1GaplessExtender.html#aaa77a2fc74630664d12527818826e28b',1,'vg::GaplessExtender']]],
- ['max_5fmissing_5fvariant_5fwarnings_3564',['max_missing_variant_warnings',['../classvg_1_1HaplotypeIndexer.html#a512203218e3b78afa0fc5c0e594e6516',1,'vg::HaplotypeIndexer']]],
- ['max_5fmotif_5fpairs_3565',['max_motif_pairs',['../classvg_1_1MultipathMapper.html#a7427a85cc5f4ff850524ecf929ca72c8',1,'vg::MultipathMapper']]],
- ['max_5fmulti_5falns_3566',['max_multi_alns',['../classvg_1_1BandedGlobalAligner.html#a7191ef47a3e2a5232e5ba74283c646b6',1,'vg::BandedGlobalAligner::max_multi_alns()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9114c48d4516fb6115fe47e910624377',1,'vg::BandedGlobalAligner::AltTracebackStack::max_multi_alns()']]],
- ['max_5fmultimaps_3567',['max_multimaps',['../classvg_1_1Mapper.html#a462268836d2c5f5f4acde6ca9060e593',1,'vg::Mapper::max_multimaps()'],['../classvg_1_1MinimizerMapper.html#aede601962425752ec75ea1d890505357',1,'vg::MinimizerMapper::max_multimaps()']]],
- ['max_5fnode_3568',['max_node',['../classvg_1_1SubgraphOverlay.html#a6eb5155328921c3a0ec46e62c7edfdca',1,'vg::SubgraphOverlay']]],
- ['max_5fnode_5fid_3569',['max_node_id',['../classvg_1_1DagifiedGraph.html#a511c81e2e65250eeeac52936bfe3ae0e',1,'vg::DagifiedGraph::max_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#a4962a5c38f363db65a1b0083a05bcfcc',1,'vg::DozeuPinningOverlay::max_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ab7384a54f90e4351cb7e6d0a99f3290d',1,'vg::ExtraNodeGraph::max_node_id()'],['../classvg_1_1SnarlGraph.html#a69ce6bde5f346eb5926b6db093122be1',1,'vg::SnarlGraph::max_node_id()'],['../classvg_1_1IdentityOverlay.html#a5aba68df4094870dd2324613d2db1d63',1,'vg::IdentityOverlay::max_node_id()'],['../classvg_1_1IncrementalSubgraph.html#aa92bb84a3ea785a09c814932ae56a5a8',1,'vg::IncrementalSubgraph::max_node_id()'],['../classvg_1_1IndexedVG.html#ab7e6f41fefb23702e708d23a0dcec9d0',1,'vg::IndexedVG::max_node_id()'],['../classvg_1_1MemoizingGraph.html#a7a9052b566d4062493432265aa1c9e70',1,'vg::MemoizingGraph::max_node_id()'],['../classvg_1_1NullMaskingGraph.html#a768717b98ae295bb52a68028db0145ec',1,'vg::NullMaskingGraph::max_node_id()'],['../classvg_1_1PathSubgraph.html#a7d5368e9b40989fa3e1ecd020468a1da',1,'vg::PathSubgraph::max_node_id()'],['../classvg_1_1ReverseGraph.html#ac276a2df66a605842304eec2d9ef340c',1,'vg::ReverseGraph::max_node_id()'],['../classvg_1_1NetGraph.html#abb16fbc7ae88f61e3ce9076d2e2a3817',1,'vg::NetGraph::max_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ab9be77971160f356b0ba0721ed17983e',1,'vg::SourceSinkOverlay::max_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#abbf5f65b4f075efb985c0978cead8513',1,'vg::JoinedSpliceGraph::max_node_id()'],['../classvg_1_1StrandSplitGraph.html#a83194bc2415f2f0fa2e23ce970d2f932',1,'vg::StrandSplitGraph::max_node_id()'],['../classvg_1_1SubHandleGraph.html#afd0e51c2e81f5b51f4e21167e3e691f3',1,'vg::SubHandleGraph::max_node_id()'],['../classvg_1_1SubgraphOverlay.html#ab2858c7e55226d9754eb388654da88ab',1,'vg::SubgraphOverlay::max_node_id()'],['../classvg_1_1SubpathOverlay.html#aa5b627c97bac0914a4b77e289a1f888b',1,'vg::SubpathOverlay::max_node_id()'],['../classvg_1_1TreeSubgraph.html#ae8f3ebca4f5d097fe9b5081cdc1f7a96',1,'vg::TreeSubgraph::max_node_id()'],['../classvg_1_1VG.html#a5a03ad90e03794944c5e0d4d61780652',1,'vg::VG::max_node_id()'],['../classvg_1_1VGset.html#a31691223aa51fca983dd145b5896cad7',1,'vg::VGset::max_node_id()'],['../classxg_1_1XG.html#ac991d9094b1959ff503d9a94d0a9ed4c',1,'xg::XG::max_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a599303e41c6f9913424933778893f1c6',1,'handlegraph::algorithms::SubHandleGraph::max_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a5a2e2b1ea6a29b3f4b34a6abcb6dbc50',1,'handlegraph::HandleGraph::max_node_id()']]],
- ['max_5fnode_5frank_3570',['max_node_rank',['../classxg_1_1XG.html#a1bc4d756800a8e55ddb33abf49865956',1,'xg::XG']]],
- ['max_5fnode_5fsize_3571',['max_node_size',['../classvg_1_1Constructor.html#a6ca9a0b7785c1c9c6e859cc75ea2a2f4',1,'vg::Constructor::max_node_size()'],['../structvg_1_1IndexingParameters.html#a6b392a212907d34c6f586cb7cefeac1f',1,'vg::IndexingParameters::max_node_size()'],['../classvg_1_1VariantAdder.html#a3e1dae34969d5779d09819de627a6bd5',1,'vg::VariantAdder::max_node_size()']]],
- ['max_5fnum_5fnodes_3572',['max_num_nodes',['../classvg_1_1IncrementalSubgraph.html#a37038271292f8c25f63b9d3e8400d13e',1,'vg::IncrementalSubgraph']]],
- ['max_5foverhang_3573',['max_overhang',['../classvg_1_1ReadFilter.html#a54c30818834f623c78a2cb0a0e9b4a91',1,'vg::ReadFilter::max_overhang()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a500747869171f1e18a4e7c56625ed3ef',1,'vg::Counts::max_overhang()']]],
- ['max_5fp_5fvalue_5fmemo_5fsize_3574',['max_p_value_memo_size',['../classvg_1_1MultipathMapper.html#ada39acac8f403bf92632024be4e448e1',1,'vg::MultipathMapper']]],
- ['max_5fparsed_5fvariant_5fsize_3575',['max_parsed_variant_size',['../classvg_1_1Constructor.html#a2725e8e6876deb0ca0ccf597955163c2',1,'vg::Constructor']]],
- ['max_5fpath_5fid_3576',['max_path_id',['../classvg_1_1Paths.html#ac5e9e182ecf09166f516c6fbf9923a29',1,'vg::Paths']]],
- ['max_5fpath_5flength_3577',['max_path_length',['../classvg_1_1Filter.html#a77225b4859a55b509396332e96c81c0e',1,'vg::Filter']]],
- ['max_5fpath_5frank_3578',['max_path_rank',['../classxg_1_1XG.html#acd75e4cc0ccf977505a5c6bda03ddb73',1,'xg::XG']]],
- ['max_5fpath_5fsearch_5fsteps_3579',['max_path_search_steps',['../classvg_1_1Genotyper.html#a500af110546f9572fe40d5ef098552d9',1,'vg::Genotyper::max_path_search_steps()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa61be13e0e070bd8af8fe890b47dfde5',1,'vg::ReadRestrictedTraversalFinder::max_path_search_steps()'],['../classvg_1_1PathRestrictedTraversalFinder.html#af24fb970905bbb3d2e04631fd3d0918b',1,'vg::PathRestrictedTraversalFinder::max_path_search_steps()']]],
- ['max_5fpossible_5fmapping_5fquality_3580',['max_possible_mapping_quality',['../classvg_1_1GSSWAligner.html#a0058c97d1dbe2be7643e9f75cee15bab',1,'vg::GSSWAligner::max_possible_mapping_quality()'],['../classvg_1_1Mapper.html#a1799afefa90f9fbfd7de41626bdb460c',1,'vg::Mapper::max_possible_mapping_quality()']]],
- ['max_5fprune_5fiterations_3581',['max_prune_iterations',['../classvg_1_1VCFTraversalFinder.html#a667a1499ac092df03deaa7ec0813d6df',1,'vg::VCFTraversalFinder']]],
- ['max_5freads_3582',['max_reads',['../classvg_1_1ReadFilter.html#a1a4d052b3060e2b8a434310ce6dc14f5',1,'vg::ReadFilter::max_reads()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a6c584adbe4422e18c6bb875bb3a482ca',1,'vg::Counts::max_reads()']]],
- ['max_5freads_5fused_3583',['max_reads_used',['../classvg_1_1ReadFilter.html#a06835480f40ef09dd073cc14a469f760',1,'vg::ReadFilter']]],
- ['max_5fref_5fhet_5fbias_3584',['max_ref_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a6012c94aabfcffde89851c587ed34f9e',1,'vg::RatioSupportSnarlCaller']]],
- ['max_5frescue_5fattempts_3585',['max_rescue_attempts',['../classvg_1_1MinimizerMapper.html#a0985bcf3a1ed28098bf0271b251dd6e2',1,'vg::MinimizerMapper::max_rescue_attempts()'],['../classvg_1_1MultipathMapper.html#a87f585b42e49cd2e642ab092e54a309a',1,'vg::MultipathMapper::max_rescue_attempts()']]],
- ['max_5frescue_5fp_5fvalue_3586',['max_rescue_p_value',['../classvg_1_1MultipathMapper.html#afe5cb57d342ca46e5ee2e132d1d238d3',1,'vg::MultipathMapper']]],
- ['max_5frgfa_5frank_3587',['max_rgfa_rank',['../classvg_1_1algorithms_1_1GFAParser.html#ae5841a4a832376b2894cbbb956c89569',1,'vg::algorithms::GFAParser']]],
- ['max_5fsample_5fsize_3588',['max_sample_size',['../classvg_1_1FragmentLengthDistribution.html#ae5f1b666c1bee15996ad997eb4c9505e',1,'vg::FragmentLengthDistribution']]],
- ['max_5fsearch_5fdepth_3589',['max_search_depth',['../classvg_1_1LegacyCaller.html#a321503fbe153735736a542d4ad5d9235',1,'vg::LegacyCaller']]],
- ['max_5fsearch_5fwidth_3590',['max_search_width',['../classvg_1_1LegacyCaller.html#a01572bf56d35cc89232fac3dce35c891',1,'vg::LegacyCaller']]],
- ['max_5fseparation_3591',['max_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a1094dccc104bf859b2bdb8b5fac6bec6',1,'vg::GreedyMinDistanceClusterer']]],
- ['max_5fshift_3592',['max_shift',['../classvg_1_1MultipathAlignmentGraph.html#a50ff4a1c2bc2b997c28af99527e595dd',1,'vg::MultipathAlignmentGraph']]],
- ['max_5fsingle_5fend_5fmappings_5ffor_5frescue_3593',['max_single_end_mappings_for_rescue',['../classvg_1_1MultipathMapper.html#a1dc8310407eabb6cbe419d5765364df7',1,'vg::MultipathMapper']]],
- ['max_5fskipped_5fbases_3594',['max_skipped_bases',['../classvg_1_1MinimizerMapper.html#ad72974afc9d7fadd23716fba49b7e82f',1,'vg::MinimizerMapper']]],
- ['max_5fslide_3595',['max_slide',['../classvg_1_1Surjector.html#a0e40286284b27ccef7fbcc028fc40142',1,'vg::Surjector']]],
- ['max_5fsnarl_5fcut_5fsize_3596',['max_snarl_cut_size',['../classvg_1_1MultipathMapper.html#a507872f1a20d6b0e34b6f9b8dac2639f',1,'vg::MultipathMapper']]],
- ['max_5fsnarl_5fedges_3597',['max_snarl_edges',['../classvg_1_1FlowCaller.html#a07f59c5945984d13f67ec660923c0f81',1,'vg::FlowCaller']]],
- ['max_5fsnarl_5fshallow_5fsize_3598',['max_snarl_shallow_size',['../classvg_1_1NestedFlowCaller.html#ab5e10be4ba6c1d33235e5844cfb8b8c0',1,'vg::NestedFlowCaller']]],
- ['max_5fsoftclip_5fiterations_3599',['max_softclip_iterations',['../classvg_1_1Mapper.html#a145a97f0859865815bba2562024078e9',1,'vg::Mapper']]],
- ['max_5fsoftclip_5foverlap_3600',['max_softclip_overlap',['../classvg_1_1MultipathMapper.html#afcacb8b30589b82487cca2a1755320f3',1,'vg::MultipathMapper']]],
- ['max_5fsplice_5foverhang_3601',['max_splice_overhang',['../classvg_1_1MultipathMapper.html#a8c71d1bf28c8567e878c5cd004b94e8b',1,'vg::MultipathMapper']]],
- ['max_5fsplice_5fref_5fsearch_5flength_3602',['max_splice_ref_search_length',['../classvg_1_1MultipathMapper.html#a4f4bca24b9dbe1a7a40499a30e91c4f6',1,'vg::MultipathMapper']]],
- ['max_5fsteps_5fof_5fhandle_5fmemo_5fsize_3603',['max_steps_of_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a55aadb2458a395d6fd47f9a9c5ddf415',1,'vg::MemoizingGraph']]],
- ['max_5fsub_5fmem_5frecursion_5fdepth_3604',['max_sub_mem_recursion_depth',['../classvg_1_1BaseMapper.html#ac12496865e23fd68ba1f579dcb050037',1,'vg::BaseMapper']]],
- ['max_5fsubgraph_5fbases_5fper_5fread_5fbase_3605',['max_subgraph_bases_per_read_base',['../classvg_1_1Surjector.html#a14e20f641f120ca8fa5206ace84be331',1,'vg::Surjector']]],
- ['max_5fsuboptimal_5fpath_5fscore_5fratio_3606',['max_suboptimal_path_score_ratio',['../classvg_1_1MultipathMapper.html#ac117889984b58f3c0fd3d389a8ee7f26',1,'vg::MultipathMapper']]],
- ['max_5ftag_5flength_3607',['MAX_TAG_LENGTH',['../classvg_1_1io_1_1Registry.html#a8791c3355999775f973ab74fa4111fa2',1,'vg::io::Registry']]],
- ['max_5ftail_5fanchor_5fprune_3608',['max_tail_anchor_prune',['../classvg_1_1Surjector.html#a59034e11562bb0969c25defd215f166b',1,'vg::Surjector']]],
- ['max_5ftail_5fdp_5flength_3609',['max_tail_dp_length',['../classvg_1_1MinimizerMapper.html#ab333ad05b05cdcd8d59bd0c6b2733e04',1,'vg::MinimizerMapper']]],
- ['max_5ftail_5fgap_3610',['max_tail_gap',['../classvg_1_1MinimizerMapper.html#a25dccb476876cf2797743ec916c3d661',1,'vg::MinimizerMapper']]],
- ['max_5ftail_5flength_3611',['max_tail_length',['../classvg_1_1MinimizerMapper.html#ad041c860d77e6ad2bd025bd2da337d7a',1,'vg::MinimizerMapper::max_tail_length()'],['../classvg_1_1Surjector.html#a185cc3fad9b021b08f03880ae0119db6',1,'vg::Surjector::max_tail_length()']]],
- ['max_5ftail_5fmerge_5fsupress_5flength_3612',['max_tail_merge_supress_length',['../classvg_1_1MultipathMapper.html#a8de58bf1942c4aa16b762554268d3e3d',1,'vg::MultipathMapper']]],
- ['max_5ftarget_5ffactor_3613',['max_target_factor',['../classvg_1_1Mapper.html#a5ecf825b76d29c8b8242d8167fae6cc4',1,'vg::Mapper']]],
- ['max_5fto_5ffragment_3614',['max_to_fragment',['../classvg_1_1MinimizerMapper.html#ab6b8884b622acf26ceeae7ea1f2204d6',1,'vg::MinimizerMapper']]],
- ['max_5ftrav_5fsize_3615',['max_trav_size',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a4842f02f38903b12e0c7de54bf0482e3',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['max_5ftraversal_5fcutoff_3616',['max_traversal_cutoff',['../classvg_1_1VCFTraversalFinder.html#a2ece2a9a96c909c7859bd88d54daa559',1,'vg::VCFTraversalFinder']]],
- ['max_5ftraversal_5flength_3617',['max_traversal_length',['../classvg_1_1FlowTraversalFinder.html#a1dbaa147e49e103151629a210977c58b',1,'vg::FlowTraversalFinder']]],
- ['max_5ftries_3618',['max_tries',['../classvg_1_1AbstractReadSampler.html#a68421d544f78d22ed080321929c9fd01',1,'vg::AbstractReadSampler']]],
- ['max_5funcalled_5falleles_3619',['max_uncalled_alleles',['../classvg_1_1VCFOutputCaller.html#acf04132e0a3cf52b5ba58a88f0b2d3d4',1,'vg::VCFOutputCaller']]],
- ['max_5funique_5fmin_3620',['max_unique_min',['../classvg_1_1MinimizerMapper.html#a8862622f6f711cc6a797b26990c9f195',1,'vg::MinimizerMapper']]],
- ['max_5fvalue_3621',['max_value',['../structvg_1_1SummaryStatistics.html#ad86748ae17ecc7acce49364a9fa93a74',1,'vg::SummaryStatistics::max_value()'],['../structvg_1_1varint__vector__t.html#a92149196c806e2230f53f2d62e9bf8b3',1,'vg::varint_vector_t::MAX_VALUE()']]],
- ['max_5fvcf_5fline_5flength_3622',['max_vcf_line_length',['../classvg_1_1VCFOutputCaller.html#a549336b5a84bfdef74b8ae8116b1b151',1,'vg::VCFOutputCaller']]],
- ['max_5fvertex_3623',['max_vertex',['../classvg_1_1MEMChainModel.html#abc9cf4a87ae1b38488bcf96c0a09b853',1,'vg::MEMChainModel::max_vertex()'],['../classvg_1_1AlignmentChainModel.html#a79f49cd995d623a0dae8b704ad57432e',1,'vg::AlignmentChainModel::max_vertex()']]],
- ['max_5fwalk_3624',['max_walk',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6d8dc74ae9eaaabf35ba1c89cfae8a11',1,'vg::PathOrientedDistanceMeasurer']]],
- ['max_5fwidth_3625',['max_width',['../classvg_1_1RepresentativeTraversalFinder.html#aac2939337439d7566246889b3a4655c6',1,'vg::RepresentativeTraversalFinder']]],
- ['max_5fxdrop_5fgap_5flength_3626',['max_xdrop_gap_length',['../classvg_1_1Mapper.html#a2754b67772ef25cb66d06b66b8caeb55',1,'vg::Mapper']]],
- ['maximalexactmatch_3627',['MaximalExactMatch',['../classvg_1_1MaximalExactMatch.html',1,'vg::MaximalExactMatch'],['../classvg_1_1MaximalExactMatch.html#a0eb93e97b671cbafb0de7aa5827fa5f0',1,'vg::MaximalExactMatch::MaximalExactMatch(string::const_iterator b, string::const_iterator e, gcsa::range_type r, size_t m=0)'],['../classvg_1_1MaximalExactMatch.html#aab0c8e120398563dfa7dae32a92b2fa9',1,'vg::MaximalExactMatch::MaximalExactMatch(void)=default'],['../classvg_1_1MaximalExactMatch.html#a058f43692dd5943fa4e4ecc1b5fc68c0',1,'vg::MaximalExactMatch::MaximalExactMatch(const MaximalExactMatch &)=default'],['../classvg_1_1MaximalExactMatch.html#a9b0816ee01550f8ce43d32984d6fc333',1,'vg::MaximalExactMatch::MaximalExactMatch(MaximalExactMatch &&)=default']]],
- ['maximum_5fdistance_3628',['maximum_distance',['../namespacevg.html#a004ed92d4db665ce8ec4e527f150a7c4',1,'vg']]],
- ['maximum_5fmapping_5fquality_5fapprox_3629',['maximum_mapping_quality_approx',['../classvg_1_1GSSWAligner.html#a3104dc6ddfd6a15e1ed02950006a4063',1,'vg::GSSWAligner']]],
- ['maximum_5fmapping_5fquality_5fexact_3630',['maximum_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#ac17619c1908446d3e61a882c879f2eb1',1,'vg::GSSWAligner']]],
- ['maximum_5fquality_3631',['maximum_quality',['../classvg_1_1Packer.html#a0de02be2009ac1d477d5cc8fefccab1c',1,'vg::Packer']]],
- ['maximum_5fsample_5fsize_3632',['maximum_sample_size',['../classvg_1_1FragmentLengthDistribution.html#a82ad9fe36dc81ea108a530b7f9792b78',1,'vg::FragmentLengthDistribution']]],
- ['maybe_5fmq_5fthreshold_3633',['maybe_mq_threshold',['../classvg_1_1Mapper.html#a26d2d7d3964d9210c963b325c64678b0',1,'vg::Mapper']]],
- ['mcmc_5fcaller_2ecpp_3634',['mcmc_caller.cpp',['../mcmc__caller_8cpp.html',1,'']]],
- ['mcmc_5fcaller_2ehpp_3635',['mcmc_caller.hpp',['../mcmc__caller_8hpp.html',1,'']]],
- ['mcmc_5fgenotyper_2ecpp_3636',['mcmc_genotyper.cpp',['../mcmc__genotyper_8cpp.html',1,'']]],
- ['mcmc_5fgenotyper_2ehpp_3637',['mcmc_genotyper.hpp',['../mcmc__genotyper_8hpp.html',1,'']]],
- ['mcmc_5fmain_2ecpp_3638',['mcmc_main.cpp',['../mcmc__main_8cpp.html',1,'']]],
- ['mcmccaller_3639',['MCMCCaller',['../classvg_1_1MCMCCaller.html',1,'vg::MCMCCaller'],['../classvg_1_1MCMCCaller.html#add4fcb2e5a2a8633e659a986bb347c40',1,'vg::MCMCCaller::MCMCCaller()']]],
- ['mcmcgenotyper_3640',['MCMCGenotyper',['../classvg_1_1MCMCGenotyper.html',1,'vg::MCMCGenotyper'],['../classvg_1_1MCMCGenotyper.html#abb6ddf1a8e99fc5c183ec188ae87bb22',1,'vg::MCMCGenotyper::MCMCGenotyper()']]],
- ['mean_3641',['mean',['../structvg_1_1SummaryStatistics.html#a275cb7138ffd1285cbdad3ae7017cbe8',1,'vg::SummaryStatistics::mean()'],['../classvg_1_1FragmentLengthDistribution.html#abe1b685c70bdafff09e089038ae68971',1,'vg::FragmentLengthDistribution::mean()'],['../classvg_1_1normal__distribution.html#a8b5bd06d0c3589eab21131a033bd706a',1,'vg::normal_distribution::mean()'],['../classvg_1_1truncated__normal__distribution.html#ad842920993df04cbcc18cc4182f9d005',1,'vg::truncated_normal_distribution::mean()']]],
- ['mean_5fnode_5flength_3642',['mean_node_length',['../classvg_1_1Transcriptome.html#af173c32d4ccfa7f94f68220e7e564895',1,'vg::Transcriptome']]],
- ['measurements_5fbegin_3643',['measurements_begin',['../classvg_1_1FragmentLengthDistribution.html#a9a57a0e4a86983fc13a87d5ee4c5b8a7',1,'vg::FragmentLengthDistribution']]],
- ['measurements_5fend_3644',['measurements_end',['../classvg_1_1FragmentLengthDistribution.html#a929562555917920f58a5d3692cd14fb4',1,'vg::FragmentLengthDistribution']]],
- ['median_3645',['median',['../structvg_1_1SummaryStatistics.html#ae98f01cfb86f82f0e9185c63fb57445f',1,'vg::SummaryStatistics::median()'],['../namespacevg.html#a6eef175773ce8532826ba78eee0cece5',1,'vg::median()']]],
- ['median_5fmem_5fcoverage_3646',['median_mem_coverage',['../classvg_1_1MEMClusterer_1_1HitGraph.html#abe3be52c11df5f9b5fc131cfe9460d5a',1,'vg::MEMClusterer::HitGraph']]],
- ['mem_3647',['mem',['../classvg_1_1MEMChainModelVertex.html#acd9990963345deb38096763554ae4b3d',1,'vg::MEMChainModelVertex::mem()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#a9f3480f5d231cf8d4325ae558a379f10',1,'vg::MEMClusterer::HitNode::mem()']]],
- ['mem_2ecpp_3648',['mem.cpp',['../mem_8cpp.html',1,'']]],
- ['mem_2ehpp_3649',['mem.hpp',['../mem_8hpp.html',1,'']]],
- ['mem_5faccelerator_2ecpp_3650',['mem_accelerator.cpp',['../mem__accelerator_8cpp.html',1,'']]],
- ['mem_5faccelerator_2ehpp_3651',['mem_accelerator.hpp',['../mem__accelerator_8hpp.html',1,'']]],
- ['mem_5fcoverage_5fmin_5fratio_3652',['mem_coverage_min_ratio',['../classvg_1_1MultipathMapper.html#ae977e7bbf30ca7634e7422aa76c16e71',1,'vg::MultipathMapper']]],
- ['mem_5fmin_5foriented_5fdistances_3653',['mem_min_oriented_distances',['../namespacevg.html#ae1678438e6011469b88ddf3b54023013',1,'vg']]],
- ['mem_5fnode_5fstart_5fpositions_3654',['mem_node_start_positions',['../namespacevg.html#aa65ea58e40ea30264407f9fdbce2a83d',1,'vg']]],
- ['mem_5freseed_5flength_3655',['mem_reseed_length',['../classvg_1_1BaseMapper.html#abaea877646c1be5aea6200201d28c4cf',1,'vg::BaseMapper']]],
- ['mem_5fusage_5fstring_3656',['mem_usage_string',['../autoindex__main_8cpp.html#a95ea1f250ba974749a30b213bede7969',1,'autoindex_main.cpp']]],
- ['memaccelerator_3657',['MEMAccelerator',['../classvg_1_1MEMAccelerator.html',1,'vg::MEMAccelerator'],['../classvg_1_1MEMAccelerator.html#af51ef34773bca8cc723fb3ef0bfe87c8',1,'vg::MEMAccelerator::MEMAccelerator()=default'],['../classvg_1_1MEMAccelerator.html#a3928fe622799f9ac33ba7e2e5d4b3568',1,'vg::MEMAccelerator::MEMAccelerator(const gcsa::GCSA &gcsa_index, size_t k)']]],
- ['memchainmodel_3658',['MEMChainModel',['../classvg_1_1MEMChainModel.html',1,'vg::MEMChainModel'],['../classvg_1_1MEMChainModel.html#ae612545bdf38bad27b4fc18e19d38eff',1,'vg::MEMChainModel::MEMChainModel()']]],
- ['memchainmodelvertex_3659',['MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html',1,'vg::MEMChainModelVertex'],['../classvg_1_1MEMChainModelVertex.html#a9ec1a9cd36b3328911409e598109c1c9',1,'vg::MEMChainModelVertex::MEMChainModelVertex(void)=default'],['../classvg_1_1MEMChainModelVertex.html#a01ed669199f3319be51dbd2aafc268de',1,'vg::MEMChainModelVertex::MEMChainModelVertex(const MEMChainModelVertex &)=default'],['../classvg_1_1MEMChainModelVertex.html#adb5651ba734c5700f334b0074dfaaca8',1,'vg::MEMChainModelVertex::MEMChainModelVertex(MEMChainModelVertex &&)=default']]],
- ['memcluster_5ft_3660',['memcluster_t',['../classvg_1_1MultipathMapper.html#acae95760b8750cf3b2bb48d00fe499fd',1,'vg::MultipathMapper']]],
- ['memclusterer_3661',['MEMClusterer',['../classvg_1_1MEMClusterer.html',1,'vg::MEMClusterer'],['../classvg_1_1MEMClusterer.html#ae035e62365ff4617433e18d102bec452',1,'vg::MEMClusterer::MEMClusterer()']]],
- ['memo_3662',['memo',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a382739dd7136e759c6a01725ddebd301',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['memoized_5flf_3663',['memoized_LF',['../classvg_1_1MEMAccelerator.html#a89dfd34874f065088799dfce96c11649',1,'vg::MEMAccelerator']]],
- ['memoizing_5fgraph_2ecpp_3664',['memoizing_graph.cpp',['../memoizing__graph_8cpp.html',1,'']]],
- ['memoizing_5fgraph_2ehpp_3665',['memoizing_graph.hpp',['../memoizing__graph_8hpp.html',1,'']]],
- ['memoizinggraph_3666',['MemoizingGraph',['../classvg_1_1MemoizingGraph.html',1,'vg::MemoizingGraph'],['../classvg_1_1MemoizingGraph.html#aef84e6abc0084e0f910bc99edc760345',1,'vg::MemoizingGraph::MemoizingGraph(const PathPositionHandleGraph *graph)'],['../classvg_1_1MemoizingGraph.html#aa6030fdc5e73a8d88059bc31f1886746',1,'vg::MemoizingGraph::MemoizingGraph()=default']]],
- ['memory_5fhigh_5fwater_5fkb_3667',['memory_high_water_kb',['../classvg_1_1Watchdog.html#aa759f3d73ebe15aeb95a13a8c86a0b59',1,'vg::Watchdog']]],
- ['mems_5fid_5fclusters_5fto_5falignments_3668',['mems_id_clusters_to_alignments',['../classvg_1_1Mapper.html#a0dc4c04ebad76435afafe9cec62a5eaa',1,'vg::Mapper']]],
- ['mems_5foverlap_3669',['mems_overlap',['../namespacevg.html#aa412de4741b61d2a8b863f50f31209e0',1,'vg']]],
- ['mems_5foverlap_5flength_3670',['mems_overlap_length',['../namespacevg.html#af5d04132733b3487e3dab20729645850',1,'vg']]],
- ['mems_5fto_5fjson_3671',['mems_to_json',['../namespacevg.html#ab0bec9992b4441128754ac4ed1a330e8',1,'vg']]],
- ['memusage_2ecpp_3672',['memusage.cpp',['../memusage_8cpp.html',1,'']]],
- ['memusage_2ehpp_3673',['memusage.hpp',['../memusage_8hpp.html',1,'']]],
- ['merge_3674',['merge',['../structGBWTConfig.html#a850f9f30af38996cc64f1fabb20a6458',1,'GBWTConfig::merge()'],['../classvg_1_1Funnel.html#ae75f133fdc545176a27f0121a61a98e4',1,'vg::Funnel::merge()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a658429a7896e87dc276f749f5ba8dc27',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::merge()'],['../classvg_1_1VG.html#a0abc84684faea29b49032ec254d5e13b',1,'vg::VG::merge(Graph &g)'],['../classvg_1_1VG.html#a40f22f6bb4a3e7a2aea7b3887237faec',1,'vg::VG::merge(VG &g)'],['../namespacevg_1_1algorithms.html#a91a6bbd822f6380421a973f75036c3d3',1,'vg::algorithms::merge()']]],
- ['merge_2ecpp_3675',['merge.cpp',['../merge_8cpp.html',1,'']]],
- ['merge_2ehpp_3676',['merge.hpp',['../merge_8hpp.html',1,'']]],
- ['merge_5fadjacent_5fedits_3677',['merge_adjacent_edits',['../namespacevg.html#a30a83a9e127a0c7d75118dc14a8985f6',1,'vg::merge_adjacent_edits(const Mapping &m)'],['../namespacevg.html#a2c9985bf70965bd36bb54f910ab74e3b',1,'vg::merge_adjacent_edits(const Path &m)']]],
- ['merge_5falignments_3678',['merge_alignments',['../namespacevg.html#afa2d2a5d955cff1e7a99369055ebe75d',1,'vg::merge_alignments(const vector< Alignment > &alns)'],['../namespacevg.html#a9d71527a132d7e6bf364d2108b269e09',1,'vg::merge_alignments(const Alignment &a1, const Alignment &a2, bool debug)']]],
- ['merge_5fedits_5fin_5fplace_3679',['merge_edits_in_place',['../namespacevg.html#a20ebf02d59df03f906550e695a1aa00d',1,'vg']]],
- ['merge_5fequivalent_5ftraversals_5fin_5fgraph_3680',['merge_equivalent_traversals_in_graph',['../namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1',1,'vg']]],
- ['merge_5ffast_3681',['merge_fast',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fa00b833ba044e1135d12579e8baeedca6',1,'GBWTConfig']]],
- ['merge_5ffrom_5fdynamic_3682',['merge_from_dynamic',['../classvg_1_1Packer.html#a79ce5d54645f6d124c710b86b666f5d7',1,'vg::Packer']]],
- ['merge_5ffrom_5ffiles_3683',['merge_from_files',['../classvg_1_1Packer.html#af857449c08a56dd66c6a4bc0402231cb',1,'vg::Packer']]],
- ['merge_5fgroup_3684',['merge_group',['../classvg_1_1Funnel.html#a585c5484ef877a1ede56ed4467e32312',1,'vg::Funnel']]],
- ['merge_5fgroups_3685',['merge_groups',['../classvg_1_1Funnel.html#a44fcff7c06cb79e43cc1aa2fc73a8da6',1,'vg::Funnel']]],
- ['merge_5fid_5fspace_3686',['merge_id_space',['../classvg_1_1VGset.html#a968fb68f13f91ea8ded32d02c6ea683a',1,'vg::VGset']]],
- ['merge_5finsert_3687',['merge_insert',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faa05cfa7f46c6c005f05b264b71ede9d3',1,'GBWTConfig']]],
- ['merge_5fmode_3688',['merge_mode',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0f',1,'GBWTConfig']]],
- ['merge_5fnodes_3689',['merge_nodes',['../classvg_1_1VG.html#a2e506d51db427b617cc334a791c7f594',1,'vg::VG']]],
- ['merge_5fnon_5fbranching_5fsubpaths_3690',['merge_non_branching_subpaths',['../namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43',1,'vg']]],
- ['merge_5fnone_3691',['merge_none',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faace9bbb313fb5c18d2a5a9142b99762b',1,'GBWTConfig']]],
- ['merge_5fparallel_3692',['merge_parallel',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fad49ba685add4291f2ba5d4d042f6e548',1,'GBWTConfig']]],
- ['merge_5fparameters_3693',['merge_parameters',['../structGBWTConfig.html#a77aea6d71d3a6904f01eeccf1f950318',1,'GBWTConfig']]],
- ['merge_5fpartially_5fredundant_5fmatch_5fnodes_3694',['merge_partially_redundant_match_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a9f8ca4f9936aa6abcc8681e91dae3f43',1,'vg::MultipathAlignmentGraph']]],
- ['merge_5frescued_5fmappings_3695',['merge_rescued_mappings',['../classvg_1_1MultipathMapper.html#a525152a98c905ba789a0454c70336c3e',1,'vg::MultipathMapper']]],
- ['merge_5fstate_3696',['merge_state',['../classvg_1_1DinucleotideMachine.html#ab28bcc9f016d8df680d6f17b5957fc57',1,'vg::DinucleotideMachine']]],
- ['merge_5funion_3697',['merge_union',['../classvg_1_1VG.html#a5aff716eee0bf720b3836caa761d48be',1,'vg::VG']]],
- ['merged_5fgroup_3698',['merged_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#acd6301aa5e085df9fa56ba8b102cdde6',1,'vg::IndexedVG::CacheEntry']]],
- ['mergedadjacencygraph_3699',['MergedAdjacencyGraph',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#aa09eaec5fd36cfe50b4313a38ba01fe1',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const RankedHandleGraph *graph)'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ab8d7ea6f475144c3779568d9d552c1c7',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const MergedAdjacencyGraph &other)']]],
- ['mergegraphs_3700',['mergeGraphs',['../namespacevg_1_1io.html#a09b6c55dd368ec0c3e85f51a87321ba2',1,'vg::io']]],
- ['mergenodeobjects_3701',['mergeNodeObjects',['../namespacevg.html#aa539af4f481d4e955ede26ee85c320c5',1,'vg']]],
- ['message_3702',['message',['../structvg_1_1AlignmentValidity.html#a7eede46d9951c0c2b0b4c226c6987691',1,'vg::AlignmentValidity::message()'],['../classvg_1_1NoAlignmentInBandException.html#a3cc1fd5899066709228ecea9e5a25956',1,'vg::NoAlignmentInBandException::message()']]],
- ['message_5fbuffer_3703',['message_buffer',['../structvg_1_1algorithms_1_1GFAFormatError.html#a24e4e4d2285fd970978365e2747165c8',1,'vg::algorithms::GFAFormatError']]],
- ['message_5fconsumer_5ffunction_5ft_3704',['message_consumer_function_t',['../namespacevg_1_1io.html#a618e8c9e44f63328bb2c0742ab0e69c2',1,'vg::io']]],
- ['message_5femitter_3705',['message_emitter',['../classvg_1_1io_1_1ProtobufEmitter.html#a1bdc1e48041d69eeca45745580af19f3',1,'vg::io::ProtobufEmitter']]],
- ['message_5femitter_2ecpp_3706',['message_emitter.cpp',['../message__emitter_8cpp.html',1,'']]],
- ['message_5femitter_2ehpp_3707',['message_emitter.hpp',['../message__emitter_8hpp.html',1,'']]],
- ['message_5fhandlers_3708',['message_handlers',['../classvg_1_1io_1_1ProtobufEmitter.html#a73231a5a45811c280d1a6d346abc75eb',1,'vg::io::ProtobufEmitter']]],
- ['message_5fit_3709',['message_it',['../classvg_1_1io_1_1ProtobufIterator.html#a787d06e13a1799b7e65ee1aa19ec3bb8',1,'vg::io::ProtobufIterator']]],
- ['message_5fiterator_2ecpp_3710',['message_iterator.cpp',['../message__iterator_8cpp.html',1,'']]],
- ['message_5fiterator_2ehpp_3711',['message_iterator.hpp',['../message__iterator_8hpp.html',1,'']]],
- ['message_5flistener_5ft_3712',['message_listener_t',['../classvg_1_1io_1_1ProtobufEmitter.html#a735167dc9e644a83d0e9fd206b241ce1',1,'vg::io::ProtobufEmitter']]],
- ['message_5fsender_5ffunction_5ft_3713',['message_sender_function_t',['../namespacevg_1_1io.html#a26ea41d1ec4cf44b436a345f1eefccf1',1,'vg::io']]],
- ['messageemitter_3714',['MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html',1,'vg::io::MessageEmitter'],['../classvg_1_1io_1_1MessageEmitter.html#a674e6dee23ee5d3a5b49e56ff6dad2c1',1,'vg::io::MessageEmitter::MessageEmitter(ostream &out, bool compress=false, size_t max_group_size=1000)'],['../classvg_1_1io_1_1MessageEmitter.html#a4e9dd0179e7e2b815fcbf3175fd5a030',1,'vg::io::MessageEmitter::MessageEmitter(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#af48941a2e4e66c513e169d29f120d511',1,'vg::io::MessageEmitter::MessageEmitter(MessageEmitter &&other)=default']]],
- ['messageiterator_3715',['MessageIterator',['../classvg_1_1io_1_1MessageIterator.html',1,'vg::io::MessageIterator'],['../classvg_1_1io_1_1MessageIterator.html#a44eabe49bb3f28067f8ba3396915ee64',1,'vg::io::MessageIterator::MessageIterator(istream &in, bool verbose=false, size_t thread_count=0)'],['../classvg_1_1io_1_1MessageIterator.html#ae7ddb87951881f58221acd0a1beeb32f',1,'vg::io::MessageIterator::MessageIterator(unique_ptr< BlockedGzipInputStream > &&bgzf, bool verbose=false)'],['../classvg_1_1io_1_1MessageIterator.html#a46b16972d489742f42922fd9cb9b85af',1,'vg::io::MessageIterator::MessageIterator()=default']]],
- ['metadata_3716',['metadata',['../structGBWTConfig.html#a0e91b96d773182fc4e4e36314ae6bd8d',1,'GBWTConfig']]],
- ['metadata_5fmode_3717',['metadata_mode',['../structGBWTConfig.html#a102642e75fdf2b95d22a07d372ca2890',1,'GBWTConfig']]],
- ['middle_5fsignature_3718',['middle_signature',['../namespacevg.html#a7848d492a243a93f37b1ac52a541a96a',1,'vg::middle_signature(const Alignment &aln, int len)'],['../namespacevg.html#af64c67658563ff567bc0b103ef1d8af4',1,'vg::middle_signature(const Alignment &aln1, const Alignment &aln2, int len)']]],
- ['min_3719',['min',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#ad4cda218b41dfcb1dfdb3d3c5f3924c1',1,'vg::WFAExtender::ErrorModel::Event::min()'],['../classvg_1_1WideningPRNG.html#a3cd7defb4589ed56c43b27f5d7bd36fe',1,'vg::WideningPRNG::min()']]],
- ['min_5fad_5flog_5flikelihood_5ffor_5ffilter_3720',['min_ad_log_likelihood_for_filter',['../classvg_1_1RatioSupportSnarlCaller.html#a16602959db7c2bc06471474b07a3c2f7',1,'vg::RatioSupportSnarlCaller']]],
- ['min_5falt_5fpath_5fsupport_3721',['min_alt_path_support',['../classvg_1_1SupportBasedSnarlCaller.html#a17f76956318b838695d8b120d553ce24',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5fapprox_5fpath_5fdistance_3722',['min_approx_path_distance',['../classxg_1_1XG.html#ae92433487bc35ef856ee592137937a98',1,'xg::XG::min_approx_path_distance()'],['../namespacevg_1_1algorithms.html#ae18b50d29d9accb763b44d6e065dac58',1,'vg::algorithms::min_approx_path_distance()']]],
- ['min_5favg_5fqual_3723',['min_avg_qual',['../classvg_1_1Filter.html#aa2f91d1daf04d2fdd6eb75183994d834',1,'vg::Filter']]],
- ['min_5fbanded_5fmq_3724',['min_banded_mq',['../classvg_1_1Mapper.html#a4fe883a960df0bbef6d08cfbe483c179',1,'vg::Mapper']]],
- ['min_5fbase_5fqual_3725',['min_base_qual',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a81bd6ba848d5742091102b7e6e7f0528',1,'vg::Counts']]],
- ['min_5fbase_5fquality_3726',['min_base_quality',['../classvg_1_1ReadFilter.html#a7fe13f943f153913f16aa594720d350a',1,'vg::ReadFilter']]],
- ['min_5fbase_5fquality_5ffraction_3727',['min_base_quality_fraction',['../classvg_1_1ReadFilter.html#ab8c6af52884a83d9538ea7ef42ac9eb4',1,'vg::ReadFilter']]],
- ['min_5fbp_5fedge_5foverride_3728',['min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a767e1ca73abc43065673009d115c310d',1,'vg::TraversalSupportFinder']]],
- ['min_5fchain_5fscore_5fper_5fbase_3729',['min_chain_score_per_base',['../classvg_1_1MinimizerMapper.html#a2b4cc838d0959b158c0c68b1e84e9123',1,'vg::MinimizerMapper']]],
- ['min_5fchaining_5fproblems_3730',['min_chaining_problems',['../classvg_1_1MinimizerMapper.html#a821c2a05942d63254a2485a1e0987b80',1,'vg::MinimizerMapper']]],
- ['min_5fchains_3731',['min_chains',['../classvg_1_1MinimizerMapper.html#a85797857c8e3f3bc363fa634af55889c',1,'vg::MinimizerMapper']]],
- ['min_5fcluster_5flength_3732',['min_cluster_length',['../classvg_1_1Mapper.html#a70ed23d3ba482d38f7201376e179af9f',1,'vg::Mapper']]],
- ['min_5fclustering_5fmem_5flength_3733',['min_clustering_mem_length',['../classvg_1_1MultipathMapper.html#ac656fb3b81d4cf6d06fb077551b54b7f',1,'vg::MultipathMapper']]],
- ['min_5fcount_5fto_5fkeep_3734',['min_count_to_keep',['../classvg_1_1RareVariantSimplifier.html#aa481bbf8d0d969a9f9aa350fd376500e',1,'vg::RareVariantSimplifier']]],
- ['min_5fcov_3735',['min_cov',['../classvg_1_1Filter.html#a77f731ad12fc655130808337452ba734',1,'vg::Filter']]],
- ['min_5fcut_3736',['min_cut',['../classvg_1_1FlowSort.html#aa489e8c6bbf375d149410afe0a35d58b',1,'vg::FlowSort']]],
- ['min_5fcut_5fdecomposition_3737',['min_cut_decomposition',['../namespacevg_1_1algorithms.html#a5cd4d23b1a702613134895c2d5618154',1,'vg::algorithms']]],
- ['min_5fcut_5fgraph_2ecpp_3738',['min_cut_graph.cpp',['../min__cut__graph_8cpp.html',1,'']]],
- ['min_5fcut_5fgraph_2ehpp_3739',['min_cut_graph.hpp',['../min__cut__graph_8hpp.html',1,'']]],
- ['min_5fdepth_3740',['min_depth',['../classvg_1_1Filter.html#a941f203667435234a1e08cce0358d8c6',1,'vg::Filter']]],
- ['min_5fdiagonal_3741',['min_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#ae69b636772fc01c9bd756c2b6dd7fd05',1,'vg::WFATree::ScoreProperties']]],
- ['min_5fdistance_3742',['min_distance',['../classvg_1_1WFATree.html#a9578f5415befbcf1260abf8d4536f538',1,'vg::WFATree']]],
- ['min_5fdistance_5ffrom_5fstart_3743',['min_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#ab859980ced41bcd382cd5961ff3b8475',1,'vg::IncrementalSubgraph']]],
- ['min_5fdists_3744',['min_dists',['../classvg_1_1DeletionAligner.html#a42b9fef2da830c0912fb4141701c501e',1,'vg::DeletionAligner']]],
- ['min_5fedge_5fsupport_3745',['min_edge_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#aabc81064635f9311af46bf2b5f1417aa',1,'vg::SupportRestrictedTraversalFinder::min_edge_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a16cd92c3b27a0b6be9d9154a7d9da77a',1,'vg::RepresentativeTraversalFinder::min_edge_support()']]],
- ['min_5fend_5fmatches_3746',['min_end_matches',['../classvg_1_1ReadFilter.html#a05d07dd311e58f3fc04d510870ddf662',1,'vg::ReadFilter::min_end_matches()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a0035f968d8e0ae55fcaf6763f7dd01a1',1,'vg::Counts::min_end_matches()']]],
- ['min_5fextension_5fsets_3747',['min_extension_sets',['../classvg_1_1MinimizerMapper.html#a1df84f11e9476595bcde3584553d2830',1,'vg::MinimizerMapper']]],
- ['min_5fextensions_3748',['min_extensions',['../classvg_1_1MinimizerMapper.html#a03f18247f88d4817feef2d25a46fd5ca',1,'vg::MinimizerMapper']]],
- ['min_5ffold_5fcoverage_5ffor_5fdownsample_3749',['min_fold_coverage_for_downsample',['../classvg_1_1Surjector.html#ac21d8c91876c3522c56c4c1c2b8f8f58',1,'vg::Surjector']]],
- ['min_5ffrequency_5fto_5fkeep_3750',['min_frequency_to_keep',['../classvg_1_1RareVariantSimplifier.html#a7aca3c00c47d8a8c6261536952fd96d8',1,'vg::RareVariantSimplifier']]],
- ['min_5fhandle_3751',['min_handle',['../classvg_1_1DagifiedGraph.html#a80c29e6e7494413dd631ea741d77f8c0',1,'vg::DagifiedGraph::min_handle()'],['../classxg_1_1XGPath.html#a59c1b92f21b5d102f70808266b457e7e',1,'xg::XGPath::min_handle()']]],
- ['min_5fid_3752',['min_id',['../classvg_1_1SubHandleGraph.html#a81878c5b09f4863b125f9de74ce11315',1,'vg::SubHandleGraph::min_id()'],['../classxg_1_1XG.html#a89a7150cd2c37698fc33ce0953f6019b',1,'xg::XG::min_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af225cef56e4c7af36ea3252d86502238',1,'handlegraph::algorithms::SubHandleGraph::min_id()']]],
- ['min_5fidentity_3753',['min_identity',['../classvg_1_1Mapper.html#a9b1d4bad7b2b7e96253006b4625329ac',1,'vg::Mapper']]],
- ['min_5flink_5flength_3754',['min_link_length',['../classvg_1_1JoinedSpliceGraph.html#a92c8438c7a1efd3f0c5351a59b519a38',1,'vg::JoinedSpliceGraph']]],
- ['min_5fmad_5ffor_5ffilter_3755',['min_mad_for_filter',['../classvg_1_1SupportBasedSnarlCaller.html#aec268641676f41d2c24128cb9e17ac03',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5fmapq_3756',['min_mapq',['../classvg_1_1ReadFilter.html#a8da615d17aba7ed66be6174253ce64ce',1,'vg::ReadFilter::min_mapq()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a228a82cd163bae9299de79bacd32fab8',1,'vg::Counts::min_mapq()']]],
- ['min_5fmedian_5fmem_5fcoverage_5ffor_5fsplit_3757',['min_median_mem_coverage_for_split',['../classvg_1_1MultipathMapper.html#a4aa16d72dd27681fef0f5d99fec8f0ee',1,'vg::MultipathMapper']]],
- ['min_5fmem_5flength_3758',['min_mem_length',['../classvg_1_1BaseMapper.html#a6de91c39c73a95b014b1773495985a09',1,'vg::BaseMapper']]],
- ['min_5fmultimaps_3759',['min_multimaps',['../classvg_1_1Mapper.html#a34d17aa5222b5b97e8e96d70a39c99c9',1,'vg::Mapper']]],
- ['min_5fnode_3760',['min_node',['../classvg_1_1SubgraphOverlay.html#a6fa8fb25c1244dfc3569ac1d37699334',1,'vg::SubgraphOverlay']]],
- ['min_5fnode_5fid_3761',['min_node_id',['../classvg_1_1DagifiedGraph.html#a59e1c5556c2f5a984d9680cdaf8be41d',1,'vg::DagifiedGraph::min_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#ac48d1492dd478af9811307c52954e517',1,'vg::DozeuPinningOverlay::min_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ae07290cc251f0843de41551e25ffd4bf',1,'vg::ExtraNodeGraph::min_node_id()'],['../classvg_1_1SnarlGraph.html#a6e61014fadcbc2703a8fe3b208132ee4',1,'vg::SnarlGraph::min_node_id()'],['../classvg_1_1IdentityOverlay.html#a9a689ba99fa1452b5434a8a523e142c1',1,'vg::IdentityOverlay::min_node_id()'],['../classvg_1_1IncrementalSubgraph.html#a2d34ac8b129c82511c38f267644918d5',1,'vg::IncrementalSubgraph::min_node_id()'],['../classvg_1_1IndexedVG.html#ac496219064127ecd533ab41f77fc5da6',1,'vg::IndexedVG::min_node_id()'],['../classvg_1_1MemoizingGraph.html#afcbf2c9b526deaddee36140a362f4640',1,'vg::MemoizingGraph::min_node_id()'],['../classvg_1_1NullMaskingGraph.html#ab970c84b4caea2d00fd43a77f0826a95',1,'vg::NullMaskingGraph::min_node_id()'],['../classvg_1_1PathSubgraph.html#a472e93221aa3a728984d07aa6b7f0cc0',1,'vg::PathSubgraph::min_node_id()'],['../classvg_1_1ReverseGraph.html#adf486245a2201f1685e2af41a57a98f3',1,'vg::ReverseGraph::min_node_id()'],['../classvg_1_1NetGraph.html#a9b3c2b7f61f5c0133e844fa5edc4ea6d',1,'vg::NetGraph::min_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ad91d6241e1a962eaf4b4f1c92f2d94c8',1,'vg::SourceSinkOverlay::min_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#aa92df9f1002415710b4ffa4e6074cb5b',1,'vg::JoinedSpliceGraph::min_node_id()'],['../classvg_1_1StrandSplitGraph.html#aaeaf9231d44d7e0260ef5439f49e5e40',1,'vg::StrandSplitGraph::min_node_id()'],['../classvg_1_1SubHandleGraph.html#a180704728aa79aaf37189c644995cf91',1,'vg::SubHandleGraph::min_node_id()'],['../classvg_1_1SubgraphOverlay.html#a0d876d83943a078f6d9114bd08216086',1,'vg::SubgraphOverlay::min_node_id()'],['../classvg_1_1SubpathOverlay.html#a3d0fc1b94bdd931b4bd72197a07d6510',1,'vg::SubpathOverlay::min_node_id()'],['../classvg_1_1TreeSubgraph.html#a1ac845e3e2d75d7da5ff81b79aba3d08',1,'vg::TreeSubgraph::min_node_id()'],['../classvg_1_1VG.html#ac27674d67445ddc135c3c8ab4d3d5231',1,'vg::VG::min_node_id()'],['../classxg_1_1XG.html#a9195d1b18542de3b89b80bb14ce1ca0a',1,'xg::XG::min_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af944543089a7fae6c052decc4ff0a4c4',1,'handlegraph::algorithms::SubHandleGraph::min_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a85c52fe4b5f483504ed142d0ad94a969',1,'handlegraph::HandleGraph::min_node_id()']]],
- ['min_5fnode_5fsupport_3762',['min_node_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#ae0201f741f7e5cffed2577d47e8e1830',1,'vg::SupportRestrictedTraversalFinder::min_node_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a873d02fe79d020bb106879f5b478e38f',1,'vg::RepresentativeTraversalFinder::min_node_support()']]],
- ['min_5fnode_5fsupport_5fcache_3763',['min_node_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a3a150bfc048afe50f2e006f77159bf34',1,'vg::CachedPackedTraversalSupportFinder']]],
- ['min_5foriented_5fdistances_3764',['min_oriented_distances',['../namespacevg.html#a973bf2647d54324bc63c323a0aa29a35',1,'vg']]],
- ['min_5fpair_5ffragment_5flength_3765',['min_pair_fragment_length',['../classvg_1_1Mapper.html#a3682f47407c7feddc2f8a22cd546a4ec',1,'vg::Mapper']]],
- ['min_5fpercent_5fidentity_3766',['min_percent_identity',['../classvg_1_1Filter.html#afd9cc5bfa5740f71e70a601f7f0b8199',1,'vg::Filter']]],
- ['min_5fprimary_3767',['min_primary',['../classvg_1_1ReadFilter.html#a64132e9f5f27ce6930554ad3c197e694',1,'vg::ReadFilter']]],
- ['min_5fqual_3768',['min_qual',['../classvg_1_1Filter.html#ab3ced01093210b1379fbcd7de7709a30',1,'vg::Filter']]],
- ['min_5fqueue_5fitem_5fbytes_3769',['MIN_QUEUE_ITEM_BYTES',['../classvg_1_1io_1_1StreamMultiplexer.html#afd60eacdf650f68a3989c91670655146',1,'vg::io::StreamMultiplexer']]],
- ['min_5fread_5fseparation_3770',['min_read_separation',['../classvg_1_1ComponentMinDistanceClusterer.html#a6c48555f1245310c614265e3d9d69c42',1,'vg::ComponentMinDistanceClusterer']]],
- ['min_5frecurrence_3771',['min_recurrence',['../classvg_1_1Genotyper.html#afffa8d75fd4155bc7d420a41d92f198c',1,'vg::Genotyper::min_recurrence()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa00f717b20773b41578e642425fbf73b',1,'vg::ReadRestrictedTraversalFinder::min_recurrence()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a3085d06249a54ac345e3bebde7c2378c',1,'vg::PathRestrictedTraversalFinder::min_recurrence()']]],
- ['min_5fscore_3772',['min_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab6d45328b152bc6aa0e23943d77e473b',1,'vg::Counts']]],
- ['min_5fscore_5ffactor_3773',['min_score_factor',['../classvg_1_1VariantAdder.html#aae129564bcf5ec9fd9d0838754d27323',1,'vg::VariantAdder']]],
- ['min_5fscore_5fper_5fbase_3774',['min_score_per_base',['../classvg_1_1Genotyper.html#a8fc1fdccfa9829bb29903ed5d7b21b28',1,'vg::Genotyper']]],
- ['min_5fsec_5fscore_3775',['min_sec_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac355280a9dc2984da55998417433ccdb',1,'vg::Counts']]],
- ['min_5fsecondary_3776',['min_secondary',['../classvg_1_1ReadFilter.html#af85c211a4a06a1fb750958002cefba0f',1,'vg::ReadFilter']]],
- ['min_5fseparation_3777',['min_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a97ed3ff5a8770a314b138148319b9a3b',1,'vg::GreedyMinDistanceClusterer']]],
- ['min_5fshift_5ffor_5fprune_3778',['min_shift_for_prune',['../classvg_1_1Surjector.html#a731d00674b2d71044a8e404be059c2cf',1,'vg::Surjector']]],
- ['min_5fsite_5fdepth_3779',['min_site_depth',['../classvg_1_1SupportBasedSnarlCaller.html#adde07f3e5ca89a2a565e8859ee641159',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5fsize_3780',['min_size',['../classvg_1_1SmallSnarlSimplifier.html#a6efa9c6d0dc38da336a5723f87e20e46',1,'vg::SmallSnarlSimplifier']]],
- ['min_5fsoftclip_5flength_5ffor_5fsplice_3781',['min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#a2d6a193c1277d948f7155da585e60367',1,'vg::MultipathMapper']]],
- ['min_5fsoftclipped_5fscore_5ffor_5fsplice_3782',['min_softclipped_score_for_splice',['../classvg_1_1MultipathMapper.html#aaae9feaf584c64fe27628e29778359b4',1,'vg::MultipathMapper']]],
- ['min_5fsplice_5flength_3783',['min_splice_length',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a801ecf2defc628516d4a5165ff745acb',1,'vg::SplicedHTSAlignmentEmitter::min_splice_length()'],['../classvg_1_1MultipathAlignmentEmitter.html#a38e7b3d9a6dca8b5601add1a6d9023e4',1,'vg::MultipathAlignmentEmitter::min_splice_length()'],['../classvg_1_1Surjector.html#a9046bb2c7267f996a6636518e2747b89',1,'vg::Surjector::min_splice_length()']]],
- ['min_5fsplice_5frepair_5flength_3784',['min_splice_repair_length',['../classvg_1_1Surjector.html#ad5048905a75d047631f3552632f58cd3',1,'vg::Surjector']]],
- ['min_5fsplice_5frescue_5fmatches_3785',['min_splice_rescue_matches',['../classvg_1_1MultipathMapper.html#a194ce33d0517a8ccd67c4e87d26f1191',1,'vg::MultipathMapper']]],
- ['min_5fsupport_5fin_5fpath_3786',['min_support_in_path',['../classvg_1_1NestedTraversalFinder.html#a3021b0689285b7c73f8201dcea103dac',1,'vg::NestedTraversalFinder::min_support_in_path()'],['../classvg_1_1RepresentativeTraversalFinder.html#acdea076c1d46ca2b92b338bd023c081b',1,'vg::RepresentativeTraversalFinder::min_support_in_path()']]],
- ['min_5ftail_5fanchor_5flength_3787',['min_tail_anchor_length',['../classvg_1_1MultipathMapper.html#a9616c4b8786af795cfd1f007c5e0c1dc',1,'vg::MultipathMapper']]],
- ['min_5fto_5ffragment_3788',['min_to_fragment',['../classvg_1_1MinimizerMapper.html#a8b9e086aeaf58ab94283f9398890a9ca',1,'vg::MinimizerMapper']]],
- ['min_5ftotal_5fsupport_5ffor_5fcall_3789',['min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#a559c8afa8e4f1f73768d7d90ff6a6db0',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5funique_5fnode_5ffraction_3790',['min_unique_node_fraction',['../classvg_1_1MinimizerMapper.html#a0df762ac6300835ee936f77a1b3daf8d',1,'vg::MinimizerMapper']]],
- ['min_5funique_5fper_5fstrand_3791',['min_unique_per_strand',['../classvg_1_1Genotyper.html#a6b1feebb10944e684e417115e880fe39',1,'vg::Genotyper']]],
- ['min_5fversion_3792',['MIN_VERSION',['../structvg_1_1Haplotypes_1_1Header.html#a58665b0f0dbbb098f50a6b02653f624e',1,'vg::Haplotypes::Header']]],
- ['mindistanceclusterer_3793',['MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html',1,'vg::MinDistanceClusterer'],['../classvg_1_1MinDistanceClusterer.html#a8fe5349edbec12f8f15465249b8e6726',1,'vg::MinDistanceClusterer::MinDistanceClusterer()']]],
- ['minimizer_3794',['Minimizer',['../structvg_1_1MinimizerMapper_1_1Minimizer.html',1,'vg::MinimizerMapper']]],
- ['minimizer_5fcoverage_5fflank_3795',['minimizer_coverage_flank',['../classvg_1_1MinimizerMapper.html#abf19808c5cfabda803651ab3a049495e',1,'vg::MinimizerMapper']]],
- ['minimizer_5fdownsampling_5fmax_5fwindow_5flength_3796',['minimizer_downsampling_max_window_length',['../classvg_1_1MinimizerMapper.html#a3aea2ff3e3fa7c837f8005aedf16cc4e',1,'vg::MinimizerMapper']]],
- ['minimizer_5fdownsampling_5fwindow_5fcount_3797',['minimizer_downsampling_window_count',['../classvg_1_1MinimizerMapper.html#a6edefae974f20cbb3dfc0b9ac767bb98',1,'vg::MinimizerMapper']]],
- ['minimizer_5fdownweight_5fthreshold_3798',['minimizer_downweight_threshold',['../structvg_1_1IndexingParameters.html#a441e50494bc2037df74d3b77b9dea964',1,'vg::IndexingParameters']]],
- ['minimizer_5findex_3799',['minimizer_index',['../classvg_1_1MinimizerMapper.html#a30be171658ca4f82aaa05e0c42c0d61b',1,'vg::MinimizerMapper::minimizer_index()'],['../classvg_1_1HaplotypePartitioner.html#a450b3d9e8876b9679fca63dfba0962d2',1,'vg::HaplotypePartitioner::minimizer_index()']]],
- ['minimizer_5findex_5ftype_3800',['minimizer_index_type',['../classvg_1_1HaplotypePartitioner.html#a9a059ded0fd7ed983801fa4d16f7cd5d',1,'vg::HaplotypePartitioner']]],
- ['minimizer_5fmain_2ecpp_3801',['minimizer_main.cpp',['../minimizer__main_8cpp.html',1,'']]],
- ['minimizer_5fmapper_2ecpp_3802',['minimizer_mapper.cpp',['../minimizer__mapper_8cpp.html',1,'']]],
- ['minimizer_5fmapper_2ehpp_3803',['minimizer_mapper.hpp',['../minimizer__mapper_8hpp.html',1,'']]],
- ['minimizer_5fmapper_5ffrom_5fchains_2ecpp_3804',['minimizer_mapper_from_chains.cpp',['../minimizer__mapper__from__chains_8cpp.html',1,'']]],
- ['minimizer_5freverse_5fcomplement_3805',['minimizer_reverse_complement',['../namespacevg.html#ae4b8625853b4a17f731c9fbd5a040fd7',1,'vg']]],
- ['minimizer_5fs_3806',['minimizer_s',['../structvg_1_1IndexingParameters.html#a85e4148452f9a2b23d0cdb75afe0fd3d',1,'vg::IndexingParameters']]],
- ['minimizer_5fscore_5ffraction_3807',['minimizer_score_fraction',['../classvg_1_1MinimizerMapper.html#a5696bfb7029ca88ec04d0f849365b34f',1,'vg::MinimizerMapper']]],
- ['minimizermapper_3808',['MinimizerMapper',['../classvg_1_1MinimizerMapper.html',1,'vg::MinimizerMapper'],['../classvg_1_1MinimizerMapper.html#ae2ecef3023c1cd374f0c7b1a3ac6ac5d',1,'vg::MinimizerMapper::MinimizerMapper()']]],
- ['minimum_5fdistance_3809',['minimum_distance',['../namespacevg.html#abcbcd550b51078ae43f2b1d87941e1a0',1,'vg']]],
- ['minimum_5fdistance_5fbetween_3810',['minimum_distance_between',['../classvg_1_1ZipCode.html#a3f0f330d338d949d04dbe14fd606e838',1,'vg::ZipCode']]],
- ['mipayload_3811',['MIPayload',['../structvg_1_1MIPayload.html',1,'vg']]],
- ['mismatch_3812',['mismatch',['../classvg_1_1GSSWAligner.html#abf06d9e9138bbbd23a451d1d0848c503',1,'vg::GSSWAligner::mismatch()'],['../classvg_1_1WFATree.html#a58f242d50871271336260013dfbcf4a8',1,'vg::WFATree::mismatch()'],['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeba1720159dd67365a6e856bd65a56722e7',1,'vg::WFAAlignment::mismatch()'],['../classvg_1_1SSWAligner.html#a49756fbcff60e14c65b58f76c78a923f',1,'vg::SSWAligner::mismatch()'],['../structScoringOptions.html#ad4144b88190ac6bc4881e5bcb0a26b50',1,'ScoringOptions::mismatch()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): xdrop_aligner.cpp']]],
- ['mismatch_5fpositions_3813',['mismatch_positions',['../structvg_1_1GaplessExtension.html#a30b340b28d82e7070329e45aaa9e6486',1,'vg::GaplessExtension']]],
- ['mismatches_3814',['mismatches',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ae28dd39b01ceed21e1a78fd24b32bcf6',1,'vg::WFAExtender::ErrorModel::mismatches()'],['../structvg_1_1GaplessExtension.html#a4898e2fabc109703f497e19f10bb164a',1,'vg::GaplessExtension::mismatches()']]],
- ['mixture_5fweights_3815',['mixture_weights',['../classvg_1_1SpliceStats.html#ab5f243b05a8a80f0bf80ea3d82960e7e',1,'vg::SpliceStats']]],
- ['mod_5fmain_2ecpp_3816',['mod_main.cpp',['../mod__main_8cpp.html',1,'']]],
- ['mode_3817',['mode',['../structvg_1_1SummaryStatistics.html#a8aa060d244b54f34a06f0136d0572bd4',1,'vg::SummaryStatistics::mode()'],['../structHaplotypesConfig.html#ac5dd4d9940ef4d3d9f2dbfb7cde9754b',1,'HaplotypesConfig::mode()']]],
- ['mode_5fclassify_3818',['mode_classify',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667abd23aa372c8ca2d63cf4b477257d27ea',1,'HaplotypesConfig']]],
- ['mode_5fextract_3819',['mode_extract',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a8efe96a347c67fea3b49d01cb2c21dde',1,'HaplotypesConfig']]],
- ['mode_5finvalid_3820',['mode_invalid',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667afef1428e91bd487b53f44f88885ed506',1,'HaplotypesConfig']]],
- ['mode_5flog_5flikelihood_3821',['mode_log_likelihood',['../classvg_1_1SpliceStats.html#ad10b6fd62bdc23e8bb7afbf8c545f0bd',1,'vg::SpliceStats']]],
- ['mode_5fmap_5fvariants_3822',['mode_map_variants',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667ac11510277093ba13a92edaad15a143f4',1,'HaplotypesConfig']]],
- ['mode_5fname_3823',['mode_name',['../prune__main_8cpp.html#a9b89c7a3b7a8efd51b246bc312140bb8',1,'prune_main.cpp']]],
- ['mode_5fpreprocess_3824',['mode_preprocess',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a2ecb8ae543c843b61de526ce2096f8fe',1,'HaplotypesConfig']]],
- ['mode_5fprune_3825',['mode_prune',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a6a94759a7900a825dd21bf4d9eb648ef',1,'prune_main.cpp']]],
- ['mode_5frestore_3826',['mode_restore',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a7ac5442ed3dfb51eaa1c7311fefc8842',1,'prune_main.cpp']]],
- ['mode_5fsample_5fgraph_3827',['mode_sample_graph',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a043a4f84904086154417f62fbf55084b',1,'HaplotypesConfig']]],
- ['mode_5fsample_5fhaplotypes_3828',['mode_sample_haplotypes',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a684f467f5682443799839a988b490626',1,'HaplotypesConfig']]],
- ['mode_5fstatistics_3829',['mode_statistics',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a0ec67bc2861395ce21fbe3333a118713',1,'HaplotypesConfig']]],
- ['mode_5funfold_3830',['mode_unfold',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a14b7711c85d633b1e1cee3b9466c48b3',1,'prune_main.cpp']]],
- ['model_3831',['model',['../classvg_1_1MEMChainModel.html#a5f0fbf6a027827aa3a2ee1344588e7b7',1,'vg::MEMChainModel::model()'],['../classvg_1_1AlignmentChainModel.html#a18fbbeaa51ee69363983810e702fcf24',1,'vg::AlignmentChainModel::model()']]],
- ['modular_5fexponent_3832',['modular_exponent',['../namespacevg.html#abc8f8791be2575164e6070e1cef39b4e',1,'vg']]],
- ['motif_5fdata_3833',['motif_data',['../classvg_1_1SpliceStats.html#a6a48be87c666572f8e2893e8cf1df9a6',1,'vg::SpliceStats']]],
- ['motif_5ffrequency_3834',['motif_frequency',['../classvg_1_1SpliceStats.html#aeb0d77ba4fc7a6767eff466a6ba8ed9e',1,'vg::SpliceStats']]],
- ['motif_5fis_5freverse_3835',['motif_is_reverse',['../classvg_1_1SpliceStats.html#afc22a25e939fa725d3808430f9a62007',1,'vg::SpliceStats']]],
- ['motif_5fmatches_3836',['motif_matches',['../classvg_1_1SpliceRegion.html#a79697742be9ce68f77d75b430f23a896',1,'vg::SpliceRegion']]],
- ['motif_5fscore_3837',['motif_score',['../classvg_1_1SpliceStats.html#a7da67978c875a8e9bc1fac31fdb8277b',1,'vg::SpliceStats']]],
- ['motif_5fsize_3838',['motif_size',['../classvg_1_1SpliceStats.html#aae5310e0728aebc36703641a566242e3',1,'vg::SpliceStats']]],
- ['move_3839',['move',['../classvg_1_1SmallBitset.html#a5c80c7e3d6d92c7c5e58463771a2a341',1,'vg::SmallBitset']]],
- ['mp_5faln_5femitter_3840',['mp_aln_emitter',['../classvg_1_1ReadFilter.html#a7baa666446be017dea5507fe5771de57',1,'vg::ReadFilter']]],
- ['mp_5faln_5femitters_3841',['mp_aln_emitters',['../classvg_1_1MultipathAlignmentEmitter.html#abf746b78f8aaf59332dc1852c91affdd',1,'vg::MultipathAlignmentEmitter']]],
- ['mpmap_5fmain_2ecpp_3842',['mpmap_main.cpp',['../mpmap__main_8cpp.html',1,'']]],
- ['mq_5foverlap_3843',['mq_overlap',['../classvg_1_1Mapper.html#a6a23397e02e8522823d36ad4b11a698a',1,'vg::Mapper']]],
- ['msa_5fconverter_2ecpp_3844',['msa_converter.cpp',['../msa__converter_8cpp.html',1,'']]],
- ['msa_5fconverter_2ehpp_3845',['msa_converter.hpp',['../msa__converter_8hpp.html',1,'']]],
- ['msaconverter_3846',['MSAConverter',['../classvg_1_1MSAConverter.html',1,'vg::MSAConverter'],['../classvg_1_1MSAConverter.html#ac6e82d70cf93d7b8a75750b40dd89277',1,'vg::MSAConverter::MSAConverter()']]],
- ['msg_3847',['msg',['../classvg_1_1InsufficientInputException.html#a1e4d0ea31dffdc2f339bf11067c00d38',1,'vg::InsufficientInputException::msg()'],['../classvg_1_1RewindPlanException.html#a6dc3f46bfa00c1eb02030b4ff6e73f80',1,'vg::RewindPlanException::msg()'],['../classvg_1_1SizeLimitExceededException.html#ae776aba3017b9ff4c7e7b05002d0be99',1,'vg::SizeLimitExceededException::msg()']]],
- ['msga_5fmain_2ecpp_3848',['msga_main.cpp',['../msga__main_8cpp.html',1,'']]],
- ['mtx_3849',['mtx',['../classvg_1_1ParallelKFFReader.html#a616866362b3f55b76ea1df8a65c01267',1,'vg::ParallelKFFReader']]],
- ['mu_3850',['mu',['../classvg_1_1FragmentLengthDistribution.html#a8c1fb2ac76ebdec084c599686ca12bfa',1,'vg::FragmentLengthDistribution']]],
- ['multi_5fposition_5fannotations_3851',['multi_position_annotations',['../classvg_1_1AbstractReadSampler.html#a679c8195e5411d7460725453298b50f2',1,'vg::AbstractReadSampler']]],
- ['multi_5fsurject_3852',['multi_surject',['../classvg_1_1Surjector.html#a0ed6215f3860203803deb2f3078d93b4',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#ab8b34cbb819829cd493bdc901a6e3060',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a943158332e4865de071dca68454a4d77',1,'vg::Surjector::multi_surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
- ['multiallelic_5fsv_5fwarned_3853',['multiallelic_sv_warned',['../classvg_1_1Constructor.html#ad4a4e56154c62990a784f7e51e7368cd',1,'vg::Constructor']]],
- ['multinomial_5fcensored_5fsampling_5fprob_5fln_3854',['multinomial_censored_sampling_prob_ln',['../namespacevg.html#a074fcebfeb68fc970b5b2a0db3722f01',1,'vg']]],
- ['multinomial_5fchoose_5fln_3855',['multinomial_choose_ln',['../namespacevg.html#a15f09f05f7894863e9cd852c63266078',1,'vg']]],
- ['multinomial_5fsampling_5fprob_5fln_3856',['multinomial_sampling_prob_ln',['../namespacevg.html#af4d69cf9a7d7e6272960fcb9f0a0a00c',1,'vg']]],
- ['multipath_5falign_3857',['multipath_align',['../classvg_1_1MultipathMapper.html#a7af0cb7af3f7a3e3ab60627f3793aa0a',1,'vg::MultipathMapper']]],
- ['multipath_5falignment_2ecpp_3858',['multipath_alignment.cpp',['../multipath__alignment_8cpp.html',1,'']]],
- ['multipath_5falignment_2ehpp_3859',['multipath_alignment.hpp',['../multipath__alignment_8hpp.html',1,'']]],
- ['multipath_5falignment_5femitter_2ecpp_3860',['multipath_alignment_emitter.cpp',['../multipath__alignment__emitter_8cpp.html',1,'']]],
- ['multipath_5falignment_5femitter_2ehpp_3861',['multipath_alignment_emitter.hpp',['../multipath__alignment__emitter_8hpp.html',1,'']]],
- ['multipath_5falignment_5fgraph_2ecpp_3862',['multipath_alignment_graph.cpp',['../multipath__alignment__graph_8cpp.html',1,'']]],
- ['multipath_5falignment_5fgraph_2ehpp_3863',['multipath_alignment_graph.hpp',['../multipath__alignment__graph_8hpp.html',1,'']]],
- ['multipath_5falignment_5fpath_5foffsets_3864',['multipath_alignment_path_offsets',['../namespacevg_1_1algorithms.html#ad0cecedaa8dd475e634b513af5be028b',1,'vg::algorithms']]],
- ['multipath_5falignment_5ft_3865',['multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html',1,'vg::multipath_alignment_t'],['../classvg_1_1multipath__alignment__t.html#ae7f715f63023d3043c01ed29193ea6a1',1,'vg::multipath_alignment_t::multipath_alignment_t()'],['../classvg_1_1multipath__alignment__t.html#a55b4c1fee893c4b596f0a654a624bccc',1,'vg::multipath_alignment_t::multipath_alignment_t(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ad4de932d4f01d8d44a76095605294470',1,'vg::multipath_alignment_t::multipath_alignment_t(multipath_alignment_t &&other)']]],
- ['multipath_5fmap_3866',['multipath_map',['../classvg_1_1MultipathMapper.html#a9ea318c04336aa79020b7c012e468ef8',1,'vg::MultipathMapper']]],
- ['multipath_5fmap_5fpaired_3867',['multipath_map_paired',['../classvg_1_1MultipathMapper.html#a240c4502e41aa0e5961772a12b1b42a8',1,'vg::MultipathMapper']]],
- ['multipath_5fmapper_2ecpp_3868',['multipath_mapper.cpp',['../multipath__mapper_8cpp.html',1,'']]],
- ['multipath_5fmapper_2ehpp_3869',['multipath_mapper.hpp',['../multipath__mapper_8hpp.html',1,'']]],
- ['multipathalignment_3870',['MultipathAlignment',['../structvg_1_1MultipathAlignment.html',1,'vg']]],
- ['multipathalignmentemitter_3871',['MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html',1,'vg::MultipathAlignmentEmitter'],['../classvg_1_1MultipathAlignmentEmitter.html#a022247fcbd889aeb51b35b0cae1c3622',1,'vg::MultipathAlignmentEmitter::MultipathAlignmentEmitter()']]],
- ['multipathalignmentgraph_3872',['MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html',1,'vg::MultipathAlignmentGraph'],['../classvg_1_1MultipathAlignmentGraph.html#a058e6120cb359e2566c1c2d7961c608e',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a51e7308dc1c0c96d1e576970211b7705',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#afd75ac7afd23901c4b8f38eb126bdba0',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a74eec86f754011999dc6caed5d1f6c8a',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a366ddb07faadad371e896d3f453e147c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a4289e77bb6d76abfbb1d3c02d89a2586',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#ac8f4ae19921529920157bcbbf9a2f5c3',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a10f9b18c8aa4db1b80bf54ccc5dcc09c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const unordered_map< id_t, pair< id_t, bool >> &projection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a89b441f028fd26c177a9ce8d8188b7c1',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project)']]],
- ['multipathmapper_3873',['MultipathMapper',['../classvg_1_1MultipathMapper.html',1,'vg::MultipathMapper'],['../classvg_1_1MultipathMapper.html#a4d3a7e85dfc2d7cda41912a4f87fd5ac',1,'vg::MultipathMapper::MultipathMapper()']]],
- ['multipathproblem_3874',['MultipathProblem',['../structvg_1_1MultipathProblem.html',1,'vg::MultipathProblem'],['../structvg_1_1MultipathProblem.html#ac97d55858c86d218c380fd43e115d18a',1,'vg::MultipathProblem::MultipathProblem()']]],
- ['multiplexer_3875',['multiplexer',['../classvg_1_1HTSWriter.html#a6e2ff3f77a4265c8dcd1c47770a0bee5',1,'vg::HTSWriter::multiplexer()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a24cd277c06adf66414346ffeb22c0400',1,'vg::io::TSVAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a2f047c1205c512b44f29d0e8231c0cef',1,'vg::io::VGAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a286a69e0bb8071d101e27e501ce1e3ce',1,'vg::io::GafAlignmentEmitter::multiplexer()']]],
- ['mut_5fgraph_5fimpl_3876',['mut_graph_impl',['../structvg_1_1IndexingParameters.html#a9db2b318dee6f693544c8fc5a04c0a53',1,'vg::IndexingParameters']]],
- ['mut_5fsampler_3877',['mut_sampler',['../classvg_1_1NGSSimulator.html#a9501d39b8059ad161395f2b7ba89d424',1,'vg::NGSSimulator']]],
- ['mutable_5fconnection_3878',['mutable_connection',['../classvg_1_1subpath__t.html#a271236a46bdb6105f216a630c0c67a74',1,'vg::subpath_t::mutable_connection()'],['../classvg_1_1subpath__t.html#aa967fceb620f92e73e965345d4cd0b67',1,'vg::subpath_t::mutable_connection(size_t i)']]],
- ['mutable_5fedit_3879',['mutable_edit',['../classvg_1_1path__mapping__t.html#aeb9d50accda37c8829c49cd8567f72bc',1,'vg::path_mapping_t::mutable_edit()'],['../classvg_1_1path__mapping__t.html#a56c059138a051e7889f4083a74c5401f',1,'vg::path_mapping_t::mutable_edit(size_t i)']]],
- ['mutable_5fhandle_5fgraph_2ecpp_3880',['mutable_handle_graph.cpp',['../mutable__handle__graph_8cpp.html',1,'']]],
- ['mutable_5fhandle_5fgraph_2ehpp_3881',['mutable_handle_graph.hpp',['../mutable__handle__graph_8hpp.html',1,'']]],
- ['mutable_5fmapping_3882',['mutable_mapping',['../classvg_1_1path__t.html#ab3f1eeeefe1c604dacdeff019488ff07',1,'vg::path_t::mutable_mapping()'],['../classvg_1_1path__t.html#aac0ad10ace8970358d471d779061b22d',1,'vg::path_t::mutable_mapping(size_t i)']]],
- ['mutable_5fnext_3883',['mutable_next',['../classvg_1_1subpath__t.html#ae1331c79838d972ccb8be4e98ac87954',1,'vg::subpath_t']]],
- ['mutable_5fpath_3884',['mutable_path',['../classvg_1_1subpath__t.html#aa5f32fe1e7167d09187d4a69c091bde5',1,'vg::subpath_t']]],
- ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ecpp_3885',['mutable_path_deletable_handle_graph.cpp',['../mutable__path__deletable__handle__graph_8cpp.html',1,'']]],
- ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ehpp_3886',['mutable_path_deletable_handle_graph.hpp',['../mutable__path__deletable__handle__graph_8hpp.html',1,'']]],
- ['mutable_5fpath_5fhandle_5fgraph_2ecpp_3887',['mutable_path_handle_graph.cpp',['../mutable__path__handle__graph_8cpp.html',1,'']]],
- ['mutable_5fpath_5fhandle_5fgraph_2ehpp_3888',['mutable_path_handle_graph.hpp',['../mutable__path__handle__graph_8hpp.html',1,'']]],
- ['mutable_5fpath_5fmetadata_2ecpp_3889',['mutable_path_metadata.cpp',['../mutable__path__metadata_8cpp.html',1,'']]],
- ['mutable_5fpath_5fmetadata_2ehpp_3890',['mutable_path_metadata.hpp',['../mutable__path__metadata_8hpp.html',1,'']]],
- ['mutable_5fpath_5fmutable_5fhandle_5fgraph_2ehpp_3891',['mutable_path_mutable_handle_graph.hpp',['../mutable__path__mutable__handle__graph_8hpp.html',1,'']]],
- ['mutable_5fposition_3892',['mutable_position',['../classvg_1_1path__mapping__t.html#a87ef119207623109aea694cd5432421d',1,'vg::path_mapping_t']]],
- ['mutable_5fquality_3893',['mutable_quality',['../classvg_1_1multipath__alignment__t.html#a5d62a17eb3aad07f05f5580aa7f9dfbd',1,'vg::multipath_alignment_t']]],
- ['mutable_5fsequence_3894',['mutable_sequence',['../classvg_1_1multipath__alignment__t.html#a11d22790dc8b9cc631a237ef00b6e0e4',1,'vg::multipath_alignment_t::mutable_sequence()'],['../classvg_1_1edit__t.html#aa5e639217215d8d67bfe1ec2a07105fb',1,'vg::edit_t::mutable_sequence()']]],
- ['mutable_5fstart_3895',['mutable_start',['../classvg_1_1multipath__alignment__t.html#a43e30d76e7ac0596fc15c868fbbd603c',1,'vg::multipath_alignment_t']]],
- ['mutable_5fsubpath_3896',['mutable_subpath',['../classvg_1_1multipath__alignment__t.html#a65ee05140e26b51a60f7d33a7b9b9c54',1,'vg::multipath_alignment_t::mutable_subpath()'],['../classvg_1_1multipath__alignment__t.html#a727e5e6bc04955e46efe83bc5d668bdf',1,'vg::multipath_alignment_t::mutable_subpath(size_t i)']]],
- ['mutablegraphimplementation_3897',['MutableGraphImplementation',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10',1,'vg::IndexingParameters']]],
- ['mutablehandlegraph_3898',['MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html',1,'handlegraph::MutableHandleGraph'],['../namespacevg.html#a293aa7465cc63a2581914d6a85a0e4b8',1,'vg::MutableHandleGraph()']]],
- ['mutablepathdeletablehandlegraph_3899',['MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html',1,'handlegraph::MutablePathDeletableHandleGraph'],['../namespacevg.html#a2f0cc7bac7a4f92b2b523357f8940aa5',1,'vg::MutablePathDeletableHandleGraph()']]],
- ['mutablepathhandlegraph_3900',['MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html',1,'handlegraph::MutablePathHandleGraph'],['../namespacevg.html#a24350c08e6d69244e6930f41fee00e1f',1,'vg::MutablePathHandleGraph()']]],
- ['mutablepathmetadata_3901',['MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html',1,'handlegraph']]],
- ['mutablepathmutablehandlegraph_3902',['MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html',1,'handlegraph::MutablePathMutableHandleGraph'],['../namespacevg.html#aa2f83c48d4ecdcfd8f2604f10e863aea',1,'vg::MutablePathMutableHandleGraph()']]],
- ['mutate_3903',['mutate',['../classvg_1_1Sampler.html#a8f148dac7598a3465202371511e53f2a',1,'vg::Sampler']]],
- ['mutate_5fedit_3904',['mutate_edit',['../classvg_1_1Sampler.html#ad372d6fdcac5af601bdb0729f94a7e7d',1,'vg::Sampler']]],
- ['mutation_5falphabets_3905',['mutation_alphabets',['../classvg_1_1NGSSimulator.html#a4a8eacfde748b35453a54ab40c195680',1,'vg::NGSSimulator']]],
- ['mutex_5fgraph_3906',['mutex_graph',['../classvg_1_1Transcriptome.html#a881ee68ca1a43b0ab10494f62e7b127f',1,'vg::Transcriptome']]],
- ['mutex_5ftranscript_5fpaths_3907',['mutex_transcript_paths',['../classvg_1_1Transcriptome.html#a3c6d64194201d695fdcb07078463161a',1,'vg::Transcriptome']]],
- ['my_5fmapper_3908',['my_mapper',['../classvg_1_1Filter.html#a13678a95a03ae4feb7e6ebc0fa00a69f',1,'vg::Filter']]],
- ['my_5fmax_5fdistance_3909',['my_max_distance',['../classvg_1_1Filter.html#ab9ec8e13d2cd4fc50aa86981a0b6475f',1,'vg::Filter']]],
- ['my_5fnames_3910',['my_names',['../classVectorizer.html#a5702f38d3e6d29866e2135d29f7496fd',1,'Vectorizer']]],
- ['my_5fpath_5fposition_5fgraph_3911',['my_path_position_graph',['../classvg_1_1Filter.html#af17db75bb83c6d2ad00b813a4812d30d',1,'vg::Filter']]],
- ['my_5fvectors_3912',['my_vectors',['../classVectorizer.html#af370e810d055623deaa0bfaac120fe8d',1,'Vectorizer']]],
- ['my_5fvg_3913',['my_vg',['../classvg_1_1Filter.html#ac849cd8534ba9b7eb7daa8485d6c9d45',1,'vg::Filter']]],
- ['my_5fxg_3914',['my_xg',['../classVectorizer.html#adebb6c75ae3b7c1199143ab2f166d284',1,'Vectorizer']]]
+ ['m_5fa_3294',['m_a',['../classvg_1_1uniform__real__distribution.html#a7504f90f6d4dea77942a9ca0c0cc3f57',1,'vg::uniform_real_distribution::m_a()'],['../classvg_1_1uniform__int__distribution.html#a2d084a9d58cbc2f4a202d7ba640207ac',1,'vg::uniform_int_distribution::m_a()']]],
+ ['m_5falpha_3295',['m_alpha',['../classvg_1_1truncated__normal__distribution.html#a103e91e1a5b135b61ef12bb1396b073d',1,'vg::truncated_normal_distribution']]],
+ ['m_5fb_3296',['m_b',['../classvg_1_1uniform__real__distribution.html#a736effb600abacbb4ad5dbd9960449b7',1,'vg::uniform_real_distribution::m_b()'],['../classvg_1_1uniform__int__distribution.html#a8fcf808d445c2826852f79c4bac7f594',1,'vg::uniform_int_distribution::m_b()']]],
+ ['m_5fbeta_3297',['m_beta',['../classvg_1_1truncated__normal__distribution.html#ab4ba11d217ace97234dbc707180a388a',1,'vg::truncated_normal_distribution']]],
+ ['m_5fdistu1_3298',['m_distU1',['../classvg_1_1normal__distribution.html#a88845be3c45acd203b683f83a658b3bd',1,'vg::normal_distribution::m_distU1()'],['../classvg_1_1truncated__normal__distribution.html#a0020a9172587312e5342375bb0730ec5',1,'vg::truncated_normal_distribution::m_distU1()']]],
+ ['m_5fmean_3299',['m_mean',['../classvg_1_1normal__distribution.html#ac215210d6799c86403804a8700f8870f',1,'vg::normal_distribution']]],
+ ['m_5fmu_3300',['m_mu',['../classvg_1_1truncated__normal__distribution.html#a16eb85a95c575485c51f3915c27fb206',1,'vg::truncated_normal_distribution']]],
+ ['m_5fsigma_3301',['m_sigma',['../classvg_1_1truncated__normal__distribution.html#acc168175a443e25b3b7a49ddbd2d0d65',1,'vg::truncated_normal_distribution']]],
+ ['m_5fstddev_3302',['m_stddev',['../classvg_1_1normal__distribution.html#a4940854c4f61e99e8c62acb754619bed',1,'vg::normal_distribution']]],
+ ['m_5fsums_3303',['m_sums',['../classvg_1_1discrete__distribution.html#a175dbe373664d84a0a354f1d2febb1b1',1,'vg::discrete_distribution']]],
+ ['m_5fweights_3304',['m_weights',['../classvg_1_1discrete__distribution.html#aae17bac88e7ee1c979e4c44287f9a2fe',1,'vg::discrete_distribution']]],
+ ['magic_5fbytes_3305',['MAGIC_BYTES',['../classvg_1_1StreamIndexBase.html#a9bbb2b0134f0e831fc2ec5db056b7397',1,'vg::StreamIndexBase']]],
+ ['magic_5fnumber_3306',['MAGIC_NUMBER',['../structvg_1_1Haplotypes_1_1Header.html#a08c60e1b376c1a451b42810f5131758b',1,'vg::Haplotypes::Header::MAGIC_NUMBER()'],['../structvg_1_1Haplotypes_1_1Header.html#ae84cdbdc1d89ebf53496eed304acafd3',1,'vg::Haplotypes::Header::magic_number()'],['../classvg_1_1ZipCodeCollection.html#a27434270b2b8b6e6a66f783efb8150c2',1,'vg::ZipCodeCollection::magic_number()']]],
+ ['main_3307',['main',['../main_8cpp.html#a813f1942a22b88bf4ff8686af6c643bd',1,'main(int argc, char *argv[]) VG_PREFLIGHT_EVERYWHERE: main.cpp'],['../main_8cpp.html#a3c04138a5bfe5d72780bb7e82a18e627',1,'main(int argc, char **argv): main.cpp']]],
+ ['main_2ecpp_3308',['main.cpp',['../main_8cpp.html',1,'']]],
+ ['main_5fadd_3309',['main_add',['../add__main_8cpp.html#a70f2a72c5f1d86661c78534083fbe668',1,'add_main.cpp']]],
+ ['main_5falign_3310',['main_align',['../align__main_8cpp.html#acc3c08d6346e0538c36aa20a0af338f2',1,'align_main.cpp']]],
+ ['main_5fannotate_3311',['main_annotate',['../annotate__main_8cpp.html#ae4b460c351b8e163410fbacf4244f7f2',1,'annotate_main.cpp']]],
+ ['main_5faugment_3312',['main_augment',['../augment__main_8cpp.html#a39b28115682b22f672ec0f6932d0f259',1,'augment_main.cpp']]],
+ ['main_5fautoindex_3313',['main_autoindex',['../autoindex__main_8cpp.html#a0c5af200c1937f0b3c5723ce0220a7bf',1,'autoindex_main.cpp']]],
+ ['main_5fbenchmark_3314',['main_benchmark',['../benchmark__main_8cpp.html#add0702a6210234f5e42ee9c301265d6a',1,'benchmark_main.cpp']]],
+ ['main_5fcall_3315',['main_call',['../call__main_8cpp.html#ac255329e18ef1a778298cd5fdc5d3050',1,'call_main.cpp']]],
+ ['main_5fchain_3316',['main_chain',['../chain__main_8cpp.html#af61d7259730b08c0c8ff61629e51d78a',1,'chain_main.cpp']]],
+ ['main_5fchunk_3317',['main_chunk',['../chunk__main_8cpp.html#aa34cae934dcb31ac7653f079d0d4bf93',1,'chunk_main.cpp']]],
+ ['main_5fcircularize_3318',['main_circularize',['../circularize__main_8cpp.html#a1d21512b4c5eb417fa6a1b20a72c1195',1,'circularize_main.cpp']]],
+ ['main_5fclip_3319',['main_clip',['../clip__main_8cpp.html#af09a429b96343cf918b8fdea5ebf1a4b',1,'clip_main.cpp']]],
+ ['main_5fcluster_3320',['main_cluster',['../cluster__main_8cpp.html#a88693148489c263b15047d96976b9b94',1,'cluster_main.cpp']]],
+ ['main_5fcombine_3321',['main_combine',['../combine__main_8cpp.html#a7f4bcb1d0c551b46ed39797df9d0da60',1,'combine_main.cpp']]],
+ ['main_5fconcat_3322',['main_concat',['../concat__main_8cpp.html#a22a9b545fc267c18654f312d4fa8d701',1,'concat_main.cpp']]],
+ ['main_5fconstruct_3323',['main_construct',['../construct__main_8cpp.html#a385574d21007babb8ef7fa73c9b39cee',1,'construct_main.cpp']]],
+ ['main_5fconvert_3324',['main_convert',['../convert__main_8cpp.html#abd9dc3a752930342a8096088f2d4b742',1,'convert_main.cpp']]],
+ ['main_5fdeconstruct_3325',['main_deconstruct',['../deconstruct__main_8cpp.html#a80a32834c987861cb4c90d124e0aba12',1,'deconstruct_main.cpp']]],
+ ['main_5fdepth_3326',['main_depth',['../depth__main_8cpp.html#a7db982076303bea19c79ee8df88e086f',1,'depth_main.cpp']]],
+ ['main_5fdotplot_3327',['main_dotplot',['../dotplot__main_8cpp.html#a74751264f7ead208e151be5408766053',1,'dotplot_main.cpp']]],
+ ['main_5fexplode_3328',['main_explode',['../explode__main_8cpp.html#a0448cf7f521dde683e09f6c57df48d67',1,'explode_main.cpp']]],
+ ['main_5ffilter_3329',['main_filter',['../filter__main_8cpp.html#af14726647fef6f08e5f916f8a1b4ae0e',1,'filter_main.cpp']]],
+ ['main_5ffind_3330',['main_find',['../find__main_8cpp.html#a35569e011de224c166556ea563a4861e',1,'find_main.cpp']]],
+ ['main_5ffunction_3331',['main_function',['../classvg_1_1subcommand_1_1Subcommand.html#a8c500a86e1c9c51cea715508a19c75fa',1,'vg::subcommand::Subcommand']]],
+ ['main_5fgamcompare_3332',['main_gamcompare',['../gamcompare__main_8cpp.html#a0685b1cc8cff4ca811a199eb1746ddf7',1,'gamcompare_main.cpp']]],
+ ['main_5fgampcompare_3333',['main_gampcompare',['../gampcompare__main_8cpp.html#a4b081154219461589d0978c7d993d547',1,'gampcompare_main.cpp']]],
+ ['main_5fgamsort_3334',['main_gamsort',['../gamsort__main_8cpp.html#a0aa266bac1f77e7c3625c293f1050108',1,'gamsort_main.cpp']]],
+ ['main_5fgbwt_3335',['main_gbwt',['../gbwt__main_8cpp.html#a2018904e4679a19c52921f97afab4592',1,'gbwt_main.cpp']]],
+ ['main_5fgenotype_3336',['main_genotype',['../genotype__main_8cpp.html#a04819bc8264065b3aadb2b7bf3a923fa',1,'genotype_main.cpp']]],
+ ['main_5fgiraffe_3337',['main_giraffe',['../giraffe__main_8cpp.html#a03a19bdd804f12c23f77bb885e91df4a',1,'giraffe_main.cpp']]],
+ ['main_5fhaplotypes_3338',['main_haplotypes',['../haplotypes__main_8cpp.html#ae8ab8ef2233eb016b7b7f0c2bd5c9411',1,'haplotypes_main.cpp']]],
+ ['main_5fhelp_3339',['main_help',['../help__main_8cpp.html#ad13a4a4aadfb1314983f35c8cca2e5c7',1,'help_main.cpp']]],
+ ['main_5fids_3340',['main_ids',['../ids__main_8cpp.html#aaefd32fe84e813daa1089df0d0bd955f',1,'ids_main.cpp']]],
+ ['main_5findex_3341',['main_index',['../index__main_8cpp.html#a7a9da678374c285546cdf243a185b15e',1,'index_main.cpp']]],
+ ['main_5finject_3342',['main_inject',['../inject__main_8cpp.html#a214bda0795dc475a91ffd32752b2ee8e',1,'inject_main.cpp']]],
+ ['main_5fjoin_3343',['main_join',['../join__main_8cpp.html#a904b50e94b5426c0bb0a39523aada064',1,'join_main.cpp']]],
+ ['main_5fkmers_3344',['main_kmers',['../kmers__main_8cpp.html#af32e430824ef93e29253ec42f2edb21e',1,'kmers_main.cpp']]],
+ ['main_5fmap_3345',['main_map',['../map__main_8cpp.html#ac963a6cd2cd103405e86f088d5c8358a',1,'map_main.cpp']]],
+ ['main_5fmask_3346',['main_mask',['../mask__main_8cpp.html#a66e6db9d20d50a757d7ab70d7ca458f8',1,'mask_main.cpp']]],
+ ['main_5fmcmc_3347',['main_mcmc',['../mcmc__main_8cpp.html#a7a702ad991c4285feaeee55461c95a63',1,'mcmc_main.cpp']]],
+ ['main_5fminimizer_3348',['main_minimizer',['../minimizer__main_8cpp.html#a5a43d1ef287159cce46f07df1b8b088d',1,'minimizer_main.cpp']]],
+ ['main_5fmod_3349',['main_mod',['../mod__main_8cpp.html#ab561b57168cf02964d1a14e024108f2e',1,'mod_main.cpp']]],
+ ['main_5fmpmap_3350',['main_mpmap',['../mpmap__main_8cpp.html#a8deece908ee37e2d38e61b2c921e508f',1,'mpmap_main.cpp']]],
+ ['main_5fmsga_3351',['main_msga',['../msga__main_8cpp.html#a60a999194e7689bb509442f1caa2354e',1,'msga_main.cpp']]],
+ ['main_5fpack_3352',['main_pack',['../pack__main_8cpp.html#a0b3d5bb3cabcd119b839dded9853de23',1,'pack_main.cpp']]],
+ ['main_5fpaths_3353',['main_paths',['../paths__main_8cpp.html#a6357ea987a573514a31781145d74cd61',1,'paths_main.cpp']]],
+ ['main_5fprune_3354',['main_prune',['../prune__main_8cpp.html#a5b6c70447534213ea13f56ad785d881b',1,'prune_main.cpp']]],
+ ['main_5frna_3355',['main_rna',['../rna__main_8cpp.html#a6d06f637eb10cfbb38bb55619ceb3c00',1,'rna_main.cpp']]],
+ ['main_5fsift_3356',['main_sift',['../sift__main_8cpp.html#a5c78b9bf77f34696d562b5abffb7a1ef',1,'sift_main.cpp']]],
+ ['main_5fsim_3357',['main_sim',['../sim__main_8cpp.html#a1926f81c841475ca54d3100d6340d468',1,'sim_main.cpp']]],
+ ['main_5fsimplify_3358',['main_simplify',['../simplify__main_8cpp.html#a16ebf24b0dce88509b5e97fc2fc777b8',1,'simplify_main.cpp']]],
+ ['main_5fsnarl_3359',['main_snarl',['../snarls__main_8cpp.html#a4bda7d45d00c828d1e8555573c1c3caf',1,'snarls_main.cpp']]],
+ ['main_5fsort_3360',['main_sort',['../sort__main_8cpp.html#a40dc673c2ce8bc4c8ae1496857641885',1,'sort_main.cpp']]],
+ ['main_5fstats_3361',['main_stats',['../stats__main_8cpp.html#a6e64cedc2b30a69dea5b727edded704d',1,'stats_main.cpp']]],
+ ['main_5fsurject_3362',['main_surject',['../surject__main_8cpp.html#a51d014c6923a46c0f34ca4deb59d11b0',1,'surject_main.cpp']]],
+ ['main_5ftest_3363',['main_test',['../test__main_8cpp.html#abd8de8d504f1b1aa53207643a7b553b4',1,'test_main.cpp']]],
+ ['main_5ftrace_3364',['main_trace',['../trace__main_8cpp.html#a7bc03098058581a46cba55a13de823e9',1,'trace_main.cpp']]],
+ ['main_5ftranslate_3365',['main_translate',['../translate__main_8cpp.html#a2578e3814e52126bf55e62054a01ec7d',1,'translate_main.cpp']]],
+ ['main_5fvalidate_3366',['main_validate',['../validate__main_8cpp.html#a8249f1e29a84af534ef5116f778267fb',1,'validate_main.cpp']]],
+ ['main_5fvectorize_3367',['main_vectorize',['../vectorize__main_8cpp.html#a8e4da879b5896dd1e13ee84e310870ea',1,'vectorize_main.cpp']]],
+ ['main_5fversion_3368',['main_version',['../version__main_8cpp.html#a972dc6662988df17dcc0b4cc0abf6e54',1,'version_main.cpp']]],
+ ['main_5fview_3369',['main_view',['../view__main_8cpp.html#a868d2fd8e59794e18a2ecee28f838143',1,'view_main.cpp']]],
+ ['main_5fviz_3370',['main_viz',['../viz__main_8cpp.html#a9e415066b5a221e559f9a402b85f386d',1,'viz_main.cpp']]],
+ ['main_5fzipcode_3371',['main_zipcode',['../zipcode__main_8cpp.html#a8b81469e01a40dbf9eefbdf90e0c0427',1,'zipcode_main.cpp']]],
+ ['make_5fbands_3372',['make_bands',['../classvg_1_1Mapper.html#aafecbaf352024b2847928860fe6c1168',1,'vg::Mapper']]],
+ ['make_5fcircular_3373',['make_circular',['../classvg_1_1Paths.html#a1e8760e2c86dd64141c2d0df35926430',1,'vg::Paths']]],
+ ['make_5fcompact_3374',['make_compact',['../classvg_1_1Packer.html#a66e266fca00d4e74b7bda1ddbcf384e3',1,'vg::Packer']]],
+ ['make_5fdynamic_3375',['make_dynamic',['../classvg_1_1Packer.html#ac3ab6cab2e0cf0ae4e65663db73184e8',1,'vg::Packer']]],
+ ['make_5fedge_3376',['make_edge',['../classvg_1_1PhaseUnfolder.html#a82b0a653c98ead9bc4c31d283583d102',1,'vg::PhaseUnfolder']]],
+ ['make_5fempty_3377',['make_empty',['../structvg_1_1WFAAlignment.html#ae54f9060454a45ea9a2131a9b5b81c38',1,'vg::WFAAlignment']]],
+ ['make_5fgraph_3378',['make_graph',['../classvg_1_1MSAConverter.html#aa4556065637b908e37d2cbf7534b930a',1,'vg::MSAConverter']]],
+ ['make_5fhit_5fgraph_3379',['make_hit_graph',['../classvg_1_1MEMClusterer.html#ac65c43448463ef346199437b073c1467',1,'vg::MEMClusterer::make_hit_graph()'],['../classvg_1_1NullClusterer.html#a4e7540aadd3d1eb3d4616cf0d268b3f0',1,'vg::NullClusterer::make_hit_graph()'],['../classvg_1_1OrientedDistanceClusterer.html#af520fdf27e87d46d3a7a5976ec6179c2',1,'vg::OrientedDistanceClusterer::make_hit_graph()'],['../classvg_1_1TVSClusterer.html#a33dff32277c63fa9dc42969c01094900',1,'vg::TVSClusterer::make_hit_graph()'],['../classvg_1_1MinDistanceClusterer.html#a8f3bd899d336e3a30f77e2985eaceb81',1,'vg::MinDistanceClusterer::make_hit_graph()'],['../classvg_1_1GreedyMinDistanceClusterer.html#ad5a3eda064089d19eec2338ccc82e515',1,'vg::GreedyMinDistanceClusterer::make_hit_graph()'],['../classvg_1_1ComponentMinDistanceClusterer.html#afe8b8bc133b5ef94999264dabb3452b8',1,'vg::ComponentMinDistanceClusterer::make_hit_graph()']]],
+ ['make_5findexes_3380',['make_indexes',['../classvg_1_1IndexRegistry.html#a4c954dbadbab6cdcd3e81b438864668d',1,'vg::IndexRegistry']]],
+ ['make_5flinear_3381',['make_linear',['../classvg_1_1Paths.html#aa82bcbd02b83a9f0781c3696ef46d371',1,'vg::Paths']]],
+ ['make_5flong_5foptions_3382',['make_long_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aec2fb8fe7d2b574993b33658440227e0',1,'vg::subcommand::BaseOptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8db74c059e0822c3b25ea7d05bcce340',1,'vg::subcommand::OptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af521b678294674ffcd04b670b5cde737',1,'vg::subcommand::GroupedOptionGroup::make_long_options()']]],
+ ['make_5fnontrivial_5fmultipath_5falignment_3383',['make_nontrivial_multipath_alignment',['../classvg_1_1MultipathMapper.html#a4e4be08a92493e0e3b865783b4701cd7',1,'vg::MultipathMapper']]],
+ ['make_5fnull_5falignment_3384',['make_null_alignment',['../classvg_1_1Surjector.html#a139ffe849fc1164217e45ea5755fc518',1,'vg::Surjector']]],
+ ['make_5fnull_5fmp_5falignment_3385',['make_null_mp_alignment',['../classvg_1_1Surjector.html#a7db137631f3315ede2f6887334a161b4',1,'vg::Surjector']]],
+ ['make_5fplan_3386',['make_plan',['../classvg_1_1IndexRegistry.html#ab31ecdcf8f9d50a1310667d23c6410e2',1,'vg::IndexRegistry']]],
+ ['make_5fpos_5ft_3387',['make_pos_t',['../namespacevg.html#a2d9f0a2379194fb00d706e90d373b378',1,'vg::make_pos_t(const Position &pos)'],['../namespacevg.html#a1b348dcfac955a7030a3721f436e7d5d',1,'vg::make_pos_t(const position_t &pos)'],['../namespacevg.html#afc066dab7543192bf782959ef160f2d4',1,'vg::make_pos_t(gcsa::node_type node)'],['../namespacevg.html#a1d85d380ba4b936ac8a715a72062866c',1,'vg::make_pos_t(id_t id, bool is_rev, offset_t off)'],['../namespacexg.html#aace66781c520f719a1f8f64ab24f2589',1,'xg::make_pos_t()']]],
+ ['make_5fposition_3388',['make_position',['../namespacevg.html#a6247de8deb27aaabf2bc0d6fc755f693',1,'vg::make_position(const pos_t &pos)'],['../namespacevg.html#ac6af3d55800703f7534ca07a84450580',1,'vg::make_position(id_t id, bool is_rev, offset_t off)'],['../namespacevg.html#a4cdd9b08b7b6d6e15d00536554f3ca56',1,'vg::make_position(gcsa::node_type node)']]],
+ ['make_5fprefix_5fsuffix_5ftable_3389',['make_prefix_suffix_table',['../namespacevg.html#a3ff1638bd636bb4b9746545dc261aea1',1,'vg']]],
+ ['make_5fshort_5foptions_3390',['make_short_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a0a5933555ce227565029122dfd6f15e9',1,'vg::subcommand::BaseOptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8ef56a59e757ab9cd808cf9112e1f64b',1,'vg::subcommand::OptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3f2f2249f4edee37552c77bce6c4a42c',1,'vg::subcommand::GroupedOptionGroup::make_short_options()']]],
+ ['make_5fshuffle_5fseed_3391',['make_shuffle_seed',['../namespacevg.html#aeca2b8e2d5730b1d5b94c1d3861757d7',1,'vg::make_shuffle_seed(const multipath_alignment_t &aln)'],['../namespacevg.html#acc312d814d6a06a4a5159c7943675bbe',1,'vg::make_shuffle_seed(const Alignment &aln)'],['../namespacevg.html#a2ec8fc79a1f84c6ef4a02c9d7c7a2850',1,'vg::make_shuffle_seed(const T *ptr)'],['../namespacevg.html#a04ebc20fd2965b1932e27958dd0c602c',1,'vg::make_shuffle_seed(const pair< T1, T2 > &p)']]],
+ ['make_5fsingle_5fstranded_3392',['make_single_stranded',['../namespacehandlegraph_1_1algorithms.html#a8cac1e5f4dc0c5e0e501ebb9fc58fca3',1,'handlegraph::algorithms']]],
+ ['make_5fsnarl_5fgraph_3393',['make_snarl_graph',['../classvg_1_1MCMCGenotyper.html#abbbf0c2625e4039f5a79b8b360515b41',1,'vg::MCMCGenotyper']]],
+ ['make_5fsnarl_5fmap_3394',['make_snarl_map',['../classvg_1_1MCMCGenotyper.html#a5e31dd64fad5dfb14d38be487fc14e59',1,'vg::MCMCGenotyper']]],
+ ['make_5fsubset_5fgraph_3395',['make_subset_graph',['../classvg_1_1Genotyper.html#ab11a87f5f21d3a7122ec85f6d853f336',1,'vg::Genotyper']]],
+ ['make_5fsupport_3396',['make_support',['../namespacevg.html#a1c0ae5cc687e77bb7cee28e975a005b3',1,'vg']]],
+ ['make_5ftemporary_5fdistance_5findex_3397',['make_temporary_distance_index',['../namespacevg.html#ae55954f00a00c8b34d20966f7d9fe72a',1,'vg']]],
+ ['make_5ftranslation_3398',['make_translation',['../namespacevg.html#a028aa842a68b6993a37a82c7645e0633',1,'vg']]],
+ ['make_5funlocalized_5finsertion_3399',['make_unlocalized_insertion',['../structvg_1_1WFAAlignment.html#aee475e8a07f1e06f61411f581813252e',1,'vg::WFAAlignment']]],
+ ['make_5fvariant_5fid_3400',['make_variant_id',['../namespacevg.html#aa74ef603900cf05ce35dbab813d21deb',1,'vg']]],
+ ['manage_3401',['manage',['../classvg_1_1SnarlManager.html#adb68da18eef20aa324c498444a9ed77f',1,'vg::SnarlManager']]],
+ ['manager_3402',['manager',['../classvg_1_1GenomeState.html#a6c9277391547084f77ff1dbfbe481310',1,'vg::GenomeState']]],
+ ['many_5flimit_3403',['MANY_LIMIT',['../classvg_1_1MinimizerMapper.html#aecc1f538f9a05a7f3fd29b5a425ec522',1,'vg::MinimizerMapper']]],
+ ['map_3404',['map',['../classvg_1_1MinimizerMapper.html#a4c955e7607a1c07d2ca2b22a065e8b91',1,'vg::MinimizerMapper::map(Alignment &aln, AlignmentEmitter &alignment_emitter)'],['../classvg_1_1MinimizerMapper.html#a182c026fcc4e3a8dea5de373d1a79bbb',1,'vg::MinimizerMapper::map(Alignment &aln)']]],
+ ['map_5fentry_5ftype_3405',['map_entry_type',['../structvg_1_1WFAPoint.html#ac125c09256ece943d40cf65152a9837a',1,'vg::WFAPoint']]],
+ ['map_5ffrom_5fchains_3406',['map_from_chains',['../classvg_1_1MinimizerMapper.html#af098e417ff3df9ff70d18cd4cd12555b',1,'vg::MinimizerMapper']]],
+ ['map_5ffrom_5fextensions_3407',['map_from_extensions',['../classvg_1_1MinimizerMapper.html#aaaaff0f62d2003bd8814c3fd90dd8226',1,'vg::MinimizerMapper']]],
+ ['map_5fkeys_5fto_5fset_3408',['map_keys_to_set',['../namespacevg.html#ace99283a6b34f0891dc0b49f0cd60eea',1,'vg']]],
+ ['map_5fmain_2ecpp_3409',['map_main.cpp',['../map__main_8cpp.html',1,'']]],
+ ['map_5forder_5fto_5foriginal_3410',['map_order_to_original',['../classvg_1_1WindowedVcfBuffer.html#ab62203851ffc243bd9183f9174739bbd',1,'vg::WindowedVcfBuffer']]],
+ ['map_5fover_3411',['map_over',['../namespacevg.html#a4833086451a8b97af4709aa6c7385177',1,'vg']]],
+ ['map_5fpaired_3412',['map_paired',['../classvg_1_1MinimizerMapper.html#a5c90ef4f961998cc7904e78225b36f50',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer)'],['../classvg_1_1MinimizerMapper.html#ab5f4c707ec44ba8f742c79bb0153c157',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2)']]],
+ ['map_5fstage_5fresults_5fto_5fprevious_5fstage_3413',['map_stage_results_to_previous_stage',['../classvg_1_1Funnel.html#aeca18258bb42790609df5f17d2394135',1,'vg::Funnel']]],
+ ['map_5fvariants_3414',['map_variants',['../haplotypes__main_8cpp.html#a1e43abd4f18210a8a4e131afbc8d182d',1,'haplotypes_main.cpp']]],
+ ['mapper_3415',['Mapper',['../classvg_1_1Mapper.html',1,'vg::Mapper'],['../classvg_1_1Mapper.html#a1d808071bd518202414fba56f5ec333e',1,'vg::Mapper::Mapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr)'],['../classvg_1_1Mapper.html#ae47e4e50adf1a5132656e9dd9a227628',1,'vg::Mapper::Mapper(void)']]],
+ ['mapper_2ecpp_3416',['mapper.cpp',['../mapper_8cpp.html',1,'']]],
+ ['mapper_2ehpp_3417',['mapper.hpp',['../mapper_8hpp.html',1,'']]],
+ ['mapper_5falignment_5fcutoff_3418',['mapper_alignment_cutoff',['../classvg_1_1VariantAdder.html#aa4281d59699cd880523cb47a146e5462',1,'vg::VariantAdder']]],
+ ['mapping_3419',['Mapping',['../structvg_1_1Mapping.html',1,'vg::Mapping'],['../classvg_1_1PhaseUnfolder.html#ae30c8d79f4461cae38e4ec2268a22022',1,'vg::PhaseUnfolder::mapping()'],['../structvg_1_1Path.html#a5d91e68bc4c6f7a5915cb4a42cc21caf',1,'vg::Path::mapping()'],['../classvg_1_1path__t.html#ab7f2f4df754fec9f8631c8388cbe4aad',1,'vg::path_t::mapping() const'],['../classvg_1_1path__t.html#a07af6243d1650ddef63ed19804da8071',1,'vg::path_t::mapping(size_t i) const']]],
+ ['mapping_5fagainst_5fpath_3420',['mapping_against_path',['../namespacevg.html#ad2e7730a993652e18d80ca77dac73713',1,'vg']]],
+ ['mapping_5fcigar_3421',['mapping_cigar',['../namespacevg.html#a5a0bb992cac134b2eed1e7b84eaecc2c',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char >> &cigar, char mismatch_operation)'],['../namespacevg.html#a642736d2f652e5ab522e1f26b874e097',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char > > &cigar, char mismatch_operation='M')']]],
+ ['mapping_5fedits_3422',['mapping_edits',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a9eb8dcec1e61b69092af38a89e82917a',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['mapping_5fends_5fin_5fdeletion_3423',['mapping_ends_in_deletion',['../namespacevg.html#afeef6a4c023183ead5725398b14d443c',1,'vg']]],
+ ['mapping_5fenters_5fside_3424',['mapping_enters_side',['../classvg_1_1Genotyper.html#aa2b4d94f59265c107895c48a26b107a6',1,'vg::Genotyper']]],
+ ['mapping_5fexits_5fside_3425',['mapping_exits_side',['../classvg_1_1Genotyper.html#a8b054a94fb2ceb4c65731188227b0cf8',1,'vg::Genotyper']]],
+ ['mapping_5ffrom_5flength_3426',['mapping_from_length',['../namespacevg.html#aa2aa77c6d4db628d13488c0bd82538ed',1,'vg::mapping_from_length(const Mapping &m)'],['../namespacevg.html#a151a868062bd12ac34b9aea68dc8d4f0',1,'vg::mapping_from_length(const path_mapping_t &mapping)']]],
+ ['mapping_5fis_5fmatch_3427',['mapping_is_match',['../namespacevg.html#a78ea8a2cf04759a3cfecbe4bf3e926c2',1,'vg']]],
+ ['mapping_5fis_5fsimple_5fmatch_3428',['mapping_is_simple_match',['../namespacevg.html#ae8ba5042b838f859a078cf014f1a0871',1,'vg']]],
+ ['mapping_5fis_5ftotal_5fdeletion_3429',['mapping_is_total_deletion',['../namespacevg.html#a6d10b5bc5677fdb0ae164f79848bb1bb',1,'vg']]],
+ ['mapping_5fis_5ftotal_5finsertion_3430',['mapping_is_total_insertion',['../namespacevg.html#a54cdb9b97e741de6ced9fefbc2bf48f3',1,'vg']]],
+ ['mapping_5fis_5ftotal_5fmatch_3431',['mapping_is_total_match',['../classvg_1_1VG.html#acd555e66c8fa99984c8cb24aef0ab6f9',1,'vg::VG']]],
+ ['mapping_5fitr_3432',['mapping_itr',['../classvg_1_1Paths.html#ae2bd0d7232fb84776841ac7c4bfea0d2',1,'vg::Paths']]],
+ ['mapping_5flikelihoods_3433',['mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a9c55acfb3c1116daeba543b42303ce7d',1,'vg::MultipathMapper']]],
+ ['mapping_5fpath_5fid_3434',['mapping_path_id',['../classvg_1_1Paths.html#abb58996e669d1b9271772a929f6bebe2',1,'vg::Paths']]],
+ ['mapping_5fpath_5fname_3435',['mapping_path_name',['../classvg_1_1Paths.html#ab520f6e02a5a9b2e11f10a6455be5bdd',1,'vg::Paths']]],
+ ['mapping_5fpositions_3436',['mapping_positions',['../structvg_1_1PathIndex.html#acc0b1da5ad0b4f428ceb623a4d3f806f',1,'vg::PathIndex']]],
+ ['mapping_5fquality_3437',['mapping_quality',['../structvg_1_1Alignment.html#a78851a70cc8a3e8f3e71409693130230',1,'vg::Alignment::mapping_quality()'],['../structvg_1_1MultipathAlignment.html#add653bff58eeb96872463fdc21b3dfd5',1,'vg::MultipathAlignment::mapping_quality()'],['../classvg_1_1multipath__alignment__t.html#a7a9fd028a082d666d19522d27ea5aa2c',1,'vg::multipath_alignment_t::mapping_quality()']]],
+ ['mapping_5fquality_5fmethod_3438',['mapping_quality_method',['../classvg_1_1BaseMapper.html#a0b1fe81d11d92332f613d8a29dcadb37',1,'vg::BaseMapper']]],
+ ['mapping_5fquality_5fscore_5fdiff_3439',['mapping_quality_score_diff',['../classvg_1_1GSSWAligner.html#a1c341fd9f6dd51131b714d580f5ccfea',1,'vg::GSSWAligner']]],
+ ['mapping_5fsequence_3440',['mapping_sequence',['../namespacevg.html#a2b648cd1a51584623d6618565d3ca9c6',1,'vg::mapping_sequence(const Mapping &mp, const string &node_seq)'],['../namespacevg.html#ac23702705b681eacdfd1b3bcbc5254b5',1,'vg::mapping_sequence(const Mapping &mp, const Node &n)']]],
+ ['mapping_5fsize_3441',['mapping_size',['../classvg_1_1path__t.html#aa3e09b61e5f2b803461ac3e20df6117c',1,'vg::path_t']]],
+ ['mapping_5fstarts_5fin_5fdeletion_3442',['mapping_starts_in_deletion',['../namespacevg.html#aa377b3e776e312c717aedec842216f48',1,'vg']]],
+ ['mapping_5fstring_3443',['mapping_string',['../namespacevg.html#ad993b1f289a57f3413b85840984b459c',1,'vg']]],
+ ['mapping_5ft_3444',['mapping_t',['../classvg_1_1mapping__t.html',1,'vg::mapping_t'],['../classvg_1_1mapping__t.html#aa47429bfca4c4120a2e5c116d6d54450',1,'vg::mapping_t::mapping_t(void)'],['../classvg_1_1mapping__t.html#a6c9be43df27053b2bc5599faad299513',1,'vg::mapping_t::mapping_t(const Mapping &m)']]],
+ ['mapping_5fto_5fgbwt_3445',['mapping_to_gbwt',['../namespacevg.html#ace1a7180fda8bb98abba24fb19183e9d',1,'vg']]],
+ ['mapping_5fto_5fhandle_3446',['mapping_to_handle',['../namespacevg.html#acdaa29c218d5d55e76fe4ab168f7a14b',1,'vg']]],
+ ['mapping_5fto_5flength_3447',['mapping_to_length',['../namespacevg.html#a9ef1ccef545dfc30f9123eba61267b4a',1,'vg::mapping_to_length(const Mapping &m)'],['../namespacevg.html#a3f709a91987a7d669b3974fa00aa8ecd',1,'vg::mapping_to_length(const path_mapping_t &mapping)']]],
+ ['mapping_5ftype_3448',['mapping_type',['../structvg_1_1RebuildJob.html#afdbb259fb3fc369a7824f6420b2043c0',1,'vg::RebuildJob']]],
+ ['mappinghash_3449',['MappingHash',['../structvg_1_1MappingHash.html',1,'vg']]],
+ ['mappingqualitymethod_3450',['MappingQualityMethod',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39',1,'vg']]],
+ ['mappingrun_3451',['MappingRun',['../structMappingRun.html',1,'']]],
+ ['mappings_3452',['mappings',['../structvg_1_1RebuildJob.html#a82f413afdbd0c9f3c697ab84774542bf',1,'vg::RebuildJob']]],
+ ['mappings_5fby_5frank_3453',['mappings_by_rank',['../classvg_1_1Paths.html#a27d349c3f4795f1389d3824e1c1e3e8f',1,'vg::Paths']]],
+ ['mappings_5fequivalent_3454',['mappings_equivalent',['../namespacevg.html#af26a23818c9426d77ef25b07bbaaf605',1,'vg']]],
+ ['mapq_3455',['mapq',['../structgafkluge_1_1GafRecord.html#a09ffb165e71177223d73e2fea5ed1399',1,'gafkluge::GafRecord']]],
+ ['mapq_5fscaling_5ffactor_3456',['mapq_scaling_factor',['../classvg_1_1MultipathMapper.html#aadbb94f74824864d7bed5c63cb85687e',1,'vg::MultipathMapper']]],
+ ['mapq_5fscore_5fscale_3457',['mapq_score_scale',['../classvg_1_1MinimizerMapper.html#a0e13799b9b7e3f64d06d10bde825924c',1,'vg::MinimizerMapper']]],
+ ['mapq_5fscore_5fwindow_3458',['mapq_score_window',['../classvg_1_1MinimizerMapper.html#ace4a8ce19de89dd8f42f807b71c66dd3',1,'vg::MinimizerMapper']]],
+ ['maps_5fto_5fnode_3459',['maps_to_node',['../namespacevg.html#a242b97c26d74e9fc05ad16c31b21dcca',1,'vg']]],
+ ['margin_5fafter_3460',['margin_after',['../classvg_1_1algorithms_1_1Anchor.html#ade738d4df1585fa0dc6fc935da262ee0',1,'vg::algorithms::Anchor']]],
+ ['margin_5fbefore_3461',['margin_before',['../classvg_1_1algorithms_1_1Anchor.html#a545c9c26a24e8d37459944c5632c79e2',1,'vg::algorithms::Anchor']]],
+ ['mark_5fdfs_3462',['mark_dfs',['../classvg_1_1FlowSort.html#a498b6d9f0a37f2588e4ad08b6c35a0ff',1,'vg::FlowSort']]],
+ ['mark_5fsmallvariant_5falignments_3463',['mark_smallVariant_alignments',['../classvg_1_1Filter.html#a2ab59f83f673047f5c2106456c4426c3',1,'vg::Filter']]],
+ ['mark_5fsv_5falignments_3464',['mark_sv_alignments',['../classvg_1_1Filter.html#a267d55220fcf5239f12dcc852586bc71',1,'vg::Filter']]],
+ ['markovdistribution_3465',['MarkovDistribution',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator::MarkovDistribution< From, To >'],['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#aef78cda42fffdef670a3ceb7e4877ee9',1,'vg::NGSSimulator::MarkovDistribution::MarkovDistribution()']]],
+ ['markovdistribution_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_20_3e_20_3e_3466',['MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > >',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator']]],
+ ['mask_3467',['mask',['../classvg_1_1ReadMasker.html#ad6d292712ead5b6f89940f020fd8fcc2',1,'vg::ReadMasker::mask()'],['../classvg_1_1GaplessExtender.html#a9824f8144fd4f3515c7333fbeb6e2afd',1,'vg::GaplessExtender::mask()'],['../classvg_1_1WFAExtender.html#a1af2acef8bd391f46798288e9322019b',1,'vg::WFAExtender::mask()']]],
+ ['mask_5fmain_2ecpp_3468',['mask_main.cpp',['../mask__main_8cpp.html',1,'']]],
+ ['mask_5fsequences_3469',['mask_sequences',['../classvg_1_1Masker.html#a18d454c702ded8fdb3436f90135631ed',1,'vg::Masker']]],
+ ['masker_3470',['Masker',['../classvg_1_1Masker.html',1,'vg::Masker'],['../classvg_1_1Masker.html#a0c3817b4839ee4b2dd6d38d193cd61e8',1,'vg::Masker::Masker(gbwtgraph::GBWTGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#ab302923c0d437d4e997e1c11d35125ac',1,'vg::Masker::Masker(MutablePathDeletableHandleGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#a5398d6fdb929425966c9b71c0c9dc2fd',1,'vg::Masker::Masker()=default'],['../classvg_1_1Masker.html#aae42512f78c75af240e164d16a3445e1',1,'vg::Masker::Masker(Masker &&other)=default']]],
+ ['masker_2ecpp_3471',['masker.cpp',['../masker_8cpp.html',1,'']]],
+ ['masker_2ehpp_3472',['masker.hpp',['../masker_8hpp.html',1,'']]],
+ ['match_3473',['match',['../classvg_1_1GSSWAligner.html#a7323efd4ef078ab5866b8c2b9fea87a8',1,'vg::GSSWAligner::match()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a4fdc2b0adb79d04c4e928a61e891aa84',1,'vg::BandedGlobalAligner::BAMatrix::match()'],['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebae6fe3d73bbbc5c70e386589f9732e9af',1,'vg::WFAAlignment::match()'],['../classvg_1_1SSWAligner.html#a8ec16a3583a2d8347ee9eaf1853b8cc8',1,'vg::SSWAligner::match()'],['../structScoringOptions.html#a3a450e63987f79011a51819efd5420a4',1,'ScoringOptions::match()'],['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faac03946390169c005fafc9a38b114e6a',1,'vg::BandedGlobalAligner::Match()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): xdrop_aligner.cpp']]],
+ ['match_5fbackward_3474',['match_backward',['../namespacevg.html#a3495eb8e73ceeece9957079280edc921',1,'vg']]],
+ ['match_5fcount_3475',['match_count',['../classvg_1_1MaximalExactMatch.html#ab7a9c66468635a1498efdeb394c1fad6',1,'vg::MaximalExactMatch']]],
+ ['match_5ffanouts_5ft_3476',['match_fanouts_t',['../classvg_1_1MEMClusterer.html#a3127930f2b575bed2937c21382924480',1,'vg::MEMClusterer::match_fanouts_t()'],['../classvg_1_1MultipathMapper.html#a165e5c0531ff4337ce6542da263d3fbd',1,'vg::MultipathMapper::match_fanouts_t()']]],
+ ['match_5fforward_3477',['match_forward',['../structvg_1_1WFANode.html#a368dbe3b756f08e21718cbfac97978fd',1,'vg::WFANode::match_forward()'],['../namespacevg.html#abcb300141666ec86856482f6a59cec4c',1,'vg::match_forward()']]],
+ ['match_5finitial_3478',['match_initial',['../namespacevg.html#a4b1defb1ef0b163389ff84745294d1d0',1,'vg']]],
+ ['match_5fpredecessor_3479',['match_predecessor',['../classvg_1_1WFATree.html#a4242e9739a9f789386354f4582dea547',1,'vg::WFATree']]],
+ ['matches_3480',['MATCHES',['../structvg_1_1WFANode.html#a0188bfd686597181c42f2384c21e9e19',1,'vg::WFANode::MATCHES()'],['../structvg_1_1SeqComplexity.html#a03e3682e2a96bbf0595d38694d3818ad',1,'vg::SeqComplexity::matches()'],['../structgafkluge_1_1GafRecord.html#a0cac64f74ee1a099fafc4148d08a630c',1,'gafkluge::GafRecord::matches()'],['../classvg_1_1DinucleotideMachine.html#a2250f97747bf0e9390ed7326d357c557',1,'vg::DinucleotideMachine::matches(uint32_t state, const char *dinucleotide) const'],['../classvg_1_1DinucleotideMachine.html#aa30db9eff5e43b78cd23094f3d7edce5',1,'vg::DinucleotideMachine::matches(uint32_t state, const string &dinucleotide) const']]],
+ ['matches_5fannotation_3481',['matches_annotation',['../classvg_1_1ReadFilter.html#a95d1165f7c3901772a70ba863d1fc983',1,'vg::ReadFilter']]],
+ ['matches_5fname_3482',['matches_name',['../classvg_1_1ReadFilter.html#ab72c4fd96eedcb4bcd6aa565e97dfe4d',1,'vg::ReadFilter']]],
+ ['matching_3483',['matching',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a6bb2874bc8c41f0606f8f142a465e469',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['matchpos_3484',['MatchPos',['../structvg_1_1MatchPos.html',1,'vg::MatchPos'],['../structvg_1_1MatchPos.html#ab44cfadd41dfc2ec79266e4fe204458f',1,'vg::MatchPos::MatchPos()'],['../structvg_1_1MatchPos.html#a167922796c04609cdf6a129c7135f869',1,'vg::MatchPos::MatchPos(uint32_t seq_offset, uint32_t node_offset, const PathList &path)']]],
+ ['mate_5fmapped_5fto_5fdisjoint_5fsubgraph_3485',['mate_mapped_to_disjoint_subgraph',['../structvg_1_1Alignment.html#a95ed4d8c7a57e34a96871b74ff851821',1,'vg::Alignment']]],
+ ['mate_5fon_5freverse_5fstrand_3486',['mate_on_reverse_strand',['../structvg_1_1Alignment.html#aef312ed490cb8adf8b89eb36b46ee7d6',1,'vg::Alignment']]],
+ ['mate_5frescues_3487',['mate_rescues',['../classvg_1_1Mapper.html#a56cec2a0bdc2a2398bd494cf0acb80a2',1,'vg::Mapper']]],
+ ['mate_5funmapped_3488',['mate_unmapped',['../structvg_1_1Alignment.html#a061bf4ec65ccf7ff88e73e9e4ff268b7',1,'vg::Alignment']]],
+ ['mates_3489',['mates',['../structvg_1_1BREAKPOINT.html#a7469d5658b49020a71529d1704b962f9',1,'vg::BREAKPOINT']]],
+ ['matrix_5finvert_3490',['matrix_invert',['../namespacevg.html#a7effc13e3f877e676d65d9164a44b4a6',1,'vg']]],
+ ['matrix_5fmultiply_3491',['matrix_multiply',['../namespacevg.html#a02d66ca193142fb4825a62b300d60697',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< vector< double >> &B)'],['../namespacevg.html#a9a1927488f1b7b82758828d5a53ca845',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< double > &b)']]],
+ ['matrix_5fstate_3492',['matrix_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a5b8b44e10a1bc42b694728459e4b4271',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['matrix_5ft_3493',['matrix_t',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2f',1,'vg::BandedGlobalAligner']]],
+ ['max_3494',['max',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a45c40bccc3fd5b000987f633c8ec8df4',1,'vg::WFAExtender::ErrorModel::Event::max()'],['../classvg_1_1WideningPRNG.html#a3083db737b68cc80dacad05c9e1ae1ee',1,'vg::WideningPRNG::max()'],['../namespacestd.html#a032e2e35689ce96dfb488db853f83334',1,'std::max()']]],
+ ['max_5falignment_5fgap_3495',['max_alignment_gap',['../classvg_1_1MultipathMapper.html#aaf8af884f81cfd5ed869f26a8b8403d4',1,'vg::MultipathMapper']]],
+ ['max_5falignments_3496',['max_alignments',['../classvg_1_1MinimizerMapper.html#a6062b78a7f795cb2a585eb6695bde675',1,'vg::MinimizerMapper']]],
+ ['max_5falt_5fmappings_3497',['max_alt_mappings',['../classvg_1_1MultipathMapper.html#a87223306ba0d983104e48d4ded4e685d',1,'vg::MultipathMapper']]],
+ ['max_5fanchors_3498',['max_anchors',['../classvg_1_1Surjector.html#a5a735901a421d305e6cbf13a016fdc9d',1,'vg::Surjector']]],
+ ['max_5fattempts_3499',['max_attempts',['../classvg_1_1Mapper.html#ac9973fcf3d75d4396f6b6bdec58156a6',1,'vg::Mapper']]],
+ ['max_5fband_5fcells_3500',['max_band_cells',['../classvg_1_1Surjector.html#a0e22a6f6da976c0b505caa6c1ad10ed8',1,'vg::Surjector']]],
+ ['max_5fband_5fjump_3501',['max_band_jump',['../classvg_1_1Mapper.html#a916fd22fce2ebf7953863590c45f5150',1,'vg::Mapper']]],
+ ['max_5fbranch_5ftrim_5flength_3502',['max_branch_trim_length',['../classvg_1_1MultipathMapper.html#a9e260c61a4b39d27286957c4f012a26a',1,'vg::MultipathMapper']]],
+ ['max_5fbubble_5fpaths_3503',['max_bubble_paths',['../classvg_1_1LegacyCaller.html#a807ba6e24d16bac14c24fdc973cb837b',1,'vg::LegacyCaller::max_bubble_paths()'],['../classvg_1_1RepresentativeTraversalFinder.html#ad2de8e0f74e29d2338d0e9f99a764e23',1,'vg::RepresentativeTraversalFinder::max_bubble_paths()']]],
+ ['max_5fbuf_5fsize_3504',['max_buf_size',['../classvg_1_1StreamSorter.html#a192491eeef2fa2c99522f2ad23f12035',1,'vg::StreamSorter']]],
+ ['max_5fchain_5fconnection_3505',['max_chain_connection',['../classvg_1_1MinimizerMapper.html#a4d54618686eb23ac6a4a2c3579f3fec9',1,'vg::MinimizerMapper']]],
+ ['max_5fchaining_5fproblems_3506',['max_chaining_problems',['../classvg_1_1MinimizerMapper.html#a034098134b882ab3e4c8dc0542763f97',1,'vg::MinimizerMapper']]],
+ ['max_5fchains_5fper_5ftree_3507',['max_chains_per_tree',['../classvg_1_1MinimizerMapper.html#ada8578ed33c349fa8f9e5ff7562ac71f',1,'vg::MinimizerMapper']]],
+ ['max_5fcluster_5fmapping_5fquality_3508',['max_cluster_mapping_quality',['../classvg_1_1Mapper.html#a92ea8476aae3d65f0b46f6c7353c21be',1,'vg::Mapper']]],
+ ['max_5fcontext_5fradius_3509',['max_context_radius',['../classvg_1_1VariantAdder.html#a943bba24f9a1a7197744e74ee5465e5d',1,'vg::VariantAdder']]],
+ ['max_5fdagify_5fduplications_3510',['max_dagify_duplications',['../classvg_1_1MultipathMapper.html#a10c136d72e6f32ff28cd608efc1f31db',1,'vg::MultipathMapper']]],
+ ['max_5fdegree_3511',['max_degree',['../structPruningParameters.html#a58d4dca5e0623280f669e386a5eadd2f',1,'PruningParameters']]],
+ ['max_5fdeletion_5fscan_5fnodes_3512',['max_deletion_scan_nodes',['../classvg_1_1VCFTraversalFinder.html#a3e61ffdb1cf6733311b444df38928137',1,'vg::VCFTraversalFinder']]],
+ ['max_5fdepth_3513',['max_depth',['../classvg_1_1RepresentativeTraversalFinder.html#a79339337af609bc33f77cf4696962492',1,'vg::RepresentativeTraversalFinder::max_depth()'],['../classvg_1_1ZipCode.html#aa9b8e3ee702697e3692a83e2307d9084',1,'vg::ZipCode::max_depth()']]],
+ ['max_5fdiagonal_3514',['max_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#abde71e96e8aac83b5233fa782b514290',1,'vg::WFATree::ScoreProperties']]],
+ ['max_5fdirect_5fto_5fchain_3515',['max_direct_to_chain',['../classvg_1_1MinimizerMapper.html#adfe5996aca0f60eace262a8c06f76f30',1,'vg::MinimizerMapper']]],
+ ['max_5fdisplayed_5fsuggestions_5fper_5fcategory_3516',['MAX_DISPLAYED_SUGGESTIONS_PER_CATEGORY',['../classvg_1_1DiagramExplainer.html#abb72da5ad3b5613b80c4a39c7e4b8f18',1,'vg::DiagramExplainer']]],
+ ['max_5fdistance_3517',['max_distance',['../classvg_1_1WFATree.html#a761ae97d39a69d470cae27ef7cfb28a9',1,'vg::WFATree::max_distance()'],['../classvg_1_1IncrementalSubgraph.html#a06d0598eae084de70fa40ed859ce9704',1,'vg::IncrementalSubgraph::max_distance()']]],
+ ['max_5fdistance_5ffrom_5fstart_3518',['max_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#a0d573babd81fa2d0c209c75afec6c91d',1,'vg::IncrementalSubgraph']]],
+ ['max_5fdozeu_5fcells_3519',['max_dozeu_cells',['../classvg_1_1MinimizerMapper.html#aa462df061307b0b35996a6ecd33091f7',1,'vg::MinimizerMapper']]],
+ ['max_5fdp_5fcells_3520',['max_dp_cells',['../classvg_1_1MinimizerMapper.html#af673f62cfdb402e93acaf2eb81680772',1,'vg::MinimizerMapper']]],
+ ['max_5fexpected_5fdist_5fapprox_5ferror_3521',['max_expected_dist_approx_error',['../classvg_1_1OrientedDistanceClusterer.html#a74174c834516a6b4116ff6b9972ae10c',1,'vg::OrientedDistanceClusterer::max_expected_dist_approx_error()'],['../classvg_1_1MultipathMapper.html#a23d02e5f180a337a4b9eff178fc0b65d',1,'vg::MultipathMapper::max_expected_dist_approx_error()']]],
+ ['max_5fexponential_5fcdf_3522',['max_exponential_cdf',['../namespacevg.html#a82dc203eaecb442a26d8f1a3db773dda',1,'vg']]],
+ ['max_5fexponential_5flog_5flikelihood_3523',['max_exponential_log_likelihood',['../namespacevg.html#a617472d242ff7aad1126a6b70e70a7a8',1,'vg']]],
+ ['max_5fexponential_5frate_5fintercept_3524',['max_exponential_rate_intercept',['../classvg_1_1MultipathMapper.html#a3b9f8d9eb806a7dd7e05a0b1c4851bc8',1,'vg::MultipathMapper']]],
+ ['max_5fexponential_5frate_5fslope_3525',['max_exponential_rate_slope',['../classvg_1_1MultipathMapper.html#a0c2252c568582797db9b65756694eaff',1,'vg::MultipathMapper']]],
+ ['max_5fexponential_5fshape_5fintercept_3526',['max_exponential_shape_intercept',['../classvg_1_1MultipathMapper.html#a2e7f7551674fa412abd1333c0baf6672',1,'vg::MultipathMapper']]],
+ ['max_5fexponential_5fshape_5fslope_3527',['max_exponential_shape_slope',['../classvg_1_1MultipathMapper.html#a8ea8f5c8ad1906ccf0b878a6821a16e2',1,'vg::MultipathMapper']]],
+ ['max_5fextension_5fmismatches_3528',['max_extension_mismatches',['../classvg_1_1MinimizerMapper.html#a30fd35c63e316b4a1fcdeca3752ea667',1,'vg::MinimizerMapper']]],
+ ['max_5fextensions_3529',['max_extensions',['../classvg_1_1MinimizerMapper.html#a5d03747a37700e9a3f73c308709f70d1',1,'vg::MinimizerMapper']]],
+ ['max_5ffan_5fin_3530',['max_fan_in',['../classvg_1_1StreamSorter.html#a673ce446e1ba8b9917f9475b9003364d',1,'vg::StreamSorter']]],
+ ['max_5ffanout_5fbase_5fquality_3531',['max_fanout_base_quality',['../classvg_1_1MultipathMapper.html#a63f9b0403dceed8c8055ce5c423dd8fe',1,'vg::MultipathMapper']]],
+ ['max_5ffans_5fout_3532',['max_fans_out',['../classvg_1_1MultipathMapper.html#a46f2835eebe0c9ab495e697c975534b6',1,'vg::MultipathMapper']]],
+ ['max_5fflow_5fsort_3533',['max_flow_sort',['../classvg_1_1FlowSort.html#a8a5d0ba61635331b2107ad3df4972ff1',1,'vg::FlowSort']]],
+ ['max_5ffragment_5flength_3534',['max_fragment_length',['../classvg_1_1MinimizerMapper.html#a4575d140e45d04d3d36e6a99bf7b0241',1,'vg::MinimizerMapper']]],
+ ['max_5ffragments_3535',['max_fragments',['../classvg_1_1MinimizerMapper.html#a50848190e760fb1f3c45fd785f57c8a3',1,'vg::MinimizerMapper']]],
+ ['max_5fgap_3536',['max_gap',['../classvg_1_1MEMClusterer.html#a9b8459888ec7b51e739c3be04825b4fd',1,'vg::MEMClusterer']]],
+ ['max_5fgroup_5fsize_3537',['max_group_size',['../classvg_1_1io_1_1MessageEmitter.html#a4bcef07ec2af1cb44f4cd3abfe58f29c',1,'vg::io::MessageEmitter']]],
+ ['max_5fhandle_3538',['max_handle',['../classvg_1_1DozeuPinningOverlay.html#a63162330a1caec7a81abf6b5f747da32',1,'vg::DozeuPinningOverlay']]],
+ ['max_5fhandle_5fmemo_5fsize_3539',['max_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a478ef9dbdebaccadc78679868baa350d',1,'vg::MemoizingGraph']]],
+ ['max_5fhet_5fbias_3540',['max_het_bias',['../classvg_1_1Genotyper.html#a96285d96b960d50199ad3167c20ddf91',1,'vg::Genotyper::max_het_bias()'],['../classvg_1_1RatioSupportSnarlCaller.html#a78f0c7800c9c27021c66d68cbd0335b7',1,'vg::RatioSupportSnarlCaller::max_het_bias()']]],
+ ['max_5fid_3541',['max_id',['../structvg_1_1ConstructedChunk.html#aca49ac5cc43f6390443ab02496fdfd74',1,'vg::ConstructedChunk::max_id()'],['../classvg_1_1Constructor.html#a8466741ece82babe9e892a50bd06a1d9',1,'vg::Constructor::max_id()'],['../classvg_1_1DagifiedGraph.html#a154919be0eb8719eb2fa0181584a9c66',1,'vg::DagifiedGraph::max_id()'],['../classvg_1_1SubHandleGraph.html#ad0090894570f0c53d4c3011472a01d37',1,'vg::SubHandleGraph::max_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a90afa5abb895d5bb6800cd99759de14a',1,'vg::algorithms::GFAIDMapInfo::max_id()'],['../classxg_1_1XG.html#a2cf5a51e7056900fd3872792ef5fa2a5',1,'xg::XG::max_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade12e1983845ebfbf47782b8867c708c',1,'handlegraph::algorithms::SubHandleGraph::max_id()']]],
+ ['max_5fin_3542',['max_in',['../classvg_1_1algorithms_1_1TracedScore.html#a8d01a37cedeb1e7e7667f05bdb8f67e9',1,'vg::algorithms::TracedScore']]],
+ ['max_5findel_5fbases_3543',['max_indel_bases',['../classvg_1_1MinimizerMapper.html#a05b1280ff66b9ad01015c490f35fc005',1,'vg::MinimizerMapper']]],
+ ['max_5findel_5fbases_5fper_5fbase_3544',['max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a82da9f52e8af8e9dde669c903d441adc',1,'vg::MinimizerMapper']]],
+ ['max_5findel_5fhet_5fbias_3545',['max_indel_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a9298ec62feb5ab8f593fdf2c6cd2b620',1,'vg::RatioSupportSnarlCaller']]],
+ ['max_5finput_5fversion_3546',['MAX_INPUT_VERSION',['../classvg_1_1StreamIndexBase.html#aa497c1ad37621af86f5f40d45e0f30b2',1,'vg::StreamIndexBase']]],
+ ['max_5fintron_5flength_3547',['max_intron_length',['../classvg_1_1MultipathMapper.html#a51be0d0325abe9a3afa023477d9c2ab0',1,'vg::MultipathMapper']]],
+ ['max_5fiterations_3548',['max_iterations',['../classvg_1_1SmallSnarlSimplifier.html#a212bd3bc07ab19cb42edef936ee62f7a',1,'vg::SmallSnarlSimplifier::max_iterations()'],['../minimizer__main_8cpp.html#a932fcab549241f3cf9efead93803fabc',1,'MAX_ITERATIONS(): minimizer_main.cpp']]],
+ ['max_5fkmers_5fper_5fblock_3549',['max_kmers_per_block',['../classvg_1_1ParallelKFFReader.html#a0179377c78c5e599f903b70c954ffd12',1,'vg::ParallelKFFReader']]],
+ ['max_5flength_3550',['max_length',['../classvg_1_1ReadFilter.html#a2afae0acb031354f67f95f20dda1c4b8',1,'vg::ReadFilter::max_length()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9abd4efb2ac344eea5ff58477c7014a769',1,'vg::Counts::max_length()']]],
+ ['max_5flink_5flength_3551',['max_link_length',['../classvg_1_1JoinedSpliceGraph.html#a25612fe4db491aa5cbcc06f5816bd5bd',1,'vg::JoinedSpliceGraph']]],
+ ['max_5flocal_5fextensions_3552',['max_local_extensions',['../classvg_1_1MinimizerMapper.html#a4e6142c1ccdde28230769e5a8b629d9f',1,'vg::MinimizerMapper']]],
+ ['max_5flookback_5fbases_3553',['max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ae94869146878dba80c980d4e35830abe',1,'vg::MinimizerMapper']]],
+ ['max_5flookback_5fbases_5fper_5fbase_3554',['max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a48ec2ca2886d6f069546d6a424becb61',1,'vg::MinimizerMapper']]],
+ ['max_5flow_5fcomplexity_5fanchor_5fprune_3555',['max_low_complexity_anchor_prune',['../classvg_1_1Surjector.html#a0f304005022b214c309ff60a1f186b1f',1,'vg::Surjector']]],
+ ['max_5flow_5fcomplexity_5fanchor_5ftrim_3556',['max_low_complexity_anchor_trim',['../classvg_1_1Surjector.html#a9c0cf333d85aef40eda8354075dfa01e',1,'vg::Surjector']]],
+ ['max_5fma_5fbias_3557',['max_ma_bias',['../classvg_1_1RatioSupportSnarlCaller.html#ac6d48f0372786d80db440fa67523af9e',1,'vg::RatioSupportSnarlCaller']]],
+ ['max_5fmapping_5fp_5fvalue_3558',['max_mapping_p_value',['../classvg_1_1MultipathMapper.html#aa7656b2372ae8450e48a9db512ce309d',1,'vg::MultipathMapper']]],
+ ['max_5fmapping_5fquality_3559',['max_mapping_quality',['../classvg_1_1BaseMapper.html#a467884235c316072a1ed7136faa14be3',1,'vg::BaseMapper']]],
+ ['max_5fmemory_5fproportion_3560',['max_memory_proportion',['../structvg_1_1IndexingParameters.html#a28aa7110447f9ba3a74e1e3326959751',1,'vg::IndexingParameters']]],
+ ['max_5fmessage_5fsize_3561',['MAX_MESSAGE_SIZE',['../classvg_1_1io_1_1MessageEmitter.html#a67ece9e5b7c411ccb40169b650e1f5ae',1,'vg::io::MessageEmitter::MAX_MESSAGE_SIZE()'],['../classvg_1_1io_1_1MessageIterator.html#a5b2b881e4032fb2ecfa8da35ad13e602',1,'vg::io::MessageIterator::MAX_MESSAGE_SIZE()']]],
+ ['max_5fmiddle_5fdp_5flength_3562',['max_middle_dp_length',['../classvg_1_1MinimizerMapper.html#aa8bdbd3ae354863aaa50bcd0fdfb340f',1,'vg::MinimizerMapper']]],
+ ['max_5fmiddle_5fgap_3563',['max_middle_gap',['../classvg_1_1MinimizerMapper.html#a9e0bcb7de51be992126d051cf343a9c5',1,'vg::MinimizerMapper']]],
+ ['max_5fmin_5fchain_5fscore_3564',['max_min_chain_score',['../classvg_1_1MinimizerMapper.html#a5dc73dddd111a8a64b5285a2e75e3ba5',1,'vg::MinimizerMapper']]],
+ ['max_5fmismatches_3565',['MAX_MISMATCHES',['../classvg_1_1GaplessExtender.html#aaa77a2fc74630664d12527818826e28b',1,'vg::GaplessExtender']]],
+ ['max_5fmissing_5fvariant_5fwarnings_3566',['max_missing_variant_warnings',['../classvg_1_1HaplotypeIndexer.html#a512203218e3b78afa0fc5c0e594e6516',1,'vg::HaplotypeIndexer']]],
+ ['max_5fmotif_5fpairs_3567',['max_motif_pairs',['../classvg_1_1MultipathMapper.html#a7427a85cc5f4ff850524ecf929ca72c8',1,'vg::MultipathMapper']]],
+ ['max_5fmulti_5falns_3568',['max_multi_alns',['../classvg_1_1BandedGlobalAligner.html#a7191ef47a3e2a5232e5ba74283c646b6',1,'vg::BandedGlobalAligner::max_multi_alns()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9114c48d4516fb6115fe47e910624377',1,'vg::BandedGlobalAligner::AltTracebackStack::max_multi_alns()']]],
+ ['max_5fmultimaps_3569',['max_multimaps',['../classvg_1_1Mapper.html#a462268836d2c5f5f4acde6ca9060e593',1,'vg::Mapper::max_multimaps()'],['../classvg_1_1MinimizerMapper.html#aede601962425752ec75ea1d890505357',1,'vg::MinimizerMapper::max_multimaps()']]],
+ ['max_5fnode_3570',['max_node',['../classvg_1_1SubgraphOverlay.html#a6eb5155328921c3a0ec46e62c7edfdca',1,'vg::SubgraphOverlay']]],
+ ['max_5fnode_5fid_3571',['max_node_id',['../classvg_1_1DagifiedGraph.html#a511c81e2e65250eeeac52936bfe3ae0e',1,'vg::DagifiedGraph::max_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#a4962a5c38f363db65a1b0083a05bcfcc',1,'vg::DozeuPinningOverlay::max_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ab7384a54f90e4351cb7e6d0a99f3290d',1,'vg::ExtraNodeGraph::max_node_id()'],['../classvg_1_1SnarlGraph.html#a69ce6bde5f346eb5926b6db093122be1',1,'vg::SnarlGraph::max_node_id()'],['../classvg_1_1IdentityOverlay.html#a5aba68df4094870dd2324613d2db1d63',1,'vg::IdentityOverlay::max_node_id()'],['../classvg_1_1IncrementalSubgraph.html#aa92bb84a3ea785a09c814932ae56a5a8',1,'vg::IncrementalSubgraph::max_node_id()'],['../classvg_1_1IndexedVG.html#ab7e6f41fefb23702e708d23a0dcec9d0',1,'vg::IndexedVG::max_node_id()'],['../classvg_1_1MemoizingGraph.html#a7a9052b566d4062493432265aa1c9e70',1,'vg::MemoizingGraph::max_node_id()'],['../classvg_1_1NullMaskingGraph.html#a768717b98ae295bb52a68028db0145ec',1,'vg::NullMaskingGraph::max_node_id()'],['../classvg_1_1PathSubgraph.html#a7d5368e9b40989fa3e1ecd020468a1da',1,'vg::PathSubgraph::max_node_id()'],['../classvg_1_1ReverseGraph.html#ac276a2df66a605842304eec2d9ef340c',1,'vg::ReverseGraph::max_node_id()'],['../classvg_1_1NetGraph.html#abb16fbc7ae88f61e3ce9076d2e2a3817',1,'vg::NetGraph::max_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ab9be77971160f356b0ba0721ed17983e',1,'vg::SourceSinkOverlay::max_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#abbf5f65b4f075efb985c0978cead8513',1,'vg::JoinedSpliceGraph::max_node_id()'],['../classvg_1_1StrandSplitGraph.html#a83194bc2415f2f0fa2e23ce970d2f932',1,'vg::StrandSplitGraph::max_node_id()'],['../classvg_1_1SubHandleGraph.html#afd0e51c2e81f5b51f4e21167e3e691f3',1,'vg::SubHandleGraph::max_node_id()'],['../classvg_1_1SubgraphOverlay.html#ab2858c7e55226d9754eb388654da88ab',1,'vg::SubgraphOverlay::max_node_id()'],['../classvg_1_1SubpathOverlay.html#aa5b627c97bac0914a4b77e289a1f888b',1,'vg::SubpathOverlay::max_node_id()'],['../classvg_1_1TreeSubgraph.html#ae8f3ebca4f5d097fe9b5081cdc1f7a96',1,'vg::TreeSubgraph::max_node_id()'],['../classvg_1_1VG.html#a5a03ad90e03794944c5e0d4d61780652',1,'vg::VG::max_node_id()'],['../classvg_1_1VGset.html#a31691223aa51fca983dd145b5896cad7',1,'vg::VGset::max_node_id()'],['../classxg_1_1XG.html#ac991d9094b1959ff503d9a94d0a9ed4c',1,'xg::XG::max_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a599303e41c6f9913424933778893f1c6',1,'handlegraph::algorithms::SubHandleGraph::max_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a5a2e2b1ea6a29b3f4b34a6abcb6dbc50',1,'handlegraph::HandleGraph::max_node_id()']]],
+ ['max_5fnode_5frank_3572',['max_node_rank',['../classxg_1_1XG.html#a1bc4d756800a8e55ddb33abf49865956',1,'xg::XG']]],
+ ['max_5fnode_5fsize_3573',['max_node_size',['../classvg_1_1Constructor.html#a6ca9a0b7785c1c9c6e859cc75ea2a2f4',1,'vg::Constructor::max_node_size()'],['../structvg_1_1IndexingParameters.html#a6b392a212907d34c6f586cb7cefeac1f',1,'vg::IndexingParameters::max_node_size()'],['../classvg_1_1VariantAdder.html#a3e1dae34969d5779d09819de627a6bd5',1,'vg::VariantAdder::max_node_size()']]],
+ ['max_5fnum_5fnodes_3574',['max_num_nodes',['../classvg_1_1IncrementalSubgraph.html#a37038271292f8c25f63b9d3e8400d13e',1,'vg::IncrementalSubgraph']]],
+ ['max_5foverhang_3575',['max_overhang',['../classvg_1_1ReadFilter.html#a54c30818834f623c78a2cb0a0e9b4a91',1,'vg::ReadFilter::max_overhang()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a500747869171f1e18a4e7c56625ed3ef',1,'vg::Counts::max_overhang()']]],
+ ['max_5fp_5fvalue_5fmemo_5fsize_3576',['max_p_value_memo_size',['../classvg_1_1MultipathMapper.html#ada39acac8f403bf92632024be4e448e1',1,'vg::MultipathMapper']]],
+ ['max_5fparsed_5fvariant_5fsize_3577',['max_parsed_variant_size',['../classvg_1_1Constructor.html#a2725e8e6876deb0ca0ccf597955163c2',1,'vg::Constructor']]],
+ ['max_5fpath_5fid_3578',['max_path_id',['../classvg_1_1Paths.html#ac5e9e182ecf09166f516c6fbf9923a29',1,'vg::Paths']]],
+ ['max_5fpath_5flength_3579',['max_path_length',['../classvg_1_1Filter.html#a77225b4859a55b509396332e96c81c0e',1,'vg::Filter']]],
+ ['max_5fpath_5frank_3580',['max_path_rank',['../classxg_1_1XG.html#acd75e4cc0ccf977505a5c6bda03ddb73',1,'xg::XG']]],
+ ['max_5fpath_5fsearch_5fsteps_3581',['max_path_search_steps',['../classvg_1_1Genotyper.html#a500af110546f9572fe40d5ef098552d9',1,'vg::Genotyper::max_path_search_steps()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa61be13e0e070bd8af8fe890b47dfde5',1,'vg::ReadRestrictedTraversalFinder::max_path_search_steps()'],['../classvg_1_1PathRestrictedTraversalFinder.html#af24fb970905bbb3d2e04631fd3d0918b',1,'vg::PathRestrictedTraversalFinder::max_path_search_steps()']]],
+ ['max_5fpossible_5fmapping_5fquality_3582',['max_possible_mapping_quality',['../classvg_1_1GSSWAligner.html#a0058c97d1dbe2be7643e9f75cee15bab',1,'vg::GSSWAligner::max_possible_mapping_quality()'],['../classvg_1_1Mapper.html#a1799afefa90f9fbfd7de41626bdb460c',1,'vg::Mapper::max_possible_mapping_quality()']]],
+ ['max_5fprune_5fiterations_3583',['max_prune_iterations',['../classvg_1_1VCFTraversalFinder.html#a667a1499ac092df03deaa7ec0813d6df',1,'vg::VCFTraversalFinder']]],
+ ['max_5freads_3584',['max_reads',['../classvg_1_1ReadFilter.html#a1a4d052b3060e2b8a434310ce6dc14f5',1,'vg::ReadFilter::max_reads()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a6c584adbe4422e18c6bb875bb3a482ca',1,'vg::Counts::max_reads()']]],
+ ['max_5freads_5fused_3585',['max_reads_used',['../classvg_1_1ReadFilter.html#a06835480f40ef09dd073cc14a469f760',1,'vg::ReadFilter']]],
+ ['max_5fref_5fhet_5fbias_3586',['max_ref_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a6012c94aabfcffde89851c587ed34f9e',1,'vg::RatioSupportSnarlCaller']]],
+ ['max_5frescue_5fattempts_3587',['max_rescue_attempts',['../classvg_1_1MinimizerMapper.html#a0985bcf3a1ed28098bf0271b251dd6e2',1,'vg::MinimizerMapper::max_rescue_attempts()'],['../classvg_1_1MultipathMapper.html#a87f585b42e49cd2e642ab092e54a309a',1,'vg::MultipathMapper::max_rescue_attempts()']]],
+ ['max_5frescue_5fp_5fvalue_3588',['max_rescue_p_value',['../classvg_1_1MultipathMapper.html#afe5cb57d342ca46e5ee2e132d1d238d3',1,'vg::MultipathMapper']]],
+ ['max_5frgfa_5frank_3589',['max_rgfa_rank',['../classvg_1_1algorithms_1_1GFAParser.html#ae5841a4a832376b2894cbbb956c89569',1,'vg::algorithms::GFAParser']]],
+ ['max_5fsample_5fsize_3590',['max_sample_size',['../classvg_1_1FragmentLengthDistribution.html#ae5f1b666c1bee15996ad997eb4c9505e',1,'vg::FragmentLengthDistribution']]],
+ ['max_5fsearch_5fdepth_3591',['max_search_depth',['../classvg_1_1LegacyCaller.html#a321503fbe153735736a542d4ad5d9235',1,'vg::LegacyCaller']]],
+ ['max_5fsearch_5fwidth_3592',['max_search_width',['../classvg_1_1LegacyCaller.html#a01572bf56d35cc89232fac3dce35c891',1,'vg::LegacyCaller']]],
+ ['max_5fseparation_3593',['max_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a1094dccc104bf859b2bdb8b5fac6bec6',1,'vg::GreedyMinDistanceClusterer']]],
+ ['max_5fshift_3594',['max_shift',['../classvg_1_1MultipathAlignmentGraph.html#a50ff4a1c2bc2b997c28af99527e595dd',1,'vg::MultipathAlignmentGraph']]],
+ ['max_5fsingle_5fend_5fmappings_5ffor_5frescue_3595',['max_single_end_mappings_for_rescue',['../classvg_1_1MultipathMapper.html#a1dc8310407eabb6cbe419d5765364df7',1,'vg::MultipathMapper']]],
+ ['max_5fskipped_5fbases_3596',['max_skipped_bases',['../classvg_1_1MinimizerMapper.html#ad72974afc9d7fadd23716fba49b7e82f',1,'vg::MinimizerMapper']]],
+ ['max_5fslide_3597',['max_slide',['../classvg_1_1Surjector.html#a0e40286284b27ccef7fbcc028fc40142',1,'vg::Surjector']]],
+ ['max_5fsnarl_5fcut_5fsize_3598',['max_snarl_cut_size',['../classvg_1_1MultipathMapper.html#a507872f1a20d6b0e34b6f9b8dac2639f',1,'vg::MultipathMapper']]],
+ ['max_5fsnarl_5fedges_3599',['max_snarl_edges',['../classvg_1_1FlowCaller.html#a07f59c5945984d13f67ec660923c0f81',1,'vg::FlowCaller']]],
+ ['max_5fsnarl_5fshallow_5fsize_3600',['max_snarl_shallow_size',['../classvg_1_1NestedFlowCaller.html#ab5e10be4ba6c1d33235e5844cfb8b8c0',1,'vg::NestedFlowCaller']]],
+ ['max_5fsoftclip_5fiterations_3601',['max_softclip_iterations',['../classvg_1_1Mapper.html#a145a97f0859865815bba2562024078e9',1,'vg::Mapper']]],
+ ['max_5fsoftclip_5foverlap_3602',['max_softclip_overlap',['../classvg_1_1MultipathMapper.html#afcacb8b30589b82487cca2a1755320f3',1,'vg::MultipathMapper']]],
+ ['max_5fsplice_5foverhang_3603',['max_splice_overhang',['../classvg_1_1MultipathMapper.html#a8c71d1bf28c8567e878c5cd004b94e8b',1,'vg::MultipathMapper']]],
+ ['max_5fsplice_5fref_5fsearch_5flength_3604',['max_splice_ref_search_length',['../classvg_1_1MultipathMapper.html#a4f4bca24b9dbe1a7a40499a30e91c4f6',1,'vg::MultipathMapper']]],
+ ['max_5fsteps_5fof_5fhandle_5fmemo_5fsize_3605',['max_steps_of_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a55aadb2458a395d6fd47f9a9c5ddf415',1,'vg::MemoizingGraph']]],
+ ['max_5fsub_5fmem_5frecursion_5fdepth_3606',['max_sub_mem_recursion_depth',['../classvg_1_1BaseMapper.html#ac12496865e23fd68ba1f579dcb050037',1,'vg::BaseMapper']]],
+ ['max_5fsubgraph_5fbases_5fper_5fread_5fbase_3607',['max_subgraph_bases_per_read_base',['../classvg_1_1Surjector.html#a14e20f641f120ca8fa5206ace84be331',1,'vg::Surjector']]],
+ ['max_5fsuboptimal_5fpath_5fscore_5fratio_3608',['max_suboptimal_path_score_ratio',['../classvg_1_1MultipathMapper.html#ac117889984b58f3c0fd3d389a8ee7f26',1,'vg::MultipathMapper']]],
+ ['max_5ftag_5flength_3609',['MAX_TAG_LENGTH',['../classvg_1_1io_1_1Registry.html#a8791c3355999775f973ab74fa4111fa2',1,'vg::io::Registry']]],
+ ['max_5ftail_5fanchor_5fprune_3610',['max_tail_anchor_prune',['../classvg_1_1Surjector.html#a59034e11562bb0969c25defd215f166b',1,'vg::Surjector']]],
+ ['max_5ftail_5fdp_5flength_3611',['max_tail_dp_length',['../classvg_1_1MinimizerMapper.html#ab333ad05b05cdcd8d59bd0c6b2733e04',1,'vg::MinimizerMapper']]],
+ ['max_5ftail_5fgap_3612',['max_tail_gap',['../classvg_1_1MinimizerMapper.html#a25dccb476876cf2797743ec916c3d661',1,'vg::MinimizerMapper']]],
+ ['max_5ftail_5flength_3613',['max_tail_length',['../classvg_1_1MinimizerMapper.html#ad041c860d77e6ad2bd025bd2da337d7a',1,'vg::MinimizerMapper::max_tail_length()'],['../classvg_1_1Surjector.html#a185cc3fad9b021b08f03880ae0119db6',1,'vg::Surjector::max_tail_length()']]],
+ ['max_5ftail_5fmerge_5fsupress_5flength_3614',['max_tail_merge_supress_length',['../classvg_1_1MultipathMapper.html#a8de58bf1942c4aa16b762554268d3e3d',1,'vg::MultipathMapper']]],
+ ['max_5ftarget_5ffactor_3615',['max_target_factor',['../classvg_1_1Mapper.html#a5ecf825b76d29c8b8242d8167fae6cc4',1,'vg::Mapper']]],
+ ['max_5fto_5ffragment_3616',['max_to_fragment',['../classvg_1_1MinimizerMapper.html#ab6b8884b622acf26ceeae7ea1f2204d6',1,'vg::MinimizerMapper']]],
+ ['max_5ftrav_5fsize_3617',['max_trav_size',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a4842f02f38903b12e0c7de54bf0482e3',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['max_5ftraversal_5fcutoff_3618',['max_traversal_cutoff',['../classvg_1_1VCFTraversalFinder.html#a2ece2a9a96c909c7859bd88d54daa559',1,'vg::VCFTraversalFinder']]],
+ ['max_5ftraversal_5flength_3619',['max_traversal_length',['../classvg_1_1FlowTraversalFinder.html#a1dbaa147e49e103151629a210977c58b',1,'vg::FlowTraversalFinder']]],
+ ['max_5ftries_3620',['max_tries',['../classvg_1_1AbstractReadSampler.html#a68421d544f78d22ed080321929c9fd01',1,'vg::AbstractReadSampler']]],
+ ['max_5funcalled_5falleles_3621',['max_uncalled_alleles',['../classvg_1_1VCFOutputCaller.html#acf04132e0a3cf52b5ba58a88f0b2d3d4',1,'vg::VCFOutputCaller']]],
+ ['max_5funique_5fmin_3622',['max_unique_min',['../classvg_1_1MinimizerMapper.html#a8862622f6f711cc6a797b26990c9f195',1,'vg::MinimizerMapper']]],
+ ['max_5fvalue_3623',['max_value',['../structvg_1_1SummaryStatistics.html#ad86748ae17ecc7acce49364a9fa93a74',1,'vg::SummaryStatistics::max_value()'],['../structvg_1_1varint__vector__t.html#a92149196c806e2230f53f2d62e9bf8b3',1,'vg::varint_vector_t::MAX_VALUE()']]],
+ ['max_5fvcf_5fline_5flength_3624',['max_vcf_line_length',['../classvg_1_1VCFOutputCaller.html#a549336b5a84bfdef74b8ae8116b1b151',1,'vg::VCFOutputCaller']]],
+ ['max_5fvertex_3625',['max_vertex',['../classvg_1_1MEMChainModel.html#abc9cf4a87ae1b38488bcf96c0a09b853',1,'vg::MEMChainModel::max_vertex()'],['../classvg_1_1AlignmentChainModel.html#a79f49cd995d623a0dae8b704ad57432e',1,'vg::AlignmentChainModel::max_vertex()']]],
+ ['max_5fwalk_3626',['max_walk',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6d8dc74ae9eaaabf35ba1c89cfae8a11',1,'vg::PathOrientedDistanceMeasurer']]],
+ ['max_5fwidth_3627',['max_width',['../classvg_1_1RepresentativeTraversalFinder.html#aac2939337439d7566246889b3a4655c6',1,'vg::RepresentativeTraversalFinder']]],
+ ['max_5fxdrop_5fgap_5flength_3628',['max_xdrop_gap_length',['../classvg_1_1Mapper.html#a2754b67772ef25cb66d06b66b8caeb55',1,'vg::Mapper']]],
+ ['maximalexactmatch_3629',['MaximalExactMatch',['../classvg_1_1MaximalExactMatch.html',1,'vg::MaximalExactMatch'],['../classvg_1_1MaximalExactMatch.html#a0eb93e97b671cbafb0de7aa5827fa5f0',1,'vg::MaximalExactMatch::MaximalExactMatch(string::const_iterator b, string::const_iterator e, gcsa::range_type r, size_t m=0)'],['../classvg_1_1MaximalExactMatch.html#aab0c8e120398563dfa7dae32a92b2fa9',1,'vg::MaximalExactMatch::MaximalExactMatch(void)=default'],['../classvg_1_1MaximalExactMatch.html#a058f43692dd5943fa4e4ecc1b5fc68c0',1,'vg::MaximalExactMatch::MaximalExactMatch(const MaximalExactMatch &)=default'],['../classvg_1_1MaximalExactMatch.html#a9b0816ee01550f8ce43d32984d6fc333',1,'vg::MaximalExactMatch::MaximalExactMatch(MaximalExactMatch &&)=default']]],
+ ['maximum_5fdistance_3630',['maximum_distance',['../namespacevg.html#a004ed92d4db665ce8ec4e527f150a7c4',1,'vg']]],
+ ['maximum_5fmapping_5fquality_5fapprox_3631',['maximum_mapping_quality_approx',['../classvg_1_1GSSWAligner.html#a3104dc6ddfd6a15e1ed02950006a4063',1,'vg::GSSWAligner']]],
+ ['maximum_5fmapping_5fquality_5fexact_3632',['maximum_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#ac17619c1908446d3e61a882c879f2eb1',1,'vg::GSSWAligner']]],
+ ['maximum_5fquality_3633',['maximum_quality',['../classvg_1_1Packer.html#a0de02be2009ac1d477d5cc8fefccab1c',1,'vg::Packer']]],
+ ['maximum_5fsample_5fsize_3634',['maximum_sample_size',['../classvg_1_1FragmentLengthDistribution.html#a82ad9fe36dc81ea108a530b7f9792b78',1,'vg::FragmentLengthDistribution']]],
+ ['maybe_5fmq_5fthreshold_3635',['maybe_mq_threshold',['../classvg_1_1Mapper.html#a26d2d7d3964d9210c963b325c64678b0',1,'vg::Mapper']]],
+ ['mcmc_5fcaller_2ecpp_3636',['mcmc_caller.cpp',['../mcmc__caller_8cpp.html',1,'']]],
+ ['mcmc_5fcaller_2ehpp_3637',['mcmc_caller.hpp',['../mcmc__caller_8hpp.html',1,'']]],
+ ['mcmc_5fgenotyper_2ecpp_3638',['mcmc_genotyper.cpp',['../mcmc__genotyper_8cpp.html',1,'']]],
+ ['mcmc_5fgenotyper_2ehpp_3639',['mcmc_genotyper.hpp',['../mcmc__genotyper_8hpp.html',1,'']]],
+ ['mcmc_5fmain_2ecpp_3640',['mcmc_main.cpp',['../mcmc__main_8cpp.html',1,'']]],
+ ['mcmccaller_3641',['MCMCCaller',['../classvg_1_1MCMCCaller.html',1,'vg::MCMCCaller'],['../classvg_1_1MCMCCaller.html#add4fcb2e5a2a8633e659a986bb347c40',1,'vg::MCMCCaller::MCMCCaller()']]],
+ ['mcmcgenotyper_3642',['MCMCGenotyper',['../classvg_1_1MCMCGenotyper.html',1,'vg::MCMCGenotyper'],['../classvg_1_1MCMCGenotyper.html#abb6ddf1a8e99fc5c183ec188ae87bb22',1,'vg::MCMCGenotyper::MCMCGenotyper()']]],
+ ['mean_3643',['mean',['../structvg_1_1SummaryStatistics.html#a275cb7138ffd1285cbdad3ae7017cbe8',1,'vg::SummaryStatistics::mean()'],['../classvg_1_1FragmentLengthDistribution.html#abe1b685c70bdafff09e089038ae68971',1,'vg::FragmentLengthDistribution::mean()'],['../classvg_1_1normal__distribution.html#a8b5bd06d0c3589eab21131a033bd706a',1,'vg::normal_distribution::mean()'],['../classvg_1_1truncated__normal__distribution.html#ad842920993df04cbcc18cc4182f9d005',1,'vg::truncated_normal_distribution::mean()']]],
+ ['mean_5fnode_5flength_3644',['mean_node_length',['../classvg_1_1Transcriptome.html#af173c32d4ccfa7f94f68220e7e564895',1,'vg::Transcriptome']]],
+ ['measurements_5fbegin_3645',['measurements_begin',['../classvg_1_1FragmentLengthDistribution.html#a9a57a0e4a86983fc13a87d5ee4c5b8a7',1,'vg::FragmentLengthDistribution']]],
+ ['measurements_5fend_3646',['measurements_end',['../classvg_1_1FragmentLengthDistribution.html#a929562555917920f58a5d3692cd14fb4',1,'vg::FragmentLengthDistribution']]],
+ ['median_3647',['median',['../structvg_1_1SummaryStatistics.html#ae98f01cfb86f82f0e9185c63fb57445f',1,'vg::SummaryStatistics::median()'],['../namespacevg.html#a6eef175773ce8532826ba78eee0cece5',1,'vg::median()']]],
+ ['median_5fmem_5fcoverage_3648',['median_mem_coverage',['../classvg_1_1MEMClusterer_1_1HitGraph.html#abe3be52c11df5f9b5fc131cfe9460d5a',1,'vg::MEMClusterer::HitGraph']]],
+ ['mem_3649',['mem',['../classvg_1_1MEMChainModelVertex.html#acd9990963345deb38096763554ae4b3d',1,'vg::MEMChainModelVertex::mem()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#a9f3480f5d231cf8d4325ae558a379f10',1,'vg::MEMClusterer::HitNode::mem()']]],
+ ['mem_2ecpp_3650',['mem.cpp',['../mem_8cpp.html',1,'']]],
+ ['mem_2ehpp_3651',['mem.hpp',['../mem_8hpp.html',1,'']]],
+ ['mem_5faccelerator_2ecpp_3652',['mem_accelerator.cpp',['../mem__accelerator_8cpp.html',1,'']]],
+ ['mem_5faccelerator_2ehpp_3653',['mem_accelerator.hpp',['../mem__accelerator_8hpp.html',1,'']]],
+ ['mem_5fcoverage_5fmin_5fratio_3654',['mem_coverage_min_ratio',['../classvg_1_1MultipathMapper.html#ae977e7bbf30ca7634e7422aa76c16e71',1,'vg::MultipathMapper']]],
+ ['mem_5fmin_5foriented_5fdistances_3655',['mem_min_oriented_distances',['../namespacevg.html#ae1678438e6011469b88ddf3b54023013',1,'vg']]],
+ ['mem_5fnode_5fstart_5fpositions_3656',['mem_node_start_positions',['../namespacevg.html#aa65ea58e40ea30264407f9fdbce2a83d',1,'vg']]],
+ ['mem_5freseed_5flength_3657',['mem_reseed_length',['../classvg_1_1BaseMapper.html#abaea877646c1be5aea6200201d28c4cf',1,'vg::BaseMapper']]],
+ ['mem_5fusage_5fstring_3658',['mem_usage_string',['../autoindex__main_8cpp.html#a95ea1f250ba974749a30b213bede7969',1,'autoindex_main.cpp']]],
+ ['memaccelerator_3659',['MEMAccelerator',['../classvg_1_1MEMAccelerator.html',1,'vg::MEMAccelerator'],['../classvg_1_1MEMAccelerator.html#af51ef34773bca8cc723fb3ef0bfe87c8',1,'vg::MEMAccelerator::MEMAccelerator()=default'],['../classvg_1_1MEMAccelerator.html#a3928fe622799f9ac33ba7e2e5d4b3568',1,'vg::MEMAccelerator::MEMAccelerator(const gcsa::GCSA &gcsa_index, size_t k)']]],
+ ['memchainmodel_3660',['MEMChainModel',['../classvg_1_1MEMChainModel.html',1,'vg::MEMChainModel'],['../classvg_1_1MEMChainModel.html#ae612545bdf38bad27b4fc18e19d38eff',1,'vg::MEMChainModel::MEMChainModel()']]],
+ ['memchainmodelvertex_3661',['MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html',1,'vg::MEMChainModelVertex'],['../classvg_1_1MEMChainModelVertex.html#a9ec1a9cd36b3328911409e598109c1c9',1,'vg::MEMChainModelVertex::MEMChainModelVertex(void)=default'],['../classvg_1_1MEMChainModelVertex.html#a01ed669199f3319be51dbd2aafc268de',1,'vg::MEMChainModelVertex::MEMChainModelVertex(const MEMChainModelVertex &)=default'],['../classvg_1_1MEMChainModelVertex.html#adb5651ba734c5700f334b0074dfaaca8',1,'vg::MEMChainModelVertex::MEMChainModelVertex(MEMChainModelVertex &&)=default']]],
+ ['memcluster_5ft_3662',['memcluster_t',['../classvg_1_1MultipathMapper.html#acae95760b8750cf3b2bb48d00fe499fd',1,'vg::MultipathMapper']]],
+ ['memclusterer_3663',['MEMClusterer',['../classvg_1_1MEMClusterer.html',1,'vg::MEMClusterer'],['../classvg_1_1MEMClusterer.html#ae035e62365ff4617433e18d102bec452',1,'vg::MEMClusterer::MEMClusterer()']]],
+ ['memo_3664',['memo',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a382739dd7136e759c6a01725ddebd301',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['memoized_5flf_3665',['memoized_LF',['../classvg_1_1MEMAccelerator.html#a89dfd34874f065088799dfce96c11649',1,'vg::MEMAccelerator']]],
+ ['memoizing_5fgraph_2ecpp_3666',['memoizing_graph.cpp',['../memoizing__graph_8cpp.html',1,'']]],
+ ['memoizing_5fgraph_2ehpp_3667',['memoizing_graph.hpp',['../memoizing__graph_8hpp.html',1,'']]],
+ ['memoizinggraph_3668',['MemoizingGraph',['../classvg_1_1MemoizingGraph.html',1,'vg::MemoizingGraph'],['../classvg_1_1MemoizingGraph.html#aef84e6abc0084e0f910bc99edc760345',1,'vg::MemoizingGraph::MemoizingGraph(const PathPositionHandleGraph *graph)'],['../classvg_1_1MemoizingGraph.html#aa6030fdc5e73a8d88059bc31f1886746',1,'vg::MemoizingGraph::MemoizingGraph()=default']]],
+ ['memory_5fhigh_5fwater_5fkb_3669',['memory_high_water_kb',['../classvg_1_1Watchdog.html#aa759f3d73ebe15aeb95a13a8c86a0b59',1,'vg::Watchdog']]],
+ ['mems_5fid_5fclusters_5fto_5falignments_3670',['mems_id_clusters_to_alignments',['../classvg_1_1Mapper.html#a0dc4c04ebad76435afafe9cec62a5eaa',1,'vg::Mapper']]],
+ ['mems_5foverlap_3671',['mems_overlap',['../namespacevg.html#aa412de4741b61d2a8b863f50f31209e0',1,'vg']]],
+ ['mems_5foverlap_5flength_3672',['mems_overlap_length',['../namespacevg.html#af5d04132733b3487e3dab20729645850',1,'vg']]],
+ ['mems_5fto_5fjson_3673',['mems_to_json',['../namespacevg.html#ab0bec9992b4441128754ac4ed1a330e8',1,'vg']]],
+ ['memusage_2ecpp_3674',['memusage.cpp',['../memusage_8cpp.html',1,'']]],
+ ['memusage_2ehpp_3675',['memusage.hpp',['../memusage_8hpp.html',1,'']]],
+ ['merge_3676',['merge',['../structGBWTConfig.html#a850f9f30af38996cc64f1fabb20a6458',1,'GBWTConfig::merge()'],['../classvg_1_1Funnel.html#ae75f133fdc545176a27f0121a61a98e4',1,'vg::Funnel::merge()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a658429a7896e87dc276f749f5ba8dc27',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::merge()'],['../classvg_1_1VG.html#a0abc84684faea29b49032ec254d5e13b',1,'vg::VG::merge(Graph &g)'],['../classvg_1_1VG.html#a40f22f6bb4a3e7a2aea7b3887237faec',1,'vg::VG::merge(VG &g)'],['../namespacevg_1_1algorithms.html#a91a6bbd822f6380421a973f75036c3d3',1,'vg::algorithms::merge()']]],
+ ['merge_2ecpp_3677',['merge.cpp',['../merge_8cpp.html',1,'']]],
+ ['merge_2ehpp_3678',['merge.hpp',['../merge_8hpp.html',1,'']]],
+ ['merge_5fadjacent_5fedits_3679',['merge_adjacent_edits',['../namespacevg.html#a30a83a9e127a0c7d75118dc14a8985f6',1,'vg::merge_adjacent_edits(const Mapping &m)'],['../namespacevg.html#a2c9985bf70965bd36bb54f910ab74e3b',1,'vg::merge_adjacent_edits(const Path &m)']]],
+ ['merge_5falignments_3680',['merge_alignments',['../namespacevg.html#afa2d2a5d955cff1e7a99369055ebe75d',1,'vg::merge_alignments(const vector< Alignment > &alns)'],['../namespacevg.html#a9d71527a132d7e6bf364d2108b269e09',1,'vg::merge_alignments(const Alignment &a1, const Alignment &a2, bool debug)']]],
+ ['merge_5fedits_5fin_5fplace_3681',['merge_edits_in_place',['../namespacevg.html#a20ebf02d59df03f906550e695a1aa00d',1,'vg']]],
+ ['merge_5fequivalent_5ftraversals_5fin_5fgraph_3682',['merge_equivalent_traversals_in_graph',['../namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1',1,'vg']]],
+ ['merge_5ffast_3683',['merge_fast',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fa00b833ba044e1135d12579e8baeedca6',1,'GBWTConfig']]],
+ ['merge_5ffrom_5fdynamic_3684',['merge_from_dynamic',['../classvg_1_1Packer.html#a79ce5d54645f6d124c710b86b666f5d7',1,'vg::Packer']]],
+ ['merge_5ffrom_5ffiles_3685',['merge_from_files',['../classvg_1_1Packer.html#af857449c08a56dd66c6a4bc0402231cb',1,'vg::Packer']]],
+ ['merge_5fgroup_3686',['merge_group',['../classvg_1_1Funnel.html#a585c5484ef877a1ede56ed4467e32312',1,'vg::Funnel']]],
+ ['merge_5fgroups_3687',['merge_groups',['../classvg_1_1Funnel.html#a44fcff7c06cb79e43cc1aa2fc73a8da6',1,'vg::Funnel']]],
+ ['merge_5fid_5fspace_3688',['merge_id_space',['../classvg_1_1VGset.html#a968fb68f13f91ea8ded32d02c6ea683a',1,'vg::VGset']]],
+ ['merge_5finsert_3689',['merge_insert',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faa05cfa7f46c6c005f05b264b71ede9d3',1,'GBWTConfig']]],
+ ['merge_5fmode_3690',['merge_mode',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0f',1,'GBWTConfig']]],
+ ['merge_5fnodes_3691',['merge_nodes',['../classvg_1_1VG.html#a2e506d51db427b617cc334a791c7f594',1,'vg::VG']]],
+ ['merge_5fnon_5fbranching_5fsubpaths_3692',['merge_non_branching_subpaths',['../namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43',1,'vg']]],
+ ['merge_5fnone_3693',['merge_none',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faace9bbb313fb5c18d2a5a9142b99762b',1,'GBWTConfig']]],
+ ['merge_5fparallel_3694',['merge_parallel',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fad49ba685add4291f2ba5d4d042f6e548',1,'GBWTConfig']]],
+ ['merge_5fparameters_3695',['merge_parameters',['../structGBWTConfig.html#a77aea6d71d3a6904f01eeccf1f950318',1,'GBWTConfig']]],
+ ['merge_5fpartially_5fredundant_5fmatch_5fnodes_3696',['merge_partially_redundant_match_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a9f8ca4f9936aa6abcc8681e91dae3f43',1,'vg::MultipathAlignmentGraph']]],
+ ['merge_5frescued_5fmappings_3697',['merge_rescued_mappings',['../classvg_1_1MultipathMapper.html#a525152a98c905ba789a0454c70336c3e',1,'vg::MultipathMapper']]],
+ ['merge_5fstate_3698',['merge_state',['../classvg_1_1DinucleotideMachine.html#ab28bcc9f016d8df680d6f17b5957fc57',1,'vg::DinucleotideMachine']]],
+ ['merge_5funion_3699',['merge_union',['../classvg_1_1VG.html#a5aff716eee0bf720b3836caa761d48be',1,'vg::VG']]],
+ ['merged_5fgroup_3700',['merged_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#acd6301aa5e085df9fa56ba8b102cdde6',1,'vg::IndexedVG::CacheEntry']]],
+ ['mergedadjacencygraph_3701',['MergedAdjacencyGraph',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#aa09eaec5fd36cfe50b4313a38ba01fe1',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const RankedHandleGraph *graph)'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ab8d7ea6f475144c3779568d9d552c1c7',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const MergedAdjacencyGraph &other)']]],
+ ['mergegraphs_3702',['mergeGraphs',['../namespacevg_1_1io.html#a09b6c55dd368ec0c3e85f51a87321ba2',1,'vg::io']]],
+ ['mergenodeobjects_3703',['mergeNodeObjects',['../namespacevg.html#aa539af4f481d4e955ede26ee85c320c5',1,'vg']]],
+ ['message_3704',['message',['../structvg_1_1AlignmentValidity.html#a7eede46d9951c0c2b0b4c226c6987691',1,'vg::AlignmentValidity::message()'],['../classvg_1_1NoAlignmentInBandException.html#a3cc1fd5899066709228ecea9e5a25956',1,'vg::NoAlignmentInBandException::message()']]],
+ ['message_5fbuffer_3705',['message_buffer',['../structvg_1_1algorithms_1_1GFAFormatError.html#a24e4e4d2285fd970978365e2747165c8',1,'vg::algorithms::GFAFormatError']]],
+ ['message_5fconsumer_5ffunction_5ft_3706',['message_consumer_function_t',['../namespacevg_1_1io.html#a618e8c9e44f63328bb2c0742ab0e69c2',1,'vg::io']]],
+ ['message_5femitter_3707',['message_emitter',['../classvg_1_1io_1_1ProtobufEmitter.html#a1bdc1e48041d69eeca45745580af19f3',1,'vg::io::ProtobufEmitter']]],
+ ['message_5femitter_2ecpp_3708',['message_emitter.cpp',['../message__emitter_8cpp.html',1,'']]],
+ ['message_5femitter_2ehpp_3709',['message_emitter.hpp',['../message__emitter_8hpp.html',1,'']]],
+ ['message_5fhandlers_3710',['message_handlers',['../classvg_1_1io_1_1ProtobufEmitter.html#a73231a5a45811c280d1a6d346abc75eb',1,'vg::io::ProtobufEmitter']]],
+ ['message_5fit_3711',['message_it',['../classvg_1_1io_1_1ProtobufIterator.html#a787d06e13a1799b7e65ee1aa19ec3bb8',1,'vg::io::ProtobufIterator']]],
+ ['message_5fiterator_2ecpp_3712',['message_iterator.cpp',['../message__iterator_8cpp.html',1,'']]],
+ ['message_5fiterator_2ehpp_3713',['message_iterator.hpp',['../message__iterator_8hpp.html',1,'']]],
+ ['message_5flistener_5ft_3714',['message_listener_t',['../classvg_1_1io_1_1ProtobufEmitter.html#a735167dc9e644a83d0e9fd206b241ce1',1,'vg::io::ProtobufEmitter']]],
+ ['message_5fsender_5ffunction_5ft_3715',['message_sender_function_t',['../namespacevg_1_1io.html#a26ea41d1ec4cf44b436a345f1eefccf1',1,'vg::io']]],
+ ['messageemitter_3716',['MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html',1,'vg::io::MessageEmitter'],['../classvg_1_1io_1_1MessageEmitter.html#a674e6dee23ee5d3a5b49e56ff6dad2c1',1,'vg::io::MessageEmitter::MessageEmitter(ostream &out, bool compress=false, size_t max_group_size=1000)'],['../classvg_1_1io_1_1MessageEmitter.html#a4e9dd0179e7e2b815fcbf3175fd5a030',1,'vg::io::MessageEmitter::MessageEmitter(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#af48941a2e4e66c513e169d29f120d511',1,'vg::io::MessageEmitter::MessageEmitter(MessageEmitter &&other)=default']]],
+ ['messageiterator_3717',['MessageIterator',['../classvg_1_1io_1_1MessageIterator.html',1,'vg::io::MessageIterator'],['../classvg_1_1io_1_1MessageIterator.html#a44eabe49bb3f28067f8ba3396915ee64',1,'vg::io::MessageIterator::MessageIterator(istream &in, bool verbose=false, size_t thread_count=0)'],['../classvg_1_1io_1_1MessageIterator.html#ae7ddb87951881f58221acd0a1beeb32f',1,'vg::io::MessageIterator::MessageIterator(unique_ptr< BlockedGzipInputStream > &&bgzf, bool verbose=false)'],['../classvg_1_1io_1_1MessageIterator.html#a46b16972d489742f42922fd9cb9b85af',1,'vg::io::MessageIterator::MessageIterator()=default']]],
+ ['metadata_3718',['metadata',['../structGBWTConfig.html#a0e91b96d773182fc4e4e36314ae6bd8d',1,'GBWTConfig']]],
+ ['metadata_5fmode_3719',['metadata_mode',['../structGBWTConfig.html#a102642e75fdf2b95d22a07d372ca2890',1,'GBWTConfig']]],
+ ['middle_5fsignature_3720',['middle_signature',['../namespacevg.html#a7848d492a243a93f37b1ac52a541a96a',1,'vg::middle_signature(const Alignment &aln, int len)'],['../namespacevg.html#af64c67658563ff567bc0b103ef1d8af4',1,'vg::middle_signature(const Alignment &aln1, const Alignment &aln2, int len)']]],
+ ['min_3721',['min',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#ad4cda218b41dfcb1dfdb3d3c5f3924c1',1,'vg::WFAExtender::ErrorModel::Event::min()'],['../classvg_1_1WideningPRNG.html#a3cd7defb4589ed56c43b27f5d7bd36fe',1,'vg::WideningPRNG::min()']]],
+ ['min_5fad_5flog_5flikelihood_5ffor_5ffilter_3722',['min_ad_log_likelihood_for_filter',['../classvg_1_1RatioSupportSnarlCaller.html#a16602959db7c2bc06471474b07a3c2f7',1,'vg::RatioSupportSnarlCaller']]],
+ ['min_5falt_5fpath_5fsupport_3723',['min_alt_path_support',['../classvg_1_1SupportBasedSnarlCaller.html#a17f76956318b838695d8b120d553ce24',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5fapprox_5fpath_5fdistance_3724',['min_approx_path_distance',['../classxg_1_1XG.html#ae92433487bc35ef856ee592137937a98',1,'xg::XG::min_approx_path_distance()'],['../namespacevg_1_1algorithms.html#ae18b50d29d9accb763b44d6e065dac58',1,'vg::algorithms::min_approx_path_distance()']]],
+ ['min_5favg_5fqual_3725',['min_avg_qual',['../classvg_1_1Filter.html#aa2f91d1daf04d2fdd6eb75183994d834',1,'vg::Filter']]],
+ ['min_5fbanded_5fmq_3726',['min_banded_mq',['../classvg_1_1Mapper.html#a4fe883a960df0bbef6d08cfbe483c179',1,'vg::Mapper']]],
+ ['min_5fbase_5fqual_3727',['min_base_qual',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a81bd6ba848d5742091102b7e6e7f0528',1,'vg::Counts']]],
+ ['min_5fbase_5fquality_3728',['min_base_quality',['../classvg_1_1ReadFilter.html#a7fe13f943f153913f16aa594720d350a',1,'vg::ReadFilter']]],
+ ['min_5fbase_5fquality_5ffraction_3729',['min_base_quality_fraction',['../classvg_1_1ReadFilter.html#ab8c6af52884a83d9538ea7ef42ac9eb4',1,'vg::ReadFilter']]],
+ ['min_5fbp_5fedge_5foverride_3730',['min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a767e1ca73abc43065673009d115c310d',1,'vg::TraversalSupportFinder']]],
+ ['min_5fchain_5fscore_5fper_5fbase_3731',['min_chain_score_per_base',['../classvg_1_1MinimizerMapper.html#a2b4cc838d0959b158c0c68b1e84e9123',1,'vg::MinimizerMapper']]],
+ ['min_5fchaining_5fproblems_3732',['min_chaining_problems',['../classvg_1_1MinimizerMapper.html#a821c2a05942d63254a2485a1e0987b80',1,'vg::MinimizerMapper']]],
+ ['min_5fchains_3733',['min_chains',['../classvg_1_1MinimizerMapper.html#a85797857c8e3f3bc363fa634af55889c',1,'vg::MinimizerMapper']]],
+ ['min_5fcluster_5flength_3734',['min_cluster_length',['../classvg_1_1Mapper.html#a70ed23d3ba482d38f7201376e179af9f',1,'vg::Mapper']]],
+ ['min_5fclustering_5fmem_5flength_3735',['min_clustering_mem_length',['../classvg_1_1MultipathMapper.html#ac656fb3b81d4cf6d06fb077551b54b7f',1,'vg::MultipathMapper']]],
+ ['min_5fcount_5fto_5fkeep_3736',['min_count_to_keep',['../classvg_1_1RareVariantSimplifier.html#aa481bbf8d0d969a9f9aa350fd376500e',1,'vg::RareVariantSimplifier']]],
+ ['min_5fcov_3737',['min_cov',['../classvg_1_1Filter.html#a77f731ad12fc655130808337452ba734',1,'vg::Filter']]],
+ ['min_5fcut_3738',['min_cut',['../classvg_1_1FlowSort.html#aa489e8c6bbf375d149410afe0a35d58b',1,'vg::FlowSort']]],
+ ['min_5fcut_5fdecomposition_3739',['min_cut_decomposition',['../namespacevg_1_1algorithms.html#a5cd4d23b1a702613134895c2d5618154',1,'vg::algorithms']]],
+ ['min_5fcut_5fgraph_2ecpp_3740',['min_cut_graph.cpp',['../min__cut__graph_8cpp.html',1,'']]],
+ ['min_5fcut_5fgraph_2ehpp_3741',['min_cut_graph.hpp',['../min__cut__graph_8hpp.html',1,'']]],
+ ['min_5fdepth_3742',['min_depth',['../classvg_1_1Filter.html#a941f203667435234a1e08cce0358d8c6',1,'vg::Filter']]],
+ ['min_5fdiagonal_3743',['min_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#ae69b636772fc01c9bd756c2b6dd7fd05',1,'vg::WFATree::ScoreProperties']]],
+ ['min_5fdistance_3744',['min_distance',['../classvg_1_1WFATree.html#a9578f5415befbcf1260abf8d4536f538',1,'vg::WFATree']]],
+ ['min_5fdistance_5ffrom_5fstart_3745',['min_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#ab859980ced41bcd382cd5961ff3b8475',1,'vg::IncrementalSubgraph']]],
+ ['min_5fdists_3746',['min_dists',['../classvg_1_1DeletionAligner.html#a42b9fef2da830c0912fb4141701c501e',1,'vg::DeletionAligner']]],
+ ['min_5fedge_5fsupport_3747',['min_edge_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#aabc81064635f9311af46bf2b5f1417aa',1,'vg::SupportRestrictedTraversalFinder::min_edge_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a16cd92c3b27a0b6be9d9154a7d9da77a',1,'vg::RepresentativeTraversalFinder::min_edge_support()']]],
+ ['min_5fend_5fmatches_3748',['min_end_matches',['../classvg_1_1ReadFilter.html#a05d07dd311e58f3fc04d510870ddf662',1,'vg::ReadFilter::min_end_matches()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a0035f968d8e0ae55fcaf6763f7dd01a1',1,'vg::Counts::min_end_matches()']]],
+ ['min_5fextension_5fsets_3749',['min_extension_sets',['../classvg_1_1MinimizerMapper.html#a1df84f11e9476595bcde3584553d2830',1,'vg::MinimizerMapper']]],
+ ['min_5fextensions_3750',['min_extensions',['../classvg_1_1MinimizerMapper.html#a03f18247f88d4817feef2d25a46fd5ca',1,'vg::MinimizerMapper']]],
+ ['min_5ffold_5fcoverage_5ffor_5fdownsample_3751',['min_fold_coverage_for_downsample',['../classvg_1_1Surjector.html#ac21d8c91876c3522c56c4c1c2b8f8f58',1,'vg::Surjector']]],
+ ['min_5ffrequency_5fto_5fkeep_3752',['min_frequency_to_keep',['../classvg_1_1RareVariantSimplifier.html#a7aca3c00c47d8a8c6261536952fd96d8',1,'vg::RareVariantSimplifier']]],
+ ['min_5fhandle_3753',['min_handle',['../classvg_1_1DagifiedGraph.html#a80c29e6e7494413dd631ea741d77f8c0',1,'vg::DagifiedGraph::min_handle()'],['../classxg_1_1XGPath.html#a59c1b92f21b5d102f70808266b457e7e',1,'xg::XGPath::min_handle()']]],
+ ['min_5fid_3754',['min_id',['../classvg_1_1SubHandleGraph.html#a81878c5b09f4863b125f9de74ce11315',1,'vg::SubHandleGraph::min_id()'],['../classxg_1_1XG.html#a89a7150cd2c37698fc33ce0953f6019b',1,'xg::XG::min_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af225cef56e4c7af36ea3252d86502238',1,'handlegraph::algorithms::SubHandleGraph::min_id()']]],
+ ['min_5fidentity_3755',['min_identity',['../classvg_1_1Mapper.html#a9b1d4bad7b2b7e96253006b4625329ac',1,'vg::Mapper']]],
+ ['min_5flink_5flength_3756',['min_link_length',['../classvg_1_1JoinedSpliceGraph.html#a92c8438c7a1efd3f0c5351a59b519a38',1,'vg::JoinedSpliceGraph']]],
+ ['min_5fmad_5ffor_5ffilter_3757',['min_mad_for_filter',['../classvg_1_1SupportBasedSnarlCaller.html#aec268641676f41d2c24128cb9e17ac03',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5fmapq_3758',['min_mapq',['../classvg_1_1ReadFilter.html#a8da615d17aba7ed66be6174253ce64ce',1,'vg::ReadFilter::min_mapq()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a228a82cd163bae9299de79bacd32fab8',1,'vg::Counts::min_mapq()']]],
+ ['min_5fmedian_5fmem_5fcoverage_5ffor_5fsplit_3759',['min_median_mem_coverage_for_split',['../classvg_1_1MultipathMapper.html#a4aa16d72dd27681fef0f5d99fec8f0ee',1,'vg::MultipathMapper']]],
+ ['min_5fmem_5flength_3760',['min_mem_length',['../classvg_1_1BaseMapper.html#a6de91c39c73a95b014b1773495985a09',1,'vg::BaseMapper']]],
+ ['min_5fmultimaps_3761',['min_multimaps',['../classvg_1_1Mapper.html#a34d17aa5222b5b97e8e96d70a39c99c9',1,'vg::Mapper']]],
+ ['min_5fnode_3762',['min_node',['../classvg_1_1SubgraphOverlay.html#a6fa8fb25c1244dfc3569ac1d37699334',1,'vg::SubgraphOverlay']]],
+ ['min_5fnode_5fid_3763',['min_node_id',['../classvg_1_1DagifiedGraph.html#a59e1c5556c2f5a984d9680cdaf8be41d',1,'vg::DagifiedGraph::min_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#ac48d1492dd478af9811307c52954e517',1,'vg::DozeuPinningOverlay::min_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ae07290cc251f0843de41551e25ffd4bf',1,'vg::ExtraNodeGraph::min_node_id()'],['../classvg_1_1SnarlGraph.html#a6e61014fadcbc2703a8fe3b208132ee4',1,'vg::SnarlGraph::min_node_id()'],['../classvg_1_1IdentityOverlay.html#a9a689ba99fa1452b5434a8a523e142c1',1,'vg::IdentityOverlay::min_node_id()'],['../classvg_1_1IncrementalSubgraph.html#a2d34ac8b129c82511c38f267644918d5',1,'vg::IncrementalSubgraph::min_node_id()'],['../classvg_1_1IndexedVG.html#ac496219064127ecd533ab41f77fc5da6',1,'vg::IndexedVG::min_node_id()'],['../classvg_1_1MemoizingGraph.html#afcbf2c9b526deaddee36140a362f4640',1,'vg::MemoizingGraph::min_node_id()'],['../classvg_1_1NullMaskingGraph.html#ab970c84b4caea2d00fd43a77f0826a95',1,'vg::NullMaskingGraph::min_node_id()'],['../classvg_1_1PathSubgraph.html#a472e93221aa3a728984d07aa6b7f0cc0',1,'vg::PathSubgraph::min_node_id()'],['../classvg_1_1ReverseGraph.html#adf486245a2201f1685e2af41a57a98f3',1,'vg::ReverseGraph::min_node_id()'],['../classvg_1_1NetGraph.html#a9b3c2b7f61f5c0133e844fa5edc4ea6d',1,'vg::NetGraph::min_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ad91d6241e1a962eaf4b4f1c92f2d94c8',1,'vg::SourceSinkOverlay::min_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#aa92df9f1002415710b4ffa4e6074cb5b',1,'vg::JoinedSpliceGraph::min_node_id()'],['../classvg_1_1StrandSplitGraph.html#aaeaf9231d44d7e0260ef5439f49e5e40',1,'vg::StrandSplitGraph::min_node_id()'],['../classvg_1_1SubHandleGraph.html#a180704728aa79aaf37189c644995cf91',1,'vg::SubHandleGraph::min_node_id()'],['../classvg_1_1SubgraphOverlay.html#a0d876d83943a078f6d9114bd08216086',1,'vg::SubgraphOverlay::min_node_id()'],['../classvg_1_1SubpathOverlay.html#a3d0fc1b94bdd931b4bd72197a07d6510',1,'vg::SubpathOverlay::min_node_id()'],['../classvg_1_1TreeSubgraph.html#a1ac845e3e2d75d7da5ff81b79aba3d08',1,'vg::TreeSubgraph::min_node_id()'],['../classvg_1_1VG.html#ac27674d67445ddc135c3c8ab4d3d5231',1,'vg::VG::min_node_id()'],['../classxg_1_1XG.html#a9195d1b18542de3b89b80bb14ce1ca0a',1,'xg::XG::min_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af944543089a7fae6c052decc4ff0a4c4',1,'handlegraph::algorithms::SubHandleGraph::min_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a85c52fe4b5f483504ed142d0ad94a969',1,'handlegraph::HandleGraph::min_node_id()']]],
+ ['min_5fnode_5fsupport_3764',['min_node_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#ae0201f741f7e5cffed2577d47e8e1830',1,'vg::SupportRestrictedTraversalFinder::min_node_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a873d02fe79d020bb106879f5b478e38f',1,'vg::RepresentativeTraversalFinder::min_node_support()']]],
+ ['min_5fnode_5fsupport_5fcache_3765',['min_node_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a3a150bfc048afe50f2e006f77159bf34',1,'vg::CachedPackedTraversalSupportFinder']]],
+ ['min_5foriented_5fdistances_3766',['min_oriented_distances',['../namespacevg.html#a973bf2647d54324bc63c323a0aa29a35',1,'vg']]],
+ ['min_5fpair_5ffragment_5flength_3767',['min_pair_fragment_length',['../classvg_1_1Mapper.html#a3682f47407c7feddc2f8a22cd546a4ec',1,'vg::Mapper']]],
+ ['min_5fpercent_5fidentity_3768',['min_percent_identity',['../classvg_1_1Filter.html#afd9cc5bfa5740f71e70a601f7f0b8199',1,'vg::Filter']]],
+ ['min_5fprimary_3769',['min_primary',['../classvg_1_1ReadFilter.html#a64132e9f5f27ce6930554ad3c197e694',1,'vg::ReadFilter']]],
+ ['min_5fqual_3770',['min_qual',['../classvg_1_1Filter.html#ab3ced01093210b1379fbcd7de7709a30',1,'vg::Filter']]],
+ ['min_5fqueue_5fitem_5fbytes_3771',['MIN_QUEUE_ITEM_BYTES',['../classvg_1_1io_1_1StreamMultiplexer.html#afd60eacdf650f68a3989c91670655146',1,'vg::io::StreamMultiplexer']]],
+ ['min_5fread_5fseparation_3772',['min_read_separation',['../classvg_1_1ComponentMinDistanceClusterer.html#a6c48555f1245310c614265e3d9d69c42',1,'vg::ComponentMinDistanceClusterer']]],
+ ['min_5frecurrence_3773',['min_recurrence',['../classvg_1_1Genotyper.html#afffa8d75fd4155bc7d420a41d92f198c',1,'vg::Genotyper::min_recurrence()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa00f717b20773b41578e642425fbf73b',1,'vg::ReadRestrictedTraversalFinder::min_recurrence()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a3085d06249a54ac345e3bebde7c2378c',1,'vg::PathRestrictedTraversalFinder::min_recurrence()']]],
+ ['min_5fscore_3774',['min_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab6d45328b152bc6aa0e23943d77e473b',1,'vg::Counts']]],
+ ['min_5fscore_5ffactor_3775',['min_score_factor',['../classvg_1_1VariantAdder.html#aae129564bcf5ec9fd9d0838754d27323',1,'vg::VariantAdder']]],
+ ['min_5fscore_5fper_5fbase_3776',['min_score_per_base',['../classvg_1_1Genotyper.html#a8fc1fdccfa9829bb29903ed5d7b21b28',1,'vg::Genotyper']]],
+ ['min_5fsec_5fscore_3777',['min_sec_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac355280a9dc2984da55998417433ccdb',1,'vg::Counts']]],
+ ['min_5fsecondary_3778',['min_secondary',['../classvg_1_1ReadFilter.html#af85c211a4a06a1fb750958002cefba0f',1,'vg::ReadFilter']]],
+ ['min_5fseparation_3779',['min_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a97ed3ff5a8770a314b138148319b9a3b',1,'vg::GreedyMinDistanceClusterer']]],
+ ['min_5fshift_5ffor_5fprune_3780',['min_shift_for_prune',['../classvg_1_1Surjector.html#a731d00674b2d71044a8e404be059c2cf',1,'vg::Surjector']]],
+ ['min_5fsite_5fdepth_3781',['min_site_depth',['../classvg_1_1SupportBasedSnarlCaller.html#adde07f3e5ca89a2a565e8859ee641159',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5fsize_3782',['min_size',['../classvg_1_1SmallSnarlSimplifier.html#a6efa9c6d0dc38da336a5723f87e20e46',1,'vg::SmallSnarlSimplifier']]],
+ ['min_5fsoftclip_5flength_5ffor_5fsplice_3783',['min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#a2d6a193c1277d948f7155da585e60367',1,'vg::MultipathMapper']]],
+ ['min_5fsoftclipped_5fscore_5ffor_5fsplice_3784',['min_softclipped_score_for_splice',['../classvg_1_1MultipathMapper.html#aaae9feaf584c64fe27628e29778359b4',1,'vg::MultipathMapper']]],
+ ['min_5fsplice_5flength_3785',['min_splice_length',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a801ecf2defc628516d4a5165ff745acb',1,'vg::SplicedHTSAlignmentEmitter::min_splice_length()'],['../classvg_1_1MultipathAlignmentEmitter.html#a38e7b3d9a6dca8b5601add1a6d9023e4',1,'vg::MultipathAlignmentEmitter::min_splice_length()'],['../classvg_1_1Surjector.html#a9046bb2c7267f996a6636518e2747b89',1,'vg::Surjector::min_splice_length()']]],
+ ['min_5fsplice_5frepair_5flength_3786',['min_splice_repair_length',['../classvg_1_1Surjector.html#ad5048905a75d047631f3552632f58cd3',1,'vg::Surjector']]],
+ ['min_5fsplice_5frescue_5fmatches_3787',['min_splice_rescue_matches',['../classvg_1_1MultipathMapper.html#a194ce33d0517a8ccd67c4e87d26f1191',1,'vg::MultipathMapper']]],
+ ['min_5fsupport_5fin_5fpath_3788',['min_support_in_path',['../classvg_1_1NestedTraversalFinder.html#a3021b0689285b7c73f8201dcea103dac',1,'vg::NestedTraversalFinder::min_support_in_path()'],['../classvg_1_1RepresentativeTraversalFinder.html#acdea076c1d46ca2b92b338bd023c081b',1,'vg::RepresentativeTraversalFinder::min_support_in_path()']]],
+ ['min_5ftail_5fanchor_5flength_3789',['min_tail_anchor_length',['../classvg_1_1MultipathMapper.html#a9616c4b8786af795cfd1f007c5e0c1dc',1,'vg::MultipathMapper']]],
+ ['min_5fto_5ffragment_3790',['min_to_fragment',['../classvg_1_1MinimizerMapper.html#a8b9e086aeaf58ab94283f9398890a9ca',1,'vg::MinimizerMapper']]],
+ ['min_5ftotal_5fsupport_5ffor_5fcall_3791',['min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#a559c8afa8e4f1f73768d7d90ff6a6db0',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5funique_5fnode_5ffraction_3792',['min_unique_node_fraction',['../classvg_1_1MinimizerMapper.html#a0df762ac6300835ee936f77a1b3daf8d',1,'vg::MinimizerMapper']]],
+ ['min_5funique_5fper_5fstrand_3793',['min_unique_per_strand',['../classvg_1_1Genotyper.html#a6b1feebb10944e684e417115e880fe39',1,'vg::Genotyper']]],
+ ['min_5fversion_3794',['MIN_VERSION',['../structvg_1_1Haplotypes_1_1Header.html#a58665b0f0dbbb098f50a6b02653f624e',1,'vg::Haplotypes::Header']]],
+ ['mindistanceclusterer_3795',['MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html',1,'vg::MinDistanceClusterer'],['../classvg_1_1MinDistanceClusterer.html#a8fe5349edbec12f8f15465249b8e6726',1,'vg::MinDistanceClusterer::MinDistanceClusterer()']]],
+ ['minimizer_3796',['Minimizer',['../structvg_1_1MinimizerMapper_1_1Minimizer.html',1,'vg::MinimizerMapper']]],
+ ['minimizer_5fcoverage_5fflank_3797',['minimizer_coverage_flank',['../classvg_1_1MinimizerMapper.html#abf19808c5cfabda803651ab3a049495e',1,'vg::MinimizerMapper']]],
+ ['minimizer_5fdownsampling_5fmax_5fwindow_5flength_3798',['minimizer_downsampling_max_window_length',['../classvg_1_1MinimizerMapper.html#a3aea2ff3e3fa7c837f8005aedf16cc4e',1,'vg::MinimizerMapper']]],
+ ['minimizer_5fdownsampling_5fwindow_5fcount_3799',['minimizer_downsampling_window_count',['../classvg_1_1MinimizerMapper.html#a6edefae974f20cbb3dfc0b9ac767bb98',1,'vg::MinimizerMapper']]],
+ ['minimizer_5fdownweight_5fthreshold_3800',['minimizer_downweight_threshold',['../structvg_1_1IndexingParameters.html#a441e50494bc2037df74d3b77b9dea964',1,'vg::IndexingParameters']]],
+ ['minimizer_5findex_3801',['minimizer_index',['../classvg_1_1MinimizerMapper.html#a30be171658ca4f82aaa05e0c42c0d61b',1,'vg::MinimizerMapper::minimizer_index()'],['../classvg_1_1HaplotypePartitioner.html#a450b3d9e8876b9679fca63dfba0962d2',1,'vg::HaplotypePartitioner::minimizer_index()']]],
+ ['minimizer_5findex_5ftype_3802',['minimizer_index_type',['../classvg_1_1HaplotypePartitioner.html#a9a059ded0fd7ed983801fa4d16f7cd5d',1,'vg::HaplotypePartitioner']]],
+ ['minimizer_5fmain_2ecpp_3803',['minimizer_main.cpp',['../minimizer__main_8cpp.html',1,'']]],
+ ['minimizer_5fmapper_2ecpp_3804',['minimizer_mapper.cpp',['../minimizer__mapper_8cpp.html',1,'']]],
+ ['minimizer_5fmapper_2ehpp_3805',['minimizer_mapper.hpp',['../minimizer__mapper_8hpp.html',1,'']]],
+ ['minimizer_5fmapper_5ffrom_5fchains_2ecpp_3806',['minimizer_mapper_from_chains.cpp',['../minimizer__mapper__from__chains_8cpp.html',1,'']]],
+ ['minimizer_5freverse_5fcomplement_3807',['minimizer_reverse_complement',['../namespacevg.html#ae4b8625853b4a17f731c9fbd5a040fd7',1,'vg']]],
+ ['minimizer_5fs_3808',['minimizer_s',['../structvg_1_1IndexingParameters.html#a85e4148452f9a2b23d0cdb75afe0fd3d',1,'vg::IndexingParameters']]],
+ ['minimizer_5fscore_5ffraction_3809',['minimizer_score_fraction',['../classvg_1_1MinimizerMapper.html#a5696bfb7029ca88ec04d0f849365b34f',1,'vg::MinimizerMapper']]],
+ ['minimizermapper_3810',['MinimizerMapper',['../classvg_1_1MinimizerMapper.html',1,'vg::MinimizerMapper'],['../classvg_1_1MinimizerMapper.html#ae2ecef3023c1cd374f0c7b1a3ac6ac5d',1,'vg::MinimizerMapper::MinimizerMapper()']]],
+ ['minimum_5fdistance_3811',['minimum_distance',['../namespacevg.html#abcbcd550b51078ae43f2b1d87941e1a0',1,'vg']]],
+ ['minimum_5fdistance_5fbetween_3812',['minimum_distance_between',['../classvg_1_1ZipCode.html#a3f0f330d338d949d04dbe14fd606e838',1,'vg::ZipCode']]],
+ ['mipayload_3813',['MIPayload',['../structvg_1_1MIPayload.html',1,'vg']]],
+ ['mismatch_3814',['mismatch',['../classvg_1_1GSSWAligner.html#abf06d9e9138bbbd23a451d1d0848c503',1,'vg::GSSWAligner::mismatch()'],['../classvg_1_1WFATree.html#a58f242d50871271336260013dfbcf4a8',1,'vg::WFATree::mismatch()'],['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeba1720159dd67365a6e856bd65a56722e7',1,'vg::WFAAlignment::mismatch()'],['../classvg_1_1SSWAligner.html#a49756fbcff60e14c65b58f76c78a923f',1,'vg::SSWAligner::mismatch()'],['../structScoringOptions.html#ad4144b88190ac6bc4881e5bcb0a26b50',1,'ScoringOptions::mismatch()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): xdrop_aligner.cpp']]],
+ ['mismatch_5fpositions_3815',['mismatch_positions',['../structvg_1_1GaplessExtension.html#a30b340b28d82e7070329e45aaa9e6486',1,'vg::GaplessExtension']]],
+ ['mismatches_3816',['mismatches',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ae28dd39b01ceed21e1a78fd24b32bcf6',1,'vg::WFAExtender::ErrorModel::mismatches()'],['../structvg_1_1GaplessExtension.html#a4898e2fabc109703f497e19f10bb164a',1,'vg::GaplessExtension::mismatches()']]],
+ ['mixture_5fweights_3817',['mixture_weights',['../classvg_1_1SpliceStats.html#ab5f243b05a8a80f0bf80ea3d82960e7e',1,'vg::SpliceStats']]],
+ ['mod_5fmain_2ecpp_3818',['mod_main.cpp',['../mod__main_8cpp.html',1,'']]],
+ ['mode_3819',['mode',['../structvg_1_1SummaryStatistics.html#a8aa060d244b54f34a06f0136d0572bd4',1,'vg::SummaryStatistics::mode()'],['../structHaplotypesConfig.html#ac5dd4d9940ef4d3d9f2dbfb7cde9754b',1,'HaplotypesConfig::mode()']]],
+ ['mode_5fclassify_3820',['mode_classify',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667abd23aa372c8ca2d63cf4b477257d27ea',1,'HaplotypesConfig']]],
+ ['mode_5fextract_3821',['mode_extract',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a8efe96a347c67fea3b49d01cb2c21dde',1,'HaplotypesConfig']]],
+ ['mode_5finvalid_3822',['mode_invalid',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667afef1428e91bd487b53f44f88885ed506',1,'HaplotypesConfig']]],
+ ['mode_5flog_5flikelihood_3823',['mode_log_likelihood',['../classvg_1_1SpliceStats.html#ad10b6fd62bdc23e8bb7afbf8c545f0bd',1,'vg::SpliceStats']]],
+ ['mode_5fmap_5fvariants_3824',['mode_map_variants',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667ac11510277093ba13a92edaad15a143f4',1,'HaplotypesConfig']]],
+ ['mode_5fname_3825',['mode_name',['../prune__main_8cpp.html#a9b89c7a3b7a8efd51b246bc312140bb8',1,'prune_main.cpp']]],
+ ['mode_5fpreprocess_3826',['mode_preprocess',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a2ecb8ae543c843b61de526ce2096f8fe',1,'HaplotypesConfig']]],
+ ['mode_5fprune_3827',['mode_prune',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a6a94759a7900a825dd21bf4d9eb648ef',1,'prune_main.cpp']]],
+ ['mode_5frestore_3828',['mode_restore',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a7ac5442ed3dfb51eaa1c7311fefc8842',1,'prune_main.cpp']]],
+ ['mode_5fsample_5fgraph_3829',['mode_sample_graph',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a043a4f84904086154417f62fbf55084b',1,'HaplotypesConfig']]],
+ ['mode_5fsample_5fhaplotypes_3830',['mode_sample_haplotypes',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a684f467f5682443799839a988b490626',1,'HaplotypesConfig']]],
+ ['mode_5fstatistics_3831',['mode_statistics',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a0ec67bc2861395ce21fbe3333a118713',1,'HaplotypesConfig']]],
+ ['mode_5funfold_3832',['mode_unfold',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a14b7711c85d633b1e1cee3b9466c48b3',1,'prune_main.cpp']]],
+ ['model_3833',['model',['../classvg_1_1MEMChainModel.html#a5f0fbf6a027827aa3a2ee1344588e7b7',1,'vg::MEMChainModel::model()'],['../classvg_1_1AlignmentChainModel.html#a18fbbeaa51ee69363983810e702fcf24',1,'vg::AlignmentChainModel::model()']]],
+ ['modular_5fexponent_3834',['modular_exponent',['../namespacevg.html#abc8f8791be2575164e6070e1cef39b4e',1,'vg']]],
+ ['motif_5fdata_3835',['motif_data',['../classvg_1_1SpliceStats.html#a6a48be87c666572f8e2893e8cf1df9a6',1,'vg::SpliceStats']]],
+ ['motif_5ffrequency_3836',['motif_frequency',['../classvg_1_1SpliceStats.html#aeb0d77ba4fc7a6767eff466a6ba8ed9e',1,'vg::SpliceStats']]],
+ ['motif_5fis_5freverse_3837',['motif_is_reverse',['../classvg_1_1SpliceStats.html#afc22a25e939fa725d3808430f9a62007',1,'vg::SpliceStats']]],
+ ['motif_5fmatches_3838',['motif_matches',['../classvg_1_1SpliceRegion.html#a79697742be9ce68f77d75b430f23a896',1,'vg::SpliceRegion']]],
+ ['motif_5fscore_3839',['motif_score',['../classvg_1_1SpliceStats.html#a7da67978c875a8e9bc1fac31fdb8277b',1,'vg::SpliceStats']]],
+ ['motif_5fsize_3840',['motif_size',['../classvg_1_1SpliceStats.html#aae5310e0728aebc36703641a566242e3',1,'vg::SpliceStats']]],
+ ['move_3841',['move',['../classvg_1_1SmallBitset.html#a5c80c7e3d6d92c7c5e58463771a2a341',1,'vg::SmallBitset']]],
+ ['mp_5faln_5femitter_3842',['mp_aln_emitter',['../classvg_1_1ReadFilter.html#a7baa666446be017dea5507fe5771de57',1,'vg::ReadFilter']]],
+ ['mp_5faln_5femitters_3843',['mp_aln_emitters',['../classvg_1_1MultipathAlignmentEmitter.html#abf746b78f8aaf59332dc1852c91affdd',1,'vg::MultipathAlignmentEmitter']]],
+ ['mpmap_5fmain_2ecpp_3844',['mpmap_main.cpp',['../mpmap__main_8cpp.html',1,'']]],
+ ['mq_5foverlap_3845',['mq_overlap',['../classvg_1_1Mapper.html#a6a23397e02e8522823d36ad4b11a698a',1,'vg::Mapper']]],
+ ['msa_5fconverter_2ecpp_3846',['msa_converter.cpp',['../msa__converter_8cpp.html',1,'']]],
+ ['msa_5fconverter_2ehpp_3847',['msa_converter.hpp',['../msa__converter_8hpp.html',1,'']]],
+ ['msaconverter_3848',['MSAConverter',['../classvg_1_1MSAConverter.html',1,'vg::MSAConverter'],['../classvg_1_1MSAConverter.html#ac6e82d70cf93d7b8a75750b40dd89277',1,'vg::MSAConverter::MSAConverter()']]],
+ ['msg_3849',['msg',['../classvg_1_1InsufficientInputException.html#a1e4d0ea31dffdc2f339bf11067c00d38',1,'vg::InsufficientInputException::msg()'],['../classvg_1_1RewindPlanException.html#a6dc3f46bfa00c1eb02030b4ff6e73f80',1,'vg::RewindPlanException::msg()'],['../classvg_1_1SizeLimitExceededException.html#ae776aba3017b9ff4c7e7b05002d0be99',1,'vg::SizeLimitExceededException::msg()']]],
+ ['msga_5fmain_2ecpp_3850',['msga_main.cpp',['../msga__main_8cpp.html',1,'']]],
+ ['mtx_3851',['mtx',['../classvg_1_1ParallelKFFReader.html#a616866362b3f55b76ea1df8a65c01267',1,'vg::ParallelKFFReader']]],
+ ['mu_3852',['mu',['../classvg_1_1FragmentLengthDistribution.html#a8c1fb2ac76ebdec084c599686ca12bfa',1,'vg::FragmentLengthDistribution']]],
+ ['multi_5fposition_5fannotations_3853',['multi_position_annotations',['../classvg_1_1AbstractReadSampler.html#a679c8195e5411d7460725453298b50f2',1,'vg::AbstractReadSampler']]],
+ ['multi_5fsurject_3854',['multi_surject',['../classvg_1_1Surjector.html#a0ed6215f3860203803deb2f3078d93b4',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#ab8b34cbb819829cd493bdc901a6e3060',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a943158332e4865de071dca68454a4d77',1,'vg::Surjector::multi_surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
+ ['multiallelic_5fsv_5fwarned_3855',['multiallelic_sv_warned',['../classvg_1_1Constructor.html#ad4a4e56154c62990a784f7e51e7368cd',1,'vg::Constructor']]],
+ ['multinomial_5fcensored_5fsampling_5fprob_5fln_3856',['multinomial_censored_sampling_prob_ln',['../namespacevg.html#a074fcebfeb68fc970b5b2a0db3722f01',1,'vg']]],
+ ['multinomial_5fchoose_5fln_3857',['multinomial_choose_ln',['../namespacevg.html#a15f09f05f7894863e9cd852c63266078',1,'vg']]],
+ ['multinomial_5fsampling_5fprob_5fln_3858',['multinomial_sampling_prob_ln',['../namespacevg.html#af4d69cf9a7d7e6272960fcb9f0a0a00c',1,'vg']]],
+ ['multipath_5falign_3859',['multipath_align',['../classvg_1_1MultipathMapper.html#a7af0cb7af3f7a3e3ab60627f3793aa0a',1,'vg::MultipathMapper']]],
+ ['multipath_5falignment_2ecpp_3860',['multipath_alignment.cpp',['../multipath__alignment_8cpp.html',1,'']]],
+ ['multipath_5falignment_2ehpp_3861',['multipath_alignment.hpp',['../multipath__alignment_8hpp.html',1,'']]],
+ ['multipath_5falignment_5femitter_2ecpp_3862',['multipath_alignment_emitter.cpp',['../multipath__alignment__emitter_8cpp.html',1,'']]],
+ ['multipath_5falignment_5femitter_2ehpp_3863',['multipath_alignment_emitter.hpp',['../multipath__alignment__emitter_8hpp.html',1,'']]],
+ ['multipath_5falignment_5fgraph_2ecpp_3864',['multipath_alignment_graph.cpp',['../multipath__alignment__graph_8cpp.html',1,'']]],
+ ['multipath_5falignment_5fgraph_2ehpp_3865',['multipath_alignment_graph.hpp',['../multipath__alignment__graph_8hpp.html',1,'']]],
+ ['multipath_5falignment_5fpath_5foffsets_3866',['multipath_alignment_path_offsets',['../namespacevg_1_1algorithms.html#ad0cecedaa8dd475e634b513af5be028b',1,'vg::algorithms']]],
+ ['multipath_5falignment_5ft_3867',['multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html',1,'vg::multipath_alignment_t'],['../classvg_1_1multipath__alignment__t.html#ae7f715f63023d3043c01ed29193ea6a1',1,'vg::multipath_alignment_t::multipath_alignment_t()'],['../classvg_1_1multipath__alignment__t.html#a55b4c1fee893c4b596f0a654a624bccc',1,'vg::multipath_alignment_t::multipath_alignment_t(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ad4de932d4f01d8d44a76095605294470',1,'vg::multipath_alignment_t::multipath_alignment_t(multipath_alignment_t &&other)']]],
+ ['multipath_5fmap_3868',['multipath_map',['../classvg_1_1MultipathMapper.html#a9ea318c04336aa79020b7c012e468ef8',1,'vg::MultipathMapper']]],
+ ['multipath_5fmap_5fpaired_3869',['multipath_map_paired',['../classvg_1_1MultipathMapper.html#a240c4502e41aa0e5961772a12b1b42a8',1,'vg::MultipathMapper']]],
+ ['multipath_5fmapper_2ecpp_3870',['multipath_mapper.cpp',['../multipath__mapper_8cpp.html',1,'']]],
+ ['multipath_5fmapper_2ehpp_3871',['multipath_mapper.hpp',['../multipath__mapper_8hpp.html',1,'']]],
+ ['multipathalignment_3872',['MultipathAlignment',['../structvg_1_1MultipathAlignment.html',1,'vg']]],
+ ['multipathalignmentemitter_3873',['MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html',1,'vg::MultipathAlignmentEmitter'],['../classvg_1_1MultipathAlignmentEmitter.html#a022247fcbd889aeb51b35b0cae1c3622',1,'vg::MultipathAlignmentEmitter::MultipathAlignmentEmitter()']]],
+ ['multipathalignmentgraph_3874',['MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html',1,'vg::MultipathAlignmentGraph'],['../classvg_1_1MultipathAlignmentGraph.html#a058e6120cb359e2566c1c2d7961c608e',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a51e7308dc1c0c96d1e576970211b7705',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#afd75ac7afd23901c4b8f38eb126bdba0',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a74eec86f754011999dc6caed5d1f6c8a',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a366ddb07faadad371e896d3f453e147c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a4289e77bb6d76abfbb1d3c02d89a2586',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#ac8f4ae19921529920157bcbbf9a2f5c3',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a10f9b18c8aa4db1b80bf54ccc5dcc09c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const unordered_map< id_t, pair< id_t, bool >> &projection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a89b441f028fd26c177a9ce8d8188b7c1',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project)']]],
+ ['multipathmapper_3875',['MultipathMapper',['../classvg_1_1MultipathMapper.html',1,'vg::MultipathMapper'],['../classvg_1_1MultipathMapper.html#a4d3a7e85dfc2d7cda41912a4f87fd5ac',1,'vg::MultipathMapper::MultipathMapper()']]],
+ ['multipathproblem_3876',['MultipathProblem',['../structvg_1_1MultipathProblem.html',1,'vg::MultipathProblem'],['../structvg_1_1MultipathProblem.html#ac97d55858c86d218c380fd43e115d18a',1,'vg::MultipathProblem::MultipathProblem()']]],
+ ['multiplexer_3877',['multiplexer',['../classvg_1_1HTSWriter.html#a6e2ff3f77a4265c8dcd1c47770a0bee5',1,'vg::HTSWriter::multiplexer()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a24cd277c06adf66414346ffeb22c0400',1,'vg::io::TSVAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a2f047c1205c512b44f29d0e8231c0cef',1,'vg::io::VGAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a286a69e0bb8071d101e27e501ce1e3ce',1,'vg::io::GafAlignmentEmitter::multiplexer()']]],
+ ['mut_5fgraph_5fimpl_3878',['mut_graph_impl',['../structvg_1_1IndexingParameters.html#a9db2b318dee6f693544c8fc5a04c0a53',1,'vg::IndexingParameters']]],
+ ['mut_5fsampler_3879',['mut_sampler',['../classvg_1_1NGSSimulator.html#a9501d39b8059ad161395f2b7ba89d424',1,'vg::NGSSimulator']]],
+ ['mutable_5fconnection_3880',['mutable_connection',['../classvg_1_1subpath__t.html#a271236a46bdb6105f216a630c0c67a74',1,'vg::subpath_t::mutable_connection()'],['../classvg_1_1subpath__t.html#aa967fceb620f92e73e965345d4cd0b67',1,'vg::subpath_t::mutable_connection(size_t i)']]],
+ ['mutable_5fedit_3881',['mutable_edit',['../classvg_1_1path__mapping__t.html#aeb9d50accda37c8829c49cd8567f72bc',1,'vg::path_mapping_t::mutable_edit()'],['../classvg_1_1path__mapping__t.html#a56c059138a051e7889f4083a74c5401f',1,'vg::path_mapping_t::mutable_edit(size_t i)']]],
+ ['mutable_5fhandle_5fgraph_2ecpp_3882',['mutable_handle_graph.cpp',['../mutable__handle__graph_8cpp.html',1,'']]],
+ ['mutable_5fhandle_5fgraph_2ehpp_3883',['mutable_handle_graph.hpp',['../mutable__handle__graph_8hpp.html',1,'']]],
+ ['mutable_5fmapping_3884',['mutable_mapping',['../classvg_1_1path__t.html#ab3f1eeeefe1c604dacdeff019488ff07',1,'vg::path_t::mutable_mapping()'],['../classvg_1_1path__t.html#aac0ad10ace8970358d471d779061b22d',1,'vg::path_t::mutable_mapping(size_t i)']]],
+ ['mutable_5fnext_3885',['mutable_next',['../classvg_1_1subpath__t.html#ae1331c79838d972ccb8be4e98ac87954',1,'vg::subpath_t']]],
+ ['mutable_5fpath_3886',['mutable_path',['../classvg_1_1subpath__t.html#aa5f32fe1e7167d09187d4a69c091bde5',1,'vg::subpath_t']]],
+ ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ecpp_3887',['mutable_path_deletable_handle_graph.cpp',['../mutable__path__deletable__handle__graph_8cpp.html',1,'']]],
+ ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ehpp_3888',['mutable_path_deletable_handle_graph.hpp',['../mutable__path__deletable__handle__graph_8hpp.html',1,'']]],
+ ['mutable_5fpath_5fhandle_5fgraph_2ecpp_3889',['mutable_path_handle_graph.cpp',['../mutable__path__handle__graph_8cpp.html',1,'']]],
+ ['mutable_5fpath_5fhandle_5fgraph_2ehpp_3890',['mutable_path_handle_graph.hpp',['../mutable__path__handle__graph_8hpp.html',1,'']]],
+ ['mutable_5fpath_5fmetadata_2ecpp_3891',['mutable_path_metadata.cpp',['../mutable__path__metadata_8cpp.html',1,'']]],
+ ['mutable_5fpath_5fmetadata_2ehpp_3892',['mutable_path_metadata.hpp',['../mutable__path__metadata_8hpp.html',1,'']]],
+ ['mutable_5fpath_5fmutable_5fhandle_5fgraph_2ehpp_3893',['mutable_path_mutable_handle_graph.hpp',['../mutable__path__mutable__handle__graph_8hpp.html',1,'']]],
+ ['mutable_5fposition_3894',['mutable_position',['../classvg_1_1path__mapping__t.html#a87ef119207623109aea694cd5432421d',1,'vg::path_mapping_t']]],
+ ['mutable_5fquality_3895',['mutable_quality',['../classvg_1_1multipath__alignment__t.html#a5d62a17eb3aad07f05f5580aa7f9dfbd',1,'vg::multipath_alignment_t']]],
+ ['mutable_5fsequence_3896',['mutable_sequence',['../classvg_1_1multipath__alignment__t.html#a11d22790dc8b9cc631a237ef00b6e0e4',1,'vg::multipath_alignment_t::mutable_sequence()'],['../classvg_1_1edit__t.html#aa5e639217215d8d67bfe1ec2a07105fb',1,'vg::edit_t::mutable_sequence()']]],
+ ['mutable_5fstart_3897',['mutable_start',['../classvg_1_1multipath__alignment__t.html#a43e30d76e7ac0596fc15c868fbbd603c',1,'vg::multipath_alignment_t']]],
+ ['mutable_5fsubpath_3898',['mutable_subpath',['../classvg_1_1multipath__alignment__t.html#a65ee05140e26b51a60f7d33a7b9b9c54',1,'vg::multipath_alignment_t::mutable_subpath()'],['../classvg_1_1multipath__alignment__t.html#a727e5e6bc04955e46efe83bc5d668bdf',1,'vg::multipath_alignment_t::mutable_subpath(size_t i)']]],
+ ['mutablegraphimplementation_3899',['MutableGraphImplementation',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10',1,'vg::IndexingParameters']]],
+ ['mutablehandlegraph_3900',['MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html',1,'handlegraph::MutableHandleGraph'],['../namespacevg.html#a293aa7465cc63a2581914d6a85a0e4b8',1,'vg::MutableHandleGraph()']]],
+ ['mutablepathdeletablehandlegraph_3901',['MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html',1,'handlegraph::MutablePathDeletableHandleGraph'],['../namespacevg.html#a2f0cc7bac7a4f92b2b523357f8940aa5',1,'vg::MutablePathDeletableHandleGraph()']]],
+ ['mutablepathhandlegraph_3902',['MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html',1,'handlegraph::MutablePathHandleGraph'],['../namespacevg.html#a24350c08e6d69244e6930f41fee00e1f',1,'vg::MutablePathHandleGraph()']]],
+ ['mutablepathmetadata_3903',['MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html',1,'handlegraph']]],
+ ['mutablepathmutablehandlegraph_3904',['MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html',1,'handlegraph::MutablePathMutableHandleGraph'],['../namespacevg.html#aa2f83c48d4ecdcfd8f2604f10e863aea',1,'vg::MutablePathMutableHandleGraph()']]],
+ ['mutate_3905',['mutate',['../classvg_1_1Sampler.html#a8f148dac7598a3465202371511e53f2a',1,'vg::Sampler']]],
+ ['mutate_5fedit_3906',['mutate_edit',['../classvg_1_1Sampler.html#ad372d6fdcac5af601bdb0729f94a7e7d',1,'vg::Sampler']]],
+ ['mutation_5falphabets_3907',['mutation_alphabets',['../classvg_1_1NGSSimulator.html#a4a8eacfde748b35453a54ab40c195680',1,'vg::NGSSimulator']]],
+ ['mutex_5fgraph_3908',['mutex_graph',['../classvg_1_1Transcriptome.html#a881ee68ca1a43b0ab10494f62e7b127f',1,'vg::Transcriptome']]],
+ ['mutex_5ftranscript_5fpaths_3909',['mutex_transcript_paths',['../classvg_1_1Transcriptome.html#a3c6d64194201d695fdcb07078463161a',1,'vg::Transcriptome']]],
+ ['my_5fmapper_3910',['my_mapper',['../classvg_1_1Filter.html#a13678a95a03ae4feb7e6ebc0fa00a69f',1,'vg::Filter']]],
+ ['my_5fmax_5fdistance_3911',['my_max_distance',['../classvg_1_1Filter.html#ab9ec8e13d2cd4fc50aa86981a0b6475f',1,'vg::Filter']]],
+ ['my_5fnames_3912',['my_names',['../classVectorizer.html#a5702f38d3e6d29866e2135d29f7496fd',1,'Vectorizer']]],
+ ['my_5fpath_5fposition_5fgraph_3913',['my_path_position_graph',['../classvg_1_1Filter.html#af17db75bb83c6d2ad00b813a4812d30d',1,'vg::Filter']]],
+ ['my_5fvectors_3914',['my_vectors',['../classVectorizer.html#af370e810d055623deaa0bfaac120fe8d',1,'Vectorizer']]],
+ ['my_5fvg_3915',['my_vg',['../classvg_1_1Filter.html#ac849cd8534ba9b7eb7daa8485d6c9d45',1,'vg::Filter']]],
+ ['my_5fxg_3916',['my_xg',['../classVectorizer.html#adebb6c75ae3b7c1199143ab2f166d284',1,'Vectorizer']]]
];
diff --git a/search/all_e.js b/search/all_e.js
index c114ba8eaa..aac4ef311c 100644
--- a/search/all_e.js
+++ b/search/all_e.js
@@ -1,209 +1,209 @@
var searchData=
[
- ['n_3915',['n',['../namespacehaplotypes__defaults.html#a08f2ff580a81523291eed7ef0d644bd2',1,'haplotypes_defaults']]],
- ['n_5fbins_3916',['n_bins',['../classvg_1_1Packer.html#a3e753cd974d4411036081d252b6eb7bf',1,'vg::Packer']]],
- ['n_5fiterations_3917',['n_iterations',['../classvg_1_1MCMCGenotyper.html#a1d5684e63858e5362578bc85d638a870',1,'vg::MCMCGenotyper']]],
- ['name_3918',['name',['../structvg_1_1BenchmarkResult.html#a406a53ba511e3f0f28d20a542b41355a',1,'vg::BenchmarkResult::name()'],['../structvg_1_1BREAKPOINT.html#a098f871767e6bbb25ec840acfabae12b',1,'vg::BREAKPOINT::name()'],['../structvg_1_1Funnel_1_1Stage.html#a709200eef7b97eb16aaaeaad95aab6fe',1,'vg::Funnel::Stage::name()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ac72259c3b34d4ec70dcb14225a546c0a',1,'vg::Recombinator::LocalHaplotype::name()'],['../structvg_1_1Transcript.html#a91a919300bda880406cf56a4f78cffda',1,'vg::Transcript::name()'],['../classvg_1_1VG.html#a1f6fcd5a907e9bee524cf37a62ad5be2',1,'vg::VG::name()'],['../structvg_1_1VG_1_1Plan.html#aba1bea59a4b1db998936d5d99eff9c4e',1,'vg::VG::Plan::name()'],['../classvg_1_1subcommand_1_1Subcommand.html#a1873ba1dfd0eec7c8db3303f18971e08',1,'vg::subcommand::Subcommand::name()'],['../structgafkluge_1_1GafStep.html#a9cf80aad32be2824f3a2196e669851ca',1,'gafkluge::GafStep::name()'],['../structvg_1_1Node.html#a3a4827f5d3eb097a4ef9e542e56c1e2c',1,'vg::Node::name()'],['../structvg_1_1Position.html#ae2e1a55adad827628c58ec06489c54ed',1,'vg::Position::name()'],['../structvg_1_1Path.html#a24e6f7ffbbe8fcbd7444937b7fcd1601',1,'vg::Path::name()'],['../structvg_1_1Alignment.html#ad20cac38e0bd25d2b32862fe1f5409ab',1,'vg::Alignment::name()'],['../structvg_1_1MultipathAlignment.html#a9427bb485b73bc6d3e2f077ee5df303d',1,'vg::MultipathAlignment::name()'],['../structvg_1_1Snarl.html#ac6e2f21c606af930c7f77f8f4027f833',1,'vg::Snarl::name()'],['../structvg_1_1Visit.html#ac0dae7bcea098cf39bbba443e7b45cbf',1,'vg::Visit::name()'],['../structvg_1_1SnarlTraversal.html#a1c8921481ba23cd8fe8725212f376b21',1,'vg::SnarlTraversal::name()'],['../structvg_1_1Locus.html#a39e5699f029942f81777d7e0ab203189',1,'vg::Locus::name()']]],
- ['name_5fmapper_2ecpp_3919',['name_mapper.cpp',['../name__mapper_8cpp.html',1,'']]],
- ['name_5fmapper_2ehpp_3920',['name_mapper.hpp',['../name__mapper_8hpp.html',1,'']]],
- ['name_5fprefixes_3921',['name_prefixes',['../classvg_1_1ReadFilter.html#a59dd97c0eadf3aebd852ae3b0aabe31d',1,'vg::ReadFilter']]],
- ['name_5fto_5fid_3922',['name_to_id',['../classvg_1_1Paths.html#a032139e6fadea366f224508c8f8385df',1,'vg::Paths::name_to_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a349cfce46078beef8d6169874b5b29b9',1,'vg::algorithms::GFAIDMapInfo::name_to_id()']]],
- ['named_5fnode_5fback_5ftranslation_2ehpp_3923',['named_node_back_translation.hpp',['../named__node__back__translation_8hpp.html',1,'']]],
- ['namednodebacktranslation_3924',['NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html',1,'handlegraph::NamedNodeBackTranslation'],['../namespacevg.html#a2c7b4f84e5a75aee3d3abf4b65b0000f',1,'vg::NamedNodeBackTranslation()']]],
- ['namemapper_3925',['NameMapper',['../classvg_1_1NameMapper.html',1,'vg']]],
- ['nearest_5foffsets_5fin_5fpaths_3926',['nearest_offsets_in_paths',['../classxg_1_1XG.html#ab885cecf687ffb8583fb95cce8ca34b2',1,'xg::XG::nearest_offsets_in_paths()'],['../namespacevg_1_1algorithms.html#a477330d3ab29cbd3c48e4830d51b3e0f',1,'vg::algorithms::nearest_offsets_in_paths()']]],
- ['nearest_5foffsets_5fin_5fpaths_2ecpp_3927',['nearest_offsets_in_paths.cpp',['../nearest__offsets__in__paths_8cpp.html',1,'']]],
- ['nearest_5foffsets_5fin_5fpaths_2ehpp_3928',['nearest_offsets_in_paths.hpp',['../nearest__offsets__in__paths_8hpp.html',1,'']]],
- ['nearest_5fpath_5fnode_3929',['nearest_path_node',['../classxg_1_1XG.html#a03f2f8a4cc3d06e4f1748474082efdb9',1,'xg::XG']]],
- ['need_5fcomma_3930',['need_comma',['../classvg_1_1ProblemDumpExplainer.html#af1f3a4b525a0c5b4daeee2a3ae9a3a18',1,'vg::ProblemDumpExplainer']]],
- ['need_5fline_3931',['need_line',['../classvg_1_1TSVExplainer.html#a810b272c339e543614686bce35a82f76',1,'vg::TSVExplainer']]],
- ['need_5ftab_3932',['need_tab',['../classvg_1_1TSVExplainer.html#ad9f986f075d4dbe3033a2102376e12e5',1,'vg::TSVExplainer']]],
- ['nested_5fdecomposition_3933',['nested_decomposition',['../classvg_1_1Deconstructor.html#aa6cf4f15fa2a53976ee40443e63df36f',1,'vg::Deconstructor']]],
- ['nested_5fsupport_5ffinder_3934',['nested_support_finder',['../classvg_1_1NestedFlowCaller.html#a2c0bda955a72c10f4040ea42203b8f39',1,'vg::NestedFlowCaller']]],
- ['nested_5ftraversal_5ffinder_2ecpp_3935',['nested_traversal_finder.cpp',['../nested__traversal__finder_8cpp.html',1,'']]],
- ['nested_5ftraversal_5ffinder_2ehpp_3936',['nested_traversal_finder.hpp',['../nested__traversal__finder_8hpp.html',1,'']]],
- ['nestedcachedpackedtraversalsupportfinder_3937',['NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html',1,'vg::NestedCachedPackedTraversalSupportFinder'],['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#a6893d620886b1bb326f735e36757f6e2',1,'vg::NestedCachedPackedTraversalSupportFinder::NestedCachedPackedTraversalSupportFinder()']]],
- ['nestedflowcaller_3938',['NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html',1,'vg::NestedFlowCaller'],['../classvg_1_1NestedFlowCaller.html#ab56c3d2fe181450dc33167539bc8f74c',1,'vg::NestedFlowCaller::NestedFlowCaller()']]],
- ['nestedtraversalfinder_3939',['NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html',1,'vg::NestedTraversalFinder'],['../classvg_1_1NestedTraversalFinder.html#a0ab18d1355be2772f9ca78c5eb269e6c',1,'vg::NestedTraversalFinder::NestedTraversalFinder()']]],
- ['nestinginfo_3940',['NestingInfo',['../structvg_1_1Deconstructor_1_1NestingInfo.html',1,'vg::Deconstructor']]],
- ['net_5fgraph_5fof_3941',['net_graph_of',['../classvg_1_1SnarlManager.html#aa8872188679a5ad4d0da08c1235f2019',1,'vg::SnarlManager']]],
- ['net_5fgraphs_3942',['net_graphs',['../classvg_1_1GenomeState.html#a7745fd8de0051a478dbf5b4e47ebce8c',1,'vg::GenomeState']]],
- ['net_5fhandle_3943',['net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#a9288aae0c2945e8b6213368b9bf99eec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['net_5fhandle_5ft_3944',['net_handle_t',['../structhandlegraph_1_1net__handle__t.html',1,'handlegraph']]],
- ['net_5fhandle_5fto_5fnode_5fproblem_5findex_3945',['net_handle_to_node_problem_index',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#ada18575df8f9870a5063c99ac6167612',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['net_5fidentifier_5ft_3946',['net_identifier_t',['../namespacevg.html#a064c859d9612d9c2b240b9c0d01f8a85',1,'vg']]],
- ['net_5fnode_5flanes_3947',['net_node_lanes',['../classvg_1_1SnarlState.html#a01d595bd630d0d550176cade6897b491',1,'vg::SnarlState']]],
- ['netgraph_3948',['NetGraph',['../classvg_1_1NetGraph.html',1,'vg::NetGraph'],['../classvg_1_1NetGraph.html#a9059c913779ce4095224a5ae6638a27d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains_mixed, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#a29abf89e03eedc7ac2af4682a1b5bb04',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains, const SnarlContainer &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aa1e17ccb08d595123db3d8cd6e2593b2',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const vector< vector< pair< Snarl, bool >>> &child_chains, const vector< Snarl > &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aba1479f586d07f276ba6925cfc1a8e6d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const HandleGraph *graph, bool use_internal_connectivity=false)']]],
- ['new_5fheight_3949',['new_height',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae444abfaf71eedae674fb4703e910248',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['new_5flength_3950',['new_length',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a9d8c1bf7222ee28236691c30185194d3',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['new_5fnode_3951',['new_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ab98205bb3934c92fec2a63a0360339b4',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['new_5foutput_5fgraph_3952',['new_output_graph',['../namespacevg_1_1io.html#a4b6ad53e3fc9e4c143221b213932db70',1,'vg::io']]],
- ['new_5fside_3953',['new_side',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af0ea102c59fcbcb1a5387ea5b465e950',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['next_3954',['Next',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a91e4dc4f48957737a80e99a8ad32ba53',1,'vg::io::BlockedGzipInputStream::Next()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a0c3e80161a999b884abf3965dd0a5a39',1,'vg::io::BlockedGzipOutputStream::Next()'],['../structvg_1_1PathBranch.html#acf21b2d9bb36f687d4727c56a4b2e940',1,'vg::PathBranch::next()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#ae6ca62f71e4ab5a266170af025ec97dd',1,'vg::PhasedGenome::HaplotypeNode::next()'],['../structvg_1_1Subpath.html#ae8d4a9f246eae61420b666aa0665930d',1,'vg::Subpath::next()'],['../structvg_1_1Connection.html#a151e393bbacd7904d71afd4939950509',1,'vg::Connection::next()'],['../classvg_1_1WFATree.html#acec4f54d7784d6c7310418ddec2716b9',1,'vg::WFATree::next()'],['../classvg_1_1connection__t.html#a18d278044df80b1334542e6d25043a32',1,'vg::connection_t::next()'],['../classvg_1_1subpath__t.html#a60a4ec0114c307ae532ea307128bfe24',1,'vg::subpath_t::next() const'],['../classvg_1_1subpath__t.html#aabe3e1337325511c83d7e949195fdf37',1,'vg::subpath_t::next(size_t i) const'],['../classvg_1_1WindowedVcfBuffer.html#a0d66b5a177f55cb726122577840d8911',1,'vg::WindowedVcfBuffer::next()']]],
- ['next_5fchar_3955',['next_char',['../structvg_1_1kmer__t.html#a844852956a93c48eadc3557a0da7ab66',1,'vg::kmer_t']]],
- ['next_5fchars_3956',['next_chars',['../structvg_1_1KmerPosition.html#ae56be5485cffba06cdab7c949487ea3f',1,'vg::KmerPosition']]],
- ['next_5fcost_3957',['next_cost',['../classvg_1_1MEMChainModelVertex.html#af972fee5a48a5eb92466395cdffe38c4',1,'vg::MEMChainModelVertex::next_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#ab4300ed3dcbce1f434b6db7d28aa6a0f',1,'vg::AlignmentChainModelVertex::next_cost()']]],
- ['next_5fempty_5falignment_3958',['next_empty_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a08e8eed8f95a621c9786bca1b0850dd2',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['next_5fexplanation_5fnumber_3959',['next_explanation_number',['../classvg_1_1Explainer.html#ad6f34855ed8bf99838f158ed027b3a6a',1,'vg::Explainer']]],
- ['next_5fgroup_3960',['next_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a5dee6816359ccf56409120cff36a759b',1,'vg::IndexedVG::CacheEntry']]],
- ['next_5fis_5fempty_3961',['next_is_empty',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a016150b6b6f4551ee3eb7600d7037b67',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['next_5fpath_5fposition_3962',['next_path_position',['../classxg_1_1XG.html#ae973d41358ddab92f0a2dca094806102',1,'xg::XG']]],
- ['next_5fpos_3963',['next_pos',['../structvg_1_1kmer__t.html#a4af3ee75920ba66867f991ec823b2bf4',1,'vg::kmer_t']]],
- ['next_5fpos_5fchars_3964',['next_pos_chars',['../classvg_1_1Sampler.html#ab5455f8f6faf176b418e3dbcb6bf1ce8',1,'vg::Sampler::next_pos_chars()'],['../namespacevg_1_1algorithms.html#a22d03c4f50c51d0d537811ba88895688',1,'vg::algorithms::next_pos_chars()']]],
- ['next_5fpos_5fchars_2ecpp_3965',['next_pos_chars.cpp',['../next__pos__chars_8cpp.html',1,'']]],
- ['next_5fpos_5fchars_2ehpp_3966',['next_pos_chars.hpp',['../next__pos__chars_8hpp.html',1,'']]],
- ['next_5fpositions_3967',['next_positions',['../structvg_1_1KmerPosition.html#ad6a841261ad5205e4dc10503f5ec8ba7',1,'vg::KmerPosition']]],
- ['next_5fscore_3968',['next_score',['../classvg_1_1WFATree.html#aba63fbf6ca1e1382e62727ea95c4b0af',1,'vg::WFATree']]],
- ['next_5fsize_3969',['next_size',['../classvg_1_1subpath__t.html#aab697710ebd5e8f968bed5c5262bbe2a',1,'vg::subpath_t']]],
- ['next_5fsnarl_3970',['next_snarl',['../classvg_1_1SnarlManager.html#afcca3b74e960b6931598188e0b9ae7a8',1,'vg::SnarlManager']]],
- ['next_5ftraceback_5falignment_3971',['next_traceback_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a8d6cbc921387724da8db3c8c0f20f363',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['ngssimulator_3972',['NGSSimulator',['../classvg_1_1NGSSimulator.html',1,'vg::NGSSimulator'],['../classvg_1_1NGSSimulator.html#a51e3a4117f9339b3195d73f2c6cf560e',1,'vg::NGSSimulator::NGSSimulator(PathPositionHandleGraph &graph, const string &ngs_fastq_file, const string &ngs_paired_fastq_file="", bool interleaved_fastq=false, const vector< string > &source_paths={}, const vector< double > &source_path_ploidies={}, const vector< pair< string, double >> &transcript_expressions={}, const vector< tuple< string, string, size_t >> &haplotype_transcripts={}, double substition_polymorphism_rate=0.001, double indel_polymorphism_rate=0.0002, double indel_error_proportion=0.01, double fragment_length_mean=300.0, double fragment_length_stdev=50.0, double error_multiplier=1.0, bool retry_on_Ns=true, bool sample_unsheared_paths=false, uint64_t seed=0)'],['../classvg_1_1NGSSimulator.html#a5417af00068600ab1e6d0acb24836698',1,'vg::NGSSimulator::NGSSimulator(void)=delete']]],
- ['nid_5ft_3973',['nid_t',['../namespacevg.html#a26f660292f00451f15d1c95d9b8c6ffb',1,'vg::nid_t()'],['../namespacexg.html#a8f8752f074f0e121862f9dd3aabfbb45',1,'xg::nid_t()'],['../namespacehandlegraph.html#a93c2889b752934c4b2488b37cbdd278b',1,'handlegraph::nid_t()'],['../namespacevg_1_1io.html#a43c8209ab6c2c1d48c0ca50c24fd0d13',1,'vg::io::nid_t()']]],
- ['no_5fchain_5finfo_3974',['no_chain_info',['../classvg_1_1MinimizerMapper.html#a3b9a4518b171aa85909da6ccde88e0a8',1,'vg::MinimizerMapper']]],
- ['no_5fclustering_3975',['no_clustering',['../classvg_1_1MultipathMapper.html#ad4a0793bd06a62ca2e267e5a1ceb4643',1,'vg::MultipathMapper']]],
- ['no_5fcode_3976',['NO_CODE',['../structvg_1_1MIPayload.html#aad1e599cc16dec3115ea845eada83bb3',1,'vg::MIPayload']]],
- ['no_5fend_5fposition_3977',['NO_END_POSITION',['../classhandlegraph_1_1PathMetadata.html#a2b966a3af9aac1a11236de902cae6f8b',1,'handlegraph::PathMetadata']]],
- ['no_5fhaplotype_3978',['NO_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#a22d67bfb9356f42b46aaa6cefc1ee24b',1,'handlegraph::PathMetadata']]],
- ['no_5findex_3979',['NO_INDEX',['../namespacevg.html#a0fc209aaa8c7c17499d70452d2816f44',1,'vg']]],
- ['no_5flocus_5fname_3980',['NO_LOCUS_NAME',['../classhandlegraph_1_1PathMetadata.html#ae7ee0795aa13f7ad34189f2982d64c42',1,'handlegraph::PathMetadata']]],
- ['no_5fmultiple_5fcover_5ftypes_3981',['no_multiple_cover_types',['../gbwt__main_8cpp.html#a0124aac03621e82b84ef0de974a08574',1,'gbwt_main.cpp']]],
- ['no_5fmultiple_5finput_5ftypes_3982',['no_multiple_input_types',['../gbwt__main_8cpp.html#ae1c5768186dc339c157bf4b72517b5ab',1,'gbwt_main.cpp']]],
- ['no_5fmultiple_5finputs_3983',['no_multiple_inputs',['../convert__main_8cpp.html#aca425ac5df78dde7681385a5341abb1b',1,'convert_main.cpp']]],
- ['no_5fns_3984',['no_Ns',['../classvg_1_1Sampler.html#aa71ef9078ed81b2406357f0dd4fdda3a',1,'vg::Sampler']]],
- ['no_5fphase_5fblock_3985',['NO_PHASE_BLOCK',['../classhandlegraph_1_1PathMetadata.html#a03fdf276dc586f22039aa3e70dd9bf77',1,'handlegraph::PathMetadata']]],
- ['no_5fpos_3986',['no_pos',['../classvg_1_1WFATree.html#ad0383cee94782b3f0e8d48078d4d2348',1,'vg::WFATree']]],
- ['no_5fprogress_3987',['NO_PROGRESS',['../namespacevg_1_1io.html#a33939950704e2d4439b93cde15139172',1,'vg::io']]],
- ['no_5fread_5findex_3988',['NO_READ_INDEX',['../namespacevg.html#aa32104605c22b25e9ec17d69fbc61a4b',1,'vg']]],
- ['no_5fsample_5fname_3989',['NO_SAMPLE_NAME',['../classhandlegraph_1_1PathMetadata.html#a9770508967dec07997d8ad31dbbe5a95',1,'handlegraph::PathMetadata']]],
- ['no_5fsplice_5flog_5fodds_3990',['no_splice_log_odds',['../classvg_1_1MultipathMapper.html#a3130f372f82437af2f7733901a47c142',1,'vg::MultipathMapper']]],
- ['no_5fsplice_5fnatural_5flog_5fodds_3991',['no_splice_natural_log_odds',['../classvg_1_1MultipathMapper.html#a3903979b6a7b5e297335f823864cd511',1,'vg::MultipathMapper']]],
- ['no_5fsubrange_3992',['NO_SUBRANGE',['../classhandlegraph_1_1PathMetadata.html#a8524bdffc330d58553459074c57fc889',1,'handlegraph::PathMetadata']]],
- ['no_5fvalue_3993',['NO_VALUE',['../structvg_1_1MIPayload.html#a90c2f3f622099c6920b28356d49d9a4e',1,'vg::MIPayload']]],
- ['no_5fwait_3994',['NO_WAIT',['../namespacevg_1_1io.html#a21ec64ee292cf76a61bff68a727471e9',1,'vg::io']]],
- ['noalignmentinbandexception_3995',['NoAlignmentInBandException',['../classvg_1_1NoAlignmentInBandException.html',1,'vg']]],
- ['node_3996',['Node',['../structvg_1_1Node.html',1,'vg::Node'],['../structvg_1_1algorithms_1_1Node.html',1,'vg::algorithms::Node'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a15ee21b9bf2ed37f9892ca0291964d28',1,'vg::BandedGlobalAligner::BAMatrix::node()'],['../structvg_1_1CactusSide.html#a1e590f9e0956cdd491c9758a89bc4e1e',1,'vg::CactusSide::node()'],['../classvg_1_1NodeSide.html#a11a48024eddd85edf22b6e0748049fa0',1,'vg::NodeSide::node()'],['../classvg_1_1NodeTraversal.html#a73ca27b85d0f387740425dea434763ed',1,'vg::NodeTraversal::node()'],['../structvg_1_1Graph.html#ac16f6921068e2ae84b0d2166b2eb3b4e',1,'vg::Graph::node()'],['../structvg_1_1MatchPos.html#abd73a2a9a1d86e1747631f89b045e4fd',1,'vg::MatchPos::node()'],['../classxg_1_1XGPath.html#a621253a080fdb8b81eb5efe2359b93a8',1,'xg::XGPath::node()'],['../structvg_1_1Tree.html#ad5b04c67e4c1390c2ae46d1db40548f7',1,'vg::Tree::Node()'],['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a2995e7f61da600fe7b67e5fd40d4b319',1,'vg::ZipCode::NODE()']]],
- ['node_5fat_5fvector_5foffset_3997',['node_at_vector_offset',['../classxg_1_1XG.html#a2f2c0b014af5d0032f9beaefb074cc59',1,'xg::XG::node_at_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a3095e541eee436a9f49ef0846539ef44',1,'handlegraph::VectorizableHandleGraph::node_at_vector_offset()']]],
- ['node_5fby_5fid_3998',['node_by_id',['../classvg_1_1VG.html#ad84c5c18cddf1ef2c469e0db0fd7b9dc',1,'vg::VG']]],
- ['node_5fcache_3999',['node_cache',['../classvg_1_1Sampler.html#a7fe30513fb778b219886100865cb33e8',1,'vg::Sampler']]],
- ['node_5fchain_5fcomponent_5foffset_4000',['NODE_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#aa4fb1284d9b1da36db4e87fb5f8a1510',1,'vg::ZipCode']]],
- ['node_5fcode_5ft_4001',['node_code_t',['../structvg_1_1ZipCode_1_1node__code__t.html',1,'vg::ZipCode']]],
- ['node_5fcount_4002',['NODE_COUNT',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada57ddf26ffbd2c06cff7bf2cc21613b6c',1,'vg::ZipCodeTree::NODE_COUNT()'],['../classvg_1_1DagifiedGraph.html#add99aae0a2ea95cbb54a1eeebc29087a',1,'vg::DagifiedGraph::node_count()'],['../classxg_1_1XG.html#a8324b23c3162c729f8336df7355b13a1',1,'xg::XG::node_count()'],['../classvg_1_1VG.html#abb3e9e655bcaad0bc522307743acd6a0',1,'vg::VG::node_count()']]],
- ['node_5fcount_5fnext_4003',['node_count_next',['../classvg_1_1VG.html#a4c614759c77b4b0a95b25360c2fa1fa0',1,'vg::VG']]],
- ['node_5fcount_5fprev_4004',['node_count_prev',['../classvg_1_1VG.html#a1091113608fae5b9cbafc87cf4cf82a2',1,'vg::VG']]],
- ['node_5fend_4005',['node_end',['../namespacevg.html#a434e32ac84fd027508a6506e80107331',1,'vg']]],
- ['node_5fgraph_5fidx_4006',['node_graph_idx',['../classxg_1_1XG.html#a191b03b4ada2d076ae6cc53a5a0f5b3d',1,'xg::XG']]],
- ['node_5fhandle_4007',['node_handle',['../structvg_1_1MIPayload.html#a360ac8861d30614205e7637d6ac443b4',1,'vg::MIPayload']]],
- ['node_5fid_4008',['node_id',['../structvg_1_1Position.html#aef891b22e577fdcce6062cf78edd2474',1,'vg::Position::node_id()'],['../structvg_1_1KmerMatch.html#a6d59f7a7bc30d06c055d768324410853',1,'vg::KmerMatch::node_id()'],['../structvg_1_1NodePileup.html#a3ed5e4d46aadb0402badb75e3138dac2',1,'vg::NodePileup::node_id()'],['../structvg_1_1Visit.html#a0dc6e6745e330afc09f338fd50f7fa6c',1,'vg::Visit::node_id()'],['../structvg_1_1LocationSupport.html#a5729cf43650d3357ae350f91291823d3',1,'vg::LocationSupport::node_id()'],['../classvg_1_1mapping__t.html#a878754e2bea167b11b7cb83af5556a6f',1,'vg::mapping_t::node_id()'],['../classvg_1_1position__t.html#a241b513ec1180294fc6e43f7df1935a7',1,'vg::position_t::node_id()']]],
- ['node_5fid_5fto_5fidx_4009',['node_id_to_idx',['../classvg_1_1BandedGlobalAligner.html#ad892d2f28a60a26de8f9afb4461765d0',1,'vg::BandedGlobalAligner']]],
- ['node_5fids_4010',['node_ids',['../classvg_1_1ContractingGraph.html#a639c5892160dd053bc66066b53493253',1,'vg::ContractingGraph::node_ids()'],['../classvg_1_1SparseUnionFind.html#a650957ef3de935c615ef8e28e35d4721',1,'vg::SparseUnionFind::node_ids()']]],
- ['node_5findex_4011',['node_index',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a24f308c69c1dfc5da67e3bb5eda3e017',1,'vg::DozeuInterface::graph_pos_s::node_index()'],['../classvg_1_1VG.html#a2ce9aecf57e0684821ee277d983eb248',1,'vg::VG::node_index()'],['../classvg_1_1Packer.html#abc210cd0133e161824e80c366738d158',1,'vg::Packer::node_index()']]],
- ['node_5fis_5fin_5fcyclic_5fsnarl_4012',['node_is_in_cyclic_snarl',['../classvg_1_1ZipCodeTree.html#aadc6866376dcdda602ff117838ced129',1,'vg::ZipCodeTree']]],
- ['node_5fis_5finvalid_4013',['node_is_invalid',['../classvg_1_1ZipCodeTree.html#ad12d46904662a2f622a2ec83567177f3',1,'vg::ZipCodeTree']]],
- ['node_5fis_5freversed_5foffset_4014',['NODE_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a26bad855c31c5f57abbadbc681c08803',1,'vg::ZipCode']]],
- ['node_5flength_4015',['node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af4071b87357c2a091b98ddb1032d5bdf',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::node_length()'],['../classvg_1_1SourceSinkOverlay.html#aeba2436177cd49e0ec49c1447ba55180',1,'vg::SourceSinkOverlay::node_length()'],['../structvg_1_1MIPayload.html#a787342925dee2293cd58ecc2346f0c4e',1,'vg::MIPayload::node_length()'],['../structvg_1_1PathIndex.html#a398380d0a0f4b4fefc15eef8b37cd2f3',1,'vg::PathIndex::node_length()'],['../classvg_1_1Sampler.html#a490f1a1d093d2c8bf4369c32ad2c257e',1,'vg::Sampler::node_length()']]],
- ['node_5flength_5foffset_4016',['NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a94d890670c72b9e6639b55200cac921c',1,'vg::ZipCode']]],
- ['node_5flengths_4017',['node_lengths',['../structhaplo_1_1gbwt__thread__t.html#afb9949e8024637afcf7f254f91fd0c97',1,'haplo::gbwt_thread_t']]],
- ['node_5flisteners_4018',['node_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#af8e9a128ae89863a958de09962a50dae',1,'vg::algorithms::GFAParser']]],
- ['node_5flocations_4019',['node_locations',['../classvg_1_1PhasedGenome.html#a00b61ff3ca8566865774b0661d5f47c6',1,'vg::PhasedGenome']]],
- ['node_5fmapping_4020',['node_mapping',['../classvg_1_1Paths.html#a724b545027d19a3fd4658494d676f61a',1,'vg::Paths']]],
- ['node_5fmappings_4021',['node_mappings',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a1704e01ce31452b48d51de4258295b09',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['node_5fmissing_4022',['NODE_MISSING',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a0fc049aba7e02c479f48dd02c5facab1',1,'vg::AlignmentValidity']]],
- ['node_5foccurrences_4023',['node_occurrences',['../structvg_1_1PathIndex.html#a057c79ab3b7c3d4a2827af2e7698b1f1',1,'vg::PathIndex']]],
- ['node_5foffset_4024',['node_offset',['../structvg_1_1MatchPos.html#aee7d8f1091e860ccd367ea9042a451bc',1,'vg::MatchPos::node_offset()'],['../structvg_1_1WFAPoint.html#a70ee87f31f5aa70364a43e7416af677e',1,'vg::WFAPoint::node_offset()'],['../structvg_1_1WFAAlignment.html#a7c7ab8f31a4259c0ddd4d188c7596a7f',1,'vg::WFAAlignment::node_offset()'],['../classvg_1_1Viz.html#aa4fc0be6ae2f6acc7fe790e5f50f67f5',1,'vg::Viz::node_offset()']]],
- ['node_5foffset_5foffset_4025',['NODE_OFFSET_OFFSET',['../classvg_1_1ZipCode.html#a23f1322b4bb418f265261d790a5477ae',1,'vg::ZipCode']]],
- ['node_5fpath_5ftraversal_5fcounts_4026',['node_path_traversal_counts',['../classvg_1_1Paths.html#a787ba9aa7f693c4a92c5e17957bb0877',1,'vg::Paths']]],
- ['node_5fpath_5ftraversals_4027',['node_path_traversals',['../classvg_1_1Paths.html#a6856b1b2f59defaeccedc1e31a8a88d3',1,'vg::Paths']]],
- ['node_5fpileups_4028',['node_pileups',['../structvg_1_1Pileup.html#aa70628ddc77e14378831220ea88480c6',1,'vg::Pileup']]],
- ['node_5fqual_5fbin_5fsize_4029',['node_qual_bin_size',['../classvg_1_1Packer.html#ab74d4e3fe0a2a0942e82cdcae0d1bad6',1,'vg::Packer']]],
- ['node_5fquality_5fbin_5foffset_4030',['node_quality_bin_offset',['../classvg_1_1Packer.html#ac3f39972f863ff761e8c32dee7702296',1,'vg::Packer']]],
- ['node_5fquality_5fbin_5fsize_4031',['node_quality_bin_size',['../classvg_1_1Packer.html#a1526efc7e55974a7f3b009f769900dda',1,'vg::Packer']]],
- ['node_5fquality_5fciv_4032',['node_quality_civ',['../classvg_1_1Packer.html#a8491169478e16d232cdb9b1100acdade',1,'vg::Packer']]],
- ['node_5fquality_5fdynamic_4033',['node_quality_dynamic',['../classvg_1_1Packer.html#a7ff3c9e1c9147389485b0da01d5eb2db',1,'vg::Packer']]],
- ['node_5fquality_5flocks_4034',['node_quality_locks',['../classvg_1_1Packer.html#ac06fff3568beec54bb343011fc8f6786',1,'vg::Packer']]],
- ['node_5fquality_5fvector_5fsize_4035',['node_quality_vector_size',['../classvg_1_1Packer.html#ada965622937baaf933fd36cd84315cde',1,'vg::Packer']]],
- ['node_5frank_4036',['node_rank',['../classvg_1_1VG.html#a0202180fa7153f464c3b1d3ff70dc9cb',1,'vg::VG::node_rank(Node *node)'],['../classvg_1_1VG.html#ad7ac4861a64a07f344c21cf2f41b91f1',1,'vg::VG::node_rank(nid_t id)']]],
- ['node_5fsequence_4037',['node_sequence',['../structvg_1_1WFANode.html#a1a923918d714be1ab7c32f27a5ed31e9',1,'vg::WFANode']]],
- ['node_5fsize_4038',['NODE_SIZE',['../classvg_1_1ZipCode.html#a0237b30c6e57eb94d71e67af989cbf03',1,'vg::ZipCode']]],
- ['node_5fstart_4039',['node_start',['../namespacevg.html#a30f5b0dc3732e48a6d9b8d1c895cd8d1',1,'vg']]],
- ['node_5fstart_5fat_5fpath_5fposition_4040',['node_start_at_path_position',['../classxg_1_1XG.html#aa9b17c02171a7073eeb9d4614e619f34',1,'xg::XG']]],
- ['node_5fstarts_5fin_5fpath_4041',['node_starts_in_path',['../classvg_1_1VG.html#a093f4e4dffe0d03806df32edc33cdb9a',1,'vg::VG::node_starts_in_path(const list< NodeTraversal > &path, map< Node *, int > &node_start)'],['../classvg_1_1VG.html#ac27c591957478a17605c2453749f7d20',1,'vg::VG::node_starts_in_path(list< NodeTraversal > &path, map< NodeTraversal *, int > &node_start)']]],
- ['node_5fsubset_4042',['node_subset',['../classvg_1_1SubgraphOverlay.html#a68a505e96443fd85b5498cf785fc372d',1,'vg::SubgraphOverlay']]],
- ['node_5fsupports_4043',['node_supports',['../structvg_1_1SupportAugmentedGraph.html#ad904715950e1e9ffcb6ed6676868debe',1,'vg::SupportAugmentedGraph']]],
- ['node_5fto_5fposition_4044',['node_to_position',['../classvg_1_1Filter.html#aa3a0cf6a83085d33f0983e681c078625',1,'vg::Filter']]],
- ['node_5fto_5fsegment_5fand_5foffsets_4045',['node_to_segment_and_offsets',['../classvg_1_1FlatFileBackTranslation.html#a019b9f65e0fbd404da5fe42f8a338e22',1,'vg::FlatFileBackTranslation']]],
- ['node_5fto_5fsnarl_4046',['node_to_snarl',['../classvg_1_1SnarlGraph.html#afccf2e9cf0326a49a9d2226869e11c5f',1,'vg::SnarlGraph']]],
- ['node_5fto_5fvariant_4047',['node_to_variant',['../classvg_1_1VCFTraversalFinder.html#a133068b1a172eb5f5490ff7c47fd567f',1,'vg::VCFTraversalFinder']]],
- ['node_5ftoo_5fshort_4048',['NODE_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae6b4882026edf127e7a8d7a120636586',1,'vg::AlignmentValidity']]],
- ['node_5ftraversal_4049',['node_traversal',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a6347ba68d0d1a79fa623928b2d2eadcc',1,'vg::PhasedGenome::HaplotypeNode']]],
- ['node_5fvector_5foffset_4050',['node_vector_offset',['../classxg_1_1XG.html#abc79b8d077e089d9a847a6a4a4be70cc',1,'xg::XG::node_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a8666da4a9f55361893544fbb4eff76ce',1,'handlegraph::VectorizableHandleGraph::node_vector_offset()']]],
- ['node_5fweight_5fcallback_4051',['node_weight_callback',['../classvg_1_1FlowTraversalFinder.html#a345a65197b9a0cd215d616dfcfcd5519',1,'vg::FlowTraversalFinder']]],
- ['nodelength_4052',['nodelength',['../structhaplo_1_1gbwt__thread__t.html#afcc24f78011916b909ac56b22c8f82c3',1,'haplo::gbwt_thread_t']]],
- ['nodepileup_4053',['NodePileup',['../structvg_1_1NodePileup.html',1,'vg']]],
- ['nodes_4054',['nodes',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aa1c634ccdab6c61d7fc0b9971014b276',1,'vg::MEMClusterer::HitGraph::nodes()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a348fbee890bd78dc50c7c84368c5b2f6',1,'vg::MEMClusterer::DPScoreComparator::nodes()'],['../classvg_1_1DiagramExplainer.html#ac48c36394b081ec619056ce38cde5d13',1,'vg::DiagramExplainer::nodes()'],['../structvg_1_1FlowSort_1_1Growth.html#ace41b35679169dfbe0a6dda4c4837681',1,'vg::FlowSort::Growth::nodes()'],['../classvg_1_1WFATree.html#a786ffc1f75cffa39bb4fe43cf22b0926',1,'vg::WFATree::nodes()'],['../structhaplo_1_1gbwt__thread__t.html#a88bae446203703780f81cbcee5ff75cd',1,'haplo::gbwt_thread_t::nodes()'],['../classvg_1_1MaximalExactMatch.html#a1c34a3529b17b7ca55a3d29c0777f5e8',1,'vg::MaximalExactMatch::nodes()'],['../structvg_1_1algorithms_1_1Graph.html#a838a14a80429547309f3e9a1c75e491e',1,'vg::algorithms::Graph::nodes()']]],
- ['nodes_5fare_5fperfect_5fpath_5fneighbors_4055',['nodes_are_perfect_path_neighbors',['../namespacehandlegraph_1_1algorithms.html#afbf906cc6a283954093403396ee5ce0e',1,'handlegraph::algorithms']]],
- ['nodes_5fbefore_5foffset_4056',['nodes_before_offset',['../classvg_1_1Viz.html#aa315096c3932839c5cf98b28da52b078',1,'vg::Viz']]],
- ['nodes_5fnext_4057',['nodes_next',['../classvg_1_1VG.html#a0b084d958fd8069839884dc3a01ed745',1,'vg::VG::nodes_next(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a62f1bb7fa27d4d4312017b113aab099a',1,'vg::VG::nodes_next(NodeTraversal n)']]],
- ['nodes_5fprev_4058',['nodes_prev',['../classvg_1_1VG.html#ac08e778396904ad3b3f20f605f54628d',1,'vg::VG::nodes_prev(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a0f3e69ced0c3135f3f363c14bf752aad',1,'vg::VG::nodes_prev(NodeTraversal n)']]],
- ['nodeside_4059',['NodeSide',['../classvg_1_1NodeSide.html',1,'vg::NodeSide'],['../classvg_1_1NodeSide.html#ac4bde3f59ff17ea8c7415fcd9fdd4a0b',1,'vg::NodeSide::NodeSide(id_t node, bool is_end=false)'],['../classvg_1_1NodeSide.html#a3ecb3102be6a85788a003754925c5872',1,'vg::NodeSide::NodeSide()']]],
- ['nodeside_2ehpp_4060',['nodeside.hpp',['../nodeside_8hpp.html',1,'']]],
- ['nodetraversal_4061',['NodeTraversal',['../classvg_1_1NodeTraversal.html',1,'vg::NodeTraversal'],['../classvg_1_1NodeTraversal.html#afca10c8751d4d0f0a86da02277d11513',1,'vg::NodeTraversal::NodeTraversal(Node *node, bool backward=false)'],['../classvg_1_1NodeTraversal.html#a795cce0d085b9113a41fc187e0669f12',1,'vg::NodeTraversal::NodeTraversal()']]],
- ['nodetraversal_2ehpp_4062',['nodetraversal.hpp',['../nodetraversal_8hpp.html',1,'']]],
- ['nodetype_4063',['nodeType',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8',1,'haplo::linear_haplo_structure::nodeType()'],['../structhaplo_1_1linear__haplo__structure.html#a2eb8780c98a02ad3a070d3d2b027170e',1,'haplo::linear_haplo_structure::nodeType()']]],
- ['non_5fintermediate_5faliases_4064',['non_intermediate_aliases',['../classvg_1_1AliasGraph.html#ac400ab0ecb048175fc460f69820204e8',1,'vg::AliasGraph']]],
- ['non_5fmatch_5fend_4065',['non_match_end',['../namespacevg.html#a3ec2e2ef9679291d966bc348a47c3537',1,'vg']]],
- ['non_5fmatch_5fstart_4066',['non_match_start',['../namespacevg.html#ae838e7d89edc59dd87747238cee49b49',1,'vg']]],
- ['nonatgcnton_4067',['nonATGCNtoN',['../namespacevg.html#a453b457823e1ddf916ebf298befb4512',1,'vg']]],
- ['nonce_4068',['nonce',['../classvg_1_1Sampler.html#a36388c416226dd9c343b2da154aada5c',1,'vg::Sampler']]],
- ['nondisjoint_4069',['nondisjoint',['../structhaplo_1_1int__itvl__t.html#af18e576db32fb19f602ed249e07567a7',1,'haplo::int_itvl_t']]],
- ['none_4070',['None',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3a7ec02cb6759bbdcec376638fb9e76d4e',1,'vg::IndexingParameters::None()'],['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85ab50339a10e1de285ac99d4c3990b8693',1,'vg::Funnel::NONE()'],['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39aa676d6ce23c4076e354ffb65936c03d1',1,'vg::None()']]],
- ['nonoverlapping_5fnode_5fcontext_5fwithout_5fpaths_4071',['nonoverlapping_node_context_without_paths',['../classvg_1_1VG.html#a44edad9ba2a6df332234b43715dd71db',1,'vg::VG']]],
- ['normal_4072',['normal',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea867c09ce684d19db107c790ac73e29c2',1,'vg::Haplotypes::Subchain']]],
- ['normal_5faligners_4073',['normal_aligners',['../classvg_1_1Genotyper.html#a91d6174a20ca4f121f68766fbf7fb4b0',1,'vg::Genotyper']]],
- ['normal_5fdistribution_4074',['normal_distribution',['../classvg_1_1normal__distribution.html',1,'vg::normal_distribution< T >'],['../classvg_1_1normal__distribution.html#a7c7bb2c253ac80e0752fd2ba2f84ed56',1,'vg::normal_distribution::normal_distribution()']]],
- ['normal_5fpdf_4075',['normal_pdf',['../namespacevg.html#ae825181ee40a5f0d5087fc657db9a7db',1,'vg']]],
- ['normal_5fsupports_4076',['normal_supports',['../structvg_1_1BREAKPOINT.html#a08a0810aad3ba05efd04908b4911d57d',1,'vg::BREAKPOINT']]],
- ['normalize_4077',['normalize',['../namespacevg_1_1algorithms.html#afb6a93eb17739d744908d61ca6650f4c',1,'vg::algorithms']]],
- ['normalize_2ecpp_4078',['normalize.cpp',['../normalize_8cpp.html',1,'']]],
- ['normalize_2ehpp_4079',['normalize.hpp',['../normalize_8hpp.html',1,'']]],
- ['normalize_5falignment_4080',['normalize_alignment',['../namespacevg.html#afa0c54720b2b1007ae540dc70b5b8024',1,'vg']]],
- ['nowhere_4081',['nowhere',['../classvg_1_1algorithms_1_1TracedScore.html#ad2f398d1d22f2a027a870182e7fd26d4',1,'vg::algorithms::TracedScore']]],
- ['np_5fbv_4082',['np_bv',['../classxg_1_1XG.html#a7c8fe296641f19779727ab5857b834ea',1,'xg::XG']]],
- ['np_5fbv_5fselect_4083',['np_bv_select',['../classxg_1_1XG.html#a077bdb48fbea43751a6cf5c5d731cfbe',1,'xg::XG']]],
- ['np_5fiv_4084',['np_iv',['../classxg_1_1XG.html#a1bb51062742302890454d1d5552c011d',1,'xg::XG']]],
- ['nr_5fiv_4085',['nr_iv',['../classxg_1_1XG.html#a8516a2b79e6326c6b2e7c2a3033ef9d4',1,'xg::XG']]],
- ['nt_5ftable_4086',['nt_table',['../classvg_1_1GSSWAligner.html#a73b117b8b0b894ce486bdb2c4eeeeb10',1,'vg::GSSWAligner::nt_table()'],['../classvg_1_1DinucleotideMachine.html#a42eb3d5ffd684edcd69e43c3bc28eb95',1,'vg::DinucleotideMachine::nt_table()']]],
- ['nth_5fcopy_5fof_5fhandle_4087',['nth_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a716193b4f3dcecfd26de15acf83964b9',1,'vg::DagifiedGraph']]],
- ['null_4088',['Null',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095ea4da67a14c941c99eb8e041314fa98640',1,'vg::multipath_alignment_t']]],
- ['null_5fmasking_5fgraph_2ecpp_4089',['null_masking_graph.cpp',['../null__masking__graph_8cpp.html',1,'']]],
- ['null_5fmasking_5fgraph_2ehpp_4090',['null_masking_graph.hpp',['../null__masking__graph_8hpp.html',1,'']]],
- ['nullalignmentemitter_4091',['NullAlignmentEmitter',['../classvg_1_1io_1_1NullAlignmentEmitter.html',1,'vg::io']]],
- ['nullclusterer_4092',['NullClusterer',['../classvg_1_1NullClusterer.html',1,'vg::NullClusterer'],['../classvg_1_1NullClusterer.html#a63ae2e8bfe748f6557df52cddf4b41e8',1,'vg::NullClusterer::NullClusterer()']]],
- ['nullmaskinggraph_4093',['NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html',1,'vg::NullMaskingGraph'],['../classvg_1_1NullMaskingGraph.html#a2d348fa5aa3bd9216fc4133d320575ef',1,'vg::NullMaskingGraph::NullMaskingGraph(const HandleGraph *graph)'],['../classvg_1_1NullMaskingGraph.html#addeb1ab4002f516c686a5af59018597f',1,'vg::NullMaskingGraph::NullMaskingGraph()=default']]],
- ['num_5falt_5falns_4094',['num_alt_alns',['../classvg_1_1MultipathMapper.html#ad29e0a45fcb921023bd6479a15cfef78',1,'vg::MultipathMapper']]],
- ['num_5fbases_4095',['num_bases',['../structvg_1_1BasePileup.html#aca3e40a479d777aaaa687ca8ab7ce49a',1,'vg::BasePileup']]],
- ['num_5fbases_5fdynamic_4096',['num_bases_dynamic',['../classvg_1_1Packer.html#a34e4dcd2100f889a0f3e673f1a794d29',1,'vg::Packer']]],
- ['num_5fbp_5fper_5fmin_4097',['num_bp_per_min',['../classvg_1_1MinimizerMapper.html#af96dfe389dbee27c52f253bb473d94de',1,'vg::MinimizerMapper']]],
- ['num_5fcandidates_4098',['NUM_CANDIDATES',['../classvg_1_1Recombinator.html#a5768e471a3447a31b14f1d8d94a11588',1,'vg::Recombinator']]],
- ['num_5fcomponents_4099',['num_components',['../namespacevg_1_1algorithms.html#aa84bd9740e748431857b5fd8a0397183',1,'vg::algorithms']]],
- ['num_5fconnected_5fcomponents_4100',['num_connected_components',['../namespacevg.html#a1ac45a06bc04f88ba6c2321d7af304c6',1,'vg']]],
- ['num_5fedges_5fdynamic_4101',['num_edges_dynamic',['../classvg_1_1Packer.html#ae05325e714e72b76815740f03dc10a3b',1,'vg::Packer']]],
- ['num_5fforward_5freads_4102',['num_forward_reads',['../structvg_1_1EdgePileup.html#a5a61f1d9489561ede0ca1afcbcd7c1d9',1,'vg::EdgePileup']]],
- ['num_5fhaplotypes_4103',['NUM_HAPLOTYPES',['../classvg_1_1Recombinator.html#a06515509b2d56e644d5a89d1bab3b239',1,'vg::Recombinator::NUM_HAPLOTYPES()'],['../structvg_1_1Recombinator_1_1Parameters.html#a253f1e11aa0a36a9f1cf0251de316066',1,'vg::Recombinator::Parameters::num_haplotypes()'],['../classvg_1_1PhasedGenome.html#af17e5f99a07028d41f94885480cdddf7',1,'vg::PhasedGenome::num_haplotypes()']]],
- ['num_5finline_4104',['NUM_INLINE',['../structvg_1_1MatchPos_1_1PathList.html#ac2b88a61013598a9ed786f65137c888f',1,'vg::MatchPos::PathList']]],
- ['num_5fitems_4105',['num_items',['../classvg_1_1ShuffledPairs.html#af7af129e1f60b59e78ed6d92d693d599',1,'vg::ShuffledPairs']]],
- ['num_5fjobs_4106',['num_jobs',['../structvg_1_1RebuildParameters.html#a25c12cba31a60be2c6bdfd5ece960ad7',1,'vg::RebuildParameters']]],
- ['num_5fleft_5fhandles_4107',['num_left_handles',['../classvg_1_1JoinedSpliceGraph.html#acb848555db862533ceda5be3136b7040',1,'vg::JoinedSpliceGraph']]],
- ['num_5fmapping_5fattempts_4108',['num_mapping_attempts',['../classvg_1_1MultipathMapper.html#acd259da737785206d02cc2807ab831fa',1,'vg::MultipathMapper']]],
- ['num_5fnodes_5fdynamic_4109',['num_nodes_dynamic',['../classvg_1_1Packer.html#a9f406ddaf008b85d23ea1262ab95ad68',1,'vg::Packer']]],
- ['num_5fnull_5fnodes_4110',['num_null_nodes',['../classvg_1_1DozeuPinningOverlay.html#aad4a7969c5c7263cfd5072169b60f6fa',1,'vg::DozeuPinningOverlay::num_null_nodes()'],['../classvg_1_1NullMaskingGraph.html#a789adb0e97e25f480f18c7158aec51ac',1,'vg::NullMaskingGraph::num_null_nodes()']]],
- ['num_5fpairs_4111',['num_pairs',['../classvg_1_1ShuffledPairs.html#abf8913c70ff6595d8b288bdab3c88981',1,'vg::ShuffledPairs']]],
- ['num_5fpaths_4112',['num_paths',['../structGBWTConfig.html#ad3dc88b3f829f932b976fc182257b987',1,'GBWTConfig']]],
- ['num_5fpaths_5fset_4113',['num_paths_set',['../structGBWTConfig.html#aefbd9bdd79f88ab07ee18a12df56e513',1,'GBWTConfig']]],
- ['num_5freads_4114',['num_reads',['../structvg_1_1EdgePileup.html#aa95aa0337a5bc6229762abaa56dcdbff',1,'vg::EdgePileup']]],
- ['num_5fsnarls_4115',['num_snarls',['../classvg_1_1SnarlManager.html#a727734d76e892a3fc0d421c6382349a1',1,'vg::SnarlManager']]],
- ['num_5fthreads_4116',['num_threads',['../classvg_1_1Transcriptome.html#ac2261cd2e4236c02dbfded216253c923',1,'vg::Transcriptome']]],
- ['number_5fbool_5fpacking_4117',['number_bool_packing',['../structhandlegraph_1_1number__bool__packing.html',1,'handlegraph']]],
- ['number_5fof_5fvalues_4118',['number_of_values',['../structvg_1_1SummaryStatistics.html#a0960315b33bca238ec069a1c23eefba5',1,'vg::SummaryStatistics']]],
- ['numeric_5fmode_4119',['numeric_mode',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#af2a10466f1ac4f49fb670ffd43d48a19',1,'vg::algorithms::GFAIDMapInfo']]],
- ['nx_5fiv_4120',['nx_iv',['../classxg_1_1XG.html#a48563ff2d8a9e68e67ec75ad93b6272e',1,'xg::XG']]]
+ ['n_3917',['n',['../namespacehaplotypes__defaults.html#a08f2ff580a81523291eed7ef0d644bd2',1,'haplotypes_defaults']]],
+ ['n_5fbins_3918',['n_bins',['../classvg_1_1Packer.html#a3e753cd974d4411036081d252b6eb7bf',1,'vg::Packer']]],
+ ['n_5fiterations_3919',['n_iterations',['../classvg_1_1MCMCGenotyper.html#a1d5684e63858e5362578bc85d638a870',1,'vg::MCMCGenotyper']]],
+ ['name_3920',['name',['../structvg_1_1BenchmarkResult.html#a406a53ba511e3f0f28d20a542b41355a',1,'vg::BenchmarkResult::name()'],['../structvg_1_1BREAKPOINT.html#a098f871767e6bbb25ec840acfabae12b',1,'vg::BREAKPOINT::name()'],['../structvg_1_1Funnel_1_1Stage.html#a709200eef7b97eb16aaaeaad95aab6fe',1,'vg::Funnel::Stage::name()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ac72259c3b34d4ec70dcb14225a546c0a',1,'vg::Recombinator::LocalHaplotype::name()'],['../structvg_1_1Transcript.html#a91a919300bda880406cf56a4f78cffda',1,'vg::Transcript::name()'],['../classvg_1_1VG.html#a1f6fcd5a907e9bee524cf37a62ad5be2',1,'vg::VG::name()'],['../structvg_1_1VG_1_1Plan.html#aba1bea59a4b1db998936d5d99eff9c4e',1,'vg::VG::Plan::name()'],['../classvg_1_1subcommand_1_1Subcommand.html#a1873ba1dfd0eec7c8db3303f18971e08',1,'vg::subcommand::Subcommand::name()'],['../structgafkluge_1_1GafStep.html#a9cf80aad32be2824f3a2196e669851ca',1,'gafkluge::GafStep::name()'],['../structvg_1_1Node.html#a3a4827f5d3eb097a4ef9e542e56c1e2c',1,'vg::Node::name()'],['../structvg_1_1Position.html#ae2e1a55adad827628c58ec06489c54ed',1,'vg::Position::name()'],['../structvg_1_1Path.html#a24e6f7ffbbe8fcbd7444937b7fcd1601',1,'vg::Path::name()'],['../structvg_1_1Alignment.html#ad20cac38e0bd25d2b32862fe1f5409ab',1,'vg::Alignment::name()'],['../structvg_1_1MultipathAlignment.html#a9427bb485b73bc6d3e2f077ee5df303d',1,'vg::MultipathAlignment::name()'],['../structvg_1_1Snarl.html#ac6e2f21c606af930c7f77f8f4027f833',1,'vg::Snarl::name()'],['../structvg_1_1Visit.html#ac0dae7bcea098cf39bbba443e7b45cbf',1,'vg::Visit::name()'],['../structvg_1_1SnarlTraversal.html#a1c8921481ba23cd8fe8725212f376b21',1,'vg::SnarlTraversal::name()'],['../structvg_1_1Locus.html#a39e5699f029942f81777d7e0ab203189',1,'vg::Locus::name()']]],
+ ['name_5fmapper_2ecpp_3921',['name_mapper.cpp',['../name__mapper_8cpp.html',1,'']]],
+ ['name_5fmapper_2ehpp_3922',['name_mapper.hpp',['../name__mapper_8hpp.html',1,'']]],
+ ['name_5fprefixes_3923',['name_prefixes',['../classvg_1_1ReadFilter.html#a59dd97c0eadf3aebd852ae3b0aabe31d',1,'vg::ReadFilter']]],
+ ['name_5fto_5fid_3924',['name_to_id',['../classvg_1_1Paths.html#a032139e6fadea366f224508c8f8385df',1,'vg::Paths::name_to_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a349cfce46078beef8d6169874b5b29b9',1,'vg::algorithms::GFAIDMapInfo::name_to_id()']]],
+ ['named_5fnode_5fback_5ftranslation_2ehpp_3925',['named_node_back_translation.hpp',['../named__node__back__translation_8hpp.html',1,'']]],
+ ['namednodebacktranslation_3926',['NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html',1,'handlegraph::NamedNodeBackTranslation'],['../namespacevg.html#a2c7b4f84e5a75aee3d3abf4b65b0000f',1,'vg::NamedNodeBackTranslation()']]],
+ ['namemapper_3927',['NameMapper',['../classvg_1_1NameMapper.html',1,'vg']]],
+ ['nearest_5foffsets_5fin_5fpaths_3928',['nearest_offsets_in_paths',['../classxg_1_1XG.html#ab885cecf687ffb8583fb95cce8ca34b2',1,'xg::XG::nearest_offsets_in_paths()'],['../namespacevg_1_1algorithms.html#a477330d3ab29cbd3c48e4830d51b3e0f',1,'vg::algorithms::nearest_offsets_in_paths()']]],
+ ['nearest_5foffsets_5fin_5fpaths_2ecpp_3929',['nearest_offsets_in_paths.cpp',['../nearest__offsets__in__paths_8cpp.html',1,'']]],
+ ['nearest_5foffsets_5fin_5fpaths_2ehpp_3930',['nearest_offsets_in_paths.hpp',['../nearest__offsets__in__paths_8hpp.html',1,'']]],
+ ['nearest_5fpath_5fnode_3931',['nearest_path_node',['../classxg_1_1XG.html#a03f2f8a4cc3d06e4f1748474082efdb9',1,'xg::XG']]],
+ ['need_5fcomma_3932',['need_comma',['../classvg_1_1ProblemDumpExplainer.html#af1f3a4b525a0c5b4daeee2a3ae9a3a18',1,'vg::ProblemDumpExplainer']]],
+ ['need_5fline_3933',['need_line',['../classvg_1_1TSVExplainer.html#a810b272c339e543614686bce35a82f76',1,'vg::TSVExplainer']]],
+ ['need_5ftab_3934',['need_tab',['../classvg_1_1TSVExplainer.html#ad9f986f075d4dbe3033a2102376e12e5',1,'vg::TSVExplainer']]],
+ ['nested_5fdecomposition_3935',['nested_decomposition',['../classvg_1_1Deconstructor.html#aa6cf4f15fa2a53976ee40443e63df36f',1,'vg::Deconstructor']]],
+ ['nested_5fsupport_5ffinder_3936',['nested_support_finder',['../classvg_1_1NestedFlowCaller.html#a2c0bda955a72c10f4040ea42203b8f39',1,'vg::NestedFlowCaller']]],
+ ['nested_5ftraversal_5ffinder_2ecpp_3937',['nested_traversal_finder.cpp',['../nested__traversal__finder_8cpp.html',1,'']]],
+ ['nested_5ftraversal_5ffinder_2ehpp_3938',['nested_traversal_finder.hpp',['../nested__traversal__finder_8hpp.html',1,'']]],
+ ['nestedcachedpackedtraversalsupportfinder_3939',['NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html',1,'vg::NestedCachedPackedTraversalSupportFinder'],['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#a6893d620886b1bb326f735e36757f6e2',1,'vg::NestedCachedPackedTraversalSupportFinder::NestedCachedPackedTraversalSupportFinder()']]],
+ ['nestedflowcaller_3940',['NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html',1,'vg::NestedFlowCaller'],['../classvg_1_1NestedFlowCaller.html#ab56c3d2fe181450dc33167539bc8f74c',1,'vg::NestedFlowCaller::NestedFlowCaller()']]],
+ ['nestedtraversalfinder_3941',['NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html',1,'vg::NestedTraversalFinder'],['../classvg_1_1NestedTraversalFinder.html#a0ab18d1355be2772f9ca78c5eb269e6c',1,'vg::NestedTraversalFinder::NestedTraversalFinder()']]],
+ ['nestinginfo_3942',['NestingInfo',['../structvg_1_1Deconstructor_1_1NestingInfo.html',1,'vg::Deconstructor']]],
+ ['net_5fgraph_5fof_3943',['net_graph_of',['../classvg_1_1SnarlManager.html#aa8872188679a5ad4d0da08c1235f2019',1,'vg::SnarlManager']]],
+ ['net_5fgraphs_3944',['net_graphs',['../classvg_1_1GenomeState.html#a7745fd8de0051a478dbf5b4e47ebce8c',1,'vg::GenomeState']]],
+ ['net_5fhandle_3945',['net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#a9288aae0c2945e8b6213368b9bf99eec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['net_5fhandle_5ft_3946',['net_handle_t',['../structhandlegraph_1_1net__handle__t.html',1,'handlegraph']]],
+ ['net_5fhandle_5fto_5fnode_5fproblem_5findex_3947',['net_handle_to_node_problem_index',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#ada18575df8f9870a5063c99ac6167612',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['net_5fidentifier_5ft_3948',['net_identifier_t',['../namespacevg.html#a064c859d9612d9c2b240b9c0d01f8a85',1,'vg']]],
+ ['net_5fnode_5flanes_3949',['net_node_lanes',['../classvg_1_1SnarlState.html#a01d595bd630d0d550176cade6897b491',1,'vg::SnarlState']]],
+ ['netgraph_3950',['NetGraph',['../classvg_1_1NetGraph.html',1,'vg::NetGraph'],['../classvg_1_1NetGraph.html#a9059c913779ce4095224a5ae6638a27d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains_mixed, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#a29abf89e03eedc7ac2af4682a1b5bb04',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains, const SnarlContainer &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aa1e17ccb08d595123db3d8cd6e2593b2',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const vector< vector< pair< Snarl, bool >>> &child_chains, const vector< Snarl > &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aba1479f586d07f276ba6925cfc1a8e6d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const HandleGraph *graph, bool use_internal_connectivity=false)']]],
+ ['new_5fheight_3951',['new_height',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae444abfaf71eedae674fb4703e910248',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['new_5flength_3952',['new_length',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a9d8c1bf7222ee28236691c30185194d3',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['new_5fnode_3953',['new_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ab98205bb3934c92fec2a63a0360339b4',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['new_5foutput_5fgraph_3954',['new_output_graph',['../namespacevg_1_1io.html#a4b6ad53e3fc9e4c143221b213932db70',1,'vg::io']]],
+ ['new_5fside_3955',['new_side',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af0ea102c59fcbcb1a5387ea5b465e950',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['next_3956',['Next',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a91e4dc4f48957737a80e99a8ad32ba53',1,'vg::io::BlockedGzipInputStream::Next()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a0c3e80161a999b884abf3965dd0a5a39',1,'vg::io::BlockedGzipOutputStream::Next()'],['../structvg_1_1PathBranch.html#acf21b2d9bb36f687d4727c56a4b2e940',1,'vg::PathBranch::next()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#ae6ca62f71e4ab5a266170af025ec97dd',1,'vg::PhasedGenome::HaplotypeNode::next()'],['../structvg_1_1Subpath.html#ae8d4a9f246eae61420b666aa0665930d',1,'vg::Subpath::next()'],['../structvg_1_1Connection.html#a151e393bbacd7904d71afd4939950509',1,'vg::Connection::next()'],['../classvg_1_1WFATree.html#acec4f54d7784d6c7310418ddec2716b9',1,'vg::WFATree::next()'],['../classvg_1_1connection__t.html#a18d278044df80b1334542e6d25043a32',1,'vg::connection_t::next()'],['../classvg_1_1subpath__t.html#a60a4ec0114c307ae532ea307128bfe24',1,'vg::subpath_t::next() const'],['../classvg_1_1subpath__t.html#aabe3e1337325511c83d7e949195fdf37',1,'vg::subpath_t::next(size_t i) const'],['../classvg_1_1WindowedVcfBuffer.html#a0d66b5a177f55cb726122577840d8911',1,'vg::WindowedVcfBuffer::next()']]],
+ ['next_5fchar_3957',['next_char',['../structvg_1_1kmer__t.html#a844852956a93c48eadc3557a0da7ab66',1,'vg::kmer_t']]],
+ ['next_5fchars_3958',['next_chars',['../structvg_1_1KmerPosition.html#ae56be5485cffba06cdab7c949487ea3f',1,'vg::KmerPosition']]],
+ ['next_5fcost_3959',['next_cost',['../classvg_1_1MEMChainModelVertex.html#af972fee5a48a5eb92466395cdffe38c4',1,'vg::MEMChainModelVertex::next_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#ab4300ed3dcbce1f434b6db7d28aa6a0f',1,'vg::AlignmentChainModelVertex::next_cost()']]],
+ ['next_5fempty_5falignment_3960',['next_empty_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a08e8eed8f95a621c9786bca1b0850dd2',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['next_5fexplanation_5fnumber_3961',['next_explanation_number',['../classvg_1_1Explainer.html#ad6f34855ed8bf99838f158ed027b3a6a',1,'vg::Explainer']]],
+ ['next_5fgroup_3962',['next_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a5dee6816359ccf56409120cff36a759b',1,'vg::IndexedVG::CacheEntry']]],
+ ['next_5fis_5fempty_3963',['next_is_empty',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a016150b6b6f4551ee3eb7600d7037b67',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['next_5fpath_5fposition_3964',['next_path_position',['../classxg_1_1XG.html#ae973d41358ddab92f0a2dca094806102',1,'xg::XG']]],
+ ['next_5fpos_3965',['next_pos',['../structvg_1_1kmer__t.html#a4af3ee75920ba66867f991ec823b2bf4',1,'vg::kmer_t']]],
+ ['next_5fpos_5fchars_3966',['next_pos_chars',['../classvg_1_1Sampler.html#ab5455f8f6faf176b418e3dbcb6bf1ce8',1,'vg::Sampler::next_pos_chars()'],['../namespacevg_1_1algorithms.html#a22d03c4f50c51d0d537811ba88895688',1,'vg::algorithms::next_pos_chars()']]],
+ ['next_5fpos_5fchars_2ecpp_3967',['next_pos_chars.cpp',['../next__pos__chars_8cpp.html',1,'']]],
+ ['next_5fpos_5fchars_2ehpp_3968',['next_pos_chars.hpp',['../next__pos__chars_8hpp.html',1,'']]],
+ ['next_5fpositions_3969',['next_positions',['../structvg_1_1KmerPosition.html#ad6a841261ad5205e4dc10503f5ec8ba7',1,'vg::KmerPosition']]],
+ ['next_5fscore_3970',['next_score',['../classvg_1_1WFATree.html#aba63fbf6ca1e1382e62727ea95c4b0af',1,'vg::WFATree']]],
+ ['next_5fsize_3971',['next_size',['../classvg_1_1subpath__t.html#aab697710ebd5e8f968bed5c5262bbe2a',1,'vg::subpath_t']]],
+ ['next_5fsnarl_3972',['next_snarl',['../classvg_1_1SnarlManager.html#afcca3b74e960b6931598188e0b9ae7a8',1,'vg::SnarlManager']]],
+ ['next_5ftraceback_5falignment_3973',['next_traceback_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a8d6cbc921387724da8db3c8c0f20f363',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['ngssimulator_3974',['NGSSimulator',['../classvg_1_1NGSSimulator.html',1,'vg::NGSSimulator'],['../classvg_1_1NGSSimulator.html#a51e3a4117f9339b3195d73f2c6cf560e',1,'vg::NGSSimulator::NGSSimulator(PathPositionHandleGraph &graph, const string &ngs_fastq_file, const string &ngs_paired_fastq_file="", bool interleaved_fastq=false, const vector< string > &source_paths={}, const vector< double > &source_path_ploidies={}, const vector< pair< string, double >> &transcript_expressions={}, const vector< tuple< string, string, size_t >> &haplotype_transcripts={}, double substition_polymorphism_rate=0.001, double indel_polymorphism_rate=0.0002, double indel_error_proportion=0.01, double fragment_length_mean=300.0, double fragment_length_stdev=50.0, double error_multiplier=1.0, bool retry_on_Ns=true, bool sample_unsheared_paths=false, uint64_t seed=0)'],['../classvg_1_1NGSSimulator.html#a5417af00068600ab1e6d0acb24836698',1,'vg::NGSSimulator::NGSSimulator(void)=delete']]],
+ ['nid_5ft_3975',['nid_t',['../namespacevg.html#a26f660292f00451f15d1c95d9b8c6ffb',1,'vg::nid_t()'],['../namespacexg.html#a8f8752f074f0e121862f9dd3aabfbb45',1,'xg::nid_t()'],['../namespacehandlegraph.html#a93c2889b752934c4b2488b37cbdd278b',1,'handlegraph::nid_t()'],['../namespacevg_1_1io.html#a43c8209ab6c2c1d48c0ca50c24fd0d13',1,'vg::io::nid_t()']]],
+ ['no_5fchain_5finfo_3976',['no_chain_info',['../classvg_1_1MinimizerMapper.html#a3b9a4518b171aa85909da6ccde88e0a8',1,'vg::MinimizerMapper']]],
+ ['no_5fclustering_3977',['no_clustering',['../classvg_1_1MultipathMapper.html#ad4a0793bd06a62ca2e267e5a1ceb4643',1,'vg::MultipathMapper']]],
+ ['no_5fcode_3978',['NO_CODE',['../structvg_1_1MIPayload.html#aad1e599cc16dec3115ea845eada83bb3',1,'vg::MIPayload']]],
+ ['no_5fend_5fposition_3979',['NO_END_POSITION',['../classhandlegraph_1_1PathMetadata.html#a2b966a3af9aac1a11236de902cae6f8b',1,'handlegraph::PathMetadata']]],
+ ['no_5fhaplotype_3980',['NO_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#a22d67bfb9356f42b46aaa6cefc1ee24b',1,'handlegraph::PathMetadata']]],
+ ['no_5findex_3981',['NO_INDEX',['../namespacevg.html#a0fc209aaa8c7c17499d70452d2816f44',1,'vg']]],
+ ['no_5flocus_5fname_3982',['NO_LOCUS_NAME',['../classhandlegraph_1_1PathMetadata.html#ae7ee0795aa13f7ad34189f2982d64c42',1,'handlegraph::PathMetadata']]],
+ ['no_5fmultiple_5fcover_5ftypes_3983',['no_multiple_cover_types',['../gbwt__main_8cpp.html#a0124aac03621e82b84ef0de974a08574',1,'gbwt_main.cpp']]],
+ ['no_5fmultiple_5finput_5ftypes_3984',['no_multiple_input_types',['../gbwt__main_8cpp.html#ae1c5768186dc339c157bf4b72517b5ab',1,'gbwt_main.cpp']]],
+ ['no_5fmultiple_5finputs_3985',['no_multiple_inputs',['../convert__main_8cpp.html#aca425ac5df78dde7681385a5341abb1b',1,'convert_main.cpp']]],
+ ['no_5fns_3986',['no_Ns',['../classvg_1_1Sampler.html#aa71ef9078ed81b2406357f0dd4fdda3a',1,'vg::Sampler']]],
+ ['no_5fphase_5fblock_3987',['NO_PHASE_BLOCK',['../classhandlegraph_1_1PathMetadata.html#a03fdf276dc586f22039aa3e70dd9bf77',1,'handlegraph::PathMetadata']]],
+ ['no_5fpos_3988',['no_pos',['../classvg_1_1WFATree.html#ad0383cee94782b3f0e8d48078d4d2348',1,'vg::WFATree']]],
+ ['no_5fprogress_3989',['NO_PROGRESS',['../namespacevg_1_1io.html#a33939950704e2d4439b93cde15139172',1,'vg::io']]],
+ ['no_5fread_5findex_3990',['NO_READ_INDEX',['../namespacevg.html#aa32104605c22b25e9ec17d69fbc61a4b',1,'vg']]],
+ ['no_5fsample_5fname_3991',['NO_SAMPLE_NAME',['../classhandlegraph_1_1PathMetadata.html#a9770508967dec07997d8ad31dbbe5a95',1,'handlegraph::PathMetadata']]],
+ ['no_5fsplice_5flog_5fodds_3992',['no_splice_log_odds',['../classvg_1_1MultipathMapper.html#a3130f372f82437af2f7733901a47c142',1,'vg::MultipathMapper']]],
+ ['no_5fsplice_5fnatural_5flog_5fodds_3993',['no_splice_natural_log_odds',['../classvg_1_1MultipathMapper.html#a3903979b6a7b5e297335f823864cd511',1,'vg::MultipathMapper']]],
+ ['no_5fsubrange_3994',['NO_SUBRANGE',['../classhandlegraph_1_1PathMetadata.html#a8524bdffc330d58553459074c57fc889',1,'handlegraph::PathMetadata']]],
+ ['no_5fvalue_3995',['NO_VALUE',['../structvg_1_1MIPayload.html#a90c2f3f622099c6920b28356d49d9a4e',1,'vg::MIPayload']]],
+ ['no_5fwait_3996',['NO_WAIT',['../namespacevg_1_1io.html#a21ec64ee292cf76a61bff68a727471e9',1,'vg::io']]],
+ ['noalignmentinbandexception_3997',['NoAlignmentInBandException',['../classvg_1_1NoAlignmentInBandException.html',1,'vg']]],
+ ['node_3998',['Node',['../structvg_1_1Node.html',1,'vg::Node'],['../structvg_1_1algorithms_1_1Node.html',1,'vg::algorithms::Node'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a15ee21b9bf2ed37f9892ca0291964d28',1,'vg::BandedGlobalAligner::BAMatrix::node()'],['../structvg_1_1CactusSide.html#a1e590f9e0956cdd491c9758a89bc4e1e',1,'vg::CactusSide::node()'],['../classvg_1_1NodeSide.html#a11a48024eddd85edf22b6e0748049fa0',1,'vg::NodeSide::node()'],['../classvg_1_1NodeTraversal.html#a73ca27b85d0f387740425dea434763ed',1,'vg::NodeTraversal::node()'],['../structvg_1_1Graph.html#ac16f6921068e2ae84b0d2166b2eb3b4e',1,'vg::Graph::node()'],['../structvg_1_1MatchPos.html#abd73a2a9a1d86e1747631f89b045e4fd',1,'vg::MatchPos::node()'],['../classxg_1_1XGPath.html#a621253a080fdb8b81eb5efe2359b93a8',1,'xg::XGPath::node()'],['../structvg_1_1Tree.html#ad5b04c67e4c1390c2ae46d1db40548f7',1,'vg::Tree::Node()'],['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a2995e7f61da600fe7b67e5fd40d4b319',1,'vg::ZipCode::NODE()']]],
+ ['node_5fat_5fvector_5foffset_3999',['node_at_vector_offset',['../classxg_1_1XG.html#a2f2c0b014af5d0032f9beaefb074cc59',1,'xg::XG::node_at_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a3095e541eee436a9f49ef0846539ef44',1,'handlegraph::VectorizableHandleGraph::node_at_vector_offset()']]],
+ ['node_5fby_5fid_4000',['node_by_id',['../classvg_1_1VG.html#ad84c5c18cddf1ef2c469e0db0fd7b9dc',1,'vg::VG']]],
+ ['node_5fcache_4001',['node_cache',['../classvg_1_1Sampler.html#a7fe30513fb778b219886100865cb33e8',1,'vg::Sampler']]],
+ ['node_5fchain_5fcomponent_5foffset_4002',['NODE_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#aa4fb1284d9b1da36db4e87fb5f8a1510',1,'vg::ZipCode']]],
+ ['node_5fcode_5ft_4003',['node_code_t',['../structvg_1_1ZipCode_1_1node__code__t.html',1,'vg::ZipCode']]],
+ ['node_5fcount_4004',['NODE_COUNT',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada57ddf26ffbd2c06cff7bf2cc21613b6c',1,'vg::ZipCodeTree::NODE_COUNT()'],['../classvg_1_1DagifiedGraph.html#add99aae0a2ea95cbb54a1eeebc29087a',1,'vg::DagifiedGraph::node_count()'],['../classxg_1_1XG.html#a8324b23c3162c729f8336df7355b13a1',1,'xg::XG::node_count()'],['../classvg_1_1VG.html#abb3e9e655bcaad0bc522307743acd6a0',1,'vg::VG::node_count()']]],
+ ['node_5fcount_5fnext_4005',['node_count_next',['../classvg_1_1VG.html#a4c614759c77b4b0a95b25360c2fa1fa0',1,'vg::VG']]],
+ ['node_5fcount_5fprev_4006',['node_count_prev',['../classvg_1_1VG.html#a1091113608fae5b9cbafc87cf4cf82a2',1,'vg::VG']]],
+ ['node_5fend_4007',['node_end',['../namespacevg.html#a434e32ac84fd027508a6506e80107331',1,'vg']]],
+ ['node_5fgraph_5fidx_4008',['node_graph_idx',['../classxg_1_1XG.html#a191b03b4ada2d076ae6cc53a5a0f5b3d',1,'xg::XG']]],
+ ['node_5fhandle_4009',['node_handle',['../structvg_1_1MIPayload.html#a360ac8861d30614205e7637d6ac443b4',1,'vg::MIPayload']]],
+ ['node_5fid_4010',['node_id',['../structvg_1_1Position.html#aef891b22e577fdcce6062cf78edd2474',1,'vg::Position::node_id()'],['../structvg_1_1KmerMatch.html#a6d59f7a7bc30d06c055d768324410853',1,'vg::KmerMatch::node_id()'],['../structvg_1_1NodePileup.html#a3ed5e4d46aadb0402badb75e3138dac2',1,'vg::NodePileup::node_id()'],['../structvg_1_1Visit.html#a0dc6e6745e330afc09f338fd50f7fa6c',1,'vg::Visit::node_id()'],['../structvg_1_1LocationSupport.html#a5729cf43650d3357ae350f91291823d3',1,'vg::LocationSupport::node_id()'],['../classvg_1_1mapping__t.html#a878754e2bea167b11b7cb83af5556a6f',1,'vg::mapping_t::node_id()'],['../classvg_1_1position__t.html#a241b513ec1180294fc6e43f7df1935a7',1,'vg::position_t::node_id()']]],
+ ['node_5fid_5fto_5fidx_4011',['node_id_to_idx',['../classvg_1_1BandedGlobalAligner.html#ad892d2f28a60a26de8f9afb4461765d0',1,'vg::BandedGlobalAligner']]],
+ ['node_5fids_4012',['node_ids',['../classvg_1_1ContractingGraph.html#a639c5892160dd053bc66066b53493253',1,'vg::ContractingGraph::node_ids()'],['../classvg_1_1SparseUnionFind.html#a650957ef3de935c615ef8e28e35d4721',1,'vg::SparseUnionFind::node_ids()']]],
+ ['node_5findex_4013',['node_index',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a24f308c69c1dfc5da67e3bb5eda3e017',1,'vg::DozeuInterface::graph_pos_s::node_index()'],['../classvg_1_1VG.html#a2ce9aecf57e0684821ee277d983eb248',1,'vg::VG::node_index()'],['../classvg_1_1Packer.html#abc210cd0133e161824e80c366738d158',1,'vg::Packer::node_index()']]],
+ ['node_5fis_5fin_5fcyclic_5fsnarl_4014',['node_is_in_cyclic_snarl',['../classvg_1_1ZipCodeTree.html#aadc6866376dcdda602ff117838ced129',1,'vg::ZipCodeTree']]],
+ ['node_5fis_5finvalid_4015',['node_is_invalid',['../classvg_1_1ZipCodeTree.html#ad12d46904662a2f622a2ec83567177f3',1,'vg::ZipCodeTree']]],
+ ['node_5fis_5freversed_5foffset_4016',['NODE_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a26bad855c31c5f57abbadbc681c08803',1,'vg::ZipCode']]],
+ ['node_5flength_4017',['node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af4071b87357c2a091b98ddb1032d5bdf',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::node_length()'],['../classvg_1_1SourceSinkOverlay.html#aeba2436177cd49e0ec49c1447ba55180',1,'vg::SourceSinkOverlay::node_length()'],['../structvg_1_1MIPayload.html#a787342925dee2293cd58ecc2346f0c4e',1,'vg::MIPayload::node_length()'],['../structvg_1_1PathIndex.html#a398380d0a0f4b4fefc15eef8b37cd2f3',1,'vg::PathIndex::node_length()'],['../classvg_1_1Sampler.html#a490f1a1d093d2c8bf4369c32ad2c257e',1,'vg::Sampler::node_length()']]],
+ ['node_5flength_5foffset_4018',['NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a94d890670c72b9e6639b55200cac921c',1,'vg::ZipCode']]],
+ ['node_5flengths_4019',['node_lengths',['../structhaplo_1_1gbwt__thread__t.html#afb9949e8024637afcf7f254f91fd0c97',1,'haplo::gbwt_thread_t']]],
+ ['node_5flisteners_4020',['node_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#af8e9a128ae89863a958de09962a50dae',1,'vg::algorithms::GFAParser']]],
+ ['node_5flocations_4021',['node_locations',['../classvg_1_1PhasedGenome.html#a00b61ff3ca8566865774b0661d5f47c6',1,'vg::PhasedGenome']]],
+ ['node_5fmapping_4022',['node_mapping',['../classvg_1_1Paths.html#a724b545027d19a3fd4658494d676f61a',1,'vg::Paths']]],
+ ['node_5fmappings_4023',['node_mappings',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a1704e01ce31452b48d51de4258295b09',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['node_5fmissing_4024',['NODE_MISSING',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a0fc049aba7e02c479f48dd02c5facab1',1,'vg::AlignmentValidity']]],
+ ['node_5foccurrences_4025',['node_occurrences',['../structvg_1_1PathIndex.html#a057c79ab3b7c3d4a2827af2e7698b1f1',1,'vg::PathIndex']]],
+ ['node_5foffset_4026',['node_offset',['../structvg_1_1MatchPos.html#aee7d8f1091e860ccd367ea9042a451bc',1,'vg::MatchPos::node_offset()'],['../structvg_1_1WFAPoint.html#a70ee87f31f5aa70364a43e7416af677e',1,'vg::WFAPoint::node_offset()'],['../structvg_1_1WFAAlignment.html#a7c7ab8f31a4259c0ddd4d188c7596a7f',1,'vg::WFAAlignment::node_offset()'],['../classvg_1_1Viz.html#aa4fc0be6ae2f6acc7fe790e5f50f67f5',1,'vg::Viz::node_offset()']]],
+ ['node_5foffset_5foffset_4027',['NODE_OFFSET_OFFSET',['../classvg_1_1ZipCode.html#a23f1322b4bb418f265261d790a5477ae',1,'vg::ZipCode']]],
+ ['node_5fpath_5ftraversal_5fcounts_4028',['node_path_traversal_counts',['../classvg_1_1Paths.html#a787ba9aa7f693c4a92c5e17957bb0877',1,'vg::Paths']]],
+ ['node_5fpath_5ftraversals_4029',['node_path_traversals',['../classvg_1_1Paths.html#a6856b1b2f59defaeccedc1e31a8a88d3',1,'vg::Paths']]],
+ ['node_5fpileups_4030',['node_pileups',['../structvg_1_1Pileup.html#aa70628ddc77e14378831220ea88480c6',1,'vg::Pileup']]],
+ ['node_5fqual_5fbin_5fsize_4031',['node_qual_bin_size',['../classvg_1_1Packer.html#ab74d4e3fe0a2a0942e82cdcae0d1bad6',1,'vg::Packer']]],
+ ['node_5fquality_5fbin_5foffset_4032',['node_quality_bin_offset',['../classvg_1_1Packer.html#ac3f39972f863ff761e8c32dee7702296',1,'vg::Packer']]],
+ ['node_5fquality_5fbin_5fsize_4033',['node_quality_bin_size',['../classvg_1_1Packer.html#a1526efc7e55974a7f3b009f769900dda',1,'vg::Packer']]],
+ ['node_5fquality_5fciv_4034',['node_quality_civ',['../classvg_1_1Packer.html#a8491169478e16d232cdb9b1100acdade',1,'vg::Packer']]],
+ ['node_5fquality_5fdynamic_4035',['node_quality_dynamic',['../classvg_1_1Packer.html#a7ff3c9e1c9147389485b0da01d5eb2db',1,'vg::Packer']]],
+ ['node_5fquality_5flocks_4036',['node_quality_locks',['../classvg_1_1Packer.html#ac06fff3568beec54bb343011fc8f6786',1,'vg::Packer']]],
+ ['node_5fquality_5fvector_5fsize_4037',['node_quality_vector_size',['../classvg_1_1Packer.html#ada965622937baaf933fd36cd84315cde',1,'vg::Packer']]],
+ ['node_5frank_4038',['node_rank',['../classvg_1_1VG.html#a0202180fa7153f464c3b1d3ff70dc9cb',1,'vg::VG::node_rank(Node *node)'],['../classvg_1_1VG.html#ad7ac4861a64a07f344c21cf2f41b91f1',1,'vg::VG::node_rank(nid_t id)']]],
+ ['node_5fsequence_4039',['node_sequence',['../structvg_1_1WFANode.html#a1a923918d714be1ab7c32f27a5ed31e9',1,'vg::WFANode']]],
+ ['node_5fsize_4040',['NODE_SIZE',['../classvg_1_1ZipCode.html#a0237b30c6e57eb94d71e67af989cbf03',1,'vg::ZipCode']]],
+ ['node_5fstart_4041',['node_start',['../namespacevg.html#a30f5b0dc3732e48a6d9b8d1c895cd8d1',1,'vg']]],
+ ['node_5fstart_5fat_5fpath_5fposition_4042',['node_start_at_path_position',['../classxg_1_1XG.html#aa9b17c02171a7073eeb9d4614e619f34',1,'xg::XG']]],
+ ['node_5fstarts_5fin_5fpath_4043',['node_starts_in_path',['../classvg_1_1VG.html#a093f4e4dffe0d03806df32edc33cdb9a',1,'vg::VG::node_starts_in_path(const list< NodeTraversal > &path, map< Node *, int > &node_start)'],['../classvg_1_1VG.html#ac27c591957478a17605c2453749f7d20',1,'vg::VG::node_starts_in_path(list< NodeTraversal > &path, map< NodeTraversal *, int > &node_start)']]],
+ ['node_5fsubset_4044',['node_subset',['../classvg_1_1SubgraphOverlay.html#a68a505e96443fd85b5498cf785fc372d',1,'vg::SubgraphOverlay']]],
+ ['node_5fsupports_4045',['node_supports',['../structvg_1_1SupportAugmentedGraph.html#ad904715950e1e9ffcb6ed6676868debe',1,'vg::SupportAugmentedGraph']]],
+ ['node_5fto_5fposition_4046',['node_to_position',['../classvg_1_1Filter.html#aa3a0cf6a83085d33f0983e681c078625',1,'vg::Filter']]],
+ ['node_5fto_5fsegment_5fand_5foffsets_4047',['node_to_segment_and_offsets',['../classvg_1_1FlatFileBackTranslation.html#a019b9f65e0fbd404da5fe42f8a338e22',1,'vg::FlatFileBackTranslation']]],
+ ['node_5fto_5fsnarl_4048',['node_to_snarl',['../classvg_1_1SnarlGraph.html#afccf2e9cf0326a49a9d2226869e11c5f',1,'vg::SnarlGraph']]],
+ ['node_5fto_5fvariant_4049',['node_to_variant',['../classvg_1_1VCFTraversalFinder.html#a133068b1a172eb5f5490ff7c47fd567f',1,'vg::VCFTraversalFinder']]],
+ ['node_5ftoo_5fshort_4050',['NODE_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae6b4882026edf127e7a8d7a120636586',1,'vg::AlignmentValidity']]],
+ ['node_5ftraversal_4051',['node_traversal',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a6347ba68d0d1a79fa623928b2d2eadcc',1,'vg::PhasedGenome::HaplotypeNode']]],
+ ['node_5fvector_5foffset_4052',['node_vector_offset',['../classxg_1_1XG.html#abc79b8d077e089d9a847a6a4a4be70cc',1,'xg::XG::node_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a8666da4a9f55361893544fbb4eff76ce',1,'handlegraph::VectorizableHandleGraph::node_vector_offset()']]],
+ ['node_5fweight_5fcallback_4053',['node_weight_callback',['../classvg_1_1FlowTraversalFinder.html#a345a65197b9a0cd215d616dfcfcd5519',1,'vg::FlowTraversalFinder']]],
+ ['nodelength_4054',['nodelength',['../structhaplo_1_1gbwt__thread__t.html#afcc24f78011916b909ac56b22c8f82c3',1,'haplo::gbwt_thread_t']]],
+ ['nodepileup_4055',['NodePileup',['../structvg_1_1NodePileup.html',1,'vg']]],
+ ['nodes_4056',['nodes',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aa1c634ccdab6c61d7fc0b9971014b276',1,'vg::MEMClusterer::HitGraph::nodes()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a348fbee890bd78dc50c7c84368c5b2f6',1,'vg::MEMClusterer::DPScoreComparator::nodes()'],['../classvg_1_1DiagramExplainer.html#ac48c36394b081ec619056ce38cde5d13',1,'vg::DiagramExplainer::nodes()'],['../structvg_1_1FlowSort_1_1Growth.html#ace41b35679169dfbe0a6dda4c4837681',1,'vg::FlowSort::Growth::nodes()'],['../classvg_1_1WFATree.html#a786ffc1f75cffa39bb4fe43cf22b0926',1,'vg::WFATree::nodes()'],['../structhaplo_1_1gbwt__thread__t.html#a88bae446203703780f81cbcee5ff75cd',1,'haplo::gbwt_thread_t::nodes()'],['../classvg_1_1MaximalExactMatch.html#a1c34a3529b17b7ca55a3d29c0777f5e8',1,'vg::MaximalExactMatch::nodes()'],['../structvg_1_1algorithms_1_1Graph.html#a838a14a80429547309f3e9a1c75e491e',1,'vg::algorithms::Graph::nodes()']]],
+ ['nodes_5fare_5fperfect_5fpath_5fneighbors_4057',['nodes_are_perfect_path_neighbors',['../namespacehandlegraph_1_1algorithms.html#afbf906cc6a283954093403396ee5ce0e',1,'handlegraph::algorithms']]],
+ ['nodes_5fbefore_5foffset_4058',['nodes_before_offset',['../classvg_1_1Viz.html#aa315096c3932839c5cf98b28da52b078',1,'vg::Viz']]],
+ ['nodes_5fnext_4059',['nodes_next',['../classvg_1_1VG.html#a0b084d958fd8069839884dc3a01ed745',1,'vg::VG::nodes_next(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a62f1bb7fa27d4d4312017b113aab099a',1,'vg::VG::nodes_next(NodeTraversal n)']]],
+ ['nodes_5fprev_4060',['nodes_prev',['../classvg_1_1VG.html#ac08e778396904ad3b3f20f605f54628d',1,'vg::VG::nodes_prev(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a0f3e69ced0c3135f3f363c14bf752aad',1,'vg::VG::nodes_prev(NodeTraversal n)']]],
+ ['nodeside_4061',['NodeSide',['../classvg_1_1NodeSide.html',1,'vg::NodeSide'],['../classvg_1_1NodeSide.html#ac4bde3f59ff17ea8c7415fcd9fdd4a0b',1,'vg::NodeSide::NodeSide(id_t node, bool is_end=false)'],['../classvg_1_1NodeSide.html#a3ecb3102be6a85788a003754925c5872',1,'vg::NodeSide::NodeSide()']]],
+ ['nodeside_2ehpp_4062',['nodeside.hpp',['../nodeside_8hpp.html',1,'']]],
+ ['nodetraversal_4063',['NodeTraversal',['../classvg_1_1NodeTraversal.html',1,'vg::NodeTraversal'],['../classvg_1_1NodeTraversal.html#afca10c8751d4d0f0a86da02277d11513',1,'vg::NodeTraversal::NodeTraversal(Node *node, bool backward=false)'],['../classvg_1_1NodeTraversal.html#a795cce0d085b9113a41fc187e0669f12',1,'vg::NodeTraversal::NodeTraversal()']]],
+ ['nodetraversal_2ehpp_4064',['nodetraversal.hpp',['../nodetraversal_8hpp.html',1,'']]],
+ ['nodetype_4065',['nodeType',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8',1,'haplo::linear_haplo_structure::nodeType()'],['../structhaplo_1_1linear__haplo__structure.html#a2eb8780c98a02ad3a070d3d2b027170e',1,'haplo::linear_haplo_structure::nodeType()']]],
+ ['non_5fintermediate_5faliases_4066',['non_intermediate_aliases',['../classvg_1_1AliasGraph.html#ac400ab0ecb048175fc460f69820204e8',1,'vg::AliasGraph']]],
+ ['non_5fmatch_5fend_4067',['non_match_end',['../namespacevg.html#a3ec2e2ef9679291d966bc348a47c3537',1,'vg']]],
+ ['non_5fmatch_5fstart_4068',['non_match_start',['../namespacevg.html#ae838e7d89edc59dd87747238cee49b49',1,'vg']]],
+ ['nonatgcnton_4069',['nonATGCNtoN',['../namespacevg.html#a453b457823e1ddf916ebf298befb4512',1,'vg']]],
+ ['nonce_4070',['nonce',['../classvg_1_1Sampler.html#a36388c416226dd9c343b2da154aada5c',1,'vg::Sampler']]],
+ ['nondisjoint_4071',['nondisjoint',['../structhaplo_1_1int__itvl__t.html#af18e576db32fb19f602ed249e07567a7',1,'haplo::int_itvl_t']]],
+ ['none_4072',['None',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3a7ec02cb6759bbdcec376638fb9e76d4e',1,'vg::IndexingParameters::None()'],['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85ab50339a10e1de285ac99d4c3990b8693',1,'vg::Funnel::NONE()'],['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39aa676d6ce23c4076e354ffb65936c03d1',1,'vg::None()']]],
+ ['nonoverlapping_5fnode_5fcontext_5fwithout_5fpaths_4073',['nonoverlapping_node_context_without_paths',['../classvg_1_1VG.html#a44edad9ba2a6df332234b43715dd71db',1,'vg::VG']]],
+ ['normal_4074',['normal',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea867c09ce684d19db107c790ac73e29c2',1,'vg::Haplotypes::Subchain']]],
+ ['normal_5faligners_4075',['normal_aligners',['../classvg_1_1Genotyper.html#a91d6174a20ca4f121f68766fbf7fb4b0',1,'vg::Genotyper']]],
+ ['normal_5fdistribution_4076',['normal_distribution',['../classvg_1_1normal__distribution.html',1,'vg::normal_distribution< T >'],['../classvg_1_1normal__distribution.html#a7c7bb2c253ac80e0752fd2ba2f84ed56',1,'vg::normal_distribution::normal_distribution()']]],
+ ['normal_5fpdf_4077',['normal_pdf',['../namespacevg.html#ae825181ee40a5f0d5087fc657db9a7db',1,'vg']]],
+ ['normal_5fsupports_4078',['normal_supports',['../structvg_1_1BREAKPOINT.html#a08a0810aad3ba05efd04908b4911d57d',1,'vg::BREAKPOINT']]],
+ ['normalize_4079',['normalize',['../namespacevg_1_1algorithms.html#afb6a93eb17739d744908d61ca6650f4c',1,'vg::algorithms']]],
+ ['normalize_2ecpp_4080',['normalize.cpp',['../normalize_8cpp.html',1,'']]],
+ ['normalize_2ehpp_4081',['normalize.hpp',['../normalize_8hpp.html',1,'']]],
+ ['normalize_5falignment_4082',['normalize_alignment',['../namespacevg.html#afa0c54720b2b1007ae540dc70b5b8024',1,'vg']]],
+ ['nowhere_4083',['nowhere',['../classvg_1_1algorithms_1_1TracedScore.html#ad2f398d1d22f2a027a870182e7fd26d4',1,'vg::algorithms::TracedScore']]],
+ ['np_5fbv_4084',['np_bv',['../classxg_1_1XG.html#a7c8fe296641f19779727ab5857b834ea',1,'xg::XG']]],
+ ['np_5fbv_5fselect_4085',['np_bv_select',['../classxg_1_1XG.html#a077bdb48fbea43751a6cf5c5d731cfbe',1,'xg::XG']]],
+ ['np_5fiv_4086',['np_iv',['../classxg_1_1XG.html#a1bb51062742302890454d1d5552c011d',1,'xg::XG']]],
+ ['nr_5fiv_4087',['nr_iv',['../classxg_1_1XG.html#a8516a2b79e6326c6b2e7c2a3033ef9d4',1,'xg::XG']]],
+ ['nt_5ftable_4088',['nt_table',['../classvg_1_1GSSWAligner.html#a73b117b8b0b894ce486bdb2c4eeeeb10',1,'vg::GSSWAligner::nt_table()'],['../classvg_1_1DinucleotideMachine.html#a42eb3d5ffd684edcd69e43c3bc28eb95',1,'vg::DinucleotideMachine::nt_table()']]],
+ ['nth_5fcopy_5fof_5fhandle_4089',['nth_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a716193b4f3dcecfd26de15acf83964b9',1,'vg::DagifiedGraph']]],
+ ['null_4090',['Null',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095ea4da67a14c941c99eb8e041314fa98640',1,'vg::multipath_alignment_t']]],
+ ['null_5fmasking_5fgraph_2ecpp_4091',['null_masking_graph.cpp',['../null__masking__graph_8cpp.html',1,'']]],
+ ['null_5fmasking_5fgraph_2ehpp_4092',['null_masking_graph.hpp',['../null__masking__graph_8hpp.html',1,'']]],
+ ['nullalignmentemitter_4093',['NullAlignmentEmitter',['../classvg_1_1io_1_1NullAlignmentEmitter.html',1,'vg::io']]],
+ ['nullclusterer_4094',['NullClusterer',['../classvg_1_1NullClusterer.html',1,'vg::NullClusterer'],['../classvg_1_1NullClusterer.html#a63ae2e8bfe748f6557df52cddf4b41e8',1,'vg::NullClusterer::NullClusterer()']]],
+ ['nullmaskinggraph_4095',['NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html',1,'vg::NullMaskingGraph'],['../classvg_1_1NullMaskingGraph.html#a2d348fa5aa3bd9216fc4133d320575ef',1,'vg::NullMaskingGraph::NullMaskingGraph(const HandleGraph *graph)'],['../classvg_1_1NullMaskingGraph.html#addeb1ab4002f516c686a5af59018597f',1,'vg::NullMaskingGraph::NullMaskingGraph()=default']]],
+ ['num_5falt_5falns_4096',['num_alt_alns',['../classvg_1_1MultipathMapper.html#ad29e0a45fcb921023bd6479a15cfef78',1,'vg::MultipathMapper']]],
+ ['num_5fbases_4097',['num_bases',['../structvg_1_1BasePileup.html#aca3e40a479d777aaaa687ca8ab7ce49a',1,'vg::BasePileup']]],
+ ['num_5fbases_5fdynamic_4098',['num_bases_dynamic',['../classvg_1_1Packer.html#a34e4dcd2100f889a0f3e673f1a794d29',1,'vg::Packer']]],
+ ['num_5fbp_5fper_5fmin_4099',['num_bp_per_min',['../classvg_1_1MinimizerMapper.html#af96dfe389dbee27c52f253bb473d94de',1,'vg::MinimizerMapper']]],
+ ['num_5fcandidates_4100',['NUM_CANDIDATES',['../classvg_1_1Recombinator.html#a5768e471a3447a31b14f1d8d94a11588',1,'vg::Recombinator']]],
+ ['num_5fcomponents_4101',['num_components',['../namespacevg_1_1algorithms.html#aa84bd9740e748431857b5fd8a0397183',1,'vg::algorithms']]],
+ ['num_5fconnected_5fcomponents_4102',['num_connected_components',['../namespacevg.html#a1ac45a06bc04f88ba6c2321d7af304c6',1,'vg']]],
+ ['num_5fedges_5fdynamic_4103',['num_edges_dynamic',['../classvg_1_1Packer.html#ae05325e714e72b76815740f03dc10a3b',1,'vg::Packer']]],
+ ['num_5fforward_5freads_4104',['num_forward_reads',['../structvg_1_1EdgePileup.html#a5a61f1d9489561ede0ca1afcbcd7c1d9',1,'vg::EdgePileup']]],
+ ['num_5fhaplotypes_4105',['NUM_HAPLOTYPES',['../classvg_1_1Recombinator.html#a06515509b2d56e644d5a89d1bab3b239',1,'vg::Recombinator::NUM_HAPLOTYPES()'],['../structvg_1_1Recombinator_1_1Parameters.html#a253f1e11aa0a36a9f1cf0251de316066',1,'vg::Recombinator::Parameters::num_haplotypes()'],['../classvg_1_1PhasedGenome.html#af17e5f99a07028d41f94885480cdddf7',1,'vg::PhasedGenome::num_haplotypes()']]],
+ ['num_5finline_4106',['NUM_INLINE',['../structvg_1_1MatchPos_1_1PathList.html#ac2b88a61013598a9ed786f65137c888f',1,'vg::MatchPos::PathList']]],
+ ['num_5fitems_4107',['num_items',['../classvg_1_1ShuffledPairs.html#af7af129e1f60b59e78ed6d92d693d599',1,'vg::ShuffledPairs']]],
+ ['num_5fjobs_4108',['num_jobs',['../structvg_1_1RebuildParameters.html#a25c12cba31a60be2c6bdfd5ece960ad7',1,'vg::RebuildParameters']]],
+ ['num_5fleft_5fhandles_4109',['num_left_handles',['../classvg_1_1JoinedSpliceGraph.html#acb848555db862533ceda5be3136b7040',1,'vg::JoinedSpliceGraph']]],
+ ['num_5fmapping_5fattempts_4110',['num_mapping_attempts',['../classvg_1_1MultipathMapper.html#acd259da737785206d02cc2807ab831fa',1,'vg::MultipathMapper']]],
+ ['num_5fnodes_5fdynamic_4111',['num_nodes_dynamic',['../classvg_1_1Packer.html#a9f406ddaf008b85d23ea1262ab95ad68',1,'vg::Packer']]],
+ ['num_5fnull_5fnodes_4112',['num_null_nodes',['../classvg_1_1DozeuPinningOverlay.html#aad4a7969c5c7263cfd5072169b60f6fa',1,'vg::DozeuPinningOverlay::num_null_nodes()'],['../classvg_1_1NullMaskingGraph.html#a789adb0e97e25f480f18c7158aec51ac',1,'vg::NullMaskingGraph::num_null_nodes()']]],
+ ['num_5fpairs_4113',['num_pairs',['../classvg_1_1ShuffledPairs.html#abf8913c70ff6595d8b288bdab3c88981',1,'vg::ShuffledPairs']]],
+ ['num_5fpaths_4114',['num_paths',['../structGBWTConfig.html#ad3dc88b3f829f932b976fc182257b987',1,'GBWTConfig']]],
+ ['num_5fpaths_5fset_4115',['num_paths_set',['../structGBWTConfig.html#aefbd9bdd79f88ab07ee18a12df56e513',1,'GBWTConfig']]],
+ ['num_5freads_4116',['num_reads',['../structvg_1_1EdgePileup.html#aa95aa0337a5bc6229762abaa56dcdbff',1,'vg::EdgePileup']]],
+ ['num_5fsnarls_4117',['num_snarls',['../classvg_1_1SnarlManager.html#a727734d76e892a3fc0d421c6382349a1',1,'vg::SnarlManager']]],
+ ['num_5fthreads_4118',['num_threads',['../classvg_1_1Transcriptome.html#ac2261cd2e4236c02dbfded216253c923',1,'vg::Transcriptome']]],
+ ['number_5fbool_5fpacking_4119',['number_bool_packing',['../structhandlegraph_1_1number__bool__packing.html',1,'handlegraph']]],
+ ['number_5fof_5fvalues_4120',['number_of_values',['../structvg_1_1SummaryStatistics.html#a0960315b33bca238ec069a1c23eefba5',1,'vg::SummaryStatistics']]],
+ ['numeric_5fmode_4121',['numeric_mode',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#af2a10466f1ac4f49fb670ffd43d48a19',1,'vg::algorithms::GFAIDMapInfo']]],
+ ['nx_5fiv_4122',['nx_iv',['../classxg_1_1XG.html#a48563ff2d8a9e68e67ec75ad93b6272e',1,'xg::XG']]]
];
diff --git a/search/all_f.js b/search/all_f.js
index 16d6994df0..05a87d5e29 100644
--- a/search/all_f.js
+++ b/search/all_f.js
@@ -1,199 +1,199 @@
var searchData=
[
- ['object_5fend_4121',['object_end',['../classvg_1_1ProblemDumpExplainer.html#adb13795992af2eafcbfe0f6716a127f9',1,'vg::ProblemDumpExplainer']]],
- ['object_5fstart_4122',['object_start',['../classvg_1_1ProblemDumpExplainer.html#a5ebde44f8627a596cdb75267a55f887d',1,'vg::ProblemDumpExplainer']]],
- ['occs_4123',['occs',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ad0254616466743533fd8b6fd59c70e0c',1,'vg::MinimizerMapper::Minimizer']]],
- ['of_5fnode_4124',['of_node',['../classvg_1_1Paths.html#abda01c563a3455d491b152a23b22a27a',1,'vg::Paths']]],
- ['off_5fref_5fpaths_4125',['off_ref_paths',['../classvg_1_1Deconstructor.html#adb3fbf24c904974bf655ef76145dac5a',1,'vg::Deconstructor']]],
- ['off_5ft_4126',['off_t',['../namespacehandlegraph.html#a0dcae34b861ba40c47d177dc06537bf7',1,'handlegraph']]],
- ['offset_4127',['offset',['../structvg_1_1GaplessExtension.html#a713e8ef2aad7aa94ae4ef91fbe83e159',1,'vg::GaplessExtension::offset()'],['../structvg_1_1PathBranch.html#ad07bed1fbba0e7c94c218f285c2e51cd',1,'vg::PathBranch::offset()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a5a3aa6577a357cc3067c7a8fbaae1349',1,'vg::Haplotypes::TopLevelChain::offset()'],['../structvg_1_1VectorView_1_1const__iterator.html#a658783ba6132302706230422eae39ce2',1,'vg::VectorView::const_iterator::offset()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a67955816b4446c3b57660e18d9626450',1,'vg::ZipCode::decoder_t::offset()'],['../structvg_1_1Position.html#a1244220d4c8ae90633fd7a7e361d309a',1,'vg::Position::offset()'],['../classvg_1_1position__t.html#a8de3e2b8d4801ca2951d4c21d57bd404',1,'vg::position_t::offset()'],['../namespacevg.html#ad48a54a3ddd5e6ffd8e3e6296fb9c037',1,'vg::offset()'],['../namespacexg.html#ac689f45eccbedaba6fab410913961f8c',1,'xg::offset()']]],
- ['offset_5ft_4128',['offset_t',['../namespacevg.html#afe223f2c7890c76de5e00b43ceb37add',1,'vg::offset_t()'],['../namespacehandlegraph.html#a5aba28c40bd7f181cac4e8d73d6edef8',1,'handlegraph::offset_t()']]],
- ['offsets_4129',['offsets',['../classxg_1_1XGPath.html#a062c1a4ce4f13b67a90f8b57ec57e91e',1,'xg::XGPath']]],
- ['offsets_5fin_5fpaths_4130',['offsets_in_paths',['../classxg_1_1XG.html#af77c93c34b8009c590fa4ee2b01fd64e',1,'xg::XG::offsets_in_paths()'],['../namespacevg_1_1algorithms.html#aef24fa77dadb09d5920ec94b88af2128',1,'vg::algorithms::offsets_in_paths()']]],
- ['offsets_5frank_4131',['offsets_rank',['../classxg_1_1XGPath.html#aa6f1e3a71e8ceb8242a4b1f5157a789b',1,'xg::XGPath']]],
- ['offsets_5fselect_4132',['offsets_select',['../classxg_1_1XGPath.html#a22511bf04c45ce0c8620069781e3cdee',1,'xg::XGPath']]],
- ['ok_4133',['ok',['../structvg_1_1WFAAlignment.html#a64f88d651eb19e3045ab6f9b5552e6c6',1,'vg::WFAAlignment::ok()'],['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae41b7fcb28f19fd52e9b25b6bb0ada27',1,'vg::AlignmentValidity::OK()']]],
- ['old_5fedge_5ftype_5fend_5fend_4134',['OLD_EDGE_TYPE_END_END',['../classxg_1_1XG.html#a42c04fbecadef083a270c715b250e0cd',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fend_5fstart_4135',['OLD_EDGE_TYPE_END_START',['../classxg_1_1XG.html#a00a6fd4ed46f08eff821566c078b744c',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fmax_4136',['OLD_EDGE_TYPE_MAX',['../classxg_1_1XG.html#a720a6ad7d985ff3f67b3cc1f49328992',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fmin_4137',['OLD_EDGE_TYPE_MIN',['../classxg_1_1XG.html#a5ea5ab4b3c152cff2dd9568c99b14f36',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fstart_5fend_4138',['OLD_EDGE_TYPE_START_END',['../classxg_1_1XG.html#a204c73be3278d6e2edb0302f467acf8f',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fstart_5fstart_4139',['OLD_EDGE_TYPE_START_START',['../classxg_1_1XG.html#a2201290a423753452c4a2943735d0c6e',1,'xg::XG']]],
- ['old_5fg_5fedge_5flength_4140',['OLD_G_EDGE_LENGTH',['../classxg_1_1XG.html#a2996e32eb2afb8b783956fb997b0a1f9',1,'xg::XG']]],
- ['old_5fg_5fedge_5foffset_5foffset_4141',['OLD_G_EDGE_OFFSET_OFFSET',['../classxg_1_1XG.html#a44e391542f4cd27cbbbb493319e37d3a',1,'xg::XG']]],
- ['old_5fg_5fedge_5ftype_5foffset_4142',['OLD_G_EDGE_TYPE_OFFSET',['../classxg_1_1XG.html#a41a462402155eb20a1549048ef12f4da',1,'xg::XG']]],
- ['old_5fg_5fnode_5ffrom_5fcount_5foffset_4143',['OLD_G_NODE_FROM_COUNT_OFFSET',['../classxg_1_1XG.html#a4885ba0ab6f74adc04b97504d6fd4f38',1,'xg::XG']]],
- ['old_5fg_5fnode_5fto_5fcount_5foffset_4144',['OLD_G_NODE_TO_COUNT_OFFSET',['../classxg_1_1XG.html#af3b654ed719981eecf06b7b5d9ddd0a8',1,'xg::XG']]],
- ['old_5fnode_4145',['old_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac101c3ba66f96fa569c1de71bf6c51fe',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['old_5fscore_4146',['old_score',['../structvg_1_1GaplessExtension.html#a868af12d5411848f3b8e0e682d053337',1,'vg::GaplessExtension']]],
- ['old_5fversion_5fpath_5fname_5fend_4147',['old_version_path_name_end',['../classxg_1_1XG.html#ac0112b557633896a5c03e7e806b76f73',1,'xg::XG']]],
- ['old_5fversion_5fpath_5fname_5fstart_4148',['old_version_path_name_start',['../classxg_1_1XG.html#aa5ca99b933d49ff2b036650008b68cbd',1,'xg::XG']]],
- ['on_5fgroup_4149',['on_group',['../classvg_1_1io_1_1MessageEmitter.html#a5b5f11b2f9b08a870fc68a980c91f1e4',1,'vg::io::MessageEmitter::on_group()'],['../classvg_1_1io_1_1ProtobufEmitter.html#af22328bc428af2be817a7a0d097ca370',1,'vg::io::ProtobufEmitter::on_group()']]],
- ['on_5fmessage_4150',['on_message',['../classvg_1_1io_1_1ProtobufEmitter.html#a6a3a16550dcd7dd7a320109125d4e2a1',1,'vg::io::ProtobufEmitter']]],
- ['on_5fpath_5fedit_4151',['on_path_edit',['../classvg_1_1FeatureSet.html#a72b47862b3121905222f7662c4ff65ca',1,'vg::FeatureSet']]],
- ['one_5fend_5fanchored_5ffilter_4152',['one_end_anchored_filter',['../classvg_1_1Filter.html#adf0ea872057dafedc321b256ec072b8c',1,'vg::Filter']]],
- ['oneof_5flocation_4153',['oneof_location',['../structvg_1_1LocationSupport.html#a9a000a5b773e07f7cc30614d77c927a0',1,'vg::LocationSupport']]],
- ['only_5fcorrectly_5fmapped_4154',['only_correctly_mapped',['../classvg_1_1ReadFilter.html#ab0f19128ff55e1e2c1cad90adcfc0d6e',1,'vg::ReadFilter']]],
- ['only_5ffirst_5falignment_4155',['only_first_alignment',['../classvg_1_1ReadFilter.html#a5747bfc6146fa25db9fd96f1f760f6f0',1,'vg::ReadFilter']]],
- ['only_5fmapped_4156',['only_mapped',['../classvg_1_1ReadFilter.html#ab19be8fc638af431bb1a629aeff77f4f',1,'vg::ReadFilter']]],
- ['only_5fproper_5fpairs_4157',['only_proper_pairs',['../classvg_1_1ReadFilter.html#ac41003be9ee710a1003288e2a6ba9c7d',1,'vg::ReadFilter']]],
- ['open_5fall_4158',['open_all',['../classvg_1_1StreamSorter.html#a112c5a39918bb37f4aa3bf1413d31b37',1,'vg::StreamSorter']]],
- ['open_5fchain_4159',['open_chain',['../classvg_1_1ZipCodeForest.html#a56fb93ecb975f5f6c12deeef5b1f9b20',1,'vg::ZipCodeForest']]],
- ['open_5fchains_4160',['open_chains',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a43af493f53945324b203009c974ab0d2',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['open_5ffd_4161',['open_fd',['../classhandlegraph_1_1TriviallySerializable.html#aa1f5b9cdb957540dfea7e0e4b478e9b2',1,'handlegraph::TriviallySerializable']]],
- ['open_5fintervals_4162',['open_intervals',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a75768315ee176ee34dc33da021696810',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['open_5fsnarl_4163',['open_snarl',['../classvg_1_1ZipCodeForest.html#ab219e010a4e80804f7c5f6ada581f18d',1,'vg::ZipCodeForest']]],
- ['operatingmode_4164',['OperatingMode',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667',1,'HaplotypesConfig']]],
- ['operator_20bool_4165',['operator bool',['../structvg_1_1AlignmentValidity.html#a2f6b53f193bad40111118e3293ad361c',1,'vg::AlignmentValidity::operator bool()'],['../classvg_1_1Explainer.html#aeca40f040dd309c5f457e8ea0bd8627f',1,'vg::Explainer::operator bool()'],['../structvg_1_1WFAAlignment.html#a7f1464e6b2a86671cdf376137409eeeb',1,'vg::WFAAlignment::operator bool()']]],
- ['operator_20number_4166',['operator Number',['../structvg_1_1Range.html#acb0f6ebb720df6227410bf9403079a32',1,'vg::Range']]],
- ['operator_20value_20_26_4167',['operator Value &',['../classvg_1_1BaseOption.html#a760720e496d3058589d34d823f61566b',1,'vg::BaseOption']]],
- ['operator_21_3d_4168',['operator!=',['../classvg_1_1ShuffledPairs_1_1iterator.html#a2714f2334dae600fc66c3508ecd4494a',1,'vg::ShuffledPairs::iterator::operator!=()'],['../structvg_1_1GaplessExtension.html#a5fc94cd2cfd5898459cac75c65be55a5',1,'vg::GaplessExtension::operator!=()'],['../structvg_1_1read__alignment__index__t.html#ac967a7e4d2339bf2ab83208991b0ce69',1,'vg::read_alignment_index_t::operator!=()'],['../structvg_1_1alignment__index__t.html#ab09e271d0c6eb6f08fd1bde411c6c5f7',1,'vg::alignment_index_t::operator!=()'],['../classvg_1_1NodeSide.html#a48481b0155b782c27644080c98d20656',1,'vg::NodeSide::operator!=()'],['../classvg_1_1NodeTraversal.html#aaa81c382e219ed6f832b1401872fe898',1,'vg::NodeTraversal::operator!=()'],['../classvg_1_1edit__t.html#ac6b81fe1407a1ae901f72ed555a30dae',1,'vg::edit_t::operator!=()'],['../classvg_1_1path__mapping__t.html#a78466c5a9e83d7367bd70799dfd4a76b',1,'vg::path_mapping_t::operator!=()'],['../classvg_1_1path__t.html#a5a0f6368c497cfe5eac4025080c20bc1',1,'vg::path_t::operator!=()'],['../classvg_1_1PhasedGenome_1_1iterator.html#aff3ae0b92ca06496a22d1aad89016737',1,'vg::PhasedGenome::iterator::operator!=()'],['../classvg_1_1position__t.html#a9011acaf2ade42c99a74596214196fa8',1,'vg::position_t::operator!=()'],['../structvg_1_1ChainIterator.html#aec215507b5b43e388afb2933d25c21d0',1,'vg::ChainIterator::operator!=()'],['../classvg_1_1BitString.html#a57b03c3b055ab267c199bd429ff5e4c6',1,'vg::BitString::operator!=()'],['../structvg_1_1VectorView_1_1const__iterator.html#a620b2bd9b99aff0ab077ce6d9441b684',1,'vg::VectorView::const_iterator::operator!=()'],['../structvg_1_1IncrementIter.html#a97c041dbf0473d997321d19072fe85e6',1,'vg::IncrementIter::operator!=()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#aced4d93ad8d1fb3b5b530ff0dd912912',1,'vg::ZipCodeTree::oriented_seed_t::operator!=()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#ac730025c4f3c9144cd742a6c0b15f3d3',1,'vg::ZipCodeTree::seed_result_t::operator!=()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a1eddeaefb5ff95cbde90e0112efa2433',1,'vg::ZipCodeTree::iterator::operator!=()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4925ff71b13d15855904e7e7497b295b',1,'vg::ZipCodeTree::reverse_iterator::operator!=()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4a74c0a77c2df092ecc5d2be1a4b793c',1,'vg::algorithms::TracedScore::operator!=()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a2c24b07521aa704e517c386e1369d227',1,'handlegraph::PathForEachSocket::iterator::operator!=()'],['../classvg_1_1io_1_1MessageIterator.html#ad6a23c45ab954ce158faec0b8935cd90',1,'vg::io::MessageIterator::operator!=()'],['../classvg_1_1io_1_1ProtobufIterator.html#a1f67a6fcda4cfa7d6d1b37bcdb74c0ac',1,'vg::io::ProtobufIterator::operator!=()'],['../namespacevg.html#abb6063b76b70947010198b46c053b578',1,'vg::operator!=(const Visit &a, const Visit &b)'],['../namespacevg.html#a24e1e38ea29c615b2c5f5cd8dbaeeb2a',1,'vg::operator!=(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a654eca8448629e42ae87cadd893ee10e',1,'vg::operator!=(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a22cb5c700c1dee4fec8d3af77057ea2a',1,'vg::operator!=(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#a4f594795be32cb04b7baf0ef71ad77b0',1,'vg::operator!=(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a581944f1e71285f8c4887c2f5ce1467f',1,'vg::operator!=(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a67115fb742d1bf6d7e4e489fda99b78e',1,'vg::operator!=(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#a913cf04aa9946eebf68cc319d7929f11',1,'handlegraph::operator!=(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a18f417ab023834f355f735c2baa18324',1,'handlegraph::operator!=(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#acbbe7b08c190039a0a3700e078818aa5',1,'handlegraph::operator!=(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#acc5274f38cf004b29d2bf398a96f4da5',1,'handlegraph::operator!=(const net_handle_t &a, const net_handle_t &b)']]],
- ['operator_26_3d_4169',['operator&=',['../classvg_1_1SmallBitset.html#a44c58c409898c13b98b3937669bf7b8f',1,'vg::SmallBitset']]],
- ['operator_28_29_4170',['operator()',['../structvg_1_1BBEdgeHash.html#af0c713bc536e343b416520dd0f14732b',1,'vg::BBEdgeHash::operator()()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a748c3131cdb69751197546f36a1298bb',1,'vg::MEMClusterer::DPScoreComparator::operator()()'],['../classvg_1_1DistanceHeuristic.html#afb17aa7db222de3ef43a70115c7eec6a',1,'vg::DistanceHeuristic::operator()()'],['../classvg_1_1SnarlMinDistance.html#a4a87d093a5ee90f158ce5e5a1fdc8fd4',1,'vg::SnarlMinDistance::operator()()'],['../classvg_1_1TipAnchoredMaxDistance.html#a165cc0f3d3e70810f72bd7ad49b9416e',1,'vg::TipAnchoredMaxDistance::operator()()'],['../structvg_1_1state__hash.html#a5ddcb7dd42852b3f35fd414663677e8c',1,'vg::state_hash::operator()()'],['../classvg_1_1ReadMasker.html#a8d7a36b958e3405106494e93fffcda5f',1,'vg::ReadMasker::operator()()'],['../structvg_1_1Genotyper_1_1hash__node__traversal.html#a62f374bedac308110f484df59f6c905f',1,'vg::Genotyper::hash_node_traversal::operator()()'],['../structvg_1_1Genotyper_1_1hash__oriented__edge.html#a070a16b42f8aeace08dfee4f22badc8d',1,'vg::Genotyper::hash_oriented_edge::operator()()'],['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html#a44aad1a7e112842dc576fd9cbebdbbfc',1,'vg::Genotyper::hash_ambiguous_allele_set::operator()()'],['../structvg_1_1wang__hash_3_01handle__t_01_4.html#a2abb45aa397420108850ce590f7f3bf7',1,'vg::wang_hash< handle_t >::operator()()'],['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html#a5a9ad96629401a307c94b17a2d91fc53',1,'vg::wang_hash< path_handle_t >::operator()()'],['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html#a847da6dc45718131135dba8e17aa93a6',1,'std::hash< pair< A, B > >::operator()()'],['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html#afdf58525bd44e80be2af8355db0eba2e',1,'std::hash< std::tuple< TT... > >::operator()()'],['../structvg_1_1wang__hash_3_01T_01_5_01_4.html#a55ef00b42c8f6103e78eb7f7b7597984',1,'vg::wang_hash< T * >::operator()()'],['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html#a87443673fa41e2f7a7ee5cf4e2bd533c',1,'vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >::operator()()'],['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html#af62856c68653d586e53d842a16e54cf7',1,'vg::wang_hash< std::pair< A, B > >::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1FCmp.html#a65b7021e0e5237b4b7f0fbb34a8f99ec',1,'vg::IncrementalSubgraph::FCmp::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html#a9a34770a4c767bf069601106bbdde191',1,'vg::IncrementalSubgraph::IterFCmp::operator()()'],['../structvg_1_1wang__hash_3_01NodeSide_01_4.html#a7880d169d8ebf669908ae4262c49c7b8',1,'vg::wang_hash< NodeSide >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html#a7db7a7f185329bda1e74c4fb99e2d7ed',1,'std::hash< vg::NodeSide >::operator()()'],['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html#ae175f5bef4a05d469ebec4341ff47062',1,'vg::wang_hash< NodeTraversal >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html#a0286ba89a52b8479c5bb4f0e474add3e',1,'std::hash< vg::NodeTraversal >::operator()()'],['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html#a14d9633d19737075532f81dc0a97cb0c',1,'vg::wang_hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html#a16e12560069fba289b6e248fb1534347',1,'std::hash< const vg::Snarl >::operator()()'],['../classvg_1_1uniform__real__distribution.html#a2943db49f42d531d7358b64dbbd87d66',1,'vg::uniform_real_distribution::operator()()'],['../classvg_1_1normal__distribution.html#a022c67bb09abf48906156257c76f0ce0',1,'vg::normal_distribution::operator()()'],['../classvg_1_1truncated__normal__distribution.html#a594bdf20c6d6ce7088dde9b1bdb8ae16',1,'vg::truncated_normal_distribution::operator()()'],['../classvg_1_1WideningPRNG.html#a6d58ed2b6a9704e40e751974d5f77927',1,'vg::WideningPRNG::operator()()'],['../classvg_1_1uniform__int__distribution.html#a51f168ff739db2810fc443c8a17a7981',1,'vg::uniform_int_distribution::operator()()'],['../classvg_1_1discrete__distribution.html#a9f9d62f067a25f9a996367d6d187638b',1,'vg::discrete_distribution::operator()()'],['../structvg_1_1MappingHash.html#ab4877c05349b1d70a4fc9fc1d91bfabf',1,'vg::MappingHash::operator()()'],['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html#a5593776feee196b357efe27af34375dd',1,'vg::NestedCachedPackedTraversalSupportFinder::snarl_less::operator()()'],['../classvg_1_1LazyRNG.html#a76642be6e0b23e61b217e22256faccce',1,'vg::LazyRNG::operator()()'],['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html#a43c26f94ae3a429cd5f02e164fbc8893',1,'vg::wang_hash< net_identifier_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html#a267e3d69b89d37dbfc9d6aee50403bfe',1,'std::hash< vg::ZipCodeTree::oriented_seed_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html#a2db521dc14ad90c29f532932a2cb116f',1,'std::hash< vg::ZipCodeTree::seed_result_t >::operator()()'],['../structcompare__gaf.html#abd0df39e112998e5f3cd4e8fc145454c',1,'compare_gaf::operator()()'],['../structgreater__gaffile.html#af92140ef197df65a58d0687a93f4194e',1,'greater_gaffile::operator()()'],['../classvg_1_1subcommand_1_1Subcommand.html#a2a236ec06c3d6d7ff148712a2ae2e492',1,'vg::subcommand::Subcommand::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html#a825db1e0338e86d296b57cd96a8e0899',1,'std::hash< handlegraph::handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html#a6ad769a3d7b2f71b5696eb33bc977d76',1,'std::hash< handlegraph::path_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html#a4dfc6072381e899f6771b7fef4a1df96',1,'std::hash< handlegraph::step_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html#a9530041f163d977cee6147e78e7f3458',1,'std::hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html#ae02ac63af6a68ca8788a3d16e0d282dc',1,'std::hash< handlegraph::edge_t >::operator()()']]],
- ['operator_2a_4171',['operator*',['../classvg_1_1ShuffledPairs_1_1iterator.html#a7a364e5a3933631209f6356bcbab4195',1,'vg::ShuffledPairs::iterator::operator*()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a6f0c09512af20809ebd66342e0b48e72',1,'vg::PhasedGenome::iterator::operator*()'],['../structvg_1_1ChainIterator.html#a4026eb3698271db72e04c8bf189a7638',1,'vg::ChainIterator::operator*()'],['../classvg_1_1count__back__inserter.html#a23ab94b37972f651d60dc06aea28f567',1,'vg::count_back_inserter::operator*()'],['../structvg_1_1VectorView_1_1const__iterator.html#a6c46dcd71c5b170627061551c7ce0755',1,'vg::VectorView::const_iterator::operator*()'],['../structvg_1_1IncrementIter.html#a5a174a8f85492d7242b52cf1531d50e1',1,'vg::IncrementIter::operator*()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aabf844f9503fb882498e9ad7348644c0',1,'vg::ZipCodeTree::iterator::operator*()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a952c338af40fc2b3c6ab3dda1e36991a',1,'vg::ZipCodeTree::reverse_iterator::operator*()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a9e1c7bf243cdf38e9844e6e253b4f48e',1,'handlegraph::PathForEachSocket::iterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#af9bd6f7d8acd6b65d86ace13aae12a49',1,'vg::io::MessageIterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#a1bde69631cd194d596192908e5a70f0a',1,'vg::io::MessageIterator::operator*() const'],['../classvg_1_1io_1_1ProtobufIterator.html#ab75942ce88acea7c4766895033c51c6f',1,'vg::io::ProtobufIterator::operator*()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6df5500c6398933f60d761188c68895b',1,'vg::io::ProtobufIterator::operator*() const'],['../namespacevg.html#a84dfc966c7511b05c234d215e3b6aec7',1,'vg::operator*(const Support &support, const Scalar &scale)'],['../namespacevg.html#a10844a7c14d7ff54051bad20c75d012e',1,'vg::operator*(const Scalar &scale, const Support &support)']]],
- ['operator_2a_3d_4172',['operator*=',['../namespacevg.html#abe7831ba6fe294e8be36fa0359a63848',1,'vg']]],
- ['operator_2b_4173',['operator+',['../structvg_1_1VectorView_1_1const__iterator.html#aa97c1950851a2eb9d5731c12340b81ff',1,'vg::VectorView::const_iterator::operator+()'],['../namespacevg.html#a27dd5c8f7c6d984a396665cbab5eba01',1,'vg::operator+(const Support &one, const Support &other)'],['../namespacevg.html#a64380ba1816d3fd97847a6dc6b2665d8',1,'vg::operator+(typename VectorView< Item >::const_iterator::difference_type a, const typename VectorView< Item >::const_iterator &b)']]],
- ['operator_2b_2b_4174',['operator++',['../classvg_1_1ShuffledPairs_1_1iterator.html#a1b39b43991061c9b38c0f66be116aa07',1,'vg::ShuffledPairs::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ae7af24b8cfca1872c3b7ecd34cc691b4',1,'vg::PhasedGenome::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a5d6220ad0e3ce9c6fad9c7bd33cd10c2',1,'vg::PhasedGenome::iterator::operator++(int)'],['../structvg_1_1ChainIterator.html#a93335ca3360cd50d0561ad1d4691d017',1,'vg::ChainIterator::operator++()'],['../classvg_1_1count__back__inserter.html#a58b46f86e84878928184f16cd71d2025',1,'vg::count_back_inserter::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab5b2928f08fa931ca8a3da78b9a6e540',1,'vg::VectorView::const_iterator::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#aadee453c16ff3359ea59c37123b1a684',1,'vg::VectorView::const_iterator::operator++(int)'],['../structvg_1_1IncrementIter.html#aa6e20c55ec21957277f5cf07d13ad04d',1,'vg::IncrementIter::operator++()'],['../structvg_1_1IncrementIter.html#a3e40dfadfa140aa600d2bc98ad7a7f90',1,'vg::IncrementIter::operator++(int)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a4fc98efef75fa50606213903af2ec146',1,'vg::ZipCodeTree::iterator::operator++()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa47b19eb964a614f69c6dc2326ed6c83',1,'vg::ZipCodeTree::reverse_iterator::operator++()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#abf9ece90b8080b6f93cbfc516777eac2',1,'handlegraph::PathForEachSocket::iterator::operator++()'],['../classvg_1_1io_1_1MessageIterator.html#a89872d57d9e7d9e49f38b6700e40c99d',1,'vg::io::MessageIterator::operator++()'],['../classvg_1_1io_1_1ProtobufIterator.html#a513fd9e86996eda664b8e5eef5d532e9',1,'vg::io::ProtobufIterator::operator++()']]],
- ['operator_2b_3d_4175',['operator+=',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a54b9cf8b8a2f6c13c1dfce6e73c203e8',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const double &value)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#aff1c525641da64850545049b20a485fb',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const stat_collection_t &other)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a180b0b1ea0fd2c5a3a2c1a1aa2cbbc94',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t::operator+=()'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af3eb35c3215c0b4cdd6628bcfc896c71',1,'vg::MinimizerMapper::aligner_stats_t::operator+=()'],['../structvg_1_1Counts.html#a0bfb40ac3e3eafe2606af33f8c4fde06',1,'vg::Counts::operator+=()'],['../structvg_1_1VectorView_1_1const__iterator.html#ac0ff4c93cb85429b2436b93a0500ab8c',1,'vg::VectorView::const_iterator::operator+=()'],['../namespacevg.html#a4f550213560bfa3c3ad8446478be24d8',1,'vg::operator+=()']]],
- ['operator_2d_4176',['operator-',['../structvg_1_1VectorView_1_1const__iterator.html#a5950d800357a74c5df1a46f3fee1e690',1,'vg::VectorView::const_iterator::operator-(const difference_type &difference) const'],['../structvg_1_1VectorView_1_1const__iterator.html#a6ca91702bea775756791a2505fec98a4',1,'vg::VectorView::const_iterator::operator-(const const_iterator &other) const'],['../classvg_1_1algorithms_1_1TracedScore.html#ade52d5662380757204b3a9eb7e632b5f',1,'vg::algorithms::TracedScore::operator-()']]],
- ['operator_2d_2d_4177',['operator--',['../structvg_1_1VectorView_1_1const__iterator.html#a3f07387c29c6f82c4cb7aa6102e2ff83',1,'vg::VectorView::const_iterator::operator--()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab04cc90a3cb13d7e5a08d51be8cadf0c',1,'vg::VectorView::const_iterator::operator--(int)']]],
- ['operator_2d_3d_4178',['operator-=',['../structvg_1_1VectorView_1_1const__iterator.html#a5da176cea2552046f8080d5be2dc67f7',1,'vg::VectorView::const_iterator']]],
- ['operator_2d_3e_4179',['operator->',['../structvg_1_1ChainIterator.html#a2e521810ed86af3b3bfcbd47285236bb',1,'vg::ChainIterator::operator->()'],['../structvg_1_1VectorView_1_1const__iterator.html#a4029e7dd6c859ed5019bb9169211e235',1,'vg::VectorView::const_iterator::operator->()']]],
- ['operator_2f_4180',['operator/',['../namespacevg.html#a5a9eefddbec41755309a378fb150071c',1,'vg']]],
- ['operator_2f_3d_4181',['operator/=',['../namespacevg.html#a1807752a0b6b83fd5952d36cc64b758d',1,'vg']]],
- ['operator_3c_4182',['operator<',['../structvg_1_1MatchPos.html#a91c8cec7a4cf39616157279004751d56',1,'vg::MatchPos::operator<()'],['../structvg_1_1WFAPoint.html#a4c1eb3733361639c504e79502946747a',1,'vg::WFAPoint::operator<()'],['../structvg_1_1GaplessExtension.html#a60ac9a1eba5b7ca5a0bd1f196a8dc94d',1,'vg::GaplessExtension::operator<()'],['../classvg_1_1MaximalExactMatch.html#ace421d32490547fc94b4003484e97dcb',1,'vg::MaximalExactMatch::operator<()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a94ddd290e4408f2a758083d2022b6c46',1,'vg::MinimizerMapper::Minimizer::operator<()'],['../classvg_1_1NodeSide.html#aa567438110aee30bceb1c00a2c6d4eec',1,'vg::NodeSide::operator<()'],['../classvg_1_1NodeTraversal.html#aaf0141ddf2587f8284bd4c111d6cdff2',1,'vg::NodeTraversal::operator<()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4e460a44f0c5027a3864e5b1b65beee8',1,'vg::algorithms::TracedScore::operator<()'],['../structjob__type.html#aed73e63d2b1d652b075a3346c5f36335',1,'job_type::operator<()'],['../namespacevg.html#ab554a977204c1f756bd0e2738a797447',1,'vg::operator<(const Support &a, const Support &b)'],['../namespacevg.html#ac476fcc21a47f34d00b4a449b28c686b',1,'vg::operator<(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a9d2e2066b3b4534b62cde6e4423efd81',1,'vg::operator<(const Visit &a, const Visit &b)'],['../namespacevg.html#aea87c61d2cc1d5acf1af1d2d351bdb75',1,'vg::operator<(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a0fd908e60f72bd98dcba364a16ab7190',1,'vg::operator<(const Snarl &a, const Snarl &b)'],['../namespacevg.html#ad29d63c9b09132ab0457b3d28ea704ff',1,'vg::operator<(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ad3728100975bea667f2f60fdc1df2dd1',1,'vg::operator<(const Transcript &lhs, const Transcript &rhs)'],['../namespacehandlegraph.html#a3e16d241ab6863b8954754d42c9a0764',1,'handlegraph::operator<(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#abe4f45c9fe64c8cf37fe277b870cf56b',1,'handlegraph::operator<(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a8fc5f1eb104107d55fb043c2a24321aa',1,'handlegraph::operator<(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a926cfa5c0852fd9dfe7685d6eec73fe9',1,'handlegraph::operator<(const net_handle_t &a, const net_handle_t &b)']]],
- ['operator_3c_3c_4183',['operator<<',['../classvg_1_1MaximalExactMatch.html#a415b6e9f064006bb599e11971822669a',1,'vg::MaximalExactMatch::operator<<()'],['../namespacevg.html#a7cc9c4d4d792e1e7f38c2c6009207706',1,'vg::operator<<(ostream &out, const BenchmarkResult &result)'],['../namespacevg.html#a3caa19999a88016c7aedf3fefb8ca69c',1,'vg::operator<<(std::ostream &out, const Funnel::State &state)'],['../namespacevg.html#a1fbb5dfd532a055d9e8251d2dcab3e58',1,'vg::operator<<(std::ostream &out, const WFAAlignment::Edit &edit)'],['../namespacevg.html#a141fbf9c40f389909c5c46132ab6c615',1,'vg::operator<<(ostream &stream, const Support &support)'],['../namespacevg.html#a0e459d4a7dda13edf5b79ea8996cfd82',1,'vg::operator<<(ostream &out, const kmer_t &kmer)'],['../namespacevg.html#af0a4b11db620d43a7e20886d5563e5b8',1,'vg::operator<<(ostream &out, const MaximalExactMatch &mem)'],['../namespacevg.html#a9b4bea48392e7bb9e745b3b04e5bf223',1,'vg::operator<<(ostream &out, const NodeSide &nodeside)'],['../namespacevg.html#ad1bdeb550c6f5fa632ad61454321e001',1,'vg::operator<<(ostream &out, const NodeTraversal &nodetraversal)'],['../namespacevg.html#a81357f8477c9ed2c3839489e0ada1ced',1,'vg::operator<<(ostream &out, mapping_t mapping)'],['../namespacevg.html#a1e7a5fc9017560cc1b505641cc4ef6d0',1,'vg::operator<<(std::ostream &out, PathBranch branch)'],['../namespacevg.html#a35d8d71a9d6d51760cc7354910d029e9',1,'vg::operator<<(ostream &os, const Counts &counts)'],['../namespacevg.html#ab38d6991537581f9ce3f4c549f966a33',1,'vg::operator<<(ostream &out, const Visit &visit)'],['../namespacevg.html#ae0744fdee12e0f4136de643a91c15f77',1,'vg::operator<<(ostream &out, const Snarl &snarl)'],['../namespacevg.html#ac5fc02ee1a5713060cd5f4b33e2eaaab',1,'vg::operator<<(ostream &out, const BitString &bs)'],['../namespacevg.html#a19349c6c73bac7da9651ee91c4272156',1,'vg::operator<<(std::ostream &out, const pos_t &pos)'],['../namespacevg.html#a848f547eaaa9c1ec84809d5ad3bd6871',1,'vg::operator<<(std::ostream &out, const ZipCode &zip)'],['../namespacevg.html#a796e339855648a7b8bdee41619eed23b',1,'vg::operator<<(std::ostream &out, const ZipCode::code_type_t &type)'],['../namespacevg.html#afacdb481e4a38366ce65c39efcb5af49',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::tree_item_type_t &type)'],['../namespacevg.html#a047b1758c707866aceb6c39b2503d5c6',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::reverse_iterator::State &state)'],['../namespacevg_1_1algorithms.html#aafbc78daa41b0c018cd39b7cccbaf53a',1,'vg::algorithms::operator<<(ostream &out, const Anchor &anchor)'],['../namespacevg_1_1algorithms.html#a503ad2215490c5c599530d7331a70120',1,'vg::algorithms::operator<<(ostream &out, const TracedScore &value)'],['../namespacevg_1_1algorithms.html#a3961418e3f3af94c4275118e4693a2fe',1,'vg::algorithms::operator<<(std::ostream &out, const kmer_t &kmer)'],['../namespacevg_1_1algorithms.html#a58ec8c8d09fde1a6e83194ec7126ed4e',1,'vg::algorithms::operator<<(std::ostream &out, const walk_t &walk)'],['../namespacevg_1_1subcommand.html#af9ff4f2d2051fd67f272a581e17dd668',1,'vg::subcommand::operator<<()'],['../namespacexg.html#a72b16c0bf83f5b1d0a1bfd3773d4eb77',1,'xg::operator<<()'],['../namespacegafkluge.html#a226812c098c373a50d825916b4c92a7c',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)'],['../namespacegafkluge.html#a098de1edfb3f22da8638f01e76d9ae2a',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)']]],
- ['operator_3d_4184',['operator=',['../classvg_1_1MEMChainModelVertex.html#a607061ec174e1ea4ed0829c86e1d23de',1,'vg::MEMChainModelVertex::operator=(const MEMChainModelVertex &) &=default'],['../classvg_1_1MEMChainModelVertex.html#ac83963d8e6a0ae78e048910f7441c83a',1,'vg::MEMChainModelVertex::operator=(MEMChainModelVertex &&) &=default'],['../classvg_1_1XdropAligner.html#a5bb2cfcbd85802990c1386827ac98192',1,'vg::XdropAligner::operator=(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a39627c50a6e60a7f065332fbd99fdcba',1,'vg::XdropAligner::operator=(XdropAligner &&other)'],['../classvg_1_1QualAdjXdropAligner.html#ab68a1dff1baf74e2275c5db0c7ac4d39',1,'vg::QualAdjXdropAligner::operator=(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a55c6307a0d16cb7ac32e25f1c4f19e6f',1,'vg::QualAdjXdropAligner::operator=(QualAdjXdropAligner &&other)'],['../classvg_1_1HTSWriter.html#aaa299cc70e86ed6fe1dd1eefef0a23f5',1,'vg::HTSWriter::operator=(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a2ec4df6ab5d9c7d4b1557e9cb04ef30d',1,'vg::HTSWriter::operator=(HTSWriter &&other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#aadcc0b64b3f9178c7e30bb15cccc4e21',1,'vg::HTSAlignmentEmitter::operator=(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a19eafc506789bd80e235ebc63e2bbe7f',1,'vg::HTSAlignmentEmitter::operator=(HTSAlignmentEmitter &&other)=delete'],['../classvg_1_1IndexRegistry.html#a50fcb23d815a8eb3da616c9284157ada',1,'vg::IndexRegistry::operator=(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#a6d96c08dbecf5d59154715bb5010f1f2',1,'vg::IndexRegistry::operator=(IndexRegistry &&other)'],['../structvg_1_1IndexedVG_1_1CacheEntry.html#a6b657674e880f1c5a8026617818f19ed',1,'vg::IndexedVG::CacheEntry::operator=()'],['../classvg_1_1ParallelKFFReader.html#ae7be7ffcc93e64e55d82f9dd4983fc04',1,'vg::ParallelKFFReader::operator=()'],['../classvg_1_1AlignmentChainModelVertex.html#a6f6558dec94cc641a412c130a024a4a2',1,'vg::AlignmentChainModelVertex::operator=(const AlignmentChainModelVertex &) &=default'],['../classvg_1_1AlignmentChainModelVertex.html#af47223eaba279b5018abd209fd9a16e8',1,'vg::AlignmentChainModelVertex::operator=(AlignmentChainModelVertex &&) &=default'],['../classvg_1_1Masker.html#ae04eeec74cbbee249846d138668a2b12',1,'vg::Masker::operator=()'],['../classvg_1_1MaximalExactMatch.html#af5383e1741bfcd3f7a9d41018bc4b7e1',1,'vg::MaximalExactMatch::operator=(const MaximalExactMatch &) &=default'],['../classvg_1_1MaximalExactMatch.html#ab2fbcdac0244023338ff7958a650c8dd',1,'vg::MaximalExactMatch::operator=(MaximalExactMatch &&) &=default'],['../classvg_1_1connection__t.html#a1af38cdb2b71e4ad441e427494c9548f',1,'vg::connection_t::operator=(const connection_t &)=default'],['../classvg_1_1connection__t.html#a9326a4bf2490223f72fbd90ac2805203',1,'vg::connection_t::operator=(connection_t &&)=default'],['../classvg_1_1subpath__t.html#a23ccc424b12615a3121c733470f5329d',1,'vg::subpath_t::operator=(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a3e18ac17337fa05ed3fc58fd69b55589',1,'vg::subpath_t::operator=(subpath_t &&)=default'],['../classvg_1_1multipath__alignment__t.html#aa0528d2e50e3d355b33a4e82f1c4fd3a',1,'vg::multipath_alignment_t::operator=(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ac68c86f5c5ffa82b45aa047f020c8296',1,'vg::multipath_alignment_t::operator=(multipath_alignment_t &&other)'],['../classvg_1_1BaseOption.html#acc23a4aa53f5aadc0524d2b4abc0fe5c',1,'vg::BaseOption::operator=(const BaseOption< Value, Parser > &other)=default'],['../classvg_1_1BaseOption.html#a37b2e13a4c48f8ee49ebc5d034d88ce4',1,'vg::BaseOption::operator=(const Value &other)'],['../classvg_1_1Paths.html#a42b45e7dcb60d7f744566ea2f1e8a6ba',1,'vg::Paths::operator=(const Paths &other)'],['../classvg_1_1Paths.html#a298a38346fff38db91b2a42a56c1b9ea',1,'vg::Paths::operator=(Paths &&other) noexcept'],['../classvg_1_1edit__t.html#ad1c13528b7936c7129ea96a96c6e8671',1,'vg::edit_t::operator=(const edit_t &other)=default'],['../classvg_1_1edit__t.html#a0fc702abc036cbc6448f7129d332082d',1,'vg::edit_t::operator=(edit_t &&other)=default'],['../classvg_1_1path__mapping__t.html#a7e04cd691817a0ba29c45e08caabc1c4',1,'vg::path_mapping_t::operator=(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a572fc6feefb1ca777a6920691d08fb4d',1,'vg::path_mapping_t::operator=(path_mapping_t &&other)=default'],['../classvg_1_1path__t.html#a48b9304e0a7dd08c9593c8cbbcf1954e',1,'vg::path_t::operator=(const path_t &other)=default'],['../classvg_1_1path__t.html#acff4daba9b88bec84475641ebbd07221',1,'vg::path_t::operator=(path_t &&other)=default'],['../classvg_1_1PhasedGenome.html#aa4f75b660fd6b1fe8528a10289621d01',1,'vg::PhasedGenome::operator=(PhasedGenome &&phased_genome)=delete'],['../classvg_1_1PhasedGenome.html#af2bcd75ffe10fee6c1af5456b229c752',1,'vg::PhasedGenome::operator=(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a2802e8904098e873bf6d261dc93bc9ec',1,'vg::PhasedGenome::iterator::operator=()'],['../classvg_1_1position__t.html#a8d39338541d93824d9bc488798e5d0b7',1,'vg::position_t::operator=(const position_t &other)=default'],['../classvg_1_1position__t.html#ae75f741879494ab27fd07a6d3085a8ca',1,'vg::position_t::operator=(position_t &&other)=default'],['../classvg_1_1SmallBitset.html#a2e0933ff70a59061ccb2a20e826364e9',1,'vg::SmallBitset::operator=(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#adb79e0c1d451eb3f54e0051c2c2ede3d',1,'vg::SmallBitset::operator=(SmallBitset &&another)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a8c84bbff732b6fa701659482136d123b',1,'vg::SnarlDistanceIndexClusterer::Seed::operator=()'],['../classvg_1_1SnarlManager.html#a08acef6ec793e011aa7537f9ccb4dcfe',1,'vg::SnarlManager::operator=(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#af6f0f956456ef8ec76616fc47bc74428',1,'vg::SnarlManager::operator=(SnarlManager &&other)=default'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ad230c1701326adfb7d3bbcb57628be43',1,'vg::SnarlManager::SnarlRecord::operator=()'],['../classvg_1_1BitString.html#a0754865910378300b6b17a76df6cfa7b',1,'vg::BitString::operator=(const BitString &other)=default'],['../classvg_1_1BitString.html#ac7bb86ec9ba1b684056abea6da960d73',1,'vg::BitString::operator=(BitString &&other)=default'],['../classvg_1_1StreamIndexBase.html#ab0ac239e55d7748226a6a2d08480e026',1,'vg::StreamIndexBase::operator=()'],['../classvg_1_1count__back__inserter.html#aeb34352656680f80cb53fdec6cd2c554',1,'vg::count_back_inserter::operator=()'],['../structvg_1_1VectorView.html#acd9cb0c00656475140021a97275b66f8',1,'vg::VectorView::operator=(const VectorView &other)=default'],['../structvg_1_1VectorView.html#a4818009b7d0a655c23e8f132c9ba65c5',1,'vg::VectorView::operator=(VectorView &&other)=default'],['../structvg_1_1IncrementIter.html#a985cc14fcad953ece4e532342778929f',1,'vg::IncrementIter::operator=()'],['../classvg_1_1VcfBuffer.html#ae0157d603d27d962a8dbd83d12e0fad6',1,'vg::VcfBuffer::operator=()'],['../classvg_1_1WindowedVcfBuffer.html#ab26fcdb650d9ca250827fa4db733fdd6',1,'vg::WindowedVcfBuffer::operator=()'],['../classvg_1_1VG.html#a46f1fe88897cfe4d62625cffd3db5ebb',1,'vg::VG::operator=(const VG &other)'],['../classvg_1_1VG.html#a3b3efbadb9fd3923bbc7e8f0b73c524f',1,'vg::VG::operator=(VG &&other) noexcept'],['../classvg_1_1Watchdog.html#a05ee3b04abde016d4dad666372a38bbb',1,'vg::Watchdog::operator=(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a46119cc28dee74f545eaa3befa3ff149',1,'vg::Watchdog::operator=(Watchdog &&other)=delete'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a393cad2bfd5329385620d1f8434f1092',1,'vg::ZipCodeTree::iterator::operator=(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a3ad6d9e6a4753a9b15df622ee3ec15ec',1,'vg::ZipCodeTree::iterator::operator=(iterator &&other)=default'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4d35f9d95c053c5941706dd3c02ac8b2',1,'vg::ZipCodeTree::reverse_iterator::operator=(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a6ca3e5d86a90780d082cdb07392096fe',1,'vg::ZipCodeTree::reverse_iterator::operator=(reverse_iterator &&other)'],['../classvg_1_1algorithms_1_1Anchor.html#a8774c392a8da56c5510d47fd418cf696',1,'vg::algorithms::Anchor::operator=(const Anchor &other)=default'],['../classvg_1_1algorithms_1_1Anchor.html#a380a35dbb36f866a533c9b4ee9571850',1,'vg::algorithms::Anchor::operator=(Anchor &&other)=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a6af8d418d16c2e2bdee3389929845669',1,'vg::subcommand::TickChainLink::operator=(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#a367346c43d55fc270b39edf46be3cf29',1,'vg::subcommand::TickChainLink::operator=(TickChainLink &&other)=delete'],['../structvg_1_1Range.html#a4880259b13fcdda9fa55abf2faf6a38c',1,'vg::Range::operator=(const Range &other)'],['../structvg_1_1Range.html#ac25f332d4f29872e1e785317dc35fe00',1,'vg::Range::operator=(Range &&other)'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3d9ea843f0b9e571bd4fe01b27f8c466',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a4c926b0df4f6b70d0b4665aedbd9256c',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &&other)=delete'],['../classxg_1_1XG.html#a5dc0f63bc2e56b29638a7a4fc89bbacb',1,'xg::XG::operator=(const XG &other)=delete'],['../classxg_1_1XG.html#aa06dbf48d0e060ddec20000e4242ed5a',1,'xg::XG::operator=(XG &&other)=delete'],['../classxg_1_1XGPath.html#a2386595dfbd819402d30a76b83b3b65d',1,'xg::XGPath::operator=(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a08310ec2e3e6e968b3d412329a9fc4ad',1,'xg::XGPath::operator=(XGPath &&other)=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a3fd64baf9dcc05eceb2a653b225ed325',1,'handlegraph::PathForEachSocket::iterator::operator=()'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#aaae753008929cd78c3ece15f1e73826d',1,'vg::io::BlockedGzipInputStream::operator=(const BlockedGzipInputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#ab978351afc9df57f66dfcbaf11932c17',1,'vg::io::BlockedGzipInputStream::operator=(BlockedGzipInputStream &&other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a26746003c36d4c51964fe291412c48a0',1,'vg::io::BlockedGzipOutputStream::operator=(const BlockedGzipOutputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae54f16684d6a1f7ea66cf57ab0a481f9',1,'vg::io::BlockedGzipOutputStream::operator=(BlockedGzipOutputStream &&other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a8cc7250b2785917930d88f92d66058cb',1,'vg::io::MessageEmitter::operator=(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a7c0f2a53bd5e382b5543eb5ccf7acb3b',1,'vg::io::MessageEmitter::operator=(MessageEmitter &&other)=default'],['../classvg_1_1io_1_1ProtobufEmitter.html#ad81cc27d627747dc34683bb2e0500ff6',1,'vg::io::ProtobufEmitter::operator=(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#a7d4c3a9c587971479a5b9a2a6c50db74',1,'vg::io::ProtobufEmitter::operator=(ProtobufEmitter &&other)=default'],['../classvg_1_1io_1_1StreamMultiplexer.html#af986451d89174a2947be32aaefba6f94',1,'vg::io::StreamMultiplexer::operator=(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#aa0426a0e605e8375e1716dfb28b6482e',1,'vg::io::StreamMultiplexer::operator=(StreamMultiplexer &&other)=delete']]],
- ['operator_3d_3d_4185',['operator==',['../classvg_1_1ShuffledPairs_1_1iterator.html#a35842cde2d948d93e9919b267410a8da',1,'vg::ShuffledPairs::iterator::operator==()'],['../structvg_1_1GaplessExtension.html#af2acf967c1b81204f8f5cea754ae1ae1',1,'vg::GaplessExtension::operator==()'],['../classvg_1_1MaximalExactMatch.html#a19feb3f51f02208aa5161562991992dc',1,'vg::MaximalExactMatch::operator==()'],['../structvg_1_1read__alignment__index__t.html#a194c254826c92dcbf90f2d08fb805245',1,'vg::read_alignment_index_t::operator==()'],['../structvg_1_1alignment__index__t.html#aca2a478078ae34cef69bd3ba0e404a08',1,'vg::alignment_index_t::operator==()'],['../classvg_1_1NodeSide.html#af011a5aeaffe705507a89ed91032ad3e',1,'vg::NodeSide::operator==()'],['../classvg_1_1NodeTraversal.html#a07c1f0b8bdc0c6b851f158e0a1cbd5b5',1,'vg::NodeTraversal::operator==()'],['../classvg_1_1edit__t.html#a2ea672c3e9e8a4a4c2332d117bf85461',1,'vg::edit_t::operator==()'],['../classvg_1_1path__mapping__t.html#a40d364000efb3da1660dede1c3762d65',1,'vg::path_mapping_t::operator==()'],['../classvg_1_1path__t.html#a1aadea895d6ca0a94f5f038809308ef9',1,'vg::path_t::operator==()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0a2ad098ff6d931f04fee951eb50b80a',1,'vg::PhasedGenome::iterator::operator==()'],['../classvg_1_1position__t.html#ad53946ea84a94a664810e7bd67689f3c',1,'vg::position_t::operator==()'],['../structvg_1_1ChainIterator.html#a87ca4ac16d01af9741d45c5c7f391c2c',1,'vg::ChainIterator::operator==()'],['../classvg_1_1BitString.html#a0e19002b533b25e6258ae9e2b7b6bd4e',1,'vg::BitString::operator==()'],['../structvg_1_1VectorView_1_1const__iterator.html#a10426612008a0eb5a74ed91193ecbb96',1,'vg::VectorView::const_iterator::operator==()'],['../structvg_1_1IncrementIter.html#ae67e82103cdee625555eced2c8f51d69',1,'vg::IncrementIter::operator==()'],['../structvg_1_1varint__vector__t.html#ada0c0ea0373d2eb784f4c8459153701f',1,'vg::varint_vector_t::operator==()'],['../classvg_1_1ZipCode.html#a0b983931fc8219fafc6cde9357b553b0',1,'vg::ZipCode::operator==()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a09179a35995161986e2a2db97f5f59c1',1,'vg::ZipCode::decoder_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a4483a326cb25512a552a1594232d3fdd',1,'vg::ZipCodeTree::oriented_seed_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#a015179ff6e9a5e02cc9dfe4af73ff32e',1,'vg::ZipCodeTree::seed_result_t::operator==()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a431bbe58e47281666f1bbd7d0db511a2',1,'vg::ZipCodeTree::iterator::operator==()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ab8ad33ac681c64fafec59409e1fcdce1',1,'vg::ZipCodeTree::reverse_iterator::operator==()'],['../classvg_1_1algorithms_1_1TracedScore.html#af8d42e525e16257aa99b6965a6d6ad4c',1,'vg::algorithms::TracedScore::operator==()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aaa1690bd6bf9f463589b8c953940741c',1,'handlegraph::PathForEachSocket::iterator::operator==()'],['../classvg_1_1io_1_1MessageIterator.html#a870adfdc044f57202d26d5fb2109b425',1,'vg::io::MessageIterator::operator==()'],['../classvg_1_1io_1_1ProtobufIterator.html#ad57a7afe6c7759074d1c9ffd3c31a4e0',1,'vg::io::ProtobufIterator::operator==()'],['../namespacevg.html#af94d73312bfd787493e87d207398d73a',1,'vg::operator==(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a87b890a4bc73725bbea08984d7510df4',1,'vg::operator==(const Visit &a, const Visit &b)'],['../namespacevg.html#a845213e6efb7204868c05afcae9c926f',1,'vg::operator==(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a387ff1f8cefcf4feb705b0f1225d16c7',1,'vg::operator==(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a6ace94ff076945069d22aa548b6e0bf6',1,'vg::operator==(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ace8e1de0bfe604d8da5537fd86e251ee',1,'vg::operator==(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a8e2505b73c51b9659c94950d2f283eec',1,'vg::operator==(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a92e719e28c0d3f7d6dfa354824220211',1,'vg::operator==(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#aadbc38098e019cace58583b35000d19f',1,'handlegraph::operator==(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a5a7206835ea412fabb928f106b291349',1,'handlegraph::operator==(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a4e83573fadcc147c475d0a7678ffbe98',1,'handlegraph::operator==(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a3b87d2ae8d5a93f67ddacb95a5fd791f',1,'handlegraph::operator==(const net_handle_t &a, const net_handle_t &b)'],['../namespacevg_1_1io.html#a05438ce01e149360e263cb83346a5261',1,'vg::io::operator==()']]],
- ['operator_3e_4186',['operator>',['../classvg_1_1algorithms_1_1TracedScore.html#ad7b72c45ce0349b96aae49d2a1cc8eec',1,'vg::algorithms::TracedScore::operator>()'],['../namespacevg.html#a955d56fb4c95213de77c1fcce44c77b8',1,'vg::operator>()']]],
- ['operator_5b_5d_4187',['operator[]',['../structhaplo_1_1gbwt__thread__t.html#a9dd1cb0268973121f00304ae34c7688d',1,'haplo::gbwt_thread_t::operator[](size_t i)'],['../structhaplo_1_1gbwt__thread__t.html#a0ebbbd89e60564e347b1bc441230786c',1,'haplo::gbwt_thread_t::operator[](size_t i) const'],['../structvg_1_1VectorView.html#aa89f493da3bd725632dd1dfb02479c0d',1,'vg::VectorView::operator[]()'],['../classvg_1_1VectorViewInverse.html#a6943170a05ddc962f61fa7ab4fed926d',1,'vg::VectorViewInverse::operator[]()']]],
- ['operator_7c_3d_4188',['operator|=',['../classvg_1_1SmallBitset.html#a541303f562fa1579b94ceda2eda95927',1,'vg::SmallBitset']]],
- ['opt_5falt_5fpaths_4189',['OPT_ALT_PATHS',['../mpmap__main_8cpp.html#ae91368cb24911fe1546ae429d8715963',1,'mpmap_main.cpp']]],
- ['opt_5falways_5fcheck_5fpopulation_4190',['OPT_ALWAYS_CHECK_POPULATION',['../mpmap__main_8cpp.html#a65c6fa4dc0d10a1eaa52a46cf7492f6f',1,'mpmap_main.cpp']]],
- ['opt_5fapprox_5fexp_4191',['OPT_APPROX_EXP',['../mpmap__main_8cpp.html#a2a31a7f2f254185a590fb21601013459',1,'mpmap_main.cpp']]],
- ['opt_5fband_5fpadding_5fmultiplier_4192',['OPT_BAND_PADDING_MULTIPLIER',['../mpmap__main_8cpp.html#a4e93612c9dd1d066ba7787a13c39d793',1,'mpmap_main.cpp']]],
- ['opt_5fbuild_5fvgi_5findex_4193',['OPT_BUILD_VGI_INDEX',['../index__main_8cpp.html#afb8482664ef525883ed18ceb46cdc029',1,'index_main.cpp']]],
- ['opt_5fcomments_5fas_5ftags_4194',['OPT_COMMENTS_AS_TAGS',['../map__main_8cpp.html#a06a0a0971a1dfb922cac7996800e0bef',1,'map_main.cpp']]],
- ['opt_5fcomponent_5fmin_5fdist_4195',['OPT_COMPONENT_MIN_DIST',['../mpmap__main_8cpp.html#a9536ee962e85c03f847a9618b7f4e380',1,'mpmap_main.cpp']]],
- ['opt_5fdistance_5fnesting_4196',['OPT_DISTANCE_NESTING',['../index__main_8cpp.html#a26828de6380594afa7c08082ff616945',1,'index_main.cpp']]],
- ['opt_5fdistance_5fsnarl_5flimit_4197',['OPT_DISTANCE_SNARL_LIMIT',['../index__main_8cpp.html#a368f75b8652409b081e17a5860e54734',1,'index_main.cpp']]],
- ['opt_5fdrop_5fsubgraph_4198',['OPT_DROP_SUBGRAPH',['../mpmap__main_8cpp.html#a54db45ba649a2cb8a4553756a909a262',1,'mpmap_main.cpp']]],
- ['opt_5fexclude_5funaligned_4199',['OPT_EXCLUDE_UNALIGNED',['../map__main_8cpp.html#a548f717dd20a48c17c3db507a0c3c53d',1,'map_main.cpp']]],
- ['opt_5ffan_5fout_5fdiff_4200',['OPT_FAN_OUT_DIFF',['../mpmap__main_8cpp.html#aa3d6561990f229c8b1fe723f0ab40bb5',1,'mpmap_main.cpp']]],
- ['opt_5ffan_5fout_5fqual_4201',['OPT_FAN_OUT_QUAL',['../mpmap__main_8cpp.html#a63b2b9f4e4cf89c48efc91e7ffff29ea',1,'mpmap_main.cpp']]],
- ['opt_5ffields_4202',['opt_fields',['../structgafkluge_1_1GafRecord.html#a999647c3cab6cb89fdaaae902c867b8b',1,'gafkluge::GafRecord']]],
- ['opt_5ffirst_4203',['OPT_FIRST',['../view__main_8cpp.html#a0a7d3e9f2f4f4183c4f010f692fcf0ff',1,'view_main.cpp']]],
- ['opt_5fforce_5fhaplotype_5fcount_4204',['OPT_FORCE_HAPLOTYPE_COUNT',['../mpmap__main_8cpp.html#a2b98cdcb665cd0cb6dcab27cd9b4b38c',1,'mpmap_main.cpp']]],
- ['opt_5fforce_5fphased_4205',['OPT_FORCE_PHASED',['../autoindex__main_8cpp.html#a97d7f5886eeeb66d54d3280476fe46d4',1,'autoindex_main.cpp']]],
- ['opt_5fforce_5funphased_4206',['OPT_FORCE_UNPHASED',['../autoindex__main_8cpp.html#a5d658d26d8f3dd160cc0ccff5badfed7',1,'autoindex_main.cpp']]],
- ['opt_5fgbwt_5fbuffer_5fsize_4207',['OPT_GBWT_BUFFER_SIZE',['../autoindex__main_8cpp.html#a74dae0f3f3b952725b2b6cfc699e9341',1,'autoindex_main.cpp']]],
- ['opt_5fgcsa_5fsize_5flimit_4208',['OPT_GCSA_SIZE_LIMIT',['../autoindex__main_8cpp.html#acef79b1df54f9953c5c43cfdb9fb5b76',1,'autoindex_main.cpp']]],
- ['opt_5fgreedy_5fmem_5frestart_5fmax_5flcp_4209',['OPT_GREEDY_MEM_RESTART_MAX_LCP',['../mpmap__main_8cpp.html#ac967783d971258300927dbeb273934b6',1,'mpmap_main.cpp']]],
- ['opt_5fgreedy_5fmin_5fdist_4210',['OPT_GREEDY_MIN_DIST',['../mpmap__main_8cpp.html#ab2c8c5abc8f0978ad62ffa9700eb2bda',1,'mpmap_main.cpp']]],
- ['opt_5fhard_5fhit_5fmax_5fmultiplier_4211',['OPT_HARD_HIT_MAX_MULTIPLIER',['../mpmap__main_8cpp.html#a714607df71e90bb572044f3632cc1ac4',1,'mpmap_main.cpp']]],
- ['opt_5fkeep_5fintermediate_4212',['OPT_KEEP_INTERMEDIATE',['../autoindex__main_8cpp.html#a6ca4cd9afa3306994612c96f8b66fb88',1,'autoindex_main.cpp']]],
- ['opt_5fmax_5ffans_5fout_4213',['OPT_MAX_FANS_OUT',['../mpmap__main_8cpp.html#af23caedc131b49443146ebb1aa947728',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5fmotif_5fpairs_4214',['OPT_MAX_MOTIF_PAIRS',['../mpmap__main_8cpp.html#a84de0c3bc2a757d008cb93b63f5273f8',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5fpaths_4215',['OPT_MAX_PATHS',['../mpmap__main_8cpp.html#a22ebe5149ddd91818874b5863ab26af0',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5frescue_5fattempts_4216',['OPT_MAX_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#a01622674e6cd85d2b1d18b9ad353b7d5',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5frescue_5fp_5fvalue_4217',['OPT_MAX_RESCUE_P_VALUE',['../mpmap__main_8cpp.html#a2f3fd1ec93d65c325e4c7a23f910096c',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5ftries_4218',['OPT_MAX_TRIES',['../sim__main_8cpp.html#af8c2875728ccfaef5ba8a34e149c9f77',1,'sim_main.cpp']]],
- ['opt_5fmin_5fdist_5fcluster_4219',['OPT_MIN_DIST_CLUSTER',['../mpmap__main_8cpp.html#a6a4cfbe743edfb7bb7866bf370c1a85b',1,'mpmap_main.cpp']]],
- ['opt_5fmulti_5fposition_4220',['OPT_MULTI_POSITION',['../sim__main_8cpp.html#a003ddf1705dee4f9aa4deac88d1ee9d9',1,'sim_main.cpp']]],
- ['opt_5fno_5fcluster_4221',['OPT_NO_CLUSTER',['../mpmap__main_8cpp.html#a819f2221fe8ecbdde55f41e801ee526f',1,'mpmap_main.cpp']]],
- ['opt_5fno_5fembedded_5fhaplotypes_4222',['OPT_NO_EMBEDDED_HAPLOTYPES',['../chunk__main_8cpp.html#ab8f2d1809705b2b706d09e4f5bc3d12f',1,'chunk_main.cpp']]],
- ['opt_5fno_5fgreedy_5fmem_5frestarts_4223',['OPT_NO_GREEDY_MEM_RESTARTS',['../mpmap__main_8cpp.html#a795fe85937dd7884864a324a2e4e7e9c',1,'mpmap_main.cpp']]],
- ['opt_5fno_5foutput_4224',['OPT_NO_OUTPUT',['../mpmap__main_8cpp.html#ab3e182a23ff8ea38e53c1170d263bb8d',1,'mpmap_main.cpp']]],
- ['opt_5fpath_5frescue_5fgraph_4225',['OPT_PATH_RESCUE_GRAPH',['../mpmap__main_8cpp.html#aadbf32efd6566ba5c71b2be2c0c3e2af',1,'mpmap_main.cpp']]],
- ['opt_5fprune_5fexp_4226',['OPT_PRUNE_EXP',['../mpmap__main_8cpp.html#af3b2453f1e45ffd27c3cb9a08a39153a',1,'mpmap_main.cpp']]],
- ['opt_5frecombination_5fpenalty_4227',['OPT_RECOMBINATION_PENALTY',['../map__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): map_main.cpp'],['../mpmap__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): mpmap_main.cpp']]],
- ['opt_5fref_5fpaths_4228',['OPT_REF_PATHS',['../map__main_8cpp.html#ab0a122861e2617680fcbb125c8a35597',1,'map_main.cpp']]],
- ['opt_5frename_5fvariants_4229',['OPT_RENAME_VARIANTS',['../index__main_8cpp.html#a1a2c640fb0e31c93f6ea09e4209c9a6a',1,'index_main.cpp']]],
- ['opt_5freport_5fallelic_5fmapq_4230',['OPT_REPORT_ALLELIC_MAPQ',['../mpmap__main_8cpp.html#a75ef8adf7c285e0e422196252143479b',1,'mpmap_main.cpp']]],
- ['opt_5freseed_5flength_4231',['OPT_RESEED_LENGTH',['../mpmap__main_8cpp.html#afccac17d1c42a1ecde6864c183600654',1,'mpmap_main.cpp']]],
- ['opt_5fscore_5fmatrix_4232',['OPT_SCORE_MATRIX',['../align__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): align_main.cpp'],['../map__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): map_main.cpp']]],
- ['opt_5fsecondary_5fmax_5fdiff_4233',['OPT_SECONDARY_MAX_DIFF',['../mpmap__main_8cpp.html#a1783eb188d16ca662e0b6302086d350b',1,'mpmap_main.cpp']]],
- ['opt_5fsecondary_5frescue_5fattempts_4234',['OPT_SECONDARY_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#ad104748288226e8b7051688389fdd714',1,'mpmap_main.cpp']]],
- ['opt_5fshort_5fmem_5ffilter_5ffactor_4235',['OPT_SHORT_MEM_FILTER_FACTOR',['../mpmap__main_8cpp.html#a318c97f0fac2cb91d18d7fca8772bf7f',1,'mpmap_main.cpp']]],
- ['opt_5fsnarl_5fmax_5fcut_4236',['OPT_SNARL_MAX_CUT',['../mpmap__main_8cpp.html#a0d81815c562f38902b6acadf68474b9a',1,'mpmap_main.cpp']]],
- ['opt_5fsplice_5fodds_4237',['OPT_SPLICE_ODDS',['../mpmap__main_8cpp.html#ade429c9659d1caaf057d4be159c6c06c',1,'mpmap_main.cpp']]],
- ['opt_5fstrip_5fcount_4238',['OPT_STRIP_COUNT',['../mpmap__main_8cpp.html#ad8233b7b00bc4fa0c87c4af3ed501cfd',1,'mpmap_main.cpp']]],
- ['opt_5fstrip_5flength_4239',['OPT_STRIP_LENGTH',['../mpmap__main_8cpp.html#abe95d7c95e55ac2cc94394e657ce16fd',1,'mpmap_main.cpp']]],
- ['opt_5fstripped_5fmatch_4240',['OPT_STRIPPED_MATCH',['../mpmap__main_8cpp.html#a241677bb449101778f187f6be8cdd2a0',1,'mpmap_main.cpp']]],
- ['opt_5fsuppress_5fmismapping_5fdetection_4241',['OPT_SUPPRESS_MISMAPPING_DETECTION',['../mpmap__main_8cpp.html#a95206e9809c284c88f971c57c56cbb39',1,'mpmap_main.cpp']]],
- ['opt_5fsuppress_5fsuppression_4242',['OPT_SUPPRESS_SUPPRESSION',['../mpmap__main_8cpp.html#a5642b35bcfa16b180f0e4e6dcf0536ad',1,'mpmap_main.cpp']]],
- ['opt_5fsuppress_5ftail_5fanchors_4243',['OPT_SUPPRESS_TAIL_ANCHORS',['../mpmap__main_8cpp.html#a8ac418f2741d5efc457e6ab40a535262',1,'mpmap_main.cpp']]],
- ['opt_5ftop_5ftracebacks_4244',['OPT_TOP_TRACEBACKS',['../mpmap__main_8cpp.html#a497dfa18c690f36ffeb9370dde515b7d',1,'mpmap_main.cpp']]],
- ['opt_5fverbose_4245',['OPT_VERBOSE',['../view__main_8cpp.html#ae33534a21238a3d0a2a892bb0bfd84be',1,'view_main.cpp']]],
- ['optimal_5falignment_4246',['optimal_alignment',['../namespacevg.html#a4e3c0f0d0f60a6a6ef1c301b63e9a21e',1,'vg']]],
- ['optimal_5falignment_5finternal_4247',['optimal_alignment_internal',['../namespacevg.html#a3caee9d564f3a803a6ad69642269c5b6',1,'vg']]],
- ['optimal_5falignment_5fscore_4248',['optimal_alignment_score',['../namespacevg.html#ad3548ef9766130a155ba65420c0e7c0e',1,'vg']]],
- ['optimal_5falignments_4249',['optimal_alignments',['../namespacevg.html#ada4d6b6771c5d7e5b2367b18ca8f76f3',1,'vg']]],
- ['optimal_5falignments_5fwith_5fdisjoint_5fsubpaths_4250',['optimal_alignments_with_disjoint_subpaths',['../namespacevg.html#af711577f7d293ffc1c8002c868081bb1',1,'vg']]],
- ['optimal_5fscore_5fon_5fgenome_4251',['optimal_score_on_genome',['../classvg_1_1PhasedGenome.html#a4f8838611a252e9a574a33af3965ad4c',1,'vg::PhasedGenome']]],
- ['optimize_4252',['optimize',['../classvg_1_1VG.html#a0b4fa1970f08f3e4d0cf2f8c33a967a5',1,'vg::VG::optimize()'],['../classhandlegraph_1_1MutableHandleGraph.html#a195c81fa446b62d94fda8841eaa3bb85',1,'handlegraph::MutableHandleGraph::optimize()']]],
- ['option_4253',['Option',['../classvg_1_1Option.html',1,'vg::Option< Value, Parser >'],['../classvg_1_1Option.html#a636f83c45d4a863e53dcb2f9d1d753aa',1,'vg::Option::Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#aa01cfc188e53cf0fb37a6ccc9b4b0043',1,'vg::Option< vector< Item >, Parser >::Option()'],['../structvg_1_1subcommand_1_1BaseValuation.html#abe97905c1fa0321a619e15146a1ede7f',1,'vg::subcommand::BaseValuation::option()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ab8b3cbd45bd3048d233359cd451347a1',1,'vg::subcommand::BaseArgSpec::option()']]],
- ['option_2ecpp_4254',['option.cpp',['../option_8cpp.html',1,'']]],
- ['option_2ehpp_4255',['option.hpp',['../option_8hpp.html',1,'']]],
- ['option_3c_20vector_3c_20item_20_3e_2c_20parser_20_3e_4256',['Option< vector< Item >, Parser >',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html',1,'vg']]],
- ['option_5fid_4257',['option_id',['../structvg_1_1subcommand_1_1BaseArgSpec.html#aef2794c913cd5f8c07f79a0e88a6eba7',1,'vg::subcommand::BaseArgSpec']]],
- ['option_5foffsets_4258',['option_offsets',['../classvg_1_1Configurable.html#a6c5fb72d68761ab4b157c817259164a5',1,'vg::Configurable']]],
- ['option_5fto_5findex_4259',['option_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a06f1cbc473d47bb7579f75a22dd99811',1,'vg::subcommand::OptionGroup']]],
- ['optionformat_4260',['OptionFormat',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9f',1,'vg::subcommand']]],
- ['optiongroup_4261',['OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html',1,'vg::subcommand::OptionGroup< Receiver >'],['../structvg_1_1subcommand_1_1OptionGroup.html#a1e4abb9a235dcfe1d50809bbb36b40a8',1,'vg::subcommand::OptionGroup::OptionGroup()']]],
- ['optioninterface_4262',['OptionInterface',['../classvg_1_1OptionInterface.html',1,'vg']]],
- ['options_2ecpp_4263',['options.cpp',['../options_8cpp.html',1,'']]],
- ['options_2ehpp_4264',['options.hpp',['../options_8hpp.html',1,'']]],
- ['options_5fby_5fcode_4265',['options_by_code',['../classvg_1_1ConfigurableParser.html#a8bdfad847167513663ef67839a574e92',1,'vg::ConfigurableParser']]],
- ['optionvalueparser_4266',['OptionValueParser',['../classvg_1_1OptionValueParser.html',1,'vg']]],
- ['optionvalueparser_3c_20vector_3c_20item_20_3e_20_3e_4267',['OptionValueParser< vector< Item > >',['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html',1,'vg']]],
- ['order_4268',['Order',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046b',1,'vg::StreamSorter::Order()'],['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894a',1,'ReferenceInterval::order()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#ae776df11d1881a7ac95ca8775b6f53d6',1,'vg::DozeuInterface::OrderedGraph::order()'],['../classvg_1_1StreamSorter.html#a03c4547e213a4be6f8f9164cf599b3c3',1,'vg::StreamSorter::order()']]],
- ['order_5flength_5frepeat_5fhit_5fmax_4269',['order_length_repeat_hit_max',['../classvg_1_1MultipathMapper.html#ae87f55f358023f5c881494ccc4ed884f',1,'vg::MultipathMapper']]],
- ['order_5fof_4270',['order_of',['../classvg_1_1IncrementalSubgraph.html#afe160f21d5b4a7964c1bceef47ca54a4',1,'vg::IncrementalSubgraph']]],
- ['orderedgraph_4271',['OrderedGraph',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html',1,'vg::DozeuInterface::OrderedGraph'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a321fef7bca4632cec8f2ed02f8294ad8',1,'vg::DozeuInterface::OrderedGraph::OrderedGraph()']]],
- ['orientation_5ffrom_5fold_5fedge_5ftype_4272',['orientation_from_old_edge_type',['../classxg_1_1XG.html#a6383f68a1f2f9150a0649c6db1c43891',1,'xg::XG']]],
- ['oriented_5fdistance_4273',['oriented_distance',['../classvg_1_1OrientedDistanceMeasurer.html#af6551e771deca01e6af9054a1ad3d30e',1,'vg::OrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a8ec77086bfe160d85961a509725b529f',1,'vg::PathOrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a8f8081d5bb9b0f5526935e2691f52dc3',1,'vg::SnarlOrientedDistanceMeasurer::oriented_distance()']]],
- ['oriented_5fmotif_4274',['oriented_motif',['../classvg_1_1SpliceStats.html#a0568cd8d7b986fdd703bd4021dbb41a1',1,'vg::SpliceStats']]],
- ['oriented_5fnode_5frange_5ft_4275',['oriented_node_range_t',['../namespacevg.html#acf54b55d1c1d16a3d64f1bae268a58af',1,'vg::oriented_node_range_t()'],['../namespacehandlegraph.html#aa9a6ea7613d52c42947d4faa2a189bba',1,'handlegraph::oriented_node_range_t()']]],
- ['oriented_5fseed_5ft_4276',['oriented_seed_t',['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html',1,'vg::ZipCodeTree']]],
- ['orienteddistanceclusterer_4277',['OrientedDistanceClusterer',['../classvg_1_1OrientedDistanceClusterer.html',1,'vg::OrientedDistanceClusterer'],['../classvg_1_1OrientedDistanceClusterer.html#a0bab84127f018db9467240db290113b4',1,'vg::OrientedDistanceClusterer::OrientedDistanceClusterer()']]],
- ['orienteddistancemeasurer_4278',['OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html',1,'vg']]],
- ['os_4279',['OS',['../classvg_1_1Version.html#a60cb5fa1efa9969bcdfa529484ea4280',1,'vg::Version']]],
- ['other_4280',['other',['../structvg_1_1algorithms_1_1Edge.html#a3a831a365cea8d70a5c9817c9a7243ee',1,'vg::algorithms::Edge::other()'],['../classvg_1_1io_1_1streaminbuf.html#a91cfbc8581e4aa70e52268897747d764',1,'vg::io::streaminbuf::other()']]],
- ['other_5forientation_5ftimeout_4281',['other_orientation_timeout',['../classvg_1_1RepresentativeTraversalFinder.html#a5d5136f771fe4566506ff486fb17df49',1,'vg::RepresentativeTraversalFinder']]],
- ['other_5fsupports_4282',['other_supports',['../structvg_1_1BREAKPOINT.html#a2f08ace3f57cff47b7f703fef1ae9792',1,'vg::BREAKPOINT']]],
- ['out_4283',['out',['../classvg_1_1TSVExplainer.html#a2ee20849b7d26e1ce2915996dd0b9912',1,'vg::TSVExplainer::out()'],['../classvg_1_1ProblemDumpExplainer.html#aae8b802f7d2db844b8a576420d0a37bd',1,'vg::ProblemDumpExplainer::out()']]],
- ['out_5ffile_4284',['out_file',['../classvg_1_1HTSWriter.html#aff12605f14901844666bf6775b7c0971',1,'vg::HTSWriter::out_file()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a7b3a7d580d6a585a4d8205caf452ce63',1,'vg::io::TSVAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a1408267254d15464a52b44317e6c780d',1,'vg::io::VGAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a1cdca9c9f2e7f42feb6160a42e072027',1,'vg::io::GafAlignmentEmitter::out_file()']]],
- ['out_5fmutex_4285',['out_mutex',['../classvg_1_1io_1_1ProtobufEmitter.html#acb50db8c0f33135ae2e246ae26efb9d0',1,'vg::io::ProtobufEmitter']]],
- ['out_5fstream_4286',['out_stream',['../classvg_1_1MCMCCaller.html#a240022048423d2922858aaf9cfae0fc0',1,'vg::MCMCCaller']]],
- ['out_5fto_4287',['out_to',['../classvg_1_1ExtraNodeGraph.html#a0f31e37f1e4398d6f8e057c1c8c92495',1,'vg::ExtraNodeGraph']]],
- ['outfile_4288',['outfile',['../classvg_1_1Viz.html#a78a53d3a62a503ff6c29e93cb9a12a88',1,'vg::Viz']]],
- ['output_4289',['output',['../structvg_1_1io_1_1hFILE__cppstream.html#a1b13eb012084d4b68b0f30a1cddebb41',1,'vg::io::hFILE_cppstream']]],
- ['output_5ffields_4290',['output_fields',['../classvg_1_1ReadFilter.html#ade1a4a40379d72d2811fe0e32bece8f7',1,'vg::ReadFilter']]],
- ['output_5ffilepath_4291',['output_filepath',['../classvg_1_1IndexingPlan.html#a405ede5620e8a7263fbb734f656c9971',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier) const'],['../classvg_1_1IndexingPlan.html#a5ef2f8275a2f997e94d178089107502a',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier, size_t chunk, size_t num_chunks) const']]],
- ['output_5fformat_5ft_4292',['output_format_t',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0b',1,'vg::MultipathAlignmentEmitter']]],
- ['output_5fgraph_5fwith_5fembedded_5fpaths_4293',['output_graph_with_embedded_paths',['../namespacevg.html#ae62ff63e415416fd298c6f59c8f2da47',1,'vg::output_graph_with_embedded_paths(vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source)'],['../namespacevg.html#a134ccba76916d6d94e59581932f1b595',1,'vg::output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json)']]],
- ['output_5fhaplotype_5fcounts_4294',['output_haplotype_counts',['../namespacevg.html#ae2d79bdac899f70214959ef92dbbad2f',1,'vg']]],
- ['output_5fin_5fprogress_4295',['output_in_progress',['../classvg_1_1Funnel.html#ae946f8189275c0f4b77f29433406a24b',1,'vg::Funnel']]],
- ['output_5fis_5fbgzf_4296',['output_is_bgzf',['../classvg_1_1HTSWriter.html#a440cfc6e79f5790976ebac5e648a3696',1,'vg::HTSWriter']]],
- ['output_5fnames_4297',['output_names',['../classVectorizer.html#aadb47085d4b369b1c9ea341b06311341',1,'Vectorizer']]],
- ['output_5fpng_4298',['output_png',['../classvg_1_1Viz.html#a8b50b34356875c1c0aa3917c7c67e445',1,'vg::Viz']]],
- ['output_5fprefix_4299',['output_prefix',['../classvg_1_1IndexRegistry.html#a24555b7ccd83df8e2ccb28b900a6b5b1',1,'vg::IndexRegistry']]],
- ['output_5fsvg_4300',['output_svg',['../classvg_1_1Viz.html#a82a23ca5a5a6ababff6176743247be04',1,'vg::Viz']]],
- ['output_5ftabbed_4301',['output_tabbed',['../classVectorizer.html#a7be5208d3a51438a989dd406fb808fd9',1,'Vectorizer']]],
- ['output_5fvariants_4302',['output_variants',['../classvg_1_1VCFOutputCaller.html#aa9a532dbc58fe6031595ed819d31b02a',1,'vg::VCFOutputCaller']]],
- ['output_5fvcf_4303',['output_vcf',['../classvg_1_1VCFOutputCaller.html#a1556bdec270d47b22e5c91b6956a23c0',1,'vg::VCFOutputCaller']]],
- ['output_5fversion_4304',['OUTPUT_VERSION',['../classvg_1_1StreamIndexBase.html#ad5ce82f31552d36c073e65ced2af529e',1,'vg::StreamIndexBase']]],
- ['output_5fwabbit_5fmap_4305',['output_wabbit_map',['../classVectorizer.html#a788aaec704ce78d29f55459ff2eaedb4',1,'Vectorizer']]],
- ['outputstream_4306',['outputStream',['../namespacevg_1_1io.html#a477841175891d3e770995307eea45f38',1,'vg::io']]],
- ['over_5fdirected_5fedge_4307',['over_directed_edge',['../classvg_1_1Paths.html#a8d1fde70db5d5c4d1e26821d4f03ba7a',1,'vg::Paths']]],
- ['over_5fedge_4308',['over_edge',['../classvg_1_1Paths.html#ae7cd0d9291a31a63aa80e9d4d578575e',1,'vg::Paths']]],
- ['overall_5fsupport_4309',['overall_support',['../structvg_1_1Locus.html#a04ac3427a7318a28984c8114cd216675',1,'vg::Locus']]],
- ['overflow_4310',['overflow',['../classvg_1_1io_1_1fdoutbuf.html#aa0b27dbd39a3ad9452f0d4c0d8ca11a1',1,'vg::io::fdoutbuf']]],
- ['overlap_4311',['overlap',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aa155f6cfbc58baef62da2c775972e636b',1,'ReferenceInterval::overlap()'],['../structvg_1_1Edge.html#aafdc39a954fd8de9dc3850ad9ecb9ade',1,'vg::Edge::overlap()'],['../structvg_1_1BREAKPOINT.html#a8843c2775e6cc15ef2739e13a02b2c86',1,'vg::BREAKPOINT::overlap()'],['../structvg_1_1GaplessExtension.html#ae13cbdb46d6375425a2f82e75daadb66',1,'vg::GaplessExtension::overlap()'],['../namespacevg.html#aaac70d8b120ca61591561cba307dcc1b',1,'vg::overlap()']]],
- ['overlap_5fthreshold_4312',['OVERLAP_THRESHOLD',['../classvg_1_1GaplessExtender.html#a3d436577897604304729afc521928ee8',1,'vg::GaplessExtender']]],
- ['overlay_4313',['overlay',['../classvg_1_1Translator.html#a91965cec764734c35ace2ecb0c643d5c',1,'vg::Translator']]],
- ['overlay_5fnode_5ftranslations_4314',['overlay_node_translations',['../classvg_1_1VG.html#ae9b314bb2021525e60a0ad23e99fb994',1,'vg::VG::overlay_node_translations()'],['../namespacevg.html#a86d5f690fe272c74949e080aca561467',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#a7816225a17a671ff849a79f064770ebb',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#af224cfdc27efec675771ba4cc5143a3f',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, id_t > &under)'],['../namespacevg.html#ae996017b379b1178d5e588b96a7c7f3f',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, id_t > &under)']]],
- ['overload_5fpair_5fhash_4315',['OVERLOAD_PAIR_HASH',['../hash__map_8hpp.html#a181224ba2835ac80e940ef8505d5f119',1,'hash_map.hpp']]],
- ['own_5fsnarl_5fmanager_4316',['own_snarl_manager',['../classvg_1_1Masker.html#aa58433090d15c4a8235aec717dcef987',1,'vg::Masker']]]
+ ['object_5fend_4123',['object_end',['../classvg_1_1ProblemDumpExplainer.html#adb13795992af2eafcbfe0f6716a127f9',1,'vg::ProblemDumpExplainer']]],
+ ['object_5fstart_4124',['object_start',['../classvg_1_1ProblemDumpExplainer.html#a5ebde44f8627a596cdb75267a55f887d',1,'vg::ProblemDumpExplainer']]],
+ ['occs_4125',['occs',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ad0254616466743533fd8b6fd59c70e0c',1,'vg::MinimizerMapper::Minimizer']]],
+ ['of_5fnode_4126',['of_node',['../classvg_1_1Paths.html#abda01c563a3455d491b152a23b22a27a',1,'vg::Paths']]],
+ ['off_5fref_5fpaths_4127',['off_ref_paths',['../classvg_1_1Deconstructor.html#adb3fbf24c904974bf655ef76145dac5a',1,'vg::Deconstructor']]],
+ ['off_5ft_4128',['off_t',['../namespacehandlegraph.html#a0dcae34b861ba40c47d177dc06537bf7',1,'handlegraph']]],
+ ['offset_4129',['offset',['../structvg_1_1GaplessExtension.html#a713e8ef2aad7aa94ae4ef91fbe83e159',1,'vg::GaplessExtension::offset()'],['../structvg_1_1PathBranch.html#ad07bed1fbba0e7c94c218f285c2e51cd',1,'vg::PathBranch::offset()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a5a3aa6577a357cc3067c7a8fbaae1349',1,'vg::Haplotypes::TopLevelChain::offset()'],['../structvg_1_1VectorView_1_1const__iterator.html#a658783ba6132302706230422eae39ce2',1,'vg::VectorView::const_iterator::offset()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a67955816b4446c3b57660e18d9626450',1,'vg::ZipCode::decoder_t::offset()'],['../structvg_1_1Position.html#a1244220d4c8ae90633fd7a7e361d309a',1,'vg::Position::offset()'],['../classvg_1_1position__t.html#a8de3e2b8d4801ca2951d4c21d57bd404',1,'vg::position_t::offset()'],['../namespacevg.html#ad48a54a3ddd5e6ffd8e3e6296fb9c037',1,'vg::offset()'],['../namespacexg.html#ac689f45eccbedaba6fab410913961f8c',1,'xg::offset()']]],
+ ['offset_5ft_4130',['offset_t',['../namespacevg.html#afe223f2c7890c76de5e00b43ceb37add',1,'vg::offset_t()'],['../namespacehandlegraph.html#a5aba28c40bd7f181cac4e8d73d6edef8',1,'handlegraph::offset_t()']]],
+ ['offsets_4131',['offsets',['../classxg_1_1XGPath.html#a062c1a4ce4f13b67a90f8b57ec57e91e',1,'xg::XGPath']]],
+ ['offsets_5fin_5fpaths_4132',['offsets_in_paths',['../classxg_1_1XG.html#af77c93c34b8009c590fa4ee2b01fd64e',1,'xg::XG::offsets_in_paths()'],['../namespacevg_1_1algorithms.html#aef24fa77dadb09d5920ec94b88af2128',1,'vg::algorithms::offsets_in_paths()']]],
+ ['offsets_5frank_4133',['offsets_rank',['../classxg_1_1XGPath.html#aa6f1e3a71e8ceb8242a4b1f5157a789b',1,'xg::XGPath']]],
+ ['offsets_5fselect_4134',['offsets_select',['../classxg_1_1XGPath.html#a22511bf04c45ce0c8620069781e3cdee',1,'xg::XGPath']]],
+ ['ok_4135',['ok',['../structvg_1_1WFAAlignment.html#a64f88d651eb19e3045ab6f9b5552e6c6',1,'vg::WFAAlignment::ok()'],['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae41b7fcb28f19fd52e9b25b6bb0ada27',1,'vg::AlignmentValidity::OK()']]],
+ ['old_5fedge_5ftype_5fend_5fend_4136',['OLD_EDGE_TYPE_END_END',['../classxg_1_1XG.html#a42c04fbecadef083a270c715b250e0cd',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fend_5fstart_4137',['OLD_EDGE_TYPE_END_START',['../classxg_1_1XG.html#a00a6fd4ed46f08eff821566c078b744c',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fmax_4138',['OLD_EDGE_TYPE_MAX',['../classxg_1_1XG.html#a720a6ad7d985ff3f67b3cc1f49328992',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fmin_4139',['OLD_EDGE_TYPE_MIN',['../classxg_1_1XG.html#a5ea5ab4b3c152cff2dd9568c99b14f36',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fstart_5fend_4140',['OLD_EDGE_TYPE_START_END',['../classxg_1_1XG.html#a204c73be3278d6e2edb0302f467acf8f',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fstart_5fstart_4141',['OLD_EDGE_TYPE_START_START',['../classxg_1_1XG.html#a2201290a423753452c4a2943735d0c6e',1,'xg::XG']]],
+ ['old_5fg_5fedge_5flength_4142',['OLD_G_EDGE_LENGTH',['../classxg_1_1XG.html#a2996e32eb2afb8b783956fb997b0a1f9',1,'xg::XG']]],
+ ['old_5fg_5fedge_5foffset_5foffset_4143',['OLD_G_EDGE_OFFSET_OFFSET',['../classxg_1_1XG.html#a44e391542f4cd27cbbbb493319e37d3a',1,'xg::XG']]],
+ ['old_5fg_5fedge_5ftype_5foffset_4144',['OLD_G_EDGE_TYPE_OFFSET',['../classxg_1_1XG.html#a41a462402155eb20a1549048ef12f4da',1,'xg::XG']]],
+ ['old_5fg_5fnode_5ffrom_5fcount_5foffset_4145',['OLD_G_NODE_FROM_COUNT_OFFSET',['../classxg_1_1XG.html#a4885ba0ab6f74adc04b97504d6fd4f38',1,'xg::XG']]],
+ ['old_5fg_5fnode_5fto_5fcount_5foffset_4146',['OLD_G_NODE_TO_COUNT_OFFSET',['../classxg_1_1XG.html#af3b654ed719981eecf06b7b5d9ddd0a8',1,'xg::XG']]],
+ ['old_5fnode_4147',['old_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac101c3ba66f96fa569c1de71bf6c51fe',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['old_5fscore_4148',['old_score',['../structvg_1_1GaplessExtension.html#a868af12d5411848f3b8e0e682d053337',1,'vg::GaplessExtension']]],
+ ['old_5fversion_5fpath_5fname_5fend_4149',['old_version_path_name_end',['../classxg_1_1XG.html#ac0112b557633896a5c03e7e806b76f73',1,'xg::XG']]],
+ ['old_5fversion_5fpath_5fname_5fstart_4150',['old_version_path_name_start',['../classxg_1_1XG.html#aa5ca99b933d49ff2b036650008b68cbd',1,'xg::XG']]],
+ ['on_5fgroup_4151',['on_group',['../classvg_1_1io_1_1MessageEmitter.html#a5b5f11b2f9b08a870fc68a980c91f1e4',1,'vg::io::MessageEmitter::on_group()'],['../classvg_1_1io_1_1ProtobufEmitter.html#af22328bc428af2be817a7a0d097ca370',1,'vg::io::ProtobufEmitter::on_group()']]],
+ ['on_5fmessage_4152',['on_message',['../classvg_1_1io_1_1ProtobufEmitter.html#a6a3a16550dcd7dd7a320109125d4e2a1',1,'vg::io::ProtobufEmitter']]],
+ ['on_5fpath_5fedit_4153',['on_path_edit',['../classvg_1_1FeatureSet.html#a72b47862b3121905222f7662c4ff65ca',1,'vg::FeatureSet']]],
+ ['one_5fend_5fanchored_5ffilter_4154',['one_end_anchored_filter',['../classvg_1_1Filter.html#adf0ea872057dafedc321b256ec072b8c',1,'vg::Filter']]],
+ ['oneof_5flocation_4155',['oneof_location',['../structvg_1_1LocationSupport.html#a9a000a5b773e07f7cc30614d77c927a0',1,'vg::LocationSupport']]],
+ ['only_5fcorrectly_5fmapped_4156',['only_correctly_mapped',['../classvg_1_1ReadFilter.html#ab0f19128ff55e1e2c1cad90adcfc0d6e',1,'vg::ReadFilter']]],
+ ['only_5ffirst_5falignment_4157',['only_first_alignment',['../classvg_1_1ReadFilter.html#a5747bfc6146fa25db9fd96f1f760f6f0',1,'vg::ReadFilter']]],
+ ['only_5fmapped_4158',['only_mapped',['../classvg_1_1ReadFilter.html#ab19be8fc638af431bb1a629aeff77f4f',1,'vg::ReadFilter']]],
+ ['only_5fproper_5fpairs_4159',['only_proper_pairs',['../classvg_1_1ReadFilter.html#ac41003be9ee710a1003288e2a6ba9c7d',1,'vg::ReadFilter']]],
+ ['open_5fall_4160',['open_all',['../classvg_1_1StreamSorter.html#a112c5a39918bb37f4aa3bf1413d31b37',1,'vg::StreamSorter']]],
+ ['open_5fchain_4161',['open_chain',['../classvg_1_1ZipCodeForest.html#a56fb93ecb975f5f6c12deeef5b1f9b20',1,'vg::ZipCodeForest']]],
+ ['open_5fchains_4162',['open_chains',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a43af493f53945324b203009c974ab0d2',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['open_5ffd_4163',['open_fd',['../classhandlegraph_1_1TriviallySerializable.html#aa1f5b9cdb957540dfea7e0e4b478e9b2',1,'handlegraph::TriviallySerializable']]],
+ ['open_5fintervals_4164',['open_intervals',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a75768315ee176ee34dc33da021696810',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['open_5fsnarl_4165',['open_snarl',['../classvg_1_1ZipCodeForest.html#ab219e010a4e80804f7c5f6ada581f18d',1,'vg::ZipCodeForest']]],
+ ['operatingmode_4166',['OperatingMode',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667',1,'HaplotypesConfig']]],
+ ['operator_20bool_4167',['operator bool',['../structvg_1_1AlignmentValidity.html#a2f6b53f193bad40111118e3293ad361c',1,'vg::AlignmentValidity::operator bool()'],['../classvg_1_1Explainer.html#aeca40f040dd309c5f457e8ea0bd8627f',1,'vg::Explainer::operator bool()'],['../structvg_1_1WFAAlignment.html#a7f1464e6b2a86671cdf376137409eeeb',1,'vg::WFAAlignment::operator bool()']]],
+ ['operator_20number_4168',['operator Number',['../structvg_1_1Range.html#acb0f6ebb720df6227410bf9403079a32',1,'vg::Range']]],
+ ['operator_20value_20_26_4169',['operator Value &',['../classvg_1_1BaseOption.html#a760720e496d3058589d34d823f61566b',1,'vg::BaseOption']]],
+ ['operator_21_3d_4170',['operator!=',['../classvg_1_1ShuffledPairs_1_1iterator.html#a2714f2334dae600fc66c3508ecd4494a',1,'vg::ShuffledPairs::iterator::operator!=()'],['../structvg_1_1GaplessExtension.html#a5fc94cd2cfd5898459cac75c65be55a5',1,'vg::GaplessExtension::operator!=()'],['../structvg_1_1read__alignment__index__t.html#ac967a7e4d2339bf2ab83208991b0ce69',1,'vg::read_alignment_index_t::operator!=()'],['../structvg_1_1alignment__index__t.html#ab09e271d0c6eb6f08fd1bde411c6c5f7',1,'vg::alignment_index_t::operator!=()'],['../classvg_1_1NodeSide.html#a48481b0155b782c27644080c98d20656',1,'vg::NodeSide::operator!=()'],['../classvg_1_1NodeTraversal.html#aaa81c382e219ed6f832b1401872fe898',1,'vg::NodeTraversal::operator!=()'],['../classvg_1_1edit__t.html#ac6b81fe1407a1ae901f72ed555a30dae',1,'vg::edit_t::operator!=()'],['../classvg_1_1path__mapping__t.html#a78466c5a9e83d7367bd70799dfd4a76b',1,'vg::path_mapping_t::operator!=()'],['../classvg_1_1path__t.html#a5a0f6368c497cfe5eac4025080c20bc1',1,'vg::path_t::operator!=()'],['../classvg_1_1PhasedGenome_1_1iterator.html#aff3ae0b92ca06496a22d1aad89016737',1,'vg::PhasedGenome::iterator::operator!=()'],['../classvg_1_1position__t.html#a9011acaf2ade42c99a74596214196fa8',1,'vg::position_t::operator!=()'],['../structvg_1_1ChainIterator.html#aec215507b5b43e388afb2933d25c21d0',1,'vg::ChainIterator::operator!=()'],['../classvg_1_1BitString.html#a57b03c3b055ab267c199bd429ff5e4c6',1,'vg::BitString::operator!=()'],['../structvg_1_1VectorView_1_1const__iterator.html#a620b2bd9b99aff0ab077ce6d9441b684',1,'vg::VectorView::const_iterator::operator!=()'],['../structvg_1_1IncrementIter.html#a97c041dbf0473d997321d19072fe85e6',1,'vg::IncrementIter::operator!=()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#aced4d93ad8d1fb3b5b530ff0dd912912',1,'vg::ZipCodeTree::oriented_seed_t::operator!=()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#ac730025c4f3c9144cd742a6c0b15f3d3',1,'vg::ZipCodeTree::seed_result_t::operator!=()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a1eddeaefb5ff95cbde90e0112efa2433',1,'vg::ZipCodeTree::iterator::operator!=()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4925ff71b13d15855904e7e7497b295b',1,'vg::ZipCodeTree::reverse_iterator::operator!=()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4a74c0a77c2df092ecc5d2be1a4b793c',1,'vg::algorithms::TracedScore::operator!=()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a2c24b07521aa704e517c386e1369d227',1,'handlegraph::PathForEachSocket::iterator::operator!=()'],['../classvg_1_1io_1_1MessageIterator.html#ad6a23c45ab954ce158faec0b8935cd90',1,'vg::io::MessageIterator::operator!=()'],['../classvg_1_1io_1_1ProtobufIterator.html#a1f67a6fcda4cfa7d6d1b37bcdb74c0ac',1,'vg::io::ProtobufIterator::operator!=()'],['../namespacevg.html#abb6063b76b70947010198b46c053b578',1,'vg::operator!=(const Visit &a, const Visit &b)'],['../namespacevg.html#a24e1e38ea29c615b2c5f5cd8dbaeeb2a',1,'vg::operator!=(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a654eca8448629e42ae87cadd893ee10e',1,'vg::operator!=(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a22cb5c700c1dee4fec8d3af77057ea2a',1,'vg::operator!=(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#a4f594795be32cb04b7baf0ef71ad77b0',1,'vg::operator!=(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a581944f1e71285f8c4887c2f5ce1467f',1,'vg::operator!=(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a67115fb742d1bf6d7e4e489fda99b78e',1,'vg::operator!=(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#a913cf04aa9946eebf68cc319d7929f11',1,'handlegraph::operator!=(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a18f417ab023834f355f735c2baa18324',1,'handlegraph::operator!=(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#acbbe7b08c190039a0a3700e078818aa5',1,'handlegraph::operator!=(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#acc5274f38cf004b29d2bf398a96f4da5',1,'handlegraph::operator!=(const net_handle_t &a, const net_handle_t &b)']]],
+ ['operator_26_3d_4171',['operator&=',['../classvg_1_1SmallBitset.html#a44c58c409898c13b98b3937669bf7b8f',1,'vg::SmallBitset']]],
+ ['operator_28_29_4172',['operator()',['../structvg_1_1BBEdgeHash.html#af0c713bc536e343b416520dd0f14732b',1,'vg::BBEdgeHash::operator()()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a748c3131cdb69751197546f36a1298bb',1,'vg::MEMClusterer::DPScoreComparator::operator()()'],['../classvg_1_1DistanceHeuristic.html#afb17aa7db222de3ef43a70115c7eec6a',1,'vg::DistanceHeuristic::operator()()'],['../classvg_1_1SnarlMinDistance.html#a4a87d093a5ee90f158ce5e5a1fdc8fd4',1,'vg::SnarlMinDistance::operator()()'],['../classvg_1_1TipAnchoredMaxDistance.html#a165cc0f3d3e70810f72bd7ad49b9416e',1,'vg::TipAnchoredMaxDistance::operator()()'],['../structvg_1_1state__hash.html#a5ddcb7dd42852b3f35fd414663677e8c',1,'vg::state_hash::operator()()'],['../classvg_1_1ReadMasker.html#a8d7a36b958e3405106494e93fffcda5f',1,'vg::ReadMasker::operator()()'],['../structvg_1_1Genotyper_1_1hash__node__traversal.html#a62f374bedac308110f484df59f6c905f',1,'vg::Genotyper::hash_node_traversal::operator()()'],['../structvg_1_1Genotyper_1_1hash__oriented__edge.html#a070a16b42f8aeace08dfee4f22badc8d',1,'vg::Genotyper::hash_oriented_edge::operator()()'],['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html#a44aad1a7e112842dc576fd9cbebdbbfc',1,'vg::Genotyper::hash_ambiguous_allele_set::operator()()'],['../structvg_1_1wang__hash_3_01handle__t_01_4.html#a2abb45aa397420108850ce590f7f3bf7',1,'vg::wang_hash< handle_t >::operator()()'],['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html#a5a9ad96629401a307c94b17a2d91fc53',1,'vg::wang_hash< path_handle_t >::operator()()'],['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html#a847da6dc45718131135dba8e17aa93a6',1,'std::hash< pair< A, B > >::operator()()'],['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html#afdf58525bd44e80be2af8355db0eba2e',1,'std::hash< std::tuple< TT... > >::operator()()'],['../structvg_1_1wang__hash_3_01T_01_5_01_4.html#a55ef00b42c8f6103e78eb7f7b7597984',1,'vg::wang_hash< T * >::operator()()'],['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html#a87443673fa41e2f7a7ee5cf4e2bd533c',1,'vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >::operator()()'],['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html#af62856c68653d586e53d842a16e54cf7',1,'vg::wang_hash< std::pair< A, B > >::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1FCmp.html#a65b7021e0e5237b4b7f0fbb34a8f99ec',1,'vg::IncrementalSubgraph::FCmp::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html#a9a34770a4c767bf069601106bbdde191',1,'vg::IncrementalSubgraph::IterFCmp::operator()()'],['../structvg_1_1wang__hash_3_01NodeSide_01_4.html#a7880d169d8ebf669908ae4262c49c7b8',1,'vg::wang_hash< NodeSide >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html#a7db7a7f185329bda1e74c4fb99e2d7ed',1,'std::hash< vg::NodeSide >::operator()()'],['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html#ae175f5bef4a05d469ebec4341ff47062',1,'vg::wang_hash< NodeTraversal >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html#a0286ba89a52b8479c5bb4f0e474add3e',1,'std::hash< vg::NodeTraversal >::operator()()'],['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html#a14d9633d19737075532f81dc0a97cb0c',1,'vg::wang_hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html#a16e12560069fba289b6e248fb1534347',1,'std::hash< const vg::Snarl >::operator()()'],['../classvg_1_1uniform__real__distribution.html#a2943db49f42d531d7358b64dbbd87d66',1,'vg::uniform_real_distribution::operator()()'],['../classvg_1_1normal__distribution.html#a022c67bb09abf48906156257c76f0ce0',1,'vg::normal_distribution::operator()()'],['../classvg_1_1truncated__normal__distribution.html#a594bdf20c6d6ce7088dde9b1bdb8ae16',1,'vg::truncated_normal_distribution::operator()()'],['../classvg_1_1WideningPRNG.html#a6d58ed2b6a9704e40e751974d5f77927',1,'vg::WideningPRNG::operator()()'],['../classvg_1_1uniform__int__distribution.html#a51f168ff739db2810fc443c8a17a7981',1,'vg::uniform_int_distribution::operator()()'],['../classvg_1_1discrete__distribution.html#a9f9d62f067a25f9a996367d6d187638b',1,'vg::discrete_distribution::operator()()'],['../structvg_1_1MappingHash.html#ab4877c05349b1d70a4fc9fc1d91bfabf',1,'vg::MappingHash::operator()()'],['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html#a5593776feee196b357efe27af34375dd',1,'vg::NestedCachedPackedTraversalSupportFinder::snarl_less::operator()()'],['../classvg_1_1LazyRNG.html#a76642be6e0b23e61b217e22256faccce',1,'vg::LazyRNG::operator()()'],['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html#a43c26f94ae3a429cd5f02e164fbc8893',1,'vg::wang_hash< net_identifier_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html#a267e3d69b89d37dbfc9d6aee50403bfe',1,'std::hash< vg::ZipCodeTree::oriented_seed_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html#a2db521dc14ad90c29f532932a2cb116f',1,'std::hash< vg::ZipCodeTree::seed_result_t >::operator()()'],['../structcompare__gaf.html#abd0df39e112998e5f3cd4e8fc145454c',1,'compare_gaf::operator()()'],['../structgreater__gaffile.html#af92140ef197df65a58d0687a93f4194e',1,'greater_gaffile::operator()()'],['../classvg_1_1subcommand_1_1Subcommand.html#a2a236ec06c3d6d7ff148712a2ae2e492',1,'vg::subcommand::Subcommand::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html#a825db1e0338e86d296b57cd96a8e0899',1,'std::hash< handlegraph::handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html#a6ad769a3d7b2f71b5696eb33bc977d76',1,'std::hash< handlegraph::path_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html#a4dfc6072381e899f6771b7fef4a1df96',1,'std::hash< handlegraph::step_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html#a9530041f163d977cee6147e78e7f3458',1,'std::hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html#ae02ac63af6a68ca8788a3d16e0d282dc',1,'std::hash< handlegraph::edge_t >::operator()()']]],
+ ['operator_2a_4173',['operator*',['../classvg_1_1ShuffledPairs_1_1iterator.html#a7a364e5a3933631209f6356bcbab4195',1,'vg::ShuffledPairs::iterator::operator*()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a6f0c09512af20809ebd66342e0b48e72',1,'vg::PhasedGenome::iterator::operator*()'],['../structvg_1_1ChainIterator.html#a4026eb3698271db72e04c8bf189a7638',1,'vg::ChainIterator::operator*()'],['../classvg_1_1count__back__inserter.html#a23ab94b37972f651d60dc06aea28f567',1,'vg::count_back_inserter::operator*()'],['../structvg_1_1VectorView_1_1const__iterator.html#a6c46dcd71c5b170627061551c7ce0755',1,'vg::VectorView::const_iterator::operator*()'],['../structvg_1_1IncrementIter.html#a5a174a8f85492d7242b52cf1531d50e1',1,'vg::IncrementIter::operator*()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aabf844f9503fb882498e9ad7348644c0',1,'vg::ZipCodeTree::iterator::operator*()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a952c338af40fc2b3c6ab3dda1e36991a',1,'vg::ZipCodeTree::reverse_iterator::operator*()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a9e1c7bf243cdf38e9844e6e253b4f48e',1,'handlegraph::PathForEachSocket::iterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#af9bd6f7d8acd6b65d86ace13aae12a49',1,'vg::io::MessageIterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#a1bde69631cd194d596192908e5a70f0a',1,'vg::io::MessageIterator::operator*() const'],['../classvg_1_1io_1_1ProtobufIterator.html#ab75942ce88acea7c4766895033c51c6f',1,'vg::io::ProtobufIterator::operator*()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6df5500c6398933f60d761188c68895b',1,'vg::io::ProtobufIterator::operator*() const'],['../namespacevg.html#a84dfc966c7511b05c234d215e3b6aec7',1,'vg::operator*(const Support &support, const Scalar &scale)'],['../namespacevg.html#a10844a7c14d7ff54051bad20c75d012e',1,'vg::operator*(const Scalar &scale, const Support &support)']]],
+ ['operator_2a_3d_4174',['operator*=',['../namespacevg.html#abe7831ba6fe294e8be36fa0359a63848',1,'vg']]],
+ ['operator_2b_4175',['operator+',['../structvg_1_1VectorView_1_1const__iterator.html#aa97c1950851a2eb9d5731c12340b81ff',1,'vg::VectorView::const_iterator::operator+()'],['../namespacevg.html#a27dd5c8f7c6d984a396665cbab5eba01',1,'vg::operator+(const Support &one, const Support &other)'],['../namespacevg.html#a64380ba1816d3fd97847a6dc6b2665d8',1,'vg::operator+(typename VectorView< Item >::const_iterator::difference_type a, const typename VectorView< Item >::const_iterator &b)']]],
+ ['operator_2b_2b_4176',['operator++',['../classvg_1_1ShuffledPairs_1_1iterator.html#a1b39b43991061c9b38c0f66be116aa07',1,'vg::ShuffledPairs::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ae7af24b8cfca1872c3b7ecd34cc691b4',1,'vg::PhasedGenome::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a5d6220ad0e3ce9c6fad9c7bd33cd10c2',1,'vg::PhasedGenome::iterator::operator++(int)'],['../structvg_1_1ChainIterator.html#a93335ca3360cd50d0561ad1d4691d017',1,'vg::ChainIterator::operator++()'],['../classvg_1_1count__back__inserter.html#a58b46f86e84878928184f16cd71d2025',1,'vg::count_back_inserter::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab5b2928f08fa931ca8a3da78b9a6e540',1,'vg::VectorView::const_iterator::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#aadee453c16ff3359ea59c37123b1a684',1,'vg::VectorView::const_iterator::operator++(int)'],['../structvg_1_1IncrementIter.html#aa6e20c55ec21957277f5cf07d13ad04d',1,'vg::IncrementIter::operator++()'],['../structvg_1_1IncrementIter.html#a3e40dfadfa140aa600d2bc98ad7a7f90',1,'vg::IncrementIter::operator++(int)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a4fc98efef75fa50606213903af2ec146',1,'vg::ZipCodeTree::iterator::operator++()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa47b19eb964a614f69c6dc2326ed6c83',1,'vg::ZipCodeTree::reverse_iterator::operator++()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#abf9ece90b8080b6f93cbfc516777eac2',1,'handlegraph::PathForEachSocket::iterator::operator++()'],['../classvg_1_1io_1_1MessageIterator.html#a89872d57d9e7d9e49f38b6700e40c99d',1,'vg::io::MessageIterator::operator++()'],['../classvg_1_1io_1_1ProtobufIterator.html#a513fd9e86996eda664b8e5eef5d532e9',1,'vg::io::ProtobufIterator::operator++()']]],
+ ['operator_2b_3d_4177',['operator+=',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a54b9cf8b8a2f6c13c1dfce6e73c203e8',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const double &value)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#aff1c525641da64850545049b20a485fb',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const stat_collection_t &other)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a180b0b1ea0fd2c5a3a2c1a1aa2cbbc94',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t::operator+=()'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af3eb35c3215c0b4cdd6628bcfc896c71',1,'vg::MinimizerMapper::aligner_stats_t::operator+=()'],['../structvg_1_1Counts.html#a0bfb40ac3e3eafe2606af33f8c4fde06',1,'vg::Counts::operator+=()'],['../structvg_1_1VectorView_1_1const__iterator.html#ac0ff4c93cb85429b2436b93a0500ab8c',1,'vg::VectorView::const_iterator::operator+=()'],['../namespacevg.html#a4f550213560bfa3c3ad8446478be24d8',1,'vg::operator+=()']]],
+ ['operator_2d_4178',['operator-',['../structvg_1_1VectorView_1_1const__iterator.html#a5950d800357a74c5df1a46f3fee1e690',1,'vg::VectorView::const_iterator::operator-(const difference_type &difference) const'],['../structvg_1_1VectorView_1_1const__iterator.html#a6ca91702bea775756791a2505fec98a4',1,'vg::VectorView::const_iterator::operator-(const const_iterator &other) const'],['../classvg_1_1algorithms_1_1TracedScore.html#ade52d5662380757204b3a9eb7e632b5f',1,'vg::algorithms::TracedScore::operator-()']]],
+ ['operator_2d_2d_4179',['operator--',['../structvg_1_1VectorView_1_1const__iterator.html#a3f07387c29c6f82c4cb7aa6102e2ff83',1,'vg::VectorView::const_iterator::operator--()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab04cc90a3cb13d7e5a08d51be8cadf0c',1,'vg::VectorView::const_iterator::operator--(int)']]],
+ ['operator_2d_3d_4180',['operator-=',['../structvg_1_1VectorView_1_1const__iterator.html#a5da176cea2552046f8080d5be2dc67f7',1,'vg::VectorView::const_iterator']]],
+ ['operator_2d_3e_4181',['operator->',['../structvg_1_1ChainIterator.html#a2e521810ed86af3b3bfcbd47285236bb',1,'vg::ChainIterator::operator->()'],['../structvg_1_1VectorView_1_1const__iterator.html#a4029e7dd6c859ed5019bb9169211e235',1,'vg::VectorView::const_iterator::operator->()']]],
+ ['operator_2f_4182',['operator/',['../namespacevg.html#a5a9eefddbec41755309a378fb150071c',1,'vg']]],
+ ['operator_2f_3d_4183',['operator/=',['../namespacevg.html#a1807752a0b6b83fd5952d36cc64b758d',1,'vg']]],
+ ['operator_3c_4184',['operator<',['../structvg_1_1MatchPos.html#a91c8cec7a4cf39616157279004751d56',1,'vg::MatchPos::operator<()'],['../structvg_1_1WFAPoint.html#a4c1eb3733361639c504e79502946747a',1,'vg::WFAPoint::operator<()'],['../structvg_1_1GaplessExtension.html#a60ac9a1eba5b7ca5a0bd1f196a8dc94d',1,'vg::GaplessExtension::operator<()'],['../classvg_1_1MaximalExactMatch.html#ace421d32490547fc94b4003484e97dcb',1,'vg::MaximalExactMatch::operator<()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a94ddd290e4408f2a758083d2022b6c46',1,'vg::MinimizerMapper::Minimizer::operator<()'],['../classvg_1_1NodeSide.html#aa567438110aee30bceb1c00a2c6d4eec',1,'vg::NodeSide::operator<()'],['../classvg_1_1NodeTraversal.html#aaf0141ddf2587f8284bd4c111d6cdff2',1,'vg::NodeTraversal::operator<()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4e460a44f0c5027a3864e5b1b65beee8',1,'vg::algorithms::TracedScore::operator<()'],['../structjob__type.html#aed73e63d2b1d652b075a3346c5f36335',1,'job_type::operator<()'],['../namespacevg.html#ab554a977204c1f756bd0e2738a797447',1,'vg::operator<(const Support &a, const Support &b)'],['../namespacevg.html#ac476fcc21a47f34d00b4a449b28c686b',1,'vg::operator<(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a9d2e2066b3b4534b62cde6e4423efd81',1,'vg::operator<(const Visit &a, const Visit &b)'],['../namespacevg.html#aea87c61d2cc1d5acf1af1d2d351bdb75',1,'vg::operator<(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a0fd908e60f72bd98dcba364a16ab7190',1,'vg::operator<(const Snarl &a, const Snarl &b)'],['../namespacevg.html#ad29d63c9b09132ab0457b3d28ea704ff',1,'vg::operator<(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ad3728100975bea667f2f60fdc1df2dd1',1,'vg::operator<(const Transcript &lhs, const Transcript &rhs)'],['../namespacehandlegraph.html#a3e16d241ab6863b8954754d42c9a0764',1,'handlegraph::operator<(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#abe4f45c9fe64c8cf37fe277b870cf56b',1,'handlegraph::operator<(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a8fc5f1eb104107d55fb043c2a24321aa',1,'handlegraph::operator<(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a926cfa5c0852fd9dfe7685d6eec73fe9',1,'handlegraph::operator<(const net_handle_t &a, const net_handle_t &b)']]],
+ ['operator_3c_3c_4185',['operator<<',['../classvg_1_1MaximalExactMatch.html#a415b6e9f064006bb599e11971822669a',1,'vg::MaximalExactMatch::operator<<()'],['../namespacevg.html#a7cc9c4d4d792e1e7f38c2c6009207706',1,'vg::operator<<(ostream &out, const BenchmarkResult &result)'],['../namespacevg.html#a3caa19999a88016c7aedf3fefb8ca69c',1,'vg::operator<<(std::ostream &out, const Funnel::State &state)'],['../namespacevg.html#a1fbb5dfd532a055d9e8251d2dcab3e58',1,'vg::operator<<(std::ostream &out, const WFAAlignment::Edit &edit)'],['../namespacevg.html#a141fbf9c40f389909c5c46132ab6c615',1,'vg::operator<<(ostream &stream, const Support &support)'],['../namespacevg.html#a0e459d4a7dda13edf5b79ea8996cfd82',1,'vg::operator<<(ostream &out, const kmer_t &kmer)'],['../namespacevg.html#af0a4b11db620d43a7e20886d5563e5b8',1,'vg::operator<<(ostream &out, const MaximalExactMatch &mem)'],['../namespacevg.html#a9b4bea48392e7bb9e745b3b04e5bf223',1,'vg::operator<<(ostream &out, const NodeSide &nodeside)'],['../namespacevg.html#ad1bdeb550c6f5fa632ad61454321e001',1,'vg::operator<<(ostream &out, const NodeTraversal &nodetraversal)'],['../namespacevg.html#a81357f8477c9ed2c3839489e0ada1ced',1,'vg::operator<<(ostream &out, mapping_t mapping)'],['../namespacevg.html#a1e7a5fc9017560cc1b505641cc4ef6d0',1,'vg::operator<<(std::ostream &out, PathBranch branch)'],['../namespacevg.html#a35d8d71a9d6d51760cc7354910d029e9',1,'vg::operator<<(ostream &os, const Counts &counts)'],['../namespacevg.html#ab38d6991537581f9ce3f4c549f966a33',1,'vg::operator<<(ostream &out, const Visit &visit)'],['../namespacevg.html#ae0744fdee12e0f4136de643a91c15f77',1,'vg::operator<<(ostream &out, const Snarl &snarl)'],['../namespacevg.html#ac5fc02ee1a5713060cd5f4b33e2eaaab',1,'vg::operator<<(ostream &out, const BitString &bs)'],['../namespacevg.html#a19349c6c73bac7da9651ee91c4272156',1,'vg::operator<<(std::ostream &out, const pos_t &pos)'],['../namespacevg.html#a848f547eaaa9c1ec84809d5ad3bd6871',1,'vg::operator<<(std::ostream &out, const ZipCode &zip)'],['../namespacevg.html#a796e339855648a7b8bdee41619eed23b',1,'vg::operator<<(std::ostream &out, const ZipCode::code_type_t &type)'],['../namespacevg.html#afacdb481e4a38366ce65c39efcb5af49',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::tree_item_type_t &type)'],['../namespacevg.html#a047b1758c707866aceb6c39b2503d5c6',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::reverse_iterator::State &state)'],['../namespacevg_1_1algorithms.html#aafbc78daa41b0c018cd39b7cccbaf53a',1,'vg::algorithms::operator<<(ostream &out, const Anchor &anchor)'],['../namespacevg_1_1algorithms.html#a503ad2215490c5c599530d7331a70120',1,'vg::algorithms::operator<<(ostream &out, const TracedScore &value)'],['../namespacevg_1_1algorithms.html#a3961418e3f3af94c4275118e4693a2fe',1,'vg::algorithms::operator<<(std::ostream &out, const kmer_t &kmer)'],['../namespacevg_1_1algorithms.html#a58ec8c8d09fde1a6e83194ec7126ed4e',1,'vg::algorithms::operator<<(std::ostream &out, const walk_t &walk)'],['../namespacevg_1_1subcommand.html#af9ff4f2d2051fd67f272a581e17dd668',1,'vg::subcommand::operator<<()'],['../namespacexg.html#a72b16c0bf83f5b1d0a1bfd3773d4eb77',1,'xg::operator<<()'],['../namespacegafkluge.html#a226812c098c373a50d825916b4c92a7c',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)'],['../namespacegafkluge.html#a098de1edfb3f22da8638f01e76d9ae2a',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)']]],
+ ['operator_3d_4186',['operator=',['../classvg_1_1MEMChainModelVertex.html#a607061ec174e1ea4ed0829c86e1d23de',1,'vg::MEMChainModelVertex::operator=(const MEMChainModelVertex &) &=default'],['../classvg_1_1MEMChainModelVertex.html#ac83963d8e6a0ae78e048910f7441c83a',1,'vg::MEMChainModelVertex::operator=(MEMChainModelVertex &&) &=default'],['../classvg_1_1XdropAligner.html#a5bb2cfcbd85802990c1386827ac98192',1,'vg::XdropAligner::operator=(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a39627c50a6e60a7f065332fbd99fdcba',1,'vg::XdropAligner::operator=(XdropAligner &&other)'],['../classvg_1_1QualAdjXdropAligner.html#ab68a1dff1baf74e2275c5db0c7ac4d39',1,'vg::QualAdjXdropAligner::operator=(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a55c6307a0d16cb7ac32e25f1c4f19e6f',1,'vg::QualAdjXdropAligner::operator=(QualAdjXdropAligner &&other)'],['../classvg_1_1HTSWriter.html#aaa299cc70e86ed6fe1dd1eefef0a23f5',1,'vg::HTSWriter::operator=(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a2ec4df6ab5d9c7d4b1557e9cb04ef30d',1,'vg::HTSWriter::operator=(HTSWriter &&other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#aadcc0b64b3f9178c7e30bb15cccc4e21',1,'vg::HTSAlignmentEmitter::operator=(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a19eafc506789bd80e235ebc63e2bbe7f',1,'vg::HTSAlignmentEmitter::operator=(HTSAlignmentEmitter &&other)=delete'],['../classvg_1_1IndexRegistry.html#a50fcb23d815a8eb3da616c9284157ada',1,'vg::IndexRegistry::operator=(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#a6d96c08dbecf5d59154715bb5010f1f2',1,'vg::IndexRegistry::operator=(IndexRegistry &&other)'],['../structvg_1_1IndexedVG_1_1CacheEntry.html#a6b657674e880f1c5a8026617818f19ed',1,'vg::IndexedVG::CacheEntry::operator=()'],['../classvg_1_1ParallelKFFReader.html#ae7be7ffcc93e64e55d82f9dd4983fc04',1,'vg::ParallelKFFReader::operator=()'],['../classvg_1_1AlignmentChainModelVertex.html#a6f6558dec94cc641a412c130a024a4a2',1,'vg::AlignmentChainModelVertex::operator=(const AlignmentChainModelVertex &) &=default'],['../classvg_1_1AlignmentChainModelVertex.html#af47223eaba279b5018abd209fd9a16e8',1,'vg::AlignmentChainModelVertex::operator=(AlignmentChainModelVertex &&) &=default'],['../classvg_1_1Masker.html#ae04eeec74cbbee249846d138668a2b12',1,'vg::Masker::operator=()'],['../classvg_1_1MaximalExactMatch.html#af5383e1741bfcd3f7a9d41018bc4b7e1',1,'vg::MaximalExactMatch::operator=(const MaximalExactMatch &) &=default'],['../classvg_1_1MaximalExactMatch.html#ab2fbcdac0244023338ff7958a650c8dd',1,'vg::MaximalExactMatch::operator=(MaximalExactMatch &&) &=default'],['../classvg_1_1connection__t.html#a1af38cdb2b71e4ad441e427494c9548f',1,'vg::connection_t::operator=(const connection_t &)=default'],['../classvg_1_1connection__t.html#a9326a4bf2490223f72fbd90ac2805203',1,'vg::connection_t::operator=(connection_t &&)=default'],['../classvg_1_1subpath__t.html#a23ccc424b12615a3121c733470f5329d',1,'vg::subpath_t::operator=(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a3e18ac17337fa05ed3fc58fd69b55589',1,'vg::subpath_t::operator=(subpath_t &&)=default'],['../classvg_1_1multipath__alignment__t.html#aa0528d2e50e3d355b33a4e82f1c4fd3a',1,'vg::multipath_alignment_t::operator=(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ac68c86f5c5ffa82b45aa047f020c8296',1,'vg::multipath_alignment_t::operator=(multipath_alignment_t &&other)'],['../classvg_1_1BaseOption.html#acc23a4aa53f5aadc0524d2b4abc0fe5c',1,'vg::BaseOption::operator=(const BaseOption< Value, Parser > &other)=default'],['../classvg_1_1BaseOption.html#a37b2e13a4c48f8ee49ebc5d034d88ce4',1,'vg::BaseOption::operator=(const Value &other)'],['../classvg_1_1Paths.html#a42b45e7dcb60d7f744566ea2f1e8a6ba',1,'vg::Paths::operator=(const Paths &other)'],['../classvg_1_1Paths.html#a298a38346fff38db91b2a42a56c1b9ea',1,'vg::Paths::operator=(Paths &&other) noexcept'],['../classvg_1_1edit__t.html#ad1c13528b7936c7129ea96a96c6e8671',1,'vg::edit_t::operator=(const edit_t &other)=default'],['../classvg_1_1edit__t.html#a0fc702abc036cbc6448f7129d332082d',1,'vg::edit_t::operator=(edit_t &&other)=default'],['../classvg_1_1path__mapping__t.html#a7e04cd691817a0ba29c45e08caabc1c4',1,'vg::path_mapping_t::operator=(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a572fc6feefb1ca777a6920691d08fb4d',1,'vg::path_mapping_t::operator=(path_mapping_t &&other)=default'],['../classvg_1_1path__t.html#a48b9304e0a7dd08c9593c8cbbcf1954e',1,'vg::path_t::operator=(const path_t &other)=default'],['../classvg_1_1path__t.html#acff4daba9b88bec84475641ebbd07221',1,'vg::path_t::operator=(path_t &&other)=default'],['../classvg_1_1PhasedGenome.html#aa4f75b660fd6b1fe8528a10289621d01',1,'vg::PhasedGenome::operator=(PhasedGenome &&phased_genome)=delete'],['../classvg_1_1PhasedGenome.html#af2bcd75ffe10fee6c1af5456b229c752',1,'vg::PhasedGenome::operator=(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a2802e8904098e873bf6d261dc93bc9ec',1,'vg::PhasedGenome::iterator::operator=()'],['../classvg_1_1position__t.html#a8d39338541d93824d9bc488798e5d0b7',1,'vg::position_t::operator=(const position_t &other)=default'],['../classvg_1_1position__t.html#ae75f741879494ab27fd07a6d3085a8ca',1,'vg::position_t::operator=(position_t &&other)=default'],['../classvg_1_1SmallBitset.html#a2e0933ff70a59061ccb2a20e826364e9',1,'vg::SmallBitset::operator=(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#adb79e0c1d451eb3f54e0051c2c2ede3d',1,'vg::SmallBitset::operator=(SmallBitset &&another)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a8c84bbff732b6fa701659482136d123b',1,'vg::SnarlDistanceIndexClusterer::Seed::operator=()'],['../classvg_1_1SnarlManager.html#a08acef6ec793e011aa7537f9ccb4dcfe',1,'vg::SnarlManager::operator=(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#af6f0f956456ef8ec76616fc47bc74428',1,'vg::SnarlManager::operator=(SnarlManager &&other)=default'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ad230c1701326adfb7d3bbcb57628be43',1,'vg::SnarlManager::SnarlRecord::operator=()'],['../classvg_1_1BitString.html#a0754865910378300b6b17a76df6cfa7b',1,'vg::BitString::operator=(const BitString &other)=default'],['../classvg_1_1BitString.html#ac7bb86ec9ba1b684056abea6da960d73',1,'vg::BitString::operator=(BitString &&other)=default'],['../classvg_1_1StreamIndexBase.html#ab0ac239e55d7748226a6a2d08480e026',1,'vg::StreamIndexBase::operator=()'],['../classvg_1_1count__back__inserter.html#aeb34352656680f80cb53fdec6cd2c554',1,'vg::count_back_inserter::operator=()'],['../structvg_1_1VectorView.html#acd9cb0c00656475140021a97275b66f8',1,'vg::VectorView::operator=(const VectorView &other)=default'],['../structvg_1_1VectorView.html#a4818009b7d0a655c23e8f132c9ba65c5',1,'vg::VectorView::operator=(VectorView &&other)=default'],['../structvg_1_1IncrementIter.html#a985cc14fcad953ece4e532342778929f',1,'vg::IncrementIter::operator=()'],['../classvg_1_1VcfBuffer.html#ae0157d603d27d962a8dbd83d12e0fad6',1,'vg::VcfBuffer::operator=()'],['../classvg_1_1WindowedVcfBuffer.html#ab26fcdb650d9ca250827fa4db733fdd6',1,'vg::WindowedVcfBuffer::operator=()'],['../classvg_1_1VG.html#a46f1fe88897cfe4d62625cffd3db5ebb',1,'vg::VG::operator=(const VG &other)'],['../classvg_1_1VG.html#a3b3efbadb9fd3923bbc7e8f0b73c524f',1,'vg::VG::operator=(VG &&other) noexcept'],['../classvg_1_1Watchdog.html#a05ee3b04abde016d4dad666372a38bbb',1,'vg::Watchdog::operator=(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a46119cc28dee74f545eaa3befa3ff149',1,'vg::Watchdog::operator=(Watchdog &&other)=delete'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a393cad2bfd5329385620d1f8434f1092',1,'vg::ZipCodeTree::iterator::operator=(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a3ad6d9e6a4753a9b15df622ee3ec15ec',1,'vg::ZipCodeTree::iterator::operator=(iterator &&other)=default'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4d35f9d95c053c5941706dd3c02ac8b2',1,'vg::ZipCodeTree::reverse_iterator::operator=(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a6ca3e5d86a90780d082cdb07392096fe',1,'vg::ZipCodeTree::reverse_iterator::operator=(reverse_iterator &&other)'],['../classvg_1_1algorithms_1_1Anchor.html#a8774c392a8da56c5510d47fd418cf696',1,'vg::algorithms::Anchor::operator=(const Anchor &other)=default'],['../classvg_1_1algorithms_1_1Anchor.html#a380a35dbb36f866a533c9b4ee9571850',1,'vg::algorithms::Anchor::operator=(Anchor &&other)=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a6af8d418d16c2e2bdee3389929845669',1,'vg::subcommand::TickChainLink::operator=(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#a367346c43d55fc270b39edf46be3cf29',1,'vg::subcommand::TickChainLink::operator=(TickChainLink &&other)=delete'],['../structvg_1_1Range.html#a4880259b13fcdda9fa55abf2faf6a38c',1,'vg::Range::operator=(const Range &other)'],['../structvg_1_1Range.html#ac25f332d4f29872e1e785317dc35fe00',1,'vg::Range::operator=(Range &&other)'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3d9ea843f0b9e571bd4fe01b27f8c466',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a4c926b0df4f6b70d0b4665aedbd9256c',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &&other)=delete'],['../classxg_1_1XG.html#a5dc0f63bc2e56b29638a7a4fc89bbacb',1,'xg::XG::operator=(const XG &other)=delete'],['../classxg_1_1XG.html#aa06dbf48d0e060ddec20000e4242ed5a',1,'xg::XG::operator=(XG &&other)=delete'],['../classxg_1_1XGPath.html#a2386595dfbd819402d30a76b83b3b65d',1,'xg::XGPath::operator=(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a08310ec2e3e6e968b3d412329a9fc4ad',1,'xg::XGPath::operator=(XGPath &&other)=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a3fd64baf9dcc05eceb2a653b225ed325',1,'handlegraph::PathForEachSocket::iterator::operator=()'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#aaae753008929cd78c3ece15f1e73826d',1,'vg::io::BlockedGzipInputStream::operator=(const BlockedGzipInputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#ab978351afc9df57f66dfcbaf11932c17',1,'vg::io::BlockedGzipInputStream::operator=(BlockedGzipInputStream &&other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a26746003c36d4c51964fe291412c48a0',1,'vg::io::BlockedGzipOutputStream::operator=(const BlockedGzipOutputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae54f16684d6a1f7ea66cf57ab0a481f9',1,'vg::io::BlockedGzipOutputStream::operator=(BlockedGzipOutputStream &&other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a8cc7250b2785917930d88f92d66058cb',1,'vg::io::MessageEmitter::operator=(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a7c0f2a53bd5e382b5543eb5ccf7acb3b',1,'vg::io::MessageEmitter::operator=(MessageEmitter &&other)=default'],['../classvg_1_1io_1_1ProtobufEmitter.html#ad81cc27d627747dc34683bb2e0500ff6',1,'vg::io::ProtobufEmitter::operator=(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#a7d4c3a9c587971479a5b9a2a6c50db74',1,'vg::io::ProtobufEmitter::operator=(ProtobufEmitter &&other)=default'],['../classvg_1_1io_1_1StreamMultiplexer.html#af986451d89174a2947be32aaefba6f94',1,'vg::io::StreamMultiplexer::operator=(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#aa0426a0e605e8375e1716dfb28b6482e',1,'vg::io::StreamMultiplexer::operator=(StreamMultiplexer &&other)=delete']]],
+ ['operator_3d_3d_4187',['operator==',['../classvg_1_1ShuffledPairs_1_1iterator.html#a35842cde2d948d93e9919b267410a8da',1,'vg::ShuffledPairs::iterator::operator==()'],['../structvg_1_1GaplessExtension.html#af2acf967c1b81204f8f5cea754ae1ae1',1,'vg::GaplessExtension::operator==()'],['../classvg_1_1MaximalExactMatch.html#a19feb3f51f02208aa5161562991992dc',1,'vg::MaximalExactMatch::operator==()'],['../structvg_1_1read__alignment__index__t.html#a194c254826c92dcbf90f2d08fb805245',1,'vg::read_alignment_index_t::operator==()'],['../structvg_1_1alignment__index__t.html#aca2a478078ae34cef69bd3ba0e404a08',1,'vg::alignment_index_t::operator==()'],['../classvg_1_1NodeSide.html#af011a5aeaffe705507a89ed91032ad3e',1,'vg::NodeSide::operator==()'],['../classvg_1_1NodeTraversal.html#a07c1f0b8bdc0c6b851f158e0a1cbd5b5',1,'vg::NodeTraversal::operator==()'],['../classvg_1_1edit__t.html#a2ea672c3e9e8a4a4c2332d117bf85461',1,'vg::edit_t::operator==()'],['../classvg_1_1path__mapping__t.html#a40d364000efb3da1660dede1c3762d65',1,'vg::path_mapping_t::operator==()'],['../classvg_1_1path__t.html#a1aadea895d6ca0a94f5f038809308ef9',1,'vg::path_t::operator==()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0a2ad098ff6d931f04fee951eb50b80a',1,'vg::PhasedGenome::iterator::operator==()'],['../classvg_1_1position__t.html#ad53946ea84a94a664810e7bd67689f3c',1,'vg::position_t::operator==()'],['../structvg_1_1ChainIterator.html#a87ca4ac16d01af9741d45c5c7f391c2c',1,'vg::ChainIterator::operator==()'],['../classvg_1_1BitString.html#a0e19002b533b25e6258ae9e2b7b6bd4e',1,'vg::BitString::operator==()'],['../structvg_1_1VectorView_1_1const__iterator.html#a10426612008a0eb5a74ed91193ecbb96',1,'vg::VectorView::const_iterator::operator==()'],['../structvg_1_1IncrementIter.html#ae67e82103cdee625555eced2c8f51d69',1,'vg::IncrementIter::operator==()'],['../structvg_1_1varint__vector__t.html#ada0c0ea0373d2eb784f4c8459153701f',1,'vg::varint_vector_t::operator==()'],['../classvg_1_1ZipCode.html#a0b983931fc8219fafc6cde9357b553b0',1,'vg::ZipCode::operator==()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a09179a35995161986e2a2db97f5f59c1',1,'vg::ZipCode::decoder_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a4483a326cb25512a552a1594232d3fdd',1,'vg::ZipCodeTree::oriented_seed_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#a015179ff6e9a5e02cc9dfe4af73ff32e',1,'vg::ZipCodeTree::seed_result_t::operator==()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a431bbe58e47281666f1bbd7d0db511a2',1,'vg::ZipCodeTree::iterator::operator==()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ab8ad33ac681c64fafec59409e1fcdce1',1,'vg::ZipCodeTree::reverse_iterator::operator==()'],['../classvg_1_1algorithms_1_1TracedScore.html#af8d42e525e16257aa99b6965a6d6ad4c',1,'vg::algorithms::TracedScore::operator==()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aaa1690bd6bf9f463589b8c953940741c',1,'handlegraph::PathForEachSocket::iterator::operator==()'],['../classvg_1_1io_1_1MessageIterator.html#a870adfdc044f57202d26d5fb2109b425',1,'vg::io::MessageIterator::operator==()'],['../classvg_1_1io_1_1ProtobufIterator.html#ad57a7afe6c7759074d1c9ffd3c31a4e0',1,'vg::io::ProtobufIterator::operator==()'],['../namespacevg.html#af94d73312bfd787493e87d207398d73a',1,'vg::operator==(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a87b890a4bc73725bbea08984d7510df4',1,'vg::operator==(const Visit &a, const Visit &b)'],['../namespacevg.html#a845213e6efb7204868c05afcae9c926f',1,'vg::operator==(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a387ff1f8cefcf4feb705b0f1225d16c7',1,'vg::operator==(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a6ace94ff076945069d22aa548b6e0bf6',1,'vg::operator==(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ace8e1de0bfe604d8da5537fd86e251ee',1,'vg::operator==(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a8e2505b73c51b9659c94950d2f283eec',1,'vg::operator==(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a92e719e28c0d3f7d6dfa354824220211',1,'vg::operator==(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#aadbc38098e019cace58583b35000d19f',1,'handlegraph::operator==(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a5a7206835ea412fabb928f106b291349',1,'handlegraph::operator==(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a4e83573fadcc147c475d0a7678ffbe98',1,'handlegraph::operator==(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a3b87d2ae8d5a93f67ddacb95a5fd791f',1,'handlegraph::operator==(const net_handle_t &a, const net_handle_t &b)'],['../namespacevg_1_1io.html#a05438ce01e149360e263cb83346a5261',1,'vg::io::operator==()']]],
+ ['operator_3e_4188',['operator>',['../classvg_1_1algorithms_1_1TracedScore.html#ad7b72c45ce0349b96aae49d2a1cc8eec',1,'vg::algorithms::TracedScore::operator>()'],['../namespacevg.html#a955d56fb4c95213de77c1fcce44c77b8',1,'vg::operator>()']]],
+ ['operator_5b_5d_4189',['operator[]',['../structhaplo_1_1gbwt__thread__t.html#a9dd1cb0268973121f00304ae34c7688d',1,'haplo::gbwt_thread_t::operator[](size_t i)'],['../structhaplo_1_1gbwt__thread__t.html#a0ebbbd89e60564e347b1bc441230786c',1,'haplo::gbwt_thread_t::operator[](size_t i) const'],['../structvg_1_1VectorView.html#aa89f493da3bd725632dd1dfb02479c0d',1,'vg::VectorView::operator[]()'],['../classvg_1_1VectorViewInverse.html#a6943170a05ddc962f61fa7ab4fed926d',1,'vg::VectorViewInverse::operator[]()']]],
+ ['operator_7c_3d_4190',['operator|=',['../classvg_1_1SmallBitset.html#a541303f562fa1579b94ceda2eda95927',1,'vg::SmallBitset']]],
+ ['opt_5falt_5fpaths_4191',['OPT_ALT_PATHS',['../mpmap__main_8cpp.html#ae91368cb24911fe1546ae429d8715963',1,'mpmap_main.cpp']]],
+ ['opt_5falways_5fcheck_5fpopulation_4192',['OPT_ALWAYS_CHECK_POPULATION',['../mpmap__main_8cpp.html#a65c6fa4dc0d10a1eaa52a46cf7492f6f',1,'mpmap_main.cpp']]],
+ ['opt_5fapprox_5fexp_4193',['OPT_APPROX_EXP',['../mpmap__main_8cpp.html#a2a31a7f2f254185a590fb21601013459',1,'mpmap_main.cpp']]],
+ ['opt_5fband_5fpadding_5fmultiplier_4194',['OPT_BAND_PADDING_MULTIPLIER',['../mpmap__main_8cpp.html#a4e93612c9dd1d066ba7787a13c39d793',1,'mpmap_main.cpp']]],
+ ['opt_5fbuild_5fvgi_5findex_4195',['OPT_BUILD_VGI_INDEX',['../index__main_8cpp.html#afb8482664ef525883ed18ceb46cdc029',1,'index_main.cpp']]],
+ ['opt_5fcomments_5fas_5ftags_4196',['OPT_COMMENTS_AS_TAGS',['../map__main_8cpp.html#a06a0a0971a1dfb922cac7996800e0bef',1,'map_main.cpp']]],
+ ['opt_5fcomponent_5fmin_5fdist_4197',['OPT_COMPONENT_MIN_DIST',['../mpmap__main_8cpp.html#a9536ee962e85c03f847a9618b7f4e380',1,'mpmap_main.cpp']]],
+ ['opt_5fdistance_5fnesting_4198',['OPT_DISTANCE_NESTING',['../index__main_8cpp.html#a26828de6380594afa7c08082ff616945',1,'index_main.cpp']]],
+ ['opt_5fdistance_5fsnarl_5flimit_4199',['OPT_DISTANCE_SNARL_LIMIT',['../index__main_8cpp.html#a368f75b8652409b081e17a5860e54734',1,'index_main.cpp']]],
+ ['opt_5fdrop_5fsubgraph_4200',['OPT_DROP_SUBGRAPH',['../mpmap__main_8cpp.html#a54db45ba649a2cb8a4553756a909a262',1,'mpmap_main.cpp']]],
+ ['opt_5fexclude_5funaligned_4201',['OPT_EXCLUDE_UNALIGNED',['../map__main_8cpp.html#a548f717dd20a48c17c3db507a0c3c53d',1,'map_main.cpp']]],
+ ['opt_5ffan_5fout_5fdiff_4202',['OPT_FAN_OUT_DIFF',['../mpmap__main_8cpp.html#aa3d6561990f229c8b1fe723f0ab40bb5',1,'mpmap_main.cpp']]],
+ ['opt_5ffan_5fout_5fqual_4203',['OPT_FAN_OUT_QUAL',['../mpmap__main_8cpp.html#a63b2b9f4e4cf89c48efc91e7ffff29ea',1,'mpmap_main.cpp']]],
+ ['opt_5ffields_4204',['opt_fields',['../structgafkluge_1_1GafRecord.html#a999647c3cab6cb89fdaaae902c867b8b',1,'gafkluge::GafRecord']]],
+ ['opt_5ffirst_4205',['OPT_FIRST',['../view__main_8cpp.html#a0a7d3e9f2f4f4183c4f010f692fcf0ff',1,'view_main.cpp']]],
+ ['opt_5fforce_5fhaplotype_5fcount_4206',['OPT_FORCE_HAPLOTYPE_COUNT',['../mpmap__main_8cpp.html#a2b98cdcb665cd0cb6dcab27cd9b4b38c',1,'mpmap_main.cpp']]],
+ ['opt_5fforce_5fphased_4207',['OPT_FORCE_PHASED',['../autoindex__main_8cpp.html#a97d7f5886eeeb66d54d3280476fe46d4',1,'autoindex_main.cpp']]],
+ ['opt_5fforce_5funphased_4208',['OPT_FORCE_UNPHASED',['../autoindex__main_8cpp.html#a5d658d26d8f3dd160cc0ccff5badfed7',1,'autoindex_main.cpp']]],
+ ['opt_5fgbwt_5fbuffer_5fsize_4209',['OPT_GBWT_BUFFER_SIZE',['../autoindex__main_8cpp.html#a74dae0f3f3b952725b2b6cfc699e9341',1,'autoindex_main.cpp']]],
+ ['opt_5fgcsa_5fsize_5flimit_4210',['OPT_GCSA_SIZE_LIMIT',['../autoindex__main_8cpp.html#acef79b1df54f9953c5c43cfdb9fb5b76',1,'autoindex_main.cpp']]],
+ ['opt_5fgreedy_5fmem_5frestart_5fmax_5flcp_4211',['OPT_GREEDY_MEM_RESTART_MAX_LCP',['../mpmap__main_8cpp.html#ac967783d971258300927dbeb273934b6',1,'mpmap_main.cpp']]],
+ ['opt_5fgreedy_5fmin_5fdist_4212',['OPT_GREEDY_MIN_DIST',['../mpmap__main_8cpp.html#ab2c8c5abc8f0978ad62ffa9700eb2bda',1,'mpmap_main.cpp']]],
+ ['opt_5fhard_5fhit_5fmax_5fmultiplier_4213',['OPT_HARD_HIT_MAX_MULTIPLIER',['../mpmap__main_8cpp.html#a714607df71e90bb572044f3632cc1ac4',1,'mpmap_main.cpp']]],
+ ['opt_5fkeep_5fintermediate_4214',['OPT_KEEP_INTERMEDIATE',['../autoindex__main_8cpp.html#a6ca4cd9afa3306994612c96f8b66fb88',1,'autoindex_main.cpp']]],
+ ['opt_5fmax_5ffans_5fout_4215',['OPT_MAX_FANS_OUT',['../mpmap__main_8cpp.html#af23caedc131b49443146ebb1aa947728',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5fmotif_5fpairs_4216',['OPT_MAX_MOTIF_PAIRS',['../mpmap__main_8cpp.html#a84de0c3bc2a757d008cb93b63f5273f8',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5fpaths_4217',['OPT_MAX_PATHS',['../mpmap__main_8cpp.html#a22ebe5149ddd91818874b5863ab26af0',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5frescue_5fattempts_4218',['OPT_MAX_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#a01622674e6cd85d2b1d18b9ad353b7d5',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5frescue_5fp_5fvalue_4219',['OPT_MAX_RESCUE_P_VALUE',['../mpmap__main_8cpp.html#a2f3fd1ec93d65c325e4c7a23f910096c',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5ftries_4220',['OPT_MAX_TRIES',['../sim__main_8cpp.html#af8c2875728ccfaef5ba8a34e149c9f77',1,'sim_main.cpp']]],
+ ['opt_5fmin_5fdist_5fcluster_4221',['OPT_MIN_DIST_CLUSTER',['../mpmap__main_8cpp.html#a6a4cfbe743edfb7bb7866bf370c1a85b',1,'mpmap_main.cpp']]],
+ ['opt_5fmulti_5fposition_4222',['OPT_MULTI_POSITION',['../sim__main_8cpp.html#a003ddf1705dee4f9aa4deac88d1ee9d9',1,'sim_main.cpp']]],
+ ['opt_5fno_5fcluster_4223',['OPT_NO_CLUSTER',['../mpmap__main_8cpp.html#a819f2221fe8ecbdde55f41e801ee526f',1,'mpmap_main.cpp']]],
+ ['opt_5fno_5fembedded_5fhaplotypes_4224',['OPT_NO_EMBEDDED_HAPLOTYPES',['../chunk__main_8cpp.html#ab8f2d1809705b2b706d09e4f5bc3d12f',1,'chunk_main.cpp']]],
+ ['opt_5fno_5fgreedy_5fmem_5frestarts_4225',['OPT_NO_GREEDY_MEM_RESTARTS',['../mpmap__main_8cpp.html#a795fe85937dd7884864a324a2e4e7e9c',1,'mpmap_main.cpp']]],
+ ['opt_5fno_5foutput_4226',['OPT_NO_OUTPUT',['../mpmap__main_8cpp.html#ab3e182a23ff8ea38e53c1170d263bb8d',1,'mpmap_main.cpp']]],
+ ['opt_5fpath_5frescue_5fgraph_4227',['OPT_PATH_RESCUE_GRAPH',['../mpmap__main_8cpp.html#aadbf32efd6566ba5c71b2be2c0c3e2af',1,'mpmap_main.cpp']]],
+ ['opt_5fprune_5fexp_4228',['OPT_PRUNE_EXP',['../mpmap__main_8cpp.html#af3b2453f1e45ffd27c3cb9a08a39153a',1,'mpmap_main.cpp']]],
+ ['opt_5frecombination_5fpenalty_4229',['OPT_RECOMBINATION_PENALTY',['../map__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): map_main.cpp'],['../mpmap__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): mpmap_main.cpp']]],
+ ['opt_5fref_5fpaths_4230',['OPT_REF_PATHS',['../map__main_8cpp.html#ab0a122861e2617680fcbb125c8a35597',1,'map_main.cpp']]],
+ ['opt_5frename_5fvariants_4231',['OPT_RENAME_VARIANTS',['../index__main_8cpp.html#a1a2c640fb0e31c93f6ea09e4209c9a6a',1,'index_main.cpp']]],
+ ['opt_5freport_5fallelic_5fmapq_4232',['OPT_REPORT_ALLELIC_MAPQ',['../mpmap__main_8cpp.html#a75ef8adf7c285e0e422196252143479b',1,'mpmap_main.cpp']]],
+ ['opt_5freseed_5flength_4233',['OPT_RESEED_LENGTH',['../mpmap__main_8cpp.html#afccac17d1c42a1ecde6864c183600654',1,'mpmap_main.cpp']]],
+ ['opt_5fscore_5fmatrix_4234',['OPT_SCORE_MATRIX',['../align__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): align_main.cpp'],['../map__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): map_main.cpp']]],
+ ['opt_5fsecondary_5fmax_5fdiff_4235',['OPT_SECONDARY_MAX_DIFF',['../mpmap__main_8cpp.html#a1783eb188d16ca662e0b6302086d350b',1,'mpmap_main.cpp']]],
+ ['opt_5fsecondary_5frescue_5fattempts_4236',['OPT_SECONDARY_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#ad104748288226e8b7051688389fdd714',1,'mpmap_main.cpp']]],
+ ['opt_5fshort_5fmem_5ffilter_5ffactor_4237',['OPT_SHORT_MEM_FILTER_FACTOR',['../mpmap__main_8cpp.html#a318c97f0fac2cb91d18d7fca8772bf7f',1,'mpmap_main.cpp']]],
+ ['opt_5fsnarl_5fmax_5fcut_4238',['OPT_SNARL_MAX_CUT',['../mpmap__main_8cpp.html#a0d81815c562f38902b6acadf68474b9a',1,'mpmap_main.cpp']]],
+ ['opt_5fsplice_5fodds_4239',['OPT_SPLICE_ODDS',['../mpmap__main_8cpp.html#ade429c9659d1caaf057d4be159c6c06c',1,'mpmap_main.cpp']]],
+ ['opt_5fstrip_5fcount_4240',['OPT_STRIP_COUNT',['../mpmap__main_8cpp.html#ad8233b7b00bc4fa0c87c4af3ed501cfd',1,'mpmap_main.cpp']]],
+ ['opt_5fstrip_5flength_4241',['OPT_STRIP_LENGTH',['../mpmap__main_8cpp.html#abe95d7c95e55ac2cc94394e657ce16fd',1,'mpmap_main.cpp']]],
+ ['opt_5fstripped_5fmatch_4242',['OPT_STRIPPED_MATCH',['../mpmap__main_8cpp.html#a241677bb449101778f187f6be8cdd2a0',1,'mpmap_main.cpp']]],
+ ['opt_5fsuppress_5fmismapping_5fdetection_4243',['OPT_SUPPRESS_MISMAPPING_DETECTION',['../mpmap__main_8cpp.html#a95206e9809c284c88f971c57c56cbb39',1,'mpmap_main.cpp']]],
+ ['opt_5fsuppress_5fsuppression_4244',['OPT_SUPPRESS_SUPPRESSION',['../mpmap__main_8cpp.html#a5642b35bcfa16b180f0e4e6dcf0536ad',1,'mpmap_main.cpp']]],
+ ['opt_5fsuppress_5ftail_5fanchors_4245',['OPT_SUPPRESS_TAIL_ANCHORS',['../mpmap__main_8cpp.html#a8ac418f2741d5efc457e6ab40a535262',1,'mpmap_main.cpp']]],
+ ['opt_5ftop_5ftracebacks_4246',['OPT_TOP_TRACEBACKS',['../mpmap__main_8cpp.html#a497dfa18c690f36ffeb9370dde515b7d',1,'mpmap_main.cpp']]],
+ ['opt_5fverbose_4247',['OPT_VERBOSE',['../view__main_8cpp.html#ae33534a21238a3d0a2a892bb0bfd84be',1,'view_main.cpp']]],
+ ['optimal_5falignment_4248',['optimal_alignment',['../namespacevg.html#a4e3c0f0d0f60a6a6ef1c301b63e9a21e',1,'vg']]],
+ ['optimal_5falignment_5finternal_4249',['optimal_alignment_internal',['../namespacevg.html#a3caee9d564f3a803a6ad69642269c5b6',1,'vg']]],
+ ['optimal_5falignment_5fscore_4250',['optimal_alignment_score',['../namespacevg.html#ad3548ef9766130a155ba65420c0e7c0e',1,'vg']]],
+ ['optimal_5falignments_4251',['optimal_alignments',['../namespacevg.html#ada4d6b6771c5d7e5b2367b18ca8f76f3',1,'vg']]],
+ ['optimal_5falignments_5fwith_5fdisjoint_5fsubpaths_4252',['optimal_alignments_with_disjoint_subpaths',['../namespacevg.html#af711577f7d293ffc1c8002c868081bb1',1,'vg']]],
+ ['optimal_5fscore_5fon_5fgenome_4253',['optimal_score_on_genome',['../classvg_1_1PhasedGenome.html#a4f8838611a252e9a574a33af3965ad4c',1,'vg::PhasedGenome']]],
+ ['optimize_4254',['optimize',['../classvg_1_1VG.html#a0b4fa1970f08f3e4d0cf2f8c33a967a5',1,'vg::VG::optimize()'],['../classhandlegraph_1_1MutableHandleGraph.html#a195c81fa446b62d94fda8841eaa3bb85',1,'handlegraph::MutableHandleGraph::optimize()']]],
+ ['option_4255',['Option',['../classvg_1_1Option.html',1,'vg::Option< Value, Parser >'],['../classvg_1_1Option.html#a636f83c45d4a863e53dcb2f9d1d753aa',1,'vg::Option::Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#aa01cfc188e53cf0fb37a6ccc9b4b0043',1,'vg::Option< vector< Item >, Parser >::Option()'],['../structvg_1_1subcommand_1_1BaseValuation.html#abe97905c1fa0321a619e15146a1ede7f',1,'vg::subcommand::BaseValuation::option()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ab8b3cbd45bd3048d233359cd451347a1',1,'vg::subcommand::BaseArgSpec::option()']]],
+ ['option_2ecpp_4256',['option.cpp',['../option_8cpp.html',1,'']]],
+ ['option_2ehpp_4257',['option.hpp',['../option_8hpp.html',1,'']]],
+ ['option_3c_20vector_3c_20item_20_3e_2c_20parser_20_3e_4258',['Option< vector< Item >, Parser >',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html',1,'vg']]],
+ ['option_5fid_4259',['option_id',['../structvg_1_1subcommand_1_1BaseArgSpec.html#aef2794c913cd5f8c07f79a0e88a6eba7',1,'vg::subcommand::BaseArgSpec']]],
+ ['option_5foffsets_4260',['option_offsets',['../classvg_1_1Configurable.html#a6c5fb72d68761ab4b157c817259164a5',1,'vg::Configurable']]],
+ ['option_5fto_5findex_4261',['option_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a06f1cbc473d47bb7579f75a22dd99811',1,'vg::subcommand::OptionGroup']]],
+ ['optionformat_4262',['OptionFormat',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9f',1,'vg::subcommand']]],
+ ['optiongroup_4263',['OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html',1,'vg::subcommand::OptionGroup< Receiver >'],['../structvg_1_1subcommand_1_1OptionGroup.html#a1e4abb9a235dcfe1d50809bbb36b40a8',1,'vg::subcommand::OptionGroup::OptionGroup()']]],
+ ['optioninterface_4264',['OptionInterface',['../classvg_1_1OptionInterface.html',1,'vg']]],
+ ['options_2ecpp_4265',['options.cpp',['../options_8cpp.html',1,'']]],
+ ['options_2ehpp_4266',['options.hpp',['../options_8hpp.html',1,'']]],
+ ['options_5fby_5fcode_4267',['options_by_code',['../classvg_1_1ConfigurableParser.html#a8bdfad847167513663ef67839a574e92',1,'vg::ConfigurableParser']]],
+ ['optionvalueparser_4268',['OptionValueParser',['../classvg_1_1OptionValueParser.html',1,'vg']]],
+ ['optionvalueparser_3c_20vector_3c_20item_20_3e_20_3e_4269',['OptionValueParser< vector< Item > >',['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html',1,'vg']]],
+ ['order_4270',['Order',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046b',1,'vg::StreamSorter::Order()'],['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894a',1,'ReferenceInterval::order()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#ae776df11d1881a7ac95ca8775b6f53d6',1,'vg::DozeuInterface::OrderedGraph::order()'],['../classvg_1_1StreamSorter.html#a03c4547e213a4be6f8f9164cf599b3c3',1,'vg::StreamSorter::order()']]],
+ ['order_5flength_5frepeat_5fhit_5fmax_4271',['order_length_repeat_hit_max',['../classvg_1_1MultipathMapper.html#ae87f55f358023f5c881494ccc4ed884f',1,'vg::MultipathMapper']]],
+ ['order_5fof_4272',['order_of',['../classvg_1_1IncrementalSubgraph.html#afe160f21d5b4a7964c1bceef47ca54a4',1,'vg::IncrementalSubgraph']]],
+ ['orderedgraph_4273',['OrderedGraph',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html',1,'vg::DozeuInterface::OrderedGraph'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a321fef7bca4632cec8f2ed02f8294ad8',1,'vg::DozeuInterface::OrderedGraph::OrderedGraph()']]],
+ ['orientation_5ffrom_5fold_5fedge_5ftype_4274',['orientation_from_old_edge_type',['../classxg_1_1XG.html#a6383f68a1f2f9150a0649c6db1c43891',1,'xg::XG']]],
+ ['oriented_5fdistance_4275',['oriented_distance',['../classvg_1_1OrientedDistanceMeasurer.html#af6551e771deca01e6af9054a1ad3d30e',1,'vg::OrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a8ec77086bfe160d85961a509725b529f',1,'vg::PathOrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a8f8081d5bb9b0f5526935e2691f52dc3',1,'vg::SnarlOrientedDistanceMeasurer::oriented_distance()']]],
+ ['oriented_5fmotif_4276',['oriented_motif',['../classvg_1_1SpliceStats.html#a0568cd8d7b986fdd703bd4021dbb41a1',1,'vg::SpliceStats']]],
+ ['oriented_5fnode_5frange_5ft_4277',['oriented_node_range_t',['../namespacevg.html#acf54b55d1c1d16a3d64f1bae268a58af',1,'vg::oriented_node_range_t()'],['../namespacehandlegraph.html#aa9a6ea7613d52c42947d4faa2a189bba',1,'handlegraph::oriented_node_range_t()']]],
+ ['oriented_5fseed_5ft_4278',['oriented_seed_t',['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html',1,'vg::ZipCodeTree']]],
+ ['orienteddistanceclusterer_4279',['OrientedDistanceClusterer',['../classvg_1_1OrientedDistanceClusterer.html',1,'vg::OrientedDistanceClusterer'],['../classvg_1_1OrientedDistanceClusterer.html#a0bab84127f018db9467240db290113b4',1,'vg::OrientedDistanceClusterer::OrientedDistanceClusterer()']]],
+ ['orienteddistancemeasurer_4280',['OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html',1,'vg']]],
+ ['os_4281',['OS',['../classvg_1_1Version.html#a60cb5fa1efa9969bcdfa529484ea4280',1,'vg::Version']]],
+ ['other_4282',['other',['../structvg_1_1algorithms_1_1Edge.html#a3a831a365cea8d70a5c9817c9a7243ee',1,'vg::algorithms::Edge::other()'],['../classvg_1_1io_1_1streaminbuf.html#a91cfbc8581e4aa70e52268897747d764',1,'vg::io::streaminbuf::other()']]],
+ ['other_5forientation_5ftimeout_4283',['other_orientation_timeout',['../classvg_1_1RepresentativeTraversalFinder.html#a5d5136f771fe4566506ff486fb17df49',1,'vg::RepresentativeTraversalFinder']]],
+ ['other_5fsupports_4284',['other_supports',['../structvg_1_1BREAKPOINT.html#a2f08ace3f57cff47b7f703fef1ae9792',1,'vg::BREAKPOINT']]],
+ ['out_4285',['out',['../classvg_1_1TSVExplainer.html#a2ee20849b7d26e1ce2915996dd0b9912',1,'vg::TSVExplainer::out()'],['../classvg_1_1ProblemDumpExplainer.html#aae8b802f7d2db844b8a576420d0a37bd',1,'vg::ProblemDumpExplainer::out()']]],
+ ['out_5ffile_4286',['out_file',['../classvg_1_1HTSWriter.html#aff12605f14901844666bf6775b7c0971',1,'vg::HTSWriter::out_file()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a7b3a7d580d6a585a4d8205caf452ce63',1,'vg::io::TSVAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a1408267254d15464a52b44317e6c780d',1,'vg::io::VGAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a1cdca9c9f2e7f42feb6160a42e072027',1,'vg::io::GafAlignmentEmitter::out_file()']]],
+ ['out_5fmutex_4287',['out_mutex',['../classvg_1_1io_1_1ProtobufEmitter.html#acb50db8c0f33135ae2e246ae26efb9d0',1,'vg::io::ProtobufEmitter']]],
+ ['out_5fstream_4288',['out_stream',['../classvg_1_1MCMCCaller.html#a240022048423d2922858aaf9cfae0fc0',1,'vg::MCMCCaller']]],
+ ['out_5fto_4289',['out_to',['../classvg_1_1ExtraNodeGraph.html#a0f31e37f1e4398d6f8e057c1c8c92495',1,'vg::ExtraNodeGraph']]],
+ ['outfile_4290',['outfile',['../classvg_1_1Viz.html#a78a53d3a62a503ff6c29e93cb9a12a88',1,'vg::Viz']]],
+ ['output_4291',['output',['../structvg_1_1io_1_1hFILE__cppstream.html#a1b13eb012084d4b68b0f30a1cddebb41',1,'vg::io::hFILE_cppstream']]],
+ ['output_5ffields_4292',['output_fields',['../classvg_1_1ReadFilter.html#ade1a4a40379d72d2811fe0e32bece8f7',1,'vg::ReadFilter']]],
+ ['output_5ffilepath_4293',['output_filepath',['../classvg_1_1IndexingPlan.html#a405ede5620e8a7263fbb734f656c9971',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier) const'],['../classvg_1_1IndexingPlan.html#a5ef2f8275a2f997e94d178089107502a',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier, size_t chunk, size_t num_chunks) const']]],
+ ['output_5fformat_5ft_4294',['output_format_t',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0b',1,'vg::MultipathAlignmentEmitter']]],
+ ['output_5fgraph_5fwith_5fembedded_5fpaths_4295',['output_graph_with_embedded_paths',['../namespacevg.html#ae62ff63e415416fd298c6f59c8f2da47',1,'vg::output_graph_with_embedded_paths(vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source)'],['../namespacevg.html#a134ccba76916d6d94e59581932f1b595',1,'vg::output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json)']]],
+ ['output_5fhaplotype_5fcounts_4296',['output_haplotype_counts',['../namespacevg.html#ae2d79bdac899f70214959ef92dbbad2f',1,'vg']]],
+ ['output_5fin_5fprogress_4297',['output_in_progress',['../classvg_1_1Funnel.html#ae946f8189275c0f4b77f29433406a24b',1,'vg::Funnel']]],
+ ['output_5fis_5fbgzf_4298',['output_is_bgzf',['../classvg_1_1HTSWriter.html#a440cfc6e79f5790976ebac5e648a3696',1,'vg::HTSWriter']]],
+ ['output_5fnames_4299',['output_names',['../classVectorizer.html#aadb47085d4b369b1c9ea341b06311341',1,'Vectorizer']]],
+ ['output_5fpng_4300',['output_png',['../classvg_1_1Viz.html#a8b50b34356875c1c0aa3917c7c67e445',1,'vg::Viz']]],
+ ['output_5fprefix_4301',['output_prefix',['../classvg_1_1IndexRegistry.html#a24555b7ccd83df8e2ccb28b900a6b5b1',1,'vg::IndexRegistry']]],
+ ['output_5fsvg_4302',['output_svg',['../classvg_1_1Viz.html#a82a23ca5a5a6ababff6176743247be04',1,'vg::Viz']]],
+ ['output_5ftabbed_4303',['output_tabbed',['../classVectorizer.html#a7be5208d3a51438a989dd406fb808fd9',1,'Vectorizer']]],
+ ['output_5fvariants_4304',['output_variants',['../classvg_1_1VCFOutputCaller.html#aa9a532dbc58fe6031595ed819d31b02a',1,'vg::VCFOutputCaller']]],
+ ['output_5fvcf_4305',['output_vcf',['../classvg_1_1VCFOutputCaller.html#a1556bdec270d47b22e5c91b6956a23c0',1,'vg::VCFOutputCaller']]],
+ ['output_5fversion_4306',['OUTPUT_VERSION',['../classvg_1_1StreamIndexBase.html#ad5ce82f31552d36c073e65ced2af529e',1,'vg::StreamIndexBase']]],
+ ['output_5fwabbit_5fmap_4307',['output_wabbit_map',['../classVectorizer.html#a788aaec704ce78d29f55459ff2eaedb4',1,'Vectorizer']]],
+ ['outputstream_4308',['outputStream',['../namespacevg_1_1io.html#a477841175891d3e770995307eea45f38',1,'vg::io']]],
+ ['over_5fdirected_5fedge_4309',['over_directed_edge',['../classvg_1_1Paths.html#a8d1fde70db5d5c4d1e26821d4f03ba7a',1,'vg::Paths']]],
+ ['over_5fedge_4310',['over_edge',['../classvg_1_1Paths.html#ae7cd0d9291a31a63aa80e9d4d578575e',1,'vg::Paths']]],
+ ['overall_5fsupport_4311',['overall_support',['../structvg_1_1Locus.html#a04ac3427a7318a28984c8114cd216675',1,'vg::Locus']]],
+ ['overflow_4312',['overflow',['../classvg_1_1io_1_1fdoutbuf.html#aa0b27dbd39a3ad9452f0d4c0d8ca11a1',1,'vg::io::fdoutbuf']]],
+ ['overlap_4313',['overlap',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aa155f6cfbc58baef62da2c775972e636b',1,'ReferenceInterval::overlap()'],['../structvg_1_1Edge.html#aafdc39a954fd8de9dc3850ad9ecb9ade',1,'vg::Edge::overlap()'],['../structvg_1_1BREAKPOINT.html#a8843c2775e6cc15ef2739e13a02b2c86',1,'vg::BREAKPOINT::overlap()'],['../structvg_1_1GaplessExtension.html#ae13cbdb46d6375425a2f82e75daadb66',1,'vg::GaplessExtension::overlap()'],['../namespacevg.html#aaac70d8b120ca61591561cba307dcc1b',1,'vg::overlap()']]],
+ ['overlap_5fthreshold_4314',['OVERLAP_THRESHOLD',['../classvg_1_1GaplessExtender.html#a3d436577897604304729afc521928ee8',1,'vg::GaplessExtender']]],
+ ['overlay_4315',['overlay',['../classvg_1_1Translator.html#a91965cec764734c35ace2ecb0c643d5c',1,'vg::Translator']]],
+ ['overlay_5fnode_5ftranslations_4316',['overlay_node_translations',['../classvg_1_1VG.html#ae9b314bb2021525e60a0ad23e99fb994',1,'vg::VG::overlay_node_translations()'],['../namespacevg.html#a86d5f690fe272c74949e080aca561467',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#a7816225a17a671ff849a79f064770ebb',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#af224cfdc27efec675771ba4cc5143a3f',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, id_t > &under)'],['../namespacevg.html#ae996017b379b1178d5e588b96a7c7f3f',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, id_t > &under)']]],
+ ['overload_5fpair_5fhash_4317',['OVERLOAD_PAIR_HASH',['../hash__map_8hpp.html#a181224ba2835ac80e940ef8505d5f119',1,'hash_map.hpp']]],
+ ['own_5fsnarl_5fmanager_4318',['own_snarl_manager',['../classvg_1_1Masker.html#aa58433090d15c4a8235aec717dcef987',1,'vg::Masker']]]
];
diff --git a/search/classes_0.js b/search/classes_0.js
index 0dccc8abb1..abbf1495cf 100644
--- a/search/classes_0.js
+++ b/search/classes_0.js
@@ -1,22 +1,22 @@
var searchData=
[
- ['abstractreadsampler_6840',['AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html',1,'vg']]],
- ['affinity_6841',['Affinity',['../structvg_1_1Genotyper_1_1Affinity.html',1,'vg::Genotyper']]],
- ['aliasgraph_6842',['AliasGraph',['../classvg_1_1AliasGraph.html',1,'vg']]],
- ['aligner_6843',['Aligner',['../classvg_1_1Aligner.html',1,'vg']]],
- ['aligner_5fstats_5ft_6844',['aligner_stats_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html',1,'vg::MinimizerMapper']]],
- ['alignerclient_6845',['AlignerClient',['../classvg_1_1AlignerClient.html',1,'vg']]],
- ['alignment_6846',['Alignment',['../structvg_1_1Alignment.html',1,'vg']]],
- ['alignment_5findex_5ft_6847',['alignment_index_t',['../structvg_1_1alignment__index__t.html',1,'vg']]],
- ['alignmentchainmodel_6848',['AlignmentChainModel',['../classvg_1_1AlignmentChainModel.html',1,'vg']]],
- ['alignmentchainmodelvertex_6849',['AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html',1,'vg']]],
- ['alignmentemitter_6850',['AlignmentEmitter',['../classvg_1_1io_1_1AlignmentEmitter.html',1,'vg::io']]],
- ['alignmentvalidity_6851',['AlignmentValidity',['../structvg_1_1AlignmentValidity.html',1,'vg']]],
- ['alttracebackstack_6852',['AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html',1,'vg::BandedGlobalAligner']]],
- ['anchor_6853',['Anchor',['../classvg_1_1algorithms_1_1Anchor.html',1,'vg::algorithms']]],
- ['annotation_6854',['Annotation',['../structvg_1_1Annotation.html',1,'vg']]],
- ['appendhaplotypecommand_6855',['AppendHaplotypeCommand',['../structvg_1_1AppendHaplotypeCommand.html',1,'vg']]],
- ['argspec_6856',['ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html',1,'vg::subcommand']]],
- ['argspec_3c_20bool_2c_20receiver_20_3e_6857',['ArgSpec< bool, Receiver >',['../structvg_1_1subcommand_1_1ArgSpec.html',1,'vg::subcommand']]],
- ['augmentedgraph_6858',['AugmentedGraph',['../structvg_1_1AugmentedGraph.html',1,'vg']]]
+ ['abstractreadsampler_6842',['AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html',1,'vg']]],
+ ['affinity_6843',['Affinity',['../structvg_1_1Genotyper_1_1Affinity.html',1,'vg::Genotyper']]],
+ ['aliasgraph_6844',['AliasGraph',['../classvg_1_1AliasGraph.html',1,'vg']]],
+ ['aligner_6845',['Aligner',['../classvg_1_1Aligner.html',1,'vg']]],
+ ['aligner_5fstats_5ft_6846',['aligner_stats_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html',1,'vg::MinimizerMapper']]],
+ ['alignerclient_6847',['AlignerClient',['../classvg_1_1AlignerClient.html',1,'vg']]],
+ ['alignment_6848',['Alignment',['../structvg_1_1Alignment.html',1,'vg']]],
+ ['alignment_5findex_5ft_6849',['alignment_index_t',['../structvg_1_1alignment__index__t.html',1,'vg']]],
+ ['alignmentchainmodel_6850',['AlignmentChainModel',['../classvg_1_1AlignmentChainModel.html',1,'vg']]],
+ ['alignmentchainmodelvertex_6851',['AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html',1,'vg']]],
+ ['alignmentemitter_6852',['AlignmentEmitter',['../classvg_1_1io_1_1AlignmentEmitter.html',1,'vg::io']]],
+ ['alignmentvalidity_6853',['AlignmentValidity',['../structvg_1_1AlignmentValidity.html',1,'vg']]],
+ ['alttracebackstack_6854',['AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html',1,'vg::BandedGlobalAligner']]],
+ ['anchor_6855',['Anchor',['../classvg_1_1algorithms_1_1Anchor.html',1,'vg::algorithms']]],
+ ['annotation_6856',['Annotation',['../structvg_1_1Annotation.html',1,'vg']]],
+ ['appendhaplotypecommand_6857',['AppendHaplotypeCommand',['../structvg_1_1AppendHaplotypeCommand.html',1,'vg']]],
+ ['argspec_6858',['ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html',1,'vg::subcommand']]],
+ ['argspec_3c_20bool_2c_20receiver_20_3e_6859',['ArgSpec< bool, Receiver >',['../structvg_1_1subcommand_1_1ArgSpec.html',1,'vg::subcommand']]],
+ ['augmentedgraph_6860',['AugmentedGraph',['../structvg_1_1AugmentedGraph.html',1,'vg']]]
];
diff --git a/search/classes_1.js b/search/classes_1.js
index 2267a2bd6c..7e4f146cd5 100644
--- a/search/classes_1.js
+++ b/search/classes_1.js
@@ -1,29 +1,29 @@
var searchData=
[
- ['babuilder_6859',['BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html',1,'vg::BandedGlobalAligner']]],
- ['backtranslatingalignmentemitter_6860',['BackTranslatingAlignmentEmitter',['../classvg_1_1BackTranslatingAlignmentEmitter.html',1,'vg']]],
- ['bamatrix_6861',['BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html',1,'vg::BandedGlobalAligner']]],
- ['bandedglobalaligner_6862',['BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html',1,'vg']]],
- ['bandmatricestoobigexception_6863',['BandMatricesTooBigException',['../classvg_1_1BandMatricesTooBigException.html',1,'vg']]],
- ['basealigner_6864',['BaseAligner',['../classvg_1_1BaseAligner.html',1,'vg']]],
- ['baseargspec_6865',['BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html',1,'vg::subcommand']]],
- ['basemapper_6866',['BaseMapper',['../classvg_1_1BaseMapper.html',1,'vg']]],
- ['baseoption_6867',['BaseOption',['../classvg_1_1BaseOption.html',1,'vg']]],
- ['baseoption_3c_20value_2c_20optionvalueparser_3c_20value_20_3e_20_3e_6868',['BaseOption< Value, OptionValueParser< Value > >',['../classvg_1_1BaseOption.html',1,'vg']]],
- ['baseoption_3c_20vector_3c_20item_20_3e_2c_20parser_20_3e_6869',['BaseOption< vector< Item >, Parser >',['../classvg_1_1BaseOption.html',1,'vg']]],
- ['baseoptiongroup_6870',['BaseOptionGroup',['../structvg_1_1subcommand_1_1BaseOptionGroup.html',1,'vg::subcommand']]],
- ['basepileup_6871',['BasePileup',['../structvg_1_1BasePileup.html',1,'vg']]],
- ['basevaluation_6872',['BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html',1,'vg::subcommand']]],
- ['bbedgehash_6873',['BBEdgeHash',['../structvg_1_1BBEdgeHash.html',1,'vg']]],
- ['benchmarkresult_6874',['BenchmarkResult',['../structvg_1_1BenchmarkResult.html',1,'vg']]],
- ['bitstring_6875',['BitString',['../classvg_1_1BitString.html',1,'vg']]],
- ['bitstringtree_6876',['BitStringTree',['../classvg_1_1BitStringTree.html',1,'vg']]],
- ['bitstringtree_3c_20bin_5ft_20_3e_6877',['BitStringTree< bin_t >',['../classvg_1_1BitStringTree.html',1,'vg']]],
- ['blockedgzipinputstream_6878',['BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html',1,'vg::io']]],
- ['blockedgzipoutputstream_6879',['BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html',1,'vg::io']]],
- ['boolreturningwrapper_6880',['BoolReturningWrapper',['../structhandlegraph_1_1BoolReturningWrapper.html',1,'handlegraph']]],
- ['boolreturningwrapper_3c_20iteratee_2c_20false_20_3e_6881',['BoolReturningWrapper< Iteratee, false >',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01false_01_4.html',1,'handlegraph']]],
- ['boolreturningwrapper_3c_20iteratee_2c_20true_20_3e_6882',['BoolReturningWrapper< Iteratee, true >',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01true_01_4.html',1,'handlegraph']]],
- ['breakpoint_6883',['BREAKPOINT',['../structvg_1_1BREAKPOINT.html',1,'vg']]],
- ['buildablesnarldecomposition_6884',['BuildableSnarlDecomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html',1,'handlegraph']]]
+ ['babuilder_6861',['BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html',1,'vg::BandedGlobalAligner']]],
+ ['backtranslatingalignmentemitter_6862',['BackTranslatingAlignmentEmitter',['../classvg_1_1BackTranslatingAlignmentEmitter.html',1,'vg']]],
+ ['bamatrix_6863',['BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html',1,'vg::BandedGlobalAligner']]],
+ ['bandedglobalaligner_6864',['BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html',1,'vg']]],
+ ['bandmatricestoobigexception_6865',['BandMatricesTooBigException',['../classvg_1_1BandMatricesTooBigException.html',1,'vg']]],
+ ['basealigner_6866',['BaseAligner',['../classvg_1_1BaseAligner.html',1,'vg']]],
+ ['baseargspec_6867',['BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html',1,'vg::subcommand']]],
+ ['basemapper_6868',['BaseMapper',['../classvg_1_1BaseMapper.html',1,'vg']]],
+ ['baseoption_6869',['BaseOption',['../classvg_1_1BaseOption.html',1,'vg']]],
+ ['baseoption_3c_20value_2c_20optionvalueparser_3c_20value_20_3e_20_3e_6870',['BaseOption< Value, OptionValueParser< Value > >',['../classvg_1_1BaseOption.html',1,'vg']]],
+ ['baseoption_3c_20vector_3c_20item_20_3e_2c_20parser_20_3e_6871',['BaseOption< vector< Item >, Parser >',['../classvg_1_1BaseOption.html',1,'vg']]],
+ ['baseoptiongroup_6872',['BaseOptionGroup',['../structvg_1_1subcommand_1_1BaseOptionGroup.html',1,'vg::subcommand']]],
+ ['basepileup_6873',['BasePileup',['../structvg_1_1BasePileup.html',1,'vg']]],
+ ['basevaluation_6874',['BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html',1,'vg::subcommand']]],
+ ['bbedgehash_6875',['BBEdgeHash',['../structvg_1_1BBEdgeHash.html',1,'vg']]],
+ ['benchmarkresult_6876',['BenchmarkResult',['../structvg_1_1BenchmarkResult.html',1,'vg']]],
+ ['bitstring_6877',['BitString',['../classvg_1_1BitString.html',1,'vg']]],
+ ['bitstringtree_6878',['BitStringTree',['../classvg_1_1BitStringTree.html',1,'vg']]],
+ ['bitstringtree_3c_20bin_5ft_20_3e_6879',['BitStringTree< bin_t >',['../classvg_1_1BitStringTree.html',1,'vg']]],
+ ['blockedgzipinputstream_6880',['BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html',1,'vg::io']]],
+ ['blockedgzipoutputstream_6881',['BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html',1,'vg::io']]],
+ ['boolreturningwrapper_6882',['BoolReturningWrapper',['../structhandlegraph_1_1BoolReturningWrapper.html',1,'handlegraph']]],
+ ['boolreturningwrapper_3c_20iteratee_2c_20false_20_3e_6883',['BoolReturningWrapper< Iteratee, false >',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01false_01_4.html',1,'handlegraph']]],
+ ['boolreturningwrapper_3c_20iteratee_2c_20true_20_3e_6884',['BoolReturningWrapper< Iteratee, true >',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01true_01_4.html',1,'handlegraph']]],
+ ['breakpoint_6885',['BREAKPOINT',['../structvg_1_1BREAKPOINT.html',1,'vg']]],
+ ['buildablesnarldecomposition_6886',['BuildableSnarlDecomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html',1,'handlegraph']]]
];
diff --git a/search/classes_10.js b/search/classes_10.js
index d2502b12ee..969ffca788 100644
--- a/search/classes_10.js
+++ b/search/classes_10.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['qualadjaligner_7208',['QualAdjAligner',['../classvg_1_1QualAdjAligner.html',1,'vg']]],
- ['qualadjxdropaligner_7209',['QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html',1,'vg']]]
+ ['qualadjaligner_7210',['QualAdjAligner',['../classvg_1_1QualAdjAligner.html',1,'vg']]],
+ ['qualadjxdropaligner_7211',['QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html',1,'vg']]]
];
diff --git a/search/classes_11.js b/search/classes_11.js
index 3732870f47..223c8c37a3 100644
--- a/search/classes_11.js
+++ b/search/classes_11.js
@@ -1,33 +1,33 @@
var searchData=
[
- ['range_7210',['Range',['../structvg_1_1Range.html',1,'vg']]],
- ['range_3c_20t_20_3e_7211',['Range< T >',['../structvg_1_1Range.html',1,'vg']]],
- ['rangeargspec_7212',['RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html',1,'vg::subcommand']]],
- ['rankedhandlegraph_7213',['RankedHandleGraph',['../classhandlegraph_1_1RankedHandleGraph.html',1,'handlegraph']]],
- ['rarevariantsimplifier_7214',['RareVariantSimplifier',['../classvg_1_1RareVariantSimplifier.html',1,'vg']]],
- ['ratiosupportsnarlcaller_7215',['RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html',1,'vg']]],
- ['read_5falignment_5findex_5ft_7216',['read_alignment_index_t',['../structvg_1_1read__alignment__index__t.html',1,'vg']]],
- ['readfilter_7217',['ReadFilter',['../classvg_1_1ReadFilter.html',1,'vg']]],
- ['readmasker_7218',['ReadMasker',['../classvg_1_1ReadMasker.html',1,'vg']]],
- ['readrestrictedtraversalfinder_7219',['ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html',1,'vg']]],
- ['rebuildjob_7220',['RebuildJob',['../structvg_1_1RebuildJob.html',1,'vg']]],
- ['rebuildparameters_7221',['RebuildParameters',['../structvg_1_1RebuildParameters.html',1,'vg']]],
- ['recombinator_7222',['Recombinator',['../classvg_1_1Recombinator.html',1,'vg']]],
- ['recombinatorfragment_7223',['RecombinatorFragment',['../structvg_1_1RecombinatorFragment.html',1,'vg']]],
- ['recombinatorhaplotype_7224',['RecombinatorHaplotype',['../structvg_1_1RecombinatorHaplotype.html',1,'vg']]],
- ['referenceinterval_7225',['ReferenceInterval',['../structReferenceInterval.html',1,'']]],
- ['region_7226',['Region',['../structvg_1_1Region.html',1,'vg']]],
- ['regionexpander_7227',['RegionExpander',['../classvg_1_1RegionExpander.html',1,'vg']]],
- ['registry_7228',['Registry',['../classvg_1_1io_1_1Registry.html',1,'vg::io']]],
- ['replacelocalhaplotypecommand_7229',['ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html',1,'vg']]],
- ['replacesnarlhaplotypecommand_7230',['ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html',1,'vg']]],
- ['representativetraversalfinder_7231',['RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html',1,'vg']]],
- ['return_5ftype_5fof_7232',['return_type_of',['../structhandlegraph_1_1return__type__of.html',1,'handlegraph']]],
- ['return_5ftype_5fof_3c_20returns_28_2a_29_28args_2e_2e_2e_29_3e_7233',['return_type_of< Returns(*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
- ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_20const_20_3e_7234',['return_type_of< Returns(Owner::*)(Args...) const >',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html',1,'handlegraph']]],
- ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_3e_7235',['return_type_of< Returns(Owner::*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
- ['reverse_5fiterator_7236',['reverse_iterator',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html',1,'vg::ZipCodeTree']]],
- ['reversegraph_7237',['ReverseGraph',['../classvg_1_1ReverseGraph.html',1,'vg']]],
- ['rewindplanexception_7238',['RewindPlanException',['../classvg_1_1RewindPlanException.html',1,'vg']]],
- ['rrmemo_7239',['RRMemo',['../structhaplo_1_1haploMath_1_1RRMemo.html',1,'haplo::haploMath']]]
+ ['range_7212',['Range',['../structvg_1_1Range.html',1,'vg']]],
+ ['range_3c_20t_20_3e_7213',['Range< T >',['../structvg_1_1Range.html',1,'vg']]],
+ ['rangeargspec_7214',['RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html',1,'vg::subcommand']]],
+ ['rankedhandlegraph_7215',['RankedHandleGraph',['../classhandlegraph_1_1RankedHandleGraph.html',1,'handlegraph']]],
+ ['rarevariantsimplifier_7216',['RareVariantSimplifier',['../classvg_1_1RareVariantSimplifier.html',1,'vg']]],
+ ['ratiosupportsnarlcaller_7217',['RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html',1,'vg']]],
+ ['read_5falignment_5findex_5ft_7218',['read_alignment_index_t',['../structvg_1_1read__alignment__index__t.html',1,'vg']]],
+ ['readfilter_7219',['ReadFilter',['../classvg_1_1ReadFilter.html',1,'vg']]],
+ ['readmasker_7220',['ReadMasker',['../classvg_1_1ReadMasker.html',1,'vg']]],
+ ['readrestrictedtraversalfinder_7221',['ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html',1,'vg']]],
+ ['rebuildjob_7222',['RebuildJob',['../structvg_1_1RebuildJob.html',1,'vg']]],
+ ['rebuildparameters_7223',['RebuildParameters',['../structvg_1_1RebuildParameters.html',1,'vg']]],
+ ['recombinator_7224',['Recombinator',['../classvg_1_1Recombinator.html',1,'vg']]],
+ ['recombinatorfragment_7225',['RecombinatorFragment',['../structvg_1_1RecombinatorFragment.html',1,'vg']]],
+ ['recombinatorhaplotype_7226',['RecombinatorHaplotype',['../structvg_1_1RecombinatorHaplotype.html',1,'vg']]],
+ ['referenceinterval_7227',['ReferenceInterval',['../structReferenceInterval.html',1,'']]],
+ ['region_7228',['Region',['../structvg_1_1Region.html',1,'vg']]],
+ ['regionexpander_7229',['RegionExpander',['../classvg_1_1RegionExpander.html',1,'vg']]],
+ ['registry_7230',['Registry',['../classvg_1_1io_1_1Registry.html',1,'vg::io']]],
+ ['replacelocalhaplotypecommand_7231',['ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html',1,'vg']]],
+ ['replacesnarlhaplotypecommand_7232',['ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html',1,'vg']]],
+ ['representativetraversalfinder_7233',['RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html',1,'vg']]],
+ ['return_5ftype_5fof_7234',['return_type_of',['../structhandlegraph_1_1return__type__of.html',1,'handlegraph']]],
+ ['return_5ftype_5fof_3c_20returns_28_2a_29_28args_2e_2e_2e_29_3e_7235',['return_type_of< Returns(*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
+ ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_20const_20_3e_7236',['return_type_of< Returns(Owner::*)(Args...) const >',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html',1,'handlegraph']]],
+ ['return_5ftype_5fof_3c_20returns_28owner_3a_3a_2a_29_28args_2e_2e_2e_29_3e_7237',['return_type_of< Returns(Owner::*)(Args...)>',['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html',1,'handlegraph']]],
+ ['reverse_5fiterator_7238',['reverse_iterator',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html',1,'vg::ZipCodeTree']]],
+ ['reversegraph_7239',['ReverseGraph',['../classvg_1_1ReverseGraph.html',1,'vg']]],
+ ['rewindplanexception_7240',['RewindPlanException',['../classvg_1_1RewindPlanException.html',1,'vg']]],
+ ['rrmemo_7241',['RRMemo',['../structhaplo_1_1haploMath_1_1RRMemo.html',1,'haplo::haploMath']]]
];
diff --git a/search/classes_12.js b/search/classes_12.js
index 07456b748c..497c50f196 100644
--- a/search/classes_12.js
+++ b/search/classes_12.js
@@ -1,75 +1,75 @@
var searchData=
[
- ['sampler_7240',['Sampler',['../classvg_1_1Sampler.html',1,'vg']]],
- ['scoreproperties_7241',['ScoreProperties',['../structvg_1_1WFATree_1_1ScoreProperties.html',1,'vg::WFATree']]],
- ['scoreprovider_7242',['ScoreProvider',['../classhaplo_1_1ScoreProvider.html',1,'haplo']]],
- ['scoringoptions_7243',['ScoringOptions',['../structScoringOptions.html',1,'']]],
- ['seed_7244',['Seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html',1,'vg::SnarlDistanceIndexClusterer']]],
- ['seed_5fresult_5ft_7245',['seed_result_t',['../structvg_1_1ZipCodeTree_1_1seed__result__t.html',1,'vg::ZipCodeTree']]],
- ['seedcache_7246',['SeedCache',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html',1,'vg::SnarlDistanceIndexClusterer']]],
- ['seqcomplexity_7247',['SeqComplexity',['../structvg_1_1SeqComplexity.html',1,'vg']]],
- ['serializable_7248',['Serializable',['../classhandlegraph_1_1Serializable.html',1,'handlegraph']]],
- ['serializablehandlegraph_7249',['SerializableHandleGraph',['../classhandlegraph_1_1SerializableHandleGraph.html',1,'handlegraph']]],
- ['shuffledpairs_7250',['ShuffledPairs',['../classvg_1_1ShuffledPairs.html',1,'vg']]],
- ['simpleconsistencycalculator_7251',['SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html',1,'vg']]],
- ['simpletraversalsupportcalculator_7252',['SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html',1,'vg']]],
- ['sizelimitexceededexception_7253',['SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html',1,'vg']]],
- ['smallbitset_7254',['SmallBitset',['../classvg_1_1SmallBitset.html',1,'vg']]],
- ['smallsnarlsimplifier_7255',['SmallSnarlSimplifier',['../classvg_1_1SmallSnarlSimplifier.html',1,'vg']]],
- ['snarl_7256',['Snarl',['../structvg_1_1Snarl.html',1,'vg']]],
- ['snarl_5fcode_5ft_7257',['snarl_code_t',['../structvg_1_1ZipCode_1_1snarl__code__t.html',1,'vg::ZipCode']]],
- ['snarl_5fless_7258',['snarl_less',['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
- ['snarlcaller_7259',['SnarlCaller',['../classvg_1_1SnarlCaller.html',1,'vg']]],
- ['snarldecomposition_7260',['SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html',1,'handlegraph']]],
- ['snarldistanceindexclusterer_7261',['SnarlDistanceIndexClusterer',['../classvg_1_1SnarlDistanceIndexClusterer.html',1,'vg']]],
- ['snarlfinder_7262',['SnarlFinder',['../classvg_1_1SnarlFinder.html',1,'vg']]],
- ['snarlgraph_7263',['SnarlGraph',['../classvg_1_1SnarlGraph.html',1,'vg']]],
- ['snarlmanager_7264',['SnarlManager',['../classvg_1_1SnarlManager.html',1,'vg']]],
- ['snarlmindistance_7265',['SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html',1,'vg']]],
- ['snarlorienteddistancemeasurer_7266',['SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html',1,'vg']]],
- ['snarlrecord_7267',['SnarlRecord',['../structvg_1_1SnarlManager_1_1SnarlRecord.html',1,'vg::SnarlManager']]],
- ['snarlstate_7268',['SnarlState',['../classvg_1_1SnarlState.html',1,'vg']]],
- ['snarltraversal_7269',['SnarlTraversal',['../structvg_1_1SnarlTraversal.html',1,'vg']]],
- ['snarltreechild_7270',['SnarlTreeChild',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['snarltreenodeproblem_7271',['SnarlTreeNodeProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html',1,'vg::SnarlDistanceIndexClusterer']]],
- ['snvvector_7272',['SNVvector',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html',1,'haplo::linear_haplo_structure']]],
- ['sort_5fvalue_5ft_7273',['sort_value_t',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html',1,'vg::ZipCodeForest']]],
- ['sourcesinkoverlay_7274',['SourceSinkOverlay',['../classvg_1_1SourceSinkOverlay.html',1,'vg']]],
- ['sparseunionfind_7275',['SparseUnionFind',['../classvg_1_1SparseUnionFind.html',1,'vg']]],
- ['splicedhtsalignmentemitter_7276',['SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html',1,'vg']]],
- ['spliceregion_7277',['SpliceRegion',['../classvg_1_1SpliceRegion.html',1,'vg']]],
- ['splicestats_7278',['SpliceStats',['../classvg_1_1SpliceStats.html',1,'vg']]],
- ['sswaligner_7279',['SSWAligner',['../classvg_1_1SSWAligner.html',1,'vg']]],
- ['stage_7280',['Stage',['../structvg_1_1Funnel_1_1Stage.html',1,'vg::Funnel']]],
- ['stat_5fcollection_5ft_7281',['stat_collection_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['stat_5fset_5ft_7282',['stat_set_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['state_5fhash_7283',['state_hash',['../structvg_1_1state__hash.html',1,'vg']]],
- ['statistics_7284',['Statistics',['../structvg_1_1Recombinator_1_1Statistics.html',1,'vg::Recombinator']]],
- ['step_5fhandle_5ft_7285',['step_handle_t',['../structhandlegraph_1_1step__handle__t.html',1,'handlegraph']]],
- ['strandsplitgraph_7286',['StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html',1,'vg']]],
- ['streaminbuf_7287',['streaminbuf',['../classvg_1_1io_1_1streaminbuf.html',1,'vg::io']]],
- ['streamindex_7288',['StreamIndex',['../classvg_1_1StreamIndex.html',1,'vg']]],
- ['streamindex_3c_20vg_3a_3aalgorithms_3a_3agraph_20_3e_7289',['StreamIndex< vg::algorithms::Graph >',['../classvg_1_1StreamIndex.html',1,'vg']]],
- ['streamindexbase_7290',['StreamIndexBase',['../classvg_1_1StreamIndexBase.html',1,'vg']]],
- ['streamistream_7291',['streamistream',['../classvg_1_1io_1_1streamistream.html',1,'vg::io']]],
- ['streammultiplexer_7292',['StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html',1,'vg::io']]],
- ['streamsorter_7293',['StreamSorter',['../classvg_1_1StreamSorter.html',1,'vg']]],
- ['string_5fhash_5fmap_7294',['string_hash_map',['../classvg_1_1string__hash__map.html',1,'vg']]],
- ['string_5fhash_5fset_7295',['string_hash_set',['../classvg_1_1string__hash__set.html',1,'vg']]],
- ['subchain_7296',['Subchain',['../structvg_1_1HaplotypePartitioner_1_1Subchain.html',1,'vg::HaplotypePartitioner::Subchain'],['../structvg_1_1Haplotypes_1_1Subchain.html',1,'vg::Haplotypes::Subchain']]],
- ['subcommand_7297',['Subcommand',['../classvg_1_1subcommand_1_1Subcommand.html',1,'vg::subcommand']]],
- ['subgraphexplainer_7298',['SubgraphExplainer',['../classvg_1_1SubgraphExplainer.html',1,'vg']]],
- ['subgraphoverlay_7299',['SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html',1,'vg']]],
- ['subhandlegraph_7300',['SubHandleGraph',['../classvg_1_1SubHandleGraph.html',1,'vg::SubHandleGraph'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html',1,'handlegraph::algorithms::SubHandleGraph']]],
- ['subpath_7301',['Subpath',['../structvg_1_1Subpath.html',1,'vg']]],
- ['subpath_5ft_7302',['subpath_t',['../classvg_1_1subpath__t.html',1,'vg']]],
- ['subpathoverlay_7303',['SubpathOverlay',['../classvg_1_1SubpathOverlay.html',1,'vg']]],
- ['summarystatistics_7304',['SummaryStatistics',['../structvg_1_1SummaryStatistics.html',1,'vg']]],
- ['support_7305',['Support',['../structvg_1_1Support.html',1,'vg']]],
- ['supportaugmentedgraph_7306',['SupportAugmentedGraph',['../structvg_1_1SupportAugmentedGraph.html',1,'vg']]],
- ['supportbasedsnarlcaller_7307',['SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html',1,'vg']]],
- ['supportrestrictedtraversalfinder_7308',['SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html',1,'vg']]],
- ['surjectingalignmentemitter_7309',['SurjectingAlignmentEmitter',['../classvg_1_1SurjectingAlignmentEmitter.html',1,'vg']]],
- ['surjector_7310',['Surjector',['../classvg_1_1Surjector.html',1,'vg']]],
- ['swaphaplotypescommand_7311',['SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html',1,'vg']]]
+ ['sampler_7242',['Sampler',['../classvg_1_1Sampler.html',1,'vg']]],
+ ['scoreproperties_7243',['ScoreProperties',['../structvg_1_1WFATree_1_1ScoreProperties.html',1,'vg::WFATree']]],
+ ['scoreprovider_7244',['ScoreProvider',['../classhaplo_1_1ScoreProvider.html',1,'haplo']]],
+ ['scoringoptions_7245',['ScoringOptions',['../structScoringOptions.html',1,'']]],
+ ['seed_7246',['Seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['seed_5fresult_5ft_7247',['seed_result_t',['../structvg_1_1ZipCodeTree_1_1seed__result__t.html',1,'vg::ZipCodeTree']]],
+ ['seedcache_7248',['SeedCache',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['seqcomplexity_7249',['SeqComplexity',['../structvg_1_1SeqComplexity.html',1,'vg']]],
+ ['serializable_7250',['Serializable',['../classhandlegraph_1_1Serializable.html',1,'handlegraph']]],
+ ['serializablehandlegraph_7251',['SerializableHandleGraph',['../classhandlegraph_1_1SerializableHandleGraph.html',1,'handlegraph']]],
+ ['shuffledpairs_7252',['ShuffledPairs',['../classvg_1_1ShuffledPairs.html',1,'vg']]],
+ ['simpleconsistencycalculator_7253',['SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html',1,'vg']]],
+ ['simpletraversalsupportcalculator_7254',['SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html',1,'vg']]],
+ ['sizelimitexceededexception_7255',['SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html',1,'vg']]],
+ ['smallbitset_7256',['SmallBitset',['../classvg_1_1SmallBitset.html',1,'vg']]],
+ ['smallsnarlsimplifier_7257',['SmallSnarlSimplifier',['../classvg_1_1SmallSnarlSimplifier.html',1,'vg']]],
+ ['snarl_7258',['Snarl',['../structvg_1_1Snarl.html',1,'vg']]],
+ ['snarl_5fcode_5ft_7259',['snarl_code_t',['../structvg_1_1ZipCode_1_1snarl__code__t.html',1,'vg::ZipCode']]],
+ ['snarl_5fless_7260',['snarl_less',['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
+ ['snarlcaller_7261',['SnarlCaller',['../classvg_1_1SnarlCaller.html',1,'vg']]],
+ ['snarldecomposition_7262',['SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html',1,'handlegraph']]],
+ ['snarldistanceindexclusterer_7263',['SnarlDistanceIndexClusterer',['../classvg_1_1SnarlDistanceIndexClusterer.html',1,'vg']]],
+ ['snarlfinder_7264',['SnarlFinder',['../classvg_1_1SnarlFinder.html',1,'vg']]],
+ ['snarlgraph_7265',['SnarlGraph',['../classvg_1_1SnarlGraph.html',1,'vg']]],
+ ['snarlmanager_7266',['SnarlManager',['../classvg_1_1SnarlManager.html',1,'vg']]],
+ ['snarlmindistance_7267',['SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html',1,'vg']]],
+ ['snarlorienteddistancemeasurer_7268',['SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html',1,'vg']]],
+ ['snarlrecord_7269',['SnarlRecord',['../structvg_1_1SnarlManager_1_1SnarlRecord.html',1,'vg::SnarlManager']]],
+ ['snarlstate_7270',['SnarlState',['../classvg_1_1SnarlState.html',1,'vg']]],
+ ['snarltraversal_7271',['SnarlTraversal',['../structvg_1_1SnarlTraversal.html',1,'vg']]],
+ ['snarltreechild_7272',['SnarlTreeChild',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['snarltreenodeproblem_7273',['SnarlTreeNodeProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['snvvector_7274',['SNVvector',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html',1,'haplo::linear_haplo_structure']]],
+ ['sort_5fvalue_5ft_7275',['sort_value_t',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html',1,'vg::ZipCodeForest']]],
+ ['sourcesinkoverlay_7276',['SourceSinkOverlay',['../classvg_1_1SourceSinkOverlay.html',1,'vg']]],
+ ['sparseunionfind_7277',['SparseUnionFind',['../classvg_1_1SparseUnionFind.html',1,'vg']]],
+ ['splicedhtsalignmentemitter_7278',['SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html',1,'vg']]],
+ ['spliceregion_7279',['SpliceRegion',['../classvg_1_1SpliceRegion.html',1,'vg']]],
+ ['splicestats_7280',['SpliceStats',['../classvg_1_1SpliceStats.html',1,'vg']]],
+ ['sswaligner_7281',['SSWAligner',['../classvg_1_1SSWAligner.html',1,'vg']]],
+ ['stage_7282',['Stage',['../structvg_1_1Funnel_1_1Stage.html',1,'vg::Funnel']]],
+ ['stat_5fcollection_5ft_7283',['stat_collection_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['stat_5fset_5ft_7284',['stat_set_t',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['state_5fhash_7285',['state_hash',['../structvg_1_1state__hash.html',1,'vg']]],
+ ['statistics_7286',['Statistics',['../structvg_1_1Recombinator_1_1Statistics.html',1,'vg::Recombinator']]],
+ ['step_5fhandle_5ft_7287',['step_handle_t',['../structhandlegraph_1_1step__handle__t.html',1,'handlegraph']]],
+ ['strandsplitgraph_7288',['StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html',1,'vg']]],
+ ['streaminbuf_7289',['streaminbuf',['../classvg_1_1io_1_1streaminbuf.html',1,'vg::io']]],
+ ['streamindex_7290',['StreamIndex',['../classvg_1_1StreamIndex.html',1,'vg']]],
+ ['streamindex_3c_20vg_3a_3aalgorithms_3a_3agraph_20_3e_7291',['StreamIndex< vg::algorithms::Graph >',['../classvg_1_1StreamIndex.html',1,'vg']]],
+ ['streamindexbase_7292',['StreamIndexBase',['../classvg_1_1StreamIndexBase.html',1,'vg']]],
+ ['streamistream_7293',['streamistream',['../classvg_1_1io_1_1streamistream.html',1,'vg::io']]],
+ ['streammultiplexer_7294',['StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html',1,'vg::io']]],
+ ['streamsorter_7295',['StreamSorter',['../classvg_1_1StreamSorter.html',1,'vg']]],
+ ['string_5fhash_5fmap_7296',['string_hash_map',['../classvg_1_1string__hash__map.html',1,'vg']]],
+ ['string_5fhash_5fset_7297',['string_hash_set',['../classvg_1_1string__hash__set.html',1,'vg']]],
+ ['subchain_7298',['Subchain',['../structvg_1_1HaplotypePartitioner_1_1Subchain.html',1,'vg::HaplotypePartitioner::Subchain'],['../structvg_1_1Haplotypes_1_1Subchain.html',1,'vg::Haplotypes::Subchain']]],
+ ['subcommand_7299',['Subcommand',['../classvg_1_1subcommand_1_1Subcommand.html',1,'vg::subcommand']]],
+ ['subgraphexplainer_7300',['SubgraphExplainer',['../classvg_1_1SubgraphExplainer.html',1,'vg']]],
+ ['subgraphoverlay_7301',['SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html',1,'vg']]],
+ ['subhandlegraph_7302',['SubHandleGraph',['../classvg_1_1SubHandleGraph.html',1,'vg::SubHandleGraph'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html',1,'handlegraph::algorithms::SubHandleGraph']]],
+ ['subpath_7303',['Subpath',['../structvg_1_1Subpath.html',1,'vg']]],
+ ['subpath_5ft_7304',['subpath_t',['../classvg_1_1subpath__t.html',1,'vg']]],
+ ['subpathoverlay_7305',['SubpathOverlay',['../classvg_1_1SubpathOverlay.html',1,'vg']]],
+ ['summarystatistics_7306',['SummaryStatistics',['../structvg_1_1SummaryStatistics.html',1,'vg']]],
+ ['support_7307',['Support',['../structvg_1_1Support.html',1,'vg']]],
+ ['supportaugmentedgraph_7308',['SupportAugmentedGraph',['../structvg_1_1SupportAugmentedGraph.html',1,'vg']]],
+ ['supportbasedsnarlcaller_7309',['SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html',1,'vg']]],
+ ['supportrestrictedtraversalfinder_7310',['SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html',1,'vg']]],
+ ['surjectingalignmentemitter_7311',['SurjectingAlignmentEmitter',['../classvg_1_1SurjectingAlignmentEmitter.html',1,'vg']]],
+ ['surjector_7312',['Surjector',['../classvg_1_1Surjector.html',1,'vg']]],
+ ['swaphaplotypescommand_7313',['SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html',1,'vg']]]
];
diff --git a/search/classes_13.js b/search/classes_13.js
index f173468da1..7432aacba2 100644
--- a/search/classes_13.js
+++ b/search/classes_13.js
@@ -1,28 +1,28 @@
var searchData=
[
- ['tables_7312',['Tables',['../structvg_1_1io_1_1Registry_1_1Tables.html',1,'vg::io::Registry']]],
- ['targetvaluesearch_7313',['TargetValueSearch',['../classvg_1_1TargetValueSearch.html',1,'vg']]],
- ['thread_5fstate_5ft_7314',['thread_state_t',['../structvg_1_1Watchdog_1_1thread__state__t.html',1,'vg::Watchdog']]],
- ['tickchainlink_7315',['TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html',1,'vg::subcommand']]],
- ['tipanchoredmaxdistance_7316',['TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html',1,'vg']]],
- ['toplevelchain_7317',['TopLevelChain',['../structvg_1_1Haplotypes_1_1TopLevelChain.html',1,'vg::Haplotypes']]],
- ['tracedscore_7318',['TracedScore',['../classvg_1_1algorithms_1_1TracedScore.html',1,'vg::algorithms']]],
- ['transcript_7319',['Transcript',['../structvg_1_1Transcript.html',1,'vg']]],
- ['transcriptome_7320',['Transcriptome',['../classvg_1_1Transcriptome.html',1,'vg']]],
- ['transcriptpath_7321',['TranscriptPath',['../structvg_1_1TranscriptPath.html',1,'vg']]],
- ['translation_7322',['Translation',['../structvg_1_1Translation.html',1,'vg']]],
- ['translator_7323',['Translator',['../classvg_1_1Translator.html',1,'vg']]],
- ['traversalfinder_7324',['TraversalFinder',['../classvg_1_1TraversalFinder.html',1,'vg']]],
- ['traversalsupportcalculator_7325',['TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html',1,'vg']]],
- ['traversalsupportfinder_7326',['TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html',1,'vg']]],
- ['tree_7327',['Tree',['../structvg_1_1Tree.html',1,'vg']]],
- ['tree_5fitem_5ft_7328',['tree_item_t',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html',1,'vg::ZipCodeTree']]],
- ['treenode_7329',['TreeNode',['../structvg_1_1BitStringTree_1_1TreeNode.html',1,'vg::BitStringTree< Item >::TreeNode'],['../structvg_1_1TreeNode.html',1,'vg::TreeNode< T >']]],
- ['treesubgraph_7330',['TreeSubgraph',['../classvg_1_1TreeSubgraph.html',1,'vg']]],
- ['triviallyserializable_7331',['TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html',1,'handlegraph']]],
- ['trivialtraversalfinder_7332',['TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html',1,'vg']]],
- ['truncated_5fnormal_5fdistribution_7333',['truncated_normal_distribution',['../classvg_1_1truncated__normal__distribution.html',1,'vg']]],
- ['tsvalignmentemitter_7334',['TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html',1,'vg::io']]],
- ['tsvexplainer_7335',['TSVExplainer',['../classvg_1_1TSVExplainer.html',1,'vg']]],
- ['tvsclusterer_7336',['TVSClusterer',['../classvg_1_1TVSClusterer.html',1,'vg']]]
+ ['tables_7314',['Tables',['../structvg_1_1io_1_1Registry_1_1Tables.html',1,'vg::io::Registry']]],
+ ['targetvaluesearch_7315',['TargetValueSearch',['../classvg_1_1TargetValueSearch.html',1,'vg']]],
+ ['thread_5fstate_5ft_7316',['thread_state_t',['../structvg_1_1Watchdog_1_1thread__state__t.html',1,'vg::Watchdog']]],
+ ['tickchainlink_7317',['TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html',1,'vg::subcommand']]],
+ ['tipanchoredmaxdistance_7318',['TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html',1,'vg']]],
+ ['toplevelchain_7319',['TopLevelChain',['../structvg_1_1Haplotypes_1_1TopLevelChain.html',1,'vg::Haplotypes']]],
+ ['tracedscore_7320',['TracedScore',['../classvg_1_1algorithms_1_1TracedScore.html',1,'vg::algorithms']]],
+ ['transcript_7321',['Transcript',['../structvg_1_1Transcript.html',1,'vg']]],
+ ['transcriptome_7322',['Transcriptome',['../classvg_1_1Transcriptome.html',1,'vg']]],
+ ['transcriptpath_7323',['TranscriptPath',['../structvg_1_1TranscriptPath.html',1,'vg']]],
+ ['translation_7324',['Translation',['../structvg_1_1Translation.html',1,'vg']]],
+ ['translator_7325',['Translator',['../classvg_1_1Translator.html',1,'vg']]],
+ ['traversalfinder_7326',['TraversalFinder',['../classvg_1_1TraversalFinder.html',1,'vg']]],
+ ['traversalsupportcalculator_7327',['TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html',1,'vg']]],
+ ['traversalsupportfinder_7328',['TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html',1,'vg']]],
+ ['tree_7329',['Tree',['../structvg_1_1Tree.html',1,'vg']]],
+ ['tree_5fitem_5ft_7330',['tree_item_t',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html',1,'vg::ZipCodeTree']]],
+ ['treenode_7331',['TreeNode',['../structvg_1_1BitStringTree_1_1TreeNode.html',1,'vg::BitStringTree< Item >::TreeNode'],['../structvg_1_1TreeNode.html',1,'vg::TreeNode< T >']]],
+ ['treesubgraph_7332',['TreeSubgraph',['../classvg_1_1TreeSubgraph.html',1,'vg']]],
+ ['triviallyserializable_7333',['TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html',1,'handlegraph']]],
+ ['trivialtraversalfinder_7334',['TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html',1,'vg']]],
+ ['truncated_5fnormal_5fdistribution_7335',['truncated_normal_distribution',['../classvg_1_1truncated__normal__distribution.html',1,'vg']]],
+ ['tsvalignmentemitter_7336',['TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html',1,'vg::io']]],
+ ['tsvexplainer_7337',['TSVExplainer',['../classvg_1_1TSVExplainer.html',1,'vg']]],
+ ['tvsclusterer_7338',['TVSClusterer',['../classvg_1_1TVSClusterer.html',1,'vg']]]
];
diff --git a/search/classes_14.js b/search/classes_14.js
index e10bee7002..28a7e54112 100644
--- a/search/classes_14.js
+++ b/search/classes_14.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['uniform_5fint_5fdistribution_7337',['uniform_int_distribution',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
- ['uniform_5fint_5fdistribution_3c_20size_5ft_20_3e_7338',['uniform_int_distribution< size_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
- ['uniform_5fint_5fdistribution_3c_20uint8_5ft_20_3e_7339',['uniform_int_distribution< uint8_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
- ['uniform_5freal_5fdistribution_7340',['uniform_real_distribution',['../classvg_1_1uniform__real__distribution.html',1,'vg']]],
- ['uniform_5freal_5fdistribution_3c_20double_20_3e_7341',['uniform_real_distribution< double >',['../classvg_1_1uniform__real__distribution.html',1,'vg']]]
+ ['uniform_5fint_5fdistribution_7339',['uniform_int_distribution',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
+ ['uniform_5fint_5fdistribution_3c_20size_5ft_20_3e_7340',['uniform_int_distribution< size_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
+ ['uniform_5fint_5fdistribution_3c_20uint8_5ft_20_3e_7341',['uniform_int_distribution< uint8_t >',['../classvg_1_1uniform__int__distribution.html',1,'vg']]],
+ ['uniform_5freal_5fdistribution_7342',['uniform_real_distribution',['../classvg_1_1uniform__real__distribution.html',1,'vg']]],
+ ['uniform_5freal_5fdistribution_3c_20double_20_3e_7343',['uniform_real_distribution< double >',['../classvg_1_1uniform__real__distribution.html',1,'vg']]]
];
diff --git a/search/classes_15.js b/search/classes_15.js
index 6a6600ae1d..5c715848b2 100644
--- a/search/classes_15.js
+++ b/search/classes_15.js
@@ -1,27 +1,27 @@
var searchData=
[
- ['valuation_7342',['Valuation',['../structvg_1_1subcommand_1_1Valuation.html',1,'vg::subcommand']]],
- ['valueargspec_7343',['ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
- ['valueargspec_3c_20bool_2c_20receiver_20_3e_7344',['ValueArgSpec< bool, Receiver >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
- ['valueargspec_3c_20t_2c_20receiver_2c_20range_3c_20t_20_3e_20_3e_7345',['ValueArgSpec< T, Receiver, Range< T > >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
- ['variantadder_7346',['VariantAdder',['../classvg_1_1VariantAdder.html',1,'vg']]],
- ['varint_5fvector_5ft_7347',['varint_vector_t',['../structvg_1_1varint__vector__t.html',1,'vg']]],
- ['vcfbuffer_7348',['VcfBuffer',['../classvg_1_1VcfBuffer.html',1,'vg']]],
- ['vcfgenotyper_7349',['VCFGenotyper',['../classvg_1_1VCFGenotyper.html',1,'vg']]],
- ['vcfoutputcaller_7350',['VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html',1,'vg']]],
- ['vcfrecordconverter_7351',['VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html',1,'vg']]],
- ['vcfrecordfilter_7352',['VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html',1,'vg']]],
- ['vcftraversalfinder_7353',['VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html',1,'vg']]],
- ['vectorizablehandlegraph_7354',['VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html',1,'handlegraph']]],
- ['vectorizer_7355',['Vectorizer',['../classVectorizer.html',1,'']]],
- ['vectorview_7356',['VectorView',['../structvg_1_1VectorView.html',1,'vg']]],
- ['vectorviewinverse_7357',['VectorViewInverse',['../classvg_1_1VectorViewInverse.html',1,'vg']]],
- ['version_7358',['Version',['../classvg_1_1Version.html',1,'vg']]],
- ['vg_7359',['VG',['../classvg_1_1VG.html',1,'vg']]],
- ['vgalignmentemitter_7360',['VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html',1,'vg::io']]],
- ['vgindexes_7361',['VGIndexes',['../structvg_1_1VGIndexes.html',1,'vg']]],
- ['vgset_7362',['VGset',['../classvg_1_1VGset.html',1,'vg']]],
- ['visit_7363',['Visit',['../structvg_1_1Visit.html',1,'vg']]],
- ['viz_7364',['Viz',['../classvg_1_1Viz.html',1,'vg']]],
- ['vpkg_7365',['VPKG',['../classvg_1_1io_1_1VPKG.html',1,'vg::io']]]
+ ['valuation_7344',['Valuation',['../structvg_1_1subcommand_1_1Valuation.html',1,'vg::subcommand']]],
+ ['valueargspec_7345',['ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
+ ['valueargspec_3c_20bool_2c_20receiver_20_3e_7346',['ValueArgSpec< bool, Receiver >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
+ ['valueargspec_3c_20t_2c_20receiver_2c_20range_3c_20t_20_3e_20_3e_7347',['ValueArgSpec< T, Receiver, Range< T > >',['../structvg_1_1subcommand_1_1ValueArgSpec.html',1,'vg::subcommand']]],
+ ['variantadder_7348',['VariantAdder',['../classvg_1_1VariantAdder.html',1,'vg']]],
+ ['varint_5fvector_5ft_7349',['varint_vector_t',['../structvg_1_1varint__vector__t.html',1,'vg']]],
+ ['vcfbuffer_7350',['VcfBuffer',['../classvg_1_1VcfBuffer.html',1,'vg']]],
+ ['vcfgenotyper_7351',['VCFGenotyper',['../classvg_1_1VCFGenotyper.html',1,'vg']]],
+ ['vcfoutputcaller_7352',['VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html',1,'vg']]],
+ ['vcfrecordconverter_7353',['VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html',1,'vg']]],
+ ['vcfrecordfilter_7354',['VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html',1,'vg']]],
+ ['vcftraversalfinder_7355',['VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html',1,'vg']]],
+ ['vectorizablehandlegraph_7356',['VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html',1,'handlegraph']]],
+ ['vectorizer_7357',['Vectorizer',['../classVectorizer.html',1,'']]],
+ ['vectorview_7358',['VectorView',['../structvg_1_1VectorView.html',1,'vg']]],
+ ['vectorviewinverse_7359',['VectorViewInverse',['../classvg_1_1VectorViewInverse.html',1,'vg']]],
+ ['version_7360',['Version',['../classvg_1_1Version.html',1,'vg']]],
+ ['vg_7361',['VG',['../classvg_1_1VG.html',1,'vg']]],
+ ['vgalignmentemitter_7362',['VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html',1,'vg::io']]],
+ ['vgindexes_7363',['VGIndexes',['../structvg_1_1VGIndexes.html',1,'vg']]],
+ ['vgset_7364',['VGset',['../classvg_1_1VGset.html',1,'vg']]],
+ ['visit_7365',['Visit',['../structvg_1_1Visit.html',1,'vg']]],
+ ['viz_7366',['Viz',['../classvg_1_1Viz.html',1,'vg']]],
+ ['vpkg_7367',['VPKG',['../classvg_1_1io_1_1VPKG.html',1,'vg::io']]]
];
diff --git a/search/classes_16.js b/search/classes_16.js
index 5c48c9d92f..d79786dc7b 100644
--- a/search/classes_16.js
+++ b/search/classes_16.js
@@ -1,24 +1,24 @@
var searchData=
[
- ['walk_5ft_7366',['walk_t',['../structvg_1_1algorithms_1_1walk__t.html',1,'vg::algorithms']]],
- ['wang_5fhash_7367',['wang_hash',['../structvg_1_1wang__hash.html',1,'vg']]],
- ['wang_5fhash_3c_20handle_5ft_20_3e_7368',['wang_hash< handle_t >',['../structvg_1_1wang__hash_3_01handle__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_7369',['wang_hash< handlegraph::net_handle_t >',['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20net_5fidentifier_5ft_20_3e_7370',['wang_hash< net_identifier_t >',['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20nodeside_20_3e_7371',['wang_hash< NodeSide >',['../structvg_1_1wang__hash_3_01NodeSide_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20nodetraversal_20_3e_7372',['wang_hash< NodeTraversal >',['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20path_5fhandle_5ft_20_3e_7373',['wang_hash< path_handle_t >',['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20std_3a_3apair_3c_20a_2c_20b_20_3e_20_3e_7374',['wang_hash< std::pair< A, B > >',['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20t_20_2a_20_3e_7375',['wang_hash< T * >',['../structvg_1_1wang__hash_3_01T_01_5_01_4.html',1,'vg']]],
- ['wang_5fhash_3c_20t_2c_20typename_20std_3a_3aenable_5fif_3c_20std_3a_3ais_5fintegral_3c_20t_20_3e_3a_3avalue_20_3e_3a_3atype_20_3e_7376',['wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >',['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html',1,'vg']]],
- ['watchdog_7377',['Watchdog',['../classvg_1_1Watchdog.html',1,'vg']]],
- ['weightedgraph_7378',['WeightedGraph',['../structvg_1_1FlowSort_1_1WeightedGraph.html',1,'vg::FlowSort']]],
- ['wfaalignment_7379',['WFAAlignment',['../structvg_1_1WFAAlignment.html',1,'vg']]],
- ['wfaextender_7380',['WFAExtender',['../classvg_1_1WFAExtender.html',1,'vg']]],
- ['wfanode_7381',['WFANode',['../structvg_1_1WFANode.html',1,'vg']]],
- ['wfapoint_7382',['WFAPoint',['../structvg_1_1WFAPoint.html',1,'vg']]],
- ['wfatree_7383',['WFATree',['../classvg_1_1WFATree.html',1,'vg']]],
- ['wideningprng_7384',['WideningPRNG',['../classvg_1_1WideningPRNG.html',1,'vg']]],
- ['windowedvcfbuffer_7385',['WindowedVcfBuffer',['../classvg_1_1WindowedVcfBuffer.html',1,'vg']]],
- ['wrappingpositionscanner_7386',['WrappingPositionScanner',['../structvg_1_1WrappingPositionScanner.html',1,'vg']]]
+ ['walk_5ft_7368',['walk_t',['../structvg_1_1algorithms_1_1walk__t.html',1,'vg::algorithms']]],
+ ['wang_5fhash_7369',['wang_hash',['../structvg_1_1wang__hash.html',1,'vg']]],
+ ['wang_5fhash_3c_20handle_5ft_20_3e_7370',['wang_hash< handle_t >',['../structvg_1_1wang__hash_3_01handle__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_7371',['wang_hash< handlegraph::net_handle_t >',['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20net_5fidentifier_5ft_20_3e_7372',['wang_hash< net_identifier_t >',['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20nodeside_20_3e_7373',['wang_hash< NodeSide >',['../structvg_1_1wang__hash_3_01NodeSide_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20nodetraversal_20_3e_7374',['wang_hash< NodeTraversal >',['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20path_5fhandle_5ft_20_3e_7375',['wang_hash< path_handle_t >',['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20std_3a_3apair_3c_20a_2c_20b_20_3e_20_3e_7376',['wang_hash< std::pair< A, B > >',['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20t_20_2a_20_3e_7377',['wang_hash< T * >',['../structvg_1_1wang__hash_3_01T_01_5_01_4.html',1,'vg']]],
+ ['wang_5fhash_3c_20t_2c_20typename_20std_3a_3aenable_5fif_3c_20std_3a_3ais_5fintegral_3c_20t_20_3e_3a_3avalue_20_3e_3a_3atype_20_3e_7378',['wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >',['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html',1,'vg']]],
+ ['watchdog_7379',['Watchdog',['../classvg_1_1Watchdog.html',1,'vg']]],
+ ['weightedgraph_7380',['WeightedGraph',['../structvg_1_1FlowSort_1_1WeightedGraph.html',1,'vg::FlowSort']]],
+ ['wfaalignment_7381',['WFAAlignment',['../structvg_1_1WFAAlignment.html',1,'vg']]],
+ ['wfaextender_7382',['WFAExtender',['../classvg_1_1WFAExtender.html',1,'vg']]],
+ ['wfanode_7383',['WFANode',['../structvg_1_1WFANode.html',1,'vg']]],
+ ['wfapoint_7384',['WFAPoint',['../structvg_1_1WFAPoint.html',1,'vg']]],
+ ['wfatree_7385',['WFATree',['../classvg_1_1WFATree.html',1,'vg']]],
+ ['wideningprng_7386',['WideningPRNG',['../classvg_1_1WideningPRNG.html',1,'vg']]],
+ ['windowedvcfbuffer_7387',['WindowedVcfBuffer',['../classvg_1_1WindowedVcfBuffer.html',1,'vg']]],
+ ['wrappingpositionscanner_7388',['WrappingPositionScanner',['../structvg_1_1WrappingPositionScanner.html',1,'vg']]]
];
diff --git a/search/classes_17.js b/search/classes_17.js
index 1a5f7597ae..df40501e56 100644
--- a/search/classes_17.js
+++ b/search/classes_17.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['xdropaligner_7387',['XdropAligner',['../classvg_1_1XdropAligner.html',1,'vg']]],
- ['xg_7388',['XG',['../classxg_1_1XG.html',1,'xg']]],
- ['xgformaterror_7389',['XGFormatError',['../classxg_1_1XGFormatError.html',1,'xg']]],
- ['xgpath_7390',['XGPath',['../classxg_1_1XGPath.html',1,'xg']]]
+ ['xdropaligner_7389',['XdropAligner',['../classvg_1_1XdropAligner.html',1,'vg']]],
+ ['xg_7390',['XG',['../classxg_1_1XG.html',1,'xg']]],
+ ['xgformaterror_7391',['XGFormatError',['../classxg_1_1XGFormatError.html',1,'xg']]],
+ ['xgpath_7392',['XGPath',['../classxg_1_1XGPath.html',1,'xg']]]
];
diff --git a/search/classes_18.js b/search/classes_18.js
index 1997c3acb6..9fea1c6dc2 100644
--- a/search/classes_18.js
+++ b/search/classes_18.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['zipcode_7391',['ZipCode',['../classvg_1_1ZipCode.html',1,'vg']]],
- ['zipcodecollection_7392',['ZipCodeCollection',['../classvg_1_1ZipCodeCollection.html',1,'vg']]],
- ['zipcodeforest_7393',['ZipCodeForest',['../classvg_1_1ZipCodeForest.html',1,'vg']]],
- ['zipcodetree_7394',['ZipCodeTree',['../classvg_1_1ZipCodeTree.html',1,'vg']]]
+ ['zipcode_7393',['ZipCode',['../classvg_1_1ZipCode.html',1,'vg']]],
+ ['zipcodecollection_7394',['ZipCodeCollection',['../classvg_1_1ZipCodeCollection.html',1,'vg']]],
+ ['zipcodeforest_7395',['ZipCodeForest',['../classvg_1_1ZipCodeForest.html',1,'vg']]],
+ ['zipcodetree_7396',['ZipCodeTree',['../classvg_1_1ZipCodeTree.html',1,'vg']]]
];
diff --git a/search/classes_2.js b/search/classes_2.js
index 4e21840cab..40ad283a90 100644
--- a/search/classes_2.js
+++ b/search/classes_2.js
@@ -1,32 +1,32 @@
var searchData=
[
- ['cachedpackedtraversalsupportfinder_6885',['CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html',1,'vg']]],
- ['cacheentry_6886',['CacheEntry',['../structvg_1_1IndexedVG_1_1CacheEntry.html',1,'vg::IndexedVG']]],
- ['cactusside_6887',['CactusSide',['../structvg_1_1CactusSide.html',1,'vg']]],
- ['cactussnarlfinder_6888',['CactusSnarlFinder',['../classvg_1_1CactusSnarlFinder.html',1,'vg']]],
- ['callinfo_6889',['CallInfo',['../structvg_1_1SnarlCaller_1_1CallInfo.html',1,'vg::SnarlCaller']]],
- ['callrecord_6890',['CallRecord',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html',1,'vg::NestedFlowCaller']]],
- ['chain_5fcode_5ft_6891',['chain_code_t',['../structvg_1_1ZipCode_1_1chain__code__t.html',1,'vg::ZipCode']]],
- ['chainalignmentfailederror_6892',['ChainAlignmentFailedError',['../classvg_1_1ChainAlignmentFailedError.html',1,'vg']]],
- ['chainiterator_6893',['ChainIterator',['../structvg_1_1ChainIterator.html',1,'vg']]],
- ['child_5finfo_5ft_6894',['child_info_t',['../structvg_1_1ZipCodeForest_1_1child__info__t.html',1,'vg::ZipCodeForest']]],
- ['cluster_6895',['Cluster',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html',1,'vg::SnarlDistanceIndexClusterer']]],
- ['clusterhead_6896',['ClusterHead',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html',1,'vg::SnarlDistanceIndexClusterer']]],
- ['clusteringproblem_6897',['ClusteringProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html',1,'vg::SnarlDistanceIndexClusterer']]],
- ['colors_6898',['Colors',['../classvg_1_1Colors.html',1,'vg']]],
- ['compare_5fgaf_6899',['compare_gaf',['../structcompare__gaf.html',1,'']]],
- ['completedtranscriptpath_6900',['CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html',1,'vg']]],
- ['componentmindistanceclusterer_6901',['ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html',1,'vg']]],
- ['configurable_6902',['Configurable',['../classvg_1_1Configurable.html',1,'vg']]],
- ['configurableparser_6903',['ConfigurableParser',['../classvg_1_1ConfigurableParser.html',1,'vg']]],
- ['connection_6904',['Connection',['../structvg_1_1Connection.html',1,'vg']]],
- ['connection_5ft_6905',['connection_t',['../classvg_1_1connection__t.html',1,'vg']]],
- ['consistencycalculator_6906',['ConsistencyCalculator',['../classvg_1_1ConsistencyCalculator.html',1,'vg']]],
- ['const_5fiterator_6907',['const_iterator',['../structvg_1_1VectorView_1_1const__iterator.html',1,'vg::VectorView']]],
- ['constructedchunk_6908',['ConstructedChunk',['../structvg_1_1ConstructedChunk.html',1,'vg']]],
- ['constructor_6909',['Constructor',['../classvg_1_1Constructor.html',1,'vg']]],
- ['contractinggraph_6910',['ContractingGraph',['../classvg_1_1ContractingGraph.html',1,'vg']]],
- ['convertedhashgraph_6911',['ConvertedHashGraph',['../classvg_1_1io_1_1ConvertedHashGraph.html',1,'vg::io']]],
- ['count_5fback_5finserter_6912',['count_back_inserter',['../classvg_1_1count__back__inserter.html',1,'vg']]],
- ['counts_6913',['Counts',['../structvg_1_1Counts.html',1,'vg']]]
+ ['cachedpackedtraversalsupportfinder_6887',['CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html',1,'vg']]],
+ ['cacheentry_6888',['CacheEntry',['../structvg_1_1IndexedVG_1_1CacheEntry.html',1,'vg::IndexedVG']]],
+ ['cactusside_6889',['CactusSide',['../structvg_1_1CactusSide.html',1,'vg']]],
+ ['cactussnarlfinder_6890',['CactusSnarlFinder',['../classvg_1_1CactusSnarlFinder.html',1,'vg']]],
+ ['callinfo_6891',['CallInfo',['../structvg_1_1SnarlCaller_1_1CallInfo.html',1,'vg::SnarlCaller']]],
+ ['callrecord_6892',['CallRecord',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html',1,'vg::NestedFlowCaller']]],
+ ['chain_5fcode_5ft_6893',['chain_code_t',['../structvg_1_1ZipCode_1_1chain__code__t.html',1,'vg::ZipCode']]],
+ ['chainalignmentfailederror_6894',['ChainAlignmentFailedError',['../classvg_1_1ChainAlignmentFailedError.html',1,'vg']]],
+ ['chainiterator_6895',['ChainIterator',['../structvg_1_1ChainIterator.html',1,'vg']]],
+ ['child_5finfo_5ft_6896',['child_info_t',['../structvg_1_1ZipCodeForest_1_1child__info__t.html',1,'vg::ZipCodeForest']]],
+ ['cluster_6897',['Cluster',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['clusterhead_6898',['ClusterHead',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['clusteringproblem_6899',['ClusteringProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['colors_6900',['Colors',['../classvg_1_1Colors.html',1,'vg']]],
+ ['compare_5fgaf_6901',['compare_gaf',['../structcompare__gaf.html',1,'']]],
+ ['completedtranscriptpath_6902',['CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html',1,'vg']]],
+ ['componentmindistanceclusterer_6903',['ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html',1,'vg']]],
+ ['configurable_6904',['Configurable',['../classvg_1_1Configurable.html',1,'vg']]],
+ ['configurableparser_6905',['ConfigurableParser',['../classvg_1_1ConfigurableParser.html',1,'vg']]],
+ ['connection_6906',['Connection',['../structvg_1_1Connection.html',1,'vg']]],
+ ['connection_5ft_6907',['connection_t',['../classvg_1_1connection__t.html',1,'vg']]],
+ ['consistencycalculator_6908',['ConsistencyCalculator',['../classvg_1_1ConsistencyCalculator.html',1,'vg']]],
+ ['const_5fiterator_6909',['const_iterator',['../structvg_1_1VectorView_1_1const__iterator.html',1,'vg::VectorView']]],
+ ['constructedchunk_6910',['ConstructedChunk',['../structvg_1_1ConstructedChunk.html',1,'vg']]],
+ ['constructor_6911',['Constructor',['../classvg_1_1Constructor.html',1,'vg']]],
+ ['contractinggraph_6912',['ContractingGraph',['../classvg_1_1ContractingGraph.html',1,'vg']]],
+ ['convertedhashgraph_6913',['ConvertedHashGraph',['../classvg_1_1io_1_1ConvertedHashGraph.html',1,'vg::io']]],
+ ['count_5fback_5finserter_6914',['count_back_inserter',['../classvg_1_1count__back__inserter.html',1,'vg']]],
+ ['counts_6915',['Counts',['../structvg_1_1Counts.html',1,'vg']]]
];
diff --git a/search/classes_3.js b/search/classes_3.js
index 80ea2d8d0c..04830b7bab 100644
--- a/search/classes_3.js
+++ b/search/classes_3.js
@@ -1,18 +1,18 @@
var searchData=
[
- ['dagifiedgraph_6914',['DagifiedGraph',['../classvg_1_1DagifiedGraph.html',1,'vg']]],
- ['decoder_5ft_6915',['decoder_t',['../structvg_1_1ZipCode_1_1decoder__t.html',1,'vg::ZipCode']]],
- ['deconstructor_6916',['Deconstructor',['../classvg_1_1Deconstructor.html',1,'vg']]],
- ['deflection_6917',['Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['deletablehandlegraph_6918',['DeletableHandleGraph',['../classhandlegraph_1_1DeletableHandleGraph.html',1,'handlegraph']]],
- ['deletehaplotypecommand_6919',['DeleteHaplotypeCommand',['../structvg_1_1DeleteHaplotypeCommand.html',1,'vg']]],
- ['deletionaligner_6920',['DeletionAligner',['../classvg_1_1DeletionAligner.html',1,'vg']]],
- ['diagramexplainer_6921',['DiagramExplainer',['../classvg_1_1DiagramExplainer.html',1,'vg']]],
- ['dinucleotidemachine_6922',['DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html',1,'vg']]],
- ['discrete_5fdistribution_6923',['discrete_distribution',['../classvg_1_1discrete__distribution.html',1,'vg']]],
- ['distanceheuristic_6924',['DistanceHeuristic',['../classvg_1_1DistanceHeuristic.html',1,'vg']]],
- ['dotdumpexplainer_6925',['DotDumpExplainer',['../classvg_1_1DotDumpExplainer.html',1,'vg']]],
- ['dozeuinterface_6926',['DozeuInterface',['../classvg_1_1DozeuInterface.html',1,'vg']]],
- ['dozeupinningoverlay_6927',['DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html',1,'vg']]],
- ['dpscorecomparator_6928',['DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html',1,'vg::MEMClusterer']]]
+ ['dagifiedgraph_6916',['DagifiedGraph',['../classvg_1_1DagifiedGraph.html',1,'vg']]],
+ ['decoder_5ft_6917',['decoder_t',['../structvg_1_1ZipCode_1_1decoder__t.html',1,'vg::ZipCode']]],
+ ['deconstructor_6918',['Deconstructor',['../classvg_1_1Deconstructor.html',1,'vg']]],
+ ['deflection_6919',['Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['deletablehandlegraph_6920',['DeletableHandleGraph',['../classhandlegraph_1_1DeletableHandleGraph.html',1,'handlegraph']]],
+ ['deletehaplotypecommand_6921',['DeleteHaplotypeCommand',['../structvg_1_1DeleteHaplotypeCommand.html',1,'vg']]],
+ ['deletionaligner_6922',['DeletionAligner',['../classvg_1_1DeletionAligner.html',1,'vg']]],
+ ['diagramexplainer_6923',['DiagramExplainer',['../classvg_1_1DiagramExplainer.html',1,'vg']]],
+ ['dinucleotidemachine_6924',['DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html',1,'vg']]],
+ ['discrete_5fdistribution_6925',['discrete_distribution',['../classvg_1_1discrete__distribution.html',1,'vg']]],
+ ['distanceheuristic_6926',['DistanceHeuristic',['../classvg_1_1DistanceHeuristic.html',1,'vg']]],
+ ['dotdumpexplainer_6927',['DotDumpExplainer',['../classvg_1_1DotDumpExplainer.html',1,'vg']]],
+ ['dozeuinterface_6928',['DozeuInterface',['../classvg_1_1DozeuInterface.html',1,'vg']]],
+ ['dozeupinningoverlay_6929',['DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html',1,'vg']]],
+ ['dpscorecomparator_6930',['DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html',1,'vg::MEMClusterer']]]
];
diff --git a/search/classes_4.js b/search/classes_4.js
index ca52a57e17..31c01b0a9e 100644
--- a/search/classes_4.js
+++ b/search/classes_4.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['edge_6929',['Edge',['../structvg_1_1Edge.html',1,'vg::Edge'],['../structvg_1_1algorithms_1_1Edge.html',1,'vg::algorithms::Edge']]],
- ['edgepileup_6930',['EdgePileup',['../structvg_1_1EdgePileup.html',1,'vg']]],
- ['edit_6931',['Edit',['../structvg_1_1Edit.html',1,'vg']]],
- ['edit_5ft_6932',['edit_t',['../classvg_1_1edit__t.html',1,'vg']]],
- ['editedtranscriptpath_6933',['EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html',1,'vg']]],
- ['endianness_6934',['endianness',['../structvg_1_1endianness.html',1,'vg']]],
- ['errormodel_6935',['ErrorModel',['../structvg_1_1WFAExtender_1_1ErrorModel.html',1,'vg::WFAExtender']]],
- ['event_6936',['Event',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html',1,'vg::WFAExtender::ErrorModel']]],
- ['exhaustivetraversalfinder_6937',['ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html',1,'vg']]],
- ['exon_6938',['Exon',['../structvg_1_1Exon.html',1,'vg']]],
- ['expandingoverlaygraph_6939',['ExpandingOverlayGraph',['../classhandlegraph_1_1ExpandingOverlayGraph.html',1,'handlegraph']]],
- ['explainer_6940',['Explainer',['../classvg_1_1Explainer.html',1,'vg']]],
- ['extranodegraph_6941',['ExtraNodeGraph',['../classvg_1_1ExtraNodeGraph.html',1,'vg']]]
+ ['edge_6931',['Edge',['../structvg_1_1Edge.html',1,'vg::Edge'],['../structvg_1_1algorithms_1_1Edge.html',1,'vg::algorithms::Edge']]],
+ ['edgepileup_6932',['EdgePileup',['../structvg_1_1EdgePileup.html',1,'vg']]],
+ ['edit_6933',['Edit',['../structvg_1_1Edit.html',1,'vg']]],
+ ['edit_5ft_6934',['edit_t',['../classvg_1_1edit__t.html',1,'vg']]],
+ ['editedtranscriptpath_6935',['EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html',1,'vg']]],
+ ['endianness_6936',['endianness',['../structvg_1_1endianness.html',1,'vg']]],
+ ['errormodel_6937',['ErrorModel',['../structvg_1_1WFAExtender_1_1ErrorModel.html',1,'vg::WFAExtender']]],
+ ['event_6938',['Event',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html',1,'vg::WFAExtender::ErrorModel']]],
+ ['exhaustivetraversalfinder_6939',['ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html',1,'vg']]],
+ ['exon_6940',['Exon',['../structvg_1_1Exon.html',1,'vg']]],
+ ['expandingoverlaygraph_6941',['ExpandingOverlayGraph',['../classhandlegraph_1_1ExpandingOverlayGraph.html',1,'handlegraph']]],
+ ['explainer_6942',['Explainer',['../classvg_1_1Explainer.html',1,'vg']]],
+ ['extranodegraph_6943',['ExtraNodeGraph',['../classvg_1_1ExtraNodeGraph.html',1,'vg']]]
];
diff --git a/search/classes_5.js b/search/classes_5.js
index f65f6cf722..c17332a376 100644
--- a/search/classes_5.js
+++ b/search/classes_5.js
@@ -1,22 +1,22 @@
var searchData=
[
- ['fcmp_6942',['FCmp',['../structvg_1_1IncrementalSubgraph_1_1FCmp.html',1,'vg::IncrementalSubgraph']]],
- ['fdinbuf_6943',['fdinbuf',['../classvg_1_1io_1_1fdinbuf.html',1,'vg::io']]],
- ['fdistream_6944',['fdistream',['../classvg_1_1io_1_1fdistream.html',1,'vg::io']]],
- ['fdostream_6945',['fdostream',['../classvg_1_1io_1_1fdostream.html',1,'vg::io']]],
- ['fdoutbuf_6946',['fdoutbuf',['../classvg_1_1io_1_1fdoutbuf.html',1,'vg::io']]],
- ['feature_6947',['Feature',['../structvg_1_1FeatureSet_1_1Feature.html',1,'vg::FeatureSet']]],
- ['featureset_6948',['FeatureSet',['../classvg_1_1FeatureSet.html',1,'vg']]],
- ['filter_6949',['Filter',['../classvg_1_1Filter.html',1,'vg']]],
- ['filterperformance_6950',['FilterPerformance',['../structvg_1_1Funnel_1_1FilterPerformance.html',1,'vg::Funnel']]],
- ['fixedgenotypepriorcalculator_6951',['FixedGenotypePriorCalculator',['../classvg_1_1FixedGenotypePriorCalculator.html',1,'vg']]],
- ['flagargspec_6952',['FlagArgSpec',['../structvg_1_1subcommand_1_1FlagArgSpec.html',1,'vg::subcommand']]],
- ['flatfilebacktranslation_6953',['FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html',1,'vg']]],
- ['flowcaller_6954',['FlowCaller',['../classvg_1_1FlowCaller.html',1,'vg']]],
- ['flowsort_6955',['FlowSort',['../classvg_1_1FlowSort.html',1,'vg']]],
- ['flowtraversalfinder_6956',['FlowTraversalFinder',['../classvg_1_1FlowTraversalFinder.html',1,'vg']]],
- ['forest_5fgrowing_5fstate_5ft_6957',['forest_growing_state_t',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html',1,'vg::ZipCodeForest']]],
- ['fragmentlengthdistribution_6958',['FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html',1,'vg']]],
- ['fragmentlengthstatistics_6959',['FragmentLengthStatistics',['../classvg_1_1FragmentLengthStatistics.html',1,'vg']]],
- ['funnel_6960',['Funnel',['../classvg_1_1Funnel.html',1,'vg']]]
+ ['fcmp_6944',['FCmp',['../structvg_1_1IncrementalSubgraph_1_1FCmp.html',1,'vg::IncrementalSubgraph']]],
+ ['fdinbuf_6945',['fdinbuf',['../classvg_1_1io_1_1fdinbuf.html',1,'vg::io']]],
+ ['fdistream_6946',['fdistream',['../classvg_1_1io_1_1fdistream.html',1,'vg::io']]],
+ ['fdostream_6947',['fdostream',['../classvg_1_1io_1_1fdostream.html',1,'vg::io']]],
+ ['fdoutbuf_6948',['fdoutbuf',['../classvg_1_1io_1_1fdoutbuf.html',1,'vg::io']]],
+ ['feature_6949',['Feature',['../structvg_1_1FeatureSet_1_1Feature.html',1,'vg::FeatureSet']]],
+ ['featureset_6950',['FeatureSet',['../classvg_1_1FeatureSet.html',1,'vg']]],
+ ['filter_6951',['Filter',['../classvg_1_1Filter.html',1,'vg']]],
+ ['filterperformance_6952',['FilterPerformance',['../structvg_1_1Funnel_1_1FilterPerformance.html',1,'vg::Funnel']]],
+ ['fixedgenotypepriorcalculator_6953',['FixedGenotypePriorCalculator',['../classvg_1_1FixedGenotypePriorCalculator.html',1,'vg']]],
+ ['flagargspec_6954',['FlagArgSpec',['../structvg_1_1subcommand_1_1FlagArgSpec.html',1,'vg::subcommand']]],
+ ['flatfilebacktranslation_6955',['FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html',1,'vg']]],
+ ['flowcaller_6956',['FlowCaller',['../classvg_1_1FlowCaller.html',1,'vg']]],
+ ['flowsort_6957',['FlowSort',['../classvg_1_1FlowSort.html',1,'vg']]],
+ ['flowtraversalfinder_6958',['FlowTraversalFinder',['../classvg_1_1FlowTraversalFinder.html',1,'vg']]],
+ ['forest_5fgrowing_5fstate_5ft_6959',['forest_growing_state_t',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html',1,'vg::ZipCodeForest']]],
+ ['fragmentlengthdistribution_6960',['FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html',1,'vg']]],
+ ['fragmentlengthstatistics_6961',['FragmentLengthStatistics',['../classvg_1_1FragmentLengthStatistics.html',1,'vg']]],
+ ['funnel_6962',['Funnel',['../classvg_1_1Funnel.html',1,'vg']]]
];
diff --git a/search/classes_6.js b/search/classes_6.js
index 56ff208b98..0017f9387b 100644
--- a/search/classes_6.js
+++ b/search/classes_6.js
@@ -1,40 +1,40 @@
var searchData=
[
- ['gafalignmentemitter_6961',['GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html',1,'vg::io']]],
- ['gaffile_6962',['GafFile',['../structGafFile.html',1,'']]],
- ['gafoutputcaller_6963',['GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html',1,'vg']]],
- ['gafrecord_6964',['GafRecord',['../structgafkluge_1_1GafRecord.html',1,'gafkluge']]],
- ['gafstep_6965',['GafStep',['../structgafkluge_1_1GafStep.html',1,'gafkluge']]],
- ['gaplessextender_6966',['GaplessExtender',['../classvg_1_1GaplessExtender.html',1,'vg']]],
- ['gaplessextension_6967',['GaplessExtension',['../structvg_1_1GaplessExtension.html',1,'vg']]],
- ['gbwt_5fthread_5ft_6968',['gbwt_thread_t',['../structhaplo_1_1gbwt__thread__t.html',1,'haplo']]],
- ['gbwtconfig_6969',['GBWTConfig',['../structGBWTConfig.html',1,'']]],
- ['gbwthandler_6970',['GBWTHandler',['../structvg_1_1GBWTHandler.html',1,'vg']]],
- ['gbwtscoreprovider_6971',['GBWTScoreProvider',['../classhaplo_1_1GBWTScoreProvider.html',1,'haplo']]],
- ['gbwttraversalfinder_6972',['GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html',1,'vg']]],
- ['gbzgraph_6973',['GBZGraph',['../classvg_1_1GBZGraph.html',1,'vg']]],
- ['genomestate_6974',['GenomeState',['../classvg_1_1GenomeState.html',1,'vg']]],
- ['genomestatecommand_6975',['GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html',1,'vg']]],
- ['genotype_6976',['Genotype',['../structvg_1_1Genotype.html',1,'vg']]],
- ['genotypelikelihoodcalculator_6977',['GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html',1,'vg']]],
- ['genotypepriorcalculator_6978',['GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html',1,'vg']]],
- ['genotyper_6979',['Genotyper',['../classvg_1_1Genotyper.html',1,'vg']]],
- ['gfaduplicatepatherror_6980',['GFADuplicatePathError',['../structvg_1_1algorithms_1_1GFADuplicatePathError.html',1,'vg::algorithms']]],
- ['gfaformaterror_6981',['GFAFormatError',['../structvg_1_1algorithms_1_1GFAFormatError.html',1,'vg::algorithms']]],
- ['gfahandlegraph_6982',['GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html',1,'vg']]],
- ['gfaidmapinfo_6983',['GFAIDMapInfo',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html',1,'vg::algorithms']]],
- ['gfaparser_6984',['GFAParser',['../classvg_1_1algorithms_1_1GFAParser.html',1,'vg::algorithms']]],
- ['gffreader_6985',['GFFReader',['../classvg_1_1GFFReader.html',1,'vg']]],
- ['gffrecord_6986',['GFFRecord',['../structvg_1_1GFFRecord.html',1,'vg']]],
- ['giraffemainoptions_6987',['GiraffeMainOptions',['../structGiraffeMainOptions.html',1,'']]],
- ['graph_6988',['Graph',['../structvg_1_1Graph.html',1,'vg::Graph'],['../structvg_1_1algorithms_1_1Graph.html',1,'vg::algorithms::Graph']]],
- ['graph_5fpos_5fs_6989',['graph_pos_s',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html',1,'vg::DozeuInterface']]],
- ['graphcaller_6990',['GraphCaller',['../classvg_1_1GraphCaller.html',1,'vg']]],
- ['graphhandler_6991',['GraphHandler',['../structGraphHandler.html',1,'']]],
- ['graphsynchronizer_6992',['GraphSynchronizer',['../classvg_1_1GraphSynchronizer.html',1,'vg']]],
- ['greater_5fgaffile_6993',['greater_gaffile',['../structgreater__gaffile.html',1,'']]],
- ['greedymindistanceclusterer_6994',['GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html',1,'vg']]],
- ['groupedoptiongroup_6995',['GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html',1,'vg::subcommand']]],
- ['growth_6996',['Growth',['../structvg_1_1FlowSort_1_1Growth.html',1,'vg::FlowSort']]],
- ['gsswaligner_6997',['GSSWAligner',['../classvg_1_1GSSWAligner.html',1,'vg']]]
+ ['gafalignmentemitter_6963',['GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html',1,'vg::io']]],
+ ['gaffile_6964',['GafFile',['../structGafFile.html',1,'']]],
+ ['gafoutputcaller_6965',['GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html',1,'vg']]],
+ ['gafrecord_6966',['GafRecord',['../structgafkluge_1_1GafRecord.html',1,'gafkluge']]],
+ ['gafstep_6967',['GafStep',['../structgafkluge_1_1GafStep.html',1,'gafkluge']]],
+ ['gaplessextender_6968',['GaplessExtender',['../classvg_1_1GaplessExtender.html',1,'vg']]],
+ ['gaplessextension_6969',['GaplessExtension',['../structvg_1_1GaplessExtension.html',1,'vg']]],
+ ['gbwt_5fthread_5ft_6970',['gbwt_thread_t',['../structhaplo_1_1gbwt__thread__t.html',1,'haplo']]],
+ ['gbwtconfig_6971',['GBWTConfig',['../structGBWTConfig.html',1,'']]],
+ ['gbwthandler_6972',['GBWTHandler',['../structvg_1_1GBWTHandler.html',1,'vg']]],
+ ['gbwtscoreprovider_6973',['GBWTScoreProvider',['../classhaplo_1_1GBWTScoreProvider.html',1,'haplo']]],
+ ['gbwttraversalfinder_6974',['GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html',1,'vg']]],
+ ['gbzgraph_6975',['GBZGraph',['../classvg_1_1GBZGraph.html',1,'vg']]],
+ ['genomestate_6976',['GenomeState',['../classvg_1_1GenomeState.html',1,'vg']]],
+ ['genomestatecommand_6977',['GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html',1,'vg']]],
+ ['genotype_6978',['Genotype',['../structvg_1_1Genotype.html',1,'vg']]],
+ ['genotypelikelihoodcalculator_6979',['GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html',1,'vg']]],
+ ['genotypepriorcalculator_6980',['GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html',1,'vg']]],
+ ['genotyper_6981',['Genotyper',['../classvg_1_1Genotyper.html',1,'vg']]],
+ ['gfaduplicatepatherror_6982',['GFADuplicatePathError',['../structvg_1_1algorithms_1_1GFADuplicatePathError.html',1,'vg::algorithms']]],
+ ['gfaformaterror_6983',['GFAFormatError',['../structvg_1_1algorithms_1_1GFAFormatError.html',1,'vg::algorithms']]],
+ ['gfahandlegraph_6984',['GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html',1,'vg']]],
+ ['gfaidmapinfo_6985',['GFAIDMapInfo',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html',1,'vg::algorithms']]],
+ ['gfaparser_6986',['GFAParser',['../classvg_1_1algorithms_1_1GFAParser.html',1,'vg::algorithms']]],
+ ['gffreader_6987',['GFFReader',['../classvg_1_1GFFReader.html',1,'vg']]],
+ ['gffrecord_6988',['GFFRecord',['../structvg_1_1GFFRecord.html',1,'vg']]],
+ ['giraffemainoptions_6989',['GiraffeMainOptions',['../structGiraffeMainOptions.html',1,'']]],
+ ['graph_6990',['Graph',['../structvg_1_1Graph.html',1,'vg::Graph'],['../structvg_1_1algorithms_1_1Graph.html',1,'vg::algorithms::Graph']]],
+ ['graph_5fpos_5fs_6991',['graph_pos_s',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html',1,'vg::DozeuInterface']]],
+ ['graphcaller_6992',['GraphCaller',['../classvg_1_1GraphCaller.html',1,'vg']]],
+ ['graphhandler_6993',['GraphHandler',['../structGraphHandler.html',1,'']]],
+ ['graphsynchronizer_6994',['GraphSynchronizer',['../classvg_1_1GraphSynchronizer.html',1,'vg']]],
+ ['greater_5fgaffile_6995',['greater_gaffile',['../structgreater__gaffile.html',1,'']]],
+ ['greedymindistanceclusterer_6996',['GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html',1,'vg']]],
+ ['groupedoptiongroup_6997',['GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html',1,'vg::subcommand']]],
+ ['growth_6998',['Growth',['../structvg_1_1FlowSort_1_1Growth.html',1,'vg::FlowSort']]],
+ ['gsswaligner_6999',['GSSWAligner',['../classvg_1_1GSSWAligner.html',1,'vg']]]
];
diff --git a/search/classes_7.js b/search/classes_7.js
index d77b9288c3..766f399deb 100644
--- a/search/classes_7.js
+++ b/search/classes_7.js
@@ -1,54 +1,54 @@
var searchData=
[
- ['handle_5ft_6998',['handle_t',['../structhandlegraph_1_1handle__t.html',1,'handlegraph']]],
- ['handlegraph_6999',['HandleGraph',['../classhandlegraph_1_1HandleGraph.html',1,'handlegraph']]],
- ['handlegraphnodeset_7000',['HandleGraphNodeSet',['../classvg_1_1HandleGraphNodeSet.html',1,'vg']]],
- ['handlegraphsnarlfinder_7001',['HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html',1,'vg']]],
- ['handler_7002',['Handler',['../structvg_1_1temp__file_1_1Handler.html',1,'vg::temp_file::Handler'],['../structxg_1_1temp__file_1_1Handler.html',1,'xg::temp_file::Handler']]],
- ['haplo_5fdp_7003',['haplo_DP',['../structhaplo_1_1haplo__DP.html',1,'haplo']]],
- ['haplo_5fdp_5fcolumn_7004',['haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html',1,'haplo']]],
- ['haplo_5fdp_5frectangle_7005',['haplo_DP_rectangle',['../structhaplo_1_1haplo__DP__rectangle.html',1,'haplo']]],
- ['haplotype_7006',['Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html',1,'vg::PhasedGenome']]],
- ['haplotypeindexer_7007',['HaplotypeIndexer',['../classvg_1_1HaplotypeIndexer.html',1,'vg']]],
- ['haplotypenode_7008',['HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html',1,'vg::PhasedGenome']]],
- ['haplotypepartitioner_7009',['HaplotypePartitioner',['../classvg_1_1HaplotypePartitioner.html',1,'vg']]],
- ['haplotypes_7010',['Haplotypes',['../classvg_1_1Haplotypes.html',1,'vg']]],
- ['haplotypesconfig_7011',['HaplotypesConfig',['../structHaplotypesConfig.html',1,'']]],
- ['hash_3c_20const_20vg_3a_3asnarl_20_3e_7012',['hash< const vg::Snarl >',['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3aedge_5ft_20_3e_7013',['hash< handlegraph::edge_t >',['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3ahandle_5ft_20_3e_7014',['hash< handlegraph::handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_7015',['hash< handlegraph::net_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3apath_5fhandle_5ft_20_3e_7016',['hash< handlegraph::path_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html',1,'std']]],
- ['hash_3c_20handlegraph_3a_3astep_5fhandle_5ft_20_3e_7017',['hash< handlegraph::step_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html',1,'std']]],
- ['hash_3c_20pair_3c_20a_2c_20b_20_3e_20_3e_7018',['hash< pair< A, B > >',['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html',1,'std']]],
- ['hash_3c_20std_3a_3atuple_3c_20tt_2e_2e_2e_20_3e_20_3e_7019',['hash< std::tuple< TT... > >',['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3anodeside_20_3e_7020',['hash< vg::NodeSide >',['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3anodetraversal_20_3e_7021',['hash< vg::NodeTraversal >',['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3azipcodetree_3a_3aoriented_5fseed_5ft_20_3e_7022',['hash< vg::ZipCodeTree::oriented_seed_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html',1,'std']]],
- ['hash_3c_20vg_3a_3azipcodetree_3a_3aseed_5fresult_5ft_20_3e_7023',['hash< vg::ZipCodeTree::seed_result_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html',1,'std']]],
- ['hash_5fambiguous_5fallele_5fset_7024',['hash_ambiguous_allele_set',['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html',1,'vg::Genotyper']]],
- ['hash_5fmap_7025',['hash_map',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20const_20vg_3a_3amapping_5ft_20_2a_2c_20pair_3c_20list_3c_20vg_3a_3amapping_5ft_20_3e_3a_3aiterator_2c_20int64_5ft_20_3e_20_3e_7026',['hash_map< const vg::mapping_t *, pair< list< vg::mapping_t >::iterator, int64_t > >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20handlegraph_3a_3anet_5fhandle_5ft_2c_20size_5ft_20_3e_7027',['hash_map< handlegraph::net_handle_t, size_t >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20id_5ft_2c_20map_3c_20int64_5ft_2c_20set_3c_20vg_3a_3amapping_5ft_20_2a_20_3e_20_3e_20_3e_7028',['hash_map< id_t, map< int64_t, set< vg::mapping_t * > > >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20k_20_2a_2c_20v_20_3e_7029',['hash_map< K *, V >',['../classvg_1_1hash__map_3_01K_01_5_00_01V_01_4.html',1,'vg']]],
- ['hash_5fmap_3c_20nid_5ft_2c_20vector_3c_20pair_3c_20nid_5ft_2c_20bool_20_3e_20_3e_20_3e_7030',['hash_map< nid_t, vector< pair< nid_t, bool > > >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20nid_5ft_2c_20vg_3a_3anode_20_2a_20_3e_7031',['hash_map< nid_t, vg::Node * >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20vg_3a_3aedge_20_2a_2c_20int_20_3e_7032',['hash_map< vg::Edge *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fmap_3c_20vg_3a_3anode_20_2a_2c_20int_20_3e_7033',['hash_map< vg::Node *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
- ['hash_5fnode_5ftraversal_7034',['hash_node_traversal',['../structvg_1_1Genotyper_1_1hash__node__traversal.html',1,'vg::Genotyper']]],
- ['hash_5foriented_5fedge_7035',['hash_oriented_edge',['../structvg_1_1Genotyper_1_1hash__oriented__edge.html',1,'vg::Genotyper']]],
- ['hash_5fset_7036',['hash_set',['../classvg_1_1hash__set.html',1,'vg']]],
- ['hash_5fset_3c_20k_20_2a_20_3e_7037',['hash_set< K * >',['../classvg_1_1hash__set_3_01K_01_5_01_4.html',1,'vg']]],
- ['hash_5fset_3c_20pair_3c_20size_5ft_2c_20size_5ft_20_3e_20_3e_7038',['hash_set< pair< size_t, size_t > >',['../classvg_1_1hash__set.html',1,'vg']]],
- ['hash_5fset_3c_20vg_3a_3aid_5ft_20_3e_7039',['hash_set< vg::id_t >',['../classvg_1_1hash__set.html',1,'vg']]],
- ['hdp_5fgbwt_5fgraph_5faccessor_7040',['hDP_gbwt_graph_accessor',['../classhaplo_1_1hDP__gbwt__graph__accessor.html',1,'haplo']]],
- ['header_7041',['Header',['../structvg_1_1Haplotypes_1_1Header.html',1,'vg::Haplotypes']]],
- ['hfile_5fbackend_7042',['hFILE_backend',['../structhFILE__backend.html',1,'']]],
- ['hfile_5fcppstream_7043',['hFILE_cppstream',['../structvg_1_1io_1_1hFILE__cppstream.html',1,'vg::io']]],
- ['hitedge_7044',['HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html',1,'vg::MEMClusterer']]],
- ['hitgraph_7045',['HitGraph',['../classvg_1_1MEMClusterer_1_1HitGraph.html',1,'vg::MEMClusterer']]],
- ['hitnode_7046',['HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html',1,'vg::MEMClusterer']]],
- ['htsalignmentemitter_7047',['HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html',1,'vg']]],
- ['htswriter_7048',['HTSWriter',['../classvg_1_1HTSWriter.html',1,'vg']]]
+ ['handle_5ft_7000',['handle_t',['../structhandlegraph_1_1handle__t.html',1,'handlegraph']]],
+ ['handlegraph_7001',['HandleGraph',['../classhandlegraph_1_1HandleGraph.html',1,'handlegraph']]],
+ ['handlegraphnodeset_7002',['HandleGraphNodeSet',['../classvg_1_1HandleGraphNodeSet.html',1,'vg']]],
+ ['handlegraphsnarlfinder_7003',['HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html',1,'vg']]],
+ ['handler_7004',['Handler',['../structvg_1_1temp__file_1_1Handler.html',1,'vg::temp_file::Handler'],['../structxg_1_1temp__file_1_1Handler.html',1,'xg::temp_file::Handler']]],
+ ['haplo_5fdp_7005',['haplo_DP',['../structhaplo_1_1haplo__DP.html',1,'haplo']]],
+ ['haplo_5fdp_5fcolumn_7006',['haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html',1,'haplo']]],
+ ['haplo_5fdp_5frectangle_7007',['haplo_DP_rectangle',['../structhaplo_1_1haplo__DP__rectangle.html',1,'haplo']]],
+ ['haplotype_7008',['Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html',1,'vg::PhasedGenome']]],
+ ['haplotypeindexer_7009',['HaplotypeIndexer',['../classvg_1_1HaplotypeIndexer.html',1,'vg']]],
+ ['haplotypenode_7010',['HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html',1,'vg::PhasedGenome']]],
+ ['haplotypepartitioner_7011',['HaplotypePartitioner',['../classvg_1_1HaplotypePartitioner.html',1,'vg']]],
+ ['haplotypes_7012',['Haplotypes',['../classvg_1_1Haplotypes.html',1,'vg']]],
+ ['haplotypesconfig_7013',['HaplotypesConfig',['../structHaplotypesConfig.html',1,'']]],
+ ['hash_3c_20const_20vg_3a_3asnarl_20_3e_7014',['hash< const vg::Snarl >',['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3aedge_5ft_20_3e_7015',['hash< handlegraph::edge_t >',['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3ahandle_5ft_20_3e_7016',['hash< handlegraph::handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3anet_5fhandle_5ft_20_3e_7017',['hash< handlegraph::net_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3apath_5fhandle_5ft_20_3e_7018',['hash< handlegraph::path_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20handlegraph_3a_3astep_5fhandle_5ft_20_3e_7019',['hash< handlegraph::step_handle_t >',['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html',1,'std']]],
+ ['hash_3c_20pair_3c_20a_2c_20b_20_3e_20_3e_7020',['hash< pair< A, B > >',['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html',1,'std']]],
+ ['hash_3c_20std_3a_3atuple_3c_20tt_2e_2e_2e_20_3e_20_3e_7021',['hash< std::tuple< TT... > >',['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3anodeside_20_3e_7022',['hash< vg::NodeSide >',['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3anodetraversal_20_3e_7023',['hash< vg::NodeTraversal >',['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3azipcodetree_3a_3aoriented_5fseed_5ft_20_3e_7024',['hash< vg::ZipCodeTree::oriented_seed_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html',1,'std']]],
+ ['hash_3c_20vg_3a_3azipcodetree_3a_3aseed_5fresult_5ft_20_3e_7025',['hash< vg::ZipCodeTree::seed_result_t >',['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html',1,'std']]],
+ ['hash_5fambiguous_5fallele_5fset_7026',['hash_ambiguous_allele_set',['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html',1,'vg::Genotyper']]],
+ ['hash_5fmap_7027',['hash_map',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20const_20vg_3a_3amapping_5ft_20_2a_2c_20pair_3c_20list_3c_20vg_3a_3amapping_5ft_20_3e_3a_3aiterator_2c_20int64_5ft_20_3e_20_3e_7028',['hash_map< const vg::mapping_t *, pair< list< vg::mapping_t >::iterator, int64_t > >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20handlegraph_3a_3anet_5fhandle_5ft_2c_20size_5ft_20_3e_7029',['hash_map< handlegraph::net_handle_t, size_t >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20id_5ft_2c_20map_3c_20int64_5ft_2c_20set_3c_20vg_3a_3amapping_5ft_20_2a_20_3e_20_3e_20_3e_7030',['hash_map< id_t, map< int64_t, set< vg::mapping_t * > > >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20k_20_2a_2c_20v_20_3e_7031',['hash_map< K *, V >',['../classvg_1_1hash__map_3_01K_01_5_00_01V_01_4.html',1,'vg']]],
+ ['hash_5fmap_3c_20nid_5ft_2c_20vector_3c_20pair_3c_20nid_5ft_2c_20bool_20_3e_20_3e_20_3e_7032',['hash_map< nid_t, vector< pair< nid_t, bool > > >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20nid_5ft_2c_20vg_3a_3anode_20_2a_20_3e_7033',['hash_map< nid_t, vg::Node * >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20vg_3a_3aedge_20_2a_2c_20int_20_3e_7034',['hash_map< vg::Edge *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fmap_3c_20vg_3a_3anode_20_2a_2c_20int_20_3e_7035',['hash_map< vg::Node *, int >',['../classvg_1_1hash__map.html',1,'vg']]],
+ ['hash_5fnode_5ftraversal_7036',['hash_node_traversal',['../structvg_1_1Genotyper_1_1hash__node__traversal.html',1,'vg::Genotyper']]],
+ ['hash_5foriented_5fedge_7037',['hash_oriented_edge',['../structvg_1_1Genotyper_1_1hash__oriented__edge.html',1,'vg::Genotyper']]],
+ ['hash_5fset_7038',['hash_set',['../classvg_1_1hash__set.html',1,'vg']]],
+ ['hash_5fset_3c_20k_20_2a_20_3e_7039',['hash_set< K * >',['../classvg_1_1hash__set_3_01K_01_5_01_4.html',1,'vg']]],
+ ['hash_5fset_3c_20pair_3c_20size_5ft_2c_20size_5ft_20_3e_20_3e_7040',['hash_set< pair< size_t, size_t > >',['../classvg_1_1hash__set.html',1,'vg']]],
+ ['hash_5fset_3c_20vg_3a_3aid_5ft_20_3e_7041',['hash_set< vg::id_t >',['../classvg_1_1hash__set.html',1,'vg']]],
+ ['hdp_5fgbwt_5fgraph_5faccessor_7042',['hDP_gbwt_graph_accessor',['../classhaplo_1_1hDP__gbwt__graph__accessor.html',1,'haplo']]],
+ ['header_7043',['Header',['../structvg_1_1Haplotypes_1_1Header.html',1,'vg::Haplotypes']]],
+ ['hfile_5fbackend_7044',['hFILE_backend',['../structhFILE__backend.html',1,'']]],
+ ['hfile_5fcppstream_7045',['hFILE_cppstream',['../structvg_1_1io_1_1hFILE__cppstream.html',1,'vg::io']]],
+ ['hitedge_7046',['HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html',1,'vg::MEMClusterer']]],
+ ['hitgraph_7047',['HitGraph',['../classvg_1_1MEMClusterer_1_1HitGraph.html',1,'vg::MEMClusterer']]],
+ ['hitnode_7048',['HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html',1,'vg::MEMClusterer']]],
+ ['htsalignmentemitter_7049',['HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html',1,'vg']]],
+ ['htswriter_7050',['HTSWriter',['../classvg_1_1HTSWriter.html',1,'vg']]]
];
diff --git a/search/classes_8.js b/search/classes_8.js
index 326c56ab1b..62bff4d58b 100644
--- a/search/classes_8.js
+++ b/search/classes_8.js
@@ -1,26 +1,26 @@
var searchData=
[
- ['identityoverlay_7049',['IdentityOverlay',['../classvg_1_1IdentityOverlay.html',1,'vg']]],
- ['idscanner_7050',['IDScanner',['../structvg_1_1IDScanner.html',1,'vg']]],
- ['incrementalsubgraph_7051',['IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html',1,'vg']]],
- ['incrementiter_7052',['IncrementIter',['../structvg_1_1IncrementIter.html',1,'vg']]],
- ['indexedvg_7053',['IndexedVG',['../classvg_1_1IndexedVG.html',1,'vg']]],
- ['indexfile_7054',['IndexFile',['../classvg_1_1IndexFile.html',1,'vg']]],
- ['indexingparameters_7055',['IndexingParameters',['../structvg_1_1IndexingParameters.html',1,'vg']]],
- ['indexingplan_7056',['IndexingPlan',['../classvg_1_1IndexingPlan.html',1,'vg']]],
- ['indexrecipe_7057',['IndexRecipe',['../structvg_1_1IndexRecipe.html',1,'vg']]],
- ['indexregistry_7058',['IndexRegistry',['../classvg_1_1IndexRegistry.html',1,'vg']]],
- ['inserthaplotypecommand_7059',['InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html',1,'vg']]],
- ['insufficientinputexception_7060',['InsufficientInputException',['../classvg_1_1InsufficientInputException.html',1,'vg']]],
- ['int_5fitvl_5ft_7061',['int_itvl_t',['../structhaplo_1_1int__itvl__t.html',1,'haplo']]],
- ['integratedsnarlfinder_7062',['IntegratedSnarlFinder',['../classvg_1_1IntegratedSnarlFinder.html',1,'vg']]],
- ['interval_5fstate_5ft_7063',['interval_state_t',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html',1,'vg::ZipCodeForest']]],
- ['is_5finstantiation_5fof_7064',['is_instantiation_of',['../structvg_1_1is__instantiation__of.html',1,'vg']]],
- ['is_5finstantiation_5fof_3c_20predicate_3c_20predicateargs_2e_2e_2e_20_3e_2c_20predicate_20_3e_7065',['is_instantiation_of< Predicate< PredicateArgs... >, Predicate >',['../structvg_1_1is__instantiation__of_3_01Predicate_3_01PredicateArgs_8_8_8_01_4_00_01Predicate_01_4.html',1,'vg']]],
- ['item_7066',['Item',['../structvg_1_1Funnel_1_1Item.html',1,'vg::Funnel']]],
- ['iterator_7067',['iterator',['../classvg_1_1ShuffledPairs_1_1iterator.html',1,'vg::ShuffledPairs::iterator'],['../classvg_1_1ZipCodeTree_1_1iterator.html',1,'vg::ZipCodeTree::iterator'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html',1,'handlegraph::PathForEachSocket::iterator'],['../classvg_1_1PhasedGenome_1_1iterator.html',1,'vg::PhasedGenome::iterator']]],
- ['iterator_5ftraits_3c_20vg_3a_3aphasedgenome_3a_3aiterator_20_3e_7068',['iterator_traits< vg::PhasedGenome::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html',1,'std']]],
- ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3aiterator_20_3e_7069',['iterator_traits< vg::ZipCodeTree::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html',1,'std']]],
- ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3areverse_5fiterator_20_3e_7070',['iterator_traits< vg::ZipCodeTree::reverse_iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html',1,'std']]],
- ['iterfcmp_7071',['IterFCmp',['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html',1,'vg::IncrementalSubgraph']]]
+ ['identityoverlay_7051',['IdentityOverlay',['../classvg_1_1IdentityOverlay.html',1,'vg']]],
+ ['idscanner_7052',['IDScanner',['../structvg_1_1IDScanner.html',1,'vg']]],
+ ['incrementalsubgraph_7053',['IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html',1,'vg']]],
+ ['incrementiter_7054',['IncrementIter',['../structvg_1_1IncrementIter.html',1,'vg']]],
+ ['indexedvg_7055',['IndexedVG',['../classvg_1_1IndexedVG.html',1,'vg']]],
+ ['indexfile_7056',['IndexFile',['../classvg_1_1IndexFile.html',1,'vg']]],
+ ['indexingparameters_7057',['IndexingParameters',['../structvg_1_1IndexingParameters.html',1,'vg']]],
+ ['indexingplan_7058',['IndexingPlan',['../classvg_1_1IndexingPlan.html',1,'vg']]],
+ ['indexrecipe_7059',['IndexRecipe',['../structvg_1_1IndexRecipe.html',1,'vg']]],
+ ['indexregistry_7060',['IndexRegistry',['../classvg_1_1IndexRegistry.html',1,'vg']]],
+ ['inserthaplotypecommand_7061',['InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html',1,'vg']]],
+ ['insufficientinputexception_7062',['InsufficientInputException',['../classvg_1_1InsufficientInputException.html',1,'vg']]],
+ ['int_5fitvl_5ft_7063',['int_itvl_t',['../structhaplo_1_1int__itvl__t.html',1,'haplo']]],
+ ['integratedsnarlfinder_7064',['IntegratedSnarlFinder',['../classvg_1_1IntegratedSnarlFinder.html',1,'vg']]],
+ ['interval_5fstate_5ft_7065',['interval_state_t',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html',1,'vg::ZipCodeForest']]],
+ ['is_5finstantiation_5fof_7066',['is_instantiation_of',['../structvg_1_1is__instantiation__of.html',1,'vg']]],
+ ['is_5finstantiation_5fof_3c_20predicate_3c_20predicateargs_2e_2e_2e_20_3e_2c_20predicate_20_3e_7067',['is_instantiation_of< Predicate< PredicateArgs... >, Predicate >',['../structvg_1_1is__instantiation__of_3_01Predicate_3_01PredicateArgs_8_8_8_01_4_00_01Predicate_01_4.html',1,'vg']]],
+ ['item_7068',['Item',['../structvg_1_1Funnel_1_1Item.html',1,'vg::Funnel']]],
+ ['iterator_7069',['iterator',['../classvg_1_1ShuffledPairs_1_1iterator.html',1,'vg::ShuffledPairs::iterator'],['../classvg_1_1ZipCodeTree_1_1iterator.html',1,'vg::ZipCodeTree::iterator'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html',1,'handlegraph::PathForEachSocket::iterator'],['../classvg_1_1PhasedGenome_1_1iterator.html',1,'vg::PhasedGenome::iterator']]],
+ ['iterator_5ftraits_3c_20vg_3a_3aphasedgenome_3a_3aiterator_20_3e_7070',['iterator_traits< vg::PhasedGenome::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html',1,'std']]],
+ ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3aiterator_20_3e_7071',['iterator_traits< vg::ZipCodeTree::iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html',1,'std']]],
+ ['iterator_5ftraits_3c_20vg_3a_3azipcodetree_3a_3areverse_5fiterator_20_3e_7072',['iterator_traits< vg::ZipCodeTree::reverse_iterator >',['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html',1,'std']]],
+ ['iterfcmp_7073',['IterFCmp',['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html',1,'vg::IncrementalSubgraph']]]
];
diff --git a/search/classes_9.js b/search/classes_9.js
index 9612c0fc0b..e5d33b4d17 100644
--- a/search/classes_9.js
+++ b/search/classes_9.js
@@ -1,9 +1,9 @@
var searchData=
[
- ['j2pb_5ferror_7072',['j2pb_error',['../classj2pb__error.html',1,'']]],
- ['job_5ftype_7073',['job_type',['../structjob__type.html',1,'']]],
- ['jobschedule_7074',['JobSchedule',['../classvg_1_1JobSchedule.html',1,'vg']]],
- ['joinedsplicegraph_7075',['JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html',1,'vg']]],
- ['json_5fautoptr_7076',['json_autoptr',['../structjson__autoptr.html',1,'']]],
- ['jsonstreamhelper_7077',['JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html',1,'vg::io']]]
+ ['j2pb_5ferror_7074',['j2pb_error',['../classj2pb__error.html',1,'']]],
+ ['job_5ftype_7075',['job_type',['../structjob__type.html',1,'']]],
+ ['jobschedule_7076',['JobSchedule',['../classvg_1_1JobSchedule.html',1,'vg']]],
+ ['joinedsplicegraph_7077',['JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html',1,'vg']]],
+ ['json_5fautoptr_7078',['json_autoptr',['../structjson__autoptr.html',1,'']]],
+ ['jsonstreamhelper_7079',['JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html',1,'vg::io']]]
];
diff --git a/search/classes_a.js b/search/classes_a.js
index 4651445d77..360c425762 100644
--- a/search/classes_a.js
+++ b/search/classes_a.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['kff_5frecoding_5ft_7078',['kff_recoding_t',['../structvg_1_1kff__recoding__t.html',1,'vg']]],
- ['kmer_5ft_7079',['kmer_t',['../structvg_1_1kmer__t.html',1,'vg::kmer_t'],['../structvg_1_1algorithms_1_1kmer__t.html',1,'vg::algorithms::kmer_t']]],
- ['kmermatch_7080',['KmerMatch',['../structvg_1_1KmerMatch.html',1,'vg']]],
- ['kmerposition_7081',['KmerPosition',['../structvg_1_1KmerPosition.html',1,'vg']]]
+ ['kff_5frecoding_5ft_7080',['kff_recoding_t',['../structvg_1_1kff__recoding__t.html',1,'vg']]],
+ ['kmer_5ft_7081',['kmer_t',['../structvg_1_1kmer__t.html',1,'vg::kmer_t'],['../structvg_1_1algorithms_1_1kmer__t.html',1,'vg::algorithms::kmer_t']]],
+ ['kmermatch_7082',['KmerMatch',['../structvg_1_1KmerMatch.html',1,'vg']]],
+ ['kmerposition_7083',['KmerPosition',['../structvg_1_1KmerPosition.html',1,'vg']]]
];
diff --git a/search/classes_b.js b/search/classes_b.js
index 646028801b..02c44268b9 100644
--- a/search/classes_b.js
+++ b/search/classes_b.js
@@ -1,12 +1,12 @@
var searchData=
[
- ['lazyrng_7082',['LazyRNG',['../classvg_1_1LazyRNG.html',1,'vg']]],
- ['legacycaller_7083',['LegacyCaller',['../classvg_1_1LegacyCaller.html',1,'vg']]],
- ['linear_5fhaplo_5fstructure_7084',['linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html',1,'haplo']]],
- ['linearscoreprovider_7085',['LinearScoreProvider',['../classhaplo_1_1LinearScoreProvider.html',1,'haplo']]],
- ['linearunrepresentable_7086',['linearUnrepresentable',['../classhaplo_1_1linear__haplo__structure_1_1linearUnrepresentable.html',1,'haplo::linear_haplo_structure']]],
- ['localhaplotype_7087',['LocalHaplotype',['../structvg_1_1Recombinator_1_1LocalHaplotype.html',1,'vg::Recombinator']]],
- ['locationsupport_7088',['LocationSupport',['../structvg_1_1LocationSupport.html',1,'vg']]],
- ['lock_7089',['Lock',['../classvg_1_1GraphSynchronizer_1_1Lock.html',1,'vg::GraphSynchronizer']]],
- ['locus_7090',['Locus',['../structvg_1_1Locus.html',1,'vg']]]
+ ['lazyrng_7084',['LazyRNG',['../classvg_1_1LazyRNG.html',1,'vg']]],
+ ['legacycaller_7085',['LegacyCaller',['../classvg_1_1LegacyCaller.html',1,'vg']]],
+ ['linear_5fhaplo_5fstructure_7086',['linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html',1,'haplo']]],
+ ['linearscoreprovider_7087',['LinearScoreProvider',['../classhaplo_1_1LinearScoreProvider.html',1,'haplo']]],
+ ['linearunrepresentable_7088',['linearUnrepresentable',['../classhaplo_1_1linear__haplo__structure_1_1linearUnrepresentable.html',1,'haplo::linear_haplo_structure']]],
+ ['localhaplotype_7089',['LocalHaplotype',['../structvg_1_1Recombinator_1_1LocalHaplotype.html',1,'vg::Recombinator']]],
+ ['locationsupport_7090',['LocationSupport',['../structvg_1_1LocationSupport.html',1,'vg']]],
+ ['lock_7091',['Lock',['../classvg_1_1GraphSynchronizer_1_1Lock.html',1,'vg::GraphSynchronizer']]],
+ ['locus_7092',['Locus',['../structvg_1_1Locus.html',1,'vg']]]
];
diff --git a/search/classes_c.js b/search/classes_c.js
index 3e83ec85e6..02d33dd880 100644
--- a/search/classes_c.js
+++ b/search/classes_c.js
@@ -1,39 +1,39 @@
var searchData=
[
- ['mapper_7091',['Mapper',['../classvg_1_1Mapper.html',1,'vg']]],
- ['mapping_7092',['Mapping',['../structvg_1_1Mapping.html',1,'vg']]],
- ['mapping_5ft_7093',['mapping_t',['../classvg_1_1mapping__t.html',1,'vg']]],
- ['mappinghash_7094',['MappingHash',['../structvg_1_1MappingHash.html',1,'vg']]],
- ['mappingrun_7095',['MappingRun',['../structMappingRun.html',1,'']]],
- ['markovdistribution_7096',['MarkovDistribution',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator']]],
- ['markovdistribution_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_20_3e_20_3e_7097',['MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > >',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator']]],
- ['masker_7098',['Masker',['../classvg_1_1Masker.html',1,'vg']]],
- ['matchpos_7099',['MatchPos',['../structvg_1_1MatchPos.html',1,'vg']]],
- ['maximalexactmatch_7100',['MaximalExactMatch',['../classvg_1_1MaximalExactMatch.html',1,'vg']]],
- ['mcmccaller_7101',['MCMCCaller',['../classvg_1_1MCMCCaller.html',1,'vg']]],
- ['mcmcgenotyper_7102',['MCMCGenotyper',['../classvg_1_1MCMCGenotyper.html',1,'vg']]],
- ['memaccelerator_7103',['MEMAccelerator',['../classvg_1_1MEMAccelerator.html',1,'vg']]],
- ['memchainmodel_7104',['MEMChainModel',['../classvg_1_1MEMChainModel.html',1,'vg']]],
- ['memchainmodelvertex_7105',['MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html',1,'vg']]],
- ['memclusterer_7106',['MEMClusterer',['../classvg_1_1MEMClusterer.html',1,'vg']]],
- ['memoizinggraph_7107',['MemoizingGraph',['../classvg_1_1MemoizingGraph.html',1,'vg']]],
- ['mergedadjacencygraph_7108',['MergedAdjacencyGraph',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html',1,'vg::IntegratedSnarlFinder']]],
- ['messageemitter_7109',['MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html',1,'vg::io']]],
- ['messageiterator_7110',['MessageIterator',['../classvg_1_1io_1_1MessageIterator.html',1,'vg::io']]],
- ['mindistanceclusterer_7111',['MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html',1,'vg']]],
- ['minimizer_7112',['Minimizer',['../structvg_1_1MinimizerMapper_1_1Minimizer.html',1,'vg::MinimizerMapper']]],
- ['minimizermapper_7113',['MinimizerMapper',['../classvg_1_1MinimizerMapper.html',1,'vg']]],
- ['mipayload_7114',['MIPayload',['../structvg_1_1MIPayload.html',1,'vg']]],
- ['msaconverter_7115',['MSAConverter',['../classvg_1_1MSAConverter.html',1,'vg']]],
- ['multipath_5falignment_5ft_7116',['multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html',1,'vg']]],
- ['multipathalignment_7117',['MultipathAlignment',['../structvg_1_1MultipathAlignment.html',1,'vg']]],
- ['multipathalignmentemitter_7118',['MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html',1,'vg']]],
- ['multipathalignmentgraph_7119',['MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html',1,'vg']]],
- ['multipathmapper_7120',['MultipathMapper',['../classvg_1_1MultipathMapper.html',1,'vg']]],
- ['multipathproblem_7121',['MultipathProblem',['../structvg_1_1MultipathProblem.html',1,'vg']]],
- ['mutablehandlegraph_7122',['MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html',1,'handlegraph']]],
- ['mutablepathdeletablehandlegraph_7123',['MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html',1,'handlegraph']]],
- ['mutablepathhandlegraph_7124',['MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html',1,'handlegraph']]],
- ['mutablepathmetadata_7125',['MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html',1,'handlegraph']]],
- ['mutablepathmutablehandlegraph_7126',['MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html',1,'handlegraph']]]
+ ['mapper_7093',['Mapper',['../classvg_1_1Mapper.html',1,'vg']]],
+ ['mapping_7094',['Mapping',['../structvg_1_1Mapping.html',1,'vg']]],
+ ['mapping_5ft_7095',['mapping_t',['../classvg_1_1mapping__t.html',1,'vg']]],
+ ['mappinghash_7096',['MappingHash',['../structvg_1_1MappingHash.html',1,'vg']]],
+ ['mappingrun_7097',['MappingRun',['../structMappingRun.html',1,'']]],
+ ['markovdistribution_7098',['MarkovDistribution',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator']]],
+ ['markovdistribution_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_2c_20pair_3c_20uint8_5ft_2c_20bool_20_3e_20_3e_20_3e_7099',['MarkovDistribution< pair< uint8_t, bool >, pair< pair< uint8_t, bool >, pair< uint8_t, bool > > >',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html',1,'vg::NGSSimulator']]],
+ ['masker_7100',['Masker',['../classvg_1_1Masker.html',1,'vg']]],
+ ['matchpos_7101',['MatchPos',['../structvg_1_1MatchPos.html',1,'vg']]],
+ ['maximalexactmatch_7102',['MaximalExactMatch',['../classvg_1_1MaximalExactMatch.html',1,'vg']]],
+ ['mcmccaller_7103',['MCMCCaller',['../classvg_1_1MCMCCaller.html',1,'vg']]],
+ ['mcmcgenotyper_7104',['MCMCGenotyper',['../classvg_1_1MCMCGenotyper.html',1,'vg']]],
+ ['memaccelerator_7105',['MEMAccelerator',['../classvg_1_1MEMAccelerator.html',1,'vg']]],
+ ['memchainmodel_7106',['MEMChainModel',['../classvg_1_1MEMChainModel.html',1,'vg']]],
+ ['memchainmodelvertex_7107',['MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html',1,'vg']]],
+ ['memclusterer_7108',['MEMClusterer',['../classvg_1_1MEMClusterer.html',1,'vg']]],
+ ['memoizinggraph_7109',['MemoizingGraph',['../classvg_1_1MemoizingGraph.html',1,'vg']]],
+ ['mergedadjacencygraph_7110',['MergedAdjacencyGraph',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html',1,'vg::IntegratedSnarlFinder']]],
+ ['messageemitter_7111',['MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html',1,'vg::io']]],
+ ['messageiterator_7112',['MessageIterator',['../classvg_1_1io_1_1MessageIterator.html',1,'vg::io']]],
+ ['mindistanceclusterer_7113',['MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html',1,'vg']]],
+ ['minimizer_7114',['Minimizer',['../structvg_1_1MinimizerMapper_1_1Minimizer.html',1,'vg::MinimizerMapper']]],
+ ['minimizermapper_7115',['MinimizerMapper',['../classvg_1_1MinimizerMapper.html',1,'vg']]],
+ ['mipayload_7116',['MIPayload',['../structvg_1_1MIPayload.html',1,'vg']]],
+ ['msaconverter_7117',['MSAConverter',['../classvg_1_1MSAConverter.html',1,'vg']]],
+ ['multipath_5falignment_5ft_7118',['multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html',1,'vg']]],
+ ['multipathalignment_7119',['MultipathAlignment',['../structvg_1_1MultipathAlignment.html',1,'vg']]],
+ ['multipathalignmentemitter_7120',['MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html',1,'vg']]],
+ ['multipathalignmentgraph_7121',['MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html',1,'vg']]],
+ ['multipathmapper_7122',['MultipathMapper',['../classvg_1_1MultipathMapper.html',1,'vg']]],
+ ['multipathproblem_7123',['MultipathProblem',['../structvg_1_1MultipathProblem.html',1,'vg']]],
+ ['mutablehandlegraph_7124',['MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html',1,'handlegraph']]],
+ ['mutablepathdeletablehandlegraph_7125',['MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html',1,'handlegraph']]],
+ ['mutablepathhandlegraph_7126',['MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html',1,'handlegraph']]],
+ ['mutablepathmetadata_7127',['MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html',1,'handlegraph']]],
+ ['mutablepathmutablehandlegraph_7128',['MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html',1,'handlegraph']]]
];
diff --git a/search/classes_d.js b/search/classes_d.js
index abffc5ab6c..a93d9e3b92 100644
--- a/search/classes_d.js
+++ b/search/classes_d.js
@@ -1,23 +1,23 @@
var searchData=
[
- ['namednodebacktranslation_7127',['NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html',1,'handlegraph']]],
- ['namemapper_7128',['NameMapper',['../classvg_1_1NameMapper.html',1,'vg']]],
- ['nestedcachedpackedtraversalsupportfinder_7129',['NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html',1,'vg']]],
- ['nestedflowcaller_7130',['NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html',1,'vg']]],
- ['nestedtraversalfinder_7131',['NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html',1,'vg']]],
- ['nestinginfo_7132',['NestingInfo',['../structvg_1_1Deconstructor_1_1NestingInfo.html',1,'vg::Deconstructor']]],
- ['net_5fhandle_5ft_7133',['net_handle_t',['../structhandlegraph_1_1net__handle__t.html',1,'handlegraph']]],
- ['netgraph_7134',['NetGraph',['../classvg_1_1NetGraph.html',1,'vg']]],
- ['ngssimulator_7135',['NGSSimulator',['../classvg_1_1NGSSimulator.html',1,'vg']]],
- ['noalignmentinbandexception_7136',['NoAlignmentInBandException',['../classvg_1_1NoAlignmentInBandException.html',1,'vg']]],
- ['node_7137',['Node',['../structvg_1_1Node.html',1,'vg::Node'],['../structvg_1_1algorithms_1_1Node.html',1,'vg::algorithms::Node']]],
- ['node_5fcode_5ft_7138',['node_code_t',['../structvg_1_1ZipCode_1_1node__code__t.html',1,'vg::ZipCode']]],
- ['nodepileup_7139',['NodePileup',['../structvg_1_1NodePileup.html',1,'vg']]],
- ['nodeside_7140',['NodeSide',['../classvg_1_1NodeSide.html',1,'vg']]],
- ['nodetraversal_7141',['NodeTraversal',['../classvg_1_1NodeTraversal.html',1,'vg']]],
- ['normal_5fdistribution_7142',['normal_distribution',['../classvg_1_1normal__distribution.html',1,'vg']]],
- ['nullalignmentemitter_7143',['NullAlignmentEmitter',['../classvg_1_1io_1_1NullAlignmentEmitter.html',1,'vg::io']]],
- ['nullclusterer_7144',['NullClusterer',['../classvg_1_1NullClusterer.html',1,'vg']]],
- ['nullmaskinggraph_7145',['NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html',1,'vg']]],
- ['number_5fbool_5fpacking_7146',['number_bool_packing',['../structhandlegraph_1_1number__bool__packing.html',1,'handlegraph']]]
+ ['namednodebacktranslation_7129',['NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html',1,'handlegraph']]],
+ ['namemapper_7130',['NameMapper',['../classvg_1_1NameMapper.html',1,'vg']]],
+ ['nestedcachedpackedtraversalsupportfinder_7131',['NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html',1,'vg']]],
+ ['nestedflowcaller_7132',['NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html',1,'vg']]],
+ ['nestedtraversalfinder_7133',['NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html',1,'vg']]],
+ ['nestinginfo_7134',['NestingInfo',['../structvg_1_1Deconstructor_1_1NestingInfo.html',1,'vg::Deconstructor']]],
+ ['net_5fhandle_5ft_7135',['net_handle_t',['../structhandlegraph_1_1net__handle__t.html',1,'handlegraph']]],
+ ['netgraph_7136',['NetGraph',['../classvg_1_1NetGraph.html',1,'vg']]],
+ ['ngssimulator_7137',['NGSSimulator',['../classvg_1_1NGSSimulator.html',1,'vg']]],
+ ['noalignmentinbandexception_7138',['NoAlignmentInBandException',['../classvg_1_1NoAlignmentInBandException.html',1,'vg']]],
+ ['node_7139',['Node',['../structvg_1_1Node.html',1,'vg::Node'],['../structvg_1_1algorithms_1_1Node.html',1,'vg::algorithms::Node']]],
+ ['node_5fcode_5ft_7140',['node_code_t',['../structvg_1_1ZipCode_1_1node__code__t.html',1,'vg::ZipCode']]],
+ ['nodepileup_7141',['NodePileup',['../structvg_1_1NodePileup.html',1,'vg']]],
+ ['nodeside_7142',['NodeSide',['../classvg_1_1NodeSide.html',1,'vg']]],
+ ['nodetraversal_7143',['NodeTraversal',['../classvg_1_1NodeTraversal.html',1,'vg']]],
+ ['normal_5fdistribution_7144',['normal_distribution',['../classvg_1_1normal__distribution.html',1,'vg']]],
+ ['nullalignmentemitter_7145',['NullAlignmentEmitter',['../classvg_1_1io_1_1NullAlignmentEmitter.html',1,'vg::io']]],
+ ['nullclusterer_7146',['NullClusterer',['../classvg_1_1NullClusterer.html',1,'vg']]],
+ ['nullmaskinggraph_7147',['NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html',1,'vg']]],
+ ['number_5fbool_5fpacking_7148',['number_bool_packing',['../structhandlegraph_1_1number__bool__packing.html',1,'handlegraph']]]
];
diff --git a/search/classes_e.js b/search/classes_e.js
index 150a3b1dc7..7584b722f0 100644
--- a/search/classes_e.js
+++ b/search/classes_e.js
@@ -1,13 +1,13 @@
var searchData=
[
- ['option_7147',['Option',['../classvg_1_1Option.html',1,'vg']]],
- ['option_3c_20vector_3c_20item_20_3e_2c_20parser_20_3e_7148',['Option< vector< Item >, Parser >',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html',1,'vg']]],
- ['optiongroup_7149',['OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html',1,'vg::subcommand']]],
- ['optioninterface_7150',['OptionInterface',['../classvg_1_1OptionInterface.html',1,'vg']]],
- ['optionvalueparser_7151',['OptionValueParser',['../classvg_1_1OptionValueParser.html',1,'vg']]],
- ['optionvalueparser_3c_20vector_3c_20item_20_3e_20_3e_7152',['OptionValueParser< vector< Item > >',['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html',1,'vg']]],
- ['orderedgraph_7153',['OrderedGraph',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html',1,'vg::DozeuInterface']]],
- ['oriented_5fseed_5ft_7154',['oriented_seed_t',['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html',1,'vg::ZipCodeTree']]],
- ['orienteddistanceclusterer_7155',['OrientedDistanceClusterer',['../classvg_1_1OrientedDistanceClusterer.html',1,'vg']]],
- ['orienteddistancemeasurer_7156',['OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html',1,'vg']]]
+ ['option_7149',['Option',['../classvg_1_1Option.html',1,'vg']]],
+ ['option_3c_20vector_3c_20item_20_3e_2c_20parser_20_3e_7150',['Option< vector< Item >, Parser >',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html',1,'vg']]],
+ ['optiongroup_7151',['OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html',1,'vg::subcommand']]],
+ ['optioninterface_7152',['OptionInterface',['../classvg_1_1OptionInterface.html',1,'vg']]],
+ ['optionvalueparser_7153',['OptionValueParser',['../classvg_1_1OptionValueParser.html',1,'vg']]],
+ ['optionvalueparser_3c_20vector_3c_20item_20_3e_20_3e_7154',['OptionValueParser< vector< Item > >',['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html',1,'vg']]],
+ ['orderedgraph_7155',['OrderedGraph',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html',1,'vg::DozeuInterface']]],
+ ['oriented_5fseed_5ft_7156',['oriented_seed_t',['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html',1,'vg::ZipCodeTree']]],
+ ['orienteddistanceclusterer_7157',['OrientedDistanceClusterer',['../classvg_1_1OrientedDistanceClusterer.html',1,'vg']]],
+ ['orienteddistancemeasurer_7158',['OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html',1,'vg']]]
];
diff --git a/search/classes_f.js b/search/classes_f.js
index 2896f76f72..eae10a1060 100644
--- a/search/classes_f.js
+++ b/search/classes_f.js
@@ -1,54 +1,54 @@
var searchData=
[
- ['packedtraversalsupportfinder_7157',['PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html',1,'vg']]],
- ['packer_7158',['Packer',['../classvg_1_1Packer.html',1,'vg']]],
- ['packers_7159',['Packers',['../classvg_1_1Packers.html',1,'vg']]],
- ['paintablespace_7160',['PaintableSpace',['../structvg_1_1Funnel_1_1PaintableSpace.html',1,'vg::Funnel']]],
- ['pair_5fhash_5fmap_7161',['pair_hash_map',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vector_3c_20vg_3a_3aalignment_20_2a_20_3e_20_3e_7162',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vector< vg::Alignment * > >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vg_3a_3aedge_20_2a_20_3e_7163',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vg::Edge * >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fmap_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_2c_20gbwt_3a_3anode_5ftype_20_3e_7164',['pair_hash_map< std::pair< gbwt::node_type, gbwt::node_type >, gbwt::node_type >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
- ['pair_5fhash_5fset_7165',['pair_hash_set',['../classvg_1_1pair__hash__set.html',1,'vg']]],
- ['pair_5fhash_5fset_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_20_3e_7166',['pair_hash_set< std::pair< gbwt::node_type, gbwt::node_type > >',['../classvg_1_1pair__hash__set.html',1,'vg']]],
- ['pairedendmapper_7167',['PairedEndMapper',['../classvg_1_1PairedEndMapper.html',1,'vg']]],
- ['parallelkffreader_7168',['ParallelKFFReader',['../classvg_1_1ParallelKFFReader.html',1,'vg']]],
- ['parameters_7169',['Parameters',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html',1,'vg::HaplotypePartitioner::Parameters'],['../structvg_1_1Recombinator_1_1Parameters.html',1,'vg::Recombinator::Parameters']]],
- ['parentgenotypeinfo_7170',['ParentGenotypeInfo',['../structvg_1_1ParentGenotypeInfo.html',1,'vg']]],
- ['path_7171',['Path',['../structvg_1_1Path.html',1,'vg']]],
- ['path_5fhandle_5ft_7172',['path_handle_t',['../structhandlegraph_1_1path__handle__t.html',1,'handlegraph']]],
- ['path_5fmapping_5ft_7173',['path_mapping_t',['../classvg_1_1path__mapping__t.html',1,'vg']]],
- ['path_5ft_7174',['path_t',['../classvg_1_1path__t.html',1,'vg']]],
- ['pathbasedtraversalfinder_7175',['PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html',1,'vg']]],
- ['pathbranch_7176',['PathBranch',['../structvg_1_1PathBranch.html',1,'vg']]],
- ['pathchunker_7177',['PathChunker',['../classvg_1_1PathChunker.html',1,'vg']]],
- ['pathcomponentindex_7178',['PathComponentIndex',['../classvg_1_1PathComponentIndex.html',1,'vg']]],
- ['pathforeachsocket_7179',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html',1,'handlegraph']]],
- ['pathhandlegraph_7180',['PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html',1,'handlegraph']]],
- ['pathindex_7181',['PathIndex',['../structvg_1_1PathIndex.html',1,'vg']]],
- ['pathlist_7182',['PathList',['../structvg_1_1MatchPos_1_1PathList.html',1,'vg::MatchPos']]],
- ['pathmetadata_7183',['PathMetadata',['../classhandlegraph_1_1PathMetadata.html',1,'handlegraph']]],
- ['pathnode_7184',['PathNode',['../classvg_1_1PathNode.html',1,'vg']]],
- ['pathorienteddistancemeasurer_7185',['PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html',1,'vg']]],
- ['pathpositionhandlegraph_7186',['PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html',1,'handlegraph']]],
- ['pathrestrictedtraversalfinder_7187',['PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html',1,'vg']]],
- ['paths_7188',['Paths',['../classvg_1_1Paths.html',1,'vg']]],
- ['pathsubgraph_7189',['PathSubgraph',['../classvg_1_1PathSubgraph.html',1,'vg']]],
- ['pathsubgraphoverlay_7190',['PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html',1,'vg']]],
- ['pathtraversalfinder_7191',['PathTraversalFinder',['../classvg_1_1PathTraversalFinder.html',1,'vg']]],
- ['phasedgenome_7192',['PhasedGenome',['../classvg_1_1PhasedGenome.html',1,'vg']]],
- ['phaseunfolder_7193',['PhaseUnfolder',['../classvg_1_1PhaseUnfolder.html',1,'vg']]],
- ['pictographs_7194',['Pictographs',['../classvg_1_1Pictographs.html',1,'vg']]],
- ['pileup_7195',['Pileup',['../structvg_1_1Pileup.html',1,'vg']]],
- ['plan_7196',['Plan',['../structvg_1_1VG_1_1Plan.html',1,'vg::VG']]],
- ['poissoncallinfo_7197',['PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html',1,'vg::PoissonSupportSnarlCaller']]],
- ['poissonsupportsnarlcaller_7198',['PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html',1,'vg']]],
- ['position_7199',['Position',['../structvg_1_1Position.html',1,'vg']]],
- ['position_5ft_7200',['position_t',['../classvg_1_1position__t.html',1,'vg']]],
- ['positionidscanner_7201',['PositionIDScanner',['../structvg_1_1PositionIDScanner.html',1,'vg']]],
- ['preset_7202',['Preset',['../structvg_1_1subcommand_1_1Preset.html',1,'vg::subcommand']]],
- ['problemdumpexplainer_7203',['ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html',1,'vg']]],
- ['progressive_7204',['Progressive',['../classvg_1_1Progressive.html',1,'vg']]],
- ['protobufemitter_7205',['ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html',1,'vg::io']]],
- ['protobufiterator_7206',['ProtobufIterator',['../classvg_1_1io_1_1ProtobufIterator.html',1,'vg::io']]],
- ['pruningparameters_7207',['PruningParameters',['../structPruningParameters.html',1,'']]]
+ ['packedtraversalsupportfinder_7159',['PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html',1,'vg']]],
+ ['packer_7160',['Packer',['../classvg_1_1Packer.html',1,'vg']]],
+ ['packers_7161',['Packers',['../classvg_1_1Packers.html',1,'vg']]],
+ ['paintablespace_7162',['PaintableSpace',['../structvg_1_1Funnel_1_1PaintableSpace.html',1,'vg::Funnel']]],
+ ['pair_5fhash_5fmap_7163',['pair_hash_map',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vector_3c_20vg_3a_3aalignment_20_2a_20_3e_20_3e_7164',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vector< vg::Alignment * > >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fmap_3c_20pair_3c_20vg_3a_3anodeside_2c_20vg_3a_3anodeside_20_3e_2c_20vg_3a_3aedge_20_2a_20_3e_7165',['pair_hash_map< pair< vg::NodeSide, vg::NodeSide >, vg::Edge * >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fmap_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_2c_20gbwt_3a_3anode_5ftype_20_3e_7166',['pair_hash_map< std::pair< gbwt::node_type, gbwt::node_type >, gbwt::node_type >',['../classvg_1_1pair__hash__map.html',1,'vg']]],
+ ['pair_5fhash_5fset_7167',['pair_hash_set',['../classvg_1_1pair__hash__set.html',1,'vg']]],
+ ['pair_5fhash_5fset_3c_20std_3a_3apair_3c_20gbwt_3a_3anode_5ftype_2c_20gbwt_3a_3anode_5ftype_20_3e_20_3e_7168',['pair_hash_set< std::pair< gbwt::node_type, gbwt::node_type > >',['../classvg_1_1pair__hash__set.html',1,'vg']]],
+ ['pairedendmapper_7169',['PairedEndMapper',['../classvg_1_1PairedEndMapper.html',1,'vg']]],
+ ['parallelkffreader_7170',['ParallelKFFReader',['../classvg_1_1ParallelKFFReader.html',1,'vg']]],
+ ['parameters_7171',['Parameters',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html',1,'vg::HaplotypePartitioner::Parameters'],['../structvg_1_1Recombinator_1_1Parameters.html',1,'vg::Recombinator::Parameters']]],
+ ['parentgenotypeinfo_7172',['ParentGenotypeInfo',['../structvg_1_1ParentGenotypeInfo.html',1,'vg']]],
+ ['path_7173',['Path',['../structvg_1_1Path.html',1,'vg']]],
+ ['path_5fhandle_5ft_7174',['path_handle_t',['../structhandlegraph_1_1path__handle__t.html',1,'handlegraph']]],
+ ['path_5fmapping_5ft_7175',['path_mapping_t',['../classvg_1_1path__mapping__t.html',1,'vg']]],
+ ['path_5ft_7176',['path_t',['../classvg_1_1path__t.html',1,'vg']]],
+ ['pathbasedtraversalfinder_7177',['PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html',1,'vg']]],
+ ['pathbranch_7178',['PathBranch',['../structvg_1_1PathBranch.html',1,'vg']]],
+ ['pathchunker_7179',['PathChunker',['../classvg_1_1PathChunker.html',1,'vg']]],
+ ['pathcomponentindex_7180',['PathComponentIndex',['../classvg_1_1PathComponentIndex.html',1,'vg']]],
+ ['pathforeachsocket_7181',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html',1,'handlegraph']]],
+ ['pathhandlegraph_7182',['PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html',1,'handlegraph']]],
+ ['pathindex_7183',['PathIndex',['../structvg_1_1PathIndex.html',1,'vg']]],
+ ['pathlist_7184',['PathList',['../structvg_1_1MatchPos_1_1PathList.html',1,'vg::MatchPos']]],
+ ['pathmetadata_7185',['PathMetadata',['../classhandlegraph_1_1PathMetadata.html',1,'handlegraph']]],
+ ['pathnode_7186',['PathNode',['../classvg_1_1PathNode.html',1,'vg']]],
+ ['pathorienteddistancemeasurer_7187',['PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html',1,'vg']]],
+ ['pathpositionhandlegraph_7188',['PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html',1,'handlegraph']]],
+ ['pathrestrictedtraversalfinder_7189',['PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html',1,'vg']]],
+ ['paths_7190',['Paths',['../classvg_1_1Paths.html',1,'vg']]],
+ ['pathsubgraph_7191',['PathSubgraph',['../classvg_1_1PathSubgraph.html',1,'vg']]],
+ ['pathsubgraphoverlay_7192',['PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html',1,'vg']]],
+ ['pathtraversalfinder_7193',['PathTraversalFinder',['../classvg_1_1PathTraversalFinder.html',1,'vg']]],
+ ['phasedgenome_7194',['PhasedGenome',['../classvg_1_1PhasedGenome.html',1,'vg']]],
+ ['phaseunfolder_7195',['PhaseUnfolder',['../classvg_1_1PhaseUnfolder.html',1,'vg']]],
+ ['pictographs_7196',['Pictographs',['../classvg_1_1Pictographs.html',1,'vg']]],
+ ['pileup_7197',['Pileup',['../structvg_1_1Pileup.html',1,'vg']]],
+ ['plan_7198',['Plan',['../structvg_1_1VG_1_1Plan.html',1,'vg::VG']]],
+ ['poissoncallinfo_7199',['PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html',1,'vg::PoissonSupportSnarlCaller']]],
+ ['poissonsupportsnarlcaller_7200',['PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html',1,'vg']]],
+ ['position_7201',['Position',['../structvg_1_1Position.html',1,'vg']]],
+ ['position_5ft_7202',['position_t',['../classvg_1_1position__t.html',1,'vg']]],
+ ['positionidscanner_7203',['PositionIDScanner',['../structvg_1_1PositionIDScanner.html',1,'vg']]],
+ ['preset_7204',['Preset',['../structvg_1_1subcommand_1_1Preset.html',1,'vg::subcommand']]],
+ ['problemdumpexplainer_7205',['ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html',1,'vg']]],
+ ['progressive_7206',['Progressive',['../classvg_1_1Progressive.html',1,'vg']]],
+ ['protobufemitter_7207',['ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html',1,'vg::io']]],
+ ['protobufiterator_7208',['ProtobufIterator',['../classvg_1_1io_1_1ProtobufIterator.html',1,'vg::io']]],
+ ['pruningparameters_7209',['PruningParameters',['../structPruningParameters.html',1,'']]]
];
diff --git a/search/defines_0.js b/search/defines_0.js
index 1f01975d25..d16a46aa9e 100644
--- a/search/defines_0.js
+++ b/search/defines_0.js
@@ -1,14 +1,14 @@
var searchData=
[
- ['_5fadd_5fedit_14114',['_add_edit',['../dozeu__interface_8cpp.html#ab7df7c17c09365f268d8b40f1b74f883',1,'dozeu_interface.cpp']]],
- ['_5fappend_5fop_14115',['_append_op',['../dozeu__interface_8cpp.html#a9eb966b9747eb954eddfdfc15587480d',1,'dozeu_interface.cpp']]],
- ['_5fconvert_14116',['_CONVERT',['../json2pb_8cpp.html#ad4c2ff64d43af01294cacd1499ebb846',1,'json2pb.cpp']]],
- ['_5fconvert_5fas_5fstring_14117',['_CONVERT_AS_STRING',['../json2pb_8cpp.html#a8ef0803c85fc6aa51de9d0a69c0c8e6d',1,'json2pb.cpp']]],
- ['_5fconvert_5fwith_5fstring_14118',['_CONVERT_WITH_STRING',['../json2pb_8cpp.html#ac7232ca2969a15d4ca8850c03de8ee86',1,'json2pb.cpp']]],
- ['_5fflush_5fop_14119',['_flush_op',['../dozeu__interface_8cpp.html#a3592941015e5430b738db9e882e0305d',1,'dozeu_interface.cpp']]],
- ['_5fposix_5fc_5fsource_14120',['_POSIX_C_SOURCE',['../crash_8cpp.html#a3024ccd4a9af5109d24e6c57565d74a1',1,'crash.cpp']]],
- ['_5fpush_5fmapping_14121',['_push_mapping',['../dozeu__interface_8cpp.html#a5787add53d7bbfdc10c9720454e98918',1,'dozeu_interface.cpp']]],
- ['_5fpush_5fop_14122',['_push_op',['../dozeu__interface_8cpp.html#ac058be264b99f54156cf44838308078c',1,'dozeu_interface.cpp']]],
- ['_5fset_5for_5fadd_14123',['_SET_OR_ADD',['../json2pb_8cpp.html#a7a898a2b4507c746088e2b09e94e4c56',1,'json2pb.cpp']]],
- ['_5fxopen_5fsource_14124',['_XOPEN_SOURCE',['../crash_8cpp.html#a78c99ffd76a7bb3c8c74db76207e9ab4',1,'crash.cpp']]]
+ ['_5fadd_5fedit_14118',['_add_edit',['../dozeu__interface_8cpp.html#ab7df7c17c09365f268d8b40f1b74f883',1,'dozeu_interface.cpp']]],
+ ['_5fappend_5fop_14119',['_append_op',['../dozeu__interface_8cpp.html#a9eb966b9747eb954eddfdfc15587480d',1,'dozeu_interface.cpp']]],
+ ['_5fconvert_14120',['_CONVERT',['../json2pb_8cpp.html#ad4c2ff64d43af01294cacd1499ebb846',1,'json2pb.cpp']]],
+ ['_5fconvert_5fas_5fstring_14121',['_CONVERT_AS_STRING',['../json2pb_8cpp.html#a8ef0803c85fc6aa51de9d0a69c0c8e6d',1,'json2pb.cpp']]],
+ ['_5fconvert_5fwith_5fstring_14122',['_CONVERT_WITH_STRING',['../json2pb_8cpp.html#ac7232ca2969a15d4ca8850c03de8ee86',1,'json2pb.cpp']]],
+ ['_5fflush_5fop_14123',['_flush_op',['../dozeu__interface_8cpp.html#a3592941015e5430b738db9e882e0305d',1,'dozeu_interface.cpp']]],
+ ['_5fposix_5fc_5fsource_14124',['_POSIX_C_SOURCE',['../crash_8cpp.html#a3024ccd4a9af5109d24e6c57565d74a1',1,'crash.cpp']]],
+ ['_5fpush_5fmapping_14125',['_push_mapping',['../dozeu__interface_8cpp.html#a5787add53d7bbfdc10c9720454e98918',1,'dozeu_interface.cpp']]],
+ ['_5fpush_5fop_14126',['_push_op',['../dozeu__interface_8cpp.html#ac058be264b99f54156cf44838308078c',1,'dozeu_interface.cpp']]],
+ ['_5fset_5for_5fadd_14127',['_SET_OR_ADD',['../json2pb_8cpp.html#a7a898a2b4507c746088e2b09e94e4c56',1,'json2pb.cpp']]],
+ ['_5fxopen_5fsource_14128',['_XOPEN_SOURCE',['../crash_8cpp.html#a78c99ffd76a7bb3c8c74db76207e9ab4',1,'crash.cpp']]]
];
diff --git a/search/defines_1.js b/search/defines_1.js
index 0836b2b343..45cfd242b3 100644
--- a/search/defines_1.js
+++ b/search/defines_1.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['backward_5fhas_5fdw_14125',['BACKWARD_HAS_DW',['../crash_8cpp.html#aa5592fc113f9fea784f0727b6c3af74e',1,'crash.cpp']]]
+ ['backward_5fhas_5fdw_14129',['BACKWARD_HAS_DW',['../crash_8cpp.html#aa5592fc113f9fea784f0727b6c3af74e',1,'crash.cpp']]]
];
diff --git a/search/defines_2.js b/search/defines_2.js
index b6c87d331a..b204137b8e 100644
--- a/search/defines_2.js
+++ b/search/defines_2.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['catch_5fconfig_5frunner_14126',['CATCH_CONFIG_RUNNER',['../test__main_8cpp.html#a34b4c3eca7342fbc4cba090d02139902',1,'test_main.cpp']]],
- ['crash_5funless_14127',['crash_unless',['../crash_8hpp.html#a11a5ab008a7ea6045c711d9e4a2c1768',1,'crash.hpp']]]
+ ['catch_5fconfig_5frunner_14130',['CATCH_CONFIG_RUNNER',['../test__main_8cpp.html#a34b4c3eca7342fbc4cba090d02139902',1,'test_main.cpp']]],
+ ['crash_5funless_14131',['crash_unless',['../crash_8hpp.html#a11a5ab008a7ea6045c711d9e4a2c1768',1,'crash.hpp']]]
];
diff --git a/search/defines_3.js b/search/defines_3.js
index 70006043f6..b8dc8d90a0 100644
--- a/search/defines_3.js
+++ b/search/defines_3.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['debug_14128',['debug',['../minimizer__mapper__from__chains_8cpp.html#a322565ccf348d13e4d3de13af771e5fc',1,'minimizer_mapper_from_chains.cpp']]],
- ['dz_5fcigar_5fop_14129',['DZ_CIGAR_OP',['../dozeu__interface_8cpp.html#af0acb761758e601c8c2111de1179c3cd',1,'DZ_CIGAR_OP(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#af0acb761758e601c8c2111de1179c3cd',1,'DZ_CIGAR_OP(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#af0acb761758e601c8c2111de1179c3cd',1,'DZ_CIGAR_OP(): xdrop_aligner.cpp']]],
- ['dz_5ffull_5flength_5fbonus_14130',['DZ_FULL_LENGTH_BONUS',['../dozeu__interface_8cpp.html#a236858d6cb48a098159fc3d416f0499b',1,'DZ_FULL_LENGTH_BONUS(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#a236858d6cb48a098159fc3d416f0499b',1,'DZ_FULL_LENGTH_BONUS(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#a236858d6cb48a098159fc3d416f0499b',1,'DZ_FULL_LENGTH_BONUS(): xdrop_aligner.cpp']]],
- ['dz_5fqual_5fadj_14131',['DZ_QUAL_ADJ',['../qual__adj__xdrop__aligner_8cpp.html#a16f2990aacdc62e8cee2b10e8e2bbad1',1,'qual_adj_xdrop_aligner.cpp']]]
+ ['debug_14132',['debug',['../minimizer__mapper__from__chains_8cpp.html#a322565ccf348d13e4d3de13af771e5fc',1,'minimizer_mapper_from_chains.cpp']]],
+ ['dz_5fcigar_5fop_14133',['DZ_CIGAR_OP',['../dozeu__interface_8cpp.html#af0acb761758e601c8c2111de1179c3cd',1,'DZ_CIGAR_OP(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#af0acb761758e601c8c2111de1179c3cd',1,'DZ_CIGAR_OP(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#af0acb761758e601c8c2111de1179c3cd',1,'DZ_CIGAR_OP(): xdrop_aligner.cpp']]],
+ ['dz_5ffull_5flength_5fbonus_14134',['DZ_FULL_LENGTH_BONUS',['../dozeu__interface_8cpp.html#a236858d6cb48a098159fc3d416f0499b',1,'DZ_FULL_LENGTH_BONUS(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#a236858d6cb48a098159fc3d416f0499b',1,'DZ_FULL_LENGTH_BONUS(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#a236858d6cb48a098159fc3d416f0499b',1,'DZ_FULL_LENGTH_BONUS(): xdrop_aligner.cpp']]],
+ ['dz_5fqual_5fadj_14135',['DZ_QUAL_ADJ',['../qual__adj__xdrop__aligner_8cpp.html#a16f2990aacdc62e8cee2b10e8e2bbad1',1,'qual_adj_xdrop_aligner.cpp']]]
];
diff --git a/search/defines_4.js b/search/defines_4.js
index d62be8bd8e..cc74471cdc 100644
--- a/search/defines_4.js
+++ b/search/defines_4.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['json_5fboolean_14132',['json_boolean',['../json2pb_8cpp.html#a250fb410df685e30b6cac97ff6e76982',1,'json2pb.cpp']]]
+ ['json_5fboolean_14136',['json_boolean',['../json2pb_8cpp.html#a250fb410df685e30b6cac97ff6e76982',1,'json2pb.cpp']]]
];
diff --git a/search/defines_5.js b/search/defines_5.js
index 224153e289..9e403711df 100644
--- a/search/defines_5.js
+++ b/search/defines_5.js
@@ -1,60 +1,60 @@
var searchData=
[
- ['opt_5falt_5fpaths_14133',['OPT_ALT_PATHS',['../mpmap__main_8cpp.html#ae91368cb24911fe1546ae429d8715963',1,'mpmap_main.cpp']]],
- ['opt_5falways_5fcheck_5fpopulation_14134',['OPT_ALWAYS_CHECK_POPULATION',['../mpmap__main_8cpp.html#a65c6fa4dc0d10a1eaa52a46cf7492f6f',1,'mpmap_main.cpp']]],
- ['opt_5fapprox_5fexp_14135',['OPT_APPROX_EXP',['../mpmap__main_8cpp.html#a2a31a7f2f254185a590fb21601013459',1,'mpmap_main.cpp']]],
- ['opt_5fband_5fpadding_5fmultiplier_14136',['OPT_BAND_PADDING_MULTIPLIER',['../mpmap__main_8cpp.html#a4e93612c9dd1d066ba7787a13c39d793',1,'mpmap_main.cpp']]],
- ['opt_5fbuild_5fvgi_5findex_14137',['OPT_BUILD_VGI_INDEX',['../index__main_8cpp.html#afb8482664ef525883ed18ceb46cdc029',1,'index_main.cpp']]],
- ['opt_5fcomments_5fas_5ftags_14138',['OPT_COMMENTS_AS_TAGS',['../map__main_8cpp.html#a06a0a0971a1dfb922cac7996800e0bef',1,'map_main.cpp']]],
- ['opt_5fcomponent_5fmin_5fdist_14139',['OPT_COMPONENT_MIN_DIST',['../mpmap__main_8cpp.html#a9536ee962e85c03f847a9618b7f4e380',1,'mpmap_main.cpp']]],
- ['opt_5fdistance_5fnesting_14140',['OPT_DISTANCE_NESTING',['../index__main_8cpp.html#a26828de6380594afa7c08082ff616945',1,'index_main.cpp']]],
- ['opt_5fdistance_5fsnarl_5flimit_14141',['OPT_DISTANCE_SNARL_LIMIT',['../index__main_8cpp.html#a368f75b8652409b081e17a5860e54734',1,'index_main.cpp']]],
- ['opt_5fdrop_5fsubgraph_14142',['OPT_DROP_SUBGRAPH',['../mpmap__main_8cpp.html#a54db45ba649a2cb8a4553756a909a262',1,'mpmap_main.cpp']]],
- ['opt_5fexclude_5funaligned_14143',['OPT_EXCLUDE_UNALIGNED',['../map__main_8cpp.html#a548f717dd20a48c17c3db507a0c3c53d',1,'map_main.cpp']]],
- ['opt_5ffan_5fout_5fdiff_14144',['OPT_FAN_OUT_DIFF',['../mpmap__main_8cpp.html#aa3d6561990f229c8b1fe723f0ab40bb5',1,'mpmap_main.cpp']]],
- ['opt_5ffan_5fout_5fqual_14145',['OPT_FAN_OUT_QUAL',['../mpmap__main_8cpp.html#a63b2b9f4e4cf89c48efc91e7ffff29ea',1,'mpmap_main.cpp']]],
- ['opt_5ffirst_14146',['OPT_FIRST',['../view__main_8cpp.html#a0a7d3e9f2f4f4183c4f010f692fcf0ff',1,'view_main.cpp']]],
- ['opt_5fforce_5fhaplotype_5fcount_14147',['OPT_FORCE_HAPLOTYPE_COUNT',['../mpmap__main_8cpp.html#a2b98cdcb665cd0cb6dcab27cd9b4b38c',1,'mpmap_main.cpp']]],
- ['opt_5fforce_5fphased_14148',['OPT_FORCE_PHASED',['../autoindex__main_8cpp.html#a97d7f5886eeeb66d54d3280476fe46d4',1,'autoindex_main.cpp']]],
- ['opt_5fforce_5funphased_14149',['OPT_FORCE_UNPHASED',['../autoindex__main_8cpp.html#a5d658d26d8f3dd160cc0ccff5badfed7',1,'autoindex_main.cpp']]],
- ['opt_5fgbwt_5fbuffer_5fsize_14150',['OPT_GBWT_BUFFER_SIZE',['../autoindex__main_8cpp.html#a74dae0f3f3b952725b2b6cfc699e9341',1,'autoindex_main.cpp']]],
- ['opt_5fgcsa_5fsize_5flimit_14151',['OPT_GCSA_SIZE_LIMIT',['../autoindex__main_8cpp.html#acef79b1df54f9953c5c43cfdb9fb5b76',1,'autoindex_main.cpp']]],
- ['opt_5fgreedy_5fmem_5frestart_5fmax_5flcp_14152',['OPT_GREEDY_MEM_RESTART_MAX_LCP',['../mpmap__main_8cpp.html#ac967783d971258300927dbeb273934b6',1,'mpmap_main.cpp']]],
- ['opt_5fgreedy_5fmin_5fdist_14153',['OPT_GREEDY_MIN_DIST',['../mpmap__main_8cpp.html#ab2c8c5abc8f0978ad62ffa9700eb2bda',1,'mpmap_main.cpp']]],
- ['opt_5fhard_5fhit_5fmax_5fmultiplier_14154',['OPT_HARD_HIT_MAX_MULTIPLIER',['../mpmap__main_8cpp.html#a714607df71e90bb572044f3632cc1ac4',1,'mpmap_main.cpp']]],
- ['opt_5fkeep_5fintermediate_14155',['OPT_KEEP_INTERMEDIATE',['../autoindex__main_8cpp.html#a6ca4cd9afa3306994612c96f8b66fb88',1,'autoindex_main.cpp']]],
- ['opt_5fmax_5ffans_5fout_14156',['OPT_MAX_FANS_OUT',['../mpmap__main_8cpp.html#af23caedc131b49443146ebb1aa947728',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5fmotif_5fpairs_14157',['OPT_MAX_MOTIF_PAIRS',['../mpmap__main_8cpp.html#a84de0c3bc2a757d008cb93b63f5273f8',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5fpaths_14158',['OPT_MAX_PATHS',['../mpmap__main_8cpp.html#a22ebe5149ddd91818874b5863ab26af0',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5frescue_5fattempts_14159',['OPT_MAX_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#a01622674e6cd85d2b1d18b9ad353b7d5',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5frescue_5fp_5fvalue_14160',['OPT_MAX_RESCUE_P_VALUE',['../mpmap__main_8cpp.html#a2f3fd1ec93d65c325e4c7a23f910096c',1,'mpmap_main.cpp']]],
- ['opt_5fmax_5ftries_14161',['OPT_MAX_TRIES',['../sim__main_8cpp.html#af8c2875728ccfaef5ba8a34e149c9f77',1,'sim_main.cpp']]],
- ['opt_5fmin_5fdist_5fcluster_14162',['OPT_MIN_DIST_CLUSTER',['../mpmap__main_8cpp.html#a6a4cfbe743edfb7bb7866bf370c1a85b',1,'mpmap_main.cpp']]],
- ['opt_5fmulti_5fposition_14163',['OPT_MULTI_POSITION',['../sim__main_8cpp.html#a003ddf1705dee4f9aa4deac88d1ee9d9',1,'sim_main.cpp']]],
- ['opt_5fno_5fcluster_14164',['OPT_NO_CLUSTER',['../mpmap__main_8cpp.html#a819f2221fe8ecbdde55f41e801ee526f',1,'mpmap_main.cpp']]],
- ['opt_5fno_5fembedded_5fhaplotypes_14165',['OPT_NO_EMBEDDED_HAPLOTYPES',['../chunk__main_8cpp.html#ab8f2d1809705b2b706d09e4f5bc3d12f',1,'chunk_main.cpp']]],
- ['opt_5fno_5fgreedy_5fmem_5frestarts_14166',['OPT_NO_GREEDY_MEM_RESTARTS',['../mpmap__main_8cpp.html#a795fe85937dd7884864a324a2e4e7e9c',1,'mpmap_main.cpp']]],
- ['opt_5fno_5foutput_14167',['OPT_NO_OUTPUT',['../mpmap__main_8cpp.html#ab3e182a23ff8ea38e53c1170d263bb8d',1,'mpmap_main.cpp']]],
- ['opt_5fpath_5frescue_5fgraph_14168',['OPT_PATH_RESCUE_GRAPH',['../mpmap__main_8cpp.html#aadbf32efd6566ba5c71b2be2c0c3e2af',1,'mpmap_main.cpp']]],
- ['opt_5fprune_5fexp_14169',['OPT_PRUNE_EXP',['../mpmap__main_8cpp.html#af3b2453f1e45ffd27c3cb9a08a39153a',1,'mpmap_main.cpp']]],
- ['opt_5frecombination_5fpenalty_14170',['OPT_RECOMBINATION_PENALTY',['../map__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): map_main.cpp'],['../mpmap__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): mpmap_main.cpp']]],
- ['opt_5fref_5fpaths_14171',['OPT_REF_PATHS',['../map__main_8cpp.html#ab0a122861e2617680fcbb125c8a35597',1,'map_main.cpp']]],
- ['opt_5frename_5fvariants_14172',['OPT_RENAME_VARIANTS',['../index__main_8cpp.html#a1a2c640fb0e31c93f6ea09e4209c9a6a',1,'index_main.cpp']]],
- ['opt_5freport_5fallelic_5fmapq_14173',['OPT_REPORT_ALLELIC_MAPQ',['../mpmap__main_8cpp.html#a75ef8adf7c285e0e422196252143479b',1,'mpmap_main.cpp']]],
- ['opt_5freseed_5flength_14174',['OPT_RESEED_LENGTH',['../mpmap__main_8cpp.html#afccac17d1c42a1ecde6864c183600654',1,'mpmap_main.cpp']]],
- ['opt_5fscore_5fmatrix_14175',['OPT_SCORE_MATRIX',['../align__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): align_main.cpp'],['../map__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): map_main.cpp']]],
- ['opt_5fsecondary_5fmax_5fdiff_14176',['OPT_SECONDARY_MAX_DIFF',['../mpmap__main_8cpp.html#a1783eb188d16ca662e0b6302086d350b',1,'mpmap_main.cpp']]],
- ['opt_5fsecondary_5frescue_5fattempts_14177',['OPT_SECONDARY_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#ad104748288226e8b7051688389fdd714',1,'mpmap_main.cpp']]],
- ['opt_5fshort_5fmem_5ffilter_5ffactor_14178',['OPT_SHORT_MEM_FILTER_FACTOR',['../mpmap__main_8cpp.html#a318c97f0fac2cb91d18d7fca8772bf7f',1,'mpmap_main.cpp']]],
- ['opt_5fsnarl_5fmax_5fcut_14179',['OPT_SNARL_MAX_CUT',['../mpmap__main_8cpp.html#a0d81815c562f38902b6acadf68474b9a',1,'mpmap_main.cpp']]],
- ['opt_5fsplice_5fodds_14180',['OPT_SPLICE_ODDS',['../mpmap__main_8cpp.html#ade429c9659d1caaf057d4be159c6c06c',1,'mpmap_main.cpp']]],
- ['opt_5fstrip_5fcount_14181',['OPT_STRIP_COUNT',['../mpmap__main_8cpp.html#ad8233b7b00bc4fa0c87c4af3ed501cfd',1,'mpmap_main.cpp']]],
- ['opt_5fstrip_5flength_14182',['OPT_STRIP_LENGTH',['../mpmap__main_8cpp.html#abe95d7c95e55ac2cc94394e657ce16fd',1,'mpmap_main.cpp']]],
- ['opt_5fstripped_5fmatch_14183',['OPT_STRIPPED_MATCH',['../mpmap__main_8cpp.html#a241677bb449101778f187f6be8cdd2a0',1,'mpmap_main.cpp']]],
- ['opt_5fsuppress_5fmismapping_5fdetection_14184',['OPT_SUPPRESS_MISMAPPING_DETECTION',['../mpmap__main_8cpp.html#a95206e9809c284c88f971c57c56cbb39',1,'mpmap_main.cpp']]],
- ['opt_5fsuppress_5fsuppression_14185',['OPT_SUPPRESS_SUPPRESSION',['../mpmap__main_8cpp.html#a5642b35bcfa16b180f0e4e6dcf0536ad',1,'mpmap_main.cpp']]],
- ['opt_5fsuppress_5ftail_5fanchors_14186',['OPT_SUPPRESS_TAIL_ANCHORS',['../mpmap__main_8cpp.html#a8ac418f2741d5efc457e6ab40a535262',1,'mpmap_main.cpp']]],
- ['opt_5ftop_5ftracebacks_14187',['OPT_TOP_TRACEBACKS',['../mpmap__main_8cpp.html#a497dfa18c690f36ffeb9370dde515b7d',1,'mpmap_main.cpp']]],
- ['opt_5fverbose_14188',['OPT_VERBOSE',['../view__main_8cpp.html#ae33534a21238a3d0a2a892bb0bfd84be',1,'view_main.cpp']]],
- ['overload_5fpair_5fhash_14189',['OVERLOAD_PAIR_HASH',['../hash__map_8hpp.html#a181224ba2835ac80e940ef8505d5f119',1,'hash_map.hpp']]]
+ ['opt_5falt_5fpaths_14137',['OPT_ALT_PATHS',['../mpmap__main_8cpp.html#ae91368cb24911fe1546ae429d8715963',1,'mpmap_main.cpp']]],
+ ['opt_5falways_5fcheck_5fpopulation_14138',['OPT_ALWAYS_CHECK_POPULATION',['../mpmap__main_8cpp.html#a65c6fa4dc0d10a1eaa52a46cf7492f6f',1,'mpmap_main.cpp']]],
+ ['opt_5fapprox_5fexp_14139',['OPT_APPROX_EXP',['../mpmap__main_8cpp.html#a2a31a7f2f254185a590fb21601013459',1,'mpmap_main.cpp']]],
+ ['opt_5fband_5fpadding_5fmultiplier_14140',['OPT_BAND_PADDING_MULTIPLIER',['../mpmap__main_8cpp.html#a4e93612c9dd1d066ba7787a13c39d793',1,'mpmap_main.cpp']]],
+ ['opt_5fbuild_5fvgi_5findex_14141',['OPT_BUILD_VGI_INDEX',['../index__main_8cpp.html#afb8482664ef525883ed18ceb46cdc029',1,'index_main.cpp']]],
+ ['opt_5fcomments_5fas_5ftags_14142',['OPT_COMMENTS_AS_TAGS',['../map__main_8cpp.html#a06a0a0971a1dfb922cac7996800e0bef',1,'map_main.cpp']]],
+ ['opt_5fcomponent_5fmin_5fdist_14143',['OPT_COMPONENT_MIN_DIST',['../mpmap__main_8cpp.html#a9536ee962e85c03f847a9618b7f4e380',1,'mpmap_main.cpp']]],
+ ['opt_5fdistance_5fnesting_14144',['OPT_DISTANCE_NESTING',['../index__main_8cpp.html#a26828de6380594afa7c08082ff616945',1,'index_main.cpp']]],
+ ['opt_5fdistance_5fsnarl_5flimit_14145',['OPT_DISTANCE_SNARL_LIMIT',['../index__main_8cpp.html#a368f75b8652409b081e17a5860e54734',1,'index_main.cpp']]],
+ ['opt_5fdrop_5fsubgraph_14146',['OPT_DROP_SUBGRAPH',['../mpmap__main_8cpp.html#a54db45ba649a2cb8a4553756a909a262',1,'mpmap_main.cpp']]],
+ ['opt_5fexclude_5funaligned_14147',['OPT_EXCLUDE_UNALIGNED',['../map__main_8cpp.html#a548f717dd20a48c17c3db507a0c3c53d',1,'map_main.cpp']]],
+ ['opt_5ffan_5fout_5fdiff_14148',['OPT_FAN_OUT_DIFF',['../mpmap__main_8cpp.html#aa3d6561990f229c8b1fe723f0ab40bb5',1,'mpmap_main.cpp']]],
+ ['opt_5ffan_5fout_5fqual_14149',['OPT_FAN_OUT_QUAL',['../mpmap__main_8cpp.html#a63b2b9f4e4cf89c48efc91e7ffff29ea',1,'mpmap_main.cpp']]],
+ ['opt_5ffirst_14150',['OPT_FIRST',['../view__main_8cpp.html#a0a7d3e9f2f4f4183c4f010f692fcf0ff',1,'view_main.cpp']]],
+ ['opt_5fforce_5fhaplotype_5fcount_14151',['OPT_FORCE_HAPLOTYPE_COUNT',['../mpmap__main_8cpp.html#a2b98cdcb665cd0cb6dcab27cd9b4b38c',1,'mpmap_main.cpp']]],
+ ['opt_5fforce_5fphased_14152',['OPT_FORCE_PHASED',['../autoindex__main_8cpp.html#a97d7f5886eeeb66d54d3280476fe46d4',1,'autoindex_main.cpp']]],
+ ['opt_5fforce_5funphased_14153',['OPT_FORCE_UNPHASED',['../autoindex__main_8cpp.html#a5d658d26d8f3dd160cc0ccff5badfed7',1,'autoindex_main.cpp']]],
+ ['opt_5fgbwt_5fbuffer_5fsize_14154',['OPT_GBWT_BUFFER_SIZE',['../autoindex__main_8cpp.html#a74dae0f3f3b952725b2b6cfc699e9341',1,'autoindex_main.cpp']]],
+ ['opt_5fgcsa_5fsize_5flimit_14155',['OPT_GCSA_SIZE_LIMIT',['../autoindex__main_8cpp.html#acef79b1df54f9953c5c43cfdb9fb5b76',1,'autoindex_main.cpp']]],
+ ['opt_5fgreedy_5fmem_5frestart_5fmax_5flcp_14156',['OPT_GREEDY_MEM_RESTART_MAX_LCP',['../mpmap__main_8cpp.html#ac967783d971258300927dbeb273934b6',1,'mpmap_main.cpp']]],
+ ['opt_5fgreedy_5fmin_5fdist_14157',['OPT_GREEDY_MIN_DIST',['../mpmap__main_8cpp.html#ab2c8c5abc8f0978ad62ffa9700eb2bda',1,'mpmap_main.cpp']]],
+ ['opt_5fhard_5fhit_5fmax_5fmultiplier_14158',['OPT_HARD_HIT_MAX_MULTIPLIER',['../mpmap__main_8cpp.html#a714607df71e90bb572044f3632cc1ac4',1,'mpmap_main.cpp']]],
+ ['opt_5fkeep_5fintermediate_14159',['OPT_KEEP_INTERMEDIATE',['../autoindex__main_8cpp.html#a6ca4cd9afa3306994612c96f8b66fb88',1,'autoindex_main.cpp']]],
+ ['opt_5fmax_5ffans_5fout_14160',['OPT_MAX_FANS_OUT',['../mpmap__main_8cpp.html#af23caedc131b49443146ebb1aa947728',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5fmotif_5fpairs_14161',['OPT_MAX_MOTIF_PAIRS',['../mpmap__main_8cpp.html#a84de0c3bc2a757d008cb93b63f5273f8',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5fpaths_14162',['OPT_MAX_PATHS',['../mpmap__main_8cpp.html#a22ebe5149ddd91818874b5863ab26af0',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5frescue_5fattempts_14163',['OPT_MAX_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#a01622674e6cd85d2b1d18b9ad353b7d5',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5frescue_5fp_5fvalue_14164',['OPT_MAX_RESCUE_P_VALUE',['../mpmap__main_8cpp.html#a2f3fd1ec93d65c325e4c7a23f910096c',1,'mpmap_main.cpp']]],
+ ['opt_5fmax_5ftries_14165',['OPT_MAX_TRIES',['../sim__main_8cpp.html#af8c2875728ccfaef5ba8a34e149c9f77',1,'sim_main.cpp']]],
+ ['opt_5fmin_5fdist_5fcluster_14166',['OPT_MIN_DIST_CLUSTER',['../mpmap__main_8cpp.html#a6a4cfbe743edfb7bb7866bf370c1a85b',1,'mpmap_main.cpp']]],
+ ['opt_5fmulti_5fposition_14167',['OPT_MULTI_POSITION',['../sim__main_8cpp.html#a003ddf1705dee4f9aa4deac88d1ee9d9',1,'sim_main.cpp']]],
+ ['opt_5fno_5fcluster_14168',['OPT_NO_CLUSTER',['../mpmap__main_8cpp.html#a819f2221fe8ecbdde55f41e801ee526f',1,'mpmap_main.cpp']]],
+ ['opt_5fno_5fembedded_5fhaplotypes_14169',['OPT_NO_EMBEDDED_HAPLOTYPES',['../chunk__main_8cpp.html#ab8f2d1809705b2b706d09e4f5bc3d12f',1,'chunk_main.cpp']]],
+ ['opt_5fno_5fgreedy_5fmem_5frestarts_14170',['OPT_NO_GREEDY_MEM_RESTARTS',['../mpmap__main_8cpp.html#a795fe85937dd7884864a324a2e4e7e9c',1,'mpmap_main.cpp']]],
+ ['opt_5fno_5foutput_14171',['OPT_NO_OUTPUT',['../mpmap__main_8cpp.html#ab3e182a23ff8ea38e53c1170d263bb8d',1,'mpmap_main.cpp']]],
+ ['opt_5fpath_5frescue_5fgraph_14172',['OPT_PATH_RESCUE_GRAPH',['../mpmap__main_8cpp.html#aadbf32efd6566ba5c71b2be2c0c3e2af',1,'mpmap_main.cpp']]],
+ ['opt_5fprune_5fexp_14173',['OPT_PRUNE_EXP',['../mpmap__main_8cpp.html#af3b2453f1e45ffd27c3cb9a08a39153a',1,'mpmap_main.cpp']]],
+ ['opt_5frecombination_5fpenalty_14174',['OPT_RECOMBINATION_PENALTY',['../map__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): map_main.cpp'],['../mpmap__main_8cpp.html#aa2bc6ed2ecef5672fcbf4c1d07b8d964',1,'OPT_RECOMBINATION_PENALTY(): mpmap_main.cpp']]],
+ ['opt_5fref_5fpaths_14175',['OPT_REF_PATHS',['../map__main_8cpp.html#ab0a122861e2617680fcbb125c8a35597',1,'map_main.cpp']]],
+ ['opt_5frename_5fvariants_14176',['OPT_RENAME_VARIANTS',['../index__main_8cpp.html#a1a2c640fb0e31c93f6ea09e4209c9a6a',1,'index_main.cpp']]],
+ ['opt_5freport_5fallelic_5fmapq_14177',['OPT_REPORT_ALLELIC_MAPQ',['../mpmap__main_8cpp.html#a75ef8adf7c285e0e422196252143479b',1,'mpmap_main.cpp']]],
+ ['opt_5freseed_5flength_14178',['OPT_RESEED_LENGTH',['../mpmap__main_8cpp.html#afccac17d1c42a1ecde6864c183600654',1,'mpmap_main.cpp']]],
+ ['opt_5fscore_5fmatrix_14179',['OPT_SCORE_MATRIX',['../align__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): align_main.cpp'],['../map__main_8cpp.html#abda380f5cc9d8b15937d4f67d559fef5',1,'OPT_SCORE_MATRIX(): map_main.cpp']]],
+ ['opt_5fsecondary_5fmax_5fdiff_14180',['OPT_SECONDARY_MAX_DIFF',['../mpmap__main_8cpp.html#a1783eb188d16ca662e0b6302086d350b',1,'mpmap_main.cpp']]],
+ ['opt_5fsecondary_5frescue_5fattempts_14181',['OPT_SECONDARY_RESCUE_ATTEMPTS',['../mpmap__main_8cpp.html#ad104748288226e8b7051688389fdd714',1,'mpmap_main.cpp']]],
+ ['opt_5fshort_5fmem_5ffilter_5ffactor_14182',['OPT_SHORT_MEM_FILTER_FACTOR',['../mpmap__main_8cpp.html#a318c97f0fac2cb91d18d7fca8772bf7f',1,'mpmap_main.cpp']]],
+ ['opt_5fsnarl_5fmax_5fcut_14183',['OPT_SNARL_MAX_CUT',['../mpmap__main_8cpp.html#a0d81815c562f38902b6acadf68474b9a',1,'mpmap_main.cpp']]],
+ ['opt_5fsplice_5fodds_14184',['OPT_SPLICE_ODDS',['../mpmap__main_8cpp.html#ade429c9659d1caaf057d4be159c6c06c',1,'mpmap_main.cpp']]],
+ ['opt_5fstrip_5fcount_14185',['OPT_STRIP_COUNT',['../mpmap__main_8cpp.html#ad8233b7b00bc4fa0c87c4af3ed501cfd',1,'mpmap_main.cpp']]],
+ ['opt_5fstrip_5flength_14186',['OPT_STRIP_LENGTH',['../mpmap__main_8cpp.html#abe95d7c95e55ac2cc94394e657ce16fd',1,'mpmap_main.cpp']]],
+ ['opt_5fstripped_5fmatch_14187',['OPT_STRIPPED_MATCH',['../mpmap__main_8cpp.html#a241677bb449101778f187f6be8cdd2a0',1,'mpmap_main.cpp']]],
+ ['opt_5fsuppress_5fmismapping_5fdetection_14188',['OPT_SUPPRESS_MISMAPPING_DETECTION',['../mpmap__main_8cpp.html#a95206e9809c284c88f971c57c56cbb39',1,'mpmap_main.cpp']]],
+ ['opt_5fsuppress_5fsuppression_14189',['OPT_SUPPRESS_SUPPRESSION',['../mpmap__main_8cpp.html#a5642b35bcfa16b180f0e4e6dcf0536ad',1,'mpmap_main.cpp']]],
+ ['opt_5fsuppress_5ftail_5fanchors_14190',['OPT_SUPPRESS_TAIL_ANCHORS',['../mpmap__main_8cpp.html#a8ac418f2741d5efc457e6ab40a535262',1,'mpmap_main.cpp']]],
+ ['opt_5ftop_5ftracebacks_14191',['OPT_TOP_TRACEBACKS',['../mpmap__main_8cpp.html#a497dfa18c690f36ffeb9370dde515b7d',1,'mpmap_main.cpp']]],
+ ['opt_5fverbose_14192',['OPT_VERBOSE',['../view__main_8cpp.html#ae33534a21238a3d0a2a892bb0bfd84be',1,'view_main.cpp']]],
+ ['overload_5fpair_5fhash_14193',['OVERLOAD_PAIR_HASH',['../hash__map_8hpp.html#a181224ba2835ac80e940ef8505d5f119',1,'hash_map.hpp']]]
];
diff --git a/search/defines_6.js b/search/defines_6.js
index efa92042a8..80bd3630bf 100644
--- a/search/defines_6.js
+++ b/search/defines_6.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['quote_14190',['QUOTE',['../version_8cpp.html#a1e7841038b1293b9a250d8999f6c8ac8',1,'version.cpp']]]
+ ['quote_14194',['QUOTE',['../version_8cpp.html#a1e7841038b1293b9a250d8999f6c8ac8',1,'version.cpp']]]
];
diff --git a/search/defines_7.js b/search/defines_7.js
index 1e2d7b8c66..5d31e8c9e3 100644
--- a/search/defines_7.js
+++ b/search/defines_7.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['settotalbyteslimit_14191',['SetTotalBytesLimit',['../message__iterator_8hpp.html#ad3271079865fad5b2725dab227556443',1,'message_iterator.hpp']]],
- ['str_14192',['STR',['../version_8cpp.html#a6a96991688ffe6ae2293f0a4b5f813d2',1,'version.cpp']]]
+ ['settotalbyteslimit_14195',['SetTotalBytesLimit',['../message__iterator_8hpp.html#ad3271079865fad5b2725dab227556443',1,'message_iterator.hpp']]],
+ ['str_14196',['STR',['../version_8cpp.html#a6a96991688ffe6ae2293f0a4b5f813d2',1,'version.cpp']]]
];
diff --git a/search/defines_8.js b/search/defines_8.js
index 61b9023b30..b46b3dfd9c 100644
--- a/search/defines_8.js
+++ b/search/defines_8.js
@@ -1,11 +1,11 @@
var searchData=
[
- ['vg_5fbuild_5fhost_14193',['VG_BUILD_HOST',['../vg__environment__version_8hpp.html#a2baea5938fa1a9b70e6a27ccc59c65d9',1,'vg_environment_version.hpp']]],
- ['vg_5fbuild_5fuser_14194',['VG_BUILD_USER',['../vg__environment__version_8hpp.html#a95dd87e623e9d0c99f662e3d2ca6676d',1,'vg_environment_version.hpp']]],
- ['vg_5fcompiler_5fversion_14195',['VG_COMPILER_VERSION',['../vg__environment__version_8hpp.html#a018858ebcbef9ca466d11e0f9effd990',1,'vg_environment_version.hpp']]],
- ['vg_5fgit_5fversion_14196',['VG_GIT_VERSION',['../vg__git__version_8hpp.html#a5df50394a80dec8f6151eb57db04a38a',1,'vg_git_version.hpp']]],
- ['vg_5fhtslib_5fversion_14197',['VG_HTSLIB_VERSION',['../version_8cpp.html#a0b12716ad9e947816319b2c448b942f3',1,'version.cpp']]],
- ['vg_5fos_14198',['VG_OS',['../vg__environment__version_8hpp.html#a4b1110f54b4fd6d1242837dee0dbc820',1,'vg_environment_version.hpp']]],
- ['vg_5fpreflight_5feverywhere_14199',['VG_PREFLIGHT_EVERYWHERE',['../preflight_8hpp.html#a15a8edc41d783e0cc08568efe26a83fd',1,'preflight.hpp']]],
- ['vg_5fstandard_5flibrary_5fversion_14200',['VG_STANDARD_LIBRARY_VERSION',['../version_8cpp.html#a923fcc9a50a1ddbec3aa567d4f91d576',1,'version.cpp']]]
+ ['vg_5fbuild_5fhost_14197',['VG_BUILD_HOST',['../vg__environment__version_8hpp.html#a2baea5938fa1a9b70e6a27ccc59c65d9',1,'vg_environment_version.hpp']]],
+ ['vg_5fbuild_5fuser_14198',['VG_BUILD_USER',['../vg__environment__version_8hpp.html#a95dd87e623e9d0c99f662e3d2ca6676d',1,'vg_environment_version.hpp']]],
+ ['vg_5fcompiler_5fversion_14199',['VG_COMPILER_VERSION',['../vg__environment__version_8hpp.html#a018858ebcbef9ca466d11e0f9effd990',1,'vg_environment_version.hpp']]],
+ ['vg_5fgit_5fversion_14200',['VG_GIT_VERSION',['../vg__git__version_8hpp.html#a5df50394a80dec8f6151eb57db04a38a',1,'vg_git_version.hpp']]],
+ ['vg_5fhtslib_5fversion_14201',['VG_HTSLIB_VERSION',['../version_8cpp.html#a0b12716ad9e947816319b2c448b942f3',1,'version.cpp']]],
+ ['vg_5fos_14202',['VG_OS',['../vg__environment__version_8hpp.html#a4b1110f54b4fd6d1242837dee0dbc820',1,'vg_environment_version.hpp']]],
+ ['vg_5fpreflight_5feverywhere_14203',['VG_PREFLIGHT_EVERYWHERE',['../preflight_8hpp.html#a15a8edc41d783e0cc08568efe26a83fd',1,'preflight.hpp']]],
+ ['vg_5fstandard_5flibrary_5fversion_14204',['VG_STANDARD_LIBRARY_VERSION',['../version_8cpp.html#a923fcc9a50a1ddbec3aa567d4f91d576',1,'version.cpp']]]
];
diff --git a/search/enums_0.js b/search/enums_0.js
index e0baea70ad..f514d57ec9 100644
--- a/search/enums_0.js
+++ b/search/enums_0.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['algorithm_5ftype_13883',['algorithm_type',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165',1,'convert_main.cpp']]],
- ['alignment_5femitter_5fflags_5ft_13884',['alignment_emitter_flags_t',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5',1,'vg']]],
- ['anno_5ftype_5ft_13885',['anno_type_t',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095e',1,'vg::multipath_alignment_t']]]
+ ['algorithm_5ftype_13887',['algorithm_type',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165',1,'convert_main.cpp']]],
+ ['alignment_5femitter_5fflags_5ft_13888',['alignment_emitter_flags_t',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5',1,'vg']]],
+ ['anno_5ftype_5ft_13889',['anno_type_t',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095e',1,'vg::multipath_alignment_t']]]
];
diff --git a/search/enums_1.js b/search/enums_1.js
index 7aa822e360..ad63b5ea35 100644
--- a/search/enums_1.js
+++ b/search/enums_1.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['build_5fmode_13886',['build_mode',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685',1,'GBWTConfig']]]
+ ['build_5fmode_13890',['build_mode',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685',1,'GBWTConfig']]]
];
diff --git a/search/enums_2.js b/search/enums_2.js
index c4478d2a42..b37fb93049 100644
--- a/search/enums_2.js
+++ b/search/enums_2.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['code_5ftype_5ft_13887',['code_type_t',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3',1,'vg::ZipCode']]],
- ['commandcategory_13888',['CommandCategory',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838',1,'vg::subcommand']]]
+ ['code_5ftype_5ft_13891',['code_type_t',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3',1,'vg::ZipCode']]],
+ ['commandcategory_13892',['CommandCategory',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838',1,'vg::subcommand']]]
];
diff --git a/search/enums_3.js b/search/enums_3.js
index 28f7f73964..071bedfb24 100644
--- a/search/enums_3.js
+++ b/search/enums_3.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['edit_13889',['Edit',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeb',1,'vg::WFAAlignment']]],
- ['endpoint_5ft_13890',['endpoint_t',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3',1,'handlegraph::SnarlDecomposition']]]
+ ['edit_13893',['Edit',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeb',1,'vg::WFAAlignment']]],
+ ['endpoint_5ft_13894',['endpoint_t',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3',1,'handlegraph::SnarlDecomposition']]]
];
diff --git a/search/enums_4.js b/search/enums_4.js
index 943341dfaf..1f73bc537e 100644
--- a/search/enums_4.js
+++ b/search/enums_4.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['filtername_13891',['FilterName',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9',1,'vg::Counts']]]
+ ['filtername_13895',['FilterName',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9',1,'vg::Counts']]]
];
diff --git a/search/enums_5.js b/search/enums_5.js
index 4903af3388..b6535d12f2 100644
--- a/search/enums_5.js
+++ b/search/enums_5.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['graph_5ftype_13892',['graph_type',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50',1,'GraphHandler']]]
+ ['graph_5ftype_13896',['graph_type',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50',1,'GraphHandler']]]
];
diff --git a/search/enums_6.js b/search/enums_6.js
index 7fa4c597a1..5900d19399 100644
--- a/search/enums_6.js
+++ b/search/enums_6.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['index_5ftype_13893',['index_type',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033',1,'vg::GBWTHandler']]],
- ['input_5ftype_13894',['input_type',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8ef',1,'convert_main.cpp']]]
+ ['index_5ftype_13897',['index_type',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033',1,'vg::GBWTHandler']]],
+ ['input_5ftype_13898',['input_type',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8ef',1,'convert_main.cpp']]]
];
diff --git a/search/enums_7.js b/search/enums_7.js
index 51b4e7f857..db0332f891 100644
--- a/search/enums_7.js
+++ b/search/enums_7.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['kmer_5fpresence_13895',['kmer_presence',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5f',1,'vg::Recombinator']]]
+ ['kmer_5fpresence_13899',['kmer_presence',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5f',1,'vg::Recombinator']]]
];
diff --git a/search/enums_8.js b/search/enums_8.js
index f316f87fd9..7b0d3e37a2 100644
--- a/search/enums_8.js
+++ b/search/enums_8.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['mappingqualitymethod_13896',['MappingQualityMethod',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39',1,'vg']]],
- ['matrix_5ft_13897',['matrix_t',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2f',1,'vg::BandedGlobalAligner']]],
- ['merge_5fmode_13898',['merge_mode',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0f',1,'GBWTConfig']]],
- ['mutablegraphimplementation_13899',['MutableGraphImplementation',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10',1,'vg::IndexingParameters']]]
+ ['mappingqualitymethod_13900',['MappingQualityMethod',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39',1,'vg']]],
+ ['matrix_5ft_13901',['matrix_t',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2f',1,'vg::BandedGlobalAligner']]],
+ ['merge_5fmode_13902',['merge_mode',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0f',1,'GBWTConfig']]],
+ ['mutablegraphimplementation_13903',['MutableGraphImplementation',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10',1,'vg::IndexingParameters']]]
];
diff --git a/search/enums_9.js b/search/enums_9.js
index eaad879ac2..79bd794b29 100644
--- a/search/enums_9.js
+++ b/search/enums_9.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['nodetype_13900',['nodeType',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8',1,'haplo::linear_haplo_structure']]]
+ ['nodetype_13904',['nodeType',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8',1,'haplo::linear_haplo_structure']]]
];
diff --git a/search/enums_a.js b/search/enums_a.js
index b4db6efd15..36e0d41212 100644
--- a/search/enums_a.js
+++ b/search/enums_a.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['operatingmode_13901',['OperatingMode',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667',1,'HaplotypesConfig']]],
- ['optionformat_13902',['OptionFormat',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9f',1,'vg::subcommand']]],
- ['order_13903',['Order',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046b',1,'vg::StreamSorter::Order()'],['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894a',1,'ReferenceInterval::order()']]],
- ['output_5fformat_5ft_13904',['output_format_t',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0b',1,'vg::MultipathAlignmentEmitter']]]
+ ['operatingmode_13905',['OperatingMode',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667',1,'HaplotypesConfig']]],
+ ['optionformat_13906',['OptionFormat',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9f',1,'vg::subcommand']]],
+ ['order_13907',['Order',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046b',1,'vg::StreamSorter::Order()'],['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894a',1,'ReferenceInterval::order()']]],
+ ['output_5fformat_5ft_13908',['output_format_t',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0b',1,'vg::MultipathAlignmentEmitter']]]
];
diff --git a/search/enums_b.js b/search/enums_b.js
index 90ea3a1d64..c7349f0a6c 100644
--- a/search/enums_b.js
+++ b/search/enums_b.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['path_5fcover_5fmode_13905',['path_cover_mode',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1',1,'GBWTConfig']]],
- ['pathsense_13906',['PathSense',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271c',1,'handlegraph']]],
- ['preset_5ft_13907',['preset_t',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4',1,'vg::Recombinator::Parameters']]],
- ['problem_13908',['Problem',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9',1,'vg::AlignmentValidity']]],
- ['pruningmode_13909',['PruningMode',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248',1,'prune_main.cpp']]]
+ ['path_5fcover_5fmode_13909',['path_cover_mode',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1',1,'GBWTConfig']]],
+ ['pathsense_13910',['PathSense',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271c',1,'handlegraph']]],
+ ['preset_5ft_13911',['preset_t',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4',1,'vg::Recombinator::Parameters']]],
+ ['problem_13912',['Problem',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9',1,'vg::AlignmentValidity']]],
+ ['pruningmode_13913',['PruningMode',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248',1,'prune_main.cpp']]]
];
diff --git a/search/enums_c.js b/search/enums_c.js
index e80e865371..b114d64ff9 100644
--- a/search/enums_c.js
+++ b/search/enums_c.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['recursetype_13910',['RecurseType',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5',1,'vg::GraphCaller']]],
- ['rescuealgorithm_13911',['RescueAlgorithm',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4',1,'vg::MinimizerMapper']]]
+ ['recursetype_13914',['RecurseType',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5',1,'vg::GraphCaller']]],
+ ['rescuealgorithm_13915',['RescueAlgorithm',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4',1,'vg::MinimizerMapper']]]
];
diff --git a/search/enums_d.js b/search/enums_d.js
index fa09431265..c6899f651e 100644
--- a/search/enums_d.js
+++ b/search/enums_d.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['snarltype_13912',['SnarlType',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97',1,'vg']]],
- ['splicestrand_13913',['SpliceStrand',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccd',1,'vg::MultipathMapper']]],
- ['state_13914',['State',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85',1,'vg::Funnel::State()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19',1,'vg::ZipCodeTree::reverse_iterator::State()']]],
- ['subchain_5ft_13915',['subchain_t',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbde',1,'vg::Haplotypes::Subchain']]]
+ ['snarltype_13916',['SnarlType',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97',1,'vg']]],
+ ['splicestrand_13917',['SpliceStrand',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccd',1,'vg::MultipathMapper']]],
+ ['state_13918',['State',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85',1,'vg::Funnel::State()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19',1,'vg::ZipCodeTree::reverse_iterator::State()']]],
+ ['subchain_5ft_13919',['subchain_t',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbde',1,'vg::Haplotypes::Subchain']]]
];
diff --git a/search/enums_e.js b/search/enums_e.js
index 9908a95b36..aa2289830f 100644
--- a/search/enums_e.js
+++ b/search/enums_e.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['traversalalg_13916',['TraversalAlg',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4',1,'vg::Genotyper']]],
- ['tree_5fitem_5ftype_5ft_13917',['tree_item_type_t',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ad',1,'vg::ZipCodeTree']]]
+ ['traversalalg_13920',['TraversalAlg',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4',1,'vg::Genotyper']]],
+ ['tree_5fitem_5ftype_5ft_13921',['tree_item_type_t',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ad',1,'vg::ZipCodeTree']]]
];
diff --git a/search/enums_f.js b/search/enums_f.js
index 360b0c6834..bf906c89fc 100644
--- a/search/enums_f.js
+++ b/search/enums_f.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['verbosity_13918',['Verbosity',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3',1,'vg::IndexingParameters::Verbosity()'],['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28a',1,'vg::Haplotypes::Verbosity()']]]
+ ['verbosity_13922',['Verbosity',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3',1,'vg::IndexingParameters::Verbosity()'],['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28a',1,'vg::Haplotypes::Verbosity()']]]
];
diff --git a/search/enumvalues_0.js b/search/enumvalues_0.js
index 5882e60067..8a6f320491 100644
--- a/search/enumvalues_0.js
+++ b/search/enumvalues_0.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['absent_13919',['absent',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa38113783fd68477aac0ec616b4ed4fb9',1,'vg::Recombinator']]],
- ['adaptive_13920',['Adaptive',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4ab530b2114d4cd7f36bb3a41c01928995',1,'vg::Genotyper::Adaptive()'],['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39a0f1da9e8a7bb929e940b4fa8be187340',1,'vg::Adaptive()']]],
- ['after_13921',['after',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aa1fc4c09b7bf2d74b74b8eda9e06df74d',1,'ReferenceInterval']]],
- ['algorithm_5fauto_13922',['algorithm_auto',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165a4ab9b7aa476786439997fe37d2eb0e2a',1,'convert_main.cpp']]],
- ['algorithm_5fgbwtgraph_13923',['algorithm_gbwtgraph',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165aec7546f54d00ba7695453b0642db76bb',1,'convert_main.cpp']]],
- ['algorithm_5fvg_13924',['algorithm_vg',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165a2987c27c5c0e7d37f1dede8a94966e86',1,'convert_main.cpp']]],
- ['alignment_5femitter_5fflag_5fhts_5fprune_5fsuspicious_5fanchors_13925',['ALIGNMENT_EMITTER_FLAG_HTS_PRUNE_SUSPICIOUS_ANCHORS',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5ad2539e657e6f87051e9f12489f9bb557',1,'vg']]],
- ['alignment_5femitter_5fflag_5fhts_5fraw_13926',['ALIGNMENT_EMITTER_FLAG_HTS_RAW',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a311ead9579740c16ac55d9eaff3953e0',1,'vg']]],
- ['alignment_5femitter_5fflag_5fhts_5fspliced_13927',['ALIGNMENT_EMITTER_FLAG_HTS_SPLICED',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a3388a03ab2e5b8dec8d422db673b00b3',1,'vg']]],
- ['alignment_5femitter_5fflag_5fnone_13928',['ALIGNMENT_EMITTER_FLAG_NONE',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a77d3ea80cba8f3d89e573bf723ea7f4f',1,'vg']]],
- ['alignment_5femitter_5fflag_5fvg_5fuse_5fsegment_5fnames_13929',['ALIGNMENT_EMITTER_FLAG_VG_USE_SEGMENT_NAMES',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a3ea893f3dade371704d31df4070e95fd',1,'vg']]],
- ['annotation_13930',['annotation',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a40f61be34cdcd40a99f5ec2fb6069cc1',1,'vg::Counts']]],
- ['approx_13931',['Approx',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39a9ab31888ec6c2da1a29c051c49f2d5ea',1,'vg']]]
+ ['absent_13923',['absent',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa38113783fd68477aac0ec616b4ed4fb9',1,'vg::Recombinator']]],
+ ['adaptive_13924',['Adaptive',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4ab530b2114d4cd7f36bb3a41c01928995',1,'vg::Genotyper::Adaptive()'],['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39a0f1da9e8a7bb929e940b4fa8be187340',1,'vg::Adaptive()']]],
+ ['after_13925',['after',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aa1fc4c09b7bf2d74b74b8eda9e06df74d',1,'ReferenceInterval']]],
+ ['algorithm_5fauto_13926',['algorithm_auto',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165a4ab9b7aa476786439997fe37d2eb0e2a',1,'convert_main.cpp']]],
+ ['algorithm_5fgbwtgraph_13927',['algorithm_gbwtgraph',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165aec7546f54d00ba7695453b0642db76bb',1,'convert_main.cpp']]],
+ ['algorithm_5fvg_13928',['algorithm_vg',['../convert__main_8cpp.html#ac6768b485302681fa674deef6df58165a2987c27c5c0e7d37f1dede8a94966e86',1,'convert_main.cpp']]],
+ ['alignment_5femitter_5fflag_5fhts_5fprune_5fsuspicious_5fanchors_13929',['ALIGNMENT_EMITTER_FLAG_HTS_PRUNE_SUSPICIOUS_ANCHORS',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5ad2539e657e6f87051e9f12489f9bb557',1,'vg']]],
+ ['alignment_5femitter_5fflag_5fhts_5fraw_13930',['ALIGNMENT_EMITTER_FLAG_HTS_RAW',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a311ead9579740c16ac55d9eaff3953e0',1,'vg']]],
+ ['alignment_5femitter_5fflag_5fhts_5fspliced_13931',['ALIGNMENT_EMITTER_FLAG_HTS_SPLICED',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a3388a03ab2e5b8dec8d422db673b00b3',1,'vg']]],
+ ['alignment_5femitter_5fflag_5fnone_13932',['ALIGNMENT_EMITTER_FLAG_NONE',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a77d3ea80cba8f3d89e573bf723ea7f4f',1,'vg']]],
+ ['alignment_5femitter_5fflag_5fvg_5fuse_5fsegment_5fnames_13933',['ALIGNMENT_EMITTER_FLAG_VG_USE_SEGMENT_NAMES',['../namespacevg.html#a43fe994695e911cc22e05195e327f5b5a3ea893f3dade371704d31df4070e95fd',1,'vg']]],
+ ['annotation_13934',['annotation',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a40f61be34cdcd40a99f5ec2fb6069cc1',1,'vg::Counts']]],
+ ['approx_13935',['Approx',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39a9ab31888ec6c2da1a29c051c49f2d5ea',1,'vg']]]
];
diff --git a/search/enumvalues_1.js b/search/enumvalues_1.js
index b91e628c14..9157faa7cc 100644
--- a/search/enumvalues_1.js
+++ b/search/enumvalues_1.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['bad_5fedit_13932',['BAD_EDIT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a7ee27fac2af6c17f855873dfa5f78a9d',1,'vg::AlignmentValidity']]],
- ['bam_13933',['BAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba9729e98f8ce900812000b2fea7c38442',1,'vg::MultipathAlignmentEmitter']]],
- ['basic_13934',['Basic',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3acc2841d7d13fb6afa6ae0bdaac318bec',1,'vg::IndexingParameters']]],
- ['before_13935',['before',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aabcfb82d021a235be54b2d58e4cbff6f2',1,'ReferenceInterval']]],
- ['bool_13936',['Bool',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eadfc9c0789c3e775ebfc319b74d2deeb6',1,'vg::multipath_alignment_t']]],
- ['build_5falignments_13937',['build_alignments',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a201fc68403f7cdb0cf4ef1de93a31715',1,'GBWTConfig']]],
- ['build_5fgbwtgraph_13938',['build_gbwtgraph',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a53ad04440251531f5f139c800eea46b8',1,'GBWTConfig']]],
- ['build_5fgbz_13939',['build_gbz',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685aae3fd4fc7fbce391a0d89a09dab5b5d7',1,'GBWTConfig']]],
- ['build_5fgfa_13940',['build_gfa',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685ab965c2d8000262a4380e189256353a8c',1,'GBWTConfig']]],
- ['build_5fnone_13941',['build_none',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685aaf0448be26e9729af1802ade9cd7d5a1',1,'GBWTConfig']]],
- ['build_5fpaths_13942',['build_paths',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a3d8e97f8cfdd8470a45ff88c44fa92b5',1,'GBWTConfig']]],
- ['build_5fvcf_13943',['build_vcf',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a172c54861f7988c1d60fb92d9881e8d9',1,'GBWTConfig']]],
- ['by_5fgraph_5fposition_13944',['BY_GRAPH_POSITION',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046ba4e42a788d54e696711a23e780451582b',1,'vg::StreamSorter']]]
+ ['bad_5fedit_13936',['BAD_EDIT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a7ee27fac2af6c17f855873dfa5f78a9d',1,'vg::AlignmentValidity']]],
+ ['bam_13937',['BAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba9729e98f8ce900812000b2fea7c38442',1,'vg::MultipathAlignmentEmitter']]],
+ ['basic_13938',['Basic',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3acc2841d7d13fb6afa6ae0bdaac318bec',1,'vg::IndexingParameters']]],
+ ['before_13939',['before',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aabcfb82d021a235be54b2d58e4cbff6f2',1,'ReferenceInterval']]],
+ ['bool_13940',['Bool',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eadfc9c0789c3e775ebfc319b74d2deeb6',1,'vg::multipath_alignment_t']]],
+ ['build_5falignments_13941',['build_alignments',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a201fc68403f7cdb0cf4ef1de93a31715',1,'GBWTConfig']]],
+ ['build_5fgbwtgraph_13942',['build_gbwtgraph',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a53ad04440251531f5f139c800eea46b8',1,'GBWTConfig']]],
+ ['build_5fgbz_13943',['build_gbz',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685aae3fd4fc7fbce391a0d89a09dab5b5d7',1,'GBWTConfig']]],
+ ['build_5fgfa_13944',['build_gfa',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685ab965c2d8000262a4380e189256353a8c',1,'GBWTConfig']]],
+ ['build_5fnone_13945',['build_none',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685aaf0448be26e9729af1802ade9cd7d5a1',1,'GBWTConfig']]],
+ ['build_5fpaths_13946',['build_paths',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a3d8e97f8cfdd8470a45ff88c44fa92b5',1,'GBWTConfig']]],
+ ['build_5fvcf_13947',['build_vcf',['../structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a172c54861f7988c1d60fb92d9881e8d9',1,'GBWTConfig']]],
+ ['by_5fgraph_5fposition_13948',['BY_GRAPH_POSITION',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046ba4e42a788d54e696711a23e780451582b',1,'vg::StreamSorter']]]
];
diff --git a/search/enumvalues_10.js b/search/enumvalues_10.js
index 5c5e36c21e..1cd88f1f1c 100644
--- a/search/enumvalues_10.js
+++ b/search/enumvalues_10.js
@@ -1,20 +1,20 @@
var searchData=
[
- ['s_5fscan_5fchain_14066',['S_SCAN_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a5a2a20c895df5cb7d5b27e3335827d84',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fscan_5fsnarl_14067',['S_SCAN_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a3eb7a4cb13ea66f6f4e7e44d06aa41bc',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fskip_5fchain_14068',['S_SKIP_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a98d325e41f9d476ccc2b82e79c873341',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fstack_5fsnarl_14069',['S_STACK_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a45d7d8cf2973c828ad7bd10774a879e4',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['s_5fstart_14070',['S_START',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a159863dec1d44845928b1b3df0d24a2a',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['sam_14071',['SAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baa4f1866efe56ebd234e7d5135ecca03e',1,'vg::MultipathAlignmentEmitter']]],
- ['seed_14072',['SEED',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adab044c319f32f470727c5c2ba078487f5',1,'vg::ZipCodeTree']]],
- ['seq_5fdoes_5fnot_5fmatch_14073',['SEQ_DOES_NOT_MATCH',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9acc8619639d089c16381dd05298fe3df8',1,'vg::AlignmentValidity']]],
- ['slug_14074',['SLUG',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa9c42a12326ffdacf390a8b88c9fe1804',1,'vg::subcommand']]],
- ['snarl_5fend_14075',['SNARL_END',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adaaa317dff9d3024c633f537d3b8b08cc7',1,'vg::ZipCodeTree']]],
- ['snarl_5fstart_14076',['SNARL_START',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adad9686e72ac57aa50bd713fce51da5666',1,'vg::ZipCodeTree']]],
- ['snv_14077',['snv',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a80993050ce71b03df8d926cbe0cde822',1,'haplo::linear_haplo_structure']]],
- ['split_14078',['split',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aaf22613489ec859693457e82fd026e3b',1,'vg::Counts']]],
- ['start_14079',['START',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3ab5854c3018055ccefae586f717850711',1,'handlegraph::SnarlDecomposition']]],
- ['string_14080',['String',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eab41cf4db950b9da3d95a7c1400a5369e',1,'vg::multipath_alignment_t']]],
- ['subsequence_14081',['subsequence',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9acf76097b099973339661134c01b30e59',1,'vg::Counts']]],
- ['suffix_14082',['suffix',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea831a2ebb5fe5a6b08270dfa5b9b6c7ac',1,'vg::Haplotypes::Subchain']]]
+ ['s_5fscan_5fchain_14070',['S_SCAN_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a5a2a20c895df5cb7d5b27e3335827d84',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fscan_5fsnarl_14071',['S_SCAN_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a3eb7a4cb13ea66f6f4e7e44d06aa41bc',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fskip_5fchain_14072',['S_SKIP_CHAIN',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a98d325e41f9d476ccc2b82e79c873341',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fstack_5fsnarl_14073',['S_STACK_SNARL',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a45d7d8cf2973c828ad7bd10774a879e4',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['s_5fstart_14074',['S_START',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a7befe01ebe22c002ec95471a8800cb19a159863dec1d44845928b1b3df0d24a2a',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['sam_14075',['SAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baa4f1866efe56ebd234e7d5135ecca03e',1,'vg::MultipathAlignmentEmitter']]],
+ ['seed_14076',['SEED',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adab044c319f32f470727c5c2ba078487f5',1,'vg::ZipCodeTree']]],
+ ['seq_5fdoes_5fnot_5fmatch_14077',['SEQ_DOES_NOT_MATCH',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9acc8619639d089c16381dd05298fe3df8',1,'vg::AlignmentValidity']]],
+ ['slug_14078',['SLUG',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa9c42a12326ffdacf390a8b88c9fe1804',1,'vg::subcommand']]],
+ ['snarl_5fend_14079',['SNARL_END',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adaaa317dff9d3024c633f537d3b8b08cc7',1,'vg::ZipCodeTree']]],
+ ['snarl_5fstart_14080',['SNARL_START',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adad9686e72ac57aa50bd713fce51da5666',1,'vg::ZipCodeTree']]],
+ ['snv_14081',['snv',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a80993050ce71b03df8d926cbe0cde822',1,'haplo::linear_haplo_structure']]],
+ ['split_14082',['split',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aaf22613489ec859693457e82fd026e3b',1,'vg::Counts']]],
+ ['start_14083',['START',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3ab5854c3018055ccefae586f717850711',1,'handlegraph::SnarlDecomposition']]],
+ ['string_14084',['String',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eab41cf4db950b9da3d95a7c1400a5369e',1,'vg::multipath_alignment_t']]],
+ ['subsequence_14085',['subsequence',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9acf76097b099973339661134c01b30e59',1,'vg::Counts']]],
+ ['suffix_14086',['suffix',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea831a2ebb5fe5a6b08270dfa5b9b6c7ac',1,'vg::Haplotypes::Subchain']]]
];
diff --git a/search/enumvalues_11.js b/search/enumvalues_11.js
index d3d86d83b2..e02370070e 100644
--- a/search/enumvalues_11.js
+++ b/search/enumvalues_11.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['tip_14083',['TIP',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3a41062278414d99cdb309732619f1ce5f',1,'handlegraph::SnarlDecomposition']]],
- ['toolkit_14084',['TOOLKIT',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838af5626d22da713c4acb1ccc508f2816d2',1,'vg::subcommand']]]
+ ['tip_14087',['TIP',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3a41062278414d99cdb309732619f1ce5f',1,'handlegraph::SnarlDecomposition']]],
+ ['toolkit_14088',['TOOLKIT',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838af5626d22da713c4acb1ccc508f2816d2',1,'vg::subcommand']]]
];
diff --git a/search/enumvalues_12.js b/search/enumvalues_12.js
index 4c72e0c00c..d6f79ab1f0 100644
--- a/search/enumvalues_12.js
+++ b/search/enumvalues_12.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['ultrabubble_14085',['ULTRABUBBLE',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97aea6b4b85aa567a940c7434df2fcb56fb',1,'vg']]],
- ['unary_14086',['UNARY',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a0e62c0ff8521d5960a5cc819a7bf7230',1,'vg']]],
- ['unclassified_14087',['UNCLASSIFIED',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a7db3292851220acc20f75deebe0924ff',1,'vg']]],
- ['undetermined_14088',['Undetermined',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda6fa550428b55152a0c55175786170a75',1,'vg::MultipathMapper']]],
- ['unmapped_14089',['unmapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aa653bbbb9be3aa57e63377efbf2122bb',1,'vg::Counts']]]
+ ['ultrabubble_14089',['ULTRABUBBLE',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97aea6b4b85aa567a940c7434df2fcb56fb',1,'vg']]],
+ ['unary_14090',['UNARY',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a0e62c0ff8521d5960a5cc819a7bf7230',1,'vg']]],
+ ['unclassified_14091',['UNCLASSIFIED',['../namespacevg.html#ac47f059d08b97304ea21d00dfc19cd97a7db3292851220acc20f75deebe0924ff',1,'vg']]],
+ ['undetermined_14092',['Undetermined',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda6fa550428b55152a0c55175786170a75',1,'vg::MultipathMapper']]],
+ ['unmapped_14093',['unmapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9aa653bbbb9be3aa57e63377efbf2122bb',1,'vg::Counts']]]
];
diff --git a/search/enumvalues_13.js b/search/enumvalues_13.js
index 52f708892b..7a5987189d 100644
--- a/search/enumvalues_13.js
+++ b/search/enumvalues_13.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['verbosity_5fbasic_14090',['verbosity_basic',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa718364c23222ec5e7444240be0799449',1,'vg::Haplotypes']]],
- ['verbosity_5fdebug_14091',['verbosity_debug',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aaa92669d64637a1583a113eb279234241',1,'vg::Haplotypes']]],
- ['verbosity_5fdetailed_14092',['verbosity_detailed',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa8c3562efded9b2b9ae9fd7ee05594ce0',1,'vg::Haplotypes']]],
- ['verbosity_5fsilent_14093',['verbosity_silent',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aadd4472c60bf6446f52a09a0d41140a21',1,'vg::Haplotypes']]],
- ['vg_14094',['VG',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a5e978449ccc729202c33e2dc543b8327',1,'vg::IndexingParameters']]]
+ ['verbosity_5fbasic_14094',['verbosity_basic',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa718364c23222ec5e7444240be0799449',1,'vg::Haplotypes']]],
+ ['verbosity_5fdebug_14095',['verbosity_debug',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aaa92669d64637a1583a113eb279234241',1,'vg::Haplotypes']]],
+ ['verbosity_5fdetailed_14096',['verbosity_detailed',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa8c3562efded9b2b9ae9fd7ee05594ce0',1,'vg::Haplotypes']]],
+ ['verbosity_5fsilent_14097',['verbosity_silent',['../classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aadd4472c60bf6446f52a09a0d41140a21',1,'vg::Haplotypes']]],
+ ['vg_14098',['VG',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a5e978449ccc729202c33e2dc543b8327',1,'vg::IndexingParameters']]]
];
diff --git a/search/enumvalues_14.js b/search/enumvalues_14.js
index 84def34888..339caabb62 100644
--- a/search/enumvalues_14.js
+++ b/search/enumvalues_14.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['widget_14095',['WIDGET',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838afa639842a4d69790c890c94b80e27792',1,'vg::subcommand']]],
- ['wrong_5fname_14096',['wrong_name',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a5d133dedebb885c312dbfca70d5abe15',1,'vg::Counts']]],
- ['wrong_5frefpos_14097',['wrong_refpos',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a069ad2b94f1414f1ba774043f5047d15',1,'vg::Counts']]]
+ ['widget_14099',['WIDGET',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838afa639842a4d69790c890c94b80e27792',1,'vg::subcommand']]],
+ ['wrong_5fname_14100',['wrong_name',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a5d133dedebb885c312dbfca70d5abe15',1,'vg::Counts']]],
+ ['wrong_5frefpos_14101',['wrong_refpos',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a069ad2b94f1414f1ba774043f5047d15',1,'vg::Counts']]]
];
diff --git a/search/enumvalues_2.js b/search/enumvalues_2.js
index 43b5798dd6..bc528b67ae 100644
--- a/search/enumvalues_2.js
+++ b/search/enumvalues_2.js
@@ -1,10 +1,10 @@
var searchData=
[
- ['chain_13945',['CHAIN',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a0fadb599003438c0ef1ebccfab78b8d6',1,'vg::ZipCode']]],
- ['chain_5fend_13946',['CHAIN_END',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada7c7e392d74a0520922c3383f3aafd681',1,'vg::ZipCodeTree']]],
- ['chain_5fstart_13947',['CHAIN_START',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada60080b65470ee6064c333eae0665001b',1,'vg::ZipCodeTree']]],
- ['cli_13948',['CLI',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa91af5705f16502125e8b2187e64202c0',1,'vg::subcommand']]],
- ['correct_13949',['CORRECT',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85a0d536515ce0fb6e96a5510b6556f30f2',1,'vg::Funnel']]],
- ['cram_13950',['CRAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba76a6da9f06ff14996667d262d476371c',1,'vg::MultipathAlignmentEmitter']]],
- ['cyclic_5fsnarl_13951',['CYCLIC_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a5fb7cef86123c58871519b0a317708d0',1,'vg::ZipCode']]]
+ ['chain_13949',['CHAIN',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a0fadb599003438c0ef1ebccfab78b8d6',1,'vg::ZipCode']]],
+ ['chain_5fend_13950',['CHAIN_END',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada7c7e392d74a0520922c3383f3aafd681',1,'vg::ZipCodeTree']]],
+ ['chain_5fstart_13951',['CHAIN_START',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada60080b65470ee6064c333eae0665001b',1,'vg::ZipCodeTree']]],
+ ['cli_13952',['CLI',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa91af5705f16502125e8b2187e64202c0',1,'vg::subcommand']]],
+ ['correct_13953',['CORRECT',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85a0d536515ce0fb6e96a5510b6556f30f2',1,'vg::Funnel']]],
+ ['cram_13954',['CRAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba76a6da9f06ff14996667d262d476371c',1,'vg::MultipathAlignmentEmitter']]],
+ ['cyclic_5fsnarl_13955',['CYCLIC_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a5fb7cef86123c58871519b0a317708d0',1,'vg::ZipCode']]]
];
diff --git a/search/enumvalues_3.js b/search/enumvalues_3.js
index 5dc158adc9..930bfc3582 100644
--- a/search/enumvalues_3.js
+++ b/search/enumvalues_3.js
@@ -1,11 +1,11 @@
var searchData=
[
- ['debug_13952',['Debug',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3a332234c0232e64560e7e9d902049c8f2',1,'vg::IndexingParameters']]],
- ['defray_13953',['defray',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ace9ad44126edf4f7b034b1a8d631b6ed',1,'vg::Counts']]],
- ['defray_5fall_13954',['defray_all',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a7f98e55e3573df75b4c7d82d9dbfbb86',1,'vg::Counts']]],
- ['del_13955',['DEL',['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba11563127ec3be864b514a1784c5d37a6',1,'DEL(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a11563127ec3be864b514a1784c5d37a6',1,'DEL(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a11563127ec3be864b514a1784c5d37a6',1,'DEL(): xdrop_aligner.cpp']]],
- ['deletion_13956',['deletion',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeba73758a6ad62787d1a52133552bc3dccb',1,'vg::WFAAlignment']]],
- ['deprecated_13957',['DEPRECATED',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838a1427d7dc483097fa9ca2fad19ce88f3f',1,'vg::subcommand']]],
- ['development_13958',['DEVELOPMENT',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838af31a3aa08995011009d0fe7af8892a74',1,'vg::subcommand']]],
- ['double_13959',['Double',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eab6d8b844500a0b813305bde5129ce099',1,'vg::multipath_alignment_t']]]
+ ['debug_13956',['Debug',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3a332234c0232e64560e7e9d902049c8f2',1,'vg::IndexingParameters']]],
+ ['defray_13957',['defray',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ace9ad44126edf4f7b034b1a8d631b6ed',1,'vg::Counts']]],
+ ['defray_5fall_13958',['defray_all',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a7f98e55e3573df75b4c7d82d9dbfbb86',1,'vg::Counts']]],
+ ['del_13959',['DEL',['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba11563127ec3be864b514a1784c5d37a6',1,'DEL(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a11563127ec3be864b514a1784c5d37a6',1,'DEL(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a11563127ec3be864b514a1784c5d37a6',1,'DEL(): xdrop_aligner.cpp']]],
+ ['deletion_13960',['deletion',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeba73758a6ad62787d1a52133552bc3dccb',1,'vg::WFAAlignment']]],
+ ['deprecated_13961',['DEPRECATED',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838a1427d7dc483097fa9ca2fad19ce88f3f',1,'vg::subcommand']]],
+ ['development_13962',['DEVELOPMENT',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838af31a3aa08995011009d0fe7af8892a74',1,'vg::subcommand']]],
+ ['double_13963',['Double',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095eab6d8b844500a0b813305bde5129ce099',1,'vg::multipath_alignment_t']]]
];
diff --git a/search/enumvalues_4.js b/search/enumvalues_4.js
index 50f0cdc9ba..02b8b76d38 100644
--- a/search/enumvalues_4.js
+++ b/search/enumvalues_4.js
@@ -1,9 +1,9 @@
var searchData=
[
- ['edge_13960',['EDGE',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adaa0bd6d0deb2e6c6f2b3c441346707376',1,'vg::ZipCodeTree']]],
- ['empty_13961',['EMPTY',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3add89c8b2a06030b4a1d698a011538aaa',1,'vg::ZipCode']]],
- ['end_13962',['END',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3aa14d92884083adfe371667c2ce1d70a5',1,'handlegraph::SnarlDecomposition']]],
- ['exact_13963',['Exact',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39a71ab21548d5ec730cee91982aa78275e',1,'vg']]],
- ['excluded_5ffeature_13964',['excluded_feature',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab17a307a45fc0197d05d31bf93203d63',1,'vg::Counts']]],
- ['exhaustive_13965',['Exhaustive',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4a03b965f4f4d03d6869811e0dedbfb0dd',1,'vg::Genotyper']]]
+ ['edge_13964',['EDGE',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117adaa0bd6d0deb2e6c6f2b3c441346707376',1,'vg::ZipCodeTree']]],
+ ['empty_13965',['EMPTY',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3add89c8b2a06030b4a1d698a011538aaa',1,'vg::ZipCode']]],
+ ['end_13966',['END',['../classhandlegraph_1_1SnarlDecomposition.html#a17b276026a2c6d99be0f63ffbc92ccd3aa14d92884083adfe371667c2ce1d70a5',1,'handlegraph::SnarlDecomposition']]],
+ ['exact_13967',['Exact',['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39a71ab21548d5ec730cee91982aa78275e',1,'vg']]],
+ ['excluded_5ffeature_13968',['excluded_feature',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab17a307a45fc0197d05d31bf93203d63',1,'vg::Counts']]],
+ ['exhaustive_13969',['Exhaustive',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4a03b965f4f4d03d6869811e0dedbfb0dd',1,'vg::Genotyper']]]
];
diff --git a/search/enumvalues_5.js b/search/enumvalues_5.js
index 2f06d2d147..ec0afd0c3a 100644
--- a/search/enumvalues_5.js
+++ b/search/enumvalues_5.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['filtered_13966',['filtered',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a1a3ab41c6f9d712e6419fb1a2b359fd7',1,'vg::Counts']]],
- ['first_5falignment_13967',['first_alignment',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab088f3cfa83ae97113bb1d55511153e6',1,'vg::Counts']]],
- ['forward_13968',['Forward',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda1927367ddd77070a67deacaefa9300a5',1,'vg::MultipathMapper']]],
- ['frequent_13969',['frequent',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa892a529e9382089dc28f99204da4dbaa',1,'vg::Recombinator']]],
- ['full_5fhaplotype_13970',['full_haplotype',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea5f4dff4ab82d6475d46abc492168ad11',1,'vg::Haplotypes::Subchain']]]
+ ['filtered_13970',['filtered',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a1a3ab41c6f9d712e6419fb1a2b359fd7',1,'vg::Counts']]],
+ ['first_5falignment_13971',['first_alignment',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab088f3cfa83ae97113bb1d55511153e6',1,'vg::Counts']]],
+ ['forward_13972',['Forward',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda1927367ddd77070a67deacaefa9300a5',1,'vg::MultipathMapper']]],
+ ['frequent_13973',['frequent',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa892a529e9382089dc28f99204da4dbaa',1,'vg::Recombinator']]],
+ ['full_5fhaplotype_13974',['full_haplotype',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea5f4dff4ab82d6475d46abc492168ad11',1,'vg::Haplotypes::Subchain']]]
];
diff --git a/search/enumvalues_6.js b/search/enumvalues_6.js
index 7273cb7b43..867188f8cd 100644
--- a/search/enumvalues_6.js
+++ b/search/enumvalues_6.js
@@ -1,12 +1,12 @@
var searchData=
[
- ['gaf_13971',['GAF',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0bab98a867ffc7b5c1ac2a3e5e171148245',1,'vg::MultipathAlignmentEmitter']]],
- ['gam_13972',['GAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baf8d906e37d32ff64beb1baf4c50958fd',1,'vg::MultipathAlignmentEmitter']]],
- ['gamp_13973',['GAMP',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba00b7d3df4dc1aead7feb32d379bb1a35',1,'vg::MultipathAlignmentEmitter']]],
- ['generic_13974',['GENERIC',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cac942dc2a9f958acddc67e11472d3ca0b',1,'handlegraph']]],
- ['graph_5fgbwtgraph_13975',['graph_gbwtgraph',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a91483c9c92517470579d46e605443620',1,'GraphHandler']]],
- ['graph_5fgbz_13976',['graph_gbz',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a759ff53fb7d1c506e3be18f608607ac5',1,'GraphHandler']]],
- ['graph_5fnone_13977',['graph_none',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50abbfbe5112e8f9046f822fc511ab21631',1,'GraphHandler']]],
- ['graph_5fpath_13978',['graph_path',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50af316f5a8669d38d1c1801caf9d5671d7',1,'GraphHandler']]],
- ['graph_5fsource_13979',['graph_source',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a66269d0a2331df8645dfca4cdbc4a2ea',1,'GraphHandler']]]
+ ['gaf_13975',['GAF',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0bab98a867ffc7b5c1ac2a3e5e171148245',1,'vg::MultipathAlignmentEmitter']]],
+ ['gam_13976',['GAM',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0baf8d906e37d32ff64beb1baf4c50958fd',1,'vg::MultipathAlignmentEmitter']]],
+ ['gamp_13977',['GAMP',['../classvg_1_1MultipathAlignmentEmitter.html#a9a078e9c7bfe62603e8f359b62519b0ba00b7d3df4dc1aead7feb32d379bb1a35',1,'vg::MultipathAlignmentEmitter']]],
+ ['generic_13978',['GENERIC',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cac942dc2a9f958acddc67e11472d3ca0b',1,'handlegraph']]],
+ ['graph_5fgbwtgraph_13979',['graph_gbwtgraph',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a91483c9c92517470579d46e605443620',1,'GraphHandler']]],
+ ['graph_5fgbz_13980',['graph_gbz',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a759ff53fb7d1c506e3be18f608607ac5',1,'GraphHandler']]],
+ ['graph_5fnone_13981',['graph_none',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50abbfbe5112e8f9046f822fc511ab21631',1,'GraphHandler']]],
+ ['graph_5fpath_13982',['graph_path',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50af316f5a8669d38d1c1801caf9d5671d7',1,'GraphHandler']]],
+ ['graph_5fsource_13983',['graph_source',['../structGraphHandler.html#a745df84ccf4f5a446e8f4b7c2aa1ea50a66269d0a2331df8645dfca4cdbc4a2ea',1,'GraphHandler']]]
];
diff --git a/search/enumvalues_7.js b/search/enumvalues_7.js
index 16639dc485..f78377eade 100644
--- a/search/enumvalues_7.js
+++ b/search/enumvalues_7.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['haplotype_13980',['HAPLOTYPE',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271ca00c31e80a8b69bfe7bd279f2bfa4b3ba',1,'handlegraph']]],
- ['hashgraph_13981',['HashGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a88fe737c0668785017687666e0aa74a8',1,'vg::IndexingParameters']]],
- ['heterozygous_13982',['heterozygous',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa3f649a400509ec3cc8b778d14ce2dd26',1,'vg::Recombinator']]]
+ ['haplotype_13984',['HAPLOTYPE',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271ca00c31e80a8b69bfe7bd279f2bfa4b3ba',1,'handlegraph']]],
+ ['hashgraph_13985',['HashGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a88fe737c0668785017687666e0aa74a8',1,'vg::IndexingParameters']]],
+ ['heterozygous_13986',['heterozygous',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa3f649a400509ec3cc8b778d14ce2dd26',1,'vg::Recombinator']]]
];
diff --git a/search/enumvalues_8.js b/search/enumvalues_8.js
index 4eca2ebf98..db693e27a0 100644
--- a/search/enumvalues_8.js
+++ b/search/enumvalues_8.js
@@ -1,18 +1,18 @@
var searchData=
[
- ['incorrectly_5fmapped_13983',['incorrectly_mapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac1473f460d502f5988365b86acaa27ea',1,'vg::Counts']]],
- ['index_5fcompressed_13984',['index_compressed',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a8733ef08a80d49962c42b2f3286f9dff',1,'vg::GBWTHandler']]],
- ['index_5fdynamic_13985',['index_dynamic',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a79071bcf44e60960f566a4fe9590d63d',1,'vg::GBWTHandler']]],
- ['index_5fnone_13986',['index_none',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a1dc536bf1ea474d215a9a7e0c7663924',1,'vg::GBWTHandler']]],
- ['input_5fgaf_13987',['input_gaf',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa68ce48b22e2cb1ea6edb3f351cff52ed',1,'convert_main.cpp']]],
- ['input_5fgam_13988',['input_gam',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaa45b4c6e90a30a90deb1183ec3b127a6',1,'convert_main.cpp']]],
- ['input_5fgbwtgraph_13989',['input_gbwtgraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa2cdb682495850f7e3a5dea532a556eb2',1,'convert_main.cpp']]],
- ['input_5fgfa_13990',['input_gfa',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaf3349e3c8dbf0909922809cb8776aebd',1,'convert_main.cpp']]],
- ['input_5fhandlegraph_13991',['input_handlegraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa6c28171b952beaf1784c655853a0e66c',1,'convert_main.cpp']]],
- ['ins_13992',['INS',['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): xdrop_aligner.cpp']]],
- ['insertcol_13993',['InsertCol',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faa0a1ece7d481572fa684460331afbfa4',1,'vg::BandedGlobalAligner']]],
- ['insertion_13994',['insertion',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebaf8105fdf086223fa49c6b63a3097a645',1,'vg::WFAAlignment']]],
- ['insertrow_13995',['InsertRow',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2fac7adaac601fdfa40491cb7906ca9e989',1,'vg::BandedGlobalAligner']]],
- ['invalid_13996',['invalid',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a26ab26b5bf5a066a0902a79defda6b5d',1,'haplo::linear_haplo_structure']]],
- ['irregular_5fsnarl_13997',['IRREGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a96d1de8b0fd352dc3449d17eab32f6f4',1,'vg::ZipCode']]]
+ ['incorrectly_5fmapped_13987',['incorrectly_mapped',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac1473f460d502f5988365b86acaa27ea',1,'vg::Counts']]],
+ ['index_5fcompressed_13988',['index_compressed',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a8733ef08a80d49962c42b2f3286f9dff',1,'vg::GBWTHandler']]],
+ ['index_5fdynamic_13989',['index_dynamic',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a79071bcf44e60960f566a4fe9590d63d',1,'vg::GBWTHandler']]],
+ ['index_5fnone_13990',['index_none',['../structvg_1_1GBWTHandler.html#aad418d9725da4ccbb6c60055eb5e9033a1dc536bf1ea474d215a9a7e0c7663924',1,'vg::GBWTHandler']]],
+ ['input_5fgaf_13991',['input_gaf',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa68ce48b22e2cb1ea6edb3f351cff52ed',1,'convert_main.cpp']]],
+ ['input_5fgam_13992',['input_gam',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaa45b4c6e90a30a90deb1183ec3b127a6',1,'convert_main.cpp']]],
+ ['input_5fgbwtgraph_13993',['input_gbwtgraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa2cdb682495850f7e3a5dea532a556eb2',1,'convert_main.cpp']]],
+ ['input_5fgfa_13994',['input_gfa',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efaf3349e3c8dbf0909922809cb8776aebd',1,'convert_main.cpp']]],
+ ['input_5fhandlegraph_13995',['input_handlegraph',['../convert__main_8cpp.html#a0ae208dfa21925e3cb4a7c4ea17ea8efa6c28171b952beaf1784c655853a0e66c',1,'convert_main.cpp']]],
+ ['ins_13996',['INS',['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a958fa7aa9ac4b5cd6e56237041b90584',1,'INS(): xdrop_aligner.cpp']]],
+ ['insertcol_13997',['InsertCol',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faa0a1ece7d481572fa684460331afbfa4',1,'vg::BandedGlobalAligner']]],
+ ['insertion_13998',['insertion',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebaf8105fdf086223fa49c6b63a3097a645',1,'vg::WFAAlignment']]],
+ ['insertrow_13999',['InsertRow',['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2fac7adaac601fdfa40491cb7906ca9e989',1,'vg::BandedGlobalAligner']]],
+ ['invalid_14000',['invalid',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8a26ab26b5bf5a066a0902a79defda6b5d',1,'haplo::linear_haplo_structure']]],
+ ['irregular_5fsnarl_14001',['IRREGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a96d1de8b0fd352dc3449d17eab32f6f4',1,'vg::ZipCode']]]
];
diff --git a/search/enumvalues_9.js b/search/enumvalues_9.js
index 0b9bc77031..52ce67f089 100644
--- a/search/enumvalues_9.js
+++ b/search/enumvalues_9.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['json_13998',['JSON',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa0ecd11c1d7a287401d148a23bbd7a2f8',1,'vg::subcommand']]]
+ ['json_14002',['JSON',['../namespacevg_1_1subcommand.html#a33e0e4354eca54aaf6140771963f7e9fa0ecd11c1d7a287401d148a23bbd7a2f8',1,'vg::subcommand']]]
];
diff --git a/search/enumvalues_a.js b/search/enumvalues_a.js
index 128c7ba9ad..9f1081c0ff 100644
--- a/search/enumvalues_a.js
+++ b/search/enumvalues_a.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['last_13999',['last',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a1f9f68c932a97214ed914c8ba2c882f2',1,'vg::Counts']]]
+ ['last_14003',['last',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a1f9f68c932a97214ed914c8ba2c882f2',1,'vg::Counts']]]
];
diff --git a/search/enumvalues_b.js b/search/enumvalues_b.js
index 4ba3cd6605..954706f3f1 100644
--- a/search/enumvalues_b.js
+++ b/search/enumvalues_b.js
@@ -1,28 +1,28 @@
var searchData=
[
- ['match_14000',['match',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebae6fe3d73bbbc5c70e386589f9732e9af',1,'vg::WFAAlignment::match()'],['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faac03946390169c005fafc9a38b114e6a',1,'vg::BandedGlobalAligner::Match()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): xdrop_aligner.cpp']]],
- ['max_5flength_14001',['max_length',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9abd4efb2ac344eea5ff58477c7014a769',1,'vg::Counts']]],
- ['max_5foverhang_14002',['max_overhang',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a500747869171f1e18a4e7c56625ed3ef',1,'vg::Counts']]],
- ['max_5freads_14003',['max_reads',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a6c584adbe4422e18c6bb875bb3a482ca',1,'vg::Counts']]],
- ['merge_5ffast_14004',['merge_fast',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fa00b833ba044e1135d12579e8baeedca6',1,'GBWTConfig']]],
- ['merge_5finsert_14005',['merge_insert',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faa05cfa7f46c6c005f05b264b71ede9d3',1,'GBWTConfig']]],
- ['merge_5fnone_14006',['merge_none',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faace9bbb313fb5c18d2a5a9142b99762b',1,'GBWTConfig']]],
- ['merge_5fparallel_14007',['merge_parallel',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fad49ba685add4291f2ba5d4d042f6e548',1,'GBWTConfig']]],
- ['min_5fbase_5fqual_14008',['min_base_qual',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a81bd6ba848d5742091102b7e6e7f0528',1,'vg::Counts']]],
- ['min_5fend_5fmatches_14009',['min_end_matches',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a0035f968d8e0ae55fcaf6763f7dd01a1',1,'vg::Counts']]],
- ['min_5fmapq_14010',['min_mapq',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a228a82cd163bae9299de79bacd32fab8',1,'vg::Counts']]],
- ['min_5fscore_14011',['min_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab6d45328b152bc6aa0e23943d77e473b',1,'vg::Counts']]],
- ['min_5fsec_5fscore_14012',['min_sec_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac355280a9dc2984da55998417433ccdb',1,'vg::Counts']]],
- ['mismatch_14013',['mismatch',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeba1720159dd67365a6e856bd65a56722e7',1,'vg::WFAAlignment::mismatch()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): xdrop_aligner.cpp']]],
- ['mode_5fclassify_14014',['mode_classify',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667abd23aa372c8ca2d63cf4b477257d27ea',1,'HaplotypesConfig']]],
- ['mode_5fextract_14015',['mode_extract',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a8efe96a347c67fea3b49d01cb2c21dde',1,'HaplotypesConfig']]],
- ['mode_5finvalid_14016',['mode_invalid',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667afef1428e91bd487b53f44f88885ed506',1,'HaplotypesConfig']]],
- ['mode_5fmap_5fvariants_14017',['mode_map_variants',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667ac11510277093ba13a92edaad15a143f4',1,'HaplotypesConfig']]],
- ['mode_5fpreprocess_14018',['mode_preprocess',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a2ecb8ae543c843b61de526ce2096f8fe',1,'HaplotypesConfig']]],
- ['mode_5fprune_14019',['mode_prune',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a6a94759a7900a825dd21bf4d9eb648ef',1,'prune_main.cpp']]],
- ['mode_5frestore_14020',['mode_restore',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a7ac5442ed3dfb51eaa1c7311fefc8842',1,'prune_main.cpp']]],
- ['mode_5fsample_5fgraph_14021',['mode_sample_graph',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a043a4f84904086154417f62fbf55084b',1,'HaplotypesConfig']]],
- ['mode_5fsample_5fhaplotypes_14022',['mode_sample_haplotypes',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a684f467f5682443799839a988b490626',1,'HaplotypesConfig']]],
- ['mode_5fstatistics_14023',['mode_statistics',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a0ec67bc2861395ce21fbe3333a118713',1,'HaplotypesConfig']]],
- ['mode_5funfold_14024',['mode_unfold',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a14b7711c85d633b1e1cee3b9466c48b3',1,'prune_main.cpp']]]
+ ['match_14004',['match',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eebae6fe3d73bbbc5c70e386589f9732e9af',1,'vg::WFAAlignment::match()'],['../classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faac03946390169c005fafc9a38b114e6a',1,'vg::BandedGlobalAligner::Match()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a1155ee5305ebe5bb9407faa9d395ae93',1,'MATCH(): xdrop_aligner.cpp']]],
+ ['max_5flength_14005',['max_length',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9abd4efb2ac344eea5ff58477c7014a769',1,'vg::Counts']]],
+ ['max_5foverhang_14006',['max_overhang',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a500747869171f1e18a4e7c56625ed3ef',1,'vg::Counts']]],
+ ['max_5freads_14007',['max_reads',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a6c584adbe4422e18c6bb875bb3a482ca',1,'vg::Counts']]],
+ ['merge_5ffast_14008',['merge_fast',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fa00b833ba044e1135d12579e8baeedca6',1,'GBWTConfig']]],
+ ['merge_5finsert_14009',['merge_insert',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faa05cfa7f46c6c005f05b264b71ede9d3',1,'GBWTConfig']]],
+ ['merge_5fnone_14010',['merge_none',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0faace9bbb313fb5c18d2a5a9142b99762b',1,'GBWTConfig']]],
+ ['merge_5fparallel_14011',['merge_parallel',['../structGBWTConfig.html#a8a8cf3f78613e27997bd0c6377349b0fad49ba685add4291f2ba5d4d042f6e548',1,'GBWTConfig']]],
+ ['min_5fbase_5fqual_14012',['min_base_qual',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a81bd6ba848d5742091102b7e6e7f0528',1,'vg::Counts']]],
+ ['min_5fend_5fmatches_14013',['min_end_matches',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a0035f968d8e0ae55fcaf6763f7dd01a1',1,'vg::Counts']]],
+ ['min_5fmapq_14014',['min_mapq',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a228a82cd163bae9299de79bacd32fab8',1,'vg::Counts']]],
+ ['min_5fscore_14015',['min_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ab6d45328b152bc6aa0e23943d77e473b',1,'vg::Counts']]],
+ ['min_5fsec_5fscore_14016',['min_sec_score',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9ac355280a9dc2984da55998417433ccdb',1,'vg::Counts']]],
+ ['mismatch_14017',['mismatch',['../structvg_1_1WFAAlignment.html#a1ce899c26978ebac4bc7a31623809eeba1720159dd67365a6e856bd65a56722e7',1,'vg::WFAAlignment::mismatch()'],['../dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): dozeu_interface.cpp'],['../qual__adj__xdrop__aligner_8cpp.html#adf764cbdea00d65edcd07bb9953ad2b7a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): qual_adj_xdrop_aligner.cpp'],['../xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a9f6e5ca49fdffa107270afa3f5e16cda',1,'MISMATCH(): xdrop_aligner.cpp']]],
+ ['mode_5fclassify_14018',['mode_classify',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667abd23aa372c8ca2d63cf4b477257d27ea',1,'HaplotypesConfig']]],
+ ['mode_5fextract_14019',['mode_extract',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a8efe96a347c67fea3b49d01cb2c21dde',1,'HaplotypesConfig']]],
+ ['mode_5finvalid_14020',['mode_invalid',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667afef1428e91bd487b53f44f88885ed506',1,'HaplotypesConfig']]],
+ ['mode_5fmap_5fvariants_14021',['mode_map_variants',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667ac11510277093ba13a92edaad15a143f4',1,'HaplotypesConfig']]],
+ ['mode_5fpreprocess_14022',['mode_preprocess',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a2ecb8ae543c843b61de526ce2096f8fe',1,'HaplotypesConfig']]],
+ ['mode_5fprune_14023',['mode_prune',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a6a94759a7900a825dd21bf4d9eb648ef',1,'prune_main.cpp']]],
+ ['mode_5frestore_14024',['mode_restore',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a7ac5442ed3dfb51eaa1c7311fefc8842',1,'prune_main.cpp']]],
+ ['mode_5fsample_5fgraph_14025',['mode_sample_graph',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a043a4f84904086154417f62fbf55084b',1,'HaplotypesConfig']]],
+ ['mode_5fsample_5fhaplotypes_14026',['mode_sample_haplotypes',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a684f467f5682443799839a988b490626',1,'HaplotypesConfig']]],
+ ['mode_5fstatistics_14027',['mode_statistics',['../structHaplotypesConfig.html#aa7a2de45a48b792a0d045bd13e203667a0ec67bc2861395ce21fbe3333a118713',1,'HaplotypesConfig']]],
+ ['mode_5funfold_14028',['mode_unfold',['../prune__main_8cpp.html#a2c77251411bc109287b491299718e248a14b7711c85d633b1e1cee3b9466c48b3',1,'prune_main.cpp']]]
];
diff --git a/search/enumvalues_c.js b/search/enumvalues_c.js
index a22772c975..49d41be1d8 100644
--- a/search/enumvalues_c.js
+++ b/search/enumvalues_c.js
@@ -1,10 +1,10 @@
var searchData=
[
- ['node_14025',['NODE',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a2995e7f61da600fe7b67e5fd40d4b319',1,'vg::ZipCode']]],
- ['node_5fcount_14026',['NODE_COUNT',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada57ddf26ffbd2c06cff7bf2cc21613b6c',1,'vg::ZipCodeTree']]],
- ['node_5fmissing_14027',['NODE_MISSING',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a0fc049aba7e02c479f48dd02c5facab1',1,'vg::AlignmentValidity']]],
- ['node_5ftoo_5fshort_14028',['NODE_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae6b4882026edf127e7a8d7a120636586',1,'vg::AlignmentValidity']]],
- ['none_14029',['None',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3a7ec02cb6759bbdcec376638fb9e76d4e',1,'vg::IndexingParameters::None()'],['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85ab50339a10e1de285ac99d4c3990b8693',1,'vg::Funnel::NONE()'],['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39aa676d6ce23c4076e354ffb65936c03d1',1,'vg::None()']]],
- ['normal_14030',['normal',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea867c09ce684d19db107c790ac73e29c2',1,'vg::Haplotypes::Subchain']]],
- ['null_14031',['Null',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095ea4da67a14c941c99eb8e041314fa98640',1,'vg::multipath_alignment_t']]]
+ ['node_14029',['NODE',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a2995e7f61da600fe7b67e5fd40d4b319',1,'vg::ZipCode']]],
+ ['node_5fcount_14030',['NODE_COUNT',['../classvg_1_1ZipCodeTree.html#ad2249d10c3c707b5433b916d388117ada57ddf26ffbd2c06cff7bf2cc21613b6c',1,'vg::ZipCodeTree']]],
+ ['node_5fmissing_14031',['NODE_MISSING',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a0fc049aba7e02c479f48dd02c5facab1',1,'vg::AlignmentValidity']]],
+ ['node_5ftoo_5fshort_14032',['NODE_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae6b4882026edf127e7a8d7a120636586',1,'vg::AlignmentValidity']]],
+ ['none_14033',['None',['../structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3a7ec02cb6759bbdcec376638fb9e76d4e',1,'vg::IndexingParameters::None()'],['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85ab50339a10e1de285ac99d4c3990b8693',1,'vg::Funnel::NONE()'],['../namespacevg.html#ae8af508a4586e2447fdbf2a30a213b39aa676d6ce23c4076e354ffb65936c03d1',1,'vg::None()']]],
+ ['normal_14034',['normal',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdea867c09ce684d19db107c790ac73e29c2',1,'vg::Haplotypes::Subchain']]],
+ ['null_14035',['Null',['../classvg_1_1multipath__alignment__t.html#a6949ef73371981a69cc9223e44e8095ea4da67a14c941c99eb8e041314fa98640',1,'vg::multipath_alignment_t']]]
];
diff --git a/search/enumvalues_d.js b/search/enumvalues_d.js
index 576287315a..0287651cbe 100644
--- a/search/enumvalues_d.js
+++ b/search/enumvalues_d.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['ok_14032',['OK',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae41b7fcb28f19fd52e9b25b6bb0ada27',1,'vg::AlignmentValidity']]],
- ['overlap_14033',['overlap',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aa155f6cfbc58baef62da2c775972e636b',1,'ReferenceInterval']]]
+ ['ok_14036',['OK',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9ae41b7fcb28f19fd52e9b25b6bb0ada27',1,'vg::AlignmentValidity']]],
+ ['overlap_14037',['overlap',['../structReferenceInterval.html#a3c371a05bdf7a0977a0bec01cff2894aa155f6cfbc58baef62da2c775972e636b',1,'ReferenceInterval']]]
];
diff --git a/search/enumvalues_e.js b/search/enumvalues_e.js
index ae4afad900..7b8eceb71f 100644
--- a/search/enumvalues_e.js
+++ b/search/enumvalues_e.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['packedgraph_14034',['PackedGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a3355e9401e49629ee5dcd20b107f3f67',1,'vg::IndexingParameters']]],
- ['path_5fcover_5faugment_14035',['path_cover_augment',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a074342f434050b0213b77e7267c3d65a',1,'GBWTConfig']]],
- ['path_5fcover_5fgreedy_14036',['path_cover_greedy',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a0984604f4f41a7c9813edce20845b146',1,'GBWTConfig']]],
- ['path_5fcover_5flocal_14037',['path_cover_local',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a6f385ad96dac65846244dfafee7f4775',1,'GBWTConfig']]],
- ['path_5fcover_5fnone_14038',['path_cover_none',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1afd10e18b78dd3425247224d94f7e3dfc',1,'GBWTConfig']]],
- ['pipeline_14039',['PIPELINE',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838a797a289a67a7dd20502b2436f0c9d305',1,'vg::subcommand']]],
- ['placed_14040',['PLACED',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85a0a4373ca716769f93112e16e251bb8a1',1,'vg::Funnel']]],
- ['prefix_14041',['prefix',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdead1db5c374c93da6cefc39869d1704f18',1,'vg::Haplotypes::Subchain']]],
- ['present_14042',['present',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa24ced965e66bc34d849a25192e59fbdf',1,'vg::Recombinator']]],
- ['preset_5fdefault_14043',['preset_default',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a7b22070ac7d633aa776868df9225baa9',1,'vg::Recombinator::Parameters']]],
- ['preset_5fdiploid_14044',['preset_diploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a645ffd73f63c0f007f249345c81d4f8a',1,'vg::Recombinator::Parameters']]],
- ['preset_5fhaploid_14045',['preset_haploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a115a5b3be57084265c380192cabde366',1,'vg::Recombinator::Parameters']]],
- ['proper_5fpair_14046',['proper_pair',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a92eba6d5ad7d830d3824261542991875',1,'vg::Counts']]]
+ ['packedgraph_14038',['PackedGraph',['../structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a3355e9401e49629ee5dcd20b107f3f67',1,'vg::IndexingParameters']]],
+ ['path_5fcover_5faugment_14039',['path_cover_augment',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a074342f434050b0213b77e7267c3d65a',1,'GBWTConfig']]],
+ ['path_5fcover_5fgreedy_14040',['path_cover_greedy',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a0984604f4f41a7c9813edce20845b146',1,'GBWTConfig']]],
+ ['path_5fcover_5flocal_14041',['path_cover_local',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1a6f385ad96dac65846244dfafee7f4775',1,'GBWTConfig']]],
+ ['path_5fcover_5fnone_14042',['path_cover_none',['../structGBWTConfig.html#a6607b41ac0d4eaad9b9ec03e4513a8e1afd10e18b78dd3425247224d94f7e3dfc',1,'GBWTConfig']]],
+ ['pipeline_14043',['PIPELINE',['../namespacevg_1_1subcommand.html#a98d12492502a2d7f7c46386d2faed838a797a289a67a7dd20502b2436f0c9d305',1,'vg::subcommand']]],
+ ['placed_14044',['PLACED',['../classvg_1_1Funnel.html#a23e7fd0c49df53dd8a9e25934fe06c85a0a4373ca716769f93112e16e251bb8a1',1,'vg::Funnel']]],
+ ['prefix_14045',['prefix',['../structvg_1_1Haplotypes_1_1Subchain.html#ae7dc63ea57faea66afbaf0b84bb9cbdead1db5c374c93da6cefc39869d1704f18',1,'vg::Haplotypes::Subchain']]],
+ ['present_14046',['present',['../classvg_1_1Recombinator.html#a15178d62423d603319fd8a23664afd5fa24ced965e66bc34d849a25192e59fbdf',1,'vg::Recombinator']]],
+ ['preset_5fdefault_14047',['preset_default',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a7b22070ac7d633aa776868df9225baa9',1,'vg::Recombinator::Parameters']]],
+ ['preset_5fdiploid_14048',['preset_diploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a645ffd73f63c0f007f249345c81d4f8a',1,'vg::Recombinator::Parameters']]],
+ ['preset_5fhaploid_14049',['preset_haploid',['../structvg_1_1Recombinator_1_1Parameters.html#a57123b9eee2179efef985d785f8c44e4a115a5b3be57084265c380192cabde366',1,'vg::Recombinator::Parameters']]],
+ ['proper_5fpair_14050',['proper_pair',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a92eba6d5ad7d830d3824261542991875',1,'vg::Counts']]]
];
diff --git a/search/enumvalues_f.js b/search/enumvalues_f.js
index f4097f289e..5b992fa44b 100644
--- a/search/enumvalues_f.js
+++ b/search/enumvalues_f.js
@@ -1,22 +1,22 @@
var searchData=
[
- ['random_14047',['RANDOM',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046ba170e02e86972c2be8559884cc3c12254',1,'vg::StreamSorter::RANDOM()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a7fbab14a93d170a9ab8395e8bad9b15d',1,'vg::Counts::random()']]],
- ['read_14048',['read',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9afdd907960f4e4f4792f9986a37c69b3c',1,'vg::Counts']]],
- ['read_5ftoo_5fshort_14049',['READ_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a997b7fe4b82277b56702572e730d3eb7',1,'vg::AlignmentValidity']]],
- ['reads_14050',['Reads',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4a9989ae14c6b6c27998126ab745488926',1,'vg::Genotyper']]],
- ['recursealways_14051',['RecurseAlways',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ade8537831952f7d91199da0ded53a8d2',1,'vg::GraphCaller']]],
- ['recursenever_14052',['RecurseNever',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ad50ac99caa8bae55f8d5d8ed7a4aef04',1,'vg::GraphCaller']]],
- ['recurseonfail_14053',['RecurseOnFail',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ae25246a2b8e3ba65437d72bf513be31c',1,'vg::GraphCaller']]],
- ['ref_5fspan_14054',['ref_span',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8aabba00d1035f3425a2ff43984b99a3d4',1,'haplo::linear_haplo_structure']]],
- ['reference_14055',['REFERENCE',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cadcd320d017d7f3c317bc8b234287bc9f',1,'handlegraph']]],
- ['regular_5fsnarl_14056',['REGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a857cb70dc6bd3383a768a8696e67689c',1,'vg::ZipCode']]],
- ['repeat_14057',['repeat',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9af8ac0bddf37c11c94f041c84a20a636b',1,'vg::Counts']]],
- ['representative_14058',['Representative',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4aca000fa2f53ba37764dedd204e1fd27e',1,'vg::Genotyper']]],
- ['rescue_5fdozeu_14059',['rescue_dozeu',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a4120cab71587100aa2d1308010fec524',1,'vg::MinimizerMapper']]],
- ['rescue_5fgssw_14060',['rescue_gssw',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4aa3089b08bc714c195447adf06eff27d9',1,'vg::MinimizerMapper']]],
- ['rescue_5fnone_14061',['rescue_none',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a830c2c22efd3590551f37663c11f61e7',1,'vg::MinimizerMapper']]],
- ['reverse_14062',['Reverse',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda3720d917b5b410fbff17c73d58c1eaf2',1,'vg::MultipathMapper']]],
- ['root_5fchain_14063',['ROOT_CHAIN',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3350f37a328be806a1a8bb7534d7fb8c',1,'vg::ZipCode']]],
- ['root_5fnode_14064',['ROOT_NODE',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3c192049eca2f2b4aafe984ff4a965d3',1,'vg::ZipCode']]],
- ['root_5fsnarl_14065',['ROOT_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a438bae58eb821bbbc90b1b4bc486d682',1,'vg::ZipCode']]]
+ ['random_14051',['RANDOM',['../classvg_1_1StreamSorter.html#a1a4cb8aac1bb3f9bd9c01456b8cc046ba170e02e86972c2be8559884cc3c12254',1,'vg::StreamSorter::RANDOM()'],['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9a7fbab14a93d170a9ab8395e8bad9b15d',1,'vg::Counts::random()']]],
+ ['read_14052',['read',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9afdd907960f4e4f4792f9986a37c69b3c',1,'vg::Counts']]],
+ ['read_5ftoo_5fshort_14053',['READ_TOO_SHORT',['../structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9a997b7fe4b82277b56702572e730d3eb7',1,'vg::AlignmentValidity']]],
+ ['reads_14054',['Reads',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4a9989ae14c6b6c27998126ab745488926',1,'vg::Genotyper']]],
+ ['recursealways_14055',['RecurseAlways',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ade8537831952f7d91199da0ded53a8d2',1,'vg::GraphCaller']]],
+ ['recursenever_14056',['RecurseNever',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ad50ac99caa8bae55f8d5d8ed7a4aef04',1,'vg::GraphCaller']]],
+ ['recurseonfail_14057',['RecurseOnFail',['../classvg_1_1GraphCaller.html#a12de4df65cc92e2d62f057c56cb46ac5ae25246a2b8e3ba65437d72bf513be31c',1,'vg::GraphCaller']]],
+ ['ref_5fspan_14058',['ref_span',['../structhaplo_1_1linear__haplo__structure.html#a3180d362cdac21750aebf6d4fe77e0d8aabba00d1035f3425a2ff43984b99a3d4',1,'haplo::linear_haplo_structure']]],
+ ['reference_14059',['REFERENCE',['../namespacehandlegraph.html#ab3d3683c53bb48b8af63a6d94497271cadcd320d017d7f3c317bc8b234287bc9f',1,'handlegraph']]],
+ ['regular_5fsnarl_14060',['REGULAR_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a857cb70dc6bd3383a768a8696e67689c',1,'vg::ZipCode']]],
+ ['repeat_14061',['repeat',['../structvg_1_1Counts.html#a91171929bace72fa1d2443a075e589a9af8ac0bddf37c11c94f041c84a20a636b',1,'vg::Counts']]],
+ ['representative_14062',['Representative',['../classvg_1_1Genotyper.html#a6e4dce6cd9cc24ab6857ceeaed6db3b4aca000fa2f53ba37764dedd204e1fd27e',1,'vg::Genotyper']]],
+ ['rescue_5fdozeu_14063',['rescue_dozeu',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a4120cab71587100aa2d1308010fec524',1,'vg::MinimizerMapper']]],
+ ['rescue_5fgssw_14064',['rescue_gssw',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4aa3089b08bc714c195447adf06eff27d9',1,'vg::MinimizerMapper']]],
+ ['rescue_5fnone_14065',['rescue_none',['../classvg_1_1MinimizerMapper.html#ad9b497a766015dfbcefce5586e2396f4a830c2c22efd3590551f37663c11f61e7',1,'vg::MinimizerMapper']]],
+ ['reverse_14066',['Reverse',['../classvg_1_1MultipathMapper.html#a3448fc563b9a57181b01ea5bb969fccda3720d917b5b410fbff17c73d58c1eaf2',1,'vg::MultipathMapper']]],
+ ['root_5fchain_14067',['ROOT_CHAIN',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3350f37a328be806a1a8bb7534d7fb8c',1,'vg::ZipCode']]],
+ ['root_5fnode_14068',['ROOT_NODE',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a3c192049eca2f2b4aafe984ff4a965d3',1,'vg::ZipCode']]],
+ ['root_5fsnarl_14069',['ROOT_SNARL',['../classvg_1_1ZipCode.html#a3a7913620a6b9e7988e14c210c51e9c3a438bae58eb821bbbc90b1b4bc486d682',1,'vg::ZipCode']]]
];
diff --git a/search/files_0.js b/search/files_0.js
index fe63d8daea..551e501201 100644
--- a/search/files_0.js
+++ b/search/files_0.js
@@ -1,27 +1,27 @@
var searchData=
[
- ['a_5fstar_2ehpp_7413',['a_star.hpp',['../a__star_8hpp.html',1,'']]],
- ['add_5fmain_2ecpp_7414',['add_main.cpp',['../add__main_8cpp.html',1,'']]],
- ['align_5fmain_2ecpp_7415',['align_main.cpp',['../align__main_8cpp.html',1,'']]],
- ['aligner_2ecpp_7416',['aligner.cpp',['../aligner_8cpp.html',1,'']]],
- ['aligner_2ehpp_7417',['aligner.hpp',['../aligner_8hpp.html',1,'']]],
- ['alignment_2ecpp_7418',['alignment.cpp',['../alignment_8cpp.html',1,'']]],
- ['alignment_2ehpp_7419',['alignment.hpp',['../alignment_8hpp.html',1,'']]],
- ['alignment_5femitter_2ecpp_7420',['alignment_emitter.cpp',['../alignment__emitter_8cpp.html',1,'']]],
- ['alignment_5femitter_2ehpp_7421',['alignment_emitter.hpp',['../alignment__emitter_8hpp.html',1,'']]],
- ['alignment_5fio_2ecpp_7422',['alignment_io.cpp',['../alignment__io_8cpp.html',1,'']]],
- ['alignment_5fio_2ehpp_7423',['alignment_io.hpp',['../alignment__io_8hpp.html',1,'']]],
- ['alignment_5fpath_5foffsets_2ecpp_7424',['alignment_path_offsets.cpp',['../alignment__path__offsets_8cpp.html',1,'']]],
- ['alignment_5fpath_5foffsets_2ehpp_7425',['alignment_path_offsets.hpp',['../alignment__path__offsets_8hpp.html',1,'']]],
- ['annotate_5fmain_2ecpp_7426',['annotate_main.cpp',['../annotate__main_8cpp.html',1,'']]],
- ['annotation_2ehpp_7427',['annotation.hpp',['../annotation_8hpp.html',1,'']]],
- ['append_5fgraph_2ecpp_7428',['append_graph.cpp',['../append__graph_8cpp.html',1,'']]],
- ['apply_5forientations_2ecpp_7429',['apply_orientations.cpp',['../apply__orientations_8cpp.html',1,'']]],
- ['approx_5fpath_5fdistance_2ecpp_7430',['approx_path_distance.cpp',['../approx__path__distance_8cpp.html',1,'']]],
- ['approx_5fpath_5fdistance_2ehpp_7431',['approx_path_distance.hpp',['../approx__path__distance_8hpp.html',1,'']]],
- ['are_5fequivalent_2ecpp_7432',['are_equivalent.cpp',['../are__equivalent_8cpp.html',1,'']]],
- ['augment_2ecpp_7433',['augment.cpp',['../augment_8cpp.html',1,'']]],
- ['augment_2ehpp_7434',['augment.hpp',['../augment_8hpp.html',1,'']]],
- ['augment_5fmain_2ecpp_7435',['augment_main.cpp',['../augment__main_8cpp.html',1,'']]],
- ['autoindex_5fmain_2ecpp_7436',['autoindex_main.cpp',['../autoindex__main_8cpp.html',1,'']]]
+ ['a_5fstar_2ehpp_7415',['a_star.hpp',['../a__star_8hpp.html',1,'']]],
+ ['add_5fmain_2ecpp_7416',['add_main.cpp',['../add__main_8cpp.html',1,'']]],
+ ['align_5fmain_2ecpp_7417',['align_main.cpp',['../align__main_8cpp.html',1,'']]],
+ ['aligner_2ecpp_7418',['aligner.cpp',['../aligner_8cpp.html',1,'']]],
+ ['aligner_2ehpp_7419',['aligner.hpp',['../aligner_8hpp.html',1,'']]],
+ ['alignment_2ecpp_7420',['alignment.cpp',['../alignment_8cpp.html',1,'']]],
+ ['alignment_2ehpp_7421',['alignment.hpp',['../alignment_8hpp.html',1,'']]],
+ ['alignment_5femitter_2ecpp_7422',['alignment_emitter.cpp',['../alignment__emitter_8cpp.html',1,'']]],
+ ['alignment_5femitter_2ehpp_7423',['alignment_emitter.hpp',['../alignment__emitter_8hpp.html',1,'']]],
+ ['alignment_5fio_2ecpp_7424',['alignment_io.cpp',['../alignment__io_8cpp.html',1,'']]],
+ ['alignment_5fio_2ehpp_7425',['alignment_io.hpp',['../alignment__io_8hpp.html',1,'']]],
+ ['alignment_5fpath_5foffsets_2ecpp_7426',['alignment_path_offsets.cpp',['../alignment__path__offsets_8cpp.html',1,'']]],
+ ['alignment_5fpath_5foffsets_2ehpp_7427',['alignment_path_offsets.hpp',['../alignment__path__offsets_8hpp.html',1,'']]],
+ ['annotate_5fmain_2ecpp_7428',['annotate_main.cpp',['../annotate__main_8cpp.html',1,'']]],
+ ['annotation_2ehpp_7429',['annotation.hpp',['../annotation_8hpp.html',1,'']]],
+ ['append_5fgraph_2ecpp_7430',['append_graph.cpp',['../append__graph_8cpp.html',1,'']]],
+ ['apply_5forientations_2ecpp_7431',['apply_orientations.cpp',['../apply__orientations_8cpp.html',1,'']]],
+ ['approx_5fpath_5fdistance_2ecpp_7432',['approx_path_distance.cpp',['../approx__path__distance_8cpp.html',1,'']]],
+ ['approx_5fpath_5fdistance_2ehpp_7433',['approx_path_distance.hpp',['../approx__path__distance_8hpp.html',1,'']]],
+ ['are_5fequivalent_2ecpp_7434',['are_equivalent.cpp',['../are__equivalent_8cpp.html',1,'']]],
+ ['augment_2ecpp_7435',['augment.cpp',['../augment_8cpp.html',1,'']]],
+ ['augment_2ehpp_7436',['augment.hpp',['../augment_8hpp.html',1,'']]],
+ ['augment_5fmain_2ecpp_7437',['augment_main.cpp',['../augment__main_8cpp.html',1,'']]],
+ ['autoindex_5fmain_2ecpp_7438',['autoindex_main.cpp',['../autoindex__main_8cpp.html',1,'']]]
];
diff --git a/search/files_1.js b/search/files_1.js
index 1e535f2978..4ddada3b89 100644
--- a/search/files_1.js
+++ b/search/files_1.js
@@ -1,22 +1,22 @@
var searchData=
[
- ['back_5ftranslate_2ecpp_7437',['back_translate.cpp',['../back__translate_8cpp.html',1,'']]],
- ['back_5ftranslate_2ehpp_7438',['back_translate.hpp',['../back__translate_8hpp.html',1,'']]],
- ['back_5ftranslating_5falignment_5femitter_2ecpp_7439',['back_translating_alignment_emitter.cpp',['../back__translating__alignment__emitter_8cpp.html',1,'']]],
- ['back_5ftranslating_5falignment_5femitter_2ehpp_7440',['back_translating_alignment_emitter.hpp',['../back__translating__alignment__emitter_8hpp.html',1,'']]],
- ['banded_5fglobal_5faligner_2ecpp_7441',['banded_global_aligner.cpp',['../banded__global__aligner_8cpp.html',1,'']]],
- ['banded_5fglobal_5faligner_2ehpp_7442',['banded_global_aligner.hpp',['../banded__global__aligner_8hpp.html',1,'']]],
- ['basic_5fstream_2ecpp_7443',['basic_stream.cpp',['../basic__stream_8cpp.html',1,'']]],
- ['basic_5fstream_2ehpp_7444',['basic_stream.hpp',['../basic__stream_8hpp.html',1,'']]],
- ['benchmark_2ecpp_7445',['benchmark.cpp',['../benchmark_8cpp.html',1,'']]],
- ['benchmark_2ehpp_7446',['benchmark.hpp',['../benchmark_8hpp.html',1,'']]],
- ['benchmark_5fmain_2ecpp_7447',['benchmark_main.cpp',['../benchmark__main_8cpp.html',1,'']]],
- ['bin2ascii_2eh_7448',['bin2ascii.h',['../bin2ascii_8h.html',1,'']]],
- ['blocked_5fgzip_5finput_5fstream_2ecpp_7449',['blocked_gzip_input_stream.cpp',['../blocked__gzip__input__stream_8cpp.html',1,'']]],
- ['blocked_5fgzip_5finput_5fstream_2ehpp_7450',['blocked_gzip_input_stream.hpp',['../blocked__gzip__input__stream_8hpp.html',1,'']]],
- ['blocked_5fgzip_5foutput_5fstream_2ecpp_7451',['blocked_gzip_output_stream.cpp',['../blocked__gzip__output__stream_8cpp.html',1,'']]],
- ['blocked_5fgzip_5foutput_5fstream_2ehpp_7452',['blocked_gzip_output_stream.hpp',['../blocked__gzip__output__stream_8hpp.html',1,'']]],
- ['build_5findex_2ecpp_7453',['build_index.cpp',['../build__index_8cpp.html',1,'']]],
- ['build_5findex_2ehpp_7454',['build_index.hpp',['../build__index_8hpp.html',1,'']]],
- ['buildable_5fsnarl_5fdecomposition_2ehpp_7455',['buildable_snarl_decomposition.hpp',['../buildable__snarl__decomposition_8hpp.html',1,'']]]
+ ['back_5ftranslate_2ecpp_7439',['back_translate.cpp',['../back__translate_8cpp.html',1,'']]],
+ ['back_5ftranslate_2ehpp_7440',['back_translate.hpp',['../back__translate_8hpp.html',1,'']]],
+ ['back_5ftranslating_5falignment_5femitter_2ecpp_7441',['back_translating_alignment_emitter.cpp',['../back__translating__alignment__emitter_8cpp.html',1,'']]],
+ ['back_5ftranslating_5falignment_5femitter_2ehpp_7442',['back_translating_alignment_emitter.hpp',['../back__translating__alignment__emitter_8hpp.html',1,'']]],
+ ['banded_5fglobal_5faligner_2ecpp_7443',['banded_global_aligner.cpp',['../banded__global__aligner_8cpp.html',1,'']]],
+ ['banded_5fglobal_5faligner_2ehpp_7444',['banded_global_aligner.hpp',['../banded__global__aligner_8hpp.html',1,'']]],
+ ['basic_5fstream_2ecpp_7445',['basic_stream.cpp',['../basic__stream_8cpp.html',1,'']]],
+ ['basic_5fstream_2ehpp_7446',['basic_stream.hpp',['../basic__stream_8hpp.html',1,'']]],
+ ['benchmark_2ecpp_7447',['benchmark.cpp',['../benchmark_8cpp.html',1,'']]],
+ ['benchmark_2ehpp_7448',['benchmark.hpp',['../benchmark_8hpp.html',1,'']]],
+ ['benchmark_5fmain_2ecpp_7449',['benchmark_main.cpp',['../benchmark__main_8cpp.html',1,'']]],
+ ['bin2ascii_2eh_7450',['bin2ascii.h',['../bin2ascii_8h.html',1,'']]],
+ ['blocked_5fgzip_5finput_5fstream_2ecpp_7451',['blocked_gzip_input_stream.cpp',['../blocked__gzip__input__stream_8cpp.html',1,'']]],
+ ['blocked_5fgzip_5finput_5fstream_2ehpp_7452',['blocked_gzip_input_stream.hpp',['../blocked__gzip__input__stream_8hpp.html',1,'']]],
+ ['blocked_5fgzip_5foutput_5fstream_2ecpp_7453',['blocked_gzip_output_stream.cpp',['../blocked__gzip__output__stream_8cpp.html',1,'']]],
+ ['blocked_5fgzip_5foutput_5fstream_2ehpp_7454',['blocked_gzip_output_stream.hpp',['../blocked__gzip__output__stream_8hpp.html',1,'']]],
+ ['build_5findex_2ecpp_7455',['build_index.cpp',['../build__index_8cpp.html',1,'']]],
+ ['build_5findex_2ehpp_7456',['build_index.hpp',['../build__index_8hpp.html',1,'']]],
+ ['buildable_5fsnarl_5fdecomposition_2ehpp_7457',['buildable_snarl_decomposition.hpp',['../buildable__snarl__decomposition_8hpp.html',1,'']]]
];
diff --git a/search/files_10.js b/search/files_10.js
index 4e32d21d41..050a7a0daf 100644
--- a/search/files_10.js
+++ b/search/files_10.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['qual_5fadj_5fxdrop_5faligner_2ecpp_7771',['qual_adj_xdrop_aligner.cpp',['../qual__adj__xdrop__aligner_8cpp.html',1,'']]]
+ ['qual_5fadj_5fxdrop_5faligner_2ecpp_7773',['qual_adj_xdrop_aligner.cpp',['../qual__adj__xdrop__aligner_8cpp.html',1,'']]]
];
diff --git a/search/files_11.js b/search/files_11.js
index 79a54ffc1f..a3446e7a9c 100644
--- a/search/files_11.js
+++ b/search/files_11.js
@@ -1,58 +1,58 @@
var searchData=
[
- ['ranked_5fhandle_5fgraph_2ecpp_7772',['ranked_handle_graph.cpp',['../ranked__handle__graph_8cpp.html',1,'']]],
- ['rare_5fvariant_5fsimplifier_2ecpp_7773',['rare_variant_simplifier.cpp',['../rare__variant__simplifier_8cpp.html',1,'']]],
- ['rare_5fvariant_5fsimplifier_2ehpp_7774',['rare_variant_simplifier.hpp',['../rare__variant__simplifier_8hpp.html',1,'']]],
- ['readfilter_2ecpp_7775',['readfilter.cpp',['../readfilter_8cpp.html',1,'']]],
- ['readfilter_2ehpp_7776',['readfilter.hpp',['../readfilter_8hpp.html',1,'']]],
- ['recombinator_2ecpp_7777',['recombinator.cpp',['../recombinator_8cpp.html',1,'']]],
- ['recombinator_2ehpp_7778',['recombinator.hpp',['../recombinator_8hpp.html',1,'']]],
- ['ref_5fpath_5fdistance_2ecpp_7779',['ref_path_distance.cpp',['../ref__path__distance_8cpp.html',1,'']]],
- ['ref_5fpath_5fdistance_2ehpp_7780',['ref_path_distance.hpp',['../ref__path__distance_8hpp.html',1,'']]],
- ['region_2ecpp_7781',['region.cpp',['../region_8cpp.html',1,'']]],
- ['region_2ehpp_7782',['region.hpp',['../region_8hpp.html',1,'']]],
- ['region_5fexpander_2ecpp_7783',['region_expander.cpp',['../region__expander_8cpp.html',1,'']]],
- ['region_5fexpander_2ehpp_7784',['region_expander.hpp',['../region__expander_8hpp.html',1,'']]],
- ['register_5flibvg_5fio_2ecpp_7785',['register_libvg_io.cpp',['../register__libvg__io_8cpp.html',1,'']]],
- ['register_5flibvg_5fio_2ehpp_7786',['register_libvg_io.hpp',['../register__libvg__io_8hpp.html',1,'']]],
- ['register_5floader_5fparams_5fjson_2ecpp_7787',['register_loader_params_json.cpp',['../register__loader__params__json_8cpp.html',1,'']]],
- ['register_5floader_5fparams_5fjson_2ehpp_7788',['register_loader_params_json.hpp',['../register__loader__params__json_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fdistance_5findex_2ecpp_7789',['register_loader_saver_distance_index.cpp',['../register__loader__saver__distance__index_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fdistance_5findex_2ehpp_7790',['register_loader_saver_distance_index.hpp',['../register__loader__saver__distance__index_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwt_2ecpp_7791',['register_loader_saver_gbwt.cpp',['../register__loader__saver__gbwt_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwt_2ehpp_7792',['register_loader_saver_gbwt.hpp',['../register__loader__saver__gbwt_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwtgraph_2ecpp_7793',['register_loader_saver_gbwtgraph.cpp',['../register__loader__saver__gbwtgraph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbwtgraph_2ehpp_7794',['register_loader_saver_gbwtgraph.hpp',['../register__loader__saver__gbwtgraph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbz_2ecpp_7795',['register_loader_saver_gbz.cpp',['../register__loader__saver__gbz_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbz_2ehpp_7796',['register_loader_saver_gbz.hpp',['../register__loader__saver__gbz_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbzgraph_2ecpp_7797',['register_loader_saver_gbzgraph.cpp',['../register__loader__saver__gbzgraph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgbzgraph_2ehpp_7798',['register_loader_saver_gbzgraph.hpp',['../register__loader__saver__gbzgraph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgcsa_2ecpp_7799',['register_loader_saver_gcsa.cpp',['../register__loader__saver__gcsa_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgcsa_2ehpp_7800',['register_loader_saver_gcsa.hpp',['../register__loader__saver__gcsa_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgfa_2ecpp_7801',['register_loader_saver_gfa.cpp',['../register__loader__saver__gfa_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fgfa_2ehpp_7802',['register_loader_saver_gfa.hpp',['../register__loader__saver__gfa_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fhash_5fgraph_2ecpp_7803',['register_loader_saver_hash_graph.cpp',['../register__loader__saver__hash__graph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fhash_5fgraph_2ehpp_7804',['register_loader_saver_hash_graph.hpp',['../register__loader__saver__hash__graph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5flcp_2ecpp_7805',['register_loader_saver_lcp.cpp',['../register__loader__saver__lcp_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5flcp_2ehpp_7806',['register_loader_saver_lcp.hpp',['../register__loader__saver__lcp_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fminimizer_2ecpp_7807',['register_loader_saver_minimizer.cpp',['../register__loader__saver__minimizer_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fminimizer_2ehpp_7808',['register_loader_saver_minimizer.hpp',['../register__loader__saver__minimizer_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fpacked_5fgraph_2ecpp_7809',['register_loader_saver_packed_graph.cpp',['../register__loader__saver__packed__graph_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fpacked_5fgraph_2ehpp_7810',['register_loader_saver_packed_graph.hpp',['../register__loader__saver__packed__graph_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fr_5findex_2ecpp_7811',['register_loader_saver_r_index.cpp',['../register__loader__saver__r__index_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fr_5findex_2ehpp_7812',['register_loader_saver_r_index.hpp',['../register__loader__saver__r__index_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fsnarl_5fmanager_2ecpp_7813',['register_loader_saver_snarl_manager.cpp',['../register__loader__saver__snarl__manager_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fsnarl_5fmanager_2ehpp_7814',['register_loader_saver_snarl_manager.hpp',['../register__loader__saver__snarl__manager_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fvg_2ecpp_7815',['register_loader_saver_vg.cpp',['../register__loader__saver__vg_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fvg_2ehpp_7816',['register_loader_saver_vg.hpp',['../register__loader__saver__vg_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fxg_2ecpp_7817',['register_loader_saver_xg.cpp',['../register__loader__saver__xg_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fxg_2ehpp_7818',['register_loader_saver_xg.hpp',['../register__loader__saver__xg_8hpp.html',1,'']]],
- ['register_5floader_5fsaver_5fzip_5fcodes_2ecpp_7819',['register_loader_saver_zip_codes.cpp',['../register__loader__saver__zip__codes_8cpp.html',1,'']]],
- ['register_5floader_5fsaver_5fzip_5fcodes_2ehpp_7820',['register_loader_saver_zip_codes.hpp',['../register__loader__saver__zip__codes_8hpp.html',1,'']]],
- ['registry_2ecpp_7821',['registry.cpp',['../registry_8cpp.html',1,'']]],
- ['registry_2ehpp_7822',['registry.hpp',['../registry_8hpp.html',1,'']]],
- ['reverse_5fcomplement_2ecpp_7823',['reverse_complement.cpp',['../reverse__complement_8cpp.html',1,'']]],
- ['reverse_5fgraph_2ecpp_7824',['reverse_graph.cpp',['../reverse__graph_8cpp.html',1,'']]],
- ['reverse_5fgraph_2ehpp_7825',['reverse_graph.hpp',['../reverse__graph_8hpp.html',1,'']]],
- ['rna_5fmain_2ecpp_7826',['rna_main.cpp',['../rna__main_8cpp.html',1,'']]]
+ ['ranked_5fhandle_5fgraph_2ecpp_7774',['ranked_handle_graph.cpp',['../ranked__handle__graph_8cpp.html',1,'']]],
+ ['rare_5fvariant_5fsimplifier_2ecpp_7775',['rare_variant_simplifier.cpp',['../rare__variant__simplifier_8cpp.html',1,'']]],
+ ['rare_5fvariant_5fsimplifier_2ehpp_7776',['rare_variant_simplifier.hpp',['../rare__variant__simplifier_8hpp.html',1,'']]],
+ ['readfilter_2ecpp_7777',['readfilter.cpp',['../readfilter_8cpp.html',1,'']]],
+ ['readfilter_2ehpp_7778',['readfilter.hpp',['../readfilter_8hpp.html',1,'']]],
+ ['recombinator_2ecpp_7779',['recombinator.cpp',['../recombinator_8cpp.html',1,'']]],
+ ['recombinator_2ehpp_7780',['recombinator.hpp',['../recombinator_8hpp.html',1,'']]],
+ ['ref_5fpath_5fdistance_2ecpp_7781',['ref_path_distance.cpp',['../ref__path__distance_8cpp.html',1,'']]],
+ ['ref_5fpath_5fdistance_2ehpp_7782',['ref_path_distance.hpp',['../ref__path__distance_8hpp.html',1,'']]],
+ ['region_2ecpp_7783',['region.cpp',['../region_8cpp.html',1,'']]],
+ ['region_2ehpp_7784',['region.hpp',['../region_8hpp.html',1,'']]],
+ ['region_5fexpander_2ecpp_7785',['region_expander.cpp',['../region__expander_8cpp.html',1,'']]],
+ ['region_5fexpander_2ehpp_7786',['region_expander.hpp',['../region__expander_8hpp.html',1,'']]],
+ ['register_5flibvg_5fio_2ecpp_7787',['register_libvg_io.cpp',['../register__libvg__io_8cpp.html',1,'']]],
+ ['register_5flibvg_5fio_2ehpp_7788',['register_libvg_io.hpp',['../register__libvg__io_8hpp.html',1,'']]],
+ ['register_5floader_5fparams_5fjson_2ecpp_7789',['register_loader_params_json.cpp',['../register__loader__params__json_8cpp.html',1,'']]],
+ ['register_5floader_5fparams_5fjson_2ehpp_7790',['register_loader_params_json.hpp',['../register__loader__params__json_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fdistance_5findex_2ecpp_7791',['register_loader_saver_distance_index.cpp',['../register__loader__saver__distance__index_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fdistance_5findex_2ehpp_7792',['register_loader_saver_distance_index.hpp',['../register__loader__saver__distance__index_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwt_2ecpp_7793',['register_loader_saver_gbwt.cpp',['../register__loader__saver__gbwt_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwt_2ehpp_7794',['register_loader_saver_gbwt.hpp',['../register__loader__saver__gbwt_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwtgraph_2ecpp_7795',['register_loader_saver_gbwtgraph.cpp',['../register__loader__saver__gbwtgraph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbwtgraph_2ehpp_7796',['register_loader_saver_gbwtgraph.hpp',['../register__loader__saver__gbwtgraph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbz_2ecpp_7797',['register_loader_saver_gbz.cpp',['../register__loader__saver__gbz_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbz_2ehpp_7798',['register_loader_saver_gbz.hpp',['../register__loader__saver__gbz_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbzgraph_2ecpp_7799',['register_loader_saver_gbzgraph.cpp',['../register__loader__saver__gbzgraph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgbzgraph_2ehpp_7800',['register_loader_saver_gbzgraph.hpp',['../register__loader__saver__gbzgraph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgcsa_2ecpp_7801',['register_loader_saver_gcsa.cpp',['../register__loader__saver__gcsa_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgcsa_2ehpp_7802',['register_loader_saver_gcsa.hpp',['../register__loader__saver__gcsa_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgfa_2ecpp_7803',['register_loader_saver_gfa.cpp',['../register__loader__saver__gfa_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fgfa_2ehpp_7804',['register_loader_saver_gfa.hpp',['../register__loader__saver__gfa_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fhash_5fgraph_2ecpp_7805',['register_loader_saver_hash_graph.cpp',['../register__loader__saver__hash__graph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fhash_5fgraph_2ehpp_7806',['register_loader_saver_hash_graph.hpp',['../register__loader__saver__hash__graph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5flcp_2ecpp_7807',['register_loader_saver_lcp.cpp',['../register__loader__saver__lcp_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5flcp_2ehpp_7808',['register_loader_saver_lcp.hpp',['../register__loader__saver__lcp_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fminimizer_2ecpp_7809',['register_loader_saver_minimizer.cpp',['../register__loader__saver__minimizer_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fminimizer_2ehpp_7810',['register_loader_saver_minimizer.hpp',['../register__loader__saver__minimizer_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fpacked_5fgraph_2ecpp_7811',['register_loader_saver_packed_graph.cpp',['../register__loader__saver__packed__graph_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fpacked_5fgraph_2ehpp_7812',['register_loader_saver_packed_graph.hpp',['../register__loader__saver__packed__graph_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fr_5findex_2ecpp_7813',['register_loader_saver_r_index.cpp',['../register__loader__saver__r__index_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fr_5findex_2ehpp_7814',['register_loader_saver_r_index.hpp',['../register__loader__saver__r__index_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fsnarl_5fmanager_2ecpp_7815',['register_loader_saver_snarl_manager.cpp',['../register__loader__saver__snarl__manager_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fsnarl_5fmanager_2ehpp_7816',['register_loader_saver_snarl_manager.hpp',['../register__loader__saver__snarl__manager_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fvg_2ecpp_7817',['register_loader_saver_vg.cpp',['../register__loader__saver__vg_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fvg_2ehpp_7818',['register_loader_saver_vg.hpp',['../register__loader__saver__vg_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fxg_2ecpp_7819',['register_loader_saver_xg.cpp',['../register__loader__saver__xg_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fxg_2ehpp_7820',['register_loader_saver_xg.hpp',['../register__loader__saver__xg_8hpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fzip_5fcodes_2ecpp_7821',['register_loader_saver_zip_codes.cpp',['../register__loader__saver__zip__codes_8cpp.html',1,'']]],
+ ['register_5floader_5fsaver_5fzip_5fcodes_2ehpp_7822',['register_loader_saver_zip_codes.hpp',['../register__loader__saver__zip__codes_8hpp.html',1,'']]],
+ ['registry_2ecpp_7823',['registry.cpp',['../registry_8cpp.html',1,'']]],
+ ['registry_2ehpp_7824',['registry.hpp',['../registry_8hpp.html',1,'']]],
+ ['reverse_5fcomplement_2ecpp_7825',['reverse_complement.cpp',['../reverse__complement_8cpp.html',1,'']]],
+ ['reverse_5fgraph_2ecpp_7826',['reverse_graph.cpp',['../reverse__graph_8cpp.html',1,'']]],
+ ['reverse_5fgraph_2ehpp_7827',['reverse_graph.hpp',['../reverse__graph_8hpp.html',1,'']]],
+ ['rna_5fmain_2ecpp_7828',['rna_main.cpp',['../rna__main_8cpp.html',1,'']]]
];
diff --git a/search/files_12.js b/search/files_12.js
index a1dd8d170a..53e55d6524 100644
--- a/search/files_12.js
+++ b/search/files_12.js
@@ -1,75 +1,75 @@
var searchData=
[
- ['sample_5fminimal_2ecpp_7827',['sample_minimal.cpp',['../sample__minimal_8cpp.html',1,'']]],
- ['sample_5fminimal_2ehpp_7828',['sample_minimal.hpp',['../sample__minimal_8hpp.html',1,'']]],
- ['sampler_2ecpp_7829',['sampler.cpp',['../sampler_8cpp.html',1,'']]],
- ['sampler_2ehpp_7830',['sampler.hpp',['../sampler_8hpp.html',1,'']]],
- ['save_5fhandle_5fgraph_2ehpp_7831',['save_handle_graph.hpp',['../save__handle__graph_8hpp.html',1,'']]],
- ['scanner_2ecpp_7832',['scanner.cpp',['../scanner_8cpp.html',1,'']]],
- ['scanner_2ehpp_7833',['scanner.hpp',['../scanner_8hpp.html',1,'']]],
- ['sequence_5fcomplexity_2ehpp_7834',['sequence_complexity.hpp',['../sequence__complexity_8hpp.html',1,'']]],
- ['serializable_2ecpp_7835',['serializable.cpp',['../serializable_8cpp.html',1,'']]],
- ['serializable_2ehpp_7836',['serializable.hpp',['../serializable_8hpp.html',1,'']]],
- ['serializable_5fhandle_5fgraph_2ehpp_7837',['serializable_handle_graph.hpp',['../serializable__handle__graph_8hpp.html',1,'']]],
- ['shortest_5fcycle_2ecpp_7838',['shortest_cycle.cpp',['../shortest__cycle_8cpp.html',1,'']]],
- ['shortest_5fcycle_2ehpp_7839',['shortest_cycle.hpp',['../shortest__cycle_8hpp.html',1,'']]],
- ['sift_5fmain_2ecpp_7840',['sift_main.cpp',['../sift__main_8cpp.html',1,'']]],
- ['sim_5fmain_2ecpp_7841',['sim_main.cpp',['../sim__main_8cpp.html',1,'']]],
- ['simplify_5fmain_2ecpp_7842',['simplify_main.cpp',['../simplify__main_8cpp.html',1,'']]],
- ['simplify_5fsiblings_2ecpp_7843',['simplify_siblings.cpp',['../simplify__siblings_8cpp.html',1,'']]],
- ['simplify_5fsiblings_2ehpp_7844',['simplify_siblings.hpp',['../simplify__siblings_8hpp.html',1,'']]],
- ['small_5fbitset_2ehpp_7845',['small_bitset.hpp',['../small__bitset_8hpp.html',1,'']]],
- ['small_5fsnarl_5fsimplifier_2ecpp_7846',['small_snarl_simplifier.cpp',['../small__snarl__simplifier_8cpp.html',1,'']]],
- ['small_5fsnarl_5fsimplifier_2ehpp_7847',['small_snarl_simplifier.hpp',['../small__snarl__simplifier_8hpp.html',1,'']]],
- ['snarl_5fcaller_2ecpp_7848',['snarl_caller.cpp',['../snarl__caller_8cpp.html',1,'']]],
- ['snarl_5fcaller_2ehpp_7849',['snarl_caller.hpp',['../snarl__caller_8hpp.html',1,'']]],
- ['snarl_5fdecomposition_2ecpp_7850',['snarl_decomposition.cpp',['../snarl__decomposition_8cpp.html',1,'']]],
- ['snarl_5fdecomposition_2ehpp_7851',['snarl_decomposition.hpp',['../snarl__decomposition_8hpp.html',1,'']]],
- ['snarl_5fdistance_5findex_2ecpp_7852',['snarl_distance_index.cpp',['../snarl__distance__index_8cpp.html',1,'']]],
- ['snarl_5fdistance_5findex_2ehpp_7853',['snarl_distance_index.hpp',['../snarl__distance__index_8hpp.html',1,'']]],
- ['snarl_5fseed_5fclusterer_2ecpp_7854',['snarl_seed_clusterer.cpp',['../snarl__seed__clusterer_8cpp.html',1,'']]],
- ['snarl_5fseed_5fclusterer_2ehpp_7855',['snarl_seed_clusterer.hpp',['../snarl__seed__clusterer_8hpp.html',1,'']]],
- ['snarls_2ecpp_7856',['snarls.cpp',['../snarls_8cpp.html',1,'']]],
- ['snarls_2ehpp_7857',['snarls.hpp',['../snarls_8hpp.html',1,'']]],
- ['snarls_5fmain_2ecpp_7858',['snarls_main.cpp',['../snarls__main_8cpp.html',1,'']]],
- ['sort_5fmain_2ecpp_7859',['sort_main.cpp',['../sort__main_8cpp.html',1,'']]],
- ['sorted_5fid_5franges_2ecpp_7860',['sorted_id_ranges.cpp',['../sorted__id__ranges_8cpp.html',1,'']]],
- ['sorted_5fid_5franges_2ehpp_7861',['sorted_id_ranges.hpp',['../sorted__id__ranges_8hpp.html',1,'']]],
- ['source_5fsink_5foverlay_2ecpp_7862',['source_sink_overlay.cpp',['../source__sink__overlay_8cpp.html',1,'']]],
- ['source_5fsink_5foverlay_2ehpp_7863',['source_sink_overlay.hpp',['../source__sink__overlay_8hpp.html',1,'']]],
- ['sparse_5funion_5ffind_2ecpp_7864',['sparse_union_find.cpp',['../sparse__union__find_8cpp.html',1,'']]],
- ['sparse_5funion_5ffind_2ehpp_7865',['sparse_union_find.hpp',['../sparse__union__find_8hpp.html',1,'']]],
- ['splicing_2ecpp_7866',['splicing.cpp',['../splicing_8cpp.html',1,'']]],
- ['splicing_2ehpp_7867',['splicing.hpp',['../splicing_8hpp.html',1,'']]],
- ['split_5fstrand_5fgraph_2ecpp_7868',['split_strand_graph.cpp',['../split__strand__graph_8cpp.html',1,'']]],
- ['split_5fstrand_5fgraph_2ehpp_7869',['split_strand_graph.hpp',['../split__strand__graph_8hpp.html',1,'']]],
- ['split_5fstrands_2ecpp_7870',['split_strands.cpp',['../split__strands_8cpp.html',1,'']]],
- ['ssw_5faligner_2ecpp_7871',['ssw_aligner.cpp',['../ssw__aligner_8cpp.html',1,'']]],
- ['ssw_5faligner_2ehpp_7872',['ssw_aligner.hpp',['../ssw__aligner_8hpp.html',1,'']]],
- ['statistics_2ecpp_7873',['statistics.cpp',['../statistics_8cpp.html',1,'']]],
- ['statistics_2ehpp_7874',['statistics.hpp',['../statistics_8hpp.html',1,'']]],
- ['stats_5fmain_2ecpp_7875',['stats_main.cpp',['../stats__main_8cpp.html',1,'']]],
- ['stream_2ecpp_7876',['stream.cpp',['../stream_8cpp.html',1,'']]],
- ['stream_2ehpp_7877',['stream.hpp',['../stream_8hpp.html',1,'']]],
- ['stream_5findex_2ecpp_7878',['stream_index.cpp',['../stream__index_8cpp.html',1,'']]],
- ['stream_5findex_2ehpp_7879',['stream_index.hpp',['../stream__index_8hpp.html',1,'']]],
- ['stream_5fmultiplexer_2ecpp_7880',['stream_multiplexer.cpp',['../stream__multiplexer_8cpp.html',1,'']]],
- ['stream_5fmultiplexer_2ehpp_7881',['stream_multiplexer.hpp',['../stream__multiplexer_8hpp.html',1,'']]],
- ['stream_5fsorter_2ecpp_7882',['stream_sorter.cpp',['../stream__sorter_8cpp.html',1,'']]],
- ['stream_5fsorter_2ehpp_7883',['stream_sorter.hpp',['../stream__sorter_8hpp.html',1,'']]],
- ['strongly_5fconnected_5fcomponents_2ecpp_7884',['strongly_connected_components.cpp',['../strongly__connected__components_8cpp.html',1,'']]],
- ['subcommand_2ecpp_7885',['subcommand.cpp',['../subcommand_8cpp.html',1,'']]],
- ['subcommand_2ehpp_7886',['subcommand.hpp',['../subcommand_8hpp.html',1,'']]],
- ['subgraph_2ecpp_7887',['subgraph.cpp',['../subgraph_8cpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8cpp.html',1,'(Global Namespace)']]],
- ['subgraph_2ehpp_7888',['subgraph.hpp',['../subgraph_8hpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8hpp.html',1,'(Global Namespace)']]],
- ['subgraph_5foverlay_2ecpp_7889',['subgraph_overlay.cpp',['../subgraph__overlay_8cpp.html',1,'']]],
- ['subgraph_5foverlay_2ehpp_7890',['subgraph_overlay.hpp',['../subgraph__overlay_8hpp.html',1,'']]],
- ['subpath_5foverlay_2ecpp_7891',['subpath_overlay.cpp',['../subpath__overlay_8cpp.html',1,'']]],
- ['subpath_5foverlay_2ehpp_7892',['subpath_overlay.hpp',['../subpath__overlay_8hpp.html',1,'']]],
- ['surject_5fmain_2ecpp_7893',['surject_main.cpp',['../surject__main_8cpp.html',1,'']]],
- ['surjecting_5falignment_5femitter_2ecpp_7894',['surjecting_alignment_emitter.cpp',['../surjecting__alignment__emitter_8cpp.html',1,'']]],
- ['surjecting_5falignment_5femitter_2ehpp_7895',['surjecting_alignment_emitter.hpp',['../surjecting__alignment__emitter_8hpp.html',1,'']]],
- ['surjector_2ecpp_7896',['surjector.cpp',['../surjector_8cpp.html',1,'']]],
- ['surjector_2ehpp_7897',['surjector.hpp',['../surjector_8hpp.html',1,'']]],
- ['swap_5fremove_2ehpp_7898',['swap_remove.hpp',['../swap__remove_8hpp.html',1,'']]]
+ ['sample_5fminimal_2ecpp_7829',['sample_minimal.cpp',['../sample__minimal_8cpp.html',1,'']]],
+ ['sample_5fminimal_2ehpp_7830',['sample_minimal.hpp',['../sample__minimal_8hpp.html',1,'']]],
+ ['sampler_2ecpp_7831',['sampler.cpp',['../sampler_8cpp.html',1,'']]],
+ ['sampler_2ehpp_7832',['sampler.hpp',['../sampler_8hpp.html',1,'']]],
+ ['save_5fhandle_5fgraph_2ehpp_7833',['save_handle_graph.hpp',['../save__handle__graph_8hpp.html',1,'']]],
+ ['scanner_2ecpp_7834',['scanner.cpp',['../scanner_8cpp.html',1,'']]],
+ ['scanner_2ehpp_7835',['scanner.hpp',['../scanner_8hpp.html',1,'']]],
+ ['sequence_5fcomplexity_2ehpp_7836',['sequence_complexity.hpp',['../sequence__complexity_8hpp.html',1,'']]],
+ ['serializable_2ecpp_7837',['serializable.cpp',['../serializable_8cpp.html',1,'']]],
+ ['serializable_2ehpp_7838',['serializable.hpp',['../serializable_8hpp.html',1,'']]],
+ ['serializable_5fhandle_5fgraph_2ehpp_7839',['serializable_handle_graph.hpp',['../serializable__handle__graph_8hpp.html',1,'']]],
+ ['shortest_5fcycle_2ecpp_7840',['shortest_cycle.cpp',['../shortest__cycle_8cpp.html',1,'']]],
+ ['shortest_5fcycle_2ehpp_7841',['shortest_cycle.hpp',['../shortest__cycle_8hpp.html',1,'']]],
+ ['sift_5fmain_2ecpp_7842',['sift_main.cpp',['../sift__main_8cpp.html',1,'']]],
+ ['sim_5fmain_2ecpp_7843',['sim_main.cpp',['../sim__main_8cpp.html',1,'']]],
+ ['simplify_5fmain_2ecpp_7844',['simplify_main.cpp',['../simplify__main_8cpp.html',1,'']]],
+ ['simplify_5fsiblings_2ecpp_7845',['simplify_siblings.cpp',['../simplify__siblings_8cpp.html',1,'']]],
+ ['simplify_5fsiblings_2ehpp_7846',['simplify_siblings.hpp',['../simplify__siblings_8hpp.html',1,'']]],
+ ['small_5fbitset_2ehpp_7847',['small_bitset.hpp',['../small__bitset_8hpp.html',1,'']]],
+ ['small_5fsnarl_5fsimplifier_2ecpp_7848',['small_snarl_simplifier.cpp',['../small__snarl__simplifier_8cpp.html',1,'']]],
+ ['small_5fsnarl_5fsimplifier_2ehpp_7849',['small_snarl_simplifier.hpp',['../small__snarl__simplifier_8hpp.html',1,'']]],
+ ['snarl_5fcaller_2ecpp_7850',['snarl_caller.cpp',['../snarl__caller_8cpp.html',1,'']]],
+ ['snarl_5fcaller_2ehpp_7851',['snarl_caller.hpp',['../snarl__caller_8hpp.html',1,'']]],
+ ['snarl_5fdecomposition_2ecpp_7852',['snarl_decomposition.cpp',['../snarl__decomposition_8cpp.html',1,'']]],
+ ['snarl_5fdecomposition_2ehpp_7853',['snarl_decomposition.hpp',['../snarl__decomposition_8hpp.html',1,'']]],
+ ['snarl_5fdistance_5findex_2ecpp_7854',['snarl_distance_index.cpp',['../snarl__distance__index_8cpp.html',1,'']]],
+ ['snarl_5fdistance_5findex_2ehpp_7855',['snarl_distance_index.hpp',['../snarl__distance__index_8hpp.html',1,'']]],
+ ['snarl_5fseed_5fclusterer_2ecpp_7856',['snarl_seed_clusterer.cpp',['../snarl__seed__clusterer_8cpp.html',1,'']]],
+ ['snarl_5fseed_5fclusterer_2ehpp_7857',['snarl_seed_clusterer.hpp',['../snarl__seed__clusterer_8hpp.html',1,'']]],
+ ['snarls_2ecpp_7858',['snarls.cpp',['../snarls_8cpp.html',1,'']]],
+ ['snarls_2ehpp_7859',['snarls.hpp',['../snarls_8hpp.html',1,'']]],
+ ['snarls_5fmain_2ecpp_7860',['snarls_main.cpp',['../snarls__main_8cpp.html',1,'']]],
+ ['sort_5fmain_2ecpp_7861',['sort_main.cpp',['../sort__main_8cpp.html',1,'']]],
+ ['sorted_5fid_5franges_2ecpp_7862',['sorted_id_ranges.cpp',['../sorted__id__ranges_8cpp.html',1,'']]],
+ ['sorted_5fid_5franges_2ehpp_7863',['sorted_id_ranges.hpp',['../sorted__id__ranges_8hpp.html',1,'']]],
+ ['source_5fsink_5foverlay_2ecpp_7864',['source_sink_overlay.cpp',['../source__sink__overlay_8cpp.html',1,'']]],
+ ['source_5fsink_5foverlay_2ehpp_7865',['source_sink_overlay.hpp',['../source__sink__overlay_8hpp.html',1,'']]],
+ ['sparse_5funion_5ffind_2ecpp_7866',['sparse_union_find.cpp',['../sparse__union__find_8cpp.html',1,'']]],
+ ['sparse_5funion_5ffind_2ehpp_7867',['sparse_union_find.hpp',['../sparse__union__find_8hpp.html',1,'']]],
+ ['splicing_2ecpp_7868',['splicing.cpp',['../splicing_8cpp.html',1,'']]],
+ ['splicing_2ehpp_7869',['splicing.hpp',['../splicing_8hpp.html',1,'']]],
+ ['split_5fstrand_5fgraph_2ecpp_7870',['split_strand_graph.cpp',['../split__strand__graph_8cpp.html',1,'']]],
+ ['split_5fstrand_5fgraph_2ehpp_7871',['split_strand_graph.hpp',['../split__strand__graph_8hpp.html',1,'']]],
+ ['split_5fstrands_2ecpp_7872',['split_strands.cpp',['../split__strands_8cpp.html',1,'']]],
+ ['ssw_5faligner_2ecpp_7873',['ssw_aligner.cpp',['../ssw__aligner_8cpp.html',1,'']]],
+ ['ssw_5faligner_2ehpp_7874',['ssw_aligner.hpp',['../ssw__aligner_8hpp.html',1,'']]],
+ ['statistics_2ecpp_7875',['statistics.cpp',['../statistics_8cpp.html',1,'']]],
+ ['statistics_2ehpp_7876',['statistics.hpp',['../statistics_8hpp.html',1,'']]],
+ ['stats_5fmain_2ecpp_7877',['stats_main.cpp',['../stats__main_8cpp.html',1,'']]],
+ ['stream_2ecpp_7878',['stream.cpp',['../stream_8cpp.html',1,'']]],
+ ['stream_2ehpp_7879',['stream.hpp',['../stream_8hpp.html',1,'']]],
+ ['stream_5findex_2ecpp_7880',['stream_index.cpp',['../stream__index_8cpp.html',1,'']]],
+ ['stream_5findex_2ehpp_7881',['stream_index.hpp',['../stream__index_8hpp.html',1,'']]],
+ ['stream_5fmultiplexer_2ecpp_7882',['stream_multiplexer.cpp',['../stream__multiplexer_8cpp.html',1,'']]],
+ ['stream_5fmultiplexer_2ehpp_7883',['stream_multiplexer.hpp',['../stream__multiplexer_8hpp.html',1,'']]],
+ ['stream_5fsorter_2ecpp_7884',['stream_sorter.cpp',['../stream__sorter_8cpp.html',1,'']]],
+ ['stream_5fsorter_2ehpp_7885',['stream_sorter.hpp',['../stream__sorter_8hpp.html',1,'']]],
+ ['strongly_5fconnected_5fcomponents_2ecpp_7886',['strongly_connected_components.cpp',['../strongly__connected__components_8cpp.html',1,'']]],
+ ['subcommand_2ecpp_7887',['subcommand.cpp',['../subcommand_8cpp.html',1,'']]],
+ ['subcommand_2ehpp_7888',['subcommand.hpp',['../subcommand_8hpp.html',1,'']]],
+ ['subgraph_2ecpp_7889',['subgraph.cpp',['../subgraph_8cpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8cpp.html',1,'(Global Namespace)']]],
+ ['subgraph_2ehpp_7890',['subgraph.hpp',['../subgraph_8hpp.html',1,'(Global Namespace)'],['../algorithms_2subgraph_8hpp.html',1,'(Global Namespace)']]],
+ ['subgraph_5foverlay_2ecpp_7891',['subgraph_overlay.cpp',['../subgraph__overlay_8cpp.html',1,'']]],
+ ['subgraph_5foverlay_2ehpp_7892',['subgraph_overlay.hpp',['../subgraph__overlay_8hpp.html',1,'']]],
+ ['subpath_5foverlay_2ecpp_7893',['subpath_overlay.cpp',['../subpath__overlay_8cpp.html',1,'']]],
+ ['subpath_5foverlay_2ehpp_7894',['subpath_overlay.hpp',['../subpath__overlay_8hpp.html',1,'']]],
+ ['surject_5fmain_2ecpp_7895',['surject_main.cpp',['../surject__main_8cpp.html',1,'']]],
+ ['surjecting_5falignment_5femitter_2ecpp_7896',['surjecting_alignment_emitter.cpp',['../surjecting__alignment__emitter_8cpp.html',1,'']]],
+ ['surjecting_5falignment_5femitter_2ehpp_7897',['surjecting_alignment_emitter.hpp',['../surjecting__alignment__emitter_8hpp.html',1,'']]],
+ ['surjector_2ecpp_7898',['surjector.cpp',['../surjector_8cpp.html',1,'']]],
+ ['surjector_2ehpp_7899',['surjector.hpp',['../surjector_8hpp.html',1,'']]],
+ ['swap_5fremove_2ehpp_7900',['swap_remove.hpp',['../swap__remove_8hpp.html',1,'']]]
];
diff --git a/search/files_13.js b/search/files_13.js
index cea2ffe792..f0273c398a 100644
--- a/search/files_13.js
+++ b/search/files_13.js
@@ -1,25 +1,25 @@
var searchData=
[
- ['test_5fmain_2ecpp_7899',['test_main.cpp',['../test__main_8cpp.html',1,'']]],
- ['three_5fedge_5fconnected_5fcomponents_2ecpp_7900',['three_edge_connected_components.cpp',['../three__edge__connected__components_8cpp.html',1,'']]],
- ['three_5fedge_5fconnected_5fcomponents_2ehpp_7901',['three_edge_connected_components.hpp',['../three__edge__connected__components_8hpp.html',1,'']]],
- ['topological_5fsort_2ecpp_7902',['topological_sort.cpp',['../topological__sort_8cpp.html',1,'']]],
- ['trace_5fmain_2ecpp_7903',['trace_main.cpp',['../trace__main_8cpp.html',1,'']]],
- ['transcriptome_2ecpp_7904',['transcriptome.cpp',['../transcriptome_8cpp.html',1,'']]],
- ['transcriptome_2ehpp_7905',['transcriptome.hpp',['../transcriptome_8hpp.html',1,'']]],
- ['translate_5fmain_2ecpp_7906',['translate_main.cpp',['../translate__main_8cpp.html',1,'']]],
- ['translator_2ecpp_7907',['translator.cpp',['../translator_8cpp.html',1,'']]],
- ['translator_2ehpp_7908',['translator.hpp',['../translator_8hpp.html',1,'']]],
- ['traversal_5fclusters_2ecpp_7909',['traversal_clusters.cpp',['../traversal__clusters_8cpp.html',1,'']]],
- ['traversal_5fclusters_2ehpp_7910',['traversal_clusters.hpp',['../traversal__clusters_8hpp.html',1,'']]],
- ['traversal_5ffinder_2ecpp_7911',['traversal_finder.cpp',['../traversal__finder_8cpp.html',1,'']]],
- ['traversal_5ffinder_2ehpp_7912',['traversal_finder.hpp',['../traversal__finder_8hpp.html',1,'']]],
- ['traversal_5fsupport_2ecpp_7913',['traversal_support.cpp',['../traversal__support_8cpp.html',1,'']]],
- ['traversal_5fsupport_2ehpp_7914',['traversal_support.hpp',['../traversal__support_8hpp.html',1,'']]],
- ['tree_5fsubgraph_2ecpp_7915',['tree_subgraph.cpp',['../tree__subgraph_8cpp.html',1,'']]],
- ['tree_5fsubgraph_2ehpp_7916',['tree_subgraph.hpp',['../tree__subgraph_8hpp.html',1,'']]],
- ['trivially_5fserializable_2ecpp_7917',['trivially_serializable.cpp',['../trivially__serializable_8cpp.html',1,'']]],
- ['trivially_5fserializable_2ehpp_7918',['trivially_serializable.hpp',['../trivially__serializable_8hpp.html',1,'']]],
- ['types_2ecpp_7919',['types.cpp',['../types_8cpp.html',1,'']]],
- ['types_2ehpp_7920',['types.hpp',['../src_2types_8hpp.html',1,'(Global Namespace)'],['../deps_2libhandlegraph_2src_2include_2handlegraph_2types_8hpp.html',1,'(Global Namespace)']]]
+ ['test_5fmain_2ecpp_7901',['test_main.cpp',['../test__main_8cpp.html',1,'']]],
+ ['three_5fedge_5fconnected_5fcomponents_2ecpp_7902',['three_edge_connected_components.cpp',['../three__edge__connected__components_8cpp.html',1,'']]],
+ ['three_5fedge_5fconnected_5fcomponents_2ehpp_7903',['three_edge_connected_components.hpp',['../three__edge__connected__components_8hpp.html',1,'']]],
+ ['topological_5fsort_2ecpp_7904',['topological_sort.cpp',['../topological__sort_8cpp.html',1,'']]],
+ ['trace_5fmain_2ecpp_7905',['trace_main.cpp',['../trace__main_8cpp.html',1,'']]],
+ ['transcriptome_2ecpp_7906',['transcriptome.cpp',['../transcriptome_8cpp.html',1,'']]],
+ ['transcriptome_2ehpp_7907',['transcriptome.hpp',['../transcriptome_8hpp.html',1,'']]],
+ ['translate_5fmain_2ecpp_7908',['translate_main.cpp',['../translate__main_8cpp.html',1,'']]],
+ ['translator_2ecpp_7909',['translator.cpp',['../translator_8cpp.html',1,'']]],
+ ['translator_2ehpp_7910',['translator.hpp',['../translator_8hpp.html',1,'']]],
+ ['traversal_5fclusters_2ecpp_7911',['traversal_clusters.cpp',['../traversal__clusters_8cpp.html',1,'']]],
+ ['traversal_5fclusters_2ehpp_7912',['traversal_clusters.hpp',['../traversal__clusters_8hpp.html',1,'']]],
+ ['traversal_5ffinder_2ecpp_7913',['traversal_finder.cpp',['../traversal__finder_8cpp.html',1,'']]],
+ ['traversal_5ffinder_2ehpp_7914',['traversal_finder.hpp',['../traversal__finder_8hpp.html',1,'']]],
+ ['traversal_5fsupport_2ecpp_7915',['traversal_support.cpp',['../traversal__support_8cpp.html',1,'']]],
+ ['traversal_5fsupport_2ehpp_7916',['traversal_support.hpp',['../traversal__support_8hpp.html',1,'']]],
+ ['tree_5fsubgraph_2ecpp_7917',['tree_subgraph.cpp',['../tree__subgraph_8cpp.html',1,'']]],
+ ['tree_5fsubgraph_2ehpp_7918',['tree_subgraph.hpp',['../tree__subgraph_8hpp.html',1,'']]],
+ ['trivially_5fserializable_2ecpp_7919',['trivially_serializable.cpp',['../trivially__serializable_8cpp.html',1,'']]],
+ ['trivially_5fserializable_2ehpp_7920',['trivially_serializable.hpp',['../trivially__serializable_8hpp.html',1,'']]],
+ ['types_2ecpp_7921',['types.cpp',['../types_8cpp.html',1,'']]],
+ ['types_2ehpp_7922',['types.hpp',['../src_2types_8hpp.html',1,'(Global Namespace)'],['../deps_2libhandlegraph_2src_2include_2handlegraph_2types_8hpp.html',1,'(Global Namespace)']]]
];
diff --git a/search/files_14.js b/search/files_14.js
index 62d6a1bb8d..1f482853e3 100644
--- a/search/files_14.js
+++ b/search/files_14.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['util_2ehpp_7921',['util.hpp',['../util_8hpp.html',1,'']]],
- ['utility_2ecpp_7922',['utility.cpp',['../utility_8cpp.html',1,'']]],
- ['utility_2ehpp_7923',['utility.hpp',['../utility_8hpp.html',1,'']]]
+ ['util_2ehpp_7923',['util.hpp',['../util_8hpp.html',1,'']]],
+ ['utility_2ecpp_7924',['utility.cpp',['../utility_8cpp.html',1,'']]],
+ ['utility_2ehpp_7925',['utility.hpp',['../utility_8hpp.html',1,'']]]
];
diff --git a/search/files_15.js b/search/files_15.js
index 2d613cea18..f8907369c0 100644
--- a/search/files_15.js
+++ b/search/files_15.js
@@ -1,31 +1,31 @@
var searchData=
[
- ['validate_5fmain_2ecpp_7924',['validate_main.cpp',['../validate__main_8cpp.html',1,'']]],
- ['variant_5fadder_2ecpp_7925',['variant_adder.cpp',['../variant__adder_8cpp.html',1,'']]],
- ['variant_5fadder_2ehpp_7926',['variant_adder.hpp',['../variant__adder_8hpp.html',1,'']]],
- ['variant_5frecall_2ecpp_7927',['variant_recall.cpp',['../variant__recall_8cpp.html',1,'']]],
- ['variant_5frecall_2ehpp_7928',['variant_recall.hpp',['../variant__recall_8hpp.html',1,'']]],
- ['varint_2ecpp_7929',['varint.cpp',['../varint_8cpp.html',1,'']]],
- ['varint_2ehpp_7930',['varint.hpp',['../varint_8hpp.html',1,'']]],
- ['vcf_5fbuffer_2ecpp_7931',['vcf_buffer.cpp',['../vcf__buffer_8cpp.html',1,'']]],
- ['vcf_5fbuffer_2ehpp_7932',['vcf_buffer.hpp',['../vcf__buffer_8hpp.html',1,'']]],
- ['vectorize_5fmain_2ecpp_7933',['vectorize_main.cpp',['../vectorize__main_8cpp.html',1,'']]],
- ['vectorizer_2ecpp_7934',['vectorizer.cpp',['../vectorizer_8cpp.html',1,'']]],
- ['vectorizer_2ehpp_7935',['vectorizer.hpp',['../vectorizer_8hpp.html',1,'']]],
- ['version_2ecpp_7936',['version.cpp',['../version_8cpp.html',1,'']]],
- ['version_2ehpp_7937',['version.hpp',['../version_8hpp.html',1,'']]],
- ['version_5fmain_2ecpp_7938',['version_main.cpp',['../version__main_8cpp.html',1,'']]],
- ['vg_2ecpp_7939',['vg.cpp',['../vg_8cpp.html',1,'']]],
- ['vg_2ehpp_7940',['vg.hpp',['../vg_8hpp.html',1,'']]],
- ['vg_2eproto_7941',['vg.proto',['../vg_8proto.html',1,'']]],
- ['vg_5fenvironment_5fversion_2ehpp_7942',['vg_environment_version.hpp',['../vg__environment__version_8hpp.html',1,'']]],
- ['vg_5fgit_5fversion_2ehpp_7943',['vg_git_version.hpp',['../vg__git__version_8hpp.html',1,'']]],
- ['vg_5fset_2ecpp_7944',['vg_set.cpp',['../vg__set_8cpp.html',1,'']]],
- ['vg_5fset_2ehpp_7945',['vg_set.hpp',['../vg__set_8hpp.html',1,'']]],
- ['view_5fmain_2ecpp_7946',['view_main.cpp',['../view__main_8cpp.html',1,'']]],
- ['viz_2ecpp_7947',['viz.cpp',['../viz_8cpp.html',1,'']]],
- ['viz_2ehpp_7948',['viz.hpp',['../viz_8hpp.html',1,'']]],
- ['viz_5fmain_2ecpp_7949',['viz_main.cpp',['../viz__main_8cpp.html',1,'']]],
- ['vpkg_2ecpp_7950',['vpkg.cpp',['../vpkg_8cpp.html',1,'']]],
- ['vpkg_2ehpp_7951',['vpkg.hpp',['../vpkg_8hpp.html',1,'']]]
+ ['validate_5fmain_2ecpp_7926',['validate_main.cpp',['../validate__main_8cpp.html',1,'']]],
+ ['variant_5fadder_2ecpp_7927',['variant_adder.cpp',['../variant__adder_8cpp.html',1,'']]],
+ ['variant_5fadder_2ehpp_7928',['variant_adder.hpp',['../variant__adder_8hpp.html',1,'']]],
+ ['variant_5frecall_2ecpp_7929',['variant_recall.cpp',['../variant__recall_8cpp.html',1,'']]],
+ ['variant_5frecall_2ehpp_7930',['variant_recall.hpp',['../variant__recall_8hpp.html',1,'']]],
+ ['varint_2ecpp_7931',['varint.cpp',['../varint_8cpp.html',1,'']]],
+ ['varint_2ehpp_7932',['varint.hpp',['../varint_8hpp.html',1,'']]],
+ ['vcf_5fbuffer_2ecpp_7933',['vcf_buffer.cpp',['../vcf__buffer_8cpp.html',1,'']]],
+ ['vcf_5fbuffer_2ehpp_7934',['vcf_buffer.hpp',['../vcf__buffer_8hpp.html',1,'']]],
+ ['vectorize_5fmain_2ecpp_7935',['vectorize_main.cpp',['../vectorize__main_8cpp.html',1,'']]],
+ ['vectorizer_2ecpp_7936',['vectorizer.cpp',['../vectorizer_8cpp.html',1,'']]],
+ ['vectorizer_2ehpp_7937',['vectorizer.hpp',['../vectorizer_8hpp.html',1,'']]],
+ ['version_2ecpp_7938',['version.cpp',['../version_8cpp.html',1,'']]],
+ ['version_2ehpp_7939',['version.hpp',['../version_8hpp.html',1,'']]],
+ ['version_5fmain_2ecpp_7940',['version_main.cpp',['../version__main_8cpp.html',1,'']]],
+ ['vg_2ecpp_7941',['vg.cpp',['../vg_8cpp.html',1,'']]],
+ ['vg_2ehpp_7942',['vg.hpp',['../vg_8hpp.html',1,'']]],
+ ['vg_2eproto_7943',['vg.proto',['../vg_8proto.html',1,'']]],
+ ['vg_5fenvironment_5fversion_2ehpp_7944',['vg_environment_version.hpp',['../vg__environment__version_8hpp.html',1,'']]],
+ ['vg_5fgit_5fversion_2ehpp_7945',['vg_git_version.hpp',['../vg__git__version_8hpp.html',1,'']]],
+ ['vg_5fset_2ecpp_7946',['vg_set.cpp',['../vg__set_8cpp.html',1,'']]],
+ ['vg_5fset_2ehpp_7947',['vg_set.hpp',['../vg__set_8hpp.html',1,'']]],
+ ['view_5fmain_2ecpp_7948',['view_main.cpp',['../view__main_8cpp.html',1,'']]],
+ ['viz_2ecpp_7949',['viz.cpp',['../viz_8cpp.html',1,'']]],
+ ['viz_2ehpp_7950',['viz.hpp',['../viz_8hpp.html',1,'']]],
+ ['viz_5fmain_2ecpp_7951',['viz_main.cpp',['../viz__main_8cpp.html',1,'']]],
+ ['vpkg_2ecpp_7952',['vpkg.cpp',['../vpkg_8cpp.html',1,'']]],
+ ['vpkg_2ehpp_7953',['vpkg.hpp',['../vpkg_8hpp.html',1,'']]]
];
diff --git a/search/files_16.js b/search/files_16.js
index d85ffbe3c9..155cfdeaeb 100644
--- a/search/files_16.js
+++ b/search/files_16.js
@@ -1,9 +1,9 @@
var searchData=
[
- ['walk_2ecpp_7952',['walk.cpp',['../walk_8cpp.html',1,'']]],
- ['walk_2ehpp_7953',['walk.hpp',['../walk_8hpp.html',1,'']]],
- ['wang_5fhash_2ehpp_7954',['wang_hash.hpp',['../wang__hash_8hpp.html',1,'']]],
- ['watchdog_2ecpp_7955',['watchdog.cpp',['../watchdog_8cpp.html',1,'']]],
- ['watchdog_2ehpp_7956',['watchdog.hpp',['../watchdog_8hpp.html',1,'']]],
- ['weakly_5fconnected_5fcomponents_2ecpp_7957',['weakly_connected_components.cpp',['../weakly__connected__components_8cpp.html',1,'']]]
+ ['walk_2ecpp_7954',['walk.cpp',['../walk_8cpp.html',1,'']]],
+ ['walk_2ehpp_7955',['walk.hpp',['../walk_8hpp.html',1,'']]],
+ ['wang_5fhash_2ehpp_7956',['wang_hash.hpp',['../wang__hash_8hpp.html',1,'']]],
+ ['watchdog_2ecpp_7957',['watchdog.cpp',['../watchdog_8cpp.html',1,'']]],
+ ['watchdog_2ehpp_7958',['watchdog.hpp',['../watchdog_8hpp.html',1,'']]],
+ ['weakly_5fconnected_5fcomponents_2ecpp_7959',['weakly_connected_components.cpp',['../weakly__connected__components_8cpp.html',1,'']]]
];
diff --git a/search/files_17.js b/search/files_17.js
index 063f266c85..430d91a951 100644
--- a/search/files_17.js
+++ b/search/files_17.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['xdrop_5faligner_2ecpp_7958',['xdrop_aligner.cpp',['../xdrop__aligner_8cpp.html',1,'']]],
- ['xg_2ecpp_7959',['xg.cpp',['../xg_8cpp.html',1,'']]],
- ['xg_2ehpp_7960',['xg.hpp',['../xg_8hpp.html',1,'']]]
+ ['xdrop_5faligner_2ecpp_7960',['xdrop_aligner.cpp',['../xdrop__aligner_8cpp.html',1,'']]],
+ ['xg_2ecpp_7961',['xg.cpp',['../xg_8cpp.html',1,'']]],
+ ['xg_2ehpp_7962',['xg.hpp',['../xg_8hpp.html',1,'']]]
];
diff --git a/search/files_18.js b/search/files_18.js
index 33bd582e44..0ba0a36a87 100644
--- a/search/files_18.js
+++ b/search/files_18.js
@@ -1,10 +1,10 @@
var searchData=
[
- ['zip_5fcode_2ecpp_7961',['zip_code.cpp',['../zip__code_8cpp.html',1,'']]],
- ['zip_5fcode_2ehpp_7962',['zip_code.hpp',['../zip__code_8hpp.html',1,'']]],
- ['zip_5fcode_5ftree_2ecpp_7963',['zip_code_tree.cpp',['../zip__code__tree_8cpp.html',1,'']]],
- ['zip_5fcode_5ftree_2ehpp_7964',['zip_code_tree.hpp',['../zip__code__tree_8hpp.html',1,'']]],
- ['zipcode_5fmain_2ecpp_7965',['zipcode_main.cpp',['../zipcode__main_8cpp.html',1,'']]],
- ['zstdutil_2ecpp_7966',['zstdutil.cpp',['../zstdutil_8cpp.html',1,'']]],
- ['zstdutil_2ehpp_7967',['zstdutil.hpp',['../zstdutil_8hpp.html',1,'']]]
+ ['zip_5fcode_2ecpp_7963',['zip_code.cpp',['../zip__code_8cpp.html',1,'']]],
+ ['zip_5fcode_2ehpp_7964',['zip_code.hpp',['../zip__code_8hpp.html',1,'']]],
+ ['zip_5fcode_5ftree_2ecpp_7965',['zip_code_tree.cpp',['../zip__code__tree_8cpp.html',1,'']]],
+ ['zip_5fcode_5ftree_2ehpp_7966',['zip_code_tree.hpp',['../zip__code__tree_8hpp.html',1,'']]],
+ ['zipcode_5fmain_2ecpp_7967',['zipcode_main.cpp',['../zipcode__main_8cpp.html',1,'']]],
+ ['zstdutil_2ecpp_7968',['zstdutil.cpp',['../zstdutil_8cpp.html',1,'']]],
+ ['zstdutil_2ehpp_7969',['zstdutil.hpp',['../zstdutil_8hpp.html',1,'']]]
];
diff --git a/search/files_2.js b/search/files_2.js
index aceda8973b..810826b7a8 100644
--- a/search/files_2.js
+++ b/search/files_2.js
@@ -1,42 +1,42 @@
var searchData=
[
- ['cactus_2ecpp_7456',['cactus.cpp',['../cactus_8cpp.html',1,'']]],
- ['cactus_2ehpp_7457',['cactus.hpp',['../cactus_8hpp.html',1,'']]],
- ['cactus_5fsnarl_5ffinder_2ecpp_7458',['cactus_snarl_finder.cpp',['../cactus__snarl__finder_8cpp.html',1,'']]],
- ['cactus_5fsnarl_5ffinder_2ehpp_7459',['cactus_snarl_finder.hpp',['../cactus__snarl__finder_8hpp.html',1,'']]],
- ['call_5fmain_2ecpp_7460',['call_main.cpp',['../call__main_8cpp.html',1,'']]],
- ['chain_5fitems_2ecpp_7461',['chain_items.cpp',['../chain__items_8cpp.html',1,'']]],
- ['chain_5fitems_2ehpp_7462',['chain_items.hpp',['../chain__items_8hpp.html',1,'']]],
- ['chain_5fmain_2ecpp_7463',['chain_main.cpp',['../chain__main_8cpp.html',1,'']]],
- ['chop_2ecpp_7464',['chop.cpp',['../chop_8cpp.html',1,'']]],
- ['chunk_5fmain_2ecpp_7465',['chunk_main.cpp',['../chunk__main_8cpp.html',1,'']]],
- ['chunker_2ecpp_7466',['chunker.cpp',['../chunker_8cpp.html',1,'']]],
- ['chunker_2ehpp_7467',['chunker.hpp',['../chunker_8hpp.html',1,'']]],
- ['circularize_5fmain_2ecpp_7468',['circularize_main.cpp',['../circularize__main_8cpp.html',1,'']]],
- ['clip_2ecpp_7469',['clip.cpp',['../clip_8cpp.html',1,'']]],
- ['clip_2ehpp_7470',['clip.hpp',['../clip_8hpp.html',1,'']]],
- ['clip_5fmain_2ecpp_7471',['clip_main.cpp',['../clip__main_8cpp.html',1,'']]],
- ['cluster_2ecpp_7472',['cluster.cpp',['../cluster_8cpp.html',1,'']]],
- ['cluster_2ehpp_7473',['cluster.hpp',['../cluster_8hpp.html',1,'']]],
- ['cluster_5fmain_2ecpp_7474',['cluster_main.cpp',['../cluster__main_8cpp.html',1,'']]],
- ['colors_2ehpp_7475',['colors.hpp',['../colors_8hpp.html',1,'']]],
- ['combine_5fmain_2ecpp_7476',['combine_main.cpp',['../combine__main_8cpp.html',1,'']]],
- ['component_2ecpp_7477',['component.cpp',['../component_8cpp.html',1,'']]],
- ['component_2ehpp_7478',['component.hpp',['../component_8hpp.html',1,'']]],
- ['concat_5fmain_2ecpp_7479',['concat_main.cpp',['../concat__main_8cpp.html',1,'']]],
- ['construct_5fmain_2ecpp_7480',['construct_main.cpp',['../construct__main_8cpp.html',1,'']]],
- ['constructor_2ecpp_7481',['constructor.cpp',['../constructor_8cpp.html',1,'']]],
- ['constructor_2ehpp_7482',['constructor.hpp',['../constructor_8hpp.html',1,'']]],
- ['contracting_5fgraph_2ecpp_7483',['contracting_graph.cpp',['../contracting__graph_8cpp.html',1,'']]],
- ['contracting_5fgraph_2ehpp_7484',['contracting_graph.hpp',['../contracting__graph_8hpp.html',1,'']]],
- ['convert_2ehpp_7485',['convert.hpp',['../convert_8hpp.html',1,'']]],
- ['convert_5fmain_2ecpp_7486',['convert_main.cpp',['../convert__main_8cpp.html',1,'']]],
- ['converted_5fhash_5fgraph_2ehpp_7487',['converted_hash_graph.hpp',['../converted__hash__graph_8hpp.html',1,'']]],
- ['copy_5fgraph_2ecpp_7488',['copy_graph.cpp',['../copy__graph_8cpp.html',1,'']]],
- ['count_5fcovered_2ehpp_7489',['count_covered.hpp',['../count__covered_8hpp.html',1,'']]],
- ['count_5fwalks_2ecpp_7490',['count_walks.cpp',['../count__walks_8cpp.html',1,'']]],
- ['coverage_5fdepth_2ecpp_7491',['coverage_depth.cpp',['../coverage__depth_8cpp.html',1,'']]],
- ['coverage_5fdepth_2ehpp_7492',['coverage_depth.hpp',['../coverage__depth_8hpp.html',1,'']]],
- ['crash_2ecpp_7493',['crash.cpp',['../crash_8cpp.html',1,'']]],
- ['crash_2ehpp_7494',['crash.hpp',['../crash_8hpp.html',1,'']]]
+ ['cactus_2ecpp_7458',['cactus.cpp',['../cactus_8cpp.html',1,'']]],
+ ['cactus_2ehpp_7459',['cactus.hpp',['../cactus_8hpp.html',1,'']]],
+ ['cactus_5fsnarl_5ffinder_2ecpp_7460',['cactus_snarl_finder.cpp',['../cactus__snarl__finder_8cpp.html',1,'']]],
+ ['cactus_5fsnarl_5ffinder_2ehpp_7461',['cactus_snarl_finder.hpp',['../cactus__snarl__finder_8hpp.html',1,'']]],
+ ['call_5fmain_2ecpp_7462',['call_main.cpp',['../call__main_8cpp.html',1,'']]],
+ ['chain_5fitems_2ecpp_7463',['chain_items.cpp',['../chain__items_8cpp.html',1,'']]],
+ ['chain_5fitems_2ehpp_7464',['chain_items.hpp',['../chain__items_8hpp.html',1,'']]],
+ ['chain_5fmain_2ecpp_7465',['chain_main.cpp',['../chain__main_8cpp.html',1,'']]],
+ ['chop_2ecpp_7466',['chop.cpp',['../chop_8cpp.html',1,'']]],
+ ['chunk_5fmain_2ecpp_7467',['chunk_main.cpp',['../chunk__main_8cpp.html',1,'']]],
+ ['chunker_2ecpp_7468',['chunker.cpp',['../chunker_8cpp.html',1,'']]],
+ ['chunker_2ehpp_7469',['chunker.hpp',['../chunker_8hpp.html',1,'']]],
+ ['circularize_5fmain_2ecpp_7470',['circularize_main.cpp',['../circularize__main_8cpp.html',1,'']]],
+ ['clip_2ecpp_7471',['clip.cpp',['../clip_8cpp.html',1,'']]],
+ ['clip_2ehpp_7472',['clip.hpp',['../clip_8hpp.html',1,'']]],
+ ['clip_5fmain_2ecpp_7473',['clip_main.cpp',['../clip__main_8cpp.html',1,'']]],
+ ['cluster_2ecpp_7474',['cluster.cpp',['../cluster_8cpp.html',1,'']]],
+ ['cluster_2ehpp_7475',['cluster.hpp',['../cluster_8hpp.html',1,'']]],
+ ['cluster_5fmain_2ecpp_7476',['cluster_main.cpp',['../cluster__main_8cpp.html',1,'']]],
+ ['colors_2ehpp_7477',['colors.hpp',['../colors_8hpp.html',1,'']]],
+ ['combine_5fmain_2ecpp_7478',['combine_main.cpp',['../combine__main_8cpp.html',1,'']]],
+ ['component_2ecpp_7479',['component.cpp',['../component_8cpp.html',1,'']]],
+ ['component_2ehpp_7480',['component.hpp',['../component_8hpp.html',1,'']]],
+ ['concat_5fmain_2ecpp_7481',['concat_main.cpp',['../concat__main_8cpp.html',1,'']]],
+ ['construct_5fmain_2ecpp_7482',['construct_main.cpp',['../construct__main_8cpp.html',1,'']]],
+ ['constructor_2ecpp_7483',['constructor.cpp',['../constructor_8cpp.html',1,'']]],
+ ['constructor_2ehpp_7484',['constructor.hpp',['../constructor_8hpp.html',1,'']]],
+ ['contracting_5fgraph_2ecpp_7485',['contracting_graph.cpp',['../contracting__graph_8cpp.html',1,'']]],
+ ['contracting_5fgraph_2ehpp_7486',['contracting_graph.hpp',['../contracting__graph_8hpp.html',1,'']]],
+ ['convert_2ehpp_7487',['convert.hpp',['../convert_8hpp.html',1,'']]],
+ ['convert_5fmain_2ecpp_7488',['convert_main.cpp',['../convert__main_8cpp.html',1,'']]],
+ ['converted_5fhash_5fgraph_2ehpp_7489',['converted_hash_graph.hpp',['../converted__hash__graph_8hpp.html',1,'']]],
+ ['copy_5fgraph_2ecpp_7490',['copy_graph.cpp',['../copy__graph_8cpp.html',1,'']]],
+ ['count_5fcovered_2ehpp_7491',['count_covered.hpp',['../count__covered_8hpp.html',1,'']]],
+ ['count_5fwalks_2ecpp_7492',['count_walks.cpp',['../count__walks_8cpp.html',1,'']]],
+ ['coverage_5fdepth_2ecpp_7493',['coverage_depth.cpp',['../coverage__depth_8cpp.html',1,'']]],
+ ['coverage_5fdepth_2ehpp_7494',['coverage_depth.hpp',['../coverage__depth_8hpp.html',1,'']]],
+ ['crash_2ecpp_7495',['crash.cpp',['../crash_8cpp.html',1,'']]],
+ ['crash_2ehpp_7496',['crash.hpp',['../crash_8hpp.html',1,'']]]
];
diff --git a/search/files_3.js b/search/files_3.js
index c2e2cf5c9d..b851e33f1b 100644
--- a/search/files_3.js
+++ b/search/files_3.js
@@ -1,30 +1,30 @@
var searchData=
[
- ['dagified_5fgraph_2ecpp_7495',['dagified_graph.cpp',['../dagified__graph_8cpp.html',1,'']]],
- ['dagified_5fgraph_2ehpp_7496',['dagified_graph.hpp',['../dagified__graph_8hpp.html',1,'']]],
- ['dagify_2ecpp_7497',['dagify.cpp',['../dagify_8cpp.html',1,'']]],
- ['deconstruct_5fmain_2ecpp_7498',['deconstruct_main.cpp',['../deconstruct__main_8cpp.html',1,'']]],
- ['deconstructor_2ecpp_7499',['deconstructor.cpp',['../deconstructor_8cpp.html',1,'']]],
- ['deconstructor_2ehpp_7500',['deconstructor.hpp',['../deconstructor_8hpp.html',1,'']]],
- ['deletable_5fhandle_5fgraph_2ecpp_7501',['deletable_handle_graph.cpp',['../deletable__handle__graph_8cpp.html',1,'']]],
- ['deletable_5fhandle_5fgraph_2ehpp_7502',['deletable_handle_graph.hpp',['../deletable__handle__graph_8hpp.html',1,'']]],
- ['deletion_5faligner_2ecpp_7503',['deletion_aligner.cpp',['../deletion__aligner_8cpp.html',1,'']]],
- ['deletion_5faligner_2ehpp_7504',['deletion_aligner.hpp',['../deletion__aligner_8hpp.html',1,'']]],
- ['depth_5fmain_2ecpp_7505',['depth_main.cpp',['../depth__main_8cpp.html',1,'']]],
- ['dfs_2ecpp_7506',['dfs.cpp',['../src_2algorithms_2dfs_8cpp.html',1,'(Global Namespace)'],['../deps_2libhandlegraph_2src_2dfs_8cpp.html',1,'(Global Namespace)']]],
- ['dfs_2ehpp_7507',['dfs.hpp',['../dfs_8hpp.html',1,'']]],
- ['dijkstra_2ecpp_7508',['dijkstra.cpp',['../dijkstra_8cpp.html',1,'']]],
- ['dinucleotide_5fmachine_2ecpp_7509',['dinucleotide_machine.cpp',['../dinucleotide__machine_8cpp.html',1,'']]],
- ['dinucleotide_5fmachine_2ehpp_7510',['dinucleotide_machine.hpp',['../dinucleotide__machine_8hpp.html',1,'']]],
- ['disjoint_5fcomponents_2ecpp_7511',['disjoint_components.cpp',['../disjoint__components_8cpp.html',1,'']]],
- ['disjoint_5fcomponents_2ehpp_7512',['disjoint_components.hpp',['../disjoint__components_8hpp.html',1,'']]],
- ['distance_5fto_5fhead_2ecpp_7513',['distance_to_head.cpp',['../distance__to__head_8cpp.html',1,'']]],
- ['distance_5fto_5fhead_2ehpp_7514',['distance_to_head.hpp',['../distance__to__head_8hpp.html',1,'']]],
- ['distance_5fto_5ftail_2ecpp_7515',['distance_to_tail.cpp',['../distance__to__tail_8cpp.html',1,'']]],
- ['distance_5fto_5ftail_2ehpp_7516',['distance_to_tail.hpp',['../distance__to__tail_8hpp.html',1,'']]],
- ['dotplot_5fmain_2ecpp_7517',['dotplot_main.cpp',['../dotplot__main_8cpp.html',1,'']]],
- ['dozeu_5finterface_2ecpp_7518',['dozeu_interface.cpp',['../dozeu__interface_8cpp.html',1,'']]],
- ['dozeu_5finterface_2ehpp_7519',['dozeu_interface.hpp',['../dozeu__interface_8hpp.html',1,'']]],
- ['dozeu_5fpinning_5foverlay_2ecpp_7520',['dozeu_pinning_overlay.cpp',['../dozeu__pinning__overlay_8cpp.html',1,'']]],
- ['dozeu_5fpinning_5foverlay_2ehpp_7521',['dozeu_pinning_overlay.hpp',['../dozeu__pinning__overlay_8hpp.html',1,'']]]
+ ['dagified_5fgraph_2ecpp_7497',['dagified_graph.cpp',['../dagified__graph_8cpp.html',1,'']]],
+ ['dagified_5fgraph_2ehpp_7498',['dagified_graph.hpp',['../dagified__graph_8hpp.html',1,'']]],
+ ['dagify_2ecpp_7499',['dagify.cpp',['../dagify_8cpp.html',1,'']]],
+ ['deconstruct_5fmain_2ecpp_7500',['deconstruct_main.cpp',['../deconstruct__main_8cpp.html',1,'']]],
+ ['deconstructor_2ecpp_7501',['deconstructor.cpp',['../deconstructor_8cpp.html',1,'']]],
+ ['deconstructor_2ehpp_7502',['deconstructor.hpp',['../deconstructor_8hpp.html',1,'']]],
+ ['deletable_5fhandle_5fgraph_2ecpp_7503',['deletable_handle_graph.cpp',['../deletable__handle__graph_8cpp.html',1,'']]],
+ ['deletable_5fhandle_5fgraph_2ehpp_7504',['deletable_handle_graph.hpp',['../deletable__handle__graph_8hpp.html',1,'']]],
+ ['deletion_5faligner_2ecpp_7505',['deletion_aligner.cpp',['../deletion__aligner_8cpp.html',1,'']]],
+ ['deletion_5faligner_2ehpp_7506',['deletion_aligner.hpp',['../deletion__aligner_8hpp.html',1,'']]],
+ ['depth_5fmain_2ecpp_7507',['depth_main.cpp',['../depth__main_8cpp.html',1,'']]],
+ ['dfs_2ecpp_7508',['dfs.cpp',['../src_2algorithms_2dfs_8cpp.html',1,'(Global Namespace)'],['../deps_2libhandlegraph_2src_2dfs_8cpp.html',1,'(Global Namespace)']]],
+ ['dfs_2ehpp_7509',['dfs.hpp',['../dfs_8hpp.html',1,'']]],
+ ['dijkstra_2ecpp_7510',['dijkstra.cpp',['../dijkstra_8cpp.html',1,'']]],
+ ['dinucleotide_5fmachine_2ecpp_7511',['dinucleotide_machine.cpp',['../dinucleotide__machine_8cpp.html',1,'']]],
+ ['dinucleotide_5fmachine_2ehpp_7512',['dinucleotide_machine.hpp',['../dinucleotide__machine_8hpp.html',1,'']]],
+ ['disjoint_5fcomponents_2ecpp_7513',['disjoint_components.cpp',['../disjoint__components_8cpp.html',1,'']]],
+ ['disjoint_5fcomponents_2ehpp_7514',['disjoint_components.hpp',['../disjoint__components_8hpp.html',1,'']]],
+ ['distance_5fto_5fhead_2ecpp_7515',['distance_to_head.cpp',['../distance__to__head_8cpp.html',1,'']]],
+ ['distance_5fto_5fhead_2ehpp_7516',['distance_to_head.hpp',['../distance__to__head_8hpp.html',1,'']]],
+ ['distance_5fto_5ftail_2ecpp_7517',['distance_to_tail.cpp',['../distance__to__tail_8cpp.html',1,'']]],
+ ['distance_5fto_5ftail_2ehpp_7518',['distance_to_tail.hpp',['../distance__to__tail_8hpp.html',1,'']]],
+ ['dotplot_5fmain_2ecpp_7519',['dotplot_main.cpp',['../dotplot__main_8cpp.html',1,'']]],
+ ['dozeu_5finterface_2ecpp_7520',['dozeu_interface.cpp',['../dozeu__interface_8cpp.html',1,'']]],
+ ['dozeu_5finterface_2ehpp_7521',['dozeu_interface.hpp',['../dozeu__interface_8hpp.html',1,'']]],
+ ['dozeu_5fpinning_5foverlay_2ecpp_7522',['dozeu_pinning_overlay.cpp',['../dozeu__pinning__overlay_8cpp.html',1,'']]],
+ ['dozeu_5fpinning_5foverlay_2ehpp_7523',['dozeu_pinning_overlay.hpp',['../dozeu__pinning__overlay_8hpp.html',1,'']]]
];
diff --git a/search/files_4.js b/search/files_4.js
index 9096ed5edc..74dc5f2c18 100644
--- a/search/files_4.js
+++ b/search/files_4.js
@@ -1,24 +1,24 @@
var searchData=
[
- ['eades_5falgorithm_2ecpp_7522',['eades_algorithm.cpp',['../eades__algorithm_8cpp.html',1,'']]],
- ['edit_2ecpp_7523',['edit.cpp',['../edit_8cpp.html',1,'']]],
- ['edit_2ehpp_7524',['edit.hpp',['../edit_8hpp.html',1,'']]],
- ['endianness_2ehpp_7525',['endianness.hpp',['../endianness_8hpp.html',1,'']]],
- ['entropy_2ecpp_7526',['entropy.cpp',['../entropy_8cpp.html',1,'']]],
- ['entropy_2ehpp_7527',['entropy.hpp',['../entropy_8hpp.html',1,'']]],
- ['expand_5fcontext_2ecpp_7528',['expand_context.cpp',['../expand__context_8cpp.html',1,'']]],
- ['expand_5fcontext_2ehpp_7529',['expand_context.hpp',['../expand__context_8hpp.html',1,'']]],
- ['expanding_5foverlay_5fgraph_2ehpp_7530',['expanding_overlay_graph.hpp',['../expanding__overlay__graph_8hpp.html',1,'']]],
- ['explainer_2ecpp_7531',['explainer.cpp',['../explainer_8cpp.html',1,'']]],
- ['explainer_2ehpp_7532',['explainer.hpp',['../explainer_8hpp.html',1,'']]],
- ['explode_5fmain_2ecpp_7533',['explode_main.cpp',['../explode__main_8cpp.html',1,'']]],
- ['extend_2ecpp_7534',['extend.cpp',['../extend_8cpp.html',1,'']]],
- ['extra_5fnode_5fgraph_2ecpp_7535',['extra_node_graph.cpp',['../extra__node__graph_8cpp.html',1,'']]],
- ['extra_5fnode_5fgraph_2ehpp_7536',['extra_node_graph.hpp',['../extra__node__graph_8hpp.html',1,'']]],
- ['extract_5fconnecting_5fgraph_2ecpp_7537',['extract_connecting_graph.cpp',['../extract__connecting__graph_8cpp.html',1,'']]],
- ['extract_5fconnecting_5fgraph_2ehpp_7538',['extract_connecting_graph.hpp',['../extract__connecting__graph_8hpp.html',1,'']]],
- ['extract_5fcontaining_5fgraph_2ecpp_7539',['extract_containing_graph.cpp',['../extract__containing__graph_8cpp.html',1,'']]],
- ['extract_5fcontaining_5fgraph_2ehpp_7540',['extract_containing_graph.hpp',['../extract__containing__graph_8hpp.html',1,'']]],
- ['extract_5fextending_5fgraph_2ecpp_7541',['extract_extending_graph.cpp',['../extract__extending__graph_8cpp.html',1,'']]],
- ['extract_5fextending_5fgraph_2ehpp_7542',['extract_extending_graph.hpp',['../extract__extending__graph_8hpp.html',1,'']]]
+ ['eades_5falgorithm_2ecpp_7524',['eades_algorithm.cpp',['../eades__algorithm_8cpp.html',1,'']]],
+ ['edit_2ecpp_7525',['edit.cpp',['../edit_8cpp.html',1,'']]],
+ ['edit_2ehpp_7526',['edit.hpp',['../edit_8hpp.html',1,'']]],
+ ['endianness_2ehpp_7527',['endianness.hpp',['../endianness_8hpp.html',1,'']]],
+ ['entropy_2ecpp_7528',['entropy.cpp',['../entropy_8cpp.html',1,'']]],
+ ['entropy_2ehpp_7529',['entropy.hpp',['../entropy_8hpp.html',1,'']]],
+ ['expand_5fcontext_2ecpp_7530',['expand_context.cpp',['../expand__context_8cpp.html',1,'']]],
+ ['expand_5fcontext_2ehpp_7531',['expand_context.hpp',['../expand__context_8hpp.html',1,'']]],
+ ['expanding_5foverlay_5fgraph_2ehpp_7532',['expanding_overlay_graph.hpp',['../expanding__overlay__graph_8hpp.html',1,'']]],
+ ['explainer_2ecpp_7533',['explainer.cpp',['../explainer_8cpp.html',1,'']]],
+ ['explainer_2ehpp_7534',['explainer.hpp',['../explainer_8hpp.html',1,'']]],
+ ['explode_5fmain_2ecpp_7535',['explode_main.cpp',['../explode__main_8cpp.html',1,'']]],
+ ['extend_2ecpp_7536',['extend.cpp',['../extend_8cpp.html',1,'']]],
+ ['extra_5fnode_5fgraph_2ecpp_7537',['extra_node_graph.cpp',['../extra__node__graph_8cpp.html',1,'']]],
+ ['extra_5fnode_5fgraph_2ehpp_7538',['extra_node_graph.hpp',['../extra__node__graph_8hpp.html',1,'']]],
+ ['extract_5fconnecting_5fgraph_2ecpp_7539',['extract_connecting_graph.cpp',['../extract__connecting__graph_8cpp.html',1,'']]],
+ ['extract_5fconnecting_5fgraph_2ehpp_7540',['extract_connecting_graph.hpp',['../extract__connecting__graph_8hpp.html',1,'']]],
+ ['extract_5fcontaining_5fgraph_2ecpp_7541',['extract_containing_graph.cpp',['../extract__containing__graph_8cpp.html',1,'']]],
+ ['extract_5fcontaining_5fgraph_2ehpp_7542',['extract_containing_graph.hpp',['../extract__containing__graph_8hpp.html',1,'']]],
+ ['extract_5fextending_5fgraph_2ecpp_7543',['extract_extending_graph.cpp',['../extract__extending__graph_8cpp.html',1,'']]],
+ ['extract_5fextending_5fgraph_2ehpp_7544',['extract_extending_graph.hpp',['../extract__extending__graph_8hpp.html',1,'']]]
];
diff --git a/search/files_5.js b/search/files_5.js
index 13bdcc68b5..86c11204e0 100644
--- a/search/files_5.js
+++ b/search/files_5.js
@@ -1,24 +1,24 @@
var searchData=
[
- ['fdstream_2ehpp_7543',['fdstream.hpp',['../fdstream_8hpp.html',1,'']]],
- ['feature_5fset_2ecpp_7544',['feature_set.cpp',['../feature__set_8cpp.html',1,'']]],
- ['feature_5fset_2ehpp_7545',['feature_set.hpp',['../feature__set_8hpp.html',1,'']]],
- ['filter_2ecpp_7546',['filter.cpp',['../filter_8cpp.html',1,'']]],
- ['filter_2ehpp_7547',['filter.hpp',['../filter_8hpp.html',1,'']]],
- ['filter_5fmain_2ecpp_7548',['filter_main.cpp',['../filter__main_8cpp.html',1,'']]],
- ['find_5fgbwt_2ecpp_7549',['find_gbwt.cpp',['../find__gbwt_8cpp.html',1,'']]],
- ['find_5fgbwt_2ehpp_7550',['find_gbwt.hpp',['../find__gbwt_8hpp.html',1,'']]],
- ['find_5fgbwtgraph_2ecpp_7551',['find_gbwtgraph.cpp',['../find__gbwtgraph_8cpp.html',1,'']]],
- ['find_5fgbwtgraph_2ehpp_7552',['find_gbwtgraph.hpp',['../find__gbwtgraph_8hpp.html',1,'']]],
- ['find_5fmain_2ecpp_7553',['find_main.cpp',['../find__main_8cpp.html',1,'']]],
- ['find_5fshortest_5fpaths_2ecpp_7554',['find_shortest_paths.cpp',['../find__shortest__paths_8cpp.html',1,'']]],
- ['find_5ftips_2ecpp_7555',['find_tips.cpp',['../find__tips_8cpp.html',1,'']]],
- ['find_5ftranslation_2ecpp_7556',['find_translation.cpp',['../find__translation_8cpp.html',1,'']]],
- ['find_5ftranslation_2ehpp_7557',['find_translation.hpp',['../find__translation_8hpp.html',1,'']]],
- ['flat_5ffile_5fback_5ftranslation_2ecpp_7558',['flat_file_back_translation.cpp',['../flat__file__back__translation_8cpp.html',1,'']]],
- ['flat_5ffile_5fback_5ftranslation_2ehpp_7559',['flat_file_back_translation.hpp',['../flat__file__back__translation_8hpp.html',1,'']]],
- ['flow_5fsort_2ecpp_7560',['flow_sort.cpp',['../flow__sort_8cpp.html',1,'']]],
- ['flow_5fsort_2ehpp_7561',['flow_sort.hpp',['../flow__sort_8hpp.html',1,'']]],
- ['funnel_2ecpp_7562',['funnel.cpp',['../funnel_8cpp.html',1,'']]],
- ['funnel_2ehpp_7563',['funnel.hpp',['../funnel_8hpp.html',1,'']]]
+ ['fdstream_2ehpp_7545',['fdstream.hpp',['../fdstream_8hpp.html',1,'']]],
+ ['feature_5fset_2ecpp_7546',['feature_set.cpp',['../feature__set_8cpp.html',1,'']]],
+ ['feature_5fset_2ehpp_7547',['feature_set.hpp',['../feature__set_8hpp.html',1,'']]],
+ ['filter_2ecpp_7548',['filter.cpp',['../filter_8cpp.html',1,'']]],
+ ['filter_2ehpp_7549',['filter.hpp',['../filter_8hpp.html',1,'']]],
+ ['filter_5fmain_2ecpp_7550',['filter_main.cpp',['../filter__main_8cpp.html',1,'']]],
+ ['find_5fgbwt_2ecpp_7551',['find_gbwt.cpp',['../find__gbwt_8cpp.html',1,'']]],
+ ['find_5fgbwt_2ehpp_7552',['find_gbwt.hpp',['../find__gbwt_8hpp.html',1,'']]],
+ ['find_5fgbwtgraph_2ecpp_7553',['find_gbwtgraph.cpp',['../find__gbwtgraph_8cpp.html',1,'']]],
+ ['find_5fgbwtgraph_2ehpp_7554',['find_gbwtgraph.hpp',['../find__gbwtgraph_8hpp.html',1,'']]],
+ ['find_5fmain_2ecpp_7555',['find_main.cpp',['../find__main_8cpp.html',1,'']]],
+ ['find_5fshortest_5fpaths_2ecpp_7556',['find_shortest_paths.cpp',['../find__shortest__paths_8cpp.html',1,'']]],
+ ['find_5ftips_2ecpp_7557',['find_tips.cpp',['../find__tips_8cpp.html',1,'']]],
+ ['find_5ftranslation_2ecpp_7558',['find_translation.cpp',['../find__translation_8cpp.html',1,'']]],
+ ['find_5ftranslation_2ehpp_7559',['find_translation.hpp',['../find__translation_8hpp.html',1,'']]],
+ ['flat_5ffile_5fback_5ftranslation_2ecpp_7560',['flat_file_back_translation.cpp',['../flat__file__back__translation_8cpp.html',1,'']]],
+ ['flat_5ffile_5fback_5ftranslation_2ehpp_7561',['flat_file_back_translation.hpp',['../flat__file__back__translation_8hpp.html',1,'']]],
+ ['flow_5fsort_2ecpp_7562',['flow_sort.cpp',['../flow__sort_8cpp.html',1,'']]],
+ ['flow_5fsort_2ehpp_7563',['flow_sort.hpp',['../flow__sort_8hpp.html',1,'']]],
+ ['funnel_2ecpp_7564',['funnel.cpp',['../funnel_8cpp.html',1,'']]],
+ ['funnel_2ehpp_7565',['funnel.hpp',['../funnel_8hpp.html',1,'']]]
];
diff --git a/search/files_6.js b/search/files_6.js
index 33ec7717bf..24696a91d5 100644
--- a/search/files_6.js
+++ b/search/files_6.js
@@ -1,37 +1,37 @@
var searchData=
[
- ['gafkluge_2ehpp_7564',['gafkluge.hpp',['../gafkluge_8hpp.html',1,'']]],
- ['gamcompare_5fmain_2ecpp_7565',['gamcompare_main.cpp',['../gamcompare__main_8cpp.html',1,'']]],
- ['gampcompare_5fmain_2ecpp_7566',['gampcompare_main.cpp',['../gampcompare__main_8cpp.html',1,'']]],
- ['gamsort_5fmain_2ecpp_7567',['gamsort_main.cpp',['../gamsort__main_8cpp.html',1,'']]],
- ['gbwt_5fextender_2ecpp_7568',['gbwt_extender.cpp',['../gbwt__extender_8cpp.html',1,'']]],
- ['gbwt_5fextender_2ehpp_7569',['gbwt_extender.hpp',['../gbwt__extender_8hpp.html',1,'']]],
- ['gbwt_5fhelper_2ecpp_7570',['gbwt_helper.cpp',['../gbwt__helper_8cpp.html',1,'']]],
- ['gbwt_5fhelper_2ehpp_7571',['gbwt_helper.hpp',['../gbwt__helper_8hpp.html',1,'']]],
- ['gbwt_5fmain_2ecpp_7572',['gbwt_main.cpp',['../gbwt__main_8cpp.html',1,'']]],
- ['gbwtgraph_5fhelper_2ecpp_7573',['gbwtgraph_helper.cpp',['../gbwtgraph__helper_8cpp.html',1,'']]],
- ['gbwtgraph_5fhelper_2ehpp_7574',['gbwtgraph_helper.hpp',['../gbwtgraph__helper_8hpp.html',1,'']]],
- ['gbzgraph_2ehpp_7575',['gbzgraph.hpp',['../gbzgraph_8hpp.html',1,'']]],
- ['gcsa_5fhelper_2ecpp_7576',['gcsa_helper.cpp',['../gcsa__helper_8cpp.html',1,'']]],
- ['gcsa_5fhelper_2ehpp_7577',['gcsa_helper.hpp',['../gcsa__helper_8hpp.html',1,'']]],
- ['genome_5fstate_2ecpp_7578',['genome_state.cpp',['../genome__state_8cpp.html',1,'']]],
- ['genome_5fstate_2ehpp_7579',['genome_state.hpp',['../genome__state_8hpp.html',1,'']]],
- ['genotype_5fmain_2ecpp_7580',['genotype_main.cpp',['../genotype__main_8cpp.html',1,'']]],
- ['genotypekit_2ecpp_7581',['genotypekit.cpp',['../genotypekit_8cpp.html',1,'']]],
- ['genotypekit_2ehpp_7582',['genotypekit.hpp',['../genotypekit_8hpp.html',1,'']]],
- ['genotyper_2ecpp_7583',['genotyper.cpp',['../genotyper_8cpp.html',1,'']]],
- ['genotyper_2ehpp_7584',['genotyper.hpp',['../genotyper_8hpp.html',1,'']]],
- ['gfa_2ecpp_7585',['gfa.cpp',['../gfa_8cpp.html',1,'']]],
- ['gfa_2ehpp_7586',['gfa.hpp',['../gfa_8hpp.html',1,'']]],
- ['gfa_5fto_5fhandle_2ecpp_7587',['gfa_to_handle.cpp',['../gfa__to__handle_8cpp.html',1,'']]],
- ['gfa_5fto_5fhandle_2ehpp_7588',['gfa_to_handle.hpp',['../gfa__to__handle_8hpp.html',1,'']]],
- ['gff_5freader_2ecpp_7589',['gff_reader.cpp',['../gff__reader_8cpp.html',1,'']]],
- ['gff_5freader_2ehpp_7590',['gff_reader.hpp',['../gff__reader_8hpp.html',1,'']]],
- ['giraffe_5fmain_2ecpp_7591',['giraffe_main.cpp',['../giraffe__main_8cpp.html',1,'']]],
- ['graph_2ecpp_7592',['graph.cpp',['../graph_8cpp.html',1,'']]],
- ['graph_2ehpp_7593',['graph.hpp',['../graph_8hpp.html',1,'']]],
- ['graph_5fcaller_2ecpp_7594',['graph_caller.cpp',['../graph__caller_8cpp.html',1,'']]],
- ['graph_5fcaller_2ehpp_7595',['graph_caller.hpp',['../graph__caller_8hpp.html',1,'']]],
- ['graph_5fsynchronizer_2ecpp_7596',['graph_synchronizer.cpp',['../graph__synchronizer_8cpp.html',1,'']]],
- ['graph_5fsynchronizer_2ehpp_7597',['graph_synchronizer.hpp',['../graph__synchronizer_8hpp.html',1,'']]]
+ ['gafkluge_2ehpp_7566',['gafkluge.hpp',['../gafkluge_8hpp.html',1,'']]],
+ ['gamcompare_5fmain_2ecpp_7567',['gamcompare_main.cpp',['../gamcompare__main_8cpp.html',1,'']]],
+ ['gampcompare_5fmain_2ecpp_7568',['gampcompare_main.cpp',['../gampcompare__main_8cpp.html',1,'']]],
+ ['gamsort_5fmain_2ecpp_7569',['gamsort_main.cpp',['../gamsort__main_8cpp.html',1,'']]],
+ ['gbwt_5fextender_2ecpp_7570',['gbwt_extender.cpp',['../gbwt__extender_8cpp.html',1,'']]],
+ ['gbwt_5fextender_2ehpp_7571',['gbwt_extender.hpp',['../gbwt__extender_8hpp.html',1,'']]],
+ ['gbwt_5fhelper_2ecpp_7572',['gbwt_helper.cpp',['../gbwt__helper_8cpp.html',1,'']]],
+ ['gbwt_5fhelper_2ehpp_7573',['gbwt_helper.hpp',['../gbwt__helper_8hpp.html',1,'']]],
+ ['gbwt_5fmain_2ecpp_7574',['gbwt_main.cpp',['../gbwt__main_8cpp.html',1,'']]],
+ ['gbwtgraph_5fhelper_2ecpp_7575',['gbwtgraph_helper.cpp',['../gbwtgraph__helper_8cpp.html',1,'']]],
+ ['gbwtgraph_5fhelper_2ehpp_7576',['gbwtgraph_helper.hpp',['../gbwtgraph__helper_8hpp.html',1,'']]],
+ ['gbzgraph_2ehpp_7577',['gbzgraph.hpp',['../gbzgraph_8hpp.html',1,'']]],
+ ['gcsa_5fhelper_2ecpp_7578',['gcsa_helper.cpp',['../gcsa__helper_8cpp.html',1,'']]],
+ ['gcsa_5fhelper_2ehpp_7579',['gcsa_helper.hpp',['../gcsa__helper_8hpp.html',1,'']]],
+ ['genome_5fstate_2ecpp_7580',['genome_state.cpp',['../genome__state_8cpp.html',1,'']]],
+ ['genome_5fstate_2ehpp_7581',['genome_state.hpp',['../genome__state_8hpp.html',1,'']]],
+ ['genotype_5fmain_2ecpp_7582',['genotype_main.cpp',['../genotype__main_8cpp.html',1,'']]],
+ ['genotypekit_2ecpp_7583',['genotypekit.cpp',['../genotypekit_8cpp.html',1,'']]],
+ ['genotypekit_2ehpp_7584',['genotypekit.hpp',['../genotypekit_8hpp.html',1,'']]],
+ ['genotyper_2ecpp_7585',['genotyper.cpp',['../genotyper_8cpp.html',1,'']]],
+ ['genotyper_2ehpp_7586',['genotyper.hpp',['../genotyper_8hpp.html',1,'']]],
+ ['gfa_2ecpp_7587',['gfa.cpp',['../gfa_8cpp.html',1,'']]],
+ ['gfa_2ehpp_7588',['gfa.hpp',['../gfa_8hpp.html',1,'']]],
+ ['gfa_5fto_5fhandle_2ecpp_7589',['gfa_to_handle.cpp',['../gfa__to__handle_8cpp.html',1,'']]],
+ ['gfa_5fto_5fhandle_2ehpp_7590',['gfa_to_handle.hpp',['../gfa__to__handle_8hpp.html',1,'']]],
+ ['gff_5freader_2ecpp_7591',['gff_reader.cpp',['../gff__reader_8cpp.html',1,'']]],
+ ['gff_5freader_2ehpp_7592',['gff_reader.hpp',['../gff__reader_8hpp.html',1,'']]],
+ ['giraffe_5fmain_2ecpp_7593',['giraffe_main.cpp',['../giraffe__main_8cpp.html',1,'']]],
+ ['graph_2ecpp_7594',['graph.cpp',['../graph_8cpp.html',1,'']]],
+ ['graph_2ehpp_7595',['graph.hpp',['../graph_8hpp.html',1,'']]],
+ ['graph_5fcaller_2ecpp_7596',['graph_caller.cpp',['../graph__caller_8cpp.html',1,'']]],
+ ['graph_5fcaller_2ehpp_7597',['graph_caller.hpp',['../graph__caller_8hpp.html',1,'']]],
+ ['graph_5fsynchronizer_2ecpp_7598',['graph_synchronizer.cpp',['../graph__synchronizer_8cpp.html',1,'']]],
+ ['graph_5fsynchronizer_2ehpp_7599',['graph_synchronizer.hpp',['../graph__synchronizer_8hpp.html',1,'']]]
];
diff --git a/search/files_7.js b/search/files_7.js
index a9bb8e23b5..1a22159b9f 100644
--- a/search/files_7.js
+++ b/search/files_7.js
@@ -1,20 +1,20 @@
var searchData=
[
- ['handle_2ehpp_7598',['handle.hpp',['../handle_8hpp.html',1,'']]],
- ['handle_5fgraph_2ecpp_7599',['handle_graph.cpp',['../handle__graph_8cpp.html',1,'']]],
- ['handle_5fgraph_2ehpp_7600',['handle_graph.hpp',['../handle__graph_8hpp.html',1,'']]],
- ['haplotype_5fextracter_2ecpp_7601',['haplotype_extracter.cpp',['../haplotype__extracter_8cpp.html',1,'']]],
- ['haplotype_5fextracter_2ehpp_7602',['haplotype_extracter.hpp',['../haplotype__extracter_8hpp.html',1,'']]],
- ['haplotype_5findexer_2ecpp_7603',['haplotype_indexer.cpp',['../haplotype__indexer_8cpp.html',1,'']]],
- ['haplotype_5findexer_2ehpp_7604',['haplotype_indexer.hpp',['../haplotype__indexer_8hpp.html',1,'']]],
- ['haplotypes_2ecpp_7605',['haplotypes.cpp',['../haplotypes_8cpp.html',1,'']]],
- ['haplotypes_2ehpp_7606',['haplotypes.hpp',['../haplotypes_8hpp.html',1,'']]],
- ['haplotypes_5fmain_2ecpp_7607',['haplotypes_main.cpp',['../haplotypes__main_8cpp.html',1,'']]],
- ['hash_5fmap_2ehpp_7608',['hash_map.hpp',['../hash__map_8hpp.html',1,'']]],
- ['help_5fmain_2ecpp_7609',['help_main.cpp',['../help__main_8cpp.html',1,'']]],
- ['hfile_5fcppstream_2ecpp_7610',['hfile_cppstream.cpp',['../hfile__cppstream_8cpp.html',1,'']]],
- ['hfile_5fcppstream_2ehpp_7611',['hfile_cppstream.hpp',['../hfile__cppstream_8hpp.html',1,'']]],
- ['hfile_5finternal_2ehpp_7612',['hfile_internal.hpp',['../hfile__internal_8hpp.html',1,'']]],
- ['hts_5falignment_5femitter_2ecpp_7613',['hts_alignment_emitter.cpp',['../hts__alignment__emitter_8cpp.html',1,'']]],
- ['hts_5falignment_5femitter_2ehpp_7614',['hts_alignment_emitter.hpp',['../hts__alignment__emitter_8hpp.html',1,'']]]
+ ['handle_2ehpp_7600',['handle.hpp',['../handle_8hpp.html',1,'']]],
+ ['handle_5fgraph_2ecpp_7601',['handle_graph.cpp',['../handle__graph_8cpp.html',1,'']]],
+ ['handle_5fgraph_2ehpp_7602',['handle_graph.hpp',['../handle__graph_8hpp.html',1,'']]],
+ ['haplotype_5fextracter_2ecpp_7603',['haplotype_extracter.cpp',['../haplotype__extracter_8cpp.html',1,'']]],
+ ['haplotype_5fextracter_2ehpp_7604',['haplotype_extracter.hpp',['../haplotype__extracter_8hpp.html',1,'']]],
+ ['haplotype_5findexer_2ecpp_7605',['haplotype_indexer.cpp',['../haplotype__indexer_8cpp.html',1,'']]],
+ ['haplotype_5findexer_2ehpp_7606',['haplotype_indexer.hpp',['../haplotype__indexer_8hpp.html',1,'']]],
+ ['haplotypes_2ecpp_7607',['haplotypes.cpp',['../haplotypes_8cpp.html',1,'']]],
+ ['haplotypes_2ehpp_7608',['haplotypes.hpp',['../haplotypes_8hpp.html',1,'']]],
+ ['haplotypes_5fmain_2ecpp_7609',['haplotypes_main.cpp',['../haplotypes__main_8cpp.html',1,'']]],
+ ['hash_5fmap_2ehpp_7610',['hash_map.hpp',['../hash__map_8hpp.html',1,'']]],
+ ['help_5fmain_2ecpp_7611',['help_main.cpp',['../help__main_8cpp.html',1,'']]],
+ ['hfile_5fcppstream_2ecpp_7612',['hfile_cppstream.cpp',['../hfile__cppstream_8cpp.html',1,'']]],
+ ['hfile_5fcppstream_2ehpp_7613',['hfile_cppstream.hpp',['../hfile__cppstream_8hpp.html',1,'']]],
+ ['hfile_5finternal_2ehpp_7614',['hfile_internal.hpp',['../hfile__internal_8hpp.html',1,'']]],
+ ['hts_5falignment_5femitter_2ecpp_7615',['hts_alignment_emitter.cpp',['../hts__alignment__emitter_8cpp.html',1,'']]],
+ ['hts_5falignment_5femitter_2ehpp_7616',['hts_alignment_emitter.hpp',['../hts__alignment__emitter_8hpp.html',1,'']]]
];
diff --git a/search/files_8.js b/search/files_8.js
index da6f129be1..e031d54ffb 100644
--- a/search/files_8.js
+++ b/search/files_8.js
@@ -1,23 +1,23 @@
var searchData=
[
- ['id_5fsort_2ecpp_7615',['id_sort.cpp',['../id__sort_8cpp.html',1,'']]],
- ['id_5fsort_2ehpp_7616',['id_sort.hpp',['../id__sort_8hpp.html',1,'']]],
- ['identity_5foverlay_2ecpp_7617',['identity_overlay.cpp',['../identity__overlay_8cpp.html',1,'']]],
- ['identity_5foverlay_2ehpp_7618',['identity_overlay.hpp',['../identity__overlay_8hpp.html',1,'']]],
- ['ids_5fmain_2ecpp_7619',['ids_main.cpp',['../ids__main_8cpp.html',1,'']]],
- ['incremental_5fsubgraph_2ecpp_7620',['incremental_subgraph.cpp',['../incremental__subgraph_8cpp.html',1,'']]],
- ['incremental_5fsubgraph_2ehpp_7621',['incremental_subgraph.hpp',['../incremental__subgraph_8hpp.html',1,'']]],
- ['index_5fmain_2ecpp_7622',['index_main.cpp',['../index__main_8cpp.html',1,'']]],
- ['index_5fregistry_2ecpp_7623',['index_registry.cpp',['../index__registry_8cpp.html',1,'']]],
- ['index_5fregistry_2ehpp_7624',['index_registry.hpp',['../index__registry_8hpp.html',1,'']]],
- ['indexed_5fvg_2ecpp_7625',['indexed_vg.cpp',['../indexed__vg_8cpp.html',1,'']]],
- ['indexed_5fvg_2ehpp_7626',['indexed_vg.hpp',['../indexed__vg_8hpp.html',1,'']]],
- ['inject_5fmain_2ecpp_7627',['inject_main.cpp',['../inject__main_8cpp.html',1,'']]],
- ['integrated_5fsnarl_5ffinder_2ecpp_7628',['integrated_snarl_finder.cpp',['../integrated__snarl__finder_8cpp.html',1,'']]],
- ['integrated_5fsnarl_5ffinder_2ehpp_7629',['integrated_snarl_finder.hpp',['../integrated__snarl__finder_8hpp.html',1,'']]],
- ['intersect_5fpath_5foffsets_2ecpp_7630',['intersect_path_offsets.cpp',['../intersect__path__offsets_8cpp.html',1,'']]],
- ['intersect_5fpath_5foffsets_2ehpp_7631',['intersect_path_offsets.hpp',['../intersect__path__offsets_8hpp.html',1,'']]],
- ['is_5facyclic_2ecpp_7632',['is_acyclic.cpp',['../is__acyclic_8cpp.html',1,'']]],
- ['is_5fsingle_5fstranded_2ecpp_7633',['is_single_stranded.cpp',['../is__single__stranded_8cpp.html',1,'']]],
- ['iteratee_2ehpp_7634',['iteratee.hpp',['../iteratee_8hpp.html',1,'']]]
+ ['id_5fsort_2ecpp_7617',['id_sort.cpp',['../id__sort_8cpp.html',1,'']]],
+ ['id_5fsort_2ehpp_7618',['id_sort.hpp',['../id__sort_8hpp.html',1,'']]],
+ ['identity_5foverlay_2ecpp_7619',['identity_overlay.cpp',['../identity__overlay_8cpp.html',1,'']]],
+ ['identity_5foverlay_2ehpp_7620',['identity_overlay.hpp',['../identity__overlay_8hpp.html',1,'']]],
+ ['ids_5fmain_2ecpp_7621',['ids_main.cpp',['../ids__main_8cpp.html',1,'']]],
+ ['incremental_5fsubgraph_2ecpp_7622',['incremental_subgraph.cpp',['../incremental__subgraph_8cpp.html',1,'']]],
+ ['incremental_5fsubgraph_2ehpp_7623',['incremental_subgraph.hpp',['../incremental__subgraph_8hpp.html',1,'']]],
+ ['index_5fmain_2ecpp_7624',['index_main.cpp',['../index__main_8cpp.html',1,'']]],
+ ['index_5fregistry_2ecpp_7625',['index_registry.cpp',['../index__registry_8cpp.html',1,'']]],
+ ['index_5fregistry_2ehpp_7626',['index_registry.hpp',['../index__registry_8hpp.html',1,'']]],
+ ['indexed_5fvg_2ecpp_7627',['indexed_vg.cpp',['../indexed__vg_8cpp.html',1,'']]],
+ ['indexed_5fvg_2ehpp_7628',['indexed_vg.hpp',['../indexed__vg_8hpp.html',1,'']]],
+ ['inject_5fmain_2ecpp_7629',['inject_main.cpp',['../inject__main_8cpp.html',1,'']]],
+ ['integrated_5fsnarl_5ffinder_2ecpp_7630',['integrated_snarl_finder.cpp',['../integrated__snarl__finder_8cpp.html',1,'']]],
+ ['integrated_5fsnarl_5ffinder_2ehpp_7631',['integrated_snarl_finder.hpp',['../integrated__snarl__finder_8hpp.html',1,'']]],
+ ['intersect_5fpath_5foffsets_2ecpp_7632',['intersect_path_offsets.cpp',['../intersect__path__offsets_8cpp.html',1,'']]],
+ ['intersect_5fpath_5foffsets_2ehpp_7633',['intersect_path_offsets.hpp',['../intersect__path__offsets_8hpp.html',1,'']]],
+ ['is_5facyclic_2ecpp_7634',['is_acyclic.cpp',['../is__acyclic_8cpp.html',1,'']]],
+ ['is_5fsingle_5fstranded_2ecpp_7635',['is_single_stranded.cpp',['../is__single__stranded_8cpp.html',1,'']]],
+ ['iteratee_2ehpp_7636',['iteratee.hpp',['../iteratee_8hpp.html',1,'']]]
];
diff --git a/search/files_9.js b/search/files_9.js
index c655949411..d8109cfefc 100644
--- a/search/files_9.js
+++ b/search/files_9.js
@@ -1,12 +1,12 @@
var searchData=
[
- ['job_5fschedule_2ecpp_7635',['job_schedule.cpp',['../job__schedule_8cpp.html',1,'']]],
- ['job_5fschedule_2ehpp_7636',['job_schedule.hpp',['../job__schedule_8hpp.html',1,'']]],
- ['join_5fmain_2ecpp_7637',['join_main.cpp',['../join__main_8cpp.html',1,'']]],
- ['json2graph_2ehpp_7638',['json2graph.hpp',['../json2graph_8hpp.html',1,'']]],
- ['json2pb_2ecpp_7639',['json2pb.cpp',['../json2pb_8cpp.html',1,'']]],
- ['json2pb_2eh_7640',['json2pb.h',['../json2pb_8h.html',1,'']]],
- ['json_5fstream_5fhelper_2ehpp_7641',['json_stream_helper.hpp',['../json__stream__helper_8hpp.html',1,'']]],
- ['jump_5falong_5fpath_2ecpp_7642',['jump_along_path.cpp',['../jump__along__path_8cpp.html',1,'']]],
- ['jump_5falong_5fpath_2ehpp_7643',['jump_along_path.hpp',['../jump__along__path_8hpp.html',1,'']]]
+ ['job_5fschedule_2ecpp_7637',['job_schedule.cpp',['../job__schedule_8cpp.html',1,'']]],
+ ['job_5fschedule_2ehpp_7638',['job_schedule.hpp',['../job__schedule_8hpp.html',1,'']]],
+ ['join_5fmain_2ecpp_7639',['join_main.cpp',['../join__main_8cpp.html',1,'']]],
+ ['json2graph_2ehpp_7640',['json2graph.hpp',['../json2graph_8hpp.html',1,'']]],
+ ['json2pb_2ecpp_7641',['json2pb.cpp',['../json2pb_8cpp.html',1,'']]],
+ ['json2pb_2eh_7642',['json2pb.h',['../json2pb_8h.html',1,'']]],
+ ['json_5fstream_5fhelper_2ehpp_7643',['json_stream_helper.hpp',['../json__stream__helper_8hpp.html',1,'']]],
+ ['jump_5falong_5fpath_2ecpp_7644',['jump_along_path.cpp',['../jump__along__path_8cpp.html',1,'']]],
+ ['jump_5falong_5fpath_2ehpp_7645',['jump_along_path.hpp',['../jump__along__path_8hpp.html',1,'']]]
];
diff --git a/search/files_a.js b/search/files_a.js
index adce5207e4..1bdcbb638d 100644
--- a/search/files_a.js
+++ b/search/files_a.js
@@ -1,12 +1,12 @@
var searchData=
[
- ['k_5fwidest_5fpaths_2ecpp_7644',['k_widest_paths.cpp',['../k__widest__paths_8cpp.html',1,'']]],
- ['k_5fwidest_5fpaths_2ehpp_7645',['k_widest_paths.hpp',['../k__widest__paths_8hpp.html',1,'']]],
- ['kff_2ecpp_7646',['kff.cpp',['../kff_8cpp.html',1,'']]],
- ['kff_2ehpp_7647',['kff.hpp',['../kff_8hpp.html',1,'']]],
- ['kmer_2ecpp_7648',['kmer.cpp',['../kmer_8cpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8cpp.html',1,'(Global Namespace)']]],
- ['kmer_2ehpp_7649',['kmer.hpp',['../kmer_8hpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8hpp.html',1,'(Global Namespace)']]],
- ['kmers_5fmain_2ecpp_7650',['kmers_main.cpp',['../kmers__main_8cpp.html',1,'']]],
- ['kmp_2ecpp_7651',['kmp.cpp',['../kmp_8cpp.html',1,'']]],
- ['kmp_2ehpp_7652',['kmp.hpp',['../kmp_8hpp.html',1,'']]]
+ ['k_5fwidest_5fpaths_2ecpp_7646',['k_widest_paths.cpp',['../k__widest__paths_8cpp.html',1,'']]],
+ ['k_5fwidest_5fpaths_2ehpp_7647',['k_widest_paths.hpp',['../k__widest__paths_8hpp.html',1,'']]],
+ ['kff_2ecpp_7648',['kff.cpp',['../kff_8cpp.html',1,'']]],
+ ['kff_2ehpp_7649',['kff.hpp',['../kff_8hpp.html',1,'']]],
+ ['kmer_2ecpp_7650',['kmer.cpp',['../kmer_8cpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8cpp.html',1,'(Global Namespace)']]],
+ ['kmer_2ehpp_7651',['kmer.hpp',['../kmer_8hpp.html',1,'(Global Namespace)'],['../algorithms_2kmer_8hpp.html',1,'(Global Namespace)']]],
+ ['kmers_5fmain_2ecpp_7652',['kmers_main.cpp',['../kmers__main_8cpp.html',1,'']]],
+ ['kmp_2ecpp_7653',['kmp.cpp',['../kmp_8cpp.html',1,'']]],
+ ['kmp_2ehpp_7654',['kmp.hpp',['../kmp_8hpp.html',1,'']]]
];
diff --git a/search/files_b.js b/search/files_b.js
index c97db17871..d3fa8fe893 100644
--- a/search/files_b.js
+++ b/search/files_b.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['load_5fproto_5fto_5fgraph_2ecpp_7653',['load_proto_to_graph.cpp',['../load__proto__to__graph_8cpp.html',1,'']]],
- ['load_5fproto_5fto_5fgraph_2ehpp_7654',['load_proto_to_graph.hpp',['../load__proto__to__graph_8hpp.html',1,'']]],
- ['loader_2ehpp_7655',['loader.hpp',['../loader_8hpp.html',1,'']]],
- ['locally_5fexpand_5fgraph_2ecpp_7656',['locally_expand_graph.cpp',['../locally__expand__graph_8cpp.html',1,'']]],
- ['locally_5fexpand_5fgraph_2ehpp_7657',['locally_expand_graph.hpp',['../locally__expand__graph_8hpp.html',1,'']]]
+ ['load_5fproto_5fto_5fgraph_2ecpp_7655',['load_proto_to_graph.cpp',['../load__proto__to__graph_8cpp.html',1,'']]],
+ ['load_5fproto_5fto_5fgraph_2ehpp_7656',['load_proto_to_graph.hpp',['../load__proto__to__graph_8hpp.html',1,'']]],
+ ['loader_2ehpp_7657',['loader.hpp',['../loader_8hpp.html',1,'']]],
+ ['locally_5fexpand_5fgraph_2ecpp_7658',['locally_expand_graph.cpp',['../locally__expand__graph_8cpp.html',1,'']]],
+ ['locally_5fexpand_5fgraph_2ehpp_7659',['locally_expand_graph.hpp',['../locally__expand__graph_8hpp.html',1,'']]]
];
diff --git a/search/files_c.js b/search/files_c.js
index 7674d98913..e195a82e11 100644
--- a/search/files_c.js
+++ b/search/files_c.js
@@ -1,57 +1,57 @@
var searchData=
[
- ['main_2ecpp_7658',['main.cpp',['../main_8cpp.html',1,'']]],
- ['map_5fmain_2ecpp_7659',['map_main.cpp',['../map__main_8cpp.html',1,'']]],
- ['mapper_2ecpp_7660',['mapper.cpp',['../mapper_8cpp.html',1,'']]],
- ['mapper_2ehpp_7661',['mapper.hpp',['../mapper_8hpp.html',1,'']]],
- ['mask_5fmain_2ecpp_7662',['mask_main.cpp',['../mask__main_8cpp.html',1,'']]],
- ['masker_2ecpp_7663',['masker.cpp',['../masker_8cpp.html',1,'']]],
- ['masker_2ehpp_7664',['masker.hpp',['../masker_8hpp.html',1,'']]],
- ['mcmc_5fcaller_2ecpp_7665',['mcmc_caller.cpp',['../mcmc__caller_8cpp.html',1,'']]],
- ['mcmc_5fcaller_2ehpp_7666',['mcmc_caller.hpp',['../mcmc__caller_8hpp.html',1,'']]],
- ['mcmc_5fgenotyper_2ecpp_7667',['mcmc_genotyper.cpp',['../mcmc__genotyper_8cpp.html',1,'']]],
- ['mcmc_5fgenotyper_2ehpp_7668',['mcmc_genotyper.hpp',['../mcmc__genotyper_8hpp.html',1,'']]],
- ['mcmc_5fmain_2ecpp_7669',['mcmc_main.cpp',['../mcmc__main_8cpp.html',1,'']]],
- ['mem_2ecpp_7670',['mem.cpp',['../mem_8cpp.html',1,'']]],
- ['mem_2ehpp_7671',['mem.hpp',['../mem_8hpp.html',1,'']]],
- ['mem_5faccelerator_2ecpp_7672',['mem_accelerator.cpp',['../mem__accelerator_8cpp.html',1,'']]],
- ['mem_5faccelerator_2ehpp_7673',['mem_accelerator.hpp',['../mem__accelerator_8hpp.html',1,'']]],
- ['memoizing_5fgraph_2ecpp_7674',['memoizing_graph.cpp',['../memoizing__graph_8cpp.html',1,'']]],
- ['memoizing_5fgraph_2ehpp_7675',['memoizing_graph.hpp',['../memoizing__graph_8hpp.html',1,'']]],
- ['memusage_2ecpp_7676',['memusage.cpp',['../memusage_8cpp.html',1,'']]],
- ['memusage_2ehpp_7677',['memusage.hpp',['../memusage_8hpp.html',1,'']]],
- ['merge_2ecpp_7678',['merge.cpp',['../merge_8cpp.html',1,'']]],
- ['merge_2ehpp_7679',['merge.hpp',['../merge_8hpp.html',1,'']]],
- ['message_5femitter_2ecpp_7680',['message_emitter.cpp',['../message__emitter_8cpp.html',1,'']]],
- ['message_5femitter_2ehpp_7681',['message_emitter.hpp',['../message__emitter_8hpp.html',1,'']]],
- ['message_5fiterator_2ecpp_7682',['message_iterator.cpp',['../message__iterator_8cpp.html',1,'']]],
- ['message_5fiterator_2ehpp_7683',['message_iterator.hpp',['../message__iterator_8hpp.html',1,'']]],
- ['min_5fcut_5fgraph_2ecpp_7684',['min_cut_graph.cpp',['../min__cut__graph_8cpp.html',1,'']]],
- ['min_5fcut_5fgraph_2ehpp_7685',['min_cut_graph.hpp',['../min__cut__graph_8hpp.html',1,'']]],
- ['minimizer_5fmain_2ecpp_7686',['minimizer_main.cpp',['../minimizer__main_8cpp.html',1,'']]],
- ['minimizer_5fmapper_2ecpp_7687',['minimizer_mapper.cpp',['../minimizer__mapper_8cpp.html',1,'']]],
- ['minimizer_5fmapper_2ehpp_7688',['minimizer_mapper.hpp',['../minimizer__mapper_8hpp.html',1,'']]],
- ['minimizer_5fmapper_5ffrom_5fchains_2ecpp_7689',['minimizer_mapper_from_chains.cpp',['../minimizer__mapper__from__chains_8cpp.html',1,'']]],
- ['mod_5fmain_2ecpp_7690',['mod_main.cpp',['../mod__main_8cpp.html',1,'']]],
- ['mpmap_5fmain_2ecpp_7691',['mpmap_main.cpp',['../mpmap__main_8cpp.html',1,'']]],
- ['msa_5fconverter_2ecpp_7692',['msa_converter.cpp',['../msa__converter_8cpp.html',1,'']]],
- ['msa_5fconverter_2ehpp_7693',['msa_converter.hpp',['../msa__converter_8hpp.html',1,'']]],
- ['msga_5fmain_2ecpp_7694',['msga_main.cpp',['../msga__main_8cpp.html',1,'']]],
- ['multipath_5falignment_2ecpp_7695',['multipath_alignment.cpp',['../multipath__alignment_8cpp.html',1,'']]],
- ['multipath_5falignment_2ehpp_7696',['multipath_alignment.hpp',['../multipath__alignment_8hpp.html',1,'']]],
- ['multipath_5falignment_5femitter_2ecpp_7697',['multipath_alignment_emitter.cpp',['../multipath__alignment__emitter_8cpp.html',1,'']]],
- ['multipath_5falignment_5femitter_2ehpp_7698',['multipath_alignment_emitter.hpp',['../multipath__alignment__emitter_8hpp.html',1,'']]],
- ['multipath_5falignment_5fgraph_2ecpp_7699',['multipath_alignment_graph.cpp',['../multipath__alignment__graph_8cpp.html',1,'']]],
- ['multipath_5falignment_5fgraph_2ehpp_7700',['multipath_alignment_graph.hpp',['../multipath__alignment__graph_8hpp.html',1,'']]],
- ['multipath_5fmapper_2ecpp_7701',['multipath_mapper.cpp',['../multipath__mapper_8cpp.html',1,'']]],
- ['multipath_5fmapper_2ehpp_7702',['multipath_mapper.hpp',['../multipath__mapper_8hpp.html',1,'']]],
- ['mutable_5fhandle_5fgraph_2ecpp_7703',['mutable_handle_graph.cpp',['../mutable__handle__graph_8cpp.html',1,'']]],
- ['mutable_5fhandle_5fgraph_2ehpp_7704',['mutable_handle_graph.hpp',['../mutable__handle__graph_8hpp.html',1,'']]],
- ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ecpp_7705',['mutable_path_deletable_handle_graph.cpp',['../mutable__path__deletable__handle__graph_8cpp.html',1,'']]],
- ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ehpp_7706',['mutable_path_deletable_handle_graph.hpp',['../mutable__path__deletable__handle__graph_8hpp.html',1,'']]],
- ['mutable_5fpath_5fhandle_5fgraph_2ecpp_7707',['mutable_path_handle_graph.cpp',['../mutable__path__handle__graph_8cpp.html',1,'']]],
- ['mutable_5fpath_5fhandle_5fgraph_2ehpp_7708',['mutable_path_handle_graph.hpp',['../mutable__path__handle__graph_8hpp.html',1,'']]],
- ['mutable_5fpath_5fmetadata_2ecpp_7709',['mutable_path_metadata.cpp',['../mutable__path__metadata_8cpp.html',1,'']]],
- ['mutable_5fpath_5fmetadata_2ehpp_7710',['mutable_path_metadata.hpp',['../mutable__path__metadata_8hpp.html',1,'']]],
- ['mutable_5fpath_5fmutable_5fhandle_5fgraph_2ehpp_7711',['mutable_path_mutable_handle_graph.hpp',['../mutable__path__mutable__handle__graph_8hpp.html',1,'']]]
+ ['main_2ecpp_7660',['main.cpp',['../main_8cpp.html',1,'']]],
+ ['map_5fmain_2ecpp_7661',['map_main.cpp',['../map__main_8cpp.html',1,'']]],
+ ['mapper_2ecpp_7662',['mapper.cpp',['../mapper_8cpp.html',1,'']]],
+ ['mapper_2ehpp_7663',['mapper.hpp',['../mapper_8hpp.html',1,'']]],
+ ['mask_5fmain_2ecpp_7664',['mask_main.cpp',['../mask__main_8cpp.html',1,'']]],
+ ['masker_2ecpp_7665',['masker.cpp',['../masker_8cpp.html',1,'']]],
+ ['masker_2ehpp_7666',['masker.hpp',['../masker_8hpp.html',1,'']]],
+ ['mcmc_5fcaller_2ecpp_7667',['mcmc_caller.cpp',['../mcmc__caller_8cpp.html',1,'']]],
+ ['mcmc_5fcaller_2ehpp_7668',['mcmc_caller.hpp',['../mcmc__caller_8hpp.html',1,'']]],
+ ['mcmc_5fgenotyper_2ecpp_7669',['mcmc_genotyper.cpp',['../mcmc__genotyper_8cpp.html',1,'']]],
+ ['mcmc_5fgenotyper_2ehpp_7670',['mcmc_genotyper.hpp',['../mcmc__genotyper_8hpp.html',1,'']]],
+ ['mcmc_5fmain_2ecpp_7671',['mcmc_main.cpp',['../mcmc__main_8cpp.html',1,'']]],
+ ['mem_2ecpp_7672',['mem.cpp',['../mem_8cpp.html',1,'']]],
+ ['mem_2ehpp_7673',['mem.hpp',['../mem_8hpp.html',1,'']]],
+ ['mem_5faccelerator_2ecpp_7674',['mem_accelerator.cpp',['../mem__accelerator_8cpp.html',1,'']]],
+ ['mem_5faccelerator_2ehpp_7675',['mem_accelerator.hpp',['../mem__accelerator_8hpp.html',1,'']]],
+ ['memoizing_5fgraph_2ecpp_7676',['memoizing_graph.cpp',['../memoizing__graph_8cpp.html',1,'']]],
+ ['memoizing_5fgraph_2ehpp_7677',['memoizing_graph.hpp',['../memoizing__graph_8hpp.html',1,'']]],
+ ['memusage_2ecpp_7678',['memusage.cpp',['../memusage_8cpp.html',1,'']]],
+ ['memusage_2ehpp_7679',['memusage.hpp',['../memusage_8hpp.html',1,'']]],
+ ['merge_2ecpp_7680',['merge.cpp',['../merge_8cpp.html',1,'']]],
+ ['merge_2ehpp_7681',['merge.hpp',['../merge_8hpp.html',1,'']]],
+ ['message_5femitter_2ecpp_7682',['message_emitter.cpp',['../message__emitter_8cpp.html',1,'']]],
+ ['message_5femitter_2ehpp_7683',['message_emitter.hpp',['../message__emitter_8hpp.html',1,'']]],
+ ['message_5fiterator_2ecpp_7684',['message_iterator.cpp',['../message__iterator_8cpp.html',1,'']]],
+ ['message_5fiterator_2ehpp_7685',['message_iterator.hpp',['../message__iterator_8hpp.html',1,'']]],
+ ['min_5fcut_5fgraph_2ecpp_7686',['min_cut_graph.cpp',['../min__cut__graph_8cpp.html',1,'']]],
+ ['min_5fcut_5fgraph_2ehpp_7687',['min_cut_graph.hpp',['../min__cut__graph_8hpp.html',1,'']]],
+ ['minimizer_5fmain_2ecpp_7688',['minimizer_main.cpp',['../minimizer__main_8cpp.html',1,'']]],
+ ['minimizer_5fmapper_2ecpp_7689',['minimizer_mapper.cpp',['../minimizer__mapper_8cpp.html',1,'']]],
+ ['minimizer_5fmapper_2ehpp_7690',['minimizer_mapper.hpp',['../minimizer__mapper_8hpp.html',1,'']]],
+ ['minimizer_5fmapper_5ffrom_5fchains_2ecpp_7691',['minimizer_mapper_from_chains.cpp',['../minimizer__mapper__from__chains_8cpp.html',1,'']]],
+ ['mod_5fmain_2ecpp_7692',['mod_main.cpp',['../mod__main_8cpp.html',1,'']]],
+ ['mpmap_5fmain_2ecpp_7693',['mpmap_main.cpp',['../mpmap__main_8cpp.html',1,'']]],
+ ['msa_5fconverter_2ecpp_7694',['msa_converter.cpp',['../msa__converter_8cpp.html',1,'']]],
+ ['msa_5fconverter_2ehpp_7695',['msa_converter.hpp',['../msa__converter_8hpp.html',1,'']]],
+ ['msga_5fmain_2ecpp_7696',['msga_main.cpp',['../msga__main_8cpp.html',1,'']]],
+ ['multipath_5falignment_2ecpp_7697',['multipath_alignment.cpp',['../multipath__alignment_8cpp.html',1,'']]],
+ ['multipath_5falignment_2ehpp_7698',['multipath_alignment.hpp',['../multipath__alignment_8hpp.html',1,'']]],
+ ['multipath_5falignment_5femitter_2ecpp_7699',['multipath_alignment_emitter.cpp',['../multipath__alignment__emitter_8cpp.html',1,'']]],
+ ['multipath_5falignment_5femitter_2ehpp_7700',['multipath_alignment_emitter.hpp',['../multipath__alignment__emitter_8hpp.html',1,'']]],
+ ['multipath_5falignment_5fgraph_2ecpp_7701',['multipath_alignment_graph.cpp',['../multipath__alignment__graph_8cpp.html',1,'']]],
+ ['multipath_5falignment_5fgraph_2ehpp_7702',['multipath_alignment_graph.hpp',['../multipath__alignment__graph_8hpp.html',1,'']]],
+ ['multipath_5fmapper_2ecpp_7703',['multipath_mapper.cpp',['../multipath__mapper_8cpp.html',1,'']]],
+ ['multipath_5fmapper_2ehpp_7704',['multipath_mapper.hpp',['../multipath__mapper_8hpp.html',1,'']]],
+ ['mutable_5fhandle_5fgraph_2ecpp_7705',['mutable_handle_graph.cpp',['../mutable__handle__graph_8cpp.html',1,'']]],
+ ['mutable_5fhandle_5fgraph_2ehpp_7706',['mutable_handle_graph.hpp',['../mutable__handle__graph_8hpp.html',1,'']]],
+ ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ecpp_7707',['mutable_path_deletable_handle_graph.cpp',['../mutable__path__deletable__handle__graph_8cpp.html',1,'']]],
+ ['mutable_5fpath_5fdeletable_5fhandle_5fgraph_2ehpp_7708',['mutable_path_deletable_handle_graph.hpp',['../mutable__path__deletable__handle__graph_8hpp.html',1,'']]],
+ ['mutable_5fpath_5fhandle_5fgraph_2ecpp_7709',['mutable_path_handle_graph.cpp',['../mutable__path__handle__graph_8cpp.html',1,'']]],
+ ['mutable_5fpath_5fhandle_5fgraph_2ehpp_7710',['mutable_path_handle_graph.hpp',['../mutable__path__handle__graph_8hpp.html',1,'']]],
+ ['mutable_5fpath_5fmetadata_2ecpp_7711',['mutable_path_metadata.cpp',['../mutable__path__metadata_8cpp.html',1,'']]],
+ ['mutable_5fpath_5fmetadata_2ehpp_7712',['mutable_path_metadata.hpp',['../mutable__path__metadata_8hpp.html',1,'']]],
+ ['mutable_5fpath_5fmutable_5fhandle_5fgraph_2ehpp_7713',['mutable_path_mutable_handle_graph.hpp',['../mutable__path__mutable__handle__graph_8hpp.html',1,'']]]
];
diff --git a/search/files_d.js b/search/files_d.js
index db4ac56e8c..f20c9955d0 100644
--- a/search/files_d.js
+++ b/search/files_d.js
@@ -1,18 +1,18 @@
var searchData=
[
- ['name_5fmapper_2ecpp_7712',['name_mapper.cpp',['../name__mapper_8cpp.html',1,'']]],
- ['name_5fmapper_2ehpp_7713',['name_mapper.hpp',['../name__mapper_8hpp.html',1,'']]],
- ['named_5fnode_5fback_5ftranslation_2ehpp_7714',['named_node_back_translation.hpp',['../named__node__back__translation_8hpp.html',1,'']]],
- ['nearest_5foffsets_5fin_5fpaths_2ecpp_7715',['nearest_offsets_in_paths.cpp',['../nearest__offsets__in__paths_8cpp.html',1,'']]],
- ['nearest_5foffsets_5fin_5fpaths_2ehpp_7716',['nearest_offsets_in_paths.hpp',['../nearest__offsets__in__paths_8hpp.html',1,'']]],
- ['nested_5ftraversal_5ffinder_2ecpp_7717',['nested_traversal_finder.cpp',['../nested__traversal__finder_8cpp.html',1,'']]],
- ['nested_5ftraversal_5ffinder_2ehpp_7718',['nested_traversal_finder.hpp',['../nested__traversal__finder_8hpp.html',1,'']]],
- ['next_5fpos_5fchars_2ecpp_7719',['next_pos_chars.cpp',['../next__pos__chars_8cpp.html',1,'']]],
- ['next_5fpos_5fchars_2ehpp_7720',['next_pos_chars.hpp',['../next__pos__chars_8hpp.html',1,'']]],
- ['nodeside_2ehpp_7721',['nodeside.hpp',['../nodeside_8hpp.html',1,'']]],
- ['nodetraversal_2ehpp_7722',['nodetraversal.hpp',['../nodetraversal_8hpp.html',1,'']]],
- ['normalize_2ecpp_7723',['normalize.cpp',['../normalize_8cpp.html',1,'']]],
- ['normalize_2ehpp_7724',['normalize.hpp',['../normalize_8hpp.html',1,'']]],
- ['null_5fmasking_5fgraph_2ecpp_7725',['null_masking_graph.cpp',['../null__masking__graph_8cpp.html',1,'']]],
- ['null_5fmasking_5fgraph_2ehpp_7726',['null_masking_graph.hpp',['../null__masking__graph_8hpp.html',1,'']]]
+ ['name_5fmapper_2ecpp_7714',['name_mapper.cpp',['../name__mapper_8cpp.html',1,'']]],
+ ['name_5fmapper_2ehpp_7715',['name_mapper.hpp',['../name__mapper_8hpp.html',1,'']]],
+ ['named_5fnode_5fback_5ftranslation_2ehpp_7716',['named_node_back_translation.hpp',['../named__node__back__translation_8hpp.html',1,'']]],
+ ['nearest_5foffsets_5fin_5fpaths_2ecpp_7717',['nearest_offsets_in_paths.cpp',['../nearest__offsets__in__paths_8cpp.html',1,'']]],
+ ['nearest_5foffsets_5fin_5fpaths_2ehpp_7718',['nearest_offsets_in_paths.hpp',['../nearest__offsets__in__paths_8hpp.html',1,'']]],
+ ['nested_5ftraversal_5ffinder_2ecpp_7719',['nested_traversal_finder.cpp',['../nested__traversal__finder_8cpp.html',1,'']]],
+ ['nested_5ftraversal_5ffinder_2ehpp_7720',['nested_traversal_finder.hpp',['../nested__traversal__finder_8hpp.html',1,'']]],
+ ['next_5fpos_5fchars_2ecpp_7721',['next_pos_chars.cpp',['../next__pos__chars_8cpp.html',1,'']]],
+ ['next_5fpos_5fchars_2ehpp_7722',['next_pos_chars.hpp',['../next__pos__chars_8hpp.html',1,'']]],
+ ['nodeside_2ehpp_7723',['nodeside.hpp',['../nodeside_8hpp.html',1,'']]],
+ ['nodetraversal_2ehpp_7724',['nodetraversal.hpp',['../nodetraversal_8hpp.html',1,'']]],
+ ['normalize_2ecpp_7725',['normalize.cpp',['../normalize_8cpp.html',1,'']]],
+ ['normalize_2ehpp_7726',['normalize.hpp',['../normalize_8hpp.html',1,'']]],
+ ['null_5fmasking_5fgraph_2ecpp_7727',['null_masking_graph.cpp',['../null__masking__graph_8cpp.html',1,'']]],
+ ['null_5fmasking_5fgraph_2ehpp_7728',['null_masking_graph.hpp',['../null__masking__graph_8hpp.html',1,'']]]
];
diff --git a/search/files_e.js b/search/files_e.js
index 94cd32df90..454e0c9dbb 100644
--- a/search/files_e.js
+++ b/search/files_e.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['option_2ecpp_7727',['option.cpp',['../option_8cpp.html',1,'']]],
- ['option_2ehpp_7728',['option.hpp',['../option_8hpp.html',1,'']]],
- ['options_2ecpp_7729',['options.cpp',['../options_8cpp.html',1,'']]],
- ['options_2ehpp_7730',['options.hpp',['../options_8hpp.html',1,'']]]
+ ['option_2ecpp_7729',['option.cpp',['../option_8cpp.html',1,'']]],
+ ['option_2ehpp_7730',['option.hpp',['../option_8hpp.html',1,'']]],
+ ['options_2ecpp_7731',['options.cpp',['../options_8cpp.html',1,'']]],
+ ['options_2ehpp_7732',['options.hpp',['../options_8hpp.html',1,'']]]
];
diff --git a/search/files_f.js b/search/files_f.js
index 00546e3f0a..d473b77d7e 100644
--- a/search/files_f.js
+++ b/search/files_f.js
@@ -1,43 +1,43 @@
var searchData=
[
- ['pack_5fmain_2ecpp_7731',['pack_main.cpp',['../pack__main_8cpp.html',1,'']]],
- ['packer_2ecpp_7732',['packer.cpp',['../packer_8cpp.html',1,'']]],
- ['packer_2ehpp_7733',['packer.hpp',['../packer_8hpp.html',1,'']]],
- ['pad_5fband_2ecpp_7734',['pad_band.cpp',['../pad__band_8cpp.html',1,'']]],
- ['pad_5fband_2ehpp_7735',['pad_band.hpp',['../pad__band_8hpp.html',1,'']]],
- ['path_2ecpp_7736',['path.cpp',['../path_8cpp.html',1,'']]],
- ['path_2ehpp_7737',['path.hpp',['../path_8hpp.html',1,'']]],
- ['path_5fcomponent_5findex_2ecpp_7738',['path_component_index.cpp',['../path__component__index_8cpp.html',1,'']]],
- ['path_5fcomponent_5findex_2ehpp_7739',['path_component_index.hpp',['../path__component__index_8hpp.html',1,'']]],
- ['path_5fhandle_5fgraph_2ecpp_7740',['path_handle_graph.cpp',['../path__handle__graph_8cpp.html',1,'']]],
- ['path_5fhandle_5fgraph_2ehpp_7741',['path_handle_graph.hpp',['../path__handle__graph_8hpp.html',1,'']]],
- ['path_5findex_2ecpp_7742',['path_index.cpp',['../path__index_8cpp.html',1,'']]],
- ['path_5findex_2ehpp_7743',['path_index.hpp',['../path__index_8hpp.html',1,'']]],
- ['path_5fmetadata_2ecpp_7744',['path_metadata.cpp',['../path__metadata_8cpp.html',1,'']]],
- ['path_5fmetadata_2ehpp_7745',['path_metadata.hpp',['../path__metadata_8hpp.html',1,'']]],
- ['path_5fposition_5fhandle_5fgraph_2ecpp_7746',['path_position_handle_graph.cpp',['../path__position__handle__graph_8cpp.html',1,'']]],
- ['path_5fposition_5fhandle_5fgraph_2ehpp_7747',['path_position_handle_graph.hpp',['../path__position__handle__graph_8hpp.html',1,'']]],
- ['path_5fstring_2ecpp_7748',['path_string.cpp',['../path__string_8cpp.html',1,'']]],
- ['path_5fstring_2ehpp_7749',['path_string.hpp',['../path__string_8hpp.html',1,'']]],
- ['path_5fsubgraph_2ecpp_7750',['path_subgraph.cpp',['../path__subgraph_8cpp.html',1,'']]],
- ['path_5fsubgraph_2ehpp_7751',['path_subgraph.hpp',['../path__subgraph_8hpp.html',1,'']]],
- ['paths_5fmain_2ecpp_7752',['paths_main.cpp',['../paths__main_8cpp.html',1,'']]],
- ['phase_5funfolder_2ecpp_7753',['phase_unfolder.cpp',['../phase__unfolder_8cpp.html',1,'']]],
- ['phase_5funfolder_2ehpp_7754',['phase_unfolder.hpp',['../phase__unfolder_8hpp.html',1,'']]],
- ['phased_5fgenome_2ecpp_7755',['phased_genome.cpp',['../phased__genome_8cpp.html',1,'']]],
- ['phased_5fgenome_2ehpp_7756',['phased_genome.hpp',['../phased__genome_8hpp.html',1,'']]],
- ['pictographs_2ehpp_7757',['pictographs.hpp',['../pictographs_8hpp.html',1,'']]],
- ['position_2ecpp_7758',['position.cpp',['../position_8cpp.html',1,'']]],
- ['position_2ehpp_7759',['position.hpp',['../position_8hpp.html',1,'']]],
- ['preflight_2ecpp_7760',['preflight.cpp',['../preflight_8cpp.html',1,'']]],
- ['preflight_2ehpp_7761',['preflight.hpp',['../preflight_8hpp.html',1,'']]],
- ['progressive_2ecpp_7762',['progressive.cpp',['../progressive_8cpp.html',1,'']]],
- ['progressive_2ehpp_7763',['progressive.hpp',['../progressive_8hpp.html',1,'']]],
- ['protobuf_5femitter_2ehpp_7764',['protobuf_emitter.hpp',['../protobuf__emitter_8hpp.html',1,'']]],
- ['protobuf_5fiterator_2ehpp_7765',['protobuf_iterator.hpp',['../protobuf__iterator_8hpp.html',1,'']]],
- ['prune_2ecpp_7766',['prune.cpp',['../prune_8cpp.html',1,'']]],
- ['prune_2ehpp_7767',['prune.hpp',['../prune_8hpp.html',1,'']]],
- ['prune_5fmain_2ecpp_7768',['prune_main.cpp',['../prune__main_8cpp.html',1,'']]],
- ['prune_5fto_5fconnecting_5fgraph_2ecpp_7769',['prune_to_connecting_graph.cpp',['../prune__to__connecting__graph_8cpp.html',1,'']]],
- ['prune_5fto_5fconnecting_5fgraph_2ehpp_7770',['prune_to_connecting_graph.hpp',['../prune__to__connecting__graph_8hpp.html',1,'']]]
+ ['pack_5fmain_2ecpp_7733',['pack_main.cpp',['../pack__main_8cpp.html',1,'']]],
+ ['packer_2ecpp_7734',['packer.cpp',['../packer_8cpp.html',1,'']]],
+ ['packer_2ehpp_7735',['packer.hpp',['../packer_8hpp.html',1,'']]],
+ ['pad_5fband_2ecpp_7736',['pad_band.cpp',['../pad__band_8cpp.html',1,'']]],
+ ['pad_5fband_2ehpp_7737',['pad_band.hpp',['../pad__band_8hpp.html',1,'']]],
+ ['path_2ecpp_7738',['path.cpp',['../path_8cpp.html',1,'']]],
+ ['path_2ehpp_7739',['path.hpp',['../path_8hpp.html',1,'']]],
+ ['path_5fcomponent_5findex_2ecpp_7740',['path_component_index.cpp',['../path__component__index_8cpp.html',1,'']]],
+ ['path_5fcomponent_5findex_2ehpp_7741',['path_component_index.hpp',['../path__component__index_8hpp.html',1,'']]],
+ ['path_5fhandle_5fgraph_2ecpp_7742',['path_handle_graph.cpp',['../path__handle__graph_8cpp.html',1,'']]],
+ ['path_5fhandle_5fgraph_2ehpp_7743',['path_handle_graph.hpp',['../path__handle__graph_8hpp.html',1,'']]],
+ ['path_5findex_2ecpp_7744',['path_index.cpp',['../path__index_8cpp.html',1,'']]],
+ ['path_5findex_2ehpp_7745',['path_index.hpp',['../path__index_8hpp.html',1,'']]],
+ ['path_5fmetadata_2ecpp_7746',['path_metadata.cpp',['../path__metadata_8cpp.html',1,'']]],
+ ['path_5fmetadata_2ehpp_7747',['path_metadata.hpp',['../path__metadata_8hpp.html',1,'']]],
+ ['path_5fposition_5fhandle_5fgraph_2ecpp_7748',['path_position_handle_graph.cpp',['../path__position__handle__graph_8cpp.html',1,'']]],
+ ['path_5fposition_5fhandle_5fgraph_2ehpp_7749',['path_position_handle_graph.hpp',['../path__position__handle__graph_8hpp.html',1,'']]],
+ ['path_5fstring_2ecpp_7750',['path_string.cpp',['../path__string_8cpp.html',1,'']]],
+ ['path_5fstring_2ehpp_7751',['path_string.hpp',['../path__string_8hpp.html',1,'']]],
+ ['path_5fsubgraph_2ecpp_7752',['path_subgraph.cpp',['../path__subgraph_8cpp.html',1,'']]],
+ ['path_5fsubgraph_2ehpp_7753',['path_subgraph.hpp',['../path__subgraph_8hpp.html',1,'']]],
+ ['paths_5fmain_2ecpp_7754',['paths_main.cpp',['../paths__main_8cpp.html',1,'']]],
+ ['phase_5funfolder_2ecpp_7755',['phase_unfolder.cpp',['../phase__unfolder_8cpp.html',1,'']]],
+ ['phase_5funfolder_2ehpp_7756',['phase_unfolder.hpp',['../phase__unfolder_8hpp.html',1,'']]],
+ ['phased_5fgenome_2ecpp_7757',['phased_genome.cpp',['../phased__genome_8cpp.html',1,'']]],
+ ['phased_5fgenome_2ehpp_7758',['phased_genome.hpp',['../phased__genome_8hpp.html',1,'']]],
+ ['pictographs_2ehpp_7759',['pictographs.hpp',['../pictographs_8hpp.html',1,'']]],
+ ['position_2ecpp_7760',['position.cpp',['../position_8cpp.html',1,'']]],
+ ['position_2ehpp_7761',['position.hpp',['../position_8hpp.html',1,'']]],
+ ['preflight_2ecpp_7762',['preflight.cpp',['../preflight_8cpp.html',1,'']]],
+ ['preflight_2ehpp_7763',['preflight.hpp',['../preflight_8hpp.html',1,'']]],
+ ['progressive_2ecpp_7764',['progressive.cpp',['../progressive_8cpp.html',1,'']]],
+ ['progressive_2ehpp_7765',['progressive.hpp',['../progressive_8hpp.html',1,'']]],
+ ['protobuf_5femitter_2ehpp_7766',['protobuf_emitter.hpp',['../protobuf__emitter_8hpp.html',1,'']]],
+ ['protobuf_5fiterator_2ehpp_7767',['protobuf_iterator.hpp',['../protobuf__iterator_8hpp.html',1,'']]],
+ ['prune_2ecpp_7768',['prune.cpp',['../prune_8cpp.html',1,'']]],
+ ['prune_2ehpp_7769',['prune.hpp',['../prune_8hpp.html',1,'']]],
+ ['prune_5fmain_2ecpp_7770',['prune_main.cpp',['../prune__main_8cpp.html',1,'']]],
+ ['prune_5fto_5fconnecting_5fgraph_2ecpp_7771',['prune_to_connecting_graph.cpp',['../prune__to__connecting__graph_8cpp.html',1,'']]],
+ ['prune_5fto_5fconnecting_5fgraph_2ehpp_7772',['prune_to_connecting_graph.hpp',['../prune__to__connecting__graph_8hpp.html',1,'']]]
];
diff --git a/search/functions_0.js b/search/functions_0.js
index 46fcfed305..2bcfdfc2e0 100644
--- a/search/functions_0.js
+++ b/search/functions_0.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['_5ffor_5feach_5fkmer_7968',['_for_each_kmer',['../classvg_1_1VG.html#aaf5016c5e5d28db6db32aa7626440238',1,'vg::VG']]]
+ ['_5ffor_5feach_5fkmer_7970',['_for_each_kmer',['../classvg_1_1VG.html#aaf5016c5e5d28db6db32aa7626440238',1,'vg::VG']]]
];
diff --git a/search/functions_1.js b/search/functions_1.js
index 34f20027f3..33dadf8052 100644
--- a/search/functions_1.js
+++ b/search/functions_1.js
@@ -1,255 +1,255 @@
var searchData=
[
- ['a_7969',['a',['../classvg_1_1uniform__real__distribution.html#aac3912d0f456993e6ae7f7bbe4d732d7',1,'vg::uniform_real_distribution::a()'],['../classvg_1_1uniform__int__distribution.html#a2ac06e4375faf1706e7d6171c7e2e14b',1,'vg::uniform_int_distribution::a()'],['../classvg_1_1truncated__normal__distribution.html#a88c472b134a2672661b45695824cd3c0',1,'vg::truncated_normal_distribution::A()']]],
- ['a_5fstar_7970',['a_star',['../namespacevg_1_1algorithms.html#a5af5b6f1083925669832ae59d0e549e7',1,'vg::algorithms']]],
- ['absent_7971',['absent',['../namespacehaplotypes__defaults.html#a201800ce4570c0eb29f0279035dcaf48',1,'haplotypes_defaults']]],
- ['abstractreadsampler_7972',['AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html#add2ef81ca4c3984e851d690c695bae2d',1,'vg::AbstractReadSampler']]],
- ['accelerate_5fmem_5fquery_7973',['accelerate_mem_query',['../classvg_1_1BaseMapper.html#a3cf076ec413d3a3bb029c46880a17759',1,'vg::BaseMapper']]],
- ['accept_5frecord_7974',['accept_record',['../classvg_1_1VcfRecordFilter.html#a2e39d3d4cb41426f965959c30b0de2d2',1,'vg::VcfRecordFilter']]],
- ['add_7975',['add',['../classvg_1_1Packer.html#a8a8cb2dd528dc7cc178e32e69e42212b',1,'vg::Packer']]],
- ['add_5fallele_5fpath_5fto_5finfo_7976',['add_allele_path_to_info',['../classvg_1_1VCFOutputCaller.html#a0d1f292cf9ad7db29e0a02e5395c7f02',1,'vg::VCFOutputCaller::add_allele_path_to_info(const HandleGraph *graph, vcflib::Variant &v, int allele, const Traversal &trav, bool reversed, bool one_based) const'],['../classvg_1_1VCFOutputCaller.html#a59a286bc432e93001bc3af35b6ec2f6a',1,'vg::VCFOutputCaller::add_allele_path_to_info(vcflib::Variant &v, int allele, const SnarlTraversal &trav, bool reversed, bool one_based) const']]],
- ['add_5falt_5fallele_7977',['add_alt_allele',['../namespacevg.html#a6391a10ec421fbb6c487f491bd978ef6',1,'vg']]],
- ['add_5fand_5fadjust_5fpaths_7978',['add_and_adjust_paths',['../convert__main_8cpp.html#a97c9047b1f01a6c50b89cae4249dbdae',1,'convert_main.cpp']]],
- ['add_5fannotations_7979',['add_annotations',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#af46d15924e533706d6999dcb9619d6e6',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t::add_annotations()'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#aa9c2fadd69e58abfea065ae09917ced7',1,'vg::MinimizerMapper::aligner_stats_t::add_annotations()'],['../classvg_1_1MultipathAlignmentEmitter.html#a9d0b6648ef4cfb2ffb72227891ebc7fd',1,'vg::MultipathAlignmentEmitter::add_annotations()']]],
- ['add_5fbv_7980',['add_bv',['../classVectorizer.html#a88203fab4049c471c963135c4c52ce03',1,'Vectorizer']]],
- ['add_5fchain_5fchild_7981',['add_chain_child',['../classvg_1_1NetGraph.html#a0fadfaf9261a911ec04b4c10f75c5b9b',1,'vg::NetGraph']]],
- ['add_5fchild_5fto_5fchain_7982',['add_child_to_chain',['../classvg_1_1ZipCodeForest.html#ac70358ab79a7212af23bc6ebffcb43fd',1,'vg::ZipCodeForest']]],
- ['add_5fconnecting_5fedges_5fto_5fsubgraph_7983',['add_connecting_edges_to_subgraph',['../namespacevg_1_1algorithms.html#a6347e00229560b4adb7cc7cb6332b21a',1,'vg::algorithms']]],
- ['add_5fconnection_7984',['add_connection',['../classvg_1_1subpath__t.html#abfcffaca080591fc341c4129574c9e21',1,'vg::subpath_t']]],
- ['add_5fcontigs_5fto_5fvcf_5fheader_7985',['add_contigs_to_vcf_header',['../classvg_1_1Deconstructor.html#a2b32d4a11d7945c680274ef7ce23cbdd',1,'vg::Deconstructor']]],
- ['add_5fdecomposed_5ftail_5falignments_7986',['add_decomposed_tail_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a99e7522a1341bc3d5e7d0876156d0e24',1,'vg::MultipathAlignmentGraph']]],
- ['add_5fdescendants_5fto_5fsubgraph_7987',['add_descendants_to_subgraph',['../namespacevg.html#a9e91a5d33d2da100b1173bc336ea90ff',1,'vg']]],
- ['add_5fedge_7988',['add_edge',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a9ea6a73a76afd51e8e3faee8d76575a2',1,'vg::MEMClusterer::HitGraph::add_edge()'],['../classvg_1_1DiagramExplainer.html#ab80098946b753fd283a3241c58c629a7',1,'vg::DiagramExplainer::add_edge()'],['../classvg_1_1VG.html#a613c931c81518212917053d07e9bf8a8',1,'vg::VG::add_edge()']]],
- ['add_5fedges_7989',['add_edges',['../classvg_1_1VG.html#a7f23cdd532ca7b8d3c0bb9cceff3d378',1,'vg::VG::add_edges(const vector< Edge > &edges)'],['../classvg_1_1VG.html#a679e39a7c1771c3ecc7204bd3b999583',1,'vg::VG::add_edges(const vector< Edge * > &edges)'],['../classvg_1_1VG.html#acb8712eefbfd373c45f54d6bac8188c6',1,'vg::VG::add_edges(const set< Edge * > &edges)']]],
- ['add_5fedges_5fonly_7990',['add_edges_only',['../namespacevg.html#ae2303a00d9cf0d35e243dc6de7574471',1,'vg']]],
- ['add_5fedit_7991',['add_edit',['../classvg_1_1path__mapping__t.html#a82a73553691a54453a70c4e76f35271f',1,'vg::path_mapping_t']]],
- ['add_5fedited_5ftranscript_5fpaths_7992',['add_edited_transcript_paths',['../classvg_1_1Transcriptome.html#abfa196d9f2e46f6f72f71a80a6063c36',1,'vg::Transcriptome']]],
- ['add_5fentry_7993',['add_entry',['../structvg_1_1subcommand_1_1Preset.html#a86195268d1480849b5286b07fa744796',1,'vg::subcommand::Preset']]],
- ['add_5fexon_7994',['add_exon',['../classvg_1_1Transcriptome.html#a8c292f8d6d1d176e5df367a25dd70e5f',1,'vg::Transcriptome::add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos) const'],['../classvg_1_1Transcriptome.html#af764ab28d6d866807d09a4482dd96523',1,'vg::Transcriptome::add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos, const bdsg::PositionOverlay &graph_path_pos_overlay) const']]],
- ['add_5fflag_7995',['add_flag',['../structvg_1_1subcommand_1_1OptionGroup.html#a09b380a1b6511d2e22477694af202ffe',1,'vg::subcommand::OptionGroup::add_flag(const std::string &name, char short_option, bool Receiver::*dest, bool default_value, const std::string &help, const ValidatorFunction< bool > &validator=[](const bool &ignored) {})'],['../structvg_1_1subcommand_1_1OptionGroup.html#abed7849b9115a028191beaa1d96050be',1,'vg::subcommand::OptionGroup::add_flag(const std::string &name, bool Receiver::*dest, bool default_value, const std::string &help, const ValidatorFunction< bool > &validator=[](const bool &ignored) {})']]],
- ['add_5fglobals_7996',['add_globals',['../classvg_1_1DiagramExplainer.html#a61051fae11426259dc7318dbb51c8ab6',1,'vg::DiagramExplainer']]],
- ['add_5fgroup_7997',['add_group',['../classvg_1_1StreamIndexBase.html#ad54626f7e5eb2587d4a5d5f514c82f75',1,'vg::StreamIndexBase::add_group()'],['../classvg_1_1StreamIndex.html#a172dd150297aad85dada7ba852ec3a0c',1,'vg::StreamIndex::add_group()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a1ef2138d216deaf4efa341ae35d5f308',1,'vg::subcommand::GroupedOptionGroup::add_group()']]],
- ['add_5fhandle_7998',['add_handle',['../classvg_1_1SubHandleGraph.html#a2ab52610b56f49a48262faafc7e510df',1,'vg::SubHandleGraph::add_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a8954a9766ec7f064c756e2bb4d9a61f1',1,'handlegraph::algorithms::SubHandleGraph::add_handle()']]],
- ['add_5fhaplotype_7999',['add_haplotype',['../classvg_1_1PhasedGenome.html#ad36e2c71ff5b2714d1fe1bb6af075f9c',1,'vg::PhasedGenome']]],
- ['add_5fhaplotype_5ftranscripts_8000',['add_haplotype_transcripts',['../classvg_1_1Transcriptome.html#a2d0ed7b746222e68f5224838a70c39f4',1,'vg::Transcriptome']]],
- ['add_5fintron_5fsplice_5fjunctions_8001',['add_intron_splice_junctions',['../classvg_1_1Transcriptome.html#a6a43848fb4557db4edb73836a1f8270c',1,'vg::Transcriptome']]],
- ['add_5flog_8002',['add_log',['../namespacevg.html#a0d4ce16064ad3986381aeead6afe317f',1,'vg']]],
- ['add_5flog10_8003',['add_log10',['../namespacevg.html#ab3f3c75ff3775f447d5dabbdb4e540dc',1,'vg']]],
- ['add_5fmapping_8004',['add_mapping',['../classvg_1_1path__t.html#a8dcc03d2615b611cb3f01ccc72235f62',1,'vg::path_t']]],
- ['add_5fname_8005',['add_name',['../classVectorizer.html#a37c3afd6049c63e09910ca050a2f2b10',1,'Vectorizer']]],
- ['add_5fname_5fmapping_8006',['add_name_mapping',['../classvg_1_1NameMapper.html#ac2e2d25ef0f36649f33bb3386f0150b5',1,'vg::NameMapper']]],
- ['add_5fnext_8007',['add_next',['../classvg_1_1subpath__t.html#a3ce38f3b06d1f9cf18885be6a8391570',1,'vg::subpath_t']]],
- ['add_5fnode_8008',['add_node',['../classvg_1_1DiagramExplainer.html#a4ddb1f858fdce9d6faa612094b584ce5',1,'vg::DiagramExplainer::add_node()'],['../classvg_1_1VG.html#ad3e265ee441758d81fdb7c038e2fa8cc',1,'vg::VG::add_node()'],['../structvg_1_1algorithms_1_1Graph.html#a1e46f942c332408f39f816b7a344182e',1,'vg::algorithms::Graph::add_node()']]],
- ['add_5fnodes_8009',['add_nodes',['../classvg_1_1VG.html#ae71d30b767f067a874c933f13f6c34e5',1,'vg::VG::add_nodes(const vector< Node > &nodes)'],['../classvg_1_1VG.html#ab796330d50fdff47f5c080e251efea68',1,'vg::VG::add_nodes(const set< Node * > &nodes)']]],
- ['add_5fnodes_5fand_5fedges_8010',['add_nodes_and_edges',['../namespacevg.html#a3aa7eee80c4c79f0f863d10687714c74',1,'vg::add_nodes_and_edges(MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t >> &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, size_t max_node_size=1024)'],['../namespacevg.html#a4b080c96a3681c4bd64f38eb05acd31b',1,'vg::add_nodes_and_edges(MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t >> &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, set< NodeSide > &dangling, size_t max_node_size)']]],
- ['add_5fone_5fbyte_8011',['add_one_byte',['../structvg_1_1varint__vector__t.html#a95601cf688af672f6848e064a8b8a0ef',1,'vg::varint_vector_t']]],
- ['add_5foption_8012',['add_option',['../structvg_1_1subcommand_1_1OptionGroup.html#ae7e574b260ca7c76e7137bae2d97486d',1,'vg::subcommand::OptionGroup::add_option(const std::string &name, char short_option, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})'],['../structvg_1_1subcommand_1_1OptionGroup.html#ab1102a6791fedb9b9bcfd61a45c9c750',1,'vg::subcommand::OptionGroup::add_option(const std::string &name, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})']]],
- ['add_5fpath_8013',['add_path',['../namespacevg.html#aee40bdeb4216e0bf79124b25d1823ae4',1,'vg']]],
- ['add_5fpath_5fto_5fgraph_8014',['add_path_to_graph',['../namespacevg.html#a7ac200a1dbeaf55eb41bebbfd2ce4bdf',1,'vg']]],
- ['add_5fpoints_8015',['add_points',['../classvg_1_1algorithms_1_1TracedScore.html#a214944e7a2a98197db1c7fa804542065',1,'vg::algorithms::TracedScore']]],
- ['add_5frange_8016',['add_range',['../structvg_1_1subcommand_1_1OptionGroup.html#a7864b536a49b3e464df80f928e27e681',1,'vg::subcommand::OptionGroup::add_range(const std::string &name, char short_option, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})'],['../structvg_1_1subcommand_1_1OptionGroup.html#a92247c70c100214bf37819ea25e53437',1,'vg::subcommand::OptionGroup::add_range(const std::string &name, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})']]],
- ['add_5freachability_5fedges_8017',['add_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#a2bf6b811ae4c3f0c993d3ac4a11359f0',1,'vg::MultipathAlignmentGraph']]],
- ['add_5freference_5ftranscripts_8018',['add_reference_transcripts',['../classvg_1_1Transcriptome.html#aa2cc47e532c6a0ce46fc30e8f9edf473',1,'vg::Transcriptome']]],
- ['add_5fseed_5fto_5fchain_5fproblem_8019',['add_seed_to_chain_problem',['../classvg_1_1SnarlDistanceIndexClusterer.html#a9a95c48ea0d0de320803712285aaf6f0',1,'vg::SnarlDistanceIndexClusterer']]],
- ['add_5fsnarl_8020',['add_snarl',['../classvg_1_1SnarlManager.html#ad41eeea8a375f91349a475a1782c3160',1,'vg::SnarlManager']]],
- ['add_5fsnarl_5fdistances_8021',['add_snarl_distances',['../classvg_1_1ZipCodeForest.html#aa9a5fa1b979958b9785310fddab5f01e',1,'vg::ZipCodeForest']]],
- ['add_5fsnarl_5fto_5fchain_5fproblem_8022',['add_snarl_to_chain_problem',['../classvg_1_1SnarlDistanceIndexClusterer.html#ac22dd38425e040559e64b1e11ad1d704',1,'vg::SnarlDistanceIndexClusterer']]],
- ['add_5fsplice_5fjunction_5fedges_8023',['add_splice_junction_edges',['../classvg_1_1Transcriptome.html#afdb0ae75032057859ad882400e6c16e5',1,'vg::Transcriptome::add_splice_junction_edges(const list< EditedTranscriptPath > &edited_transcript_paths)'],['../classvg_1_1Transcriptome.html#af44d2af3eb3181b21f767f2953f4901f',1,'vg::Transcriptome::add_splice_junction_edges(const list< CompletedTranscriptPath > &completed_transcript_paths)'],['../classvg_1_1Transcriptome.html#a9be2d779faebdb40a8048ddc9727c6fb',1,'vg::Transcriptome::add_splice_junction_edges(const vector< CompletedTranscriptPath > &completed_transcript_paths)']]],
- ['add_5fstar_5ftraversals_8024',['add_star_traversals',['../classvg_1_1Deconstructor.html#aec0dffcba5b114c3297d2a494fb26f63',1,'vg::Deconstructor']]],
- ['add_5fstart_8025',['add_start',['../classvg_1_1multipath__alignment__t.html#a793ba830eaa6fd21ec7af7c7fc12cfed',1,'vg::multipath_alignment_t']]],
- ['add_5fstart_5fend_5fmarkers_8026',['add_start_end_markers',['../classvg_1_1VG.html#a91eaa395f197ca65f38c6139bc57d161',1,'vg::VG']]],
- ['add_5fsubpath_8027',['add_subpath',['../classvg_1_1multipath__alignment__t.html#ad313d9942fcd375b7b073fa2d5276fe7',1,'vg::multipath_alignment_t']]],
- ['add_5fsubpaths_5fto_5fsubgraph_8028',['add_subpaths_to_subgraph',['../namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c',1,'vg::algorithms']]],
- ['add_5fthread_5fedges_5fto_5fset_8029',['add_thread_edges_to_set',['../namespacevg.html#afe2d6096dfe672a486e44df018c713c2',1,'vg']]],
- ['add_5fthread_5fnodes_5fto_5fset_8030',['add_thread_nodes_to_set',['../namespacevg.html#a2adfa9e81b2553fefdd5e1d6b24c7a77',1,'vg']]],
- ['add_5ftranscripts_5fto_5fgbwt_8031',['add_transcripts_to_gbwt',['../classvg_1_1Transcriptome.html#ab7fbe9d1f6688cc06381ff863a345dc4',1,'vg::Transcriptome']]],
- ['add_5ftraversals_8032',['add_traversals',['../classvg_1_1ExhaustiveTraversalFinder.html#a4d93c5f43e4be897874b2468c026c0ca',1,'vg::ExhaustiveTraversalFinder']]],
- ['add_5funary_5fchild_8033',['add_unary_child',['../classvg_1_1NetGraph.html#a3780b053c5632c4425b7057d34bffe3a',1,'vg::NetGraph']]],
- ['add_5fvalue_8034',['add_value',['../structvg_1_1varint__vector__t.html#a30b862ab93cd6934985fc61abb14df6f',1,'vg::varint_vector_t']]],
- ['add_5fvariant_8035',['add_variant',['../classvg_1_1VCFOutputCaller.html#a2cc880b6121547ff0cdd5ac9a7b1b505',1,'vg::VCFOutputCaller']]],
- ['add_5fvariants_8036',['add_variants',['../classvg_1_1VariantAdder.html#a4cf25deb4e0e2270c76e2fcd0f3dbf99',1,'vg::VariantAdder']]],
- ['addarbitrarytelomerepair_8037',['addArbitraryTelomerePair',['../namespacevg.html#a948a49f6716e35c8da05e84497dc01e4',1,'vg']]],
- ['adjacent_8038',['adjacent',['../classvg_1_1VG.html#ab213a64c6240d08603530982c0b75047',1,'vg::VG']]],
- ['adjacent_5fmappings_8039',['adjacent_mappings',['../namespacevg.html#a92de94b4571057762bb3152de1376e51',1,'vg']]],
- ['adjacent_5fpositions_8040',['adjacent_positions',['../classvg_1_1Mapper.html#a3e58033862961bc28c3db2ba7b3d44df',1,'vg::Mapper']]],
- ['adjust_5fdiagonal_5frange_8041',['adjust_diagonal_range',['../classvg_1_1WFATree.html#a87ef6db73ce334779745d1a7df7e5229',1,'vg::WFATree']]],
- ['adjustment_8042',['adjustment',['../namespacehaplotypes__defaults.html#a3cd701bda653c12395917bd45c3548ba',1,'haplotypes_defaults']]],
- ['advance_8043',['advance',['../structvg_1_1PathBranch.html#a45275291566be41d4262c59078ad99bb',1,'vg::PathBranch::advance()'],['../classvg_1_1NGSSimulator.html#af52087c09b80030eb5e28da070d68fc6',1,'vg::NGSSimulator::advance()'],['../classvg_1_1io_1_1MessageIterator.html#ab4ccacd8648e7517083bfccc4676ba9a',1,'vg::io::MessageIterator::advance()'],['../classvg_1_1io_1_1ProtobufIterator.html#a300d8f5292f866bd4709c14615cdf9e0',1,'vg::io::ProtobufIterator::advance()'],['../namespacevg.html#ace5160301eaf4ef84a5e8b77bce94a7e',1,'vg::advance()']]],
- ['advance_5fby_5fdistance_8044',['advance_by_distance',['../classvg_1_1NGSSimulator.html#a3eed6eb9096bd857aba3fa6436cc9358',1,'vg::NGSSimulator']]],
- ['advance_5fon_5fgraph_8045',['advance_on_graph',['../classvg_1_1NGSSimulator.html#acadca14bcc46a1a9489227cea12d2992',1,'vg::NGSSimulator']]],
- ['advance_5fon_5fgraph_5fby_5fdistance_8046',['advance_on_graph_by_distance',['../classvg_1_1NGSSimulator.html#aba35f36f705e591b1aecebe1a0dd1c5d',1,'vg::NGSSimulator']]],
- ['advance_5fon_5fpath_8047',['advance_on_path',['../classvg_1_1NGSSimulator.html#ae1830648142d4eef8c91a439be97367f',1,'vg::NGSSimulator']]],
- ['advance_5fon_5fpath_5fby_5fdistance_8048',['advance_on_path_by_distance',['../classvg_1_1NGSSimulator.html#ab3b4e064f4b0ed000fd917d1a70cb1e7',1,'vg::NGSSimulator']]],
- ['advance_5fsplit_8049',['advance_split',['../namespacevg.html#a0df0c35a951519aa4a74bf098a253516',1,'vg']]],
- ['affinity_8050',['Affinity',['../structvg_1_1Genotyper_1_1Affinity.html#a3a8fa26d3f84c1214b1df151346a70a0',1,'vg::Genotyper::Affinity::Affinity()=default'],['../structvg_1_1Genotyper_1_1Affinity.html#a656eb6bfb6f19acffa2a492964b1047e',1,'vg::Genotyper::Affinity::Affinity(double affinity, bool is_reverse)']]],
- ['agglomerate_8051',['agglomerate',['../classvg_1_1MultipathMapper.html#af4abb58766f7ac58e418406e0e6398e2',1,'vg::MultipathMapper']]],
- ['agglomerate_5falignment_5fpairs_8052',['agglomerate_alignment_pairs',['../classvg_1_1MultipathMapper.html#aac93091ff558b107c4d6b83852a07c81',1,'vg::MultipathMapper']]],
- ['agglomerate_5falignments_8053',['agglomerate_alignments',['../classvg_1_1MultipathMapper.html#a696ef2325572ce7233d0ecb02ee615d4',1,'vg::MultipathMapper']]],
- ['agglomeration_5fwindow_5fcount_8054',['agglomeration_window_count',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a21dd6ccbbc1c96cc307dd9b825b00f12',1,'vg::MinimizerMapper::Minimizer']]],
- ['aliasgraph_8055',['AliasGraph',['../classvg_1_1AliasGraph.html#ad18207f2d96c67fcc93282ed4c9416a2',1,'vg::AliasGraph']]],
- ['align_8056',['align',['../classvg_1_1BaseAligner.html#a5b0ee67e18697f65aab62b40c2eb925a',1,'vg::BaseAligner::align()'],['../classvg_1_1Aligner.html#a0e2376f882d3164e798f2bb0d7da4359',1,'vg::Aligner::align(Alignment &alignment, const HandleGraph &g, bool traceback_aln) const'],['../classvg_1_1Aligner.html#a735b995cc89b1d526a21293b187d44d8',1,'vg::Aligner::align(Alignment &alignment, const HandleGraph &g, const std::vector< handle_t > &topological_order) const'],['../classvg_1_1QualAdjAligner.html#a46684d481ad89ddf49b98e952388c9b8',1,'vg::QualAdjAligner::align()'],['../classvg_1_1BandedGlobalAligner.html#afbd0f828e44ba486479b7bfd457d7dc5',1,'vg::BandedGlobalAligner::align()'],['../classvg_1_1DeletionAligner.html#a0c94449e8b123e0addf0d3dbc0409774',1,'vg::DeletionAligner::align()'],['../classvg_1_1DozeuInterface.html#a3b2d827b7cf43451065a2e2369895aff',1,'vg::DozeuInterface::align(Alignment &alignment, const HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length)'],['../classvg_1_1DozeuInterface.html#aa901ac96f18c5f60cbe114087aada362',1,'vg::DozeuInterface::align(Alignment &alignment, const HandleGraph &graph, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length)'],['../classvg_1_1Mapper.html#a690d9e6f314d4b010df7e8f74f5cb9b1',1,'vg::Mapper::align(const string &seq, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false)'],['../classvg_1_1Mapper.html#a32d5ed544ec9d752b34ad1848b729078',1,'vg::Mapper::align(const Alignment &read, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false)'],['../classvg_1_1MultipathAlignmentGraph.html#a0249c6ebb9691c114fe801f566bf964c',1,'vg::MultipathAlignmentGraph::align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, bool align_in_reverse=false, uint64_t max_band_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1MultipathAlignmentGraph.html#a83adb80ffc74d2709c498820216709f9',1,'vg::MultipathAlignmentGraph::align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, const function< size_t(const Alignment &, const HandleGraph &)> &band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, bool align_in_reverse=false, uint64_t max_band_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1SSWAligner.html#adc9985aac608bfb4819cd7436b969b62',1,'vg::SSWAligner::align()'],['../classvg_1_1VG.html#ac17b237e99636d20e12e4c1b94f9110b',1,'vg::VG::align(const string &sequence, const Aligner *aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a09fa1d70c31c354915773e59a1a9b55c',1,'vg::VG::align(const Alignment &alignment, const Aligner *aligner, const vector< MaximalExactMatch > &mems, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#ae6b16848db51add920b025829e2a5d55',1,'vg::VG::align(const Alignment &alignment, const Aligner *aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a3d4e6f3f52479b59a73b04c58945277b',1,'vg::VG::align(const Alignment &alignment, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#af81a72bb91912cabbec795e17c311dc9',1,'vg::VG::align(const string &sequence, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#ac24d1defbcca2158cda5fbd272fadae0',1,'vg::VG::align(const Alignment &alignment, const Aligner *aligner, const QualAdjAligner *qual_adj_aligner, const vector< MaximalExactMatch > &mems, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)']]],
- ['align_5fbanded_8057',['align_banded',['../classvg_1_1Mapper.html#ad09b7612066e797594b98151fab355cc',1,'vg::Mapper']]],
- ['align_5fcluster_8058',['align_cluster',['../classvg_1_1Mapper.html#ab10346b736664fd152f0651448b7aea1',1,'vg::Mapper']]],
- ['align_5fdownward_8059',['align_downward',['../classvg_1_1DozeuInterface.html#a907ed564c2ed19ecaf7ee880b8a1a13c',1,'vg::DozeuInterface']]],
- ['align_5fglobal_5fbanded_8060',['align_global_banded',['../classvg_1_1GSSWAligner.html#a4ae60e4ac2c961f8f63f51b1d696a485',1,'vg::GSSWAligner::align_global_banded()'],['../classvg_1_1Aligner.html#a8984447f565f2c7b870175b90178461b',1,'vg::Aligner::align_global_banded()'],['../classvg_1_1QualAdjAligner.html#ad4d16c6a39f32dc93854f21d0a7d56e2',1,'vg::QualAdjAligner::align_global_banded()']]],
- ['align_5fglobal_5fbanded_5fmulti_8061',['align_global_banded_multi',['../classvg_1_1GSSWAligner.html#a5af41c52f81a9373c608bef49ea57e94',1,'vg::GSSWAligner::align_global_banded_multi()'],['../classvg_1_1Aligner.html#a4b2637f4e841012103cf77fa09ef318f',1,'vg::Aligner::align_global_banded_multi()'],['../classvg_1_1QualAdjAligner.html#addfd42ba76bc39c040b9028dd3995742',1,'vg::QualAdjAligner::align_global_banded_multi()']]],
- ['align_5finternal_8062',['align_internal',['../classvg_1_1Aligner.html#a9e1056e34d9b67a80b4268d6408a7e7c',1,'vg::Aligner::align_internal()'],['../classvg_1_1QualAdjAligner.html#a87cc90a9c2f1107546b483fd31f57518',1,'vg::QualAdjAligner::align_internal()']]],
- ['align_5fmaybe_5fflip_8063',['align_maybe_flip',['../classvg_1_1Mapper.html#aa6bbfabc25b809bde5d2f032eb8ec79f',1,'vg::Mapper::align_maybe_flip(const Alignment &base, HandleGraph &graph, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false)'],['../classvg_1_1Mapper.html#a4816c32c8427a964a06f945833501cd7',1,'vg::Mapper::align_maybe_flip(const Alignment &base, HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false)']]],
- ['align_5fmem_5fmulti_8064',['align_mem_multi',['../classvg_1_1Mapper.html#ab4dd1cdaeb9868d9c9f4776faaf11399',1,'vg::Mapper']]],
- ['align_5fmulti_8065',['align_multi',['../classvg_1_1DeletionAligner.html#aa6b80383c0eadcdc1b028f774d9b3713',1,'vg::DeletionAligner::align_multi()'],['../classvg_1_1Mapper.html#a568ef8bf64b91b264dbcb7c8aad61774',1,'vg::Mapper::align_multi()']]],
- ['align_5fmulti_5finternal_8066',['align_multi_internal',['../classvg_1_1Mapper.html#a4890914dde25f0ea5c184b29530ec623',1,'vg::Mapper']]],
- ['align_5fns_8067',['align_ns',['../classvg_1_1VariantAdder.html#a65c5a0e7b649a97f68a4f2ab573f17d0',1,'vg::VariantAdder']]],
- ['align_5fpaired_5fmulti_8068',['align_paired_multi',['../classvg_1_1Mapper.html#abb8fa423f1591e48f33ab17090fad750',1,'vg::Mapper']]],
- ['align_5fpinned_8069',['align_pinned',['../classvg_1_1GSSWAligner.html#ae920579abfc1f15c43d0f30e3472fd65',1,'vg::GSSWAligner::align_pinned()'],['../classvg_1_1Aligner.html#a90a7be445aa931365b940fa2f26570ff',1,'vg::Aligner::align_pinned()'],['../classvg_1_1QualAdjAligner.html#af1545edb0591d1b62bb10714af6aa3bd',1,'vg::QualAdjAligner::align_pinned()'],['../classvg_1_1DozeuInterface.html#a7f8736e97ee778271e35b2d212c8603d',1,'vg::DozeuInterface::align_pinned()']]],
- ['align_5fpinned_5fmulti_8070',['align_pinned_multi',['../classvg_1_1GSSWAligner.html#a34052d83b0a62374e411ee89eead4175',1,'vg::GSSWAligner::align_pinned_multi()'],['../classvg_1_1Aligner.html#a6c2efe87216772df9cb3d3d7d0e61a26',1,'vg::Aligner::align_pinned_multi()'],['../classvg_1_1QualAdjAligner.html#a44a05f9824834133c34f487f77708383',1,'vg::QualAdjAligner::align_pinned_multi()']]],
- ['align_5fqual_5fadjusted_8071',['align_qual_adjusted',['../classvg_1_1VG.html#a5532978af43e5c4e5e4f471069e53344',1,'vg::VG::align_qual_adjusted(const Alignment &alignment, const QualAdjAligner *qual_adj_aligner, const vector< MaximalExactMatch > &mems, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a2b135ccb439e99ef1f509a11ea9ea9ce',1,'vg::VG::align_qual_adjusted(const Alignment &alignment, const QualAdjAligner *qual_adj_aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a58919649b2a29d36fd965ba453046baf',1,'vg::VG::align_qual_adjusted(const string &sequence, const QualAdjAligner *qual_adj_aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)']]],
- ['align_5fsequence_5fbetween_8072',['align_sequence_between',['../classvg_1_1MinimizerMapper.html#a3757672b798dedc0d9ce9b4306f638c4',1,'vg::MinimizerMapper']]],
- ['align_5fsequence_5fbetween_5fconsistently_8073',['align_sequence_between_consistently',['../classvg_1_1MinimizerMapper.html#a671ecec9187f2c6b3f4f7789c30ec27e',1,'vg::MinimizerMapper']]],
- ['align_5ftails_8074',['align_tails',['../classvg_1_1MultipathAlignmentGraph.html#ab340ca598eea6944dc841a9b76b73d48',1,'vg::MultipathAlignmentGraph']]],
- ['align_5fto_5fcluster_5fgraph_5fpairs_8075',['align_to_cluster_graph_pairs',['../classvg_1_1MultipathMapper.html#a6be2107ab64d6b8d2ba9eba5c8f1368a',1,'vg::MultipathMapper']]],
- ['align_5fto_5fcluster_5fgraphs_8076',['align_to_cluster_graphs',['../classvg_1_1MultipathMapper.html#a32220c809c2dc652c56c05b53dcd6567',1,'vg::MultipathMapper']]],
- ['align_5fto_5fcluster_5fgraphs_5fwith_5frescue_8077',['align_to_cluster_graphs_with_rescue',['../classvg_1_1MultipathMapper.html#af309e1b590c47f8cb6197290892c5d79',1,'vg::MultipathMapper']]],
- ['align_5fto_5fgraph_8078',['align_to_graph',['../classvg_1_1Mapper.html#a0b3adffe0ee67feab3b7486ec0d871da',1,'vg::Mapper::align_to_graph(const Alignment &aln, HandleGraph &graph, bool do_flip, bool traceback, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, bool keep_bonuses=true)'],['../classvg_1_1Mapper.html#a8cf428d786611af1fe7727e6929ef606',1,'vg::Mapper::align_to_graph(const Alignment &aln, HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool do_flip, bool traceback, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, int xdrop_alignment=0, bool keep_bonuses=true)']]],
- ['align_5fto_5fsplice_5fcandidates_8079',['align_to_splice_candidates',['../classvg_1_1MultipathMapper.html#a068b38611f12b7e4677b39d43da715f9',1,'vg::MultipathMapper']]],
- ['align_5fxdrop_8080',['align_xdrop',['../classvg_1_1GSSWAligner.html#a71da93203b17beaffac6d7e6bbfe7c0b',1,'vg::GSSWAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const =0'],['../classvg_1_1GSSWAligner.html#a2ed8a7b2fefb98c7d814449c8e884dde',1,'vg::GSSWAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const =0'],['../classvg_1_1Aligner.html#a186815e37fef05cb774d257ceca32b36',1,'vg::Aligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const'],['../classvg_1_1Aligner.html#a335087038dcf0586837abaada8d47d4b',1,'vg::Aligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const'],['../classvg_1_1QualAdjAligner.html#a2ffbaa8d9a7e2b8cf503a3bdd169e0c5',1,'vg::QualAdjAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const'],['../classvg_1_1QualAdjAligner.html#a8b497f4fb4d1e07d2bc388de3b8b604e',1,'vg::QualAdjAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const']]],
- ['aligned_5finterval_8081',['aligned_interval',['../namespacevg.html#a3b337b4ea1b6ad514093ce1b9d44b598',1,'vg']]],
- ['aligner_8082',['Aligner',['../classvg_1_1Aligner.html#a94e3d9645c15f59fe817d4dd540fecf6',1,'vg::Aligner']]],
- ['alignerclient_8083',['AlignerClient',['../classvg_1_1AlignerClient.html#a2f3a789bca074bfbbeb327e74992d9cc',1,'vg::AlignerClient']]],
- ['alignment_8084',['alignment',['../classvg_1_1Sampler.html#af69ed2ac1782e7991b0a22654846506f',1,'vg::Sampler']]],
- ['alignment_5fend_8085',['alignment_end',['../namespacevg.html#aa63fccb24f075243da0ba145eb8d6aca',1,'vg']]],
- ['alignment_5fend_5fmatches_8086',['alignment_end_matches',['../classvg_1_1ReadFilter.html#a5088cb81cac4ce8e26c6a921bf29b546',1,'vg::ReadFilter']]],
- ['alignment_5fend_5fposition_8087',['alignment_end_position',['../classvg_1_1Mapper.html#afe879219cd07b2183fbcbd09ff690a60',1,'vg::Mapper']]],
- ['alignment_5fends_8088',['alignment_ends',['../namespacevg.html#acdc3ca4569facd77e26c78ba583e4f0a',1,'vg']]],
- ['alignment_5ffrom_5flength_8089',['alignment_from_length',['../namespacevg.html#ae4defc9906e81731eab06f8acaa28369',1,'vg']]],
- ['alignment_5ffrom_5fpath_8090',['alignment_from_path',['../namespacevg.html#abcf3c5c3332d721a86740ef23fb9e6e2',1,'vg']]],
- ['alignment_5fis_5fvalid_8091',['alignment_is_valid',['../namespacevg.html#aa15ba62ae06958a1e792554996b5ee62',1,'vg']]],
- ['alignment_5fmiddle_8092',['alignment_middle',['../namespacevg.html#a15b82cc5c99cc3e8f78229ac971ec9c3',1,'vg']]],
- ['alignment_5foverhang_8093',['alignment_overhang',['../classvg_1_1ReadFilter.html#ab655011da419f60374d9238c0c21312b',1,'vg::ReadFilter']]],
- ['alignment_5fpair_8094',['alignment_pair',['../classvg_1_1Sampler.html#aecbd1aa581c396a85ab850dab54b5cd1',1,'vg::Sampler']]],
- ['alignment_5fpath_5foffsets_8095',['alignment_path_offsets',['../namespacevg_1_1algorithms.html#aead0aa069554bbc1a3fcce05ca4d1127',1,'vg::algorithms']]],
- ['alignment_5fqual_5fscore_8096',['alignment_qual_score',['../classvg_1_1Genotyper.html#a76bba1da02c9a75895896efd5b5e3641',1,'vg::Genotyper']]],
- ['alignment_5fquality_5fchar_5fto_5fshort_8097',['alignment_quality_char_to_short',['../namespacevg_1_1io.html#a982211439438e0ef8a8fd7c7e54bddc1',1,'vg::io']]],
- ['alignment_5fquality_5fper_5fnode_8098',['alignment_quality_per_node',['../namespacevg.html#a2a4413a5d745c8fdc6339efdcd13310c',1,'vg']]],
- ['alignment_5fquality_5fshort_5fto_5fchar_8099',['alignment_quality_short_to_char',['../namespacevg_1_1io.html#a7bc5a85334e06bd81e308c0f1fc9e192',1,'vg::io']]],
- ['alignment_5frefpos_5fto_5fpath_5foffsets_8100',['alignment_refpos_to_path_offsets',['../namespacevg.html#a3ad13bf14c3488a2d7a86931831ce25d',1,'vg']]],
- ['alignment_5fscore_8101',['alignment_score',['../structvg_1_1WFAPoint.html#a3cba5c83c18ec596a547ee9dfdbe1ca8',1,'vg::WFAPoint::alignment_score(const Aligner &aligner) const'],['../structvg_1_1WFAPoint.html#a550d6300508d7739b9e2549ed9475e67',1,'vg::WFAPoint::alignment_score(const Aligner &aligner, uint32_t final_insertion) const']]],
- ['alignment_5fscore_5fpartition_5ffunction_8102',['alignment_score_partition_function',['../classvg_1_1GSSWAligner.html#a610e81a719f399a5018bd722a6affad5',1,'vg::GSSWAligner']]],
- ['alignment_5fseq_8103',['alignment_seq',['../classvg_1_1Sampler.html#a514eade400df496e68c96b3ff321cb78',1,'vg::Sampler']]],
- ['alignment_5fset_5fdistance_5fto_5fcorrect_8104',['alignment_set_distance_to_correct',['../namespacevg.html#a6c45c724ede7f4892b24ad654d68fbef',1,'vg::alignment_set_distance_to_correct(Alignment &aln, const Alignment &base, const unordered_map< string, string > *translation)'],['../namespacevg.html#ab7c6a6b96f1c4c2ca04b0b6df8f384b3',1,'vg::alignment_set_distance_to_correct(Alignment &aln, const map< string, vector< pair< size_t, bool > > > &base_offsets, const unordered_map< string, string > *translation)'],['../namespacevg.html#a6c59e7d46046fad0d349a3c747ffd6b3',1,'vg::alignment_set_distance_to_correct(Alignment &aln, const map< string, vector< pair< size_t, bool >>> &base_offsets, const unordered_map< string, string > *translation=nullptr)']]],
- ['alignment_5fstart_8105',['alignment_start',['../namespacevg.html#ab7f897cb4a7bbbd40edcb938cdbd4e7c',1,'vg']]],
- ['alignment_5fto_5fa_5fhot_8106',['alignment_to_a_hot',['../classVectorizer.html#a73fd20a41c037c7dadd220b7a75306b9',1,'Vectorizer']]],
- ['alignment_5fto_5fbam_8107',['alignment_to_bam',['../namespacevg.html#a1b59157d021eca5f39da96ca23f33f08',1,'vg::alignment_to_bam(bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max)'],['../namespacevg.html#a0d064f9483fe862fe937abc9e7474e57',1,'vg::alignment_to_bam(bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar)']]],
- ['alignment_5fto_5fbam_5finternal_8108',['alignment_to_bam_internal',['../namespacevg.html#a815420ed5a7dce52d484c346271fbd71',1,'vg']]],
- ['alignment_5fto_5fcustom_5fscore_8109',['alignment_to_custom_score',['../classVectorizer.html#a040fab89a60c48dfa8bf92b4ea347b8d',1,'Vectorizer']]],
- ['alignment_5fto_5fgaf_8110',['alignment_to_gaf',['../namespacevg_1_1io.html#ac7caf6e3e258fda58ef1bd8565074f4a',1,'vg::io::alignment_to_gaf(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const Alignment &aln, const handlegraph::NamedNodeBackTranslation *translate_through, bool cs_cigar, bool base_quals, bool frag_links)'],['../namespacevg_1_1io.html#a711294fa859b37aba71867a0dd9a035a',1,'vg::io::alignment_to_gaf(const HandleGraph &graph, const Alignment &aln, const handlegraph::NamedNodeBackTranslation *translate_through, bool cs_cigar, bool base_quals, bool frag_links)']]],
- ['alignment_5fto_5fgraph_8111',['alignment_to_graph',['../classvg_1_1Sampler.html#a544836c189c15b5a4c551220047c2d62',1,'vg::Sampler']]],
- ['alignment_5fto_5fidentity_5fhot_8112',['alignment_to_identity_hot',['../classVectorizer.html#ae2bb1c5a37fa7ead081e73db8f999b4d',1,'Vectorizer']]],
- ['alignment_5fto_5flength_8113',['alignment_to_length',['../namespacevg.html#a38cb960f8c643934d65c03f0cc85442c',1,'vg']]],
- ['alignment_5fto_5fonehot_8114',['alignment_to_onehot',['../classVectorizer.html#adb25591f400faebb90a58a19a7e16873',1,'Vectorizer']]],
- ['alignment_5fto_5fpath_8115',['alignment_to_path',['../classvg_1_1Sampler.html#af0d3a16810406204c49e02354d815313',1,'vg::Sampler']]],
- ['alignment_5fto_5fsam_8116',['alignment_to_sam',['../namespacevg.html#a8d06ec05d079a41bf301a4f5f93b635b',1,'vg::alignment_to_sam(const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max)'],['../namespacevg.html#afec7360276d2d875f4368057d528572a',1,'vg::alignment_to_sam(const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar)']]],
- ['alignment_5fto_5fsam_5finternal_8117',['alignment_to_sam_internal',['../namespacevg.html#af0471358e141f59c271b38dd64854371',1,'vg']]],
- ['alignment_5fwith_5ferror_8118',['alignment_with_error',['../classvg_1_1Sampler.html#a75ac9726e906eb75d7f5ed85c7a8d0f9',1,'vg::Sampler']]],
- ['alignmentchainmodel_8119',['AlignmentChainModel',['../classvg_1_1AlignmentChainModel.html#a960347cf0986a4392544c22bbfdf7c0b',1,'vg::AlignmentChainModel']]],
- ['alignmentchainmodelvertex_8120',['AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html#a060f439601e7445f95e2bbd6925ddc6b',1,'vg::AlignmentChainModelVertex::AlignmentChainModelVertex(void)=default'],['../classvg_1_1AlignmentChainModelVertex.html#a620d3e10aa7398d73985de1c1fd8adfa',1,'vg::AlignmentChainModelVertex::AlignmentChainModelVertex(const AlignmentChainModelVertex &)=default'],['../classvg_1_1AlignmentChainModelVertex.html#a36dea81c272702fa5977067f62c54777',1,'vg::AlignmentChainModelVertex::AlignmentChainModelVertex(AlignmentChainModelVertex &&)=default']]],
- ['alignments_5fconsistent_8121',['alignments_consistent',['../classvg_1_1Mapper.html#a5edacb959a00dcee901b42948ebf9e75',1,'vg::Mapper']]],
- ['all_5fchildren_5ftrivial_8122',['all_children_trivial',['../classvg_1_1SnarlManager.html#a732645de996b9f56608d395ea4949bd9',1,'vg::SnarlManager']]],
- ['all_5ffinished_8123',['all_finished',['../classvg_1_1IndexRegistry.html#ac81872b4bf8d7917b284f609a4127023',1,'vg::IndexRegistry::all_finished(const vector< const IndexFile * > &inputs) const'],['../classvg_1_1IndexRegistry.html#a35e5dcdc072c53f562442686dff9977a',1,'vg::IndexRegistry::all_finished(const IndexGroup &inputs) const']]],
- ['all_5fgroups_8124',['all_groups',['../classvg_1_1SparseUnionFind.html#a8fe069d0444b1dae9d71e5943ebded44',1,'vg::SparseUnionFind']]],
- ['all_5fmapping_5fqualities_5fexact_8125',['all_mapping_qualities_exact',['../classvg_1_1GSSWAligner.html#ab9f99a04dd14ab7c3cc43662b6b73293',1,'vg::GSSWAligner']]],
- ['all_5fpath_5fnames_8126',['all_path_names',['../classvg_1_1Paths.html#a246f21fbf08d613e3ce8122705044cbe',1,'vg::Paths']]],
- ['allambiguouston_8127',['allAmbiguousToN',['../namespacevg.html#afb243c35d883121f8645815571b7a55f',1,'vg']]],
- ['allatgc_8128',['allATGC',['../namespacevg.html#a7a1786f1e7e453c4b76b319ba101782d',1,'vg']]],
- ['allatgcn_8129',['allATGCN',['../namespacevg.html#ae24bea33b666a03a0065a10a60d64e9d',1,'vg']]],
- ['allele_8130',['allele',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a8e1b3233ad9520a651434b00de016d7f',1,'haplo::linear_haplo_structure::SNVvector']]],
- ['allele_5fambiguity_5flog_5fprobs_8131',['allele_ambiguity_log_probs',['../classvg_1_1Genotyper.html#aa46523cd1493686b28210136d9baf713',1,'vg::Genotyper']]],
- ['allele_5fto_5fstring_8132',['allele_to_string',['../namespacevg.html#a3b46a0183527dc1713f3ab30ef85b185',1,'vg']]],
- ['allowsaliasing_8133',['AllowsAliasing',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ac30901e7d779acdfef65858e98baaf3f',1,'vg::io::BlockedGzipOutputStream']]],
- ['also_5fmerge_5fgroup_8134',['also_merge_group',['../classvg_1_1Funnel.html#abc00e34c78f024874b44ebf90443cc4e',1,'vg::Funnel::also_merge_group(Iterator prev_stage_items_begin, Iterator prev_stage_items_end)'],['../classvg_1_1Funnel.html#a68135544a4504edde8de7df48557d4ba',1,'vg::Funnel::also_merge_group(size_t earlier_stage_lookback, Iterator earlier_stage_items_begin, Iterator earlier_stage_items_end)']]],
- ['also_5frelevant_8135',['also_relevant',['../classvg_1_1Funnel.html#a0642f2a1faae54dc12e98df452d4be65',1,'vg::Funnel']]],
- ['alt_5fproposal_5fsample_8136',['alt_proposal_sample',['../classvg_1_1MCMCGenotyper.html#a26dfe5be824755df69d533e98304f5be',1,'vg::MCMCGenotyper']]],
- ['alttracebackstack_8137',['AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#add2f3215214bfdd33cd8ccc633275827',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['anchor_8138',['Anchor',['../classvg_1_1algorithms_1_1Anchor.html#a61a4dd75e3aec703eeb6e06ab24af934',1,'vg::algorithms::Anchor::Anchor(size_t read_start, const pos_t &graph_start, size_t length, size_t margin_before, size_t margin_after, int score, size_t seed_number=std::numeric_limits< size_t >::max(), ZipCode *hint=nullptr, size_t hint_start=0, bool skippable=false)'],['../classvg_1_1algorithms_1_1Anchor.html#a2ddebc7f2076e9f6e8e00f37163af28c',1,'vg::algorithms::Anchor::Anchor(const Anchor &first, const Anchor &last, size_t extra_margin_before, size_t extra_margin_after, int score)'],['../classvg_1_1algorithms_1_1Anchor.html#a590e37aed7b087657a9ad3cae8a6fbbe',1,'vg::algorithms::Anchor::Anchor()=default'],['../classvg_1_1algorithms_1_1Anchor.html#abe177a3866f3369347049d235c7bad3a',1,'vg::algorithms::Anchor::Anchor(const Anchor &other)=default'],['../classvg_1_1algorithms_1_1Anchor.html#a1e837be4b5167a4d27841886a6913701',1,'vg::algorithms::Anchor::Anchor(Anchor &&other)=default']]],
- ['anchored_5ffilter_8139',['anchored_filter',['../classvg_1_1Filter.html#a7e797bbf731c8120cf2df43e4355963a',1,'vg::Filter']]],
- ['annotate_5fmapped_5falignment_8140',['annotate_mapped_alignment',['../classvg_1_1Funnel.html#adc044b59bc97ac7e6536068fa9bdb5d2',1,'vg::Funnel']]],
- ['annotate_5fwith_5finitial_5fpath_5fpositions_8141',['annotate_with_initial_path_positions',['../namespacevg_1_1algorithms.html#a3c1bbf062eb429066c7b46da24704cdf',1,'vg::algorithms::annotate_with_initial_path_positions(const PathPositionHandleGraph &graph, Alignment &aln, int64_t search_limit, const std::function< bool(const path_handle_t &)> *path_filter)'],['../namespacevg_1_1algorithms.html#a29c8bb498d4cab7c964783dbf98dae28',1,'vg::algorithms::annotate_with_initial_path_positions(const PathPositionHandleGraph &graph, vector< Alignment > &alns, int64_t search_limit, const std::function< bool(const path_handle_t &)> *path_filter)']]],
- ['annotate_5fwith_5fminimizer_5fstatistics_8142',['annotate_with_minimizer_statistics',['../classvg_1_1MinimizerMapper.html#a2da9c99842bd5e1fac26b7f6fc358fcc',1,'vg::MinimizerMapper']]],
- ['annotate_5fwith_5fnode_5fpath_5fpositions_8143',['annotate_with_node_path_positions',['../namespacevg_1_1algorithms.html#ad2151b93596855953805b98d78ac83c6',1,'vg::algorithms']]],
- ['annotate_5fwith_5fpath_5fpositions_8144',['annotate_with_path_positions',['../classvg_1_1AbstractReadSampler.html#a29d7f66f17c49eeae229d00ea31ed252',1,'vg::AbstractReadSampler::annotate_with_path_positions()'],['../namespacevg_1_1algorithms.html#a66e67738fef35591e953849387e94d58',1,'vg::algorithms::annotate_with_path_positions()']]],
- ['append_8145',['append',['../structvg_1_1WFAAlignment.html#a13fc5825782e95adb9e985719f91cc4a',1,'vg::WFAAlignment::append()'],['../classvg_1_1SnarlState.html#a6f40f3779030f0e665d3cdc77bbaeafd',1,'vg::SnarlState::append()'],['../classvg_1_1Paths.html#a0c8569eae84b41c65291b76f0ae4da6c',1,'vg::Paths::append(const Paths &paths, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1Paths.html#a4b25b15a87b59847a3ef5384aaed856c',1,'vg::Paths::append(const Graph &g, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1VG.html#a5272032c1e57d839176fc8e39bd87e18',1,'vg::VG::append()']]],
- ['append_5fcigar_5foperation_8146',['append_cigar_operation',['../namespacevg.html#a083d5edb5192697a269a3e5b8815bccd',1,'vg']]],
- ['append_5fhandle_5fgraph_8147',['append_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a89dc4417bd6be84b3b293b20c9254011',1,'handlegraph::algorithms']]],
- ['append_5fhaplotype_8148',['append_haplotype',['../classvg_1_1GenomeState.html#aa9f6862f286a2f28ebeb75251e1fe059',1,'vg::GenomeState']]],
- ['append_5fleft_8149',['append_left',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a6eae6ee85866e8a90efd0d7d7f5de0be',1,'vg::PhasedGenome::Haplotype']]],
- ['append_5fmapping_8150',['append_mapping',['../classvg_1_1Paths.html#aec7ad289d23cf879bdefb682dc464313',1,'vg::Paths::append_mapping(const string &name, const mapping_t &m, bool warn_on_duplicates=false)'],['../classvg_1_1Paths.html#a490ae73c613867d5621e17b6ff6635dd',1,'vg::Paths::append_mapping(const string &name, id_t id, bool is_reverse, size_t length, size_t rank=0, bool warn_on_duplicates=false)']]],
- ['append_5fmapping_5fsequence_8151',['append_mapping_sequence',['../namespacevg_1_1algorithms.html#ae5ff6fdbf4ef393faf59f22365c46bbb',1,'vg::algorithms']]],
- ['append_5fmultipath_5falignment_8152',['append_multipath_alignment',['../namespacevg.html#ac93525ce8a55a9394025efe575468488',1,'vg']]],
- ['append_5fnode_8153',['append_node',['../structvg_1_1WFANode.html#a078c2ef3a3c95bb25c532b7313c93494',1,'vg::WFANode']]],
- ['append_5fpath_8154',['append_path',['../namespacevg.html#a75a663b07489d2aba3f800943eeb0eaf',1,'vg']]],
- ['append_5fpath_5fhandle_5fgraph_8155',['append_path_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a19e43312515b3c752d20760788c97c6d',1,'handlegraph::algorithms']]],
- ['append_5fright_8156',['append_right',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a8336638c37c43db1db857b380da94ab3',1,'vg::PhasedGenome::Haplotype']]],
- ['append_5fstep_8157',['append_step',['../classvg_1_1VG.html#ad11c8a716733fce2aa9dab94b42286bd',1,'vg::VG::append_step()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a83a4a14a629cde03d33e4eb3f6bb192d',1,'handlegraph::MutablePathHandleGraph::append_step()']]],
- ['apply_8158',['apply',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a8ce78918d24994e63851dacd6e0c0913',1,'vg::subcommand::BaseArgSpec::apply()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#ac03349ad6512375cc1de928c49b50f51',1,'vg::subcommand::ValueArgSpec::apply()'],['../structvg_1_1subcommand_1_1OptionGroup.html#adfbf39aed983c832777a5194d7623dbc',1,'vg::subcommand::OptionGroup::apply()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a745503da4f277b0347d56d3cb2979455',1,'vg::subcommand::GroupedOptionGroup::apply()'],['../structvg_1_1subcommand_1_1Preset.html#ada0abd10e8ffc45f18c3ea54991c5061',1,'vg::subcommand::Preset::apply()']]],
- ['apply_5faligned_5fbase_8159',['apply_aligned_base',['../classvg_1_1NGSSimulator.html#a83b83821e465fb0eb28bfa6a6a53685e',1,'vg::NGSSimulator']]],
- ['apply_5fdeletion_8160',['apply_deletion',['../classvg_1_1NGSSimulator.html#ac9767a14ddba8d462c562c8d3b60af6c',1,'vg::NGSSimulator']]],
- ['apply_5fedit_8161',['apply_edit',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a9238af0b01ae60e19f699cf715c1b2b7',1,'vg::GraphSynchronizer::Lock::apply_edit(const Path &path, set< NodeSide > &dangling, size_t max_node_size=1024)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#ac45f1f724164cda30c1f792423d6e05c',1,'vg::GraphSynchronizer::Lock::apply_edit(const Path &path, size_t max_node_size=1024)']]],
- ['apply_5ffull_5flength_5fedit_8162',['apply_full_length_edit',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a5d529df21455c13e5c1644ad91c4f55e',1,'vg::GraphSynchronizer::Lock']]],
- ['apply_5fhaplotype_5fconsistency_5fscores_8163',['apply_haplotype_consistency_scores',['../classvg_1_1BaseMapper.html#a778c534cca5d7580584bba4131b65adc',1,'vg::BaseMapper']]],
- ['apply_5finsertion_8164',['apply_insertion',['../classvg_1_1NGSSimulator.html#abd3a16dc107228d0e3678afff66314f0',1,'vg::NGSSimulator']]],
- ['apply_5fmask_5fsequences_8165',['apply_mask_sequences',['../classvg_1_1Masker.html#a9803bfb97813ff5ae381957e56ed4f0c',1,'vg::Masker']]],
- ['apply_5fmax_5freads_8166',['apply_max_reads',['../structvg_1_1Counts.html#a63cb45fa4645b31ad9e0a033cbd5de6c',1,'vg::Counts']]],
- ['apply_5fmin_5fbp_5fedge_5foverride_8167',['apply_min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a2a9c63741c55418a64b72fb409a467f6',1,'vg::TraversalSupportFinder']]],
- ['apply_5fn_5fmask_8168',['apply_N_mask',['../classvg_1_1NGSSimulator.html#aa81005880d4667e04ff07de3a0881322',1,'vg::NGSSimulator']]],
- ['apply_5fordering_8169',['apply_ordering',['../classvg_1_1VG.html#af87ad4202f541fd560d67badcde09610',1,'vg::VG::apply_ordering()'],['../classhandlegraph_1_1MutableHandleGraph.html#a588935d58708b33bc66014b254393940',1,'handlegraph::MutableHandleGraph::apply_ordering()']]],
- ['apply_5forientation_8170',['apply_orientation',['../classvg_1_1VG.html#ab5ee06ac168f037f2cff3b332079b49c',1,'vg::VG::apply_orientation()'],['../classhandlegraph_1_1MutableHandleGraph.html#a71433449cb13e22dc19caaf544b6d7bc',1,'handlegraph::MutableHandleGraph::apply_orientation()']]],
- ['apply_5forientations_8171',['apply_orientations',['../namespacehandlegraph_1_1algorithms.html#a81d399d76c97b214aa55a82976185ea6',1,'handlegraph::algorithms']]],
- ['apply_5ftranslation_8172',['apply_translation',['../structvg_1_1PathIndex.html#a827ae5af1330e03a23c35351d3152f03',1,'vg::PathIndex']]],
- ['apply_5ftranslations_8173',['apply_translations',['../structvg_1_1PathIndex.html#a8aeebd524dc064af4cdda9fd84de2a4a',1,'vg::PathIndex']]],
- ['approx_5falignment_5fposition_8174',['approx_alignment_position',['../classvg_1_1Mapper.html#ad7a2c554e02a60549d8c46459bed0491',1,'vg::Mapper']]],
- ['approx_5fdistance_8175',['approx_distance',['../classvg_1_1Mapper.html#a04be7bfcb3252ef33217cb0f5823d4f8',1,'vg::Mapper']]],
- ['approx_5ffragment_5flength_8176',['approx_fragment_length',['../classvg_1_1Mapper.html#a3f15631b08b10107963a5c17d21c3717',1,'vg::Mapper']]],
- ['approx_5fgbwt_5fmemory_8177',['approx_gbwt_memory',['../namespacevg.html#a745a31f5e7853868dbf903f33a986480',1,'vg']]],
- ['approx_5fgraph_5fload_5fmemory_8178',['approx_graph_load_memory',['../namespacevg.html#a0d0300b12116a047d137e134eebe2e1d',1,'vg']]],
- ['approx_5fgraph_5fmemory_8179',['approx_graph_memory',['../namespacevg.html#a3d3cceb7b721a218a1be1c948138526a',1,'vg::approx_graph_memory(const vector< string > &fasta_filenames, const vector< string > &vcf_filenames)'],['../namespacevg.html#a4a16cd88bceed4db044decd94211833d',1,'vg::approx_graph_memory(const string &fasta_filename, const string &vcf_filename)'],['../namespacevg.html#aa588389795ea8613480df1c7eeeafaf8',1,'vg::approx_graph_memory(const string &gfa_filename)']]],
- ['approx_5fnum_5fvars_8180',['approx_num_vars',['../namespacevg.html#a665fe802cdb44d2dba6052fc9063513d',1,'vg']]],
- ['approx_5fposition_8181',['approx_position',['../classvg_1_1Mapper.html#accd2bd6b8ec2db952fd79e0742f1a548',1,'vg::Mapper']]],
- ['arch_5fis_5fbig_5fendian_8182',['arch_is_big_endian',['../structvg_1_1endianness.html#a24b1cadacc768c204cfebeff0c9d33f9',1,'vg::endianness']]],
- ['are_5fconsecutive_5fnodes_5fin_5fpath_8183',['are_consecutive_nodes_in_path',['../classvg_1_1Paths.html#a9562c903db44e7328f82c30afea6c643',1,'vg::Paths']]],
- ['are_5fconsistent_8184',['are_consistent',['../classvg_1_1MultipathMapper.html#a0080de005fe755313ddd6bf3b41620b4',1,'vg::MultipathMapper']]],
- ['are_5fequivalent_8185',['are_equivalent',['../namespacehandlegraph_1_1algorithms.html#a3a3110dde9b4be48c07966ca05f07ce3',1,'handlegraph::algorithms']]],
- ['are_5fequivalent_5fwith_5fpaths_8186',['are_equivalent_with_paths',['../namespacehandlegraph_1_1algorithms.html#a47f57c2a75f2c22df467596639377d77',1,'handlegraph::algorithms']]],
- ['argspec_8187',['ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html#a78e4d05575c29900e19e72fe4854fb48',1,'vg::subcommand::ArgSpec::ArgSpec(const std::string &option, char short_option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)'],['../structvg_1_1subcommand_1_1ArgSpec.html#a5c2f438f67a728d5921ceefc4414dea1',1,'vg::subcommand::ArgSpec::ArgSpec(const std::string &option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)']]],
- ['array_5fend_8188',['array_end',['../classvg_1_1ProblemDumpExplainer.html#a7696c7a5ed73ae3a701d4aeb3b2f53b0',1,'vg::ProblemDumpExplainer']]],
- ['array_5fstart_8189',['array_start',['../classvg_1_1ProblemDumpExplainer.html#ae4c171c4c55ae76ce36d18889520f2a2',1,'vg::ProblemDumpExplainer']]],
- ['as_5fedge_5ftable_8190',['as_edge_table',['../classvg_1_1Packer.html#a8fa7e449fc6358a1d1b13c0447027acb',1,'vg::Packer']]],
- ['as_5fhandle_8191',['as_handle',['../namespacehandlegraph.html#acba8bb138abe07535c62ab95b6ab135c',1,'handlegraph::as_handle(uint64_t &value)'],['../namespacehandlegraph.html#a95e4115f2aba44e76c62fee839f384af',1,'handlegraph::as_handle(const uint64_t &value)']]],
- ['as_5finteger_8192',['as_integer',['../namespacehandlegraph.html#a2bfd349561c52c6e3d32e11ad31a1056',1,'handlegraph::as_integer(handle_t &handle)'],['../namespacehandlegraph.html#aa9b39d28e558d08900cf0659648edc66',1,'handlegraph::as_integer(const handle_t &handle)'],['../namespacehandlegraph.html#aa046efc20cdba831aee499ca693b851a',1,'handlegraph::as_integer(path_handle_t &handle)'],['../namespacehandlegraph.html#a1020b4ec56092e0413aa8deb3bd8097b',1,'handlegraph::as_integer(const path_handle_t &handle)'],['../namespacehandlegraph.html#a3af04d045bd99ae54e56ab415ca74515',1,'handlegraph::as_integer(net_handle_t &handle)'],['../namespacehandlegraph.html#a2964abbc51b220805b599c14fe5785b3',1,'handlegraph::as_integer(const net_handle_t &handle)']]],
- ['as_5fintegers_8193',['as_integers',['../namespacehandlegraph.html#a5a37d9e18dfe77f0342573269372f96d',1,'handlegraph::as_integers(step_handle_t &step_handle)'],['../namespacehandlegraph.html#aa470ea0407a5de15a2e0da4ca0ac5df8',1,'handlegraph::as_integers(const step_handle_t &step_handle)']]],
- ['as_5fnet_5fhandle_8194',['as_net_handle',['../namespacehandlegraph.html#a34b30f72d26f0ab83a3b4668cb0ba73b',1,'handlegraph::as_net_handle(uint64_t &value)'],['../namespacehandlegraph.html#a5a078e0cfd4fd4fbd0fbc5f6f6c03e7d',1,'handlegraph::as_net_handle(const uint64_t &value)']]],
- ['as_5fpath_5fhandle_8195',['as_path_handle',['../namespacehandlegraph.html#a4d0f261ff95d242a0ceeaa2f01b961c0',1,'handlegraph::as_path_handle(uint64_t &value)'],['../namespacehandlegraph.html#abdee6d57b3c2132b34aae90c7766d213',1,'handlegraph::as_path_handle(const uint64_t &value)']]],
- ['as_5fquality_5ftable_8196',['as_quality_table',['../classvg_1_1Packer.html#a4768a4ad03f393f7abdf1c6a977b8caf',1,'vg::Packer']]],
- ['as_5ftable_8197',['as_table',['../classvg_1_1Packer.html#a51f56dd9782bb7841c7b50678f8ed868',1,'vg::Packer::as_table()'],['../classvg_1_1Packers.html#afcd4807c5743b90833a8e0f351f4fc77',1,'vg::Packers::as_table()']]],
- ['assign_5fchild_5fsnarls_5fto_5ftraversals_8198',['assign_child_snarls_to_traversals',['../namespacevg.html#a1ac7d2a0833215a0628a25c8195a70ab',1,'vg']]],
- ['assign_5fconstructed_8199',['assign_constructed',['../classvg_1_1IndexFile.html#ac3bf2966b1a530956e099f225208395e',1,'vg::IndexFile']]],
- ['assign_5fnew_5fsequence_5fid_8200',['assign_new_sequence_id',['../classvg_1_1algorithms_1_1GFAParser.html#aa7d65677018149472a7924da28b6633b',1,'vg::algorithms::GFAParser']]],
- ['at_8201',['at',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a613f2b4b5f02b68f1868830e3213ffe2',1,'vg::Option< vector< Item >, Parser >::at(size_t i)'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a8e8fb7dad7fb3274f9dae3e11be2ed5c',1,'vg::Option< vector< Item >, Parser >::at(size_t i) const'],['../classvg_1_1ZipCodeCollection.html#a872b6e4393de003c61621d883cac4efb',1,'vg::ZipCodeCollection::at()']]],
- ['at_5fdead_5fend_8202',['at_dead_end',['../classvg_1_1WFATree.html#a98b3e5f4f226261068acfa268ec416ae',1,'vg::WFATree']]],
- ['at_5flast_5fnode_8203',['at_last_node',['../structvg_1_1MatchPos.html#a8a426f343756ea69a1d6ae73801d9451',1,'vg::MatchPos']]],
- ['at_5fnext_5fdeflection_8204',['at_next_deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a591b428cb1644725419966f805790fb1',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['at_5for_5fafter_8205',['at_or_after',['../classvg_1_1BitString.html#af27a8d8554102a67192bb3627a56ad77',1,'vg::BitString']]],
- ['at_5for_5fbefore_8206',['at_or_before',['../classvg_1_1BitString.html#a8f2a6515c588dc34d5f8a3b10035f891',1,'vg::BitString']]],
- ['at_5fposition_8207',['at_position',['../structvg_1_1PathIndex.html#aab1c5d586bdef0e4cdc31ed7531eee7c',1,'vg::PathIndex']]],
- ['attempt_5frescue_8208',['attempt_rescue',['../classvg_1_1MinimizerMapper.html#ad2a8850ee32bef9fd4b1a52034d5a930',1,'vg::MinimizerMapper::attempt_rescue()'],['../classvg_1_1MultipathMapper.html#a007fc06565e2f9b1aa084cc4cc60a55d',1,'vg::MultipathMapper::attempt_rescue()']]],
- ['attempt_5frescue_5ffor_5fsecondaries_8209',['attempt_rescue_for_secondaries',['../classvg_1_1MultipathMapper.html#a2d154aa0e761a99266c6eddab022a1c6',1,'vg::MultipathMapper']]],
- ['attempt_5frescue_5ffor_5fsplice_5fsegment_8210',['attempt_rescue_for_splice_segment',['../classvg_1_1MultipathMapper.html#a535c42c7052c82ddc71613cce3459b03',1,'vg::MultipathMapper']]],
- ['attempt_5funpaired_5fmultipath_5fmap_5fof_5fpair_8211',['attempt_unpaired_multipath_map_of_pair',['../classvg_1_1MultipathMapper.html#a9bdb30363cd02187fb0a1ca07ea2cb20',1,'vg::MultipathMapper']]],
- ['augment_8212',['augment',['../namespacevg.html#a3ad955989dbbd240c02052d94a9214e2',1,'vg::augment(MutablePathMutableHandleGraph *graph, const string &gam_path, const string &aln_format, vector< Translation > *out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only)'],['../namespacevg.html#a10c4a321eb33280d58a3ddaf97f52ed2',1,'vg::augment(MutablePathMutableHandleGraph *graph, vector< Path > &path_vector, const string &aln_format, vector< Translation > *out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only)']]],
- ['augment_5ffrom_5falignment_5fedits_8213',['augment_from_alignment_edits',['../structvg_1_1AugmentedGraph.html#a56ecda832a62dd3a22424bb8720a4601',1,'vg::AugmentedGraph']]],
- ['augment_5fgraph_8214',['augment_graph',['../classvg_1_1Transcriptome.html#ac4eff095379bd9ab5691704de1ddc293',1,'vg::Transcriptome']]],
- ['augment_5fimpl_8215',['augment_impl',['../namespacevg.html#a5be4fdda1799c2f6876f2ac4937da349',1,'vg']]],
- ['aux_5farray_5fto_5fstring_8216',['aux_array_to_string',['../namespacevg.html#a156dcf09705f414bd179a43f565ad354',1,'vg']]],
- ['aux_5fval_5fto_5fstring_8217',['aux_val_to_string',['../namespacevg.html#a10de011128f0da64a698f71d8c7c1cdf',1,'vg']]],
- ['available_8218',['available',['../classvg_1_1IndexRegistry.html#a8c88fde3123fced3178841fc76862a19',1,'vg::IndexRegistry']]],
- ['average_5fnode_5fquality_8219',['average_node_quality',['../classvg_1_1Packer.html#a5a5c771bdb82f53eeef987e598669566',1,'vg::Packer']]],
- ['avg_5fqual_5ffilter_8220',['avg_qual_filter',['../classvg_1_1Filter.html#a3401568683899d1ebe2bcaf971a8374e',1,'vg::Filter']]]
+ ['a_7971',['a',['../classvg_1_1uniform__real__distribution.html#aac3912d0f456993e6ae7f7bbe4d732d7',1,'vg::uniform_real_distribution::a()'],['../classvg_1_1uniform__int__distribution.html#a2ac06e4375faf1706e7d6171c7e2e14b',1,'vg::uniform_int_distribution::a()'],['../classvg_1_1truncated__normal__distribution.html#a88c472b134a2672661b45695824cd3c0',1,'vg::truncated_normal_distribution::A()']]],
+ ['a_5fstar_7972',['a_star',['../namespacevg_1_1algorithms.html#a5af5b6f1083925669832ae59d0e549e7',1,'vg::algorithms']]],
+ ['absent_7973',['absent',['../namespacehaplotypes__defaults.html#a201800ce4570c0eb29f0279035dcaf48',1,'haplotypes_defaults']]],
+ ['abstractreadsampler_7974',['AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html#add2ef81ca4c3984e851d690c695bae2d',1,'vg::AbstractReadSampler']]],
+ ['accelerate_5fmem_5fquery_7975',['accelerate_mem_query',['../classvg_1_1BaseMapper.html#a3cf076ec413d3a3bb029c46880a17759',1,'vg::BaseMapper']]],
+ ['accept_5frecord_7976',['accept_record',['../classvg_1_1VcfRecordFilter.html#a2e39d3d4cb41426f965959c30b0de2d2',1,'vg::VcfRecordFilter']]],
+ ['add_7977',['add',['../classvg_1_1Packer.html#a8a8cb2dd528dc7cc178e32e69e42212b',1,'vg::Packer']]],
+ ['add_5fallele_5fpath_5fto_5finfo_7978',['add_allele_path_to_info',['../classvg_1_1VCFOutputCaller.html#a0d1f292cf9ad7db29e0a02e5395c7f02',1,'vg::VCFOutputCaller::add_allele_path_to_info(const HandleGraph *graph, vcflib::Variant &v, int allele, const Traversal &trav, bool reversed, bool one_based) const'],['../classvg_1_1VCFOutputCaller.html#a59a286bc432e93001bc3af35b6ec2f6a',1,'vg::VCFOutputCaller::add_allele_path_to_info(vcflib::Variant &v, int allele, const SnarlTraversal &trav, bool reversed, bool one_based) const']]],
+ ['add_5falt_5fallele_7979',['add_alt_allele',['../namespacevg.html#a6391a10ec421fbb6c487f491bd978ef6',1,'vg']]],
+ ['add_5fand_5fadjust_5fpaths_7980',['add_and_adjust_paths',['../convert__main_8cpp.html#a97c9047b1f01a6c50b89cae4249dbdae',1,'convert_main.cpp']]],
+ ['add_5fannotations_7981',['add_annotations',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#af46d15924e533706d6999dcb9619d6e6',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t::add_annotations()'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#aa9c2fadd69e58abfea065ae09917ced7',1,'vg::MinimizerMapper::aligner_stats_t::add_annotations()'],['../classvg_1_1MultipathAlignmentEmitter.html#a9d0b6648ef4cfb2ffb72227891ebc7fd',1,'vg::MultipathAlignmentEmitter::add_annotations()']]],
+ ['add_5fbv_7982',['add_bv',['../classVectorizer.html#a88203fab4049c471c963135c4c52ce03',1,'Vectorizer']]],
+ ['add_5fchain_5fchild_7983',['add_chain_child',['../classvg_1_1NetGraph.html#a0fadfaf9261a911ec04b4c10f75c5b9b',1,'vg::NetGraph']]],
+ ['add_5fchild_5fto_5fchain_7984',['add_child_to_chain',['../classvg_1_1ZipCodeForest.html#ac70358ab79a7212af23bc6ebffcb43fd',1,'vg::ZipCodeForest']]],
+ ['add_5fconnecting_5fedges_5fto_5fsubgraph_7985',['add_connecting_edges_to_subgraph',['../namespacevg_1_1algorithms.html#a6347e00229560b4adb7cc7cb6332b21a',1,'vg::algorithms']]],
+ ['add_5fconnection_7986',['add_connection',['../classvg_1_1subpath__t.html#abfcffaca080591fc341c4129574c9e21',1,'vg::subpath_t']]],
+ ['add_5fcontigs_5fto_5fvcf_5fheader_7987',['add_contigs_to_vcf_header',['../classvg_1_1Deconstructor.html#a2b32d4a11d7945c680274ef7ce23cbdd',1,'vg::Deconstructor']]],
+ ['add_5fdecomposed_5ftail_5falignments_7988',['add_decomposed_tail_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a99e7522a1341bc3d5e7d0876156d0e24',1,'vg::MultipathAlignmentGraph']]],
+ ['add_5fdescendants_5fto_5fsubgraph_7989',['add_descendants_to_subgraph',['../namespacevg.html#a9e91a5d33d2da100b1173bc336ea90ff',1,'vg']]],
+ ['add_5fedge_7990',['add_edge',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a9ea6a73a76afd51e8e3faee8d76575a2',1,'vg::MEMClusterer::HitGraph::add_edge()'],['../classvg_1_1DiagramExplainer.html#ab80098946b753fd283a3241c58c629a7',1,'vg::DiagramExplainer::add_edge()'],['../classvg_1_1VG.html#a613c931c81518212917053d07e9bf8a8',1,'vg::VG::add_edge()']]],
+ ['add_5fedges_7991',['add_edges',['../classvg_1_1VG.html#a7f23cdd532ca7b8d3c0bb9cceff3d378',1,'vg::VG::add_edges(const vector< Edge > &edges)'],['../classvg_1_1VG.html#a679e39a7c1771c3ecc7204bd3b999583',1,'vg::VG::add_edges(const vector< Edge * > &edges)'],['../classvg_1_1VG.html#acb8712eefbfd373c45f54d6bac8188c6',1,'vg::VG::add_edges(const set< Edge * > &edges)']]],
+ ['add_5fedges_5fonly_7992',['add_edges_only',['../namespacevg.html#ae2303a00d9cf0d35e243dc6de7574471',1,'vg']]],
+ ['add_5fedit_7993',['add_edit',['../classvg_1_1path__mapping__t.html#a82a73553691a54453a70c4e76f35271f',1,'vg::path_mapping_t']]],
+ ['add_5fedited_5ftranscript_5fpaths_7994',['add_edited_transcript_paths',['../classvg_1_1Transcriptome.html#abfa196d9f2e46f6f72f71a80a6063c36',1,'vg::Transcriptome']]],
+ ['add_5fentry_7995',['add_entry',['../structvg_1_1subcommand_1_1Preset.html#a86195268d1480849b5286b07fa744796',1,'vg::subcommand::Preset']]],
+ ['add_5fexon_7996',['add_exon',['../classvg_1_1Transcriptome.html#a8c292f8d6d1d176e5df367a25dd70e5f',1,'vg::Transcriptome::add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos) const'],['../classvg_1_1Transcriptome.html#af764ab28d6d866807d09a4482dd96523',1,'vg::Transcriptome::add_exon(Transcript *transcript, const pair< int32_t, int32_t > &exon_pos, const bdsg::PositionOverlay &graph_path_pos_overlay) const']]],
+ ['add_5fflag_7997',['add_flag',['../structvg_1_1subcommand_1_1OptionGroup.html#a09b380a1b6511d2e22477694af202ffe',1,'vg::subcommand::OptionGroup::add_flag(const std::string &name, char short_option, bool Receiver::*dest, bool default_value, const std::string &help, const ValidatorFunction< bool > &validator=[](const bool &ignored) {})'],['../structvg_1_1subcommand_1_1OptionGroup.html#abed7849b9115a028191beaa1d96050be',1,'vg::subcommand::OptionGroup::add_flag(const std::string &name, bool Receiver::*dest, bool default_value, const std::string &help, const ValidatorFunction< bool > &validator=[](const bool &ignored) {})']]],
+ ['add_5fglobals_7998',['add_globals',['../classvg_1_1DiagramExplainer.html#a61051fae11426259dc7318dbb51c8ab6',1,'vg::DiagramExplainer']]],
+ ['add_5fgroup_7999',['add_group',['../classvg_1_1StreamIndexBase.html#ad54626f7e5eb2587d4a5d5f514c82f75',1,'vg::StreamIndexBase::add_group()'],['../classvg_1_1StreamIndex.html#a172dd150297aad85dada7ba852ec3a0c',1,'vg::StreamIndex::add_group()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a1ef2138d216deaf4efa341ae35d5f308',1,'vg::subcommand::GroupedOptionGroup::add_group()']]],
+ ['add_5fhandle_8000',['add_handle',['../classvg_1_1SubHandleGraph.html#a2ab52610b56f49a48262faafc7e510df',1,'vg::SubHandleGraph::add_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a8954a9766ec7f064c756e2bb4d9a61f1',1,'handlegraph::algorithms::SubHandleGraph::add_handle()']]],
+ ['add_5fhaplotype_8001',['add_haplotype',['../classvg_1_1PhasedGenome.html#ad36e2c71ff5b2714d1fe1bb6af075f9c',1,'vg::PhasedGenome']]],
+ ['add_5fhaplotype_5ftranscripts_8002',['add_haplotype_transcripts',['../classvg_1_1Transcriptome.html#a2d0ed7b746222e68f5224838a70c39f4',1,'vg::Transcriptome']]],
+ ['add_5fintron_5fsplice_5fjunctions_8003',['add_intron_splice_junctions',['../classvg_1_1Transcriptome.html#a6a43848fb4557db4edb73836a1f8270c',1,'vg::Transcriptome']]],
+ ['add_5flog_8004',['add_log',['../namespacevg.html#a0d4ce16064ad3986381aeead6afe317f',1,'vg']]],
+ ['add_5flog10_8005',['add_log10',['../namespacevg.html#ab3f3c75ff3775f447d5dabbdb4e540dc',1,'vg']]],
+ ['add_5fmapping_8006',['add_mapping',['../classvg_1_1path__t.html#a8dcc03d2615b611cb3f01ccc72235f62',1,'vg::path_t']]],
+ ['add_5fname_8007',['add_name',['../classVectorizer.html#a37c3afd6049c63e09910ca050a2f2b10',1,'Vectorizer']]],
+ ['add_5fname_5fmapping_8008',['add_name_mapping',['../classvg_1_1NameMapper.html#ac2e2d25ef0f36649f33bb3386f0150b5',1,'vg::NameMapper']]],
+ ['add_5fnext_8009',['add_next',['../classvg_1_1subpath__t.html#a3ce38f3b06d1f9cf18885be6a8391570',1,'vg::subpath_t']]],
+ ['add_5fnode_8010',['add_node',['../classvg_1_1DiagramExplainer.html#a4ddb1f858fdce9d6faa612094b584ce5',1,'vg::DiagramExplainer::add_node()'],['../classvg_1_1VG.html#ad3e265ee441758d81fdb7c038e2fa8cc',1,'vg::VG::add_node()'],['../structvg_1_1algorithms_1_1Graph.html#a1e46f942c332408f39f816b7a344182e',1,'vg::algorithms::Graph::add_node()']]],
+ ['add_5fnodes_8011',['add_nodes',['../classvg_1_1VG.html#ae71d30b767f067a874c933f13f6c34e5',1,'vg::VG::add_nodes(const vector< Node > &nodes)'],['../classvg_1_1VG.html#ab796330d50fdff47f5c080e251efea68',1,'vg::VG::add_nodes(const set< Node * > &nodes)']]],
+ ['add_5fnodes_5fand_5fedges_8012',['add_nodes_and_edges',['../namespacevg.html#a3aa7eee80c4c79f0f863d10687714c74',1,'vg::add_nodes_and_edges(MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t >> &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, size_t max_node_size=1024)'],['../namespacevg.html#a4b080c96a3681c4bd64f38eb05acd31b',1,'vg::add_nodes_and_edges(MutableHandleGraph *graph, const Path &path, const map< pos_t, id_t > &node_translation, unordered_map< pair< pos_t, string >, vector< id_t >> &added_seqs, unordered_map< id_t, Path > &added_nodes, const unordered_map< id_t, size_t > &orig_node_sizes, set< NodeSide > &dangling, size_t max_node_size)']]],
+ ['add_5fone_5fbyte_8013',['add_one_byte',['../structvg_1_1varint__vector__t.html#a95601cf688af672f6848e064a8b8a0ef',1,'vg::varint_vector_t']]],
+ ['add_5foption_8014',['add_option',['../structvg_1_1subcommand_1_1OptionGroup.html#ae7e574b260ca7c76e7137bae2d97486d',1,'vg::subcommand::OptionGroup::add_option(const std::string &name, char short_option, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})'],['../structvg_1_1subcommand_1_1OptionGroup.html#ab1102a6791fedb9b9bcfd61a45c9c750',1,'vg::subcommand::OptionGroup::add_option(const std::string &name, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})']]],
+ ['add_5fpath_8015',['add_path',['../namespacevg.html#aee40bdeb4216e0bf79124b25d1823ae4',1,'vg']]],
+ ['add_5fpath_5fto_5fgraph_8016',['add_path_to_graph',['../namespacevg.html#a7ac200a1dbeaf55eb41bebbfd2ce4bdf',1,'vg']]],
+ ['add_5fpoints_8017',['add_points',['../classvg_1_1algorithms_1_1TracedScore.html#a214944e7a2a98197db1c7fa804542065',1,'vg::algorithms::TracedScore']]],
+ ['add_5frange_8018',['add_range',['../structvg_1_1subcommand_1_1OptionGroup.html#a7864b536a49b3e464df80f928e27e681',1,'vg::subcommand::OptionGroup::add_range(const std::string &name, char short_option, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})'],['../structvg_1_1subcommand_1_1OptionGroup.html#a92247c70c100214bf37819ea25e53437',1,'vg::subcommand::OptionGroup::add_range(const std::string &name, T Receiver::*dest, T default_value, const std::string &help, const ValidatorFunction< T > &validator=[](const T &ignored) {})']]],
+ ['add_5freachability_5fedges_8019',['add_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#a2bf6b811ae4c3f0c993d3ac4a11359f0',1,'vg::MultipathAlignmentGraph']]],
+ ['add_5freference_5ftranscripts_8020',['add_reference_transcripts',['../classvg_1_1Transcriptome.html#aa2cc47e532c6a0ce46fc30e8f9edf473',1,'vg::Transcriptome']]],
+ ['add_5fseed_5fto_5fchain_5fproblem_8021',['add_seed_to_chain_problem',['../classvg_1_1SnarlDistanceIndexClusterer.html#a9a95c48ea0d0de320803712285aaf6f0',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['add_5fsnarl_8022',['add_snarl',['../classvg_1_1SnarlManager.html#ad41eeea8a375f91349a475a1782c3160',1,'vg::SnarlManager']]],
+ ['add_5fsnarl_5fdistances_8023',['add_snarl_distances',['../classvg_1_1ZipCodeForest.html#aa9a5fa1b979958b9785310fddab5f01e',1,'vg::ZipCodeForest']]],
+ ['add_5fsnarl_5fto_5fchain_5fproblem_8024',['add_snarl_to_chain_problem',['../classvg_1_1SnarlDistanceIndexClusterer.html#ac22dd38425e040559e64b1e11ad1d704',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['add_5fsplice_5fjunction_5fedges_8025',['add_splice_junction_edges',['../classvg_1_1Transcriptome.html#afdb0ae75032057859ad882400e6c16e5',1,'vg::Transcriptome::add_splice_junction_edges(const list< EditedTranscriptPath > &edited_transcript_paths)'],['../classvg_1_1Transcriptome.html#af44d2af3eb3181b21f767f2953f4901f',1,'vg::Transcriptome::add_splice_junction_edges(const list< CompletedTranscriptPath > &completed_transcript_paths)'],['../classvg_1_1Transcriptome.html#a9be2d779faebdb40a8048ddc9727c6fb',1,'vg::Transcriptome::add_splice_junction_edges(const vector< CompletedTranscriptPath > &completed_transcript_paths)']]],
+ ['add_5fstar_5ftraversals_8026',['add_star_traversals',['../classvg_1_1Deconstructor.html#aec0dffcba5b114c3297d2a494fb26f63',1,'vg::Deconstructor']]],
+ ['add_5fstart_8027',['add_start',['../classvg_1_1multipath__alignment__t.html#a793ba830eaa6fd21ec7af7c7fc12cfed',1,'vg::multipath_alignment_t']]],
+ ['add_5fstart_5fend_5fmarkers_8028',['add_start_end_markers',['../classvg_1_1VG.html#a91eaa395f197ca65f38c6139bc57d161',1,'vg::VG']]],
+ ['add_5fsubpath_8029',['add_subpath',['../classvg_1_1multipath__alignment__t.html#ad313d9942fcd375b7b073fa2d5276fe7',1,'vg::multipath_alignment_t']]],
+ ['add_5fsubpaths_5fto_5fsubgraph_8030',['add_subpaths_to_subgraph',['../namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c',1,'vg::algorithms']]],
+ ['add_5fthread_5fedges_5fto_5fset_8031',['add_thread_edges_to_set',['../namespacevg.html#afe2d6096dfe672a486e44df018c713c2',1,'vg']]],
+ ['add_5fthread_5fnodes_5fto_5fset_8032',['add_thread_nodes_to_set',['../namespacevg.html#a2adfa9e81b2553fefdd5e1d6b24c7a77',1,'vg']]],
+ ['add_5ftranscripts_5fto_5fgbwt_8033',['add_transcripts_to_gbwt',['../classvg_1_1Transcriptome.html#ab7fbe9d1f6688cc06381ff863a345dc4',1,'vg::Transcriptome']]],
+ ['add_5ftraversals_8034',['add_traversals',['../classvg_1_1ExhaustiveTraversalFinder.html#a4d93c5f43e4be897874b2468c026c0ca',1,'vg::ExhaustiveTraversalFinder']]],
+ ['add_5funary_5fchild_8035',['add_unary_child',['../classvg_1_1NetGraph.html#a3780b053c5632c4425b7057d34bffe3a',1,'vg::NetGraph']]],
+ ['add_5fvalue_8036',['add_value',['../structvg_1_1varint__vector__t.html#a30b862ab93cd6934985fc61abb14df6f',1,'vg::varint_vector_t']]],
+ ['add_5fvariant_8037',['add_variant',['../classvg_1_1VCFOutputCaller.html#a2cc880b6121547ff0cdd5ac9a7b1b505',1,'vg::VCFOutputCaller']]],
+ ['add_5fvariants_8038',['add_variants',['../classvg_1_1VariantAdder.html#a4cf25deb4e0e2270c76e2fcd0f3dbf99',1,'vg::VariantAdder']]],
+ ['addarbitrarytelomerepair_8039',['addArbitraryTelomerePair',['../namespacevg.html#a948a49f6716e35c8da05e84497dc01e4',1,'vg']]],
+ ['adjacent_8040',['adjacent',['../classvg_1_1VG.html#ab213a64c6240d08603530982c0b75047',1,'vg::VG']]],
+ ['adjacent_5fmappings_8041',['adjacent_mappings',['../namespacevg.html#a92de94b4571057762bb3152de1376e51',1,'vg']]],
+ ['adjacent_5fpositions_8042',['adjacent_positions',['../classvg_1_1Mapper.html#a3e58033862961bc28c3db2ba7b3d44df',1,'vg::Mapper']]],
+ ['adjust_5fdiagonal_5frange_8043',['adjust_diagonal_range',['../classvg_1_1WFATree.html#a87ef6db73ce334779745d1a7df7e5229',1,'vg::WFATree']]],
+ ['adjustment_8044',['adjustment',['../namespacehaplotypes__defaults.html#a3cd701bda653c12395917bd45c3548ba',1,'haplotypes_defaults']]],
+ ['advance_8045',['advance',['../structvg_1_1PathBranch.html#a45275291566be41d4262c59078ad99bb',1,'vg::PathBranch::advance()'],['../classvg_1_1NGSSimulator.html#af52087c09b80030eb5e28da070d68fc6',1,'vg::NGSSimulator::advance()'],['../classvg_1_1io_1_1MessageIterator.html#ab4ccacd8648e7517083bfccc4676ba9a',1,'vg::io::MessageIterator::advance()'],['../classvg_1_1io_1_1ProtobufIterator.html#a300d8f5292f866bd4709c14615cdf9e0',1,'vg::io::ProtobufIterator::advance()'],['../namespacevg.html#ace5160301eaf4ef84a5e8b77bce94a7e',1,'vg::advance()']]],
+ ['advance_5fby_5fdistance_8046',['advance_by_distance',['../classvg_1_1NGSSimulator.html#a3eed6eb9096bd857aba3fa6436cc9358',1,'vg::NGSSimulator']]],
+ ['advance_5fon_5fgraph_8047',['advance_on_graph',['../classvg_1_1NGSSimulator.html#acadca14bcc46a1a9489227cea12d2992',1,'vg::NGSSimulator']]],
+ ['advance_5fon_5fgraph_5fby_5fdistance_8048',['advance_on_graph_by_distance',['../classvg_1_1NGSSimulator.html#aba35f36f705e591b1aecebe1a0dd1c5d',1,'vg::NGSSimulator']]],
+ ['advance_5fon_5fpath_8049',['advance_on_path',['../classvg_1_1NGSSimulator.html#ae1830648142d4eef8c91a439be97367f',1,'vg::NGSSimulator']]],
+ ['advance_5fon_5fpath_5fby_5fdistance_8050',['advance_on_path_by_distance',['../classvg_1_1NGSSimulator.html#ab3b4e064f4b0ed000fd917d1a70cb1e7',1,'vg::NGSSimulator']]],
+ ['advance_5fsplit_8051',['advance_split',['../namespacevg.html#a0df0c35a951519aa4a74bf098a253516',1,'vg']]],
+ ['affinity_8052',['Affinity',['../structvg_1_1Genotyper_1_1Affinity.html#a3a8fa26d3f84c1214b1df151346a70a0',1,'vg::Genotyper::Affinity::Affinity()=default'],['../structvg_1_1Genotyper_1_1Affinity.html#a656eb6bfb6f19acffa2a492964b1047e',1,'vg::Genotyper::Affinity::Affinity(double affinity, bool is_reverse)']]],
+ ['agglomerate_8053',['agglomerate',['../classvg_1_1MultipathMapper.html#af4abb58766f7ac58e418406e0e6398e2',1,'vg::MultipathMapper']]],
+ ['agglomerate_5falignment_5fpairs_8054',['agglomerate_alignment_pairs',['../classvg_1_1MultipathMapper.html#aac93091ff558b107c4d6b83852a07c81',1,'vg::MultipathMapper']]],
+ ['agglomerate_5falignments_8055',['agglomerate_alignments',['../classvg_1_1MultipathMapper.html#a696ef2325572ce7233d0ecb02ee615d4',1,'vg::MultipathMapper']]],
+ ['agglomeration_5fwindow_5fcount_8056',['agglomeration_window_count',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a21dd6ccbbc1c96cc307dd9b825b00f12',1,'vg::MinimizerMapper::Minimizer']]],
+ ['aliasgraph_8057',['AliasGraph',['../classvg_1_1AliasGraph.html#ad18207f2d96c67fcc93282ed4c9416a2',1,'vg::AliasGraph']]],
+ ['align_8058',['align',['../classvg_1_1BaseAligner.html#a5b0ee67e18697f65aab62b40c2eb925a',1,'vg::BaseAligner::align()'],['../classvg_1_1Aligner.html#a0e2376f882d3164e798f2bb0d7da4359',1,'vg::Aligner::align(Alignment &alignment, const HandleGraph &g, bool traceback_aln) const'],['../classvg_1_1Aligner.html#a735b995cc89b1d526a21293b187d44d8',1,'vg::Aligner::align(Alignment &alignment, const HandleGraph &g, const std::vector< handle_t > &topological_order) const'],['../classvg_1_1QualAdjAligner.html#a46684d481ad89ddf49b98e952388c9b8',1,'vg::QualAdjAligner::align()'],['../classvg_1_1BandedGlobalAligner.html#afbd0f828e44ba486479b7bfd457d7dc5',1,'vg::BandedGlobalAligner::align()'],['../classvg_1_1DeletionAligner.html#a0c94449e8b123e0addf0d3dbc0409774',1,'vg::DeletionAligner::align()'],['../classvg_1_1DozeuInterface.html#a3b2d827b7cf43451065a2e2369895aff',1,'vg::DozeuInterface::align(Alignment &alignment, const HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length)'],['../classvg_1_1DozeuInterface.html#aa901ac96f18c5f60cbe114087aada362',1,'vg::DozeuInterface::align(Alignment &alignment, const HandleGraph &graph, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length)'],['../classvg_1_1Mapper.html#a690d9e6f314d4b010df7e8f74f5cb9b1',1,'vg::Mapper::align(const string &seq, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false)'],['../classvg_1_1Mapper.html#a32d5ed544ec9d752b34ad1848b729078',1,'vg::Mapper::align(const Alignment &read, int kmer_size=0, int stride=0, int max_mem_length=0, int band_width=1000, int band_overlap=500, bool xdrop_alignment=false)'],['../classvg_1_1MultipathAlignmentGraph.html#a0249c6ebb9691c114fe801f566bf964c',1,'vg::MultipathAlignmentGraph::align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, bool align_in_reverse=false, uint64_t max_band_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1MultipathAlignmentGraph.html#a83adb80ffc74d2709c498820216709f9',1,'vg::MultipathAlignmentGraph::align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t max_tail_length, bool simplify_topologies, size_t unmergeable_len, const function< size_t(const Alignment &, const HandleGraph &)> &band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, bool align_in_reverse=false, uint64_t max_band_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1SSWAligner.html#adc9985aac608bfb4819cd7436b969b62',1,'vg::SSWAligner::align()'],['../classvg_1_1VG.html#ac17b237e99636d20e12e4c1b94f9110b',1,'vg::VG::align(const string &sequence, const Aligner *aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a09fa1d70c31c354915773e59a1a9b55c',1,'vg::VG::align(const Alignment &alignment, const Aligner *aligner, const vector< MaximalExactMatch > &mems, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#ae6b16848db51add920b025829e2a5d55',1,'vg::VG::align(const Alignment &alignment, const Aligner *aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a3d4e6f3f52479b59a73b04c58945277b',1,'vg::VG::align(const Alignment &alignment, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#af81a72bb91912cabbec795e17c311dc9',1,'vg::VG::align(const string &sequence, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#ac24d1defbcca2158cda5fbd272fadae0',1,'vg::VG::align(const Alignment &alignment, const Aligner *aligner, const QualAdjAligner *qual_adj_aligner, const vector< MaximalExactMatch > &mems, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)']]],
+ ['align_5fbanded_8059',['align_banded',['../classvg_1_1Mapper.html#ad09b7612066e797594b98151fab355cc',1,'vg::Mapper']]],
+ ['align_5fcluster_8060',['align_cluster',['../classvg_1_1Mapper.html#ab10346b736664fd152f0651448b7aea1',1,'vg::Mapper']]],
+ ['align_5fdownward_8061',['align_downward',['../classvg_1_1DozeuInterface.html#a907ed564c2ed19ecaf7ee880b8a1a13c',1,'vg::DozeuInterface']]],
+ ['align_5fglobal_5fbanded_8062',['align_global_banded',['../classvg_1_1GSSWAligner.html#a4ae60e4ac2c961f8f63f51b1d696a485',1,'vg::GSSWAligner::align_global_banded()'],['../classvg_1_1Aligner.html#a8984447f565f2c7b870175b90178461b',1,'vg::Aligner::align_global_banded()'],['../classvg_1_1QualAdjAligner.html#ad4d16c6a39f32dc93854f21d0a7d56e2',1,'vg::QualAdjAligner::align_global_banded()']]],
+ ['align_5fglobal_5fbanded_5fmulti_8063',['align_global_banded_multi',['../classvg_1_1GSSWAligner.html#a5af41c52f81a9373c608bef49ea57e94',1,'vg::GSSWAligner::align_global_banded_multi()'],['../classvg_1_1Aligner.html#a4b2637f4e841012103cf77fa09ef318f',1,'vg::Aligner::align_global_banded_multi()'],['../classvg_1_1QualAdjAligner.html#addfd42ba76bc39c040b9028dd3995742',1,'vg::QualAdjAligner::align_global_banded_multi()']]],
+ ['align_5finternal_8064',['align_internal',['../classvg_1_1Aligner.html#a9e1056e34d9b67a80b4268d6408a7e7c',1,'vg::Aligner::align_internal()'],['../classvg_1_1QualAdjAligner.html#a87cc90a9c2f1107546b483fd31f57518',1,'vg::QualAdjAligner::align_internal()']]],
+ ['align_5fmaybe_5fflip_8065',['align_maybe_flip',['../classvg_1_1Mapper.html#aa6bbfabc25b809bde5d2f032eb8ec79f',1,'vg::Mapper::align_maybe_flip(const Alignment &base, HandleGraph &graph, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false)'],['../classvg_1_1Mapper.html#a4816c32c8427a964a06f945833501cd7',1,'vg::Mapper::align_maybe_flip(const Alignment &base, HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool flip, bool traceback, bool banded_global=false, bool xdrop_alignment=false)']]],
+ ['align_5fmem_5fmulti_8066',['align_mem_multi',['../classvg_1_1Mapper.html#ab4dd1cdaeb9868d9c9f4776faaf11399',1,'vg::Mapper']]],
+ ['align_5fmulti_8067',['align_multi',['../classvg_1_1DeletionAligner.html#aa6b80383c0eadcdc1b028f774d9b3713',1,'vg::DeletionAligner::align_multi()'],['../classvg_1_1Mapper.html#a568ef8bf64b91b264dbcb7c8aad61774',1,'vg::Mapper::align_multi()']]],
+ ['align_5fmulti_5finternal_8068',['align_multi_internal',['../classvg_1_1Mapper.html#a4890914dde25f0ea5c184b29530ec623',1,'vg::Mapper']]],
+ ['align_5fns_8069',['align_ns',['../classvg_1_1VariantAdder.html#a65c5a0e7b649a97f68a4f2ab573f17d0',1,'vg::VariantAdder']]],
+ ['align_5fpaired_5fmulti_8070',['align_paired_multi',['../classvg_1_1Mapper.html#abb8fa423f1591e48f33ab17090fad750',1,'vg::Mapper']]],
+ ['align_5fpinned_8071',['align_pinned',['../classvg_1_1GSSWAligner.html#ae920579abfc1f15c43d0f30e3472fd65',1,'vg::GSSWAligner::align_pinned()'],['../classvg_1_1Aligner.html#a90a7be445aa931365b940fa2f26570ff',1,'vg::Aligner::align_pinned()'],['../classvg_1_1QualAdjAligner.html#af1545edb0591d1b62bb10714af6aa3bd',1,'vg::QualAdjAligner::align_pinned()'],['../classvg_1_1DozeuInterface.html#a7f8736e97ee778271e35b2d212c8603d',1,'vg::DozeuInterface::align_pinned()']]],
+ ['align_5fpinned_5fmulti_8072',['align_pinned_multi',['../classvg_1_1GSSWAligner.html#a34052d83b0a62374e411ee89eead4175',1,'vg::GSSWAligner::align_pinned_multi()'],['../classvg_1_1Aligner.html#a6c2efe87216772df9cb3d3d7d0e61a26',1,'vg::Aligner::align_pinned_multi()'],['../classvg_1_1QualAdjAligner.html#a44a05f9824834133c34f487f77708383',1,'vg::QualAdjAligner::align_pinned_multi()']]],
+ ['align_5fqual_5fadjusted_8073',['align_qual_adjusted',['../classvg_1_1VG.html#a5532978af43e5c4e5e4f471069e53344',1,'vg::VG::align_qual_adjusted(const Alignment &alignment, const QualAdjAligner *qual_adj_aligner, const vector< MaximalExactMatch > &mems, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a2b135ccb439e99ef1f509a11ea9ea9ce',1,'vg::VG::align_qual_adjusted(const Alignment &alignment, const QualAdjAligner *qual_adj_aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)'],['../classvg_1_1VG.html#a58919649b2a29d36fd965ba453046baf',1,'vg::VG::align_qual_adjusted(const string &sequence, const QualAdjAligner *qual_adj_aligner, bool traceback=true, bool acyclic_and_sorted=false, size_t max_query_graph_ratio=0, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, size_t band_padding_override=0, size_t max_span=0, size_t unroll_length=0, int xdrop_alignment=0)']]],
+ ['align_5fsequence_5fbetween_8074',['align_sequence_between',['../classvg_1_1MinimizerMapper.html#a3757672b798dedc0d9ce9b4306f638c4',1,'vg::MinimizerMapper']]],
+ ['align_5fsequence_5fbetween_5fconsistently_8075',['align_sequence_between_consistently',['../classvg_1_1MinimizerMapper.html#a671ecec9187f2c6b3f4f7789c30ec27e',1,'vg::MinimizerMapper']]],
+ ['align_5ftails_8076',['align_tails',['../classvg_1_1MultipathAlignmentGraph.html#ab340ca598eea6944dc841a9b76b73d48',1,'vg::MultipathAlignmentGraph']]],
+ ['align_5fto_5fcluster_5fgraph_5fpairs_8077',['align_to_cluster_graph_pairs',['../classvg_1_1MultipathMapper.html#a6be2107ab64d6b8d2ba9eba5c8f1368a',1,'vg::MultipathMapper']]],
+ ['align_5fto_5fcluster_5fgraphs_8078',['align_to_cluster_graphs',['../classvg_1_1MultipathMapper.html#a32220c809c2dc652c56c05b53dcd6567',1,'vg::MultipathMapper']]],
+ ['align_5fto_5fcluster_5fgraphs_5fwith_5frescue_8079',['align_to_cluster_graphs_with_rescue',['../classvg_1_1MultipathMapper.html#af309e1b590c47f8cb6197290892c5d79',1,'vg::MultipathMapper']]],
+ ['align_5fto_5fgraph_8080',['align_to_graph',['../classvg_1_1Mapper.html#a0b3adffe0ee67feab3b7486ec0d871da',1,'vg::Mapper::align_to_graph(const Alignment &aln, HandleGraph &graph, bool do_flip, bool traceback, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, bool keep_bonuses=true)'],['../classvg_1_1Mapper.html#a8cf428d786611af1fe7727e6929ef606',1,'vg::Mapper::align_to_graph(const Alignment &aln, HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool do_flip, bool traceback, bool pinned_alignment=false, bool pin_left=false, bool banded_global=false, int xdrop_alignment=0, bool keep_bonuses=true)']]],
+ ['align_5fto_5fsplice_5fcandidates_8081',['align_to_splice_candidates',['../classvg_1_1MultipathMapper.html#a068b38611f12b7e4677b39d43da715f9',1,'vg::MultipathMapper']]],
+ ['align_5fxdrop_8082',['align_xdrop',['../classvg_1_1GSSWAligner.html#a71da93203b17beaffac6d7e6bbfe7c0b',1,'vg::GSSWAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const =0'],['../classvg_1_1GSSWAligner.html#a2ed8a7b2fefb98c7d814449c8e884dde',1,'vg::GSSWAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const =0'],['../classvg_1_1Aligner.html#a186815e37fef05cb774d257ceca32b36',1,'vg::Aligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const'],['../classvg_1_1Aligner.html#a335087038dcf0586837abaada8d47d4b',1,'vg::Aligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const'],['../classvg_1_1QualAdjAligner.html#a2ffbaa8d9a7e2b8cf503a3bdd169e0c5',1,'vg::QualAdjAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const'],['../classvg_1_1QualAdjAligner.html#a8b497f4fb4d1e07d2bc388de3b8b604e',1,'vg::QualAdjAligner::align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const']]],
+ ['aligned_5finterval_8083',['aligned_interval',['../namespacevg.html#a3b337b4ea1b6ad514093ce1b9d44b598',1,'vg']]],
+ ['aligner_8084',['Aligner',['../classvg_1_1Aligner.html#a94e3d9645c15f59fe817d4dd540fecf6',1,'vg::Aligner']]],
+ ['alignerclient_8085',['AlignerClient',['../classvg_1_1AlignerClient.html#a2f3a789bca074bfbbeb327e74992d9cc',1,'vg::AlignerClient']]],
+ ['alignment_8086',['alignment',['../classvg_1_1Sampler.html#af69ed2ac1782e7991b0a22654846506f',1,'vg::Sampler']]],
+ ['alignment_5fend_8087',['alignment_end',['../namespacevg.html#aa63fccb24f075243da0ba145eb8d6aca',1,'vg']]],
+ ['alignment_5fend_5fmatches_8088',['alignment_end_matches',['../classvg_1_1ReadFilter.html#a5088cb81cac4ce8e26c6a921bf29b546',1,'vg::ReadFilter']]],
+ ['alignment_5fend_5fposition_8089',['alignment_end_position',['../classvg_1_1Mapper.html#afe879219cd07b2183fbcbd09ff690a60',1,'vg::Mapper']]],
+ ['alignment_5fends_8090',['alignment_ends',['../namespacevg.html#acdc3ca4569facd77e26c78ba583e4f0a',1,'vg']]],
+ ['alignment_5ffrom_5flength_8091',['alignment_from_length',['../namespacevg.html#ae4defc9906e81731eab06f8acaa28369',1,'vg']]],
+ ['alignment_5ffrom_5fpath_8092',['alignment_from_path',['../namespacevg.html#abcf3c5c3332d721a86740ef23fb9e6e2',1,'vg']]],
+ ['alignment_5fis_5fvalid_8093',['alignment_is_valid',['../namespacevg.html#aa15ba62ae06958a1e792554996b5ee62',1,'vg']]],
+ ['alignment_5fmiddle_8094',['alignment_middle',['../namespacevg.html#a15b82cc5c99cc3e8f78229ac971ec9c3',1,'vg']]],
+ ['alignment_5foverhang_8095',['alignment_overhang',['../classvg_1_1ReadFilter.html#ab655011da419f60374d9238c0c21312b',1,'vg::ReadFilter']]],
+ ['alignment_5fpair_8096',['alignment_pair',['../classvg_1_1Sampler.html#aecbd1aa581c396a85ab850dab54b5cd1',1,'vg::Sampler']]],
+ ['alignment_5fpath_5foffsets_8097',['alignment_path_offsets',['../namespacevg_1_1algorithms.html#aead0aa069554bbc1a3fcce05ca4d1127',1,'vg::algorithms']]],
+ ['alignment_5fqual_5fscore_8098',['alignment_qual_score',['../classvg_1_1Genotyper.html#a76bba1da02c9a75895896efd5b5e3641',1,'vg::Genotyper']]],
+ ['alignment_5fquality_5fchar_5fto_5fshort_8099',['alignment_quality_char_to_short',['../namespacevg_1_1io.html#a982211439438e0ef8a8fd7c7e54bddc1',1,'vg::io']]],
+ ['alignment_5fquality_5fper_5fnode_8100',['alignment_quality_per_node',['../namespacevg.html#a2a4413a5d745c8fdc6339efdcd13310c',1,'vg']]],
+ ['alignment_5fquality_5fshort_5fto_5fchar_8101',['alignment_quality_short_to_char',['../namespacevg_1_1io.html#a7bc5a85334e06bd81e308c0f1fc9e192',1,'vg::io']]],
+ ['alignment_5frefpos_5fto_5fpath_5foffsets_8102',['alignment_refpos_to_path_offsets',['../namespacevg.html#a3ad13bf14c3488a2d7a86931831ce25d',1,'vg']]],
+ ['alignment_5fscore_8103',['alignment_score',['../structvg_1_1WFAPoint.html#a3cba5c83c18ec596a547ee9dfdbe1ca8',1,'vg::WFAPoint::alignment_score(const Aligner &aligner) const'],['../structvg_1_1WFAPoint.html#a550d6300508d7739b9e2549ed9475e67',1,'vg::WFAPoint::alignment_score(const Aligner &aligner, uint32_t final_insertion) const']]],
+ ['alignment_5fscore_5fpartition_5ffunction_8104',['alignment_score_partition_function',['../classvg_1_1GSSWAligner.html#a610e81a719f399a5018bd722a6affad5',1,'vg::GSSWAligner']]],
+ ['alignment_5fseq_8105',['alignment_seq',['../classvg_1_1Sampler.html#a514eade400df496e68c96b3ff321cb78',1,'vg::Sampler']]],
+ ['alignment_5fset_5fdistance_5fto_5fcorrect_8106',['alignment_set_distance_to_correct',['../namespacevg.html#a6c45c724ede7f4892b24ad654d68fbef',1,'vg::alignment_set_distance_to_correct(Alignment &aln, const Alignment &base, const unordered_map< string, string > *translation)'],['../namespacevg.html#ab7c6a6b96f1c4c2ca04b0b6df8f384b3',1,'vg::alignment_set_distance_to_correct(Alignment &aln, const map< string, vector< pair< size_t, bool > > > &base_offsets, const unordered_map< string, string > *translation)'],['../namespacevg.html#a6c59e7d46046fad0d349a3c747ffd6b3',1,'vg::alignment_set_distance_to_correct(Alignment &aln, const map< string, vector< pair< size_t, bool >>> &base_offsets, const unordered_map< string, string > *translation=nullptr)']]],
+ ['alignment_5fstart_8107',['alignment_start',['../namespacevg.html#ab7f897cb4a7bbbd40edcb938cdbd4e7c',1,'vg']]],
+ ['alignment_5fto_5fa_5fhot_8108',['alignment_to_a_hot',['../classVectorizer.html#a73fd20a41c037c7dadd220b7a75306b9',1,'Vectorizer']]],
+ ['alignment_5fto_5fbam_8109',['alignment_to_bam',['../namespacevg.html#a1b59157d021eca5f39da96ca23f33f08',1,'vg::alignment_to_bam(bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max)'],['../namespacevg.html#a0d064f9483fe862fe937abc9e7474e57',1,'vg::alignment_to_bam(bam_hdr_t *bam_header, const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar)']]],
+ ['alignment_5fto_5fbam_5finternal_8110',['alignment_to_bam_internal',['../namespacevg.html#a815420ed5a7dce52d484c346271fbd71',1,'vg']]],
+ ['alignment_5fto_5fcustom_5fscore_8111',['alignment_to_custom_score',['../classVectorizer.html#a040fab89a60c48dfa8bf92b4ea347b8d',1,'Vectorizer']]],
+ ['alignment_5fto_5fgaf_8112',['alignment_to_gaf',['../namespacevg_1_1io.html#ac7caf6e3e258fda58ef1bd8565074f4a',1,'vg::io::alignment_to_gaf(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const Alignment &aln, const handlegraph::NamedNodeBackTranslation *translate_through, bool cs_cigar, bool base_quals, bool frag_links)'],['../namespacevg_1_1io.html#a711294fa859b37aba71867a0dd9a035a',1,'vg::io::alignment_to_gaf(const HandleGraph &graph, const Alignment &aln, const handlegraph::NamedNodeBackTranslation *translate_through, bool cs_cigar, bool base_quals, bool frag_links)']]],
+ ['alignment_5fto_5fgraph_8113',['alignment_to_graph',['../classvg_1_1Sampler.html#a544836c189c15b5a4c551220047c2d62',1,'vg::Sampler']]],
+ ['alignment_5fto_5fidentity_5fhot_8114',['alignment_to_identity_hot',['../classVectorizer.html#ae2bb1c5a37fa7ead081e73db8f999b4d',1,'Vectorizer']]],
+ ['alignment_5fto_5flength_8115',['alignment_to_length',['../namespacevg.html#a38cb960f8c643934d65c03f0cc85442c',1,'vg']]],
+ ['alignment_5fto_5fonehot_8116',['alignment_to_onehot',['../classVectorizer.html#adb25591f400faebb90a58a19a7e16873',1,'Vectorizer']]],
+ ['alignment_5fto_5fpath_8117',['alignment_to_path',['../classvg_1_1Sampler.html#af0d3a16810406204c49e02354d815313',1,'vg::Sampler']]],
+ ['alignment_5fto_5fsam_8118',['alignment_to_sam',['../namespacevg.html#a8d06ec05d079a41bf301a4f5f93b635b',1,'vg::alignment_to_sam(const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar, const string &mateseq, const int32_t matepos, bool materev, const int32_t tlen, const int32_t tlen_max)'],['../namespacevg.html#afec7360276d2d875f4368057d528572a',1,'vg::alignment_to_sam(const Alignment &alignment, const string &refseq, const int32_t refpos, const bool refrev, const vector< pair< int, char >> &cigar)']]],
+ ['alignment_5fto_5fsam_5finternal_8119',['alignment_to_sam_internal',['../namespacevg.html#af0471358e141f59c271b38dd64854371',1,'vg']]],
+ ['alignment_5fwith_5ferror_8120',['alignment_with_error',['../classvg_1_1Sampler.html#a75ac9726e906eb75d7f5ed85c7a8d0f9',1,'vg::Sampler']]],
+ ['alignmentchainmodel_8121',['AlignmentChainModel',['../classvg_1_1AlignmentChainModel.html#a960347cf0986a4392544c22bbfdf7c0b',1,'vg::AlignmentChainModel']]],
+ ['alignmentchainmodelvertex_8122',['AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html#a060f439601e7445f95e2bbd6925ddc6b',1,'vg::AlignmentChainModelVertex::AlignmentChainModelVertex(void)=default'],['../classvg_1_1AlignmentChainModelVertex.html#a620d3e10aa7398d73985de1c1fd8adfa',1,'vg::AlignmentChainModelVertex::AlignmentChainModelVertex(const AlignmentChainModelVertex &)=default'],['../classvg_1_1AlignmentChainModelVertex.html#a36dea81c272702fa5977067f62c54777',1,'vg::AlignmentChainModelVertex::AlignmentChainModelVertex(AlignmentChainModelVertex &&)=default']]],
+ ['alignments_5fconsistent_8123',['alignments_consistent',['../classvg_1_1Mapper.html#a5edacb959a00dcee901b42948ebf9e75',1,'vg::Mapper']]],
+ ['all_5fchildren_5ftrivial_8124',['all_children_trivial',['../classvg_1_1SnarlManager.html#a732645de996b9f56608d395ea4949bd9',1,'vg::SnarlManager']]],
+ ['all_5ffinished_8125',['all_finished',['../classvg_1_1IndexRegistry.html#ac81872b4bf8d7917b284f609a4127023',1,'vg::IndexRegistry::all_finished(const vector< const IndexFile * > &inputs) const'],['../classvg_1_1IndexRegistry.html#a35e5dcdc072c53f562442686dff9977a',1,'vg::IndexRegistry::all_finished(const IndexGroup &inputs) const']]],
+ ['all_5fgroups_8126',['all_groups',['../classvg_1_1SparseUnionFind.html#a8fe069d0444b1dae9d71e5943ebded44',1,'vg::SparseUnionFind']]],
+ ['all_5fmapping_5fqualities_5fexact_8127',['all_mapping_qualities_exact',['../classvg_1_1GSSWAligner.html#ab9f99a04dd14ab7c3cc43662b6b73293',1,'vg::GSSWAligner']]],
+ ['all_5fpath_5fnames_8128',['all_path_names',['../classvg_1_1Paths.html#a246f21fbf08d613e3ce8122705044cbe',1,'vg::Paths']]],
+ ['allambiguouston_8129',['allAmbiguousToN',['../namespacevg.html#afb243c35d883121f8645815571b7a55f',1,'vg']]],
+ ['allatgc_8130',['allATGC',['../namespacevg.html#a7a1786f1e7e453c4b76b319ba101782d',1,'vg']]],
+ ['allatgcn_8131',['allATGCN',['../namespacevg.html#ae24bea33b666a03a0065a10a60d64e9d',1,'vg']]],
+ ['allele_8132',['allele',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a8e1b3233ad9520a651434b00de016d7f',1,'haplo::linear_haplo_structure::SNVvector']]],
+ ['allele_5fambiguity_5flog_5fprobs_8133',['allele_ambiguity_log_probs',['../classvg_1_1Genotyper.html#aa46523cd1493686b28210136d9baf713',1,'vg::Genotyper']]],
+ ['allele_5fto_5fstring_8134',['allele_to_string',['../namespacevg.html#a3b46a0183527dc1713f3ab30ef85b185',1,'vg']]],
+ ['allowsaliasing_8135',['AllowsAliasing',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ac30901e7d779acdfef65858e98baaf3f',1,'vg::io::BlockedGzipOutputStream']]],
+ ['also_5fmerge_5fgroup_8136',['also_merge_group',['../classvg_1_1Funnel.html#abc00e34c78f024874b44ebf90443cc4e',1,'vg::Funnel::also_merge_group(Iterator prev_stage_items_begin, Iterator prev_stage_items_end)'],['../classvg_1_1Funnel.html#a68135544a4504edde8de7df48557d4ba',1,'vg::Funnel::also_merge_group(size_t earlier_stage_lookback, Iterator earlier_stage_items_begin, Iterator earlier_stage_items_end)']]],
+ ['also_5frelevant_8137',['also_relevant',['../classvg_1_1Funnel.html#a0642f2a1faae54dc12e98df452d4be65',1,'vg::Funnel']]],
+ ['alt_5fproposal_5fsample_8138',['alt_proposal_sample',['../classvg_1_1MCMCGenotyper.html#a26dfe5be824755df69d533e98304f5be',1,'vg::MCMCGenotyper']]],
+ ['alttracebackstack_8139',['AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#add2f3215214bfdd33cd8ccc633275827',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['anchor_8140',['Anchor',['../classvg_1_1algorithms_1_1Anchor.html#a61a4dd75e3aec703eeb6e06ab24af934',1,'vg::algorithms::Anchor::Anchor(size_t read_start, const pos_t &graph_start, size_t length, size_t margin_before, size_t margin_after, int score, size_t seed_number=std::numeric_limits< size_t >::max(), ZipCode *hint=nullptr, size_t hint_start=0, bool skippable=false)'],['../classvg_1_1algorithms_1_1Anchor.html#a2ddebc7f2076e9f6e8e00f37163af28c',1,'vg::algorithms::Anchor::Anchor(const Anchor &first, const Anchor &last, size_t extra_margin_before, size_t extra_margin_after, int score)'],['../classvg_1_1algorithms_1_1Anchor.html#a590e37aed7b087657a9ad3cae8a6fbbe',1,'vg::algorithms::Anchor::Anchor()=default'],['../classvg_1_1algorithms_1_1Anchor.html#abe177a3866f3369347049d235c7bad3a',1,'vg::algorithms::Anchor::Anchor(const Anchor &other)=default'],['../classvg_1_1algorithms_1_1Anchor.html#a1e837be4b5167a4d27841886a6913701',1,'vg::algorithms::Anchor::Anchor(Anchor &&other)=default']]],
+ ['anchored_5ffilter_8141',['anchored_filter',['../classvg_1_1Filter.html#a7e797bbf731c8120cf2df43e4355963a',1,'vg::Filter']]],
+ ['annotate_5fmapped_5falignment_8142',['annotate_mapped_alignment',['../classvg_1_1Funnel.html#adc044b59bc97ac7e6536068fa9bdb5d2',1,'vg::Funnel']]],
+ ['annotate_5fwith_5finitial_5fpath_5fpositions_8143',['annotate_with_initial_path_positions',['../namespacevg_1_1algorithms.html#a3c1bbf062eb429066c7b46da24704cdf',1,'vg::algorithms::annotate_with_initial_path_positions(const PathPositionHandleGraph &graph, Alignment &aln, int64_t search_limit, const std::function< bool(const path_handle_t &)> *path_filter)'],['../namespacevg_1_1algorithms.html#a29c8bb498d4cab7c964783dbf98dae28',1,'vg::algorithms::annotate_with_initial_path_positions(const PathPositionHandleGraph &graph, vector< Alignment > &alns, int64_t search_limit, const std::function< bool(const path_handle_t &)> *path_filter)']]],
+ ['annotate_5fwith_5fminimizer_5fstatistics_8144',['annotate_with_minimizer_statistics',['../classvg_1_1MinimizerMapper.html#a2da9c99842bd5e1fac26b7f6fc358fcc',1,'vg::MinimizerMapper']]],
+ ['annotate_5fwith_5fnode_5fpath_5fpositions_8145',['annotate_with_node_path_positions',['../namespacevg_1_1algorithms.html#ad2151b93596855953805b98d78ac83c6',1,'vg::algorithms']]],
+ ['annotate_5fwith_5fpath_5fpositions_8146',['annotate_with_path_positions',['../classvg_1_1AbstractReadSampler.html#a29d7f66f17c49eeae229d00ea31ed252',1,'vg::AbstractReadSampler::annotate_with_path_positions()'],['../namespacevg_1_1algorithms.html#a66e67738fef35591e953849387e94d58',1,'vg::algorithms::annotate_with_path_positions()']]],
+ ['append_8147',['append',['../structvg_1_1WFAAlignment.html#a13fc5825782e95adb9e985719f91cc4a',1,'vg::WFAAlignment::append()'],['../classvg_1_1SnarlState.html#a6f40f3779030f0e665d3cdc77bbaeafd',1,'vg::SnarlState::append()'],['../classvg_1_1Paths.html#a0c8569eae84b41c65291b76f0ae4da6c',1,'vg::Paths::append(const Paths &paths, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1Paths.html#a4b25b15a87b59847a3ef5384aaed856c',1,'vg::Paths::append(const Graph &g, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1VG.html#a5272032c1e57d839176fc8e39bd87e18',1,'vg::VG::append()']]],
+ ['append_5fcigar_5foperation_8148',['append_cigar_operation',['../namespacevg.html#a083d5edb5192697a269a3e5b8815bccd',1,'vg']]],
+ ['append_5fhandle_5fgraph_8149',['append_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a89dc4417bd6be84b3b293b20c9254011',1,'handlegraph::algorithms']]],
+ ['append_5fhaplotype_8150',['append_haplotype',['../classvg_1_1GenomeState.html#aa9f6862f286a2f28ebeb75251e1fe059',1,'vg::GenomeState']]],
+ ['append_5fleft_8151',['append_left',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a6eae6ee85866e8a90efd0d7d7f5de0be',1,'vg::PhasedGenome::Haplotype']]],
+ ['append_5fmapping_8152',['append_mapping',['../classvg_1_1Paths.html#aec7ad289d23cf879bdefb682dc464313',1,'vg::Paths::append_mapping(const string &name, const mapping_t &m, bool warn_on_duplicates=false)'],['../classvg_1_1Paths.html#a490ae73c613867d5621e17b6ff6635dd',1,'vg::Paths::append_mapping(const string &name, id_t id, bool is_reverse, size_t length, size_t rank=0, bool warn_on_duplicates=false)']]],
+ ['append_5fmapping_5fsequence_8153',['append_mapping_sequence',['../namespacevg_1_1algorithms.html#ae5ff6fdbf4ef393faf59f22365c46bbb',1,'vg::algorithms']]],
+ ['append_5fmultipath_5falignment_8154',['append_multipath_alignment',['../namespacevg.html#ac93525ce8a55a9394025efe575468488',1,'vg']]],
+ ['append_5fnode_8155',['append_node',['../structvg_1_1WFANode.html#a078c2ef3a3c95bb25c532b7313c93494',1,'vg::WFANode']]],
+ ['append_5fpath_8156',['append_path',['../namespacevg.html#a75a663b07489d2aba3f800943eeb0eaf',1,'vg']]],
+ ['append_5fpath_5fhandle_5fgraph_8157',['append_path_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a19e43312515b3c752d20760788c97c6d',1,'handlegraph::algorithms']]],
+ ['append_5fright_8158',['append_right',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a8336638c37c43db1db857b380da94ab3',1,'vg::PhasedGenome::Haplotype']]],
+ ['append_5fstep_8159',['append_step',['../classvg_1_1VG.html#ad11c8a716733fce2aa9dab94b42286bd',1,'vg::VG::append_step()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a83a4a14a629cde03d33e4eb3f6bb192d',1,'handlegraph::MutablePathHandleGraph::append_step()']]],
+ ['apply_8160',['apply',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a8ce78918d24994e63851dacd6e0c0913',1,'vg::subcommand::BaseArgSpec::apply()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#ac03349ad6512375cc1de928c49b50f51',1,'vg::subcommand::ValueArgSpec::apply()'],['../structvg_1_1subcommand_1_1OptionGroup.html#adfbf39aed983c832777a5194d7623dbc',1,'vg::subcommand::OptionGroup::apply()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a745503da4f277b0347d56d3cb2979455',1,'vg::subcommand::GroupedOptionGroup::apply()'],['../structvg_1_1subcommand_1_1Preset.html#ada0abd10e8ffc45f18c3ea54991c5061',1,'vg::subcommand::Preset::apply()']]],
+ ['apply_5faligned_5fbase_8161',['apply_aligned_base',['../classvg_1_1NGSSimulator.html#a83b83821e465fb0eb28bfa6a6a53685e',1,'vg::NGSSimulator']]],
+ ['apply_5fdeletion_8162',['apply_deletion',['../classvg_1_1NGSSimulator.html#ac9767a14ddba8d462c562c8d3b60af6c',1,'vg::NGSSimulator']]],
+ ['apply_5fedit_8163',['apply_edit',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a9238af0b01ae60e19f699cf715c1b2b7',1,'vg::GraphSynchronizer::Lock::apply_edit(const Path &path, set< NodeSide > &dangling, size_t max_node_size=1024)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#ac45f1f724164cda30c1f792423d6e05c',1,'vg::GraphSynchronizer::Lock::apply_edit(const Path &path, size_t max_node_size=1024)']]],
+ ['apply_5ffull_5flength_5fedit_8164',['apply_full_length_edit',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a5d529df21455c13e5c1644ad91c4f55e',1,'vg::GraphSynchronizer::Lock']]],
+ ['apply_5fhaplotype_5fconsistency_5fscores_8165',['apply_haplotype_consistency_scores',['../classvg_1_1BaseMapper.html#a778c534cca5d7580584bba4131b65adc',1,'vg::BaseMapper']]],
+ ['apply_5finsertion_8166',['apply_insertion',['../classvg_1_1NGSSimulator.html#abd3a16dc107228d0e3678afff66314f0',1,'vg::NGSSimulator']]],
+ ['apply_5fmask_5fsequences_8167',['apply_mask_sequences',['../classvg_1_1Masker.html#a9803bfb97813ff5ae381957e56ed4f0c',1,'vg::Masker']]],
+ ['apply_5fmax_5freads_8168',['apply_max_reads',['../structvg_1_1Counts.html#a63cb45fa4645b31ad9e0a033cbd5de6c',1,'vg::Counts']]],
+ ['apply_5fmin_5fbp_5fedge_5foverride_8169',['apply_min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a2a9c63741c55418a64b72fb409a467f6',1,'vg::TraversalSupportFinder']]],
+ ['apply_5fn_5fmask_8170',['apply_N_mask',['../classvg_1_1NGSSimulator.html#aa81005880d4667e04ff07de3a0881322',1,'vg::NGSSimulator']]],
+ ['apply_5fordering_8171',['apply_ordering',['../classvg_1_1VG.html#af87ad4202f541fd560d67badcde09610',1,'vg::VG::apply_ordering()'],['../classhandlegraph_1_1MutableHandleGraph.html#a588935d58708b33bc66014b254393940',1,'handlegraph::MutableHandleGraph::apply_ordering()']]],
+ ['apply_5forientation_8172',['apply_orientation',['../classvg_1_1VG.html#ab5ee06ac168f037f2cff3b332079b49c',1,'vg::VG::apply_orientation()'],['../classhandlegraph_1_1MutableHandleGraph.html#a71433449cb13e22dc19caaf544b6d7bc',1,'handlegraph::MutableHandleGraph::apply_orientation()']]],
+ ['apply_5forientations_8173',['apply_orientations',['../namespacehandlegraph_1_1algorithms.html#a81d399d76c97b214aa55a82976185ea6',1,'handlegraph::algorithms']]],
+ ['apply_5ftranslation_8174',['apply_translation',['../structvg_1_1PathIndex.html#a827ae5af1330e03a23c35351d3152f03',1,'vg::PathIndex']]],
+ ['apply_5ftranslations_8175',['apply_translations',['../structvg_1_1PathIndex.html#a8aeebd524dc064af4cdda9fd84de2a4a',1,'vg::PathIndex']]],
+ ['approx_5falignment_5fposition_8176',['approx_alignment_position',['../classvg_1_1Mapper.html#ad7a2c554e02a60549d8c46459bed0491',1,'vg::Mapper']]],
+ ['approx_5fdistance_8177',['approx_distance',['../classvg_1_1Mapper.html#a04be7bfcb3252ef33217cb0f5823d4f8',1,'vg::Mapper']]],
+ ['approx_5ffragment_5flength_8178',['approx_fragment_length',['../classvg_1_1Mapper.html#a3f15631b08b10107963a5c17d21c3717',1,'vg::Mapper']]],
+ ['approx_5fgbwt_5fmemory_8179',['approx_gbwt_memory',['../namespacevg.html#a745a31f5e7853868dbf903f33a986480',1,'vg']]],
+ ['approx_5fgraph_5fload_5fmemory_8180',['approx_graph_load_memory',['../namespacevg.html#a0d0300b12116a047d137e134eebe2e1d',1,'vg']]],
+ ['approx_5fgraph_5fmemory_8181',['approx_graph_memory',['../namespacevg.html#a3d3cceb7b721a218a1be1c948138526a',1,'vg::approx_graph_memory(const vector< string > &fasta_filenames, const vector< string > &vcf_filenames)'],['../namespacevg.html#a4a16cd88bceed4db044decd94211833d',1,'vg::approx_graph_memory(const string &fasta_filename, const string &vcf_filename)'],['../namespacevg.html#aa588389795ea8613480df1c7eeeafaf8',1,'vg::approx_graph_memory(const string &gfa_filename)']]],
+ ['approx_5fnum_5fvars_8182',['approx_num_vars',['../namespacevg.html#a665fe802cdb44d2dba6052fc9063513d',1,'vg']]],
+ ['approx_5fposition_8183',['approx_position',['../classvg_1_1Mapper.html#accd2bd6b8ec2db952fd79e0742f1a548',1,'vg::Mapper']]],
+ ['arch_5fis_5fbig_5fendian_8184',['arch_is_big_endian',['../structvg_1_1endianness.html#a24b1cadacc768c204cfebeff0c9d33f9',1,'vg::endianness']]],
+ ['are_5fconsecutive_5fnodes_5fin_5fpath_8185',['are_consecutive_nodes_in_path',['../classvg_1_1Paths.html#a9562c903db44e7328f82c30afea6c643',1,'vg::Paths']]],
+ ['are_5fconsistent_8186',['are_consistent',['../classvg_1_1MultipathMapper.html#a0080de005fe755313ddd6bf3b41620b4',1,'vg::MultipathMapper']]],
+ ['are_5fequivalent_8187',['are_equivalent',['../namespacehandlegraph_1_1algorithms.html#a3a3110dde9b4be48c07966ca05f07ce3',1,'handlegraph::algorithms']]],
+ ['are_5fequivalent_5fwith_5fpaths_8188',['are_equivalent_with_paths',['../namespacehandlegraph_1_1algorithms.html#a47f57c2a75f2c22df467596639377d77',1,'handlegraph::algorithms']]],
+ ['argspec_8189',['ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html#a78e4d05575c29900e19e72fe4854fb48',1,'vg::subcommand::ArgSpec::ArgSpec(const std::string &option, char short_option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)'],['../structvg_1_1subcommand_1_1ArgSpec.html#a5c2f438f67a728d5921ceefc4414dea1',1,'vg::subcommand::ArgSpec::ArgSpec(const std::string &option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)']]],
+ ['array_5fend_8190',['array_end',['../classvg_1_1ProblemDumpExplainer.html#a7696c7a5ed73ae3a701d4aeb3b2f53b0',1,'vg::ProblemDumpExplainer']]],
+ ['array_5fstart_8191',['array_start',['../classvg_1_1ProblemDumpExplainer.html#ae4c171c4c55ae76ce36d18889520f2a2',1,'vg::ProblemDumpExplainer']]],
+ ['as_5fedge_5ftable_8192',['as_edge_table',['../classvg_1_1Packer.html#a8fa7e449fc6358a1d1b13c0447027acb',1,'vg::Packer']]],
+ ['as_5fhandle_8193',['as_handle',['../namespacehandlegraph.html#acba8bb138abe07535c62ab95b6ab135c',1,'handlegraph::as_handle(uint64_t &value)'],['../namespacehandlegraph.html#a95e4115f2aba44e76c62fee839f384af',1,'handlegraph::as_handle(const uint64_t &value)']]],
+ ['as_5finteger_8194',['as_integer',['../namespacehandlegraph.html#a2bfd349561c52c6e3d32e11ad31a1056',1,'handlegraph::as_integer(handle_t &handle)'],['../namespacehandlegraph.html#aa9b39d28e558d08900cf0659648edc66',1,'handlegraph::as_integer(const handle_t &handle)'],['../namespacehandlegraph.html#aa046efc20cdba831aee499ca693b851a',1,'handlegraph::as_integer(path_handle_t &handle)'],['../namespacehandlegraph.html#a1020b4ec56092e0413aa8deb3bd8097b',1,'handlegraph::as_integer(const path_handle_t &handle)'],['../namespacehandlegraph.html#a3af04d045bd99ae54e56ab415ca74515',1,'handlegraph::as_integer(net_handle_t &handle)'],['../namespacehandlegraph.html#a2964abbc51b220805b599c14fe5785b3',1,'handlegraph::as_integer(const net_handle_t &handle)']]],
+ ['as_5fintegers_8195',['as_integers',['../namespacehandlegraph.html#a5a37d9e18dfe77f0342573269372f96d',1,'handlegraph::as_integers(step_handle_t &step_handle)'],['../namespacehandlegraph.html#aa470ea0407a5de15a2e0da4ca0ac5df8',1,'handlegraph::as_integers(const step_handle_t &step_handle)']]],
+ ['as_5fnet_5fhandle_8196',['as_net_handle',['../namespacehandlegraph.html#a34b30f72d26f0ab83a3b4668cb0ba73b',1,'handlegraph::as_net_handle(uint64_t &value)'],['../namespacehandlegraph.html#a5a078e0cfd4fd4fbd0fbc5f6f6c03e7d',1,'handlegraph::as_net_handle(const uint64_t &value)']]],
+ ['as_5fpath_5fhandle_8197',['as_path_handle',['../namespacehandlegraph.html#a4d0f261ff95d242a0ceeaa2f01b961c0',1,'handlegraph::as_path_handle(uint64_t &value)'],['../namespacehandlegraph.html#abdee6d57b3c2132b34aae90c7766d213',1,'handlegraph::as_path_handle(const uint64_t &value)']]],
+ ['as_5fquality_5ftable_8198',['as_quality_table',['../classvg_1_1Packer.html#a4768a4ad03f393f7abdf1c6a977b8caf',1,'vg::Packer']]],
+ ['as_5ftable_8199',['as_table',['../classvg_1_1Packer.html#a51f56dd9782bb7841c7b50678f8ed868',1,'vg::Packer::as_table()'],['../classvg_1_1Packers.html#afcd4807c5743b90833a8e0f351f4fc77',1,'vg::Packers::as_table()']]],
+ ['assign_5fchild_5fsnarls_5fto_5ftraversals_8200',['assign_child_snarls_to_traversals',['../namespacevg.html#a1ac7d2a0833215a0628a25c8195a70ab',1,'vg']]],
+ ['assign_5fconstructed_8201',['assign_constructed',['../classvg_1_1IndexFile.html#ac3bf2966b1a530956e099f225208395e',1,'vg::IndexFile']]],
+ ['assign_5fnew_5fsequence_5fid_8202',['assign_new_sequence_id',['../classvg_1_1algorithms_1_1GFAParser.html#aa7d65677018149472a7924da28b6633b',1,'vg::algorithms::GFAParser']]],
+ ['at_8203',['at',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a613f2b4b5f02b68f1868830e3213ffe2',1,'vg::Option< vector< Item >, Parser >::at(size_t i)'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a8e8fb7dad7fb3274f9dae3e11be2ed5c',1,'vg::Option< vector< Item >, Parser >::at(size_t i) const'],['../classvg_1_1ZipCodeCollection.html#a872b6e4393de003c61621d883cac4efb',1,'vg::ZipCodeCollection::at()']]],
+ ['at_5fdead_5fend_8204',['at_dead_end',['../classvg_1_1WFATree.html#a98b3e5f4f226261068acfa268ec416ae',1,'vg::WFATree']]],
+ ['at_5flast_5fnode_8205',['at_last_node',['../structvg_1_1MatchPos.html#a8a426f343756ea69a1d6ae73801d9451',1,'vg::MatchPos']]],
+ ['at_5fnext_5fdeflection_8206',['at_next_deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a591b428cb1644725419966f805790fb1',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['at_5for_5fafter_8207',['at_or_after',['../classvg_1_1BitString.html#af27a8d8554102a67192bb3627a56ad77',1,'vg::BitString']]],
+ ['at_5for_5fbefore_8208',['at_or_before',['../classvg_1_1BitString.html#a8f2a6515c588dc34d5f8a3b10035f891',1,'vg::BitString']]],
+ ['at_5fposition_8209',['at_position',['../structvg_1_1PathIndex.html#aab1c5d586bdef0e4cdc31ed7531eee7c',1,'vg::PathIndex']]],
+ ['attempt_5frescue_8210',['attempt_rescue',['../classvg_1_1MinimizerMapper.html#ad2a8850ee32bef9fd4b1a52034d5a930',1,'vg::MinimizerMapper::attempt_rescue()'],['../classvg_1_1MultipathMapper.html#a007fc06565e2f9b1aa084cc4cc60a55d',1,'vg::MultipathMapper::attempt_rescue()']]],
+ ['attempt_5frescue_5ffor_5fsecondaries_8211',['attempt_rescue_for_secondaries',['../classvg_1_1MultipathMapper.html#a2d154aa0e761a99266c6eddab022a1c6',1,'vg::MultipathMapper']]],
+ ['attempt_5frescue_5ffor_5fsplice_5fsegment_8212',['attempt_rescue_for_splice_segment',['../classvg_1_1MultipathMapper.html#a535c42c7052c82ddc71613cce3459b03',1,'vg::MultipathMapper']]],
+ ['attempt_5funpaired_5fmultipath_5fmap_5fof_5fpair_8213',['attempt_unpaired_multipath_map_of_pair',['../classvg_1_1MultipathMapper.html#a9bdb30363cd02187fb0a1ca07ea2cb20',1,'vg::MultipathMapper']]],
+ ['augment_8214',['augment',['../namespacevg.html#a3ad955989dbbd240c02052d94a9214e2',1,'vg::augment(MutablePathMutableHandleGraph *graph, const string &gam_path, const string &aln_format, vector< Translation > *out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only)'],['../namespacevg.html#a10c4a321eb33280d58a3ddaf97f52ed2',1,'vg::augment(MutablePathMutableHandleGraph *graph, vector< Path > &path_vector, const string &aln_format, vector< Translation > *out_translations, const string &gam_out_path, bool embed_paths, bool break_at_ends, bool remove_softclips, bool filter_out_of_graph_alignments, double min_baseq, double min_mapq, Packer *packer, size_t min_bp_coverage, double max_frac_n, bool edges_only)']]],
+ ['augment_5ffrom_5falignment_5fedits_8215',['augment_from_alignment_edits',['../structvg_1_1AugmentedGraph.html#a56ecda832a62dd3a22424bb8720a4601',1,'vg::AugmentedGraph']]],
+ ['augment_5fgraph_8216',['augment_graph',['../classvg_1_1Transcriptome.html#ac4eff095379bd9ab5691704de1ddc293',1,'vg::Transcriptome']]],
+ ['augment_5fimpl_8217',['augment_impl',['../namespacevg.html#a5be4fdda1799c2f6876f2ac4937da349',1,'vg']]],
+ ['aux_5farray_5fto_5fstring_8218',['aux_array_to_string',['../namespacevg.html#a156dcf09705f414bd179a43f565ad354',1,'vg']]],
+ ['aux_5fval_5fto_5fstring_8219',['aux_val_to_string',['../namespacevg.html#a10de011128f0da64a698f71d8c7c1cdf',1,'vg']]],
+ ['available_8220',['available',['../classvg_1_1IndexRegistry.html#a8c88fde3123fced3178841fc76862a19',1,'vg::IndexRegistry']]],
+ ['average_5fnode_5fquality_8221',['average_node_quality',['../classvg_1_1Packer.html#a5a5c771bdb82f53eeef987e598669566',1,'vg::Packer']]],
+ ['avg_5fqual_5ffilter_8222',['avg_qual_filter',['../classvg_1_1Filter.html#a3401568683899d1ebe2bcaf971a8374e',1,'vg::Filter']]]
];
diff --git a/search/functions_10.js b/search/functions_10.js
index 9f03d539f4..d0c75be78f 100644
--- a/search/functions_10.js
+++ b/search/functions_10.js
@@ -1,258 +1,258 @@
var searchData=
[
- ['p_5fvalue_10291',['p_value',['../structvg_1_1SeqComplexity.html#a20dfb4fbec20a18a5decaccc046c10e8',1,'vg::SeqComplexity']]],
- ['pack_10292',['pack',['../structhandlegraph_1_1number__bool__packing.html#af5082dc39a2f308585402bd19de0caa8',1,'handlegraph::number_bool_packing']]],
- ['pack_5fquery_5fforward_10293',['pack_query_forward',['../classvg_1_1DozeuInterface.html#acd17348d5d2dd0ec4c10af98748fe67a',1,'vg::DozeuInterface::pack_query_forward()'],['../classvg_1_1XdropAligner.html#a9179d91b00ed33fbc3e9e6a4bd6b9321',1,'vg::XdropAligner::pack_query_forward()'],['../classvg_1_1QualAdjXdropAligner.html#a0e1140ad3ee66b2583869ccd2267841b',1,'vg::QualAdjXdropAligner::pack_query_forward()']]],
- ['pack_5fquery_5freverse_10294',['pack_query_reverse',['../classvg_1_1DozeuInterface.html#aa15876efde0e6d8f963d37ae245c8ead',1,'vg::DozeuInterface::pack_query_reverse()'],['../classvg_1_1XdropAligner.html#a3c3832ae9935773f0dd0b97ed031c70e',1,'vg::XdropAligner::pack_query_reverse()'],['../classvg_1_1QualAdjXdropAligner.html#a0d6b25927dccfe18f03eab6457486ac7',1,'vg::QualAdjXdropAligner::pack_query_reverse()']]],
- ['packed_5fdepth_5fof_5fbin_10295',['packed_depth_of_bin',['../namespacevg_1_1algorithms.html#a62ebbcbfe1250940eb8ebf0a2dcbc19a',1,'vg::algorithms']]],
- ['packed_5fdepths_10296',['packed_depths',['../namespacevg_1_1algorithms.html#abd431ebd9786d796f708a7046e643e2e',1,'vg::algorithms']]],
- ['packedtraversalsupportfinder_10297',['PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html#a5bb7b3f0b3fd9c72597403ce75f8791c',1,'vg::PackedTraversalSupportFinder']]],
- ['packer_10298',['Packer',['../classvg_1_1Packer.html#a965acab0b6c7d973a67e449785955739',1,'vg::Packer::Packer(const HandleGraph *graph=nullptr)'],['../classvg_1_1Packer.html#ad52836b610249ada7cf0ad13c329b52c',1,'vg::Packer::Packer(const HandleGraph *graph, bool record_bases, bool record_edges, bool record_edits, bool record_qualities, size_t bin_size=0, size_t coverage_bins=1, size_t data_width=8)']]],
- ['pad_5fband_5fconstant_10299',['pad_band_constant',['../namespacevg_1_1algorithms.html#aaab5b2261edb66897af9d1158e7758d8',1,'vg::algorithms']]],
- ['pad_5fband_5fmin_5frandom_5fwalk_10300',['pad_band_min_random_walk',['../namespacevg_1_1algorithms.html#a25a37b51facd101b8a29b1a57661f74f',1,'vg::algorithms']]],
- ['pad_5fband_5frandom_5fwalk_10301',['pad_band_random_walk',['../namespacevg_1_1algorithms.html#a1294ed71274673b7e4cc1d40e9472666',1,'vg::algorithms']]],
- ['pad_5fband_5frandom_5fwalk_5finternal_10302',['pad_band_random_walk_internal',['../namespacevg_1_1algorithms.html#a9957e925ee25c57698383d4e1df21f0d',1,'vg::algorithms']]],
- ['pad_5ftraversal_10303',['pad_traversal',['../classvg_1_1GAFOutputCaller.html#a697f4f2c00fa8317ba8143bbe99931fb',1,'vg::GAFOutputCaller']]],
- ['paint_10304',['paint',['../structvg_1_1Funnel_1_1PaintableSpace.html#a88c1043f7b0cae737da989f0abc44b0a',1,'vg::Funnel::PaintableSpace']]],
- ['pair_5fall_10305',['pair_all',['../classvg_1_1MinimizerMapper.html#a4493ab0315512da6b10a7cde3754afe2',1,'vg::MinimizerMapper']]],
- ['pair_5fcluster_5fmultiplicity_10306',['pair_cluster_multiplicity',['../classvg_1_1MultipathMapper.html#ae534f0c248a4b44bdf389ead66d105e3',1,'vg::MultipathMapper']]],
- ['pair_5fclusters_10307',['pair_clusters',['../classvg_1_1MEMClusterer.html#a4e84dd599bb8dc4341cbed2fd1de1ed0',1,'vg::MEMClusterer::pair_clusters()'],['../classvg_1_1NullClusterer.html#a1794ac271ce6d785e67b488a98ec87d6',1,'vg::NullClusterer::pair_clusters()'],['../classvg_1_1OrientedDistanceClusterer.html#a41e57b46abd69532d53855499d5042eb',1,'vg::OrientedDistanceClusterer::pair_clusters()'],['../classvg_1_1TVSClusterer.html#a1477ce3367e036c0ecc101e1518b49b9',1,'vg::TVSClusterer::pair_clusters()'],['../classvg_1_1MinDistanceClusterer.html#af561001a20cc91adc6238f74edca6480',1,'vg::MinDistanceClusterer::pair_clusters()']]],
- ['pair_5fconsistent_10308',['pair_consistent',['../classvg_1_1Mapper.html#ad3a62e0a91818c4e20508ab2a0f47fa5',1,'vg::Mapper']]],
- ['pair_5ffrom_5fedge_10309',['pair_from_edge',['../classvg_1_1NodeSide.html#ad48cc3d977ad0f6ffc5ce1034cbbae65',1,'vg::NodeSide::pair_from_edge(Edge *e)'],['../classvg_1_1NodeSide.html#a97eed27ab7b77be54b68062b780a9f36',1,'vg::NodeSide::pair_from_edge(const Edge &e)']]],
- ['pair_5ffrom_5fend_5fedge_10310',['pair_from_end_edge',['../classvg_1_1NodeSide.html#a23f18cf5f9ae9c7fc8475800d967275c',1,'vg::NodeSide']]],
- ['pair_5ffrom_5fstart_5fedge_10311',['pair_from_start_edge',['../classvg_1_1NodeSide.html#a3193e35c9e8349c427cc834335e25405',1,'vg::NodeSide']]],
- ['pair_5fmapping_5flikelihoods_10312',['pair_mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a05dd8b61205954b988bb996479883989',1,'vg::MultipathMapper']]],
- ['pair_5forientation_5ffilter_10313',['pair_orientation_filter',['../classvg_1_1Filter.html#a16451e95cd6c7642df9f013d5b73c0c7',1,'vg::Filter']]],
- ['pair_5frescue_10314',['pair_rescue',['../classvg_1_1Mapper.html#a36248b0eb439694bfbd493fce0ce2b02',1,'vg::Mapper']]],
- ['pair_5fto_5fstring_10315',['pair_to_string',['../haplotypes__main_8cpp.html#a7d4977594e9d93b802b94c95752f34a2',1,'haplotypes_main.cpp']]],
- ['paired_5ffor_5feach_5fparallel_5fafter_5fwait_10316',['paired_for_each_parallel_after_wait',['../namespacevg_1_1io.html#af3c3dd4ad5c9b887fd3ee389e0b67ef6',1,'vg::io']]],
- ['parallelkffreader_10317',['ParallelKFFReader',['../classvg_1_1ParallelKFFReader.html#a4b84d319b814d4b2a5f099d19d0426d5',1,'vg::ParallelKFFReader::ParallelKFFReader(const std::string &filename)'],['../classvg_1_1ParallelKFFReader.html#adcdc292236ba8b178c38666702b4e5c1',1,'vg::ParallelKFFReader::ParallelKFFReader(const ParallelKFFReader &)=delete']]],
- ['parameters_10318',['Parameters',['../structvg_1_1Recombinator_1_1Parameters.html#a3112d2a46538ce1575d53b6706f25756',1,'vg::Recombinator::Parameters']]],
- ['parent_10319',['parent',['../classvg_1_1WFATree.html#ab6c9c25e1906e3a95bc6c853a2c5db3f',1,'vg::WFATree']]],
- ['parent_5fof_10320',['parent_of',['../classvg_1_1SnarlManager.html#ad4c8dd034c160f2908164c1ebc2a0394',1,'vg::SnarlManager']]],
- ['parse_10321',['parse',['../classvg_1_1OptionInterface.html#aa658456e011e28d8e6d3073c8ccfc740',1,'vg::OptionInterface::parse()=0'],['../classvg_1_1OptionInterface.html#a5679dbc64e1f490d7caa35730de6d09b',1,'vg::OptionInterface::parse(const string &arg)=0'],['../classvg_1_1ConfigurableParser.html#a9c28ad9040822d975a38c982677065bd',1,'vg::ConfigurableParser::parse()'],['../classvg_1_1OptionValueParser.html#a4b43a211a8dca7c43a1fe3fc4fde1de5',1,'vg::OptionValueParser::parse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a27e910ec23c80fc2c829dcdb98da0ddc',1,'vg::OptionValueParser< vector< Item > >::parse()'],['../classvg_1_1BaseOption.html#a6682e454cf748d2a29623849d72f8d1d',1,'vg::BaseOption::parse()'],['../classvg_1_1BaseOption.html#ab17b0a67fe5bdb8de8ffb39f98a804e7',1,'vg::BaseOption::parse(const string &arg)'],['../classvg_1_1algorithms_1_1GFAParser.html#a575aa78bfa6a567735133c8cffa6da77',1,'vg::algorithms::GFAParser::parse()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a040fd55d950392ade69dad277adfb848',1,'vg::subcommand::BaseArgSpec::parse()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a8ddbad123ba28ff099c263d24b751889',1,'vg::subcommand::ValueArgSpec::parse()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a96a1df206d4ef889c7f3f6cf08dc1426',1,'vg::subcommand::FlagArgSpec::parse()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a6fa17a5e6d8fbc293d69063c947cb0aa',1,'vg::subcommand::BaseOptionGroup::parse()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aa4b885a991453bbc8cde726e35dd115f',1,'vg::subcommand::OptionGroup::parse()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aada2ded9febbec1c9bab141da4bfc0ce',1,'vg::subcommand::GroupedOptionGroup::parse()'],['../classvg_1_1OptionValueParser.html#a5a34866bb0ac6c4feae8b5a20aba93c7',1,'vg::OptionValueParser::parse()'],['../namespacevg.html#a1dd328fd8abb43338a3ae9e0a3b0be1f',1,'vg::parse(const string &arg, double &dest)'],['../namespacevg.html#a2d3193c0a90ba95bd11b8b3201de52c0',1,'vg::parse(const string &arg, float &dest)'],['../namespacevg.html#aa1de4a1752e875116c767ec49a8e2961',1,'vg::parse(const string &arg, std::regex &dest)'],['../namespacevg.html#aa4a3393960dd54c941e9d7c317923c2e',1,'vg::parse(const string &arg, pos_t &dest)'],['../namespacevg.html#a8873caafc22d22b52e0f6f3f164f6dc8',1,'vg::parse(const string &arg)'],['../namespacevg.html#a8c5c364797f623025b67b9aff0657112',1,'vg::parse(const char *arg)'],['../namespacevg.html#a627f5ad6fe6f1e6b4cc23ac97dfca4b8',1,'vg::parse(const string &arg, Result &dest)'],['../namespacevg.html#a2cd6368e7395f1d90c4e3be1a7293d0a',1,'vg::parse(const string &arg, typename enable_if< sizeof(Result)<=sizeof(long long) &&is_integral< Result >::value &&is_signed< Result >::value, Result >::type &dest)'],['../namespacevg.html#a1384531a1c8d8387bdd04961590bdf93',1,'vg::parse(const string &arg, typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &dest)']]],
- ['parse_5fattribute_5fvalue_10322',['parse_attribute_value',['../classvg_1_1Transcriptome.html#a401bd93346ea5e02f586823d8f3b458e',1,'vg::Transcriptome']]],
- ['parse_5fattributes_10323',['parse_attributes',['../structvg_1_1GFFRecord.html#ade5c97a34abe718fbb607977f11fb8f1',1,'vg::GFFRecord']]],
- ['parse_5fbed_10324',['parse_bed',['../mask__main_8cpp.html#a210b34f1b7dfefc99804b335b0cf6e19',1,'mask_main.cpp']]],
- ['parse_5fbed_5fregions_10325',['parse_bed_regions',['../namespacevg.html#a736f4c7b5d03a7efe78315b4c5490f15',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#ad88fe24ca988562008c8b734c22cb403',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)'],['../namespacevg.html#a8fd1e3436d98304996aaecece048cb45',1,'vg::parse_bed_regions(const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)']]],
- ['parse_5fdefault_10326',['parse_default',['../classvg_1_1OptionValueParser.html#ad2b7db7247de0c8cb7fe4e9501314b6b',1,'vg::OptionValueParser::parse_default()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#aa9624ebfad0e2421af39a86e7327edaf',1,'vg::OptionValueParser< vector< Item > >::parse_default()'],['../classvg_1_1OptionValueParser.html#acddd63568b5e1a7ece023abeccccd15b',1,'vg::OptionValueParser::parse_default()']]],
- ['parse_5ffrom_5fstring_10327',['parse_from_string',['../classvg_1_1io_1_1ProtobufIterator.html#ab37e50d3f1375c13a223a79938d5094d',1,'vg::io::ProtobufIterator']]],
- ['parse_5fgaf_5frecord_10328',['parse_gaf_record',['../namespacegafkluge.html#ab8a6f72dddac182a6d8d74a52a6fc92d',1,'gafkluge']]],
- ['parse_5fgbwt_5fconfig_10329',['parse_gbwt_config',['../gbwt__main_8cpp.html#a8153bcd09dec28c64e4a9bfad67cee40',1,'gbwt_main.cpp']]],
- ['parse_5fgff_5fregions_10330',['parse_gff_regions',['../namespacevg.html#a55cc20d96f38b54c590af4f3f3ac2498',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#a629c9fee8a51c4ca363511ae01ad4a09',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)']]],
- ['parse_5fh_10331',['parse_h',['../classvg_1_1algorithms_1_1GFAParser.html#a122490db3d620bc310b106e2231a9140',1,'vg::algorithms::GFAParser']]],
- ['parse_5fhaplotype_10332',['parse_haplotype',['../classhandlegraph_1_1PathMetadata.html#a69e57ea70c57b01b309cdf39da4eeeb5',1,'handlegraph::PathMetadata']]],
- ['parse_5fhaplotype_5ftranscript_5ffile_10333',['parse_haplotype_transcript_file',['../sim__main_8cpp.html#ae98175893da0d162097014dd65ba8ce2',1,'sim_main.cpp']]],
- ['parse_5fintron_5fdistr_5ffile_10334',['parse_intron_distr_file',['../mpmap__main_8cpp.html#a48bc366d5c5d1acbc0c60556944bcfe9',1,'mpmap_main.cpp']]],
- ['parse_5fintrons_10335',['parse_introns',['../classvg_1_1Transcriptome.html#ad040b82553e6b03ccd926c0fe622e84c',1,'vg::Transcriptome']]],
- ['parse_5fl_10336',['parse_l',['../classvg_1_1algorithms_1_1GFAParser.html#a6033f9ec4740e70dc79fbaae78f91773',1,'vg::algorithms::GFAParser']]],
- ['parse_5flocus_5fname_10337',['parse_locus_name',['../classhandlegraph_1_1PathMetadata.html#a978b48ca96f8817f7099587dae77b8b4',1,'handlegraph::PathMetadata']]],
- ['parse_5fmatrix_10338',['parse_matrix',['../classvg_1_1AlignerClient.html#a4a56c0bf099b670763c0f5ce3653811b',1,'vg::AlignerClient']]],
- ['parse_5fmemory_5fusage_10339',['parse_memory_usage',['../autoindex__main_8cpp.html#ad25ab5b852b7a1bc223505f7a2e23853',1,'autoindex_main.cpp']]],
- ['parse_5fp_10340',['parse_p',['../classvg_1_1algorithms_1_1GFAParser.html#a3f28df872d86abde347b3bbcc7f42948',1,'vg::algorithms::GFAParser']]],
- ['parse_5fpath_5fname_10341',['parse_path_name',['../classhandlegraph_1_1PathMetadata.html#ab6bcceaaedfbb03a4ea3f70499b06ade',1,'handlegraph::PathMetadata']]],
- ['parse_5fphase_5fblock_10342',['parse_phase_block',['../classhandlegraph_1_1PathMetadata.html#a3d9a3a974ab62d008104fa7dab849465',1,'handlegraph::PathMetadata']]],
- ['parse_5fprovide_5fstring_10343',['parse_provide_string',['../autoindex__main_8cpp.html#a8f62d94c211a4113595cbdf100129fc3',1,'autoindex_main.cpp']]],
- ['parse_5fregion_10344',['parse_region',['../namespacevg.html#a253257615743a1cfb948b749be7700e2',1,'vg::parse_region(const string &target, string &name, int64_t &start, int64_t &end)'],['../namespacevg.html#af0a3beb8908adf7a6e4d641243937830',1,'vg::parse_region(string ®ion, Region &out_region)']]],
- ['parse_5frg_5fsample_5fmap_10345',['parse_rg_sample_map',['../namespacevg.html#a637c855dffc0296c6575ae8a4cac6b43',1,'vg']]],
- ['parse_5frsem_5fexpression_5ffile_10346',['parse_rsem_expression_file',['../sim__main_8cpp.html#aa1964053fdd12fb9dde544ce6d18ab70',1,'sim_main.cpp']]],
- ['parse_5fs_10347',['parse_s',['../classvg_1_1algorithms_1_1GFAParser.html#af4ce322cdb902c01881afcbb4fea85f5',1,'vg::algorithms::GFAParser']]],
- ['parse_5fsam_5ftags_10348',['parse_sam_tags',['../namespacevg.html#a175da49ded2be9251e68ae642108248a',1,'vg']]],
- ['parse_5fsample_5fname_10349',['parse_sample_name',['../classhandlegraph_1_1PathMetadata.html#acbc675d9d41c36eebb174b4871c42435',1,'handlegraph::PathMetadata']]],
- ['parse_5fsense_10350',['parse_sense',['../classhandlegraph_1_1PathMetadata.html#aae6aa5f2738ce962e4e74d46a9c5e3e0',1,'handlegraph::PathMetadata']]],
- ['parse_5fsubrange_10351',['parse_subrange',['../classhandlegraph_1_1PathMetadata.html#a010d050ee3bf526da9ae45fde6dd1dc6',1,'handlegraph::PathMetadata']]],
- ['parse_5ftags_10352',['parse_tags',['../classvg_1_1algorithms_1_1GFAParser.html#a4fecb9e4836c67853d300ffd29b046e7',1,'vg::algorithms::GFAParser']]],
- ['parse_5ftid_5fpath_5fhandle_5fmap_10353',['parse_tid_path_handle_map',['../namespacevg.html#abc66619671bdc564023a9b3259558785',1,'vg']]],
- ['parse_5ftranscripts_10354',['parse_transcripts',['../classvg_1_1Transcriptome.html#ae7b6c679e3d635342029bbc7cc39d75d',1,'vg::Transcriptome']]],
- ['parse_5ftranslation_10355',['parse_translation',['../structvg_1_1PathIndex.html#aa5272234ddb7686f1ae88881ebf99a61',1,'vg::PathIndex']]],
- ['parse_5fvcf_10356',['parse_vcf',['../classvg_1_1HaplotypeIndexer.html#ad3eda4acd04b8bae303b4604410ece41',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::string &job_name="GBWT") const'],['../classvg_1_1HaplotypeIndexer.html#ad81dbd24bba40aaa14536d79754d387b',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::vector< path_handle_t > &paths, const std::string &job_name="GBWT") const']]],
- ['parse_5fw_10357',['parse_w',['../classvg_1_1algorithms_1_1GFAParser.html#ae03c9247eb49aed8f868039365f89cdd',1,'vg::algorithms::GFAParser']]],
- ['parsegenotypes_10358',['parseGenotypes',['../namespacevg.html#a8bcecf9fe02b7f50dd5e72e40dcd98e1',1,'vg']]],
- ['partition_5fgbwt_5fsequences_10359',['partition_gbwt_sequences',['../namespacevg.html#a802baeeacfe4ee75781afabac562588b',1,'vg']]],
- ['partition_5fhaplotypes_10360',['partition_haplotypes',['../classvg_1_1HaplotypePartitioner.html#a1c0a32c7f0ca0f86fd5abb9b746895c8',1,'vg::HaplotypePartitioner']]],
- ['pass_10361',['pass',['../classvg_1_1Funnel.html#aec19daea826d5951ecf1477769722d9a',1,'vg::Funnel']]],
- ['patch_5falignment_10362',['patch_alignment',['../classvg_1_1Mapper.html#ad8f03f4ff100a15ea885a5404222a0ad',1,'vg::Mapper']]],
- ['path_10363',['path',['../classvg_1_1subpath__t.html#ad9d97e89f59cf75b1d00f0e54d979048',1,'vg::subpath_t::path()'],['../classvg_1_1Paths.html#a218a01d5d53bf945ef4f0acafd18d6bc',1,'vg::Paths::path()']]],
- ['path_5fback_10364',['path_back',['../classvg_1_1MemoizingGraph.html#a90d25a87afe426eb79582739848734c4',1,'vg::MemoizingGraph::path_back()'],['../classvg_1_1PathSubgraphOverlay.html#a7e9706b6c571a62a93c7dafb3be62f29',1,'vg::PathSubgraphOverlay::path_back()'],['../classvg_1_1VG.html#a1af5ef2df0289b964cab09d9400344c5',1,'vg::VG::path_back()'],['../classxg_1_1XG.html#aceaf4782f2fb6cbd169b6121fea8e4e8',1,'xg::XG::path_back()'],['../classhandlegraph_1_1PathHandleGraph.html#a31bb33a87ad8efd68876fc5ae1deeb09',1,'handlegraph::PathHandleGraph::path_back()']]],
- ['path_5fbegin_10365',['path_begin',['../classvg_1_1MemoizingGraph.html#ac40575d724c1d7053b9765e622cc3713',1,'vg::MemoizingGraph::path_begin()'],['../classvg_1_1PathSubgraphOverlay.html#a492b11a38ba4d31ee75341fc8777f19c',1,'vg::PathSubgraphOverlay::path_begin()'],['../classvg_1_1VG.html#af0fc3a05ce45e0100fb82812c5b1e35d',1,'vg::VG::path_begin()'],['../classxg_1_1XG.html#ad4894f85d76ca8101a5dd164a29379c5',1,'xg::XG::path_begin()'],['../classhandlegraph_1_1PathHandleGraph.html#a815759484087ed92214c2c1c6b9d1a11',1,'handlegraph::PathHandleGraph::path_begin()']]],
- ['path_5fcontains_5fhandle_10366',['path_contains_handle',['../classxg_1_1XG.html#ad55f3e5461c20199ccdb3a6fb4dacdf6',1,'xg::XG']]],
- ['path_5fcontains_5fnode_10367',['path_contains_node',['../structvg_1_1PathIndex.html#ab1bb8b7aec345a4b59242287ae1693c7',1,'vg::PathIndex']]],
- ['path_5fcontains_5fnode_5fin_5forientation_10368',['path_contains_node_in_orientation',['../structvg_1_1PathIndex.html#a0dbda80790b6d81aa0f9d83ac21f85a3',1,'vg::PathIndex']]],
- ['path_5fcover_5fparameters_10369',['path_cover_parameters',['../structGBWTConfig.html#a27d5429660a51913c09fa1b33477d27a',1,'GBWTConfig']]],
- ['path_5fdepth_5fof_5fbin_10370',['path_depth_of_bin',['../namespacevg_1_1algorithms.html#a8c66507d55ed6e10e9d77e1281d4bcfc',1,'vg::algorithms']]],
- ['path_5fdepths_10371',['path_depths',['../namespacevg_1_1algorithms.html#a85250c33b7d32346be371ab7e4404471',1,'vg::algorithms']]],
- ['path_5fdivergence_5ffilter_10372',['path_divergence_filter',['../classvg_1_1Filter.html#a961710b28527b3f9961948a068c3b860',1,'vg::Filter']]],
- ['path_5fedge_5fcount_10373',['path_edge_count',['../classvg_1_1VG.html#a5f1df72d85d8a72524b76abca972f33d',1,'vg::VG']]],
- ['path_5fend_10374',['path_end',['../classvg_1_1MemoizingGraph.html#a2e4006fc68d2db22228dcef6bed02666',1,'vg::MemoizingGraph::path_end()'],['../classvg_1_1PathSubgraphOverlay.html#a5d74d2d221394980ff65e2e9adc1818f',1,'vg::PathSubgraphOverlay::path_end()'],['../classvg_1_1VG.html#a2f532a7aeb7765b99c6c4e43ba961fdb',1,'vg::VG::path_end()'],['../classxg_1_1XG.html#a32e53f5b1a5cd650b5d731f0354c5c2d',1,'xg::XG::path_end()'],['../classhandlegraph_1_1PathHandleGraph.html#a5c3a5e04838d9e4a0a0ddf574c4de827',1,'handlegraph::PathHandleGraph::path_end()']]],
- ['path_5fend_5fnode_5foffset_10375',['path_end_node_offset',['../classvg_1_1VG.html#a8f45b42614f4ac36c8060634ec0d9805',1,'vg::VG']]],
- ['path_5fend_5fposition_10376',['path_end_position',['../namespacevg.html#af505a96db454fbd06e026f11cb6fbfba',1,'vg']]],
- ['path_5ffor_5fcontig_10377',['path_for_contig',['../haplotypes__main_8cpp.html#a38d910b58a339b55e1135bad308a2aab',1,'haplotypes_main.cpp']]],
- ['path_5ffor_5fsample_5fcontig_10378',['path_for_sample_contig',['../haplotypes__main_8cpp.html#a3336c94d43159885886cca6dfef27b87',1,'haplotypes_main.cpp']]],
- ['path_5ffrom_5flength_10379',['path_from_length',['../namespacevg.html#a1524b7b1b7e67c048c0c5e88b204de08',1,'vg::path_from_length(const Path &path)'],['../namespacevg.html#ae87f325eb11aaf966e6d77d99be40c54',1,'vg::path_from_length(const path_t &path)']]],
- ['path_5ffrom_5fnode_5ftraversals_10380',['path_from_node_traversals',['../namespacevg.html#a3aef5ee16ad883f8defeaa0f52fc342c',1,'vg']]],
- ['path_5ffrom_5fpath_5fhandle_10381',['path_from_path_handle',['../namespacevg.html#a864fe6e3e163b18e84db0783f9a2e17d',1,'vg']]],
- ['path_5ffrom_5fthread_5ft_10382',['path_from_thread_t',['../namespacevg.html#ab0f225fb74f28ea09c6c8917ec14db73',1,'vg']]],
- ['path_5ffront_5fend_10383',['path_front_end',['../classvg_1_1MemoizingGraph.html#ac3db812ecb9ba33c323ed21f2fb30de2',1,'vg::MemoizingGraph::path_front_end()'],['../classvg_1_1PathSubgraphOverlay.html#a4e25154f03620214b41b52efe030ef2a',1,'vg::PathSubgraphOverlay::path_front_end()'],['../classvg_1_1VG.html#a5e1a4d7c14f1aaf601e9a6e231b6b7d3',1,'vg::VG::path_front_end()'],['../classxg_1_1XG.html#a7c14874c12caf4b94eb87af8d2daa686',1,'xg::XG::path_front_end()'],['../classhandlegraph_1_1PathHandleGraph.html#ad7412bf19084f2b38ffec42517a6a9e9',1,'handlegraph::PathHandleGraph::path_front_end()']]],
- ['path_5fidentity_10384',['path_identity',['../classvg_1_1VG.html#ad9bd4133841d1d781fb0df4171773139',1,'vg::VG']]],
- ['path_5fis_5fsimple_5fmatch_10385',['path_is_simple_match',['../namespacevg.html#a43c4a438edc31c7b0d2aa0731c522e8a',1,'vg']]],
- ['path_5flength_5ffilter_10386',['path_length_filter',['../classvg_1_1Filter.html#a4b9e7a11ee8f1d58a4ae99d6a0a7aabf',1,'vg::Filter']]],
- ['path_5flengths_5fto_5fsinks_10387',['path_lengths_to_sinks',['../classvg_1_1BandedGlobalAligner.html#a52406c8606e4aa4c817251289651b4cc',1,'vg::BandedGlobalAligner']]],
- ['path_5fmapping_5fnode_5fid_10388',['path_mapping_node_id',['../structhaplo_1_1linear__haplo__structure.html#ae72d0e22919bc536e6ebc765f56b6271',1,'haplo::linear_haplo_structure']]],
- ['path_5fmapping_5foffset_10389',['path_mapping_offset',['../structhaplo_1_1linear__haplo__structure.html#a2d1b328d1268ef04ac035550eda05ebf',1,'haplo::linear_haplo_structure']]],
- ['path_5fmapping_5ft_10390',['path_mapping_t',['../classvg_1_1path__mapping__t.html#af53a6e6f24b6bc9fbd611bcf826845bd',1,'vg::path_mapping_t::path_mapping_t()=default'],['../classvg_1_1path__mapping__t.html#ab2a0922f085a4f2838437613525ff25c',1,'vg::path_mapping_t::path_mapping_t(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a64f8b90a2817811dd06ae831094c5fa5',1,'vg::path_mapping_t::path_mapping_t(path_mapping_t &&other)=default']]],
- ['path_5fname_10391',['path_name',['../classxg_1_1XG.html#adf5cee0fdfb7bac641cf0e7e10371f8a',1,'xg::XG']]],
- ['path_5fnames_5fby_5fprefix_10392',['path_names_by_prefix',['../classxg_1_1XG.html#a70a2bac209d84ee2b9165a7dfca5969e',1,'xg::XG']]],
- ['path_5fnode_10393',['path_node',['../namespacevg.html#a3bd8aa63fec8b9f6c3ed5808689975e6',1,'vg::path_node(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#ac6bdd8e00dd9f63a0d9049ffe3461d47',1,'vg::path_node(const gbwt::vector_type &path, size_t i)']]],
- ['path_5fpredecessors_10394',['path_predecessors',['../namespacevg.html#a72aa312e964fab8a03b93ec897f355ec',1,'vg']]],
- ['path_5franks_5fby_5fprefix_10395',['path_ranks_by_prefix',['../classxg_1_1XG.html#a93b333ee3c02b8309a139401f1dc661f',1,'xg::XG']]],
- ['path_5freverse_10396',['path_reverse',['../namespacevg.html#ae8fcec2fbe4151075a0b33bc6a0dd145',1,'vg::path_reverse(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#aa0439b7fcf30da565152d9800ff4473d',1,'vg::path_reverse(const gbwt::vector_type &path, size_t i)']]],
- ['path_5fscore_5fannotations_10397',['path_score_annotations',['../classvg_1_1Surjector.html#a9a83875480f04c8dad0207ead58003b8',1,'vg::Surjector']]],
- ['path_5fsequence_10398',['path_sequence',['../classvg_1_1VG.html#a4ce6fe02b243b4f0f82bbf801fd507fa',1,'vg::VG::path_sequence()'],['../namespacevg.html#aad7dc3b95a62cfd99b5fa6377c1a9545',1,'vg::path_sequence()']]],
- ['path_5fsize_10399',['path_size',['../namespacevg.html#aae876005c9e34df70bdc9e2e97776121',1,'vg::path_size(const vector< pair< vg::id_t, bool >> &path)'],['../namespacevg.html#a0c911ba34849a4afd407812fe6373579',1,'vg::path_size(const gbwt::vector_type &path)']]],
- ['path_5fstart_5fposition_10400',['path_start_position',['../namespacevg.html#a2c3b1708b878655d0f6a50a2ba589bf9',1,'vg']]],
- ['path_5fstring_10401',['path_string',['../namespacevg_1_1algorithms.html#a7acc0acf3d99939a0943ca9e0b86e48a',1,'vg::algorithms']]],
- ['path_5ft_10402',['path_t',['../classvg_1_1path__t.html#ac49a26cfbfc0dc2d3bc16ec5b38fceda',1,'vg::path_t::path_t()=default'],['../classvg_1_1path__t.html#a75929a646a781440f67c3b374a6c9166',1,'vg::path_t::path_t(const path_t &other)=default'],['../classvg_1_1path__t.html#ad9d1b8c169d9819e70dda68bca1af668',1,'vg::path_t::path_t(path_t &&other)=default']]],
- ['path_5fto_5fgbwt_10403',['path_to_gbwt',['../namespacevg.html#a529e3aef69e8c01934184726b7937c37',1,'vg']]],
- ['path_5fto_5fgbwt_5fthread_5ft_10404',['path_to_gbwt_thread_t',['../namespacehaplo.html#a86bbe3de0c810d215fd574fe4dfadfee',1,'haplo']]],
- ['path_5fto_5finput_5fhaplotype_10405',['path_to_input_haplotype',['../structhaplo_1_1linear__haplo__structure.html#acf88c54b278bcacae66383f2668970b2',1,'haplo::linear_haplo_structure']]],
- ['path_5fto_5flength_10406',['path_to_length',['../namespacevg.html#a48108a0abc0fdfc187437d174f88e590',1,'vg::path_to_length(const Path &path)'],['../namespacevg.html#a16b3cfa2fc1c70ce96f7ebc695c8766d',1,'vg::path_to_length(const path_t &path)']]],
- ['path_5fto_5fstring_10407',['path_to_string',['../namespacevg.html#afbe0993e79f4ef7bb4b37456b0b08402',1,'vg']]],
- ['pathbasedtraversalfinder_10408',['PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html#ae9824d8e0620854391925d43c7200da6',1,'vg::PathBasedTraversalFinder']]],
- ['pathchunker_10409',['PathChunker',['../classvg_1_1PathChunker.html#a5b31a6a4f865a99818f69be54b7f9e40',1,'vg::PathChunker']]],
- ['pathcomponentindex_10410',['PathComponentIndex',['../classvg_1_1PathComponentIndex.html#aa8aa8ec6a8bc50004db3e07d081d1942',1,'vg::PathComponentIndex::PathComponentIndex(const PathHandleGraph *graph)'],['../classvg_1_1PathComponentIndex.html#a9b093ea34524c9e95cd10375dd000c87',1,'vg::PathComponentIndex::PathComponentIndex()']]],
- ['pathforeachsocket_10411',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html#a1ae98a885a8b37c66d522c3a282c5fd5',1,'handlegraph::PathForEachSocket::PathForEachSocket()=delete'],['../classhandlegraph_1_1PathForEachSocket.html#adea5ed0aea8a5167d7c09a731b9ab65e',1,'handlegraph::PathForEachSocket::PathForEachSocket(const PathHandleGraph *graph, const path_handle_t &path)']]],
- ['pathindex_10412',['PathIndex',['../structvg_1_1PathIndex.html#ac9bdc9df55bcad668ab35b713c366994',1,'vg::PathIndex::PathIndex(const Path &path)'],['../structvg_1_1PathIndex.html#a99878fd10f43e040987e334a70d22d87',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings)'],['../structvg_1_1PathIndex.html#a91e9971a2ddb597ea1c229659b9c9b93',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings, VG &vg)'],['../structvg_1_1PathIndex.html#a72ba06ae7c3fed7abba0cbe2dd6cac88',1,'vg::PathIndex::PathIndex(const Path &path, const HandleGraph &graph)'],['../structvg_1_1PathIndex.html#a9b82679a8d5040f0160edc008d8b348d',1,'vg::PathIndex::PathIndex(VG &vg, const string &path_name, bool extract_sequence=false)'],['../structvg_1_1PathIndex.html#a88a67933e88510cd99800348eb40aa57',1,'vg::PathIndex::PathIndex(const PathHandleGraph &graph, const string &path_name, bool extract_sequence=false)']]],
- ['pathorienteddistancemeasurer_10413',['PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html#a483512f5650b15d5f56935ce2d7ce1bf',1,'vg::PathOrientedDistanceMeasurer']]],
- ['pathrestrictedtraversalfinder_10414',['PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html#aba5b15255fc6b93f745649eed9d0c535',1,'vg::PathRestrictedTraversalFinder']]],
- ['paths_10415',['Paths',['../classvg_1_1Paths.html#af048f547f9c4976c17aaa34f1cbec312',1,'vg::Paths::Paths(void)'],['../classvg_1_1Paths.html#a92fa1ad35d1cf495d96e8fbd468f2700',1,'vg::Paths::Paths(const Paths &other)'],['../classvg_1_1Paths.html#a7b932a39b910d477cd7f3e65a0af3c93',1,'vg::Paths::Paths(Paths &&other) noexcept']]],
- ['paths_5fas_5falignments_10416',['paths_as_alignments',['../classvg_1_1VG.html#a871d05e0a2d0b76092e20fe86bd12e2b',1,'vg::VG']]],
- ['paths_5fbetween_10417',['paths_between',['../classvg_1_1VG.html#a8dc8d762d07088089247b632c835a19d',1,'vg::VG::paths_between(Node *from, Node *to, vector< Path > &paths)'],['../classvg_1_1VG.html#a0a5a5cb1bac139c5a3a947a0d5a3313d',1,'vg::VG::paths_between(nid_t from, nid_t to, vector< Path > &paths)']]],
- ['paths_5ffrom_5fgraph_10418',['paths_from_graph',['../namespacevg.html#a1b5ffc03255d72f1901a7b1ce34c058a',1,'vg']]],
- ['paths_5fof_5fhandle_10419',['paths_of_handle',['../classxg_1_1XG.html#a519fa3151a3b49f5939277a14dced503',1,'xg::XG']]],
- ['paths_5fon_5fsame_5fcomponent_10420',['paths_on_same_component',['../classvg_1_1PathComponentIndex.html#a77de0e355ad6b0893cc506ce18adb050',1,'vg::PathComponentIndex']]],
- ['pathsubgraph_10421',['PathSubgraph',['../classvg_1_1PathSubgraph.html#a861b07c24488c1454b6c04b1f7f01b68',1,'vg::PathSubgraph']]],
- ['pathsubgraphoverlay_10422',['PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html#a71b48d68fc02b88cf0b1c15ca26aa2c6',1,'vg::PathSubgraphOverlay']]],
- ['pathtraversalfinder_10423',['PathTraversalFinder',['../classvg_1_1PathTraversalFinder.html#a49d66e050feec7374fb0d2ed3483b897',1,'vg::PathTraversalFinder']]],
- ['pb2json_10424',['pb2json',['../json2pb_8cpp.html#af6bb66946ffaf36b1fe45881291fee0d',1,'pb2json(const Message &msg): json2pb.cpp'],['../json2pb_8h.html#a7cc576c6ed1e52ba82cf5f264f8ba21d',1,'pb2json(const google::protobuf::Message &msg): json2pb.h']]],
- ['peek_10425',['peek',['../classvg_1_1BitString.html#a2b6d10b59df3727c8f07c3fbe646d03c',1,'vg::BitString']]],
- ['percent_5fidentity_5ffilter_10426',['percent_identity_filter',['../classvg_1_1Filter.html#aba2f93a1c4087075ccf4924fd0e44392',1,'vg::Filter']]],
- ['percent_5furl_5fencode_10427',['percent_url_encode',['../namespacevg.html#a2ba15a613567689d941f30a5a17c6ead',1,'vg']]],
- ['perfect_5ffilter_10428',['perfect_filter',['../classvg_1_1Filter.html#af33b08ad08247167fbe7d90ac86047a3',1,'vg::Filter']]],
- ['perform_5fdp_10429',['perform_dp',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6a5314b3408ca05c265648b8b6053e1d',1,'vg::MEMClusterer::HitGraph']]],
- ['performed_5fduplications_10430',['performed_duplications',['../classvg_1_1DozeuPinningOverlay.html#af98692ca5587716febd938e4e216cf99',1,'vg::DozeuPinningOverlay']]],
- ['pessimistic_5fgap_10431',['pessimistic_gap',['../classvg_1_1MultipathMapper.html#ac4311460002c8df22a29b3e55cc4e1ff',1,'vg::MultipathMapper']]],
- ['pessimistic_5ftail_5fgap_10432',['pessimistic_tail_gap',['../classvg_1_1MultipathAlignmentGraph.html#a4c591d080bc48994fcdb2c9dc08d34a1',1,'vg::MultipathAlignmentGraph']]],
- ['phasedgenome_10433',['PhasedGenome',['../classvg_1_1PhasedGenome.html#aa7a7cce5f88f52d20c659e64966ece28',1,'vg::PhasedGenome::PhasedGenome(const SnarlManager &snarl_manager)'],['../classvg_1_1PhasedGenome.html#a0e96410c065eb722e527be06b710c5d7',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome.html#ace57a61caa7e82942f94ea1e128bc3e3',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &&other)=delete']]],
- ['phaseunfolder_10434',['PhaseUnfolder',['../classvg_1_1PhaseUnfolder.html#a7d6868ce2e12eeae8a8df8b00c6b5003',1,'vg::PhaseUnfolder']]],
- ['phi_10435',['Phi',['../namespacevg.html#afea3e6d4a8ac9b486d1a2b9b89eadd2f',1,'vg']]],
- ['phi_5finv_10436',['Phi_inv',['../namespacevg.html#a4ae7976a3a19fe08c4b2bce4b3f3c00f',1,'vg']]],
- ['phred_5fadd_10437',['phred_add',['../namespacevg.html#a211ba38329cdc76a7ad0b64bbb227bfd',1,'vg']]],
- ['phred_5ffor_5fat_5fleast_5fone_10438',['phred_for_at_least_one',['../namespacevg.html#a9a6ab3a0f45f6ab7b38320db7cc14583',1,'vg']]],
- ['phred_5fgeometric_5fmean_10439',['phred_geometric_mean',['../namespacevg.html#a04edc3daae77e9d3813a97da0f473def',1,'vg']]],
- ['phred_5fsum_10440',['phred_sum',['../namespacevg.html#aaeddefa307b95defd68c8a2022db732c',1,'vg::phred_sum(const Iterator &begin_it, const Iterator &end_it)'],['../namespacevg.html#ad78072e330ae86c9ef80aeeb84f89e8f',1,'vg::phred_sum(const Collection &collection)']]],
- ['phred_5fto_5flogprob_10441',['phred_to_logprob',['../namespacevg.html#a35b531c82b765cd54702665668a98448',1,'vg']]],
- ['phred_5fto_5fprob_10442',['phred_to_prob',['../namespacevg.html#ab713ebc6e2988cc2c959be14bfa01200',1,'vg::phred_to_prob(uint8_t phred)'],['../namespacevg.html#afba77c5a550d5dd72f8cf7438f600676',1,'vg::phred_to_prob(double phred)']]],
- ['pick_5fmappings_5ffrom_5falignments_10443',['pick_mappings_from_alignments',['../classvg_1_1MinimizerMapper.html#a967245a85231b63dd7606b5cd4b4c672',1,'vg::MinimizerMapper']]],
- ['pictographs_10444',['Pictographs',['../classvg_1_1Pictographs.html#a9784714a3a94bd173fecdd31655a770b',1,'vg::Pictographs::Pictographs(void)'],['../classvg_1_1Pictographs.html#a997d5ba6f6e9c5cbdb039ed9c51625e9',1,'vg::Pictographs::Pictographs(int seed_val)']]],
- ['pin_5foffset_10445',['pin_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aff4877147fc6b731179a8e89dfb99757',1,'vg::MinimizerMapper::Minimizer']]],
- ['plan_10446',['Plan',['../structvg_1_1VG_1_1Plan.html#aa757327a3bf40e1828d8aacc5cf5dec5',1,'vg::VG::Plan']]],
- ['pmax_10447',['pmax',['../namespacevg.html#ac7f5da8e25414026729f0c4d09243f6d',1,'vg']]],
- ['pointerfy_10448',['pointerfy',['../namespacevg.html#ae6a210206858f806b345f8eb5c2c292a',1,'vg']]],
- ['poisson_5fprob_5fln_10449',['poisson_prob_ln',['../namespacevg.html#a9238b15cc78a87f27c335fc1e3627a62',1,'vg']]],
- ['poissonsupportsnarlcaller_10450',['PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html#aebde111c1431bf4af46929d8e56c7031',1,'vg::PoissonSupportSnarlCaller']]],
- ['pop_10451',['pop',['../structvg_1_1MatchPos_1_1PathList.html#a6fa2799b0d2b17e437a6c7a92ef75a4d',1,'vg::MatchPos::PathList::pop()'],['../structvg_1_1MatchPos.html#a0bf4234ad56f10dd4d602102bfaf2297',1,'vg::MatchPos::pop()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3a64ce2b4dfae9f7712598d8d6b676a6',1,'vg::ZipCodeTree::reverse_iterator::pop()']]],
- ['pop_5fback_5fstep_10452',['pop_back_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a2db5e7a66ccee26fa257c50e0d084c59',1,'handlegraph::MutablePathHandleGraph']]],
- ['pop_5ffront_5fstep_10453',['pop_front_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a67c8bfd58c5ed8136c9324f427037a7a',1,'handlegraph::MutablePathHandleGraph']]],
- ['populate_5fpath_5ffrom_5ftraceback_10454',['populate_path_from_traceback',['../namespacevg.html#a191bf7b238ea717afbf8118df0afa999',1,'vg']]],
- ['populate_5fsnarl_5findex_10455',['populate_snarl_index',['../namespacevg.html#a7c9f1f64df265187309db52705a1bef7',1,'vg']]],
- ['pos_10456',['pos',['../structvg_1_1WFAPoint.html#a4ea055d164ce5425235ec19d65a7073f',1,'vg::WFAPoint']]],
- ['pos_5fat_10457',['pos_at',['../structMappingRun.html#ac8d70e01cbc733abc3612693b39a465c',1,'MappingRun']]],
- ['pos_5fchar_10458',['pos_char',['../classvg_1_1Sampler.html#a72d922b802775f51f2b02046398d3417',1,'vg::Sampler::pos_char()'],['../classxg_1_1XG.html#abf551ac03c1db6030da1cedb81efc779',1,'xg::XG::pos_char()']]],
- ['pos_5fkey_10459',['pos_key',['../classvg_1_1Packer.html#a128c9b21b9a784c6ea27501463b23862',1,'vg::Packer']]],
- ['pos_5fsubstr_10460',['pos_substr',['../classxg_1_1XG.html#aa61897c26d2cee1e8cc8c9fc7eec540b',1,'xg::XG']]],
- ['pos_5fto_5fgbwt_10461',['pos_to_gbwt',['../namespacevg.html#ae1296fd4e352a120122d4be0a0007819',1,'vg']]],
- ['position_10462',['position',['../classvg_1_1Funnel.html#adee7882f4f431a866847baec1fc77718',1,'vg::Funnel::position()'],['../classvg_1_1path__mapping__t.html#a64f6d0dd6e7ffd6bf6d538c5a25d39f3',1,'vg::path_mapping_t::position()'],['../classvg_1_1Sampler.html#a3d983fa5e24b8802ed2516bf0bb362bf',1,'vg::Sampler::position()']]],
- ['position_5fassuming_5facyclic_10463',['position_assuming_acyclic',['../structhaplo_1_1linear__haplo__structure.html#aa450a108f8b2bab6e98271fcef6b26aa',1,'haplo::linear_haplo_structure']]],
- ['position_5fat_10464',['position_at',['../namespacevg.html#a9a33db744c41ff651da5dacda9578712',1,'vg']]],
- ['position_5fin_5fbasis_10465',['position_in_basis',['../classvg_1_1Packer.html#a6cb79c18881c68ac41b9f2ffa002ef02',1,'vg::Packer']]],
- ['position_5fin_5fpath_10466',['position_in_path',['../classxg_1_1XG.html#a870b3eae5f72331f2c498043b45b3d8d',1,'xg::XG']]],
- ['position_5fin_5fpaths_10467',['position_in_paths',['../classxg_1_1XG.html#a1bda47534cd275fdeca72b463303dc1e',1,'xg::XG']]],
- ['position_5ft_10468',['position_t',['../classvg_1_1position__t.html#a34def1328db6dda2482ccb6c64951704',1,'vg::position_t::position_t()'],['../classvg_1_1position__t.html#a47188716e3327201048ba032c10eb8fe',1,'vg::position_t::position_t(const position_t &other)=default'],['../classvg_1_1position__t.html#a1ad8e0a1fe655c7ebb31ff094e43f466',1,'vg::position_t::position_t(position_t &&other)=default']]],
- ['pow_5fln_10469',['pow_ln',['../namespacevg.html#a3a7a8c98d80a9daacbc72386bc6ad00c',1,'vg']]],
- ['precollapse_5forder_5flength_5fruns_10470',['precollapse_order_length_runs',['../classvg_1_1BaseMapper.html#af4372862ebd4f21da3e9ed105249a5af',1,'vg::BaseMapper']]],
- ['predecessor_5foffset_10471',['predecessor_offset',['../classvg_1_1WFATree.html#a5caa4118319b9fa8e5cc87f257c31225',1,'vg::WFATree']]],
- ['prefilter_5fredundant_5fsub_5fmems_10472',['prefilter_redundant_sub_mems',['../classvg_1_1BaseMapper.html#ae3103b73da0ef6137ad1d1bd16e35d56',1,'vg::BaseMapper']]],
- ['prefix_10473',['prefix',['../structvg_1_1GaplessExtension.html#af975b0dd4c3aab5d89093d9725372017',1,'vg::GaplessExtension::prefix()'],['../classvg_1_1WFAExtender.html#a5be8ff4d5922082dedf5e15665536be8',1,'vg::WFAExtender::prefix()'],['../structvg_1_1RecombinatorHaplotype.html#ad2a0e140251ae5dd203144bcbf49aab3',1,'vg::RecombinatorHaplotype::prefix()']]],
- ['preflight_5fcheck_10474',['preflight_check',['../namespacevg.html#a65ac31e5878660a97207b6ade1418c81',1,'vg']]],
- ['preload_5fprogress_10475',['preload_progress',['../classvg_1_1Progressive.html#a4eb5050eb36ed519cbfa398748ef183b',1,'vg::Progressive']]],
- ['prepend_5fmapping_10476',['prepend_mapping',['../classvg_1_1Paths.html#acd1f02b9d6d41036a24a9aee1a261dc3',1,'vg::Paths::prepend_mapping(const string &name, const Mapping &m, bool warn_on_duplicates=false)'],['../classvg_1_1Paths.html#ab5679411e308c578583066e020dc4d4f',1,'vg::Paths::prepend_mapping(const string &name, id_t id, bool is_reverse, size_t length, size_t rank=0, bool warn_on_duplicates=false)']]],
- ['prepend_5fstep_10477',['prepend_step',['../classvg_1_1VG.html#a43c2858dc8e80ba160359ccf5e1508d2',1,'vg::VG::prepend_step()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#aed17038a0104017d37ff74e15f7f436a',1,'handlegraph::MutablePathHandleGraph::prepend_step()']]],
- ['preprocess_5fgraph_10478',['preprocess_graph',['../haplotypes__main_8cpp.html#abbe87c8ead89e4916934c55ee923b0c1',1,'haplotypes_main.cpp']]],
- ['present_5fkmers_10479',['present_kmers',['../namespacevg.html#acc85734af557e4a1047554706a9b4580',1,'vg']]],
- ['present_5fsymbols_10480',['present_symbols',['../namespacevg.html#ace6690ca3c2bc1ce18c66801e500dce5',1,'vg']]],
- ['preset_10481',['preset',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a7346ca8a4f692c5a10e0df88bc6c915d',1,'vg::subcommand::BaseArgSpec::preset()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a9e5bd3a2b4884185bc07417893cf476c',1,'vg::subcommand::ArgSpec::preset()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aac88ac0803a38344b6c87057bdfb9327',1,'vg::subcommand::BaseOptionGroup::preset()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a421492b900071c23ae1250b4882ffe52',1,'vg::subcommand::OptionGroup::preset()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a2ab60146762bd02d7ec5b1e870998021',1,'vg::subcommand::GroupedOptionGroup::preset()']]],
- ['prev_5fidx_10482',['prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#a6e44d4112d111f6b5796bfbd63b7e24d',1,'haplo::haplo_DP_rectangle']]],
- ['prev_5fsnarl_10483',['prev_snarl',['../classvg_1_1SnarlManager.html#af49cb83d06b303717c94da67974fb0d6',1,'vg::SnarlManager']]],
- ['previous_5fr_10484',['previous_R',['../structhaplo_1_1haplo__DP__column.html#a0bcd7266aea2d97a6b234779739e7628',1,'haplo::haplo_DP_column']]],
- ['print_10485',['print',['../structvg_1_1WFAAlignment.html#a455ada9f59d934bd167217583b2fbd92',1,'vg::WFAAlignment::print(const HandleGraph &graph, std::ostream &out) const'],['../structvg_1_1WFAAlignment.html#a37156be6786114a37da73499f8fe49da',1,'vg::WFAAlignment::print(std::ostream &out) const'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae35f9e4427c8c9da2dbef05000158990',1,'haplo::hDP_gbwt_graph_accessor::print()'],['../structhaplo_1_1haplo__DP__column.html#a8bdb3ddfa07590bf2d50f96bd43c096b',1,'haplo::haplo_DP_column::print()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a3f04e2d77070771ba779ebaf06f0d3ff',1,'vg::HaplotypePartitioner::Parameters::print()'],['../structvg_1_1Recombinator_1_1Statistics.html#a8cc215e629110af71f6d35da557eb0e8',1,'vg::Recombinator::Statistics::print()'],['../structvg_1_1Recombinator_1_1Parameters.html#aa00e847f40210d77acbd1432f6b485ea',1,'vg::Recombinator::Parameters::print()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a5b19dc7b348fc8a8b9b9120ae032559f',1,'vg::subcommand::BaseArgSpec::print()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#aecec3a3bb1a3d2e0e3d75a080d0206eb',1,'vg::subcommand::FlagArgSpec::print()']]],
- ['print_5fband_10486',['print_band',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac248371cbaae3b95340035f88de09e0a',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5fdefault_10487',['print_default',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a489497d47ddf82df3339a4e487274144',1,'vg::subcommand::BaseArgSpec::print_default()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a06e81f25a63218e0cba32ecd6320f9b2',1,'vg::subcommand::ValueArgSpec::print_default()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a85b5c5993e124831c65dd9e31b74aec7',1,'vg::subcommand::FlagArgSpec::print_default()']]],
- ['print_5fdefaults_10488',['print_defaults',['../prune__main_8cpp.html#a01acca05639635d047176302793da18d',1,'prune_main.cpp']]],
- ['print_5fedges_10489',['print_edges',['../classvg_1_1VG.html#a2b659686076f3d6b7b63ec9678d76a93',1,'vg::VG']]],
- ['print_5ffull_5fmatrices_10490',['print_full_matrices',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a521dac0777a22cd632a45ad72f320810',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5fgraph_10491',['print_graph',['../classxg_1_1XG.html#acb2f541cd3f91783d07532d75da80b0a',1,'xg::XG']]],
- ['print_5fhelp_10492',['print_help',['../classvg_1_1ConfigurableParser.html#a29abcf4fbb780c4e586130b095aa0098',1,'vg::ConfigurableParser']]],
- ['print_5fmatrix_10493',['print_matrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#aee399b25f2ed671ad8a17e6c55757671',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5fmetadata_10494',['print_metadata',['../gbwt__main_8cpp.html#af705c69cda26007b3ea9bb76849e21b1',1,'gbwt_main.cpp']]],
- ['print_5fmetavar_10495',['print_metavar',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a8f418067cef90e2290b3a67b8fd17b74',1,'vg::subcommand::BaseArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a4bf9aeb97acee678dfbd3d5c997e28c3',1,'vg::subcommand::ValueArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a9fcf875d6e0a843cb90af9cfe7e9e3a3',1,'vg::subcommand::FlagArgSpec::print_metavar()']]],
- ['print_5foptions_10496',['print_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad3063622c78d2a03519fcbc077c4cdcc',1,'vg::subcommand::BaseOptionGroup::print_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a99c032d391c4dd8f2936f4280e6dde77',1,'vg::subcommand::OptionGroup::print_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aaf906b5e74e2a072cd1f6a90ca685381',1,'vg::subcommand::GroupedOptionGroup::print_options()']]],
- ['print_5fphased_5fgenome_10497',['print_phased_genome',['../classvg_1_1PhasedGenome.html#a4727557def28b369312b2f4a56d86a7d',1,'vg::PhasedGenome']]],
- ['print_5frectangularized_5fbands_10498',['print_rectangularized_bands',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a6c94c4cb68bf76d3b8531f004c17b26d',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['print_5freport_10499',['print_report',['../classvg_1_1IndexedVG.html#a08b7d5f9e8ad7c9b42d58ce8d2629000',1,'vg::IndexedVG']]],
- ['print_5fself_10500',['print_self',['../structvg_1_1varint__vector__t.html#a93a071296fab5dc6fabb363bf3cb66e5',1,'vg::varint_vector_t::print_self()'],['../classvg_1_1ZipCodeTree.html#afe8400e287661b3a9525d99da5329770',1,'vg::ZipCodeTree::print_self()'],['../classvg_1_1ZipCodeForest.html#a4cabd6faae5283f02bfe5397a17908fa',1,'vg::ZipCodeForest::print_self()']]],
- ['print_5fsnarl_10501',['print_snarl',['../classvg_1_1VCFOutputCaller.html#acd9942cb6cd9427e38c868efb23d8bda',1,'vg::VCFOutputCaller::print_snarl(const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) const'],['../classvg_1_1VCFOutputCaller.html#a3b9cfe228287ac605825ed4b0c8ea990',1,'vg::VCFOutputCaller::print_snarl(const Snarl &snarl, bool in_brackets=false) const']]],
- ['print_5fstatistics_10502',['print_statistics',['../classvg_1_1Genotyper.html#aadb967b3ab9daa067f8451c29fda0a5e',1,'vg::Genotyper']]],
- ['print_5ftable_10503',['print_table',['../namespacevg_1_1subcommand.html#a44e82d81de605a19980ffc9045984b3c',1,'vg::subcommand']]],
- ['print_5fvalue_10504',['print_value',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a9a3e4636afe2471cc64ef92c35038733',1,'vg::subcommand::BaseArgSpec::print_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#ab47272ea8d46fdb7c1cf5ff206ff91b1',1,'vg::subcommand::ValueArgSpec::print_value()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ae81ab9ea31e2e812037c732c5e3961cc',1,'vg::subcommand::FlagArgSpec::print_value()']]],
- ['printalignment_10505',['PrintAlignment',['../classvg_1_1SSWAligner.html#ac52ca46f4e194c324fdd67093c54db01',1,'vg::SSWAligner']]],
- ['printid_10506',['printId',['../namespacevg.html#a8bf8f408b11966feb9695d4bb723dfac',1,'vg']]],
- ['prng_10507',['prng',['../classvg_1_1NGSSimulator.html#a8550502fd97de9b154d3df837c036859',1,'vg::NGSSimulator']]],
- ['prob_5ffor_5fat_5fleast_5fone_10508',['prob_for_at_least_one',['../namespacevg.html#ae46397f9d9aa9ac06a48b4ff30da7087',1,'vg']]],
- ['prob_5fto_5flogprob_10509',['prob_to_logprob',['../namespacevg.html#a476a2102f4f5aa82c06be87780ae6d42',1,'vg']]],
- ['prob_5fto_5fphred_10510',['prob_to_phred',['../namespacevg.html#acb81881c0a3b7cf276097d8142ddb312',1,'vg']]],
- ['problemdumpexplainer_10511',['ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html#adf8775736c7646ce19bd69c995bf7238',1,'vg::ProblemDumpExplainer']]],
- ['process_5fin_5fout_5fgrowth_10512',['process_in_out_growth',['../classvg_1_1FlowSort.html#a31800555477d90ab371c08852c9cd05b',1,'vg::FlowSort']]],
- ['process_5funtil_5fthreshold_5fa_10513',['process_until_threshold_a',['../classvg_1_1MinimizerMapper.html#ae74362b0c750fb802b8c7a38c57c8823',1,'vg::MinimizerMapper']]],
- ['process_5funtil_5fthreshold_5fb_10514',['process_until_threshold_b',['../classvg_1_1MinimizerMapper.html#a121f1d7ca1b0cd5721b7c341d227fec8',1,'vg::MinimizerMapper']]],
- ['process_5funtil_5fthreshold_5fc_10515',['process_until_threshold_c',['../classvg_1_1MinimizerMapper.html#af1a420ad7240014c67269a6d7437bef6',1,'vg::MinimizerMapper']]],
- ['processed_5finput_10516',['processed_input',['../classvg_1_1Funnel.html#a94e07fb24eee3bb9284a1ba8945b010a',1,'vg::Funnel']]],
- ['processing_5finput_10517',['processing_input',['../classvg_1_1Funnel.html#a3c21502db704cde878d989f3cc75e91c',1,'vg::Funnel']]],
- ['produced_5foutput_10518',['produced_output',['../classvg_1_1Funnel.html#ae9dec7f539cf37d822328a71e376783a',1,'vg::Funnel']]],
- ['producing_5foutput_10519',['producing_output',['../classvg_1_1Funnel.html#a919aae2ef8cf780bcaba00b1ea1603b8',1,'vg::Funnel']]],
- ['project_10520',['project',['../classvg_1_1Funnel.html#a2b9e7695a998b23314c25f7fe3de4701',1,'vg::Funnel']]],
- ['project_5fgroup_10521',['project_group',['../classvg_1_1Funnel.html#a321b1e593102927ff8677214abce5592',1,'vg::Funnel']]],
- ['project_5fhaplotype_5ftranscripts_10522',['project_haplotype_transcripts',['../classvg_1_1Transcriptome.html#acaa534fdaa3f3926d7959255ab2f6feb',1,'vg::Transcriptome']]],
- ['project_5fhaplotype_5ftranscripts_5fcallback_10523',['project_haplotype_transcripts_callback',['../classvg_1_1Transcriptome.html#ae9f0bd481ee467f32d88be2b20c110c7',1,'vg::Transcriptome']]],
- ['project_5ftranscript_5fembedded_10524',['project_transcript_embedded',['../classvg_1_1Transcriptome.html#a8e9f42b9d9f57b675856c7f766d3c710',1,'vg::Transcriptome']]],
- ['project_5ftranscript_5fgbwt_10525',['project_transcript_gbwt',['../classvg_1_1Transcriptome.html#a4edf6085f024b736bef4be82c6fd854a',1,'vg::Transcriptome']]],
- ['proposal_5fsample_10526',['proposal_sample',['../classvg_1_1MCMCGenotyper.html#a0e007a331bc2854ec8734557bd80962d',1,'vg::MCMCGenotyper']]],
- ['propose_5fdeflection_10527',['propose_deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a662b5ce1fa402a6c8e7a5f20f92773b3',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['protobufemitter_10528',['ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html#ab9d133fa3604ba677c12337ccf609ba7',1,'vg::io::ProtobufEmitter::ProtobufEmitter(std::ostream &out, bool compress=true, size_t max_group_size=1000)'],['../classvg_1_1io_1_1ProtobufEmitter.html#a1adf66f9c9242369dcdd38746f925855',1,'vg::io::ProtobufEmitter::ProtobufEmitter(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#accd8d7c57bffcfdc48ba7085f7a53561',1,'vg::io::ProtobufEmitter::ProtobufEmitter(ProtobufEmitter &&other)=default']]],
- ['protobufiterator_10529',['ProtobufIterator',['../classvg_1_1io_1_1ProtobufIterator.html#a0f2996a9653a98470e7c944879a69d70',1,'vg::io::ProtobufIterator::ProtobufIterator(istream &in)'],['../classvg_1_1io_1_1ProtobufIterator.html#a50ad0e8d7ee212617dbf9e456ea43e07',1,'vg::io::ProtobufIterator::ProtobufIterator()=default']]],
- ['provide_10530',['provide',['../classvg_1_1IndexRegistry.html#a72c4f8ea143cd9a982366234a8eed71e',1,'vg::IndexRegistry::provide(const IndexName &identifier, const string &filename)'],['../classvg_1_1IndexRegistry.html#a430536c995544af29060b78d04e3f5c1',1,'vg::IndexRegistry::provide(const IndexName &identifier, const vector< string > &filenames)'],['../classvg_1_1IndexFile.html#a116a29bacf28f3889ea318ac25a11dc7',1,'vg::IndexFile::provide()']]],
- ['prune_5fand_5ftrim_5fanchors_10531',['prune_and_trim_anchors',['../classvg_1_1Surjector.html#ae34c7f96fff02c5490477fc8ad643908',1,'vg::Surjector']]],
- ['prune_5fcomplex_10532',['prune_complex',['../namespacevg_1_1algorithms.html#a09b6e838b2991d13e272ddcb41aacfbc',1,'vg::algorithms']]],
- ['prune_5fcomplex_5fwith_5fhead_5ftail_10533',['prune_complex_with_head_tail',['../namespacevg_1_1algorithms.html#a784ee29876a24431a865541426f42dee',1,'vg::algorithms']]],
- ['prune_5fhigh_5fshift_5fedges_10534',['prune_high_shift_edges',['../classvg_1_1MultipathAlignmentGraph.html#aa42ef4313d4d24ab4c19532e2bd30652',1,'vg::MultipathAlignmentGraph']]],
- ['prune_5flow_5fscoring_5fedges_10535',['prune_low_scoring_edges',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab2949f31f3e43410189eafa260544baf',1,'vg::MEMClusterer::HitGraph']]],
- ['prune_5fshort_5fsubgraphs_10536',['prune_short_subgraphs',['../namespacevg_1_1algorithms.html#a83e87cf3f8a5ca4362776cf1a3050242',1,'vg::algorithms']]],
- ['prune_5fto_5fconnecting_5fgraph_10537',['prune_to_connecting_graph',['../namespacevg_1_1algorithms.html#a3d74c519ccaa204e7735d5bd26c5095a',1,'vg::algorithms']]],
- ['prune_5fto_5fhigh_5fscoring_5fpaths_10538',['prune_to_high_scoring_paths',['../classvg_1_1MultipathAlignmentGraph.html#a8164834df4fc94907fb96b06062c9514',1,'vg::MultipathAlignmentGraph']]],
- ['prune_5funconnectable_10539',['prune_unconnectable',['../classvg_1_1Surjector.html#ab65da876e448d86bc64985c0b14d3e78',1,'vg::Surjector']]],
- ['pseudo_5flength_10540',['pseudo_length',['../classvg_1_1MultipathMapper.html#aa5ee46fa484ee95e45da33b47bcc4eb8',1,'vg::MultipathMapper']]],
- ['pseudo_5frandom_5fsequence_10541',['pseudo_random_sequence',['../namespacevg.html#a1924855da445b625609837c0920af7b2',1,'vg']]],
- ['purge_5funmapped_5falignments_10542',['purge_unmapped_alignments',['../classvg_1_1MultipathMapper.html#a009000ee2da67a965a4f627be468d976',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< multipath_alignment_t > &multipath_alns_out)'],['../classvg_1_1MultipathMapper.html#ab1c9f02cbadcd8df05b691e4ff5294f2',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, bool proper_paired)']]],
- ['push_10543',['push',['../structvg_1_1MatchPos_1_1PathList.html#a2979222c63cb87e2f530fceda30e56a5',1,'vg::MatchPos::PathList::push()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ade3a2a60c495a494d27fb6f8a72ef2db',1,'vg::ZipCodeTree::reverse_iterator::push()']]],
- ['push_5fback_10544',['push_back',['../structhaplo_1_1gbwt__thread__t.html#a726f2772b4725564569e4889f89db7c6',1,'haplo::gbwt_thread_t::push_back()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#ade3cdc2fdb2dc88b735bee5be2c04cee',1,'haplo::linear_haplo_structure::SNVvector::push_back()']]],
- ['push_5fedit_10545',['push_edit',['../classvg_1_1DozeuInterface.html#acc84e0c73002c23f8249ea17efff6848',1,'vg::DozeuInterface']]]
+ ['p_5fvalue_10295',['p_value',['../structvg_1_1SeqComplexity.html#a20dfb4fbec20a18a5decaccc046c10e8',1,'vg::SeqComplexity']]],
+ ['pack_10296',['pack',['../structhandlegraph_1_1number__bool__packing.html#af5082dc39a2f308585402bd19de0caa8',1,'handlegraph::number_bool_packing']]],
+ ['pack_5fquery_5fforward_10297',['pack_query_forward',['../classvg_1_1DozeuInterface.html#acd17348d5d2dd0ec4c10af98748fe67a',1,'vg::DozeuInterface::pack_query_forward()'],['../classvg_1_1XdropAligner.html#a9179d91b00ed33fbc3e9e6a4bd6b9321',1,'vg::XdropAligner::pack_query_forward()'],['../classvg_1_1QualAdjXdropAligner.html#a0e1140ad3ee66b2583869ccd2267841b',1,'vg::QualAdjXdropAligner::pack_query_forward()']]],
+ ['pack_5fquery_5freverse_10298',['pack_query_reverse',['../classvg_1_1DozeuInterface.html#aa15876efde0e6d8f963d37ae245c8ead',1,'vg::DozeuInterface::pack_query_reverse()'],['../classvg_1_1XdropAligner.html#a3c3832ae9935773f0dd0b97ed031c70e',1,'vg::XdropAligner::pack_query_reverse()'],['../classvg_1_1QualAdjXdropAligner.html#a0d6b25927dccfe18f03eab6457486ac7',1,'vg::QualAdjXdropAligner::pack_query_reverse()']]],
+ ['packed_5fdepth_5fof_5fbin_10299',['packed_depth_of_bin',['../namespacevg_1_1algorithms.html#a62ebbcbfe1250940eb8ebf0a2dcbc19a',1,'vg::algorithms']]],
+ ['packed_5fdepths_10300',['packed_depths',['../namespacevg_1_1algorithms.html#abd431ebd9786d796f708a7046e643e2e',1,'vg::algorithms']]],
+ ['packedtraversalsupportfinder_10301',['PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html#a5bb7b3f0b3fd9c72597403ce75f8791c',1,'vg::PackedTraversalSupportFinder']]],
+ ['packer_10302',['Packer',['../classvg_1_1Packer.html#a965acab0b6c7d973a67e449785955739',1,'vg::Packer::Packer(const HandleGraph *graph=nullptr)'],['../classvg_1_1Packer.html#ad52836b610249ada7cf0ad13c329b52c',1,'vg::Packer::Packer(const HandleGraph *graph, bool record_bases, bool record_edges, bool record_edits, bool record_qualities, size_t bin_size=0, size_t coverage_bins=1, size_t data_width=8)']]],
+ ['pad_5fband_5fconstant_10303',['pad_band_constant',['../namespacevg_1_1algorithms.html#aaab5b2261edb66897af9d1158e7758d8',1,'vg::algorithms']]],
+ ['pad_5fband_5fmin_5frandom_5fwalk_10304',['pad_band_min_random_walk',['../namespacevg_1_1algorithms.html#a25a37b51facd101b8a29b1a57661f74f',1,'vg::algorithms']]],
+ ['pad_5fband_5frandom_5fwalk_10305',['pad_band_random_walk',['../namespacevg_1_1algorithms.html#a1294ed71274673b7e4cc1d40e9472666',1,'vg::algorithms']]],
+ ['pad_5fband_5frandom_5fwalk_5finternal_10306',['pad_band_random_walk_internal',['../namespacevg_1_1algorithms.html#a9957e925ee25c57698383d4e1df21f0d',1,'vg::algorithms']]],
+ ['pad_5ftraversal_10307',['pad_traversal',['../classvg_1_1GAFOutputCaller.html#a697f4f2c00fa8317ba8143bbe99931fb',1,'vg::GAFOutputCaller']]],
+ ['paint_10308',['paint',['../structvg_1_1Funnel_1_1PaintableSpace.html#a88c1043f7b0cae737da989f0abc44b0a',1,'vg::Funnel::PaintableSpace']]],
+ ['pair_5fall_10309',['pair_all',['../classvg_1_1MinimizerMapper.html#a4493ab0315512da6b10a7cde3754afe2',1,'vg::MinimizerMapper']]],
+ ['pair_5fcluster_5fmultiplicity_10310',['pair_cluster_multiplicity',['../classvg_1_1MultipathMapper.html#ae534f0c248a4b44bdf389ead66d105e3',1,'vg::MultipathMapper']]],
+ ['pair_5fclusters_10311',['pair_clusters',['../classvg_1_1MEMClusterer.html#a4e84dd599bb8dc4341cbed2fd1de1ed0',1,'vg::MEMClusterer::pair_clusters()'],['../classvg_1_1NullClusterer.html#a1794ac271ce6d785e67b488a98ec87d6',1,'vg::NullClusterer::pair_clusters()'],['../classvg_1_1OrientedDistanceClusterer.html#a41e57b46abd69532d53855499d5042eb',1,'vg::OrientedDistanceClusterer::pair_clusters()'],['../classvg_1_1TVSClusterer.html#a1477ce3367e036c0ecc101e1518b49b9',1,'vg::TVSClusterer::pair_clusters()'],['../classvg_1_1MinDistanceClusterer.html#af561001a20cc91adc6238f74edca6480',1,'vg::MinDistanceClusterer::pair_clusters()']]],
+ ['pair_5fconsistent_10312',['pair_consistent',['../classvg_1_1Mapper.html#ad3a62e0a91818c4e20508ab2a0f47fa5',1,'vg::Mapper']]],
+ ['pair_5ffrom_5fedge_10313',['pair_from_edge',['../classvg_1_1NodeSide.html#ad48cc3d977ad0f6ffc5ce1034cbbae65',1,'vg::NodeSide::pair_from_edge(Edge *e)'],['../classvg_1_1NodeSide.html#a97eed27ab7b77be54b68062b780a9f36',1,'vg::NodeSide::pair_from_edge(const Edge &e)']]],
+ ['pair_5ffrom_5fend_5fedge_10314',['pair_from_end_edge',['../classvg_1_1NodeSide.html#a23f18cf5f9ae9c7fc8475800d967275c',1,'vg::NodeSide']]],
+ ['pair_5ffrom_5fstart_5fedge_10315',['pair_from_start_edge',['../classvg_1_1NodeSide.html#a3193e35c9e8349c427cc834335e25405',1,'vg::NodeSide']]],
+ ['pair_5fmapping_5flikelihoods_10316',['pair_mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a05dd8b61205954b988bb996479883989',1,'vg::MultipathMapper']]],
+ ['pair_5forientation_5ffilter_10317',['pair_orientation_filter',['../classvg_1_1Filter.html#a16451e95cd6c7642df9f013d5b73c0c7',1,'vg::Filter']]],
+ ['pair_5frescue_10318',['pair_rescue',['../classvg_1_1Mapper.html#a36248b0eb439694bfbd493fce0ce2b02',1,'vg::Mapper']]],
+ ['pair_5fto_5fstring_10319',['pair_to_string',['../haplotypes__main_8cpp.html#a7d4977594e9d93b802b94c95752f34a2',1,'haplotypes_main.cpp']]],
+ ['paired_5ffor_5feach_5fparallel_5fafter_5fwait_10320',['paired_for_each_parallel_after_wait',['../namespacevg_1_1io.html#af3c3dd4ad5c9b887fd3ee389e0b67ef6',1,'vg::io']]],
+ ['parallelkffreader_10321',['ParallelKFFReader',['../classvg_1_1ParallelKFFReader.html#a4b84d319b814d4b2a5f099d19d0426d5',1,'vg::ParallelKFFReader::ParallelKFFReader(const std::string &filename)'],['../classvg_1_1ParallelKFFReader.html#adcdc292236ba8b178c38666702b4e5c1',1,'vg::ParallelKFFReader::ParallelKFFReader(const ParallelKFFReader &)=delete']]],
+ ['parameters_10322',['Parameters',['../structvg_1_1Recombinator_1_1Parameters.html#a3112d2a46538ce1575d53b6706f25756',1,'vg::Recombinator::Parameters']]],
+ ['parent_10323',['parent',['../classvg_1_1WFATree.html#ab6c9c25e1906e3a95bc6c853a2c5db3f',1,'vg::WFATree']]],
+ ['parent_5fof_10324',['parent_of',['../classvg_1_1SnarlManager.html#ad4c8dd034c160f2908164c1ebc2a0394',1,'vg::SnarlManager']]],
+ ['parse_10325',['parse',['../classvg_1_1OptionInterface.html#aa658456e011e28d8e6d3073c8ccfc740',1,'vg::OptionInterface::parse()=0'],['../classvg_1_1OptionInterface.html#a5679dbc64e1f490d7caa35730de6d09b',1,'vg::OptionInterface::parse(const string &arg)=0'],['../classvg_1_1ConfigurableParser.html#a9c28ad9040822d975a38c982677065bd',1,'vg::ConfigurableParser::parse()'],['../classvg_1_1OptionValueParser.html#a4b43a211a8dca7c43a1fe3fc4fde1de5',1,'vg::OptionValueParser::parse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a27e910ec23c80fc2c829dcdb98da0ddc',1,'vg::OptionValueParser< vector< Item > >::parse()'],['../classvg_1_1BaseOption.html#a6682e454cf748d2a29623849d72f8d1d',1,'vg::BaseOption::parse()'],['../classvg_1_1BaseOption.html#ab17b0a67fe5bdb8de8ffb39f98a804e7',1,'vg::BaseOption::parse(const string &arg)'],['../classvg_1_1algorithms_1_1GFAParser.html#a575aa78bfa6a567735133c8cffa6da77',1,'vg::algorithms::GFAParser::parse()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a040fd55d950392ade69dad277adfb848',1,'vg::subcommand::BaseArgSpec::parse()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a8ddbad123ba28ff099c263d24b751889',1,'vg::subcommand::ValueArgSpec::parse()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a96a1df206d4ef889c7f3f6cf08dc1426',1,'vg::subcommand::FlagArgSpec::parse()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a6fa17a5e6d8fbc293d69063c947cb0aa',1,'vg::subcommand::BaseOptionGroup::parse()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aa4b885a991453bbc8cde726e35dd115f',1,'vg::subcommand::OptionGroup::parse()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aada2ded9febbec1c9bab141da4bfc0ce',1,'vg::subcommand::GroupedOptionGroup::parse()'],['../classvg_1_1OptionValueParser.html#a5a34866bb0ac6c4feae8b5a20aba93c7',1,'vg::OptionValueParser::parse()'],['../namespacevg.html#a1dd328fd8abb43338a3ae9e0a3b0be1f',1,'vg::parse(const string &arg, double &dest)'],['../namespacevg.html#a2d3193c0a90ba95bd11b8b3201de52c0',1,'vg::parse(const string &arg, float &dest)'],['../namespacevg.html#aa1de4a1752e875116c767ec49a8e2961',1,'vg::parse(const string &arg, std::regex &dest)'],['../namespacevg.html#aa4a3393960dd54c941e9d7c317923c2e',1,'vg::parse(const string &arg, pos_t &dest)'],['../namespacevg.html#a8873caafc22d22b52e0f6f3f164f6dc8',1,'vg::parse(const string &arg)'],['../namespacevg.html#a8c5c364797f623025b67b9aff0657112',1,'vg::parse(const char *arg)'],['../namespacevg.html#a627f5ad6fe6f1e6b4cc23ac97dfca4b8',1,'vg::parse(const string &arg, Result &dest)'],['../namespacevg.html#a2cd6368e7395f1d90c4e3be1a7293d0a',1,'vg::parse(const string &arg, typename enable_if< sizeof(Result)<=sizeof(long long) &&is_integral< Result >::value &&is_signed< Result >::value, Result >::type &dest)'],['../namespacevg.html#a1384531a1c8d8387bdd04961590bdf93',1,'vg::parse(const string &arg, typename enable_if< is_instantiation_of< Result, Range >::value, Result >::type &dest)']]],
+ ['parse_5fattribute_5fvalue_10326',['parse_attribute_value',['../classvg_1_1Transcriptome.html#a401bd93346ea5e02f586823d8f3b458e',1,'vg::Transcriptome']]],
+ ['parse_5fattributes_10327',['parse_attributes',['../structvg_1_1GFFRecord.html#ade5c97a34abe718fbb607977f11fb8f1',1,'vg::GFFRecord']]],
+ ['parse_5fbed_10328',['parse_bed',['../mask__main_8cpp.html#a210b34f1b7dfefc99804b335b0cf6e19',1,'mask_main.cpp']]],
+ ['parse_5fbed_5fregions_10329',['parse_bed_regions',['../namespacevg.html#a736f4c7b5d03a7efe78315b4c5490f15',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#ad88fe24ca988562008c8b734c22cb403',1,'vg::parse_bed_regions(istream &bedstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)'],['../namespacevg.html#a8fd1e3436d98304996aaecece048cb45',1,'vg::parse_bed_regions(const string &bed_path, vector< Region > &out_regions, vector< string > *out_names)']]],
+ ['parse_5fdefault_10330',['parse_default',['../classvg_1_1OptionValueParser.html#ad2b7db7247de0c8cb7fe4e9501314b6b',1,'vg::OptionValueParser::parse_default()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#aa9624ebfad0e2421af39a86e7327edaf',1,'vg::OptionValueParser< vector< Item > >::parse_default()'],['../classvg_1_1OptionValueParser.html#acddd63568b5e1a7ece023abeccccd15b',1,'vg::OptionValueParser::parse_default()']]],
+ ['parse_5ffrom_5fstring_10331',['parse_from_string',['../classvg_1_1io_1_1ProtobufIterator.html#ab37e50d3f1375c13a223a79938d5094d',1,'vg::io::ProtobufIterator']]],
+ ['parse_5fgaf_5frecord_10332',['parse_gaf_record',['../namespacegafkluge.html#ab8a6f72dddac182a6d8d74a52a6fc92d',1,'gafkluge']]],
+ ['parse_5fgbwt_5fconfig_10333',['parse_gbwt_config',['../gbwt__main_8cpp.html#a8153bcd09dec28c64e4a9bfad67cee40',1,'gbwt_main.cpp']]],
+ ['parse_5fgff_5fregions_10334',['parse_gff_regions',['../namespacevg.html#a55cc20d96f38b54c590af4f3f3ac2498',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, vector< Alignment > *out_alignments)'],['../namespacevg.html#a629c9fee8a51c4ca363511ae01ad4a09',1,'vg::parse_gff_regions(istream &gffstream, const PathPositionHandleGraph *graph, const std::function< void(Alignment &)> &callback)']]],
+ ['parse_5fh_10335',['parse_h',['../classvg_1_1algorithms_1_1GFAParser.html#a122490db3d620bc310b106e2231a9140',1,'vg::algorithms::GFAParser']]],
+ ['parse_5fhaplotype_10336',['parse_haplotype',['../classhandlegraph_1_1PathMetadata.html#a69e57ea70c57b01b309cdf39da4eeeb5',1,'handlegraph::PathMetadata']]],
+ ['parse_5fhaplotype_5ftranscript_5ffile_10337',['parse_haplotype_transcript_file',['../sim__main_8cpp.html#ae98175893da0d162097014dd65ba8ce2',1,'sim_main.cpp']]],
+ ['parse_5fintron_5fdistr_5ffile_10338',['parse_intron_distr_file',['../mpmap__main_8cpp.html#a48bc366d5c5d1acbc0c60556944bcfe9',1,'mpmap_main.cpp']]],
+ ['parse_5fintrons_10339',['parse_introns',['../classvg_1_1Transcriptome.html#ad040b82553e6b03ccd926c0fe622e84c',1,'vg::Transcriptome']]],
+ ['parse_5fl_10340',['parse_l',['../classvg_1_1algorithms_1_1GFAParser.html#a6033f9ec4740e70dc79fbaae78f91773',1,'vg::algorithms::GFAParser']]],
+ ['parse_5flocus_5fname_10341',['parse_locus_name',['../classhandlegraph_1_1PathMetadata.html#a978b48ca96f8817f7099587dae77b8b4',1,'handlegraph::PathMetadata']]],
+ ['parse_5fmatrix_10342',['parse_matrix',['../classvg_1_1AlignerClient.html#a4a56c0bf099b670763c0f5ce3653811b',1,'vg::AlignerClient']]],
+ ['parse_5fmemory_5fusage_10343',['parse_memory_usage',['../autoindex__main_8cpp.html#ad25ab5b852b7a1bc223505f7a2e23853',1,'autoindex_main.cpp']]],
+ ['parse_5fp_10344',['parse_p',['../classvg_1_1algorithms_1_1GFAParser.html#a3f28df872d86abde347b3bbcc7f42948',1,'vg::algorithms::GFAParser']]],
+ ['parse_5fpath_5fname_10345',['parse_path_name',['../classhandlegraph_1_1PathMetadata.html#ab6bcceaaedfbb03a4ea3f70499b06ade',1,'handlegraph::PathMetadata']]],
+ ['parse_5fphase_5fblock_10346',['parse_phase_block',['../classhandlegraph_1_1PathMetadata.html#a3d9a3a974ab62d008104fa7dab849465',1,'handlegraph::PathMetadata']]],
+ ['parse_5fprovide_5fstring_10347',['parse_provide_string',['../autoindex__main_8cpp.html#a8f62d94c211a4113595cbdf100129fc3',1,'autoindex_main.cpp']]],
+ ['parse_5fregion_10348',['parse_region',['../namespacevg.html#a253257615743a1cfb948b749be7700e2',1,'vg::parse_region(const string &target, string &name, int64_t &start, int64_t &end)'],['../namespacevg.html#af0a3beb8908adf7a6e4d641243937830',1,'vg::parse_region(string ®ion, Region &out_region)']]],
+ ['parse_5frg_5fsample_5fmap_10349',['parse_rg_sample_map',['../namespacevg.html#a637c855dffc0296c6575ae8a4cac6b43',1,'vg']]],
+ ['parse_5frsem_5fexpression_5ffile_10350',['parse_rsem_expression_file',['../sim__main_8cpp.html#aa1964053fdd12fb9dde544ce6d18ab70',1,'sim_main.cpp']]],
+ ['parse_5fs_10351',['parse_s',['../classvg_1_1algorithms_1_1GFAParser.html#af4ce322cdb902c01881afcbb4fea85f5',1,'vg::algorithms::GFAParser']]],
+ ['parse_5fsam_5ftags_10352',['parse_sam_tags',['../namespacevg.html#a175da49ded2be9251e68ae642108248a',1,'vg']]],
+ ['parse_5fsample_5fname_10353',['parse_sample_name',['../classhandlegraph_1_1PathMetadata.html#acbc675d9d41c36eebb174b4871c42435',1,'handlegraph::PathMetadata']]],
+ ['parse_5fsense_10354',['parse_sense',['../classhandlegraph_1_1PathMetadata.html#aae6aa5f2738ce962e4e74d46a9c5e3e0',1,'handlegraph::PathMetadata']]],
+ ['parse_5fsubrange_10355',['parse_subrange',['../classhandlegraph_1_1PathMetadata.html#a010d050ee3bf526da9ae45fde6dd1dc6',1,'handlegraph::PathMetadata']]],
+ ['parse_5ftags_10356',['parse_tags',['../classvg_1_1algorithms_1_1GFAParser.html#a4fecb9e4836c67853d300ffd29b046e7',1,'vg::algorithms::GFAParser']]],
+ ['parse_5ftid_5fpath_5fhandle_5fmap_10357',['parse_tid_path_handle_map',['../namespacevg.html#abc66619671bdc564023a9b3259558785',1,'vg']]],
+ ['parse_5ftranscripts_10358',['parse_transcripts',['../classvg_1_1Transcriptome.html#ae7b6c679e3d635342029bbc7cc39d75d',1,'vg::Transcriptome']]],
+ ['parse_5ftranslation_10359',['parse_translation',['../structvg_1_1PathIndex.html#aa5272234ddb7686f1ae88881ebf99a61',1,'vg::PathIndex']]],
+ ['parse_5fvcf_10360',['parse_vcf',['../classvg_1_1HaplotypeIndexer.html#ad3eda4acd04b8bae303b4604410ece41',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::string &job_name="GBWT") const'],['../classvg_1_1HaplotypeIndexer.html#ad81dbd24bba40aaa14536d79754d387b',1,'vg::HaplotypeIndexer::parse_vcf(const std::string &filename, const PathHandleGraph &graph, const std::vector< path_handle_t > &paths, const std::string &job_name="GBWT") const']]],
+ ['parse_5fw_10361',['parse_w',['../classvg_1_1algorithms_1_1GFAParser.html#ae03c9247eb49aed8f868039365f89cdd',1,'vg::algorithms::GFAParser']]],
+ ['parsegenotypes_10362',['parseGenotypes',['../namespacevg.html#a8bcecf9fe02b7f50dd5e72e40dcd98e1',1,'vg']]],
+ ['partition_5fgbwt_5fsequences_10363',['partition_gbwt_sequences',['../namespacevg.html#a802baeeacfe4ee75781afabac562588b',1,'vg']]],
+ ['partition_5fhaplotypes_10364',['partition_haplotypes',['../classvg_1_1HaplotypePartitioner.html#a1c0a32c7f0ca0f86fd5abb9b746895c8',1,'vg::HaplotypePartitioner']]],
+ ['pass_10365',['pass',['../classvg_1_1Funnel.html#aec19daea826d5951ecf1477769722d9a',1,'vg::Funnel']]],
+ ['patch_5falignment_10366',['patch_alignment',['../classvg_1_1Mapper.html#ad8f03f4ff100a15ea885a5404222a0ad',1,'vg::Mapper']]],
+ ['path_10367',['path',['../classvg_1_1subpath__t.html#ad9d97e89f59cf75b1d00f0e54d979048',1,'vg::subpath_t::path()'],['../classvg_1_1Paths.html#a218a01d5d53bf945ef4f0acafd18d6bc',1,'vg::Paths::path()']]],
+ ['path_5fback_10368',['path_back',['../classvg_1_1MemoizingGraph.html#a90d25a87afe426eb79582739848734c4',1,'vg::MemoizingGraph::path_back()'],['../classvg_1_1PathSubgraphOverlay.html#a7e9706b6c571a62a93c7dafb3be62f29',1,'vg::PathSubgraphOverlay::path_back()'],['../classvg_1_1VG.html#a1af5ef2df0289b964cab09d9400344c5',1,'vg::VG::path_back()'],['../classxg_1_1XG.html#aceaf4782f2fb6cbd169b6121fea8e4e8',1,'xg::XG::path_back()'],['../classhandlegraph_1_1PathHandleGraph.html#a31bb33a87ad8efd68876fc5ae1deeb09',1,'handlegraph::PathHandleGraph::path_back()']]],
+ ['path_5fbegin_10369',['path_begin',['../classvg_1_1MemoizingGraph.html#ac40575d724c1d7053b9765e622cc3713',1,'vg::MemoizingGraph::path_begin()'],['../classvg_1_1PathSubgraphOverlay.html#a492b11a38ba4d31ee75341fc8777f19c',1,'vg::PathSubgraphOverlay::path_begin()'],['../classvg_1_1VG.html#af0fc3a05ce45e0100fb82812c5b1e35d',1,'vg::VG::path_begin()'],['../classxg_1_1XG.html#ad4894f85d76ca8101a5dd164a29379c5',1,'xg::XG::path_begin()'],['../classhandlegraph_1_1PathHandleGraph.html#a815759484087ed92214c2c1c6b9d1a11',1,'handlegraph::PathHandleGraph::path_begin()']]],
+ ['path_5fcontains_5fhandle_10370',['path_contains_handle',['../classxg_1_1XG.html#ad55f3e5461c20199ccdb3a6fb4dacdf6',1,'xg::XG']]],
+ ['path_5fcontains_5fnode_10371',['path_contains_node',['../structvg_1_1PathIndex.html#ab1bb8b7aec345a4b59242287ae1693c7',1,'vg::PathIndex']]],
+ ['path_5fcontains_5fnode_5fin_5forientation_10372',['path_contains_node_in_orientation',['../structvg_1_1PathIndex.html#a0dbda80790b6d81aa0f9d83ac21f85a3',1,'vg::PathIndex']]],
+ ['path_5fcover_5fparameters_10373',['path_cover_parameters',['../structGBWTConfig.html#a27d5429660a51913c09fa1b33477d27a',1,'GBWTConfig']]],
+ ['path_5fdepth_5fof_5fbin_10374',['path_depth_of_bin',['../namespacevg_1_1algorithms.html#a8c66507d55ed6e10e9d77e1281d4bcfc',1,'vg::algorithms']]],
+ ['path_5fdepths_10375',['path_depths',['../namespacevg_1_1algorithms.html#a85250c33b7d32346be371ab7e4404471',1,'vg::algorithms']]],
+ ['path_5fdivergence_5ffilter_10376',['path_divergence_filter',['../classvg_1_1Filter.html#a961710b28527b3f9961948a068c3b860',1,'vg::Filter']]],
+ ['path_5fedge_5fcount_10377',['path_edge_count',['../classvg_1_1VG.html#a5f1df72d85d8a72524b76abca972f33d',1,'vg::VG']]],
+ ['path_5fend_10378',['path_end',['../classvg_1_1MemoizingGraph.html#a2e4006fc68d2db22228dcef6bed02666',1,'vg::MemoizingGraph::path_end()'],['../classvg_1_1PathSubgraphOverlay.html#a5d74d2d221394980ff65e2e9adc1818f',1,'vg::PathSubgraphOverlay::path_end()'],['../classvg_1_1VG.html#a2f532a7aeb7765b99c6c4e43ba961fdb',1,'vg::VG::path_end()'],['../classxg_1_1XG.html#a32e53f5b1a5cd650b5d731f0354c5c2d',1,'xg::XG::path_end()'],['../classhandlegraph_1_1PathHandleGraph.html#a5c3a5e04838d9e4a0a0ddf574c4de827',1,'handlegraph::PathHandleGraph::path_end()']]],
+ ['path_5fend_5fnode_5foffset_10379',['path_end_node_offset',['../classvg_1_1VG.html#a8f45b42614f4ac36c8060634ec0d9805',1,'vg::VG']]],
+ ['path_5fend_5fposition_10380',['path_end_position',['../namespacevg.html#af505a96db454fbd06e026f11cb6fbfba',1,'vg']]],
+ ['path_5ffor_5fcontig_10381',['path_for_contig',['../haplotypes__main_8cpp.html#a38d910b58a339b55e1135bad308a2aab',1,'haplotypes_main.cpp']]],
+ ['path_5ffor_5fsample_5fcontig_10382',['path_for_sample_contig',['../haplotypes__main_8cpp.html#a3336c94d43159885886cca6dfef27b87',1,'haplotypes_main.cpp']]],
+ ['path_5ffrom_5flength_10383',['path_from_length',['../namespacevg.html#a1524b7b1b7e67c048c0c5e88b204de08',1,'vg::path_from_length(const Path &path)'],['../namespacevg.html#ae87f325eb11aaf966e6d77d99be40c54',1,'vg::path_from_length(const path_t &path)']]],
+ ['path_5ffrom_5fnode_5ftraversals_10384',['path_from_node_traversals',['../namespacevg.html#a3aef5ee16ad883f8defeaa0f52fc342c',1,'vg']]],
+ ['path_5ffrom_5fpath_5fhandle_10385',['path_from_path_handle',['../namespacevg.html#a864fe6e3e163b18e84db0783f9a2e17d',1,'vg']]],
+ ['path_5ffrom_5fthread_5ft_10386',['path_from_thread_t',['../namespacevg.html#ab0f225fb74f28ea09c6c8917ec14db73',1,'vg']]],
+ ['path_5ffront_5fend_10387',['path_front_end',['../classvg_1_1MemoizingGraph.html#ac3db812ecb9ba33c323ed21f2fb30de2',1,'vg::MemoizingGraph::path_front_end()'],['../classvg_1_1PathSubgraphOverlay.html#a4e25154f03620214b41b52efe030ef2a',1,'vg::PathSubgraphOverlay::path_front_end()'],['../classvg_1_1VG.html#a5e1a4d7c14f1aaf601e9a6e231b6b7d3',1,'vg::VG::path_front_end()'],['../classxg_1_1XG.html#a7c14874c12caf4b94eb87af8d2daa686',1,'xg::XG::path_front_end()'],['../classhandlegraph_1_1PathHandleGraph.html#ad7412bf19084f2b38ffec42517a6a9e9',1,'handlegraph::PathHandleGraph::path_front_end()']]],
+ ['path_5fidentity_10388',['path_identity',['../classvg_1_1VG.html#ad9bd4133841d1d781fb0df4171773139',1,'vg::VG']]],
+ ['path_5fis_5fsimple_5fmatch_10389',['path_is_simple_match',['../namespacevg.html#a43c4a438edc31c7b0d2aa0731c522e8a',1,'vg']]],
+ ['path_5flength_5ffilter_10390',['path_length_filter',['../classvg_1_1Filter.html#a4b9e7a11ee8f1d58a4ae99d6a0a7aabf',1,'vg::Filter']]],
+ ['path_5flengths_5fto_5fsinks_10391',['path_lengths_to_sinks',['../classvg_1_1BandedGlobalAligner.html#a52406c8606e4aa4c817251289651b4cc',1,'vg::BandedGlobalAligner']]],
+ ['path_5fmapping_5fnode_5fid_10392',['path_mapping_node_id',['../structhaplo_1_1linear__haplo__structure.html#ae72d0e22919bc536e6ebc765f56b6271',1,'haplo::linear_haplo_structure']]],
+ ['path_5fmapping_5foffset_10393',['path_mapping_offset',['../structhaplo_1_1linear__haplo__structure.html#a2d1b328d1268ef04ac035550eda05ebf',1,'haplo::linear_haplo_structure']]],
+ ['path_5fmapping_5ft_10394',['path_mapping_t',['../classvg_1_1path__mapping__t.html#af53a6e6f24b6bc9fbd611bcf826845bd',1,'vg::path_mapping_t::path_mapping_t()=default'],['../classvg_1_1path__mapping__t.html#ab2a0922f085a4f2838437613525ff25c',1,'vg::path_mapping_t::path_mapping_t(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a64f8b90a2817811dd06ae831094c5fa5',1,'vg::path_mapping_t::path_mapping_t(path_mapping_t &&other)=default']]],
+ ['path_5fname_10395',['path_name',['../classxg_1_1XG.html#adf5cee0fdfb7bac641cf0e7e10371f8a',1,'xg::XG']]],
+ ['path_5fnames_5fby_5fprefix_10396',['path_names_by_prefix',['../classxg_1_1XG.html#a70a2bac209d84ee2b9165a7dfca5969e',1,'xg::XG']]],
+ ['path_5fnode_10397',['path_node',['../namespacevg.html#a3bd8aa63fec8b9f6c3ed5808689975e6',1,'vg::path_node(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#ac6bdd8e00dd9f63a0d9049ffe3461d47',1,'vg::path_node(const gbwt::vector_type &path, size_t i)']]],
+ ['path_5fpredecessors_10398',['path_predecessors',['../namespacevg.html#a72aa312e964fab8a03b93ec897f355ec',1,'vg']]],
+ ['path_5franks_5fby_5fprefix_10399',['path_ranks_by_prefix',['../classxg_1_1XG.html#a93b333ee3c02b8309a139401f1dc661f',1,'xg::XG']]],
+ ['path_5freverse_10400',['path_reverse',['../namespacevg.html#ae8fcec2fbe4151075a0b33bc6a0dd145',1,'vg::path_reverse(const vector< pair< vg::id_t, bool >> &path, size_t i)'],['../namespacevg.html#aa0439b7fcf30da565152d9800ff4473d',1,'vg::path_reverse(const gbwt::vector_type &path, size_t i)']]],
+ ['path_5fscore_5fannotations_10401',['path_score_annotations',['../classvg_1_1Surjector.html#a9a83875480f04c8dad0207ead58003b8',1,'vg::Surjector']]],
+ ['path_5fsequence_10402',['path_sequence',['../classvg_1_1VG.html#a4ce6fe02b243b4f0f82bbf801fd507fa',1,'vg::VG::path_sequence()'],['../namespacevg.html#aad7dc3b95a62cfd99b5fa6377c1a9545',1,'vg::path_sequence()']]],
+ ['path_5fsize_10403',['path_size',['../namespacevg.html#aae876005c9e34df70bdc9e2e97776121',1,'vg::path_size(const vector< pair< vg::id_t, bool >> &path)'],['../namespacevg.html#a0c911ba34849a4afd407812fe6373579',1,'vg::path_size(const gbwt::vector_type &path)']]],
+ ['path_5fstart_5fposition_10404',['path_start_position',['../namespacevg.html#a2c3b1708b878655d0f6a50a2ba589bf9',1,'vg']]],
+ ['path_5fstring_10405',['path_string',['../namespacevg_1_1algorithms.html#a7acc0acf3d99939a0943ca9e0b86e48a',1,'vg::algorithms']]],
+ ['path_5ft_10406',['path_t',['../classvg_1_1path__t.html#ac49a26cfbfc0dc2d3bc16ec5b38fceda',1,'vg::path_t::path_t()=default'],['../classvg_1_1path__t.html#a75929a646a781440f67c3b374a6c9166',1,'vg::path_t::path_t(const path_t &other)=default'],['../classvg_1_1path__t.html#ad9d1b8c169d9819e70dda68bca1af668',1,'vg::path_t::path_t(path_t &&other)=default']]],
+ ['path_5fto_5fgbwt_10407',['path_to_gbwt',['../namespacevg.html#a529e3aef69e8c01934184726b7937c37',1,'vg']]],
+ ['path_5fto_5fgbwt_5fthread_5ft_10408',['path_to_gbwt_thread_t',['../namespacehaplo.html#a86bbe3de0c810d215fd574fe4dfadfee',1,'haplo']]],
+ ['path_5fto_5finput_5fhaplotype_10409',['path_to_input_haplotype',['../structhaplo_1_1linear__haplo__structure.html#acf88c54b278bcacae66383f2668970b2',1,'haplo::linear_haplo_structure']]],
+ ['path_5fto_5flength_10410',['path_to_length',['../namespacevg.html#a48108a0abc0fdfc187437d174f88e590',1,'vg::path_to_length(const Path &path)'],['../namespacevg.html#a16b3cfa2fc1c70ce96f7ebc695c8766d',1,'vg::path_to_length(const path_t &path)']]],
+ ['path_5fto_5fstring_10411',['path_to_string',['../namespacevg.html#afbe0993e79f4ef7bb4b37456b0b08402',1,'vg']]],
+ ['pathbasedtraversalfinder_10412',['PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html#ae9824d8e0620854391925d43c7200da6',1,'vg::PathBasedTraversalFinder']]],
+ ['pathchunker_10413',['PathChunker',['../classvg_1_1PathChunker.html#a5b31a6a4f865a99818f69be54b7f9e40',1,'vg::PathChunker']]],
+ ['pathcomponentindex_10414',['PathComponentIndex',['../classvg_1_1PathComponentIndex.html#aa8aa8ec6a8bc50004db3e07d081d1942',1,'vg::PathComponentIndex::PathComponentIndex(const PathHandleGraph *graph)'],['../classvg_1_1PathComponentIndex.html#a9b093ea34524c9e95cd10375dd000c87',1,'vg::PathComponentIndex::PathComponentIndex()']]],
+ ['pathforeachsocket_10415',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html#a1ae98a885a8b37c66d522c3a282c5fd5',1,'handlegraph::PathForEachSocket::PathForEachSocket()=delete'],['../classhandlegraph_1_1PathForEachSocket.html#adea5ed0aea8a5167d7c09a731b9ab65e',1,'handlegraph::PathForEachSocket::PathForEachSocket(const PathHandleGraph *graph, const path_handle_t &path)']]],
+ ['pathindex_10416',['PathIndex',['../structvg_1_1PathIndex.html#ac9bdc9df55bcad668ab35b713c366994',1,'vg::PathIndex::PathIndex(const Path &path)'],['../structvg_1_1PathIndex.html#a99878fd10f43e040987e334a70d22d87',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings)'],['../structvg_1_1PathIndex.html#a91e9971a2ddb597ea1c229659b9c9b93',1,'vg::PathIndex::PathIndex(const list< mapping_t > &mappings, VG &vg)'],['../structvg_1_1PathIndex.html#a72ba06ae7c3fed7abba0cbe2dd6cac88',1,'vg::PathIndex::PathIndex(const Path &path, const HandleGraph &graph)'],['../structvg_1_1PathIndex.html#a9b82679a8d5040f0160edc008d8b348d',1,'vg::PathIndex::PathIndex(VG &vg, const string &path_name, bool extract_sequence=false)'],['../structvg_1_1PathIndex.html#a88a67933e88510cd99800348eb40aa57',1,'vg::PathIndex::PathIndex(const PathHandleGraph &graph, const string &path_name, bool extract_sequence=false)']]],
+ ['pathorienteddistancemeasurer_10417',['PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html#a483512f5650b15d5f56935ce2d7ce1bf',1,'vg::PathOrientedDistanceMeasurer']]],
+ ['pathrestrictedtraversalfinder_10418',['PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html#aba5b15255fc6b93f745649eed9d0c535',1,'vg::PathRestrictedTraversalFinder']]],
+ ['paths_10419',['Paths',['../classvg_1_1Paths.html#af048f547f9c4976c17aaa34f1cbec312',1,'vg::Paths::Paths(void)'],['../classvg_1_1Paths.html#a92fa1ad35d1cf495d96e8fbd468f2700',1,'vg::Paths::Paths(const Paths &other)'],['../classvg_1_1Paths.html#a7b932a39b910d477cd7f3e65a0af3c93',1,'vg::Paths::Paths(Paths &&other) noexcept']]],
+ ['paths_5fas_5falignments_10420',['paths_as_alignments',['../classvg_1_1VG.html#a871d05e0a2d0b76092e20fe86bd12e2b',1,'vg::VG']]],
+ ['paths_5fbetween_10421',['paths_between',['../classvg_1_1VG.html#a8dc8d762d07088089247b632c835a19d',1,'vg::VG::paths_between(Node *from, Node *to, vector< Path > &paths)'],['../classvg_1_1VG.html#a0a5a5cb1bac139c5a3a947a0d5a3313d',1,'vg::VG::paths_between(nid_t from, nid_t to, vector< Path > &paths)']]],
+ ['paths_5ffrom_5fgraph_10422',['paths_from_graph',['../namespacevg.html#a1b5ffc03255d72f1901a7b1ce34c058a',1,'vg']]],
+ ['paths_5fof_5fhandle_10423',['paths_of_handle',['../classxg_1_1XG.html#a519fa3151a3b49f5939277a14dced503',1,'xg::XG']]],
+ ['paths_5fon_5fsame_5fcomponent_10424',['paths_on_same_component',['../classvg_1_1PathComponentIndex.html#a77de0e355ad6b0893cc506ce18adb050',1,'vg::PathComponentIndex']]],
+ ['pathsubgraph_10425',['PathSubgraph',['../classvg_1_1PathSubgraph.html#a861b07c24488c1454b6c04b1f7f01b68',1,'vg::PathSubgraph']]],
+ ['pathsubgraphoverlay_10426',['PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html#a71b48d68fc02b88cf0b1c15ca26aa2c6',1,'vg::PathSubgraphOverlay']]],
+ ['pathtraversalfinder_10427',['PathTraversalFinder',['../classvg_1_1PathTraversalFinder.html#a49d66e050feec7374fb0d2ed3483b897',1,'vg::PathTraversalFinder']]],
+ ['pb2json_10428',['pb2json',['../json2pb_8cpp.html#af6bb66946ffaf36b1fe45881291fee0d',1,'pb2json(const Message &msg): json2pb.cpp'],['../json2pb_8h.html#a7cc576c6ed1e52ba82cf5f264f8ba21d',1,'pb2json(const google::protobuf::Message &msg): json2pb.h']]],
+ ['peek_10429',['peek',['../classvg_1_1BitString.html#a2b6d10b59df3727c8f07c3fbe646d03c',1,'vg::BitString']]],
+ ['percent_5fidentity_5ffilter_10430',['percent_identity_filter',['../classvg_1_1Filter.html#aba2f93a1c4087075ccf4924fd0e44392',1,'vg::Filter']]],
+ ['percent_5furl_5fencode_10431',['percent_url_encode',['../namespacevg.html#a2ba15a613567689d941f30a5a17c6ead',1,'vg']]],
+ ['perfect_5ffilter_10432',['perfect_filter',['../classvg_1_1Filter.html#af33b08ad08247167fbe7d90ac86047a3',1,'vg::Filter']]],
+ ['perform_5fdp_10433',['perform_dp',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6a5314b3408ca05c265648b8b6053e1d',1,'vg::MEMClusterer::HitGraph']]],
+ ['performed_5fduplications_10434',['performed_duplications',['../classvg_1_1DozeuPinningOverlay.html#af98692ca5587716febd938e4e216cf99',1,'vg::DozeuPinningOverlay']]],
+ ['pessimistic_5fgap_10435',['pessimistic_gap',['../classvg_1_1MultipathMapper.html#ac4311460002c8df22a29b3e55cc4e1ff',1,'vg::MultipathMapper']]],
+ ['pessimistic_5ftail_5fgap_10436',['pessimistic_tail_gap',['../classvg_1_1MultipathAlignmentGraph.html#a4c591d080bc48994fcdb2c9dc08d34a1',1,'vg::MultipathAlignmentGraph']]],
+ ['phasedgenome_10437',['PhasedGenome',['../classvg_1_1PhasedGenome.html#aa7a7cce5f88f52d20c659e64966ece28',1,'vg::PhasedGenome::PhasedGenome(const SnarlManager &snarl_manager)'],['../classvg_1_1PhasedGenome.html#a0e96410c065eb722e527be06b710c5d7',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome.html#ace57a61caa7e82942f94ea1e128bc3e3',1,'vg::PhasedGenome::PhasedGenome(PhasedGenome &&other)=delete']]],
+ ['phaseunfolder_10438',['PhaseUnfolder',['../classvg_1_1PhaseUnfolder.html#a7d6868ce2e12eeae8a8df8b00c6b5003',1,'vg::PhaseUnfolder']]],
+ ['phi_10439',['Phi',['../namespacevg.html#afea3e6d4a8ac9b486d1a2b9b89eadd2f',1,'vg']]],
+ ['phi_5finv_10440',['Phi_inv',['../namespacevg.html#a4ae7976a3a19fe08c4b2bce4b3f3c00f',1,'vg']]],
+ ['phred_5fadd_10441',['phred_add',['../namespacevg.html#a211ba38329cdc76a7ad0b64bbb227bfd',1,'vg']]],
+ ['phred_5ffor_5fat_5fleast_5fone_10442',['phred_for_at_least_one',['../namespacevg.html#a9a6ab3a0f45f6ab7b38320db7cc14583',1,'vg']]],
+ ['phred_5fgeometric_5fmean_10443',['phred_geometric_mean',['../namespacevg.html#a04edc3daae77e9d3813a97da0f473def',1,'vg']]],
+ ['phred_5fsum_10444',['phred_sum',['../namespacevg.html#aaeddefa307b95defd68c8a2022db732c',1,'vg::phred_sum(const Iterator &begin_it, const Iterator &end_it)'],['../namespacevg.html#ad78072e330ae86c9ef80aeeb84f89e8f',1,'vg::phred_sum(const Collection &collection)']]],
+ ['phred_5fto_5flogprob_10445',['phred_to_logprob',['../namespacevg.html#a35b531c82b765cd54702665668a98448',1,'vg']]],
+ ['phred_5fto_5fprob_10446',['phred_to_prob',['../namespacevg.html#ab713ebc6e2988cc2c959be14bfa01200',1,'vg::phred_to_prob(uint8_t phred)'],['../namespacevg.html#afba77c5a550d5dd72f8cf7438f600676',1,'vg::phred_to_prob(double phred)']]],
+ ['pick_5fmappings_5ffrom_5falignments_10447',['pick_mappings_from_alignments',['../classvg_1_1MinimizerMapper.html#a967245a85231b63dd7606b5cd4b4c672',1,'vg::MinimizerMapper']]],
+ ['pictographs_10448',['Pictographs',['../classvg_1_1Pictographs.html#a9784714a3a94bd173fecdd31655a770b',1,'vg::Pictographs::Pictographs(void)'],['../classvg_1_1Pictographs.html#a997d5ba6f6e9c5cbdb039ed9c51625e9',1,'vg::Pictographs::Pictographs(int seed_val)']]],
+ ['pin_5foffset_10449',['pin_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aff4877147fc6b731179a8e89dfb99757',1,'vg::MinimizerMapper::Minimizer']]],
+ ['plan_10450',['Plan',['../structvg_1_1VG_1_1Plan.html#aa757327a3bf40e1828d8aacc5cf5dec5',1,'vg::VG::Plan']]],
+ ['pmax_10451',['pmax',['../namespacevg.html#ac7f5da8e25414026729f0c4d09243f6d',1,'vg']]],
+ ['pointerfy_10452',['pointerfy',['../namespacevg.html#ae6a210206858f806b345f8eb5c2c292a',1,'vg']]],
+ ['poisson_5fprob_5fln_10453',['poisson_prob_ln',['../namespacevg.html#a9238b15cc78a87f27c335fc1e3627a62',1,'vg']]],
+ ['poissonsupportsnarlcaller_10454',['PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html#aebde111c1431bf4af46929d8e56c7031',1,'vg::PoissonSupportSnarlCaller']]],
+ ['pop_10455',['pop',['../structvg_1_1MatchPos_1_1PathList.html#a6fa2799b0d2b17e437a6c7a92ef75a4d',1,'vg::MatchPos::PathList::pop()'],['../structvg_1_1MatchPos.html#a0bf4234ad56f10dd4d602102bfaf2297',1,'vg::MatchPos::pop()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3a64ce2b4dfae9f7712598d8d6b676a6',1,'vg::ZipCodeTree::reverse_iterator::pop()']]],
+ ['pop_5fback_5fstep_10456',['pop_back_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a2db5e7a66ccee26fa257c50e0d084c59',1,'handlegraph::MutablePathHandleGraph']]],
+ ['pop_5ffront_5fstep_10457',['pop_front_step',['../classhandlegraph_1_1MutablePathHandleGraph.html#a67c8bfd58c5ed8136c9324f427037a7a',1,'handlegraph::MutablePathHandleGraph']]],
+ ['populate_5fpath_5ffrom_5ftraceback_10458',['populate_path_from_traceback',['../namespacevg.html#a191bf7b238ea717afbf8118df0afa999',1,'vg']]],
+ ['populate_5fsnarl_5findex_10459',['populate_snarl_index',['../namespacevg.html#a7c9f1f64df265187309db52705a1bef7',1,'vg']]],
+ ['pos_10460',['pos',['../structvg_1_1WFAPoint.html#a4ea055d164ce5425235ec19d65a7073f',1,'vg::WFAPoint']]],
+ ['pos_5fat_10461',['pos_at',['../structMappingRun.html#ac8d70e01cbc733abc3612693b39a465c',1,'MappingRun']]],
+ ['pos_5fchar_10462',['pos_char',['../classvg_1_1Sampler.html#a72d922b802775f51f2b02046398d3417',1,'vg::Sampler::pos_char()'],['../classxg_1_1XG.html#abf551ac03c1db6030da1cedb81efc779',1,'xg::XG::pos_char()']]],
+ ['pos_5fkey_10463',['pos_key',['../classvg_1_1Packer.html#a128c9b21b9a784c6ea27501463b23862',1,'vg::Packer']]],
+ ['pos_5fsubstr_10464',['pos_substr',['../classxg_1_1XG.html#aa61897c26d2cee1e8cc8c9fc7eec540b',1,'xg::XG']]],
+ ['pos_5fto_5fgbwt_10465',['pos_to_gbwt',['../namespacevg.html#ae1296fd4e352a120122d4be0a0007819',1,'vg']]],
+ ['position_10466',['position',['../classvg_1_1Funnel.html#adee7882f4f431a866847baec1fc77718',1,'vg::Funnel::position()'],['../classvg_1_1path__mapping__t.html#a64f6d0dd6e7ffd6bf6d538c5a25d39f3',1,'vg::path_mapping_t::position()'],['../classvg_1_1Sampler.html#a3d983fa5e24b8802ed2516bf0bb362bf',1,'vg::Sampler::position()']]],
+ ['position_5fassuming_5facyclic_10467',['position_assuming_acyclic',['../structhaplo_1_1linear__haplo__structure.html#aa450a108f8b2bab6e98271fcef6b26aa',1,'haplo::linear_haplo_structure']]],
+ ['position_5fat_10468',['position_at',['../namespacevg.html#a9a33db744c41ff651da5dacda9578712',1,'vg']]],
+ ['position_5fin_5fbasis_10469',['position_in_basis',['../classvg_1_1Packer.html#a6cb79c18881c68ac41b9f2ffa002ef02',1,'vg::Packer']]],
+ ['position_5fin_5fpath_10470',['position_in_path',['../classxg_1_1XG.html#a870b3eae5f72331f2c498043b45b3d8d',1,'xg::XG']]],
+ ['position_5fin_5fpaths_10471',['position_in_paths',['../classxg_1_1XG.html#a1bda47534cd275fdeca72b463303dc1e',1,'xg::XG']]],
+ ['position_5ft_10472',['position_t',['../classvg_1_1position__t.html#a34def1328db6dda2482ccb6c64951704',1,'vg::position_t::position_t()'],['../classvg_1_1position__t.html#a47188716e3327201048ba032c10eb8fe',1,'vg::position_t::position_t(const position_t &other)=default'],['../classvg_1_1position__t.html#a1ad8e0a1fe655c7ebb31ff094e43f466',1,'vg::position_t::position_t(position_t &&other)=default']]],
+ ['pow_5fln_10473',['pow_ln',['../namespacevg.html#a3a7a8c98d80a9daacbc72386bc6ad00c',1,'vg']]],
+ ['precollapse_5forder_5flength_5fruns_10474',['precollapse_order_length_runs',['../classvg_1_1BaseMapper.html#af4372862ebd4f21da3e9ed105249a5af',1,'vg::BaseMapper']]],
+ ['predecessor_5foffset_10475',['predecessor_offset',['../classvg_1_1WFATree.html#a5caa4118319b9fa8e5cc87f257c31225',1,'vg::WFATree']]],
+ ['prefilter_5fredundant_5fsub_5fmems_10476',['prefilter_redundant_sub_mems',['../classvg_1_1BaseMapper.html#ae3103b73da0ef6137ad1d1bd16e35d56',1,'vg::BaseMapper']]],
+ ['prefix_10477',['prefix',['../structvg_1_1GaplessExtension.html#af975b0dd4c3aab5d89093d9725372017',1,'vg::GaplessExtension::prefix()'],['../classvg_1_1WFAExtender.html#a5be8ff4d5922082dedf5e15665536be8',1,'vg::WFAExtender::prefix()'],['../structvg_1_1RecombinatorHaplotype.html#ad2a0e140251ae5dd203144bcbf49aab3',1,'vg::RecombinatorHaplotype::prefix()']]],
+ ['preflight_5fcheck_10478',['preflight_check',['../namespacevg.html#a65ac31e5878660a97207b6ade1418c81',1,'vg']]],
+ ['preload_5fprogress_10479',['preload_progress',['../classvg_1_1Progressive.html#a4eb5050eb36ed519cbfa398748ef183b',1,'vg::Progressive']]],
+ ['prepend_5fmapping_10480',['prepend_mapping',['../classvg_1_1Paths.html#acd1f02b9d6d41036a24a9aee1a261dc3',1,'vg::Paths::prepend_mapping(const string &name, const Mapping &m, bool warn_on_duplicates=false)'],['../classvg_1_1Paths.html#ab5679411e308c578583066e020dc4d4f',1,'vg::Paths::prepend_mapping(const string &name, id_t id, bool is_reverse, size_t length, size_t rank=0, bool warn_on_duplicates=false)']]],
+ ['prepend_5fstep_10481',['prepend_step',['../classvg_1_1VG.html#a43c2858dc8e80ba160359ccf5e1508d2',1,'vg::VG::prepend_step()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#aed17038a0104017d37ff74e15f7f436a',1,'handlegraph::MutablePathHandleGraph::prepend_step()']]],
+ ['preprocess_5fgraph_10482',['preprocess_graph',['../haplotypes__main_8cpp.html#abbe87c8ead89e4916934c55ee923b0c1',1,'haplotypes_main.cpp']]],
+ ['present_5fkmers_10483',['present_kmers',['../namespacevg.html#acc85734af557e4a1047554706a9b4580',1,'vg']]],
+ ['present_5fsymbols_10484',['present_symbols',['../namespacevg.html#ace6690ca3c2bc1ce18c66801e500dce5',1,'vg']]],
+ ['preset_10485',['preset',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a7346ca8a4f692c5a10e0df88bc6c915d',1,'vg::subcommand::BaseArgSpec::preset()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a9e5bd3a2b4884185bc07417893cf476c',1,'vg::subcommand::ArgSpec::preset()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aac88ac0803a38344b6c87057bdfb9327',1,'vg::subcommand::BaseOptionGroup::preset()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a421492b900071c23ae1250b4882ffe52',1,'vg::subcommand::OptionGroup::preset()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a2ab60146762bd02d7ec5b1e870998021',1,'vg::subcommand::GroupedOptionGroup::preset()']]],
+ ['prev_5fidx_10486',['prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#a6e44d4112d111f6b5796bfbd63b7e24d',1,'haplo::haplo_DP_rectangle']]],
+ ['prev_5fsnarl_10487',['prev_snarl',['../classvg_1_1SnarlManager.html#af49cb83d06b303717c94da67974fb0d6',1,'vg::SnarlManager']]],
+ ['previous_5fr_10488',['previous_R',['../structhaplo_1_1haplo__DP__column.html#a0bcd7266aea2d97a6b234779739e7628',1,'haplo::haplo_DP_column']]],
+ ['print_10489',['print',['../structvg_1_1WFAAlignment.html#a455ada9f59d934bd167217583b2fbd92',1,'vg::WFAAlignment::print(const HandleGraph &graph, std::ostream &out) const'],['../structvg_1_1WFAAlignment.html#a37156be6786114a37da73499f8fe49da',1,'vg::WFAAlignment::print(std::ostream &out) const'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae35f9e4427c8c9da2dbef05000158990',1,'haplo::hDP_gbwt_graph_accessor::print()'],['../structhaplo_1_1haplo__DP__column.html#a8bdb3ddfa07590bf2d50f96bd43c096b',1,'haplo::haplo_DP_column::print()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a3f04e2d77070771ba779ebaf06f0d3ff',1,'vg::HaplotypePartitioner::Parameters::print()'],['../structvg_1_1Recombinator_1_1Statistics.html#a8cc215e629110af71f6d35da557eb0e8',1,'vg::Recombinator::Statistics::print()'],['../structvg_1_1Recombinator_1_1Parameters.html#aa00e847f40210d77acbd1432f6b485ea',1,'vg::Recombinator::Parameters::print()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a5b19dc7b348fc8a8b9b9120ae032559f',1,'vg::subcommand::BaseArgSpec::print()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#aecec3a3bb1a3d2e0e3d75a080d0206eb',1,'vg::subcommand::FlagArgSpec::print()']]],
+ ['print_5fband_10490',['print_band',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac248371cbaae3b95340035f88de09e0a',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5fdefault_10491',['print_default',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a489497d47ddf82df3339a4e487274144',1,'vg::subcommand::BaseArgSpec::print_default()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a06e81f25a63218e0cba32ecd6320f9b2',1,'vg::subcommand::ValueArgSpec::print_default()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a85b5c5993e124831c65dd9e31b74aec7',1,'vg::subcommand::FlagArgSpec::print_default()']]],
+ ['print_5fdefaults_10492',['print_defaults',['../prune__main_8cpp.html#a01acca05639635d047176302793da18d',1,'prune_main.cpp']]],
+ ['print_5fedges_10493',['print_edges',['../classvg_1_1VG.html#a2b659686076f3d6b7b63ec9678d76a93',1,'vg::VG']]],
+ ['print_5ffull_5fmatrices_10494',['print_full_matrices',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a521dac0777a22cd632a45ad72f320810',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5fgraph_10495',['print_graph',['../classxg_1_1XG.html#acb2f541cd3f91783d07532d75da80b0a',1,'xg::XG']]],
+ ['print_5fhelp_10496',['print_help',['../classvg_1_1ConfigurableParser.html#a29abcf4fbb780c4e586130b095aa0098',1,'vg::ConfigurableParser']]],
+ ['print_5fmatrix_10497',['print_matrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#aee399b25f2ed671ad8a17e6c55757671',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5fmetadata_10498',['print_metadata',['../gbwt__main_8cpp.html#af705c69cda26007b3ea9bb76849e21b1',1,'gbwt_main.cpp']]],
+ ['print_5fmetavar_10499',['print_metavar',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a8f418067cef90e2290b3a67b8fd17b74',1,'vg::subcommand::BaseArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a4bf9aeb97acee678dfbd3d5c997e28c3',1,'vg::subcommand::ValueArgSpec::print_metavar()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a9fcf875d6e0a843cb90af9cfe7e9e3a3',1,'vg::subcommand::FlagArgSpec::print_metavar()']]],
+ ['print_5foptions_10500',['print_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad3063622c78d2a03519fcbc077c4cdcc',1,'vg::subcommand::BaseOptionGroup::print_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a99c032d391c4dd8f2936f4280e6dde77',1,'vg::subcommand::OptionGroup::print_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#aaf906b5e74e2a072cd1f6a90ca685381',1,'vg::subcommand::GroupedOptionGroup::print_options()']]],
+ ['print_5fphased_5fgenome_10501',['print_phased_genome',['../classvg_1_1PhasedGenome.html#a4727557def28b369312b2f4a56d86a7d',1,'vg::PhasedGenome']]],
+ ['print_5frectangularized_5fbands_10502',['print_rectangularized_bands',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a6c94c4cb68bf76d3b8531f004c17b26d',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['print_5freport_10503',['print_report',['../classvg_1_1IndexedVG.html#a08b7d5f9e8ad7c9b42d58ce8d2629000',1,'vg::IndexedVG']]],
+ ['print_5fself_10504',['print_self',['../structvg_1_1varint__vector__t.html#a93a071296fab5dc6fabb363bf3cb66e5',1,'vg::varint_vector_t::print_self()'],['../classvg_1_1ZipCodeTree.html#afe8400e287661b3a9525d99da5329770',1,'vg::ZipCodeTree::print_self()'],['../classvg_1_1ZipCodeForest.html#a4cabd6faae5283f02bfe5397a17908fa',1,'vg::ZipCodeForest::print_self()']]],
+ ['print_5fsnarl_10505',['print_snarl',['../classvg_1_1VCFOutputCaller.html#acd9942cb6cd9427e38c868efb23d8bda',1,'vg::VCFOutputCaller::print_snarl(const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) const'],['../classvg_1_1VCFOutputCaller.html#a3b9cfe228287ac605825ed4b0c8ea990',1,'vg::VCFOutputCaller::print_snarl(const Snarl &snarl, bool in_brackets=false) const']]],
+ ['print_5fstatistics_10506',['print_statistics',['../classvg_1_1Genotyper.html#aadb967b3ab9daa067f8451c29fda0a5e',1,'vg::Genotyper']]],
+ ['print_5ftable_10507',['print_table',['../namespacevg_1_1subcommand.html#a44e82d81de605a19980ffc9045984b3c',1,'vg::subcommand']]],
+ ['print_5fvalue_10508',['print_value',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a9a3e4636afe2471cc64ef92c35038733',1,'vg::subcommand::BaseArgSpec::print_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#ab47272ea8d46fdb7c1cf5ff206ff91b1',1,'vg::subcommand::ValueArgSpec::print_value()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ae81ab9ea31e2e812037c732c5e3961cc',1,'vg::subcommand::FlagArgSpec::print_value()']]],
+ ['printalignment_10509',['PrintAlignment',['../classvg_1_1SSWAligner.html#ac52ca46f4e194c324fdd67093c54db01',1,'vg::SSWAligner']]],
+ ['printid_10510',['printId',['../namespacevg.html#a8bf8f408b11966feb9695d4bb723dfac',1,'vg']]],
+ ['prng_10511',['prng',['../classvg_1_1NGSSimulator.html#a8550502fd97de9b154d3df837c036859',1,'vg::NGSSimulator']]],
+ ['prob_5ffor_5fat_5fleast_5fone_10512',['prob_for_at_least_one',['../namespacevg.html#ae46397f9d9aa9ac06a48b4ff30da7087',1,'vg']]],
+ ['prob_5fto_5flogprob_10513',['prob_to_logprob',['../namespacevg.html#a476a2102f4f5aa82c06be87780ae6d42',1,'vg']]],
+ ['prob_5fto_5fphred_10514',['prob_to_phred',['../namespacevg.html#acb81881c0a3b7cf276097d8142ddb312',1,'vg']]],
+ ['problemdumpexplainer_10515',['ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html#adf8775736c7646ce19bd69c995bf7238',1,'vg::ProblemDumpExplainer']]],
+ ['process_5fin_5fout_5fgrowth_10516',['process_in_out_growth',['../classvg_1_1FlowSort.html#a31800555477d90ab371c08852c9cd05b',1,'vg::FlowSort']]],
+ ['process_5funtil_5fthreshold_5fa_10517',['process_until_threshold_a',['../classvg_1_1MinimizerMapper.html#ae74362b0c750fb802b8c7a38c57c8823',1,'vg::MinimizerMapper']]],
+ ['process_5funtil_5fthreshold_5fb_10518',['process_until_threshold_b',['../classvg_1_1MinimizerMapper.html#a121f1d7ca1b0cd5721b7c341d227fec8',1,'vg::MinimizerMapper']]],
+ ['process_5funtil_5fthreshold_5fc_10519',['process_until_threshold_c',['../classvg_1_1MinimizerMapper.html#af1a420ad7240014c67269a6d7437bef6',1,'vg::MinimizerMapper']]],
+ ['processed_5finput_10520',['processed_input',['../classvg_1_1Funnel.html#a94e07fb24eee3bb9284a1ba8945b010a',1,'vg::Funnel']]],
+ ['processing_5finput_10521',['processing_input',['../classvg_1_1Funnel.html#a3c21502db704cde878d989f3cc75e91c',1,'vg::Funnel']]],
+ ['produced_5foutput_10522',['produced_output',['../classvg_1_1Funnel.html#ae9dec7f539cf37d822328a71e376783a',1,'vg::Funnel']]],
+ ['producing_5foutput_10523',['producing_output',['../classvg_1_1Funnel.html#a919aae2ef8cf780bcaba00b1ea1603b8',1,'vg::Funnel']]],
+ ['project_10524',['project',['../classvg_1_1Funnel.html#a2b9e7695a998b23314c25f7fe3de4701',1,'vg::Funnel']]],
+ ['project_5fgroup_10525',['project_group',['../classvg_1_1Funnel.html#a321b1e593102927ff8677214abce5592',1,'vg::Funnel']]],
+ ['project_5fhaplotype_5ftranscripts_10526',['project_haplotype_transcripts',['../classvg_1_1Transcriptome.html#acaa534fdaa3f3926d7959255ab2f6feb',1,'vg::Transcriptome']]],
+ ['project_5fhaplotype_5ftranscripts_5fcallback_10527',['project_haplotype_transcripts_callback',['../classvg_1_1Transcriptome.html#ae9f0bd481ee467f32d88be2b20c110c7',1,'vg::Transcriptome']]],
+ ['project_5ftranscript_5fembedded_10528',['project_transcript_embedded',['../classvg_1_1Transcriptome.html#a8e9f42b9d9f57b675856c7f766d3c710',1,'vg::Transcriptome']]],
+ ['project_5ftranscript_5fgbwt_10529',['project_transcript_gbwt',['../classvg_1_1Transcriptome.html#a4edf6085f024b736bef4be82c6fd854a',1,'vg::Transcriptome']]],
+ ['proposal_5fsample_10530',['proposal_sample',['../classvg_1_1MCMCGenotyper.html#a0e007a331bc2854ec8734557bd80962d',1,'vg::MCMCGenotyper']]],
+ ['propose_5fdeflection_10531',['propose_deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a662b5ce1fa402a6c8e7a5f20f92773b3',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['protobufemitter_10532',['ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html#ab9d133fa3604ba677c12337ccf609ba7',1,'vg::io::ProtobufEmitter::ProtobufEmitter(std::ostream &out, bool compress=true, size_t max_group_size=1000)'],['../classvg_1_1io_1_1ProtobufEmitter.html#a1adf66f9c9242369dcdd38746f925855',1,'vg::io::ProtobufEmitter::ProtobufEmitter(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#accd8d7c57bffcfdc48ba7085f7a53561',1,'vg::io::ProtobufEmitter::ProtobufEmitter(ProtobufEmitter &&other)=default']]],
+ ['protobufiterator_10533',['ProtobufIterator',['../classvg_1_1io_1_1ProtobufIterator.html#a0f2996a9653a98470e7c944879a69d70',1,'vg::io::ProtobufIterator::ProtobufIterator(istream &in)'],['../classvg_1_1io_1_1ProtobufIterator.html#a50ad0e8d7ee212617dbf9e456ea43e07',1,'vg::io::ProtobufIterator::ProtobufIterator()=default']]],
+ ['provide_10534',['provide',['../classvg_1_1IndexRegistry.html#a72c4f8ea143cd9a982366234a8eed71e',1,'vg::IndexRegistry::provide(const IndexName &identifier, const string &filename)'],['../classvg_1_1IndexRegistry.html#a430536c995544af29060b78d04e3f5c1',1,'vg::IndexRegistry::provide(const IndexName &identifier, const vector< string > &filenames)'],['../classvg_1_1IndexFile.html#a116a29bacf28f3889ea318ac25a11dc7',1,'vg::IndexFile::provide()']]],
+ ['prune_5fand_5ftrim_5fanchors_10535',['prune_and_trim_anchors',['../classvg_1_1Surjector.html#ae34c7f96fff02c5490477fc8ad643908',1,'vg::Surjector']]],
+ ['prune_5fcomplex_10536',['prune_complex',['../namespacevg_1_1algorithms.html#a09b6e838b2991d13e272ddcb41aacfbc',1,'vg::algorithms']]],
+ ['prune_5fcomplex_5fwith_5fhead_5ftail_10537',['prune_complex_with_head_tail',['../namespacevg_1_1algorithms.html#a784ee29876a24431a865541426f42dee',1,'vg::algorithms']]],
+ ['prune_5fhigh_5fshift_5fedges_10538',['prune_high_shift_edges',['../classvg_1_1MultipathAlignmentGraph.html#aa42ef4313d4d24ab4c19532e2bd30652',1,'vg::MultipathAlignmentGraph']]],
+ ['prune_5flow_5fscoring_5fedges_10539',['prune_low_scoring_edges',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab2949f31f3e43410189eafa260544baf',1,'vg::MEMClusterer::HitGraph']]],
+ ['prune_5fshort_5fsubgraphs_10540',['prune_short_subgraphs',['../namespacevg_1_1algorithms.html#a83e87cf3f8a5ca4362776cf1a3050242',1,'vg::algorithms']]],
+ ['prune_5fto_5fconnecting_5fgraph_10541',['prune_to_connecting_graph',['../namespacevg_1_1algorithms.html#a3d74c519ccaa204e7735d5bd26c5095a',1,'vg::algorithms']]],
+ ['prune_5fto_5fhigh_5fscoring_5fpaths_10542',['prune_to_high_scoring_paths',['../classvg_1_1MultipathAlignmentGraph.html#a8164834df4fc94907fb96b06062c9514',1,'vg::MultipathAlignmentGraph']]],
+ ['prune_5funconnectable_10543',['prune_unconnectable',['../classvg_1_1Surjector.html#ab65da876e448d86bc64985c0b14d3e78',1,'vg::Surjector']]],
+ ['pseudo_5flength_10544',['pseudo_length',['../classvg_1_1MultipathMapper.html#aa5ee46fa484ee95e45da33b47bcc4eb8',1,'vg::MultipathMapper']]],
+ ['pseudo_5frandom_5fsequence_10545',['pseudo_random_sequence',['../namespacevg.html#a1924855da445b625609837c0920af7b2',1,'vg']]],
+ ['purge_5funmapped_5falignments_10546',['purge_unmapped_alignments',['../classvg_1_1MultipathMapper.html#a009000ee2da67a965a4f627be468d976',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< multipath_alignment_t > &multipath_alns_out)'],['../classvg_1_1MultipathMapper.html#ab1c9f02cbadcd8df05b691e4ff5294f2',1,'vg::MultipathMapper::purge_unmapped_alignments(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, bool proper_paired)']]],
+ ['push_10547',['push',['../structvg_1_1MatchPos_1_1PathList.html#a2979222c63cb87e2f530fceda30e56a5',1,'vg::MatchPos::PathList::push()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ade3a2a60c495a494d27fb6f8a72ef2db',1,'vg::ZipCodeTree::reverse_iterator::push()']]],
+ ['push_5fback_10548',['push_back',['../structhaplo_1_1gbwt__thread__t.html#a726f2772b4725564569e4889f89db7c6',1,'haplo::gbwt_thread_t::push_back()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#ade3cdc2fdb2dc88b735bee5be2c04cee',1,'haplo::linear_haplo_structure::SNVvector::push_back()']]],
+ ['push_5fedit_10549',['push_edit',['../classvg_1_1DozeuInterface.html#acc84e0c73002c23f8249ea17efff6848',1,'vg::DozeuInterface']]]
];
diff --git a/search/functions_11.js b/search/functions_11.js
index e293def778..12f7fbd494 100644
--- a/search/functions_11.js
+++ b/search/functions_11.js
@@ -1,14 +1,14 @@
var searchData=
[
- ['qual_5fadjusted_5fbonuses_10546',['qual_adjusted_bonuses',['../classvg_1_1QualAdjAligner.html#a8e36e10804dcd53c0ac30f351311f2cc',1,'vg::QualAdjAligner']]],
- ['qual_5fadjusted_5fmatrix_10547',['qual_adjusted_matrix',['../classvg_1_1QualAdjAligner.html#a44f320fb6e114e25c9ff8856954b10aa',1,'vg::QualAdjAligner']]],
- ['qual_5ffilter_10548',['qual_filter',['../classvg_1_1Filter.html#ac0b864f9350cb8d9be52e2c13e69c30c',1,'vg::Filter']]],
- ['qualadjaligner_10549',['QualAdjAligner',['../classvg_1_1QualAdjAligner.html#a1eb97ac4416d8ae7e23351c2c03e0314',1,'vg::QualAdjAligner']]],
- ['qualadjxdropaligner_10550',['QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html#a72ca9e0f8a6b3f73bba3299b7fd2698b',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const int8_t *_score_matrix, const int8_t *_qual_adj_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1QualAdjXdropAligner.html#aa7bfa5bd489eda65d0c4060532d0f556',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner()=default'],['../classvg_1_1QualAdjXdropAligner.html#aa9244a0f908625e90a714acfd92e49db',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a9c73cbd3ad52ec62d102ec4958311dd2',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(QualAdjXdropAligner &&other)']]],
- ['quality_10551',['quality',['../classvg_1_1multipath__alignment__t.html#aebdfc9e1f214a2b934e42cda1810932b',1,'vg::multipath_alignment_t']]],
- ['quality_5fchar_5fto_5fshort_10552',['quality_char_to_short',['../namespacevg_1_1io.html#a64f819396b817978940de263c04713f9',1,'vg::io']]],
- ['quality_5fshort_5fto_5fchar_10553',['quality_short_to_char',['../namespacevg_1_1io.html#a62d15de4c2614e383b6bc00e34eefe15',1,'vg::io']]],
- ['query_10554',['query',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75221ee25fded8f4d4afcf7a11357413',1,'vg::IndexedVG::CacheEntry::query()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ac21892177de65eac5e2fc9237292c7dc',1,'vg::subcommand::BaseArgSpec::query()'],['../structvg_1_1subcommand_1_1ArgSpec.html#aa3a10b563ddbdd0f555f2ef46d8e9b97',1,'vg::subcommand::ArgSpec::query()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abc7e6b6b7265d1bd3224768712748f65',1,'vg::subcommand::BaseOptionGroup::query()'],['../structvg_1_1subcommand_1_1OptionGroup.html#ae9fc4713f74d5ae9f8d94b8ee29c9775',1,'vg::subcommand::OptionGroup::query()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a8b15018e5e8f03ef99d63ab382e484f5',1,'vg::subcommand::GroupedOptionGroup::query()']]],
- ['query_5fcluster_5fgraphs_10555',['query_cluster_graphs',['../classvg_1_1MultipathMapper.html#aa07b31689dd15a1f85752cbebbb42994',1,'vg::MultipathMapper']]],
- ['query_5foverlap_10556',['query_overlap',['../namespacevg.html#acffe466a3ca83097eceac30a09b9a010',1,'vg']]]
+ ['qual_5fadjusted_5fbonuses_10550',['qual_adjusted_bonuses',['../classvg_1_1QualAdjAligner.html#a8e36e10804dcd53c0ac30f351311f2cc',1,'vg::QualAdjAligner']]],
+ ['qual_5fadjusted_5fmatrix_10551',['qual_adjusted_matrix',['../classvg_1_1QualAdjAligner.html#a44f320fb6e114e25c9ff8856954b10aa',1,'vg::QualAdjAligner']]],
+ ['qual_5ffilter_10552',['qual_filter',['../classvg_1_1Filter.html#ac0b864f9350cb8d9be52e2c13e69c30c',1,'vg::Filter']]],
+ ['qualadjaligner_10553',['QualAdjAligner',['../classvg_1_1QualAdjAligner.html#a1eb97ac4416d8ae7e23351c2c03e0314',1,'vg::QualAdjAligner']]],
+ ['qualadjxdropaligner_10554',['QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html#a72ca9e0f8a6b3f73bba3299b7fd2698b',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const int8_t *_score_matrix, const int8_t *_qual_adj_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1QualAdjXdropAligner.html#aa7bfa5bd489eda65d0c4060532d0f556',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner()=default'],['../classvg_1_1QualAdjXdropAligner.html#aa9244a0f908625e90a714acfd92e49db',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a9c73cbd3ad52ec62d102ec4958311dd2',1,'vg::QualAdjXdropAligner::QualAdjXdropAligner(QualAdjXdropAligner &&other)']]],
+ ['quality_10555',['quality',['../classvg_1_1multipath__alignment__t.html#aebdfc9e1f214a2b934e42cda1810932b',1,'vg::multipath_alignment_t']]],
+ ['quality_5fchar_5fto_5fshort_10556',['quality_char_to_short',['../namespacevg_1_1io.html#a64f819396b817978940de263c04713f9',1,'vg::io']]],
+ ['quality_5fshort_5fto_5fchar_10557',['quality_short_to_char',['../namespacevg_1_1io.html#a62d15de4c2614e383b6bc00e34eefe15',1,'vg::io']]],
+ ['query_10558',['query',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75221ee25fded8f4d4afcf7a11357413',1,'vg::IndexedVG::CacheEntry::query()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ac21892177de65eac5e2fc9237292c7dc',1,'vg::subcommand::BaseArgSpec::query()'],['../structvg_1_1subcommand_1_1ArgSpec.html#aa3a10b563ddbdd0f555f2ef46d8e9b97',1,'vg::subcommand::ArgSpec::query()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abc7e6b6b7265d1bd3224768712748f65',1,'vg::subcommand::BaseOptionGroup::query()'],['../structvg_1_1subcommand_1_1OptionGroup.html#ae9fc4713f74d5ae9f8d94b8ee29c9775',1,'vg::subcommand::OptionGroup::query()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a8b15018e5e8f03ef99d63ab382e484f5',1,'vg::subcommand::GroupedOptionGroup::query()']]],
+ ['query_5fcluster_5fgraphs_10559',['query_cluster_graphs',['../classvg_1_1MultipathMapper.html#aa07b31689dd15a1f85752cbebbb42994',1,'vg::MultipathMapper']]],
+ ['query_5foverlap_10560',['query_overlap',['../namespacevg.html#acffe466a3ca83097eceac30a09b9a010',1,'vg']]]
];
diff --git a/search/functions_12.js b/search/functions_12.js
index 2b42b677ae..0dea7626c6 100644
--- a/search/functions_12.js
+++ b/search/functions_12.js
@@ -1,197 +1,197 @@
var searchData=
[
- ['radix_5fsort_5fzipcodes_10557',['radix_sort_zipcodes',['../classvg_1_1ZipCodeForest.html#aade4c028524fd9e0c4a6267335584171',1,'vg::ZipCodeForest']]],
- ['random_10558',['random',['../classvg_1_1Colors.html#aa655272ae2bc4944fe7096d3e9e072b8',1,'vg::Colors::random()'],['../classvg_1_1Pictographs.html#ac61d6a97566ac6cc8c21158688fcfdf3',1,'vg::Pictographs::random()']]],
- ['random_5fmatch_5flength_10559',['random_match_length',['../classvg_1_1BaseMapper.html#a2884c6722e6bd9c9aab6671a85a6c3c0',1,'vg::BaseMapper']]],
- ['random_5fmatch_5fp_5fvalue_10560',['random_match_p_value',['../classvg_1_1MultipathMapper.html#afbf8bce27b441ba87f83c72d5c65c592',1,'vg::MultipathMapper']]],
- ['random_5fread_10561',['random_read',['../classvg_1_1VG.html#a8452af466a3e1ad4b0b463ea0d5da933',1,'vg::VG']]],
- ['random_5fsequence_10562',['random_sequence',['../namespacevg.html#ab80fc8c8920c7ec53cfee81dc2fce852',1,'vg']]],
- ['random_5fsequence_5fgen_10563',['random_sequence_gen',['../namespacevg.html#a4012afd56ccb35387121c71c2119e244',1,'vg']]],
- ['range_10564',['Range',['../structvg_1_1Range.html#a08e1ef06cddbc0efcb0660d34cf3bc5d',1,'vg::Range::Range()'],['../structvg_1_1Range.html#a4becc4a909e9ff23a62318da327af7ff',1,'vg::Range::Range(const Number &val)'],['../structvg_1_1Range.html#a10c624eaeb6a83b450c9d24fdbaa8555',1,'vg::Range::Range(const Range &other)'],['../structvg_1_1Range.html#a7bf784228c365aa72150fec926de77ae',1,'vg::Range::Range(Range &&other)'],['../classvg_1_1io_1_1MessageIterator.html#af88ac04ab7cbb8245a86d21a71a5dd76',1,'vg::io::MessageIterator::range()'],['../classvg_1_1io_1_1ProtobufIterator.html#acf75c4c7a16e406f9bb860e3f0c7dae9',1,'vg::io::ProtobufIterator::range()']]],
- ['range_5fvector_10565',['range_vector',['../namespacevg.html#a931d9271de88fc786030fdd0ab4bf534',1,'vg::range_vector(size_t begin, size_t end)'],['../namespacevg.html#a39adca1737de5d28d007d95b809deb7f',1,'vg::range_vector(size_t end)']]],
- ['rank_5fby_5fsupport_10566',['rank_by_support',['../classvg_1_1PoissonSupportSnarlCaller.html#a300ca3bbff527fb43fbc12e65177d053',1,'vg::PoissonSupportSnarlCaller']]],
- ['rank_5fto_5fhandle_10567',['rank_to_handle',['../classhandlegraph_1_1RankedHandleGraph.html#aacf6651545adbd407082a539222f8a69',1,'handlegraph::RankedHandleGraph']]],
- ['rank_5fto_5fid_10568',['rank_to_id',['../classxg_1_1XG.html#aee052f301d8cae7b30c50c115c6b950b',1,'xg::XG::rank_to_id()'],['../classhandlegraph_1_1RankedHandleGraph.html#a5bf563241454b21539effcad11406ec9',1,'handlegraph::RankedHandleGraph::rank_to_id()']]],
- ['rarevariantsimplifier_10569',['RareVariantSimplifier',['../classvg_1_1RareVariantSimplifier.html#a08cf82d7c40db195176b9bf177a50e32',1,'vg::RareVariantSimplifier']]],
- ['ratiosupportsnarlcaller_10570',['RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html#ad6905b3e30632f2a0a3e304cdfd15faa',1,'vg::RatioSupportSnarlCaller']]],
- ['re_5fgenotype_10571',['re_genotype',['../classvg_1_1LegacyCaller.html#a6c23ee5b732d26d4f55bd3b5b4830fca',1,'vg::LegacyCaller']]],
- ['read_10572',['read',['../classvg_1_1ParallelKFFReader.html#ae34ae06b01651343a3e07b87ce019aa7',1,'vg::ParallelKFFReader']]],
- ['read_5fend_10573',['read_end',['../classvg_1_1algorithms_1_1Anchor.html#a335ebe332424cb49cae4da84c91a5367',1,'vg::algorithms::Anchor']]],
- ['read_5fexclusion_5fend_10574',['read_exclusion_end',['../classvg_1_1algorithms_1_1Anchor.html#a12554fafcdf8309d3119b349e3bf6e59',1,'vg::algorithms::Anchor']]],
- ['read_5fexclusion_5fstart_10575',['read_exclusion_start',['../classvg_1_1algorithms_1_1Anchor.html#a1de27e657461d6de450a84aab34becb4',1,'vg::algorithms::Anchor']]],
- ['read_5flog_5flikelihood_10576',['read_log_likelihood',['../classvg_1_1PhasedGenome.html#af754f8a4e9793ebd5f4aa3b673b7e442',1,'vg::PhasedGenome']]],
- ['read_5fmapping_10577',['read_mapping',['../classvg_1_1PhaseUnfolder.html#adbf93e421183b64f73276639c3c23dfb',1,'vg::PhaseUnfolder']]],
- ['read_5fstart_10578',['read_start',['../classvg_1_1algorithms_1_1Anchor.html#a21c07ed7e05dfd2194d580022f2005c4',1,'vg::algorithms::Anchor']]],
- ['readmasker_10579',['ReadMasker',['../classvg_1_1ReadMasker.html#a99656ed3430d86e7a34b908914991945',1,'vg::ReadMasker']]],
- ['readrestrictedtraversalfinder_10580',['ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html#a8cf6a940b0fce108e8af39d8a50a380f',1,'vg::ReadRestrictedTraversalFinder']]],
- ['realigning_5fsurject_10581',['realigning_surject',['../classvg_1_1Surjector.html#a2629f80135104fb8486ef823f525b843',1,'vg::Surjector']]],
- ['reallocate_5fatomic_5fint_5fvector_10582',['reallocate_atomic_int_vector',['../namespacevg_1_1algorithms.html#acd891e00c4846e53f760d504434ead12',1,'vg::algorithms']]],
- ['reassign_5fnode_10583',['reassign_node',['../classvg_1_1Paths.html#aed5ea00a6a8dab5b54eeedd9e8f91a7b',1,'vg::Paths']]],
- ['reassign_5fnode_5fids_10584',['reassign_node_ids',['../classvg_1_1VG.html#aca4a358ff4c7f387c1c6d5d239499a07',1,'vg::VG::reassign_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a4805d276a83a1dad2462e6b8dd2443dc',1,'handlegraph::MutableHandleGraph::reassign_node_ids()']]],
- ['reassign_5fsplit_5fclusters_10585',['reassign_split_clusters',['../classvg_1_1MultipathMapper.html#a5d8b62d4d55e83f80da09173e8520874',1,'vg::MultipathMapper']]],
- ['rebuild_5fedge_5findexes_10586',['rebuild_edge_indexes',['../classvg_1_1VG.html#a6541146b6410cec4be3e2a7379ea3bcf',1,'vg::VG']]],
- ['rebuild_5fgbwt_10587',['rebuild_gbwt',['../namespacevg.html#a95d54bf0a30125f9ded043bb099cb25f',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob > &jobs, const std::unordered_map< nid_t, size_t > &node_to_job, const RebuildParameters ¶meters)'],['../namespacevg.html#ade5b1e6daa5da7101533d444d3d8ff41',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob::mapping_type > &mappings)']]],
- ['rebuild_5fgbwt_5fjob_10588',['rebuild_gbwt_job',['../namespacevg.html#a16b175479dee254341d60fc037dae233',1,'vg']]],
- ['rebuild_5findexes_10589',['rebuild_indexes',['../classvg_1_1VG.html#a63d4e45a9a410c451b1cad44ef7068ad',1,'vg::VG']]],
- ['rebuild_5fmapping_5faux_10590',['rebuild_mapping_aux',['../classvg_1_1Paths.html#a5f80df5846bdac0b502a70af97dc65de',1,'vg::Paths']]],
- ['rebuild_5fnode_5fmapping_10591',['rebuild_node_mapping',['../classvg_1_1Paths.html#a7e9d9388475dcd8f23af072430e7383c',1,'vg::Paths']]],
- ['recombinator_10592',['Recombinator',['../classvg_1_1Recombinator.html#a9248c550bcc5aa267abde6eefec69e88',1,'vg::Recombinator']]],
- ['recombinator_5fsanity_5fchecks_10593',['recombinator_sanity_checks',['../namespacevg.html#aa81f31f29a47e669812c3ef57bd1aab6',1,'vg']]],
- ['recombinatorfragment_10594',['RecombinatorFragment',['../structvg_1_1RecombinatorFragment.html#aab79ba107e9e086b432dfa9fcf4a2807',1,'vg::RecombinatorFragment']]],
- ['record_10595',['record',['../classvg_1_1SnarlManager.html#a45e3765bfd07b196b6e30b7a9b62aefd',1,'vg::SnarlManager::record(const Snarl *snarl) const'],['../classvg_1_1SnarlManager.html#a3ce002195299049e9925e94546d989b9',1,'vg::SnarlManager::record(Snarl *snarl)']]],
- ['record_5ffanouts_10596',['record_fanouts',['../classvg_1_1MultipathMapper.html#a0b4e3381a53cf532acdf7cbadc6d9985',1,'vg::MultipathMapper']]],
- ['record_5ffragment_5fconfiguration_10597',['record_fragment_configuration',['../classvg_1_1FragmentLengthStatistics.html#ae63195a980c56907de548ba00098c794',1,'vg::FragmentLengthStatistics']]],
- ['record_5fread_5fpair_5fquality_10598',['record_read_pair_quality',['../classvg_1_1NGSSimulator.html#aec434f0c212aec15e1760f4c4b1185e2',1,'vg::NGSSimulator']]],
- ['record_5fread_5fquality_10599',['record_read_quality',['../classvg_1_1NGSSimulator.html#a8f34614e3dc660e31d26d9c18970e736',1,'vg::NGSSimulator']]],
- ['record_5ftransition_10600',['record_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ab3609f759c7b20d77c1bc0ca7160c26a',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['recover_5flog_5fbase_10601',['recover_log_base',['../classvg_1_1GSSWAligner.html#ab5102e690e6e2e0e72aa35ea769179a2',1,'vg::GSSWAligner']]],
- ['recursively_5femit_5fsnarls_10602',['recursively_emit_snarls',['../classvg_1_1CactusSnarlFinder.html#aad8a90f6cd0fddf6ab908f6287e3ddf3',1,'vg::CactusSnarlFinder']]],
- ['reduce_5fto_5fsingle_5fpath_10603',['reduce_to_single_path',['../classvg_1_1MultipathMapper.html#a0a3360fde5883dc2c0927b63be0a3bd5',1,'vg::MultipathMapper']]],
- ['reencode_5fold_5fg_5fvector_10604',['reencode_old_g_vector',['../classxg_1_1XG.html#a8a5068e08156a861e35e62cc3fa94204',1,'xg::XG']]],
- ['ref_5fpath_5fdistance_10605',['ref_path_distance',['../namespacevg_1_1algorithms.html#aa5e4dc632e98b58b67a99af6749d9e05',1,'vg::algorithms']]],
- ['ref_5fposition_10606',['ref_position',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a442f4e740bc94b1671c9590f65bb65a4',1,'haplo::linear_haplo_structure::SNVvector']]],
- ['refactor_5fsplit_5falignment_10607',['refactor_split_alignment',['../classvg_1_1Filter.html#af5c53d7fa62dff67d24ff0daa4d5f925',1,'vg::Filter']]],
- ['reference_5ftranscript_5fpaths_10608',['reference_transcript_paths',['../classvg_1_1Transcriptome.html#aacf1ad40a7a5d42985c4149b03fe936e',1,'vg::Transcriptome']]],
- ['regionexpander_10609',['RegionExpander',['../classvg_1_1RegionExpander.html#a42c0f501da7fabf0045f5c434b55f705',1,'vg::RegionExpander']]],
- ['register_5falias_10610',['register_alias',['../classvg_1_1AliasGraph.html#a4f21c7d2e0aa761fd5ff4ccd43bd72af',1,'vg::AliasGraph']]],
- ['register_5fbare_5floader_10611',['register_bare_loader',['../classvg_1_1io_1_1Registry.html#a025929701767e23673356cae9e7024a5',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_10612',['register_bare_loader_saver',['../classvg_1_1io_1_1Registry.html#aab501bb8db46d45e8b1946da37f0b382',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fheader_5fcheck_10613',['register_bare_loader_saver_with_header_check',['../classvg_1_1io_1_1Registry.html#a873d317a5ec04d5af5223008310043df',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_10614',['register_bare_loader_saver_with_magic',['../classvg_1_1io_1_1Registry.html#ad3f16de5d24cb503429d358e2af8c831',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_5fand_5ffilename_10615',['register_bare_loader_saver_with_magic_and_filename',['../classvg_1_1io_1_1Registry.html#acfda4299247a88075080004beba4a136',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fsaver_5fwith_5fmagics_10616',['register_bare_loader_saver_with_magics',['../classvg_1_1io_1_1Registry.html#af4180fbb60edaa1cd1aec325945d2af5',1,'vg::io::Registry']]],
- ['register_5fbare_5floader_5fwith_5ffilename_10617',['register_bare_loader_with_filename',['../classvg_1_1io_1_1Registry.html#abb7a1aefe860153a36614efa54bcde29',1,'vg::io::Registry']]],
- ['register_5fbarrier_10618',['register_barrier',['../classvg_1_1io_1_1StreamMultiplexer.html#acb05844bf345313fc1710db7f3610ac5',1,'vg::io::StreamMultiplexer']]],
- ['register_5fbreakpoint_10619',['register_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#a562910d0ca3b3fac6b95b0c3ee3c81dd',1,'vg::io::StreamMultiplexer']]],
- ['register_5fconfigurable_10620',['register_configurable',['../classvg_1_1ConfigurableParser.html#a3c42646beeac7fb48f57c44f1420ec7b',1,'vg::ConfigurableParser']]],
- ['register_5feverything_10621',['register_everything',['../classvg_1_1io_1_1Registry.html#ad1b4d2c277bdb07c2bf4cc4b60e35745',1,'vg::io::Registry']]],
- ['register_5ffragment_5flength_10622',['register_fragment_length',['../classvg_1_1FragmentLengthDistribution.html#a888c21e626cb2fd984f9e0ffd39adefc',1,'vg::FragmentLengthDistribution']]],
- ['register_5fgeneralization_10623',['register_generalization',['../classvg_1_1IndexRegistry.html#a2e1c0e83f49e8719459e644ce143302b',1,'vg::IndexRegistry']]],
- ['register_5findex_10624',['register_index',['../classvg_1_1IndexRegistry.html#ad8f48075fe06df92c65bc5fd0207f9bc',1,'vg::IndexRegistry']]],
- ['register_5flibvg_5fio_10625',['register_libvg_io',['../namespacevg_1_1io.html#ad93f27be4f07ab9c6a91a1501b992f70',1,'vg::io']]],
- ['register_5floader_10626',['register_loader',['../classvg_1_1io_1_1Registry.html#a82c329d405f2dc83880623561a10962f',1,'vg::io::Registry::register_loader(const string &tag, load_function_t loader)'],['../classvg_1_1io_1_1Registry.html#abdbc23294daf5a1f44b34da481929891',1,'vg::io::Registry::register_loader(const std::vector< std::string > &tags, load_function_t loader)']]],
- ['register_5floader_5fparams_5fjson_10627',['register_loader_params_json',['../namespacevg_1_1io.html#a113c8011c25b00d36f77f49062726bbb',1,'vg::io']]],
- ['register_5floader_5fsaver_10628',['register_loader_saver',['../classvg_1_1io_1_1Registry.html#a3dfd842b470ff701fb805838e2d7fe61',1,'vg::io::Registry::register_loader_saver(const string &tag, load_function_t loader, save_function_t saver)'],['../classvg_1_1io_1_1Registry.html#a56e76bb9dcab4c47f400d844430536b6',1,'vg::io::Registry::register_loader_saver(const std::vector< std::string > &tags, load_function_t loader, save_function_t saver)']]],
- ['register_5floader_5fsaver_5fdistance_5findex_10629',['register_loader_saver_distance_index',['../namespacevg_1_1io.html#a45372f8f761a3bce9e7ef6e1422db47b',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbwt_10630',['register_loader_saver_gbwt',['../namespacevg_1_1io.html#a47fc4c5122bf0f0810993822d194eb20',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbwtgraph_10631',['register_loader_saver_gbwtgraph',['../namespacevg_1_1io.html#a6143362abf3060042589f1ffb22ff498',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbz_10632',['register_loader_saver_gbz',['../namespacevg_1_1io.html#adb36b3bf6da822750c5c6c9cd2d987e0',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgbzgraph_10633',['register_loader_saver_gbzgraph',['../namespacevg_1_1io.html#a81649e999e30d305e02187c16b257d07',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgcsa_10634',['register_loader_saver_gcsa',['../namespacevg_1_1io.html#affca170910f12393eb1381c4d72e4e73',1,'vg::io']]],
- ['register_5floader_5fsaver_5fgfa_10635',['register_loader_saver_gfa',['../namespacevg_1_1io.html#a1fadf5a0f7d91d61c9d2c27d35987c6a',1,'vg::io']]],
- ['register_5floader_5fsaver_5fhash_5fgraph_10636',['register_loader_saver_hash_graph',['../namespacevg_1_1io.html#a49d41e6f52ad981f96d772396fd4eee5',1,'vg::io']]],
- ['register_5floader_5fsaver_5flcp_10637',['register_loader_saver_lcp',['../namespacevg_1_1io.html#af7df97a78891ada683647c88c6393eb9',1,'vg::io']]],
- ['register_5floader_5fsaver_5fminimizer_10638',['register_loader_saver_minimizer',['../namespacevg_1_1io.html#aa69bc026abe7a1db4530704dfc7e7b3f',1,'vg::io']]],
- ['register_5floader_5fsaver_5fpacked_5fgraph_10639',['register_loader_saver_packed_graph',['../namespacevg_1_1io.html#a776b6490958856d44dc2d962d629440d',1,'vg::io']]],
- ['register_5floader_5fsaver_5fr_5findex_10640',['register_loader_saver_r_index',['../namespacevg_1_1io.html#a6ce32e4ae1d4f5d244c0d80d3ac09beb',1,'vg::io']]],
- ['register_5floader_5fsaver_5fsnarl_5fmanager_10641',['register_loader_saver_snarl_manager',['../namespacevg_1_1io.html#a8072168ee8165f81afb2688ef0825ea8',1,'vg::io']]],
- ['register_5floader_5fsaver_5fvg_10642',['register_loader_saver_vg',['../namespacevg_1_1io.html#ac3485846033fd4accb221b0a866dfeb7',1,'vg::io']]],
- ['register_5floader_5fsaver_5fxg_10643',['register_loader_saver_xg',['../namespacevg_1_1io.html#a7a23bf45ec66db4b724b7f8a9f223c33',1,'vg::io']]],
- ['register_5floader_5fsaver_5fzip_5fcodes_10644',['register_loader_saver_zip_codes',['../namespacevg_1_1io.html#ac0521f6b9e5e9e78ab0837548bef8f0e',1,'vg::io']]],
- ['register_5foption_10645',['register_option',['../classvg_1_1Configurable.html#afa7bba48c6289ea9b9095acd79a5658e',1,'vg::Configurable']]],
- ['register_5fprotobuf_10646',['register_protobuf',['../classvg_1_1io_1_1Registry.html#ae4880fe254039bfe44b73b9050ce0abc',1,'vg::io::Registry']]],
- ['register_5frecipe_10647',['register_recipe',['../classvg_1_1IndexRegistry.html#afdda05f4e7f1dfd93ecb33ad3b582aad',1,'vg::IndexRegistry']]],
- ['register_5fsampled_5fposition_10648',['register_sampled_position',['../classvg_1_1NGSSimulator.html#ab9adc2b15f1d2c31301e5801e773dcbd',1,'vg::NGSSimulator']]],
- ['register_5fsaver_10649',['register_saver',['../classvg_1_1io_1_1Registry.html#a1bba520da840207b627aface669b80c6',1,'vg::io::Registry']]],
- ['regress_10650',['regress',['../namespacevg.html#aab16fbb8659a66f16f2004fcc3e8f9db',1,'vg']]],
- ['regularize_10651',['regularize',['../classvg_1_1SnarlManager.html#ae5015eacc04d12d02ef5196fb23f3075',1,'vg::SnarlManager']]],
- ['release_10652',['release',['../structjson__autoptr.html#ad3ee76d343667fd42bdbe504f32e7042',1,'json_autoptr']]],
- ['remaining_5ftree_10653',['remaining_tree',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1f7d072e5054742f4c391b294fe5d839',1,'vg::ZipCodeTree::iterator']]],
- ['remap_10654',['remap',['../classvg_1_1Filter.html#a66768cd6584270f71d190d525c99a9c4',1,'vg::Filter::remap(Alignment &aln)'],['../classvg_1_1Filter.html#aea9d6813e578a5957131fa6c4c8eff52',1,'vg::Filter::remap(string seq)']]],
- ['remove_10655',['remove',['../classvg_1_1PhasedGenome.html#a3706e208421ac10d5695ed5d5ec45090',1,'vg::PhasedGenome::remove()'],['../namespacevg_1_1temp__file.html#a9885078330e16129fccc5fb6d8717ec5',1,'vg::temp_file::remove()'],['../namespacexg_1_1temp__file.html#aa4e7fb2251b2ba8f6d054d873eae4988',1,'xg::temp_file::remove()']]],
- ['remove_5fbonuses_10656',['remove_bonuses',['../classvg_1_1GSSWAligner.html#a35fe72b24fc734d75864275c8cc1257e',1,'vg::GSSWAligner']]],
- ['remove_5fclipped_5fportion_10657',['remove_clipped_portion',['../classvg_1_1Filter.html#ac246ae985a763a2d10edc92c81639913',1,'vg::Filter']]],
- ['remove_5fdirectory_10658',['remove_directory',['../structvg_1_1temp__file_1_1Handler.html#acb21b507190287960d50a614ccf611bf',1,'vg::temp_file::Handler']]],
- ['remove_5fdominated_5fchunks_10659',['remove_dominated_chunks',['../classvg_1_1Surjector.html#aafa4eb4d310ac530ed186170dc34dba9',1,'vg::Surjector']]],
- ['remove_5fduplicate_5fedges_10660',['remove_duplicate_edges',['../namespacevg.html#add4d3a3d1917566a8df138c80b38e548',1,'vg']]],
- ['remove_5fduplicate_5fnodes_10661',['remove_duplicate_nodes',['../namespacevg.html#a6dbe8468f2f2bcf8ceb859e6a0f8b4b1',1,'vg']]],
- ['remove_5fduplicated_5fin_10662',['remove_duplicated_in',['../classvg_1_1VG.html#a33424c3be8c3e088631dfb37c48773d3',1,'vg::VG']]],
- ['remove_5fduplicates_10663',['remove_duplicates',['../classvg_1_1VG.html#aba9fb73c326ecfab70e35e44dff6a937',1,'vg::VG::remove_duplicates()'],['../namespacevg.html#a5d00fa3c72ac473353496aab96965e60',1,'vg::remove_duplicates(std::vector< GaplessExtension > &result)'],['../namespacevg.html#aecd2e49750e94ed6f9de917dd9c72ac2',1,'vg::remove_duplicates(Graph &graph)']]],
- ['remove_5fedge_10664',['remove_edge',['../classvg_1_1FlowSort.html#ad5203a8e590cc8e2bdb7038057963aaf',1,'vg::FlowSort']]],
- ['remove_5fedit_5ftmpfiles_10665',['remove_edit_tmpfiles',['../classvg_1_1Packer.html#a2612eb978cfad2220946fab00cc3360f',1,'vg::Packer']]],
- ['remove_5fempty_5falignment_5fsections_10666',['remove_empty_alignment_sections',['../namespacevg.html#af3fb034fcd6d50c2b84f40026b40f284',1,'vg']]],
- ['remove_5ffull_5flength_5fbonuses_10667',['remove_full_length_bonuses',['../classvg_1_1Mapper.html#a2e8194d4eb73fe32467ab37ed9468e09',1,'vg::Mapper']]],
- ['remove_5fhigh_5fdegree_5fnodes_10668',['remove_high_degree_nodes',['../namespacevg_1_1algorithms.html#a96020f05a81255adfca3821f538c02b9',1,'vg::algorithms']]],
- ['remove_5finverting_5fedges_10669',['remove_inverting_edges',['../classvg_1_1VG.html#a76005ed499eea217c9f778028751137c',1,'vg::VG']]],
- ['remove_5flow_5fscoring_5fsections_10670',['remove_low_scoring_sections',['../namespacevg.html#a0ea49989e31a688e22265eb41291c0ae',1,'vg']]],
- ['remove_5fmapping_10671',['remove_mapping',['../classvg_1_1Paths.html#ad52958174f83ec940328d8610563dc1a',1,'vg::Paths']]],
- ['remove_5fnode_10672',['remove_node',['../classvg_1_1Paths.html#ab74cefb48d501d96b8dc81e3865770d1',1,'vg::Paths']]],
- ['remove_5fnode_5fforwarding_5fedges_10673',['remove_node_forwarding_edges',['../classvg_1_1VG.html#ab92694e7fd89275603c967739e60e0d2',1,'vg::VG']]],
- ['remove_5fnon_5fpath_10674',['remove_non_path',['../classvg_1_1VG.html#ad517da731d2bf9c81cc28e0a1367af33',1,'vg::VG']]],
- ['remove_5fnon_5ftranscribed_5fnodes_10675',['remove_non_transcribed_nodes',['../classvg_1_1Transcriptome.html#aed6ea709b303bcc0055ea41217b5e1be',1,'vg::Transcriptome']]],
- ['remove_5fnull_5fnodes_10676',['remove_null_nodes',['../classvg_1_1VG.html#a9b107027697644d771eb529037201f71',1,'vg::VG']]],
- ['remove_5fnull_5fnodes_5fforwarding_5fedges_10677',['remove_null_nodes_forwarding_edges',['../classvg_1_1VG.html#a0e887a7b2cfc666f2210889a2dec791b',1,'vg::VG']]],
- ['remove_5forphan_5fedges_10678',['remove_orphan_edges',['../classvg_1_1VG.html#a40dd9bc0458a4948afd676374ae8d1f0',1,'vg::VG::remove_orphan_edges()'],['../namespacevg.html#a0b38f4f0d7e63b1f7f20d2dc985f88c4',1,'vg::remove_orphan_edges()']]],
- ['remove_5fpath_10679',['remove_path',['../classvg_1_1Paths.html#ad3893e02f5e0429a13621ae333208f9e',1,'vg::Paths::remove_path()'],['../classvg_1_1VG.html#a30c369b4c1b0dfa4e9fbc0d3bce82648',1,'vg::VG::remove_path()']]],
- ['remove_5fpaths_10680',['remove_paths',['../classvg_1_1Paths.html#a975ff2ed8ee5718aae414cb0cb2fb39b',1,'vg::Paths::remove_paths()'],['../namespacevg.html#ad5e16e94675197650b9d6edb9e7a9081',1,'vg::remove_paths()']]],
- ['remove_5fredundant_5ftranscript_5fpaths_10681',['remove_redundant_transcript_paths',['../classvg_1_1Transcriptome.html#aa7bf08bef8301bcff774dff1bc92d484',1,'vg::Transcriptome']]],
- ['remove_5fsamples_10682',['remove_samples',['../gbwt__main_8cpp.html#a9750054dfc43368b363ed04acd832b15',1,'gbwt_main.cpp']]],
- ['remove_5ftransitive_5fedges_10683',['remove_transitive_edges',['../classvg_1_1MultipathAlignmentGraph.html#aeb9c58b7f20245a4c400dd14e8488069',1,'vg::MultipathAlignmentGraph']]],
- ['rename_5fpath_10684',['rename_path',['../classhandlegraph_1_1MutablePathHandleGraph.html#a95370bd388b2c113cf0556f266993418',1,'handlegraph::MutablePathHandleGraph']]],
- ['rend_10685',['rend',['../classvg_1_1ZipCodeTree.html#acb87f941c2eb8bcef3f6008c248f07c4',1,'vg::ZipCodeTree']]],
- ['reorder_5fadjacency_5flists_10686',['reorder_adjacency_lists',['../classvg_1_1MultipathAlignmentGraph.html#adba05a33bf075eb3eb7260e229245f06',1,'vg::MultipathAlignmentGraph']]],
- ['reorder_5fexons_10687',['reorder_exons',['../classvg_1_1Transcriptome.html#ae6f600db9b276fe332d4f14919bba983',1,'vg::Transcriptome']]],
- ['repetitiveness_10688',['repetitiveness',['../structvg_1_1SeqComplexity.html#a192996fb41444e1ccddd6b6e334cf2d3',1,'vg::SeqComplexity']]],
- ['replace_5fin_5fstring_10689',['replace_in_string',['../namespacevg.html#ab169ac1e2fc6ba662eebc1ede1ffe157',1,'vg']]],
- ['replace_5flocal_5fhaplotype_10690',['replace_local_haplotype',['../classvg_1_1GenomeState.html#a8048b04c0d1d0b438ec76bdc1c0b5779',1,'vg::GenomeState']]],
- ['replace_5fmapping_10691',['replace_mapping',['../classvg_1_1Paths.html#a906246385a06c6825aaf9b3c58cbdeac',1,'vg::Paths']]],
- ['replace_5foccurrence_10692',['replace_occurrence',['../structvg_1_1PathIndex.html#ae8806eb31bcd8b8f9305180fea7b746f',1,'vg::PathIndex']]],
- ['replace_5fsnarl_5fhaplotype_10693',['replace_snarl_haplotype',['../classvg_1_1GenomeState.html#a83cd070b1d65189fbba77a5bda91d405',1,'vg::GenomeState']]],
- ['report_5faffinities_10694',['report_affinities',['../classvg_1_1Genotyper.html#abe8c49eaf4799ae7202e19b6e09288a7',1,'vg::Genotyper']]],
- ['report_5fexception_10695',['report_exception',['../namespacevg.html#a638a54aabac7956dae6fd882468a86fe',1,'vg']]],
- ['report_5flibrary_10696',['report_library',['../namespacevg.html#a040485dc93c5bf925dc58fe4eaa0bd02',1,'vg']]],
- ['report_5fsnarl_10697',['report_snarl',['../classvg_1_1Genotyper.html#a6c9c525615b0c453f0685ea2ed987cde',1,'vg::Genotyper']]],
- ['report_5fsnarl_5ftraversal_10698',['report_snarl_traversal',['../classvg_1_1Genotyper.html#a1a141641a0939e35dc6ee19281001628',1,'vg::Genotyper']]],
- ['report_5ftime_5fmemory_10699',['report_time_memory',['../gbwt__main_8cpp.html#aa6ba12498251a288731312b850bba212',1,'gbwt_main.cpp']]],
- ['representativetraversalfinder_10700',['RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html#a5dd3d9602c8056d016d42ba5cb760f11',1,'vg::RepresentativeTraversalFinder']]],
- ['require_10701',['require',['../classvg_1_1IndexRegistry.html#ac52737ce471d6fb1ea968a2e57dc4b7f',1,'vg::IndexRegistry']]],
- ['rescue_5fhigh_5fcount_5forder_5flength_5fmems_10702',['rescue_high_count_order_length_mems',['../classvg_1_1BaseMapper.html#aa7a71951ec7acdbf2c31ae9318ceb035',1,'vg::BaseMapper']]],
- ['resect_5fsnarls_5ffrom_5fpaths_10703',['resect_snarls_from_paths',['../classvg_1_1MultipathAlignmentGraph.html#a9c49582fe16bcb4c87b95e8e3ee93319',1,'vg::MultipathAlignmentGraph']]],
- ['reset_10704',['reset',['../classvg_1_1IndexRegistry.html#abcba0a09cee5a43096a09d05556353c1',1,'vg::IndexRegistry::reset()'],['../classvg_1_1IndexFile.html#aa16d18589ef1a9944b8e2af8c8ea1232',1,'vg::IndexFile::reset()'],['../structvg_1_1Counts.html#a90e02c9fc99656e6325f5c8fbfccda86',1,'vg::Counts::reset()'],['../classvg_1_1uniform__real__distribution.html#ad9ba8ac53f8a0af213db9d4f8da12617',1,'vg::uniform_real_distribution::reset()'],['../classvg_1_1normal__distribution.html#a7bae578d38533043f42f09413c7c1e32',1,'vg::normal_distribution::reset()'],['../classvg_1_1truncated__normal__distribution.html#ae1ebb560eee14b873305a4b5bf97616e',1,'vg::truncated_normal_distribution::reset()'],['../classvg_1_1uniform__int__distribution.html#a38594c45008dfc36cfbb4f9b9e4193dd',1,'vg::uniform_int_distribution::reset()'],['../classvg_1_1discrete__distribution.html#a5a3ca0751a139bef583b819118188780',1,'vg::discrete_distribution::reset()'],['../structvg_1_1Range.html#a3bf0b390a74ca7ea5f806f6cd98aac2c',1,'vg::Range::reset()']]],
- ['reset_5falong_5fchain_10705',['reset_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#ade116b41b24892b20ac4fa95a9b5539e',1,'vg::subcommand::TickChainLink::reset_along_chain()'],['../structvg_1_1Range.html#a475da5fc747b64bfa869524e932077df',1,'vg::Range::reset_along_chain()']]],
- ['reset_5fchain_10706',['reset_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a5a3dd8ac3d8a86fec1d2062e6d864c73',1,'vg::subcommand::TickChainLink::reset_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a05855ac56b836299fc0fc12292555b37',1,'vg::subcommand::OptionGroup::reset_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a73c92bfa80186ac2d64f9b24233aacb8',1,'vg::subcommand::GroupedOptionGroup::reset_chain()']]],
- ['resize_5findexes_10707',['resize_indexes',['../classvg_1_1VG.html#af8879b1e6aab38b9a246deba0f05ccfe',1,'vg::VG']]],
- ['restore_5fpaths_10708',['restore_paths',['../classvg_1_1PhaseUnfolder.html#a3cdfb31928c3a4127d9888d543872e1c',1,'vg::PhaseUnfolder']]],
- ['retry_5fpairing_5fspliced_5falignments_10709',['retry_pairing_spliced_alignments',['../classvg_1_1MultipathMapper.html#ae388023023d7b1a862a77416d9ed1ede',1,'vg::MultipathMapper']]],
- ['rev_5fcomp_5fmultipath_5falignment_10710',['rev_comp_multipath_alignment',['../namespacevg.html#a785f128b2eeb9aa2a4ee5477e5b9942b',1,'vg']]],
- ['rev_5fcomp_5fmultipath_5falignment_5fin_5fplace_10711',['rev_comp_multipath_alignment_in_place',['../namespacevg.html#ab9aa92b68bb45684a3b751060508c709',1,'vg']]],
- ['rev_5fcomp_5fsubpath_10712',['rev_comp_subpath',['../namespacevg.html#a4d802144c81c58c86f814507e1f99e22',1,'vg']]],
- ['revdna3bit_10713',['revdna3bit',['../namespacexg.html#a09a061b73b78b2ba029940f09ccb6f5b',1,'xg']]],
- ['reverse_10714',['reverse',['../classvg_1_1NodeTraversal.html#a748acf3ae485ab57fe649e70cad17c5d',1,'vg::NodeTraversal::reverse()'],['../namespacevg.html#a91adfc6327b5709dc73fcc7edbe5da57',1,'vg::reverse(const Position &pos, size_t node_length)'],['../namespacevg.html#a2e300d25fd8281f9453366f68b484196',1,'vg::reverse(const Visit &visit)'],['../namespacevg.html#ac52fd5878b0be1d53de644eea3458663',1,'vg::reverse(const pos_t &pos, size_t node_length)'],['../namespacexg.html#ad11c9145dd19a26ea95db548d7aaac79',1,'xg::reverse()']]],
- ['reverse_5fadjacencies_10715',['reverse_adjacencies',['../classvg_1_1Surjector.html#a98ca84936638bdcb054e3304b6f959f1',1,'vg::Surjector']]],
- ['reverse_5falignment_10716',['reverse_alignment',['../classvg_1_1MultipathAlignmentGraph.html#a91aa5268618d2f4c1d7b8665108d455c',1,'vg::MultipathAlignmentGraph']]],
- ['reverse_5fbase_5fpos_10717',['reverse_base_pos',['../namespacevg.html#ae2f3762e2a8a852c7608d71f030e0345',1,'vg::reverse_base_pos()'],['../namespacexg.html#af6d74fb0781bfeb012e78af79758ab9c',1,'xg::reverse_base_pos()']]],
- ['reverse_5fcomplement_10718',['reverse_complement',['../namespacevg.html#aa65de7dea52585f07bee6ae7f762eb95',1,'vg::reverse_complement(const char &c)'],['../namespacevg.html#a30732a1a1e8d20d6eaaaeafecc8a50a7',1,'vg::reverse_complement(const string &seq)'],['../namespacexg.html#ac667d522781e3c31d191e4c6db520eaa',1,'xg::reverse_complement(const char &c)'],['../namespacexg.html#ab4f0205fd0abe6aaa4077cd20abcd36f',1,'xg::reverse_complement(const std::string &seq)']]],
- ['reverse_5fcomplement_5falignment_10719',['reverse_complement_alignment',['../namespacevg.html#a98e512ed0fca2503ccc370435591a6c1',1,'vg']]],
- ['reverse_5fcomplement_5falignment_5fin_5fplace_10720',['reverse_complement_alignment_in_place',['../namespacevg.html#ab96610ffc81d6207e0b13f675296c234',1,'vg']]],
- ['reverse_5fcomplement_5falignments_10721',['reverse_complement_alignments',['../namespacevg.html#aed045b02277d7704e997cbede67c2662',1,'vg']]],
- ['reverse_5fcomplement_5fedit_10722',['reverse_complement_edit',['../namespacevg_1_1io.html#a52a77b52c33c165637fb00be3e9f54e0',1,'vg::io']]],
- ['reverse_5fcomplement_5fgraph_10723',['reverse_complement_graph',['../classvg_1_1VG.html#a82185028afbc17aaf60b294297507fd2',1,'vg::VG::reverse_complement_graph()'],['../namespacehandlegraph_1_1algorithms.html#a3cb6868def99085050dca0efdd3eb0c9',1,'handlegraph::algorithms::reverse_complement_graph()']]],
- ['reverse_5fcomplement_5fin_5fplace_10724',['reverse_complement_in_place',['../namespacevg.html#ae6353d47c867f1b4cc7053d82aef42f4',1,'vg::reverse_complement_in_place()'],['../namespacexg.html#a18e172174952ffa498b10715acdc031c',1,'xg::reverse_complement_in_place()']]],
- ['reverse_5fcomplement_5fmapping_10725',['reverse_complement_mapping',['../namespacevg.html#a3ce6fa1d8f3ba4f8f361fa77a6fd5261',1,'vg::reverse_complement_mapping(const Mapping &m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a798565f048dc7844739ea4913d950d31',1,'vg::reverse_complement_mapping(const path_mapping_t &m, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fcomplement_5fmapping_5fin_5fplace_10726',['reverse_complement_mapping_in_place',['../namespacevg.html#af2dc9d6ee4403027eb5965aa6a71eb4e',1,'vg::reverse_complement_mapping_in_place(Mapping *m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#abc9bd04ab1099c6d9bd655a2accbe52e',1,'vg::reverse_complement_mapping_in_place(path_mapping_t *m, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fcomplement_5fpath_10727',['reverse_complement_path',['../namespacevg.html#a463d9eaed29cd6d46a8e2afb645c8fda',1,'vg::reverse_complement_path(const Path &path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a3df9f25ec47163ccbfa328673bd28ab5',1,'vg::reverse_complement_path(const path_t &path, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fcomplement_5fpath_5fin_5fplace_10728',['reverse_complement_path_in_place',['../namespacevg.html#af2941a3c80481d02c65d9d72bd835807',1,'vg::reverse_complement_path_in_place(Path *path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a0df8f9c5838119e79ee1f671cd823740',1,'vg::reverse_complement_path_in_place(path_t *path, const function< int64_t(id_t)> &node_length)']]],
- ['reverse_5fedge_10729',['reverse_edge',['../classvg_1_1FlowSort.html#a237e09746b80c67a96290eac62fbd2c8',1,'vg::FlowSort']]],
- ['reverse_5ffrom_5fstart_5fto_5fend_5fedge_10730',['reverse_from_start_to_end_edge',['../classvg_1_1FlowSort.html#a095e96bd8ef6f016a600bdbc6af730ee',1,'vg::FlowSort']]],
- ['reverse_5fiterator_10731',['reverse_iterator',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a58d6dc8114a797ef5fa8b3ef95d3e282',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(vector< tree_item_t >::const_reverse_iterator rbegin, vector< tree_item_t >::const_reverse_iterator rend, size_t distance_limit=std::numeric_limits< size_t >::max())'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa454b7553be8ff9226e7622476de7515',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ac2889d055d75873e7d1d834c758c17ea',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(reverse_iterator &&other)']]],
- ['reversegraph_10732',['ReverseGraph',['../classvg_1_1ReverseGraph.html#a9122b516caa1f30b202ef7ef4cd83d60',1,'vg::ReverseGraph::ReverseGraph(const HandleGraph *forward_graph, bool complement)'],['../classvg_1_1ReverseGraph.html#a4715727accf496a2b7f908688638d873',1,'vg::ReverseGraph::ReverseGraph()=default']]],
- ['reversing_5ffilter_10733',['reversing_filter',['../classvg_1_1Filter.html#a5ac9ddf9392d973aa726ad6ee4d53b9f',1,'vg::Filter']]],
- ['rewindplanexception_10734',['RewindPlanException',['../classvg_1_1RewindPlanException.html#ad1b916e8d35f9825b9352045b7e77146',1,'vg::RewindPlanException::RewindPlanException()=delete'],['../classvg_1_1RewindPlanException.html#a28ad0274056215792783b0b3bc8fd258',1,'vg::RewindPlanException::RewindPlanException(const string &msg, const IndexGroup &rewind_to) noexcept']]],
- ['rewrite_5fsegment_10735',['rewrite_segment',['../classvg_1_1VG.html#abb2dc75f200cfb7480e671fd55207410',1,'vg::VG::rewrite_segment()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#af28f1372aa6dad2654a22eb8463e2a07',1,'handlegraph::MutablePathHandleGraph::rewrite_segment()']]],
- ['right_5fdegree_10736',['right_degree',['../classvg_1_1VG.html#a23622195177dff4c7c8416edffb7fc93',1,'vg::VG']]],
- ['right_5fseed_5fnode_10737',['right_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a83d9a8edb6fb9fd1ac20ffa976355155',1,'vg::JoinedSpliceGraph']]],
- ['right_5fsplice_5fnode_10738',['right_splice_node',['../classvg_1_1JoinedSpliceGraph.html#adf8ca2fd45b0d024bf4b12ea04fbfc79',1,'vg::JoinedSpliceGraph']]],
- ['ring_5fbuffer_5fempty_10739',['ring_buffer_empty',['../classvg_1_1io_1_1StreamMultiplexer.html#a92c3f4f2de80a840aef85574935758ac',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5ffull_10740',['ring_buffer_full',['../classvg_1_1io_1_1StreamMultiplexer.html#a0d671fb79357a83af6c5becfa890a6f2',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5fpeek_10741',['ring_buffer_peek',['../classvg_1_1io_1_1StreamMultiplexer.html#aa03a8b8e99c728355ade20923bcb4c2f',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5fpop_10742',['ring_buffer_pop',['../classvg_1_1io_1_1StreamMultiplexer.html#ac4f6095e2eb79970075f9b2279e990ce',1,'vg::io::StreamMultiplexer']]],
- ['ring_5fbuffer_5fpush_10743',['ring_buffer_push',['../classvg_1_1io_1_1StreamMultiplexer.html#a925607e24a8c6e905fc45c4b77bbe62c',1,'vg::io::StreamMultiplexer']]],
- ['round_5foutward_10744',['round_outward',['../structvg_1_1PathIndex.html#ac02dd3e22c5b29670ef48b6f725a9797',1,'vg::PathIndex']]],
- ['rrmemo_10745',['RRMemo',['../structhaplo_1_1haploMath_1_1RRMemo.html#a3958ec23ff1fbaac901d909c5f134f27',1,'haplo::haploMath::RRMemo']]],
- ['run_10746',['run',['../classvg_1_1Genotyper.html#af760be5c99e086b2c41510b3d3a47e5a',1,'vg::Genotyper']]],
- ['run_5fbenchmark_10747',['run_benchmark',['../namespacevg.html#ac101c453ab2076d74f0324f73d174695',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &under_test)'],['../namespacevg.html#added44ff3bb1c0ce606563a40923c513',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &setup, const function< void(void)> &under_test)']]],
- ['run_5fdp_10748',['run_dp',['../classvg_1_1DeletionAligner.html#a0eb6b38dc11173f5da75c5cafd3053fe',1,'vg::DeletionAligner']]],
- ['run_5fgenotype_10749',['run_genotype',['../classvg_1_1MCMCGenotyper.html#a3bae6f8b2947e030935d5e9cf46fb324',1,'vg::MCMCGenotyper']]],
- ['run_5fmultipath_5fdp_10750',['run_multipath_dp',['../namespacevg.html#ae57a78071537c87e2f0f57bfea18ba71',1,'vg']]]
+ ['radix_5fsort_5fzipcodes_10561',['radix_sort_zipcodes',['../classvg_1_1ZipCodeForest.html#aade4c028524fd9e0c4a6267335584171',1,'vg::ZipCodeForest']]],
+ ['random_10562',['random',['../classvg_1_1Colors.html#aa655272ae2bc4944fe7096d3e9e072b8',1,'vg::Colors::random()'],['../classvg_1_1Pictographs.html#ac61d6a97566ac6cc8c21158688fcfdf3',1,'vg::Pictographs::random()']]],
+ ['random_5fmatch_5flength_10563',['random_match_length',['../classvg_1_1BaseMapper.html#a2884c6722e6bd9c9aab6671a85a6c3c0',1,'vg::BaseMapper']]],
+ ['random_5fmatch_5fp_5fvalue_10564',['random_match_p_value',['../classvg_1_1MultipathMapper.html#afbf8bce27b441ba87f83c72d5c65c592',1,'vg::MultipathMapper']]],
+ ['random_5fread_10565',['random_read',['../classvg_1_1VG.html#a8452af466a3e1ad4b0b463ea0d5da933',1,'vg::VG']]],
+ ['random_5fsequence_10566',['random_sequence',['../namespacevg.html#ab80fc8c8920c7ec53cfee81dc2fce852',1,'vg']]],
+ ['random_5fsequence_5fgen_10567',['random_sequence_gen',['../namespacevg.html#a4012afd56ccb35387121c71c2119e244',1,'vg']]],
+ ['range_10568',['Range',['../structvg_1_1Range.html#a08e1ef06cddbc0efcb0660d34cf3bc5d',1,'vg::Range::Range()'],['../structvg_1_1Range.html#a4becc4a909e9ff23a62318da327af7ff',1,'vg::Range::Range(const Number &val)'],['../structvg_1_1Range.html#a10c624eaeb6a83b450c9d24fdbaa8555',1,'vg::Range::Range(const Range &other)'],['../structvg_1_1Range.html#a7bf784228c365aa72150fec926de77ae',1,'vg::Range::Range(Range &&other)'],['../classvg_1_1io_1_1MessageIterator.html#af88ac04ab7cbb8245a86d21a71a5dd76',1,'vg::io::MessageIterator::range()'],['../classvg_1_1io_1_1ProtobufIterator.html#acf75c4c7a16e406f9bb860e3f0c7dae9',1,'vg::io::ProtobufIterator::range()']]],
+ ['range_5fvector_10569',['range_vector',['../namespacevg.html#a931d9271de88fc786030fdd0ab4bf534',1,'vg::range_vector(size_t begin, size_t end)'],['../namespacevg.html#a39adca1737de5d28d007d95b809deb7f',1,'vg::range_vector(size_t end)']]],
+ ['rank_5fby_5fsupport_10570',['rank_by_support',['../classvg_1_1PoissonSupportSnarlCaller.html#a300ca3bbff527fb43fbc12e65177d053',1,'vg::PoissonSupportSnarlCaller']]],
+ ['rank_5fto_5fhandle_10571',['rank_to_handle',['../classhandlegraph_1_1RankedHandleGraph.html#aacf6651545adbd407082a539222f8a69',1,'handlegraph::RankedHandleGraph']]],
+ ['rank_5fto_5fid_10572',['rank_to_id',['../classxg_1_1XG.html#aee052f301d8cae7b30c50c115c6b950b',1,'xg::XG::rank_to_id()'],['../classhandlegraph_1_1RankedHandleGraph.html#a5bf563241454b21539effcad11406ec9',1,'handlegraph::RankedHandleGraph::rank_to_id()']]],
+ ['rarevariantsimplifier_10573',['RareVariantSimplifier',['../classvg_1_1RareVariantSimplifier.html#a08cf82d7c40db195176b9bf177a50e32',1,'vg::RareVariantSimplifier']]],
+ ['ratiosupportsnarlcaller_10574',['RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html#ad6905b3e30632f2a0a3e304cdfd15faa',1,'vg::RatioSupportSnarlCaller']]],
+ ['re_5fgenotype_10575',['re_genotype',['../classvg_1_1LegacyCaller.html#a6c23ee5b732d26d4f55bd3b5b4830fca',1,'vg::LegacyCaller']]],
+ ['read_10576',['read',['../classvg_1_1ParallelKFFReader.html#ae34ae06b01651343a3e07b87ce019aa7',1,'vg::ParallelKFFReader']]],
+ ['read_5fend_10577',['read_end',['../classvg_1_1algorithms_1_1Anchor.html#a335ebe332424cb49cae4da84c91a5367',1,'vg::algorithms::Anchor']]],
+ ['read_5fexclusion_5fend_10578',['read_exclusion_end',['../classvg_1_1algorithms_1_1Anchor.html#a12554fafcdf8309d3119b349e3bf6e59',1,'vg::algorithms::Anchor']]],
+ ['read_5fexclusion_5fstart_10579',['read_exclusion_start',['../classvg_1_1algorithms_1_1Anchor.html#a1de27e657461d6de450a84aab34becb4',1,'vg::algorithms::Anchor']]],
+ ['read_5flog_5flikelihood_10580',['read_log_likelihood',['../classvg_1_1PhasedGenome.html#af754f8a4e9793ebd5f4aa3b673b7e442',1,'vg::PhasedGenome']]],
+ ['read_5fmapping_10581',['read_mapping',['../classvg_1_1PhaseUnfolder.html#adbf93e421183b64f73276639c3c23dfb',1,'vg::PhaseUnfolder']]],
+ ['read_5fstart_10582',['read_start',['../classvg_1_1algorithms_1_1Anchor.html#a21c07ed7e05dfd2194d580022f2005c4',1,'vg::algorithms::Anchor']]],
+ ['readmasker_10583',['ReadMasker',['../classvg_1_1ReadMasker.html#a99656ed3430d86e7a34b908914991945',1,'vg::ReadMasker']]],
+ ['readrestrictedtraversalfinder_10584',['ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html#a8cf6a940b0fce108e8af39d8a50a380f',1,'vg::ReadRestrictedTraversalFinder']]],
+ ['realigning_5fsurject_10585',['realigning_surject',['../classvg_1_1Surjector.html#a2629f80135104fb8486ef823f525b843',1,'vg::Surjector']]],
+ ['reallocate_5fatomic_5fint_5fvector_10586',['reallocate_atomic_int_vector',['../namespacevg_1_1algorithms.html#acd891e00c4846e53f760d504434ead12',1,'vg::algorithms']]],
+ ['reassign_5fnode_10587',['reassign_node',['../classvg_1_1Paths.html#aed5ea00a6a8dab5b54eeedd9e8f91a7b',1,'vg::Paths']]],
+ ['reassign_5fnode_5fids_10588',['reassign_node_ids',['../classvg_1_1VG.html#aca4a358ff4c7f387c1c6d5d239499a07',1,'vg::VG::reassign_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a4805d276a83a1dad2462e6b8dd2443dc',1,'handlegraph::MutableHandleGraph::reassign_node_ids()']]],
+ ['reassign_5fsplit_5fclusters_10589',['reassign_split_clusters',['../classvg_1_1MultipathMapper.html#a5d8b62d4d55e83f80da09173e8520874',1,'vg::MultipathMapper']]],
+ ['rebuild_5fedge_5findexes_10590',['rebuild_edge_indexes',['../classvg_1_1VG.html#a6541146b6410cec4be3e2a7379ea3bcf',1,'vg::VG']]],
+ ['rebuild_5fgbwt_10591',['rebuild_gbwt',['../namespacevg.html#a95d54bf0a30125f9ded043bb099cb25f',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob > &jobs, const std::unordered_map< nid_t, size_t > &node_to_job, const RebuildParameters ¶meters)'],['../namespacevg.html#ade5b1e6daa5da7101533d444d3d8ff41',1,'vg::rebuild_gbwt(const gbwt::GBWT &gbwt_index, const std::vector< RebuildJob::mapping_type > &mappings)']]],
+ ['rebuild_5fgbwt_5fjob_10592',['rebuild_gbwt_job',['../namespacevg.html#a16b175479dee254341d60fc037dae233',1,'vg']]],
+ ['rebuild_5findexes_10593',['rebuild_indexes',['../classvg_1_1VG.html#a63d4e45a9a410c451b1cad44ef7068ad',1,'vg::VG']]],
+ ['rebuild_5fmapping_5faux_10594',['rebuild_mapping_aux',['../classvg_1_1Paths.html#a5f80df5846bdac0b502a70af97dc65de',1,'vg::Paths']]],
+ ['rebuild_5fnode_5fmapping_10595',['rebuild_node_mapping',['../classvg_1_1Paths.html#a7e9d9388475dcd8f23af072430e7383c',1,'vg::Paths']]],
+ ['recombinator_10596',['Recombinator',['../classvg_1_1Recombinator.html#a9248c550bcc5aa267abde6eefec69e88',1,'vg::Recombinator']]],
+ ['recombinator_5fsanity_5fchecks_10597',['recombinator_sanity_checks',['../namespacevg.html#aa81f31f29a47e669812c3ef57bd1aab6',1,'vg']]],
+ ['recombinatorfragment_10598',['RecombinatorFragment',['../structvg_1_1RecombinatorFragment.html#aab79ba107e9e086b432dfa9fcf4a2807',1,'vg::RecombinatorFragment']]],
+ ['record_10599',['record',['../classvg_1_1SnarlManager.html#a45e3765bfd07b196b6e30b7a9b62aefd',1,'vg::SnarlManager::record(const Snarl *snarl) const'],['../classvg_1_1SnarlManager.html#a3ce002195299049e9925e94546d989b9',1,'vg::SnarlManager::record(Snarl *snarl)']]],
+ ['record_5ffanouts_10600',['record_fanouts',['../classvg_1_1MultipathMapper.html#a0b4e3381a53cf532acdf7cbadc6d9985',1,'vg::MultipathMapper']]],
+ ['record_5ffragment_5fconfiguration_10601',['record_fragment_configuration',['../classvg_1_1FragmentLengthStatistics.html#ae63195a980c56907de548ba00098c794',1,'vg::FragmentLengthStatistics']]],
+ ['record_5fread_5fpair_5fquality_10602',['record_read_pair_quality',['../classvg_1_1NGSSimulator.html#aec434f0c212aec15e1760f4c4b1185e2',1,'vg::NGSSimulator']]],
+ ['record_5fread_5fquality_10603',['record_read_quality',['../classvg_1_1NGSSimulator.html#a8f34614e3dc660e31d26d9c18970e736',1,'vg::NGSSimulator']]],
+ ['record_5ftransition_10604',['record_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ab3609f759c7b20d77c1bc0ca7160c26a',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['recover_5flog_5fbase_10605',['recover_log_base',['../classvg_1_1GSSWAligner.html#ab5102e690e6e2e0e72aa35ea769179a2',1,'vg::GSSWAligner']]],
+ ['recursively_5femit_5fsnarls_10606',['recursively_emit_snarls',['../classvg_1_1CactusSnarlFinder.html#aad8a90f6cd0fddf6ab908f6287e3ddf3',1,'vg::CactusSnarlFinder']]],
+ ['reduce_5fto_5fsingle_5fpath_10607',['reduce_to_single_path',['../classvg_1_1MultipathMapper.html#a0a3360fde5883dc2c0927b63be0a3bd5',1,'vg::MultipathMapper']]],
+ ['reencode_5fold_5fg_5fvector_10608',['reencode_old_g_vector',['../classxg_1_1XG.html#a8a5068e08156a861e35e62cc3fa94204',1,'xg::XG']]],
+ ['ref_5fpath_5fdistance_10609',['ref_path_distance',['../namespacevg_1_1algorithms.html#aa5e4dc632e98b58b67a99af6749d9e05',1,'vg::algorithms']]],
+ ['ref_5fposition_10610',['ref_position',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a442f4e740bc94b1671c9590f65bb65a4',1,'haplo::linear_haplo_structure::SNVvector']]],
+ ['refactor_5fsplit_5falignment_10611',['refactor_split_alignment',['../classvg_1_1Filter.html#af5c53d7fa62dff67d24ff0daa4d5f925',1,'vg::Filter']]],
+ ['reference_5ftranscript_5fpaths_10612',['reference_transcript_paths',['../classvg_1_1Transcriptome.html#aacf1ad40a7a5d42985c4149b03fe936e',1,'vg::Transcriptome']]],
+ ['regionexpander_10613',['RegionExpander',['../classvg_1_1RegionExpander.html#a42c0f501da7fabf0045f5c434b55f705',1,'vg::RegionExpander']]],
+ ['register_5falias_10614',['register_alias',['../classvg_1_1AliasGraph.html#a4f21c7d2e0aa761fd5ff4ccd43bd72af',1,'vg::AliasGraph']]],
+ ['register_5fbare_5floader_10615',['register_bare_loader',['../classvg_1_1io_1_1Registry.html#a025929701767e23673356cae9e7024a5',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_10616',['register_bare_loader_saver',['../classvg_1_1io_1_1Registry.html#aab501bb8db46d45e8b1946da37f0b382',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fheader_5fcheck_10617',['register_bare_loader_saver_with_header_check',['../classvg_1_1io_1_1Registry.html#a873d317a5ec04d5af5223008310043df',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_10618',['register_bare_loader_saver_with_magic',['../classvg_1_1io_1_1Registry.html#ad3f16de5d24cb503429d358e2af8c831',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fmagic_5fand_5ffilename_10619',['register_bare_loader_saver_with_magic_and_filename',['../classvg_1_1io_1_1Registry.html#acfda4299247a88075080004beba4a136',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fsaver_5fwith_5fmagics_10620',['register_bare_loader_saver_with_magics',['../classvg_1_1io_1_1Registry.html#af4180fbb60edaa1cd1aec325945d2af5',1,'vg::io::Registry']]],
+ ['register_5fbare_5floader_5fwith_5ffilename_10621',['register_bare_loader_with_filename',['../classvg_1_1io_1_1Registry.html#abb7a1aefe860153a36614efa54bcde29',1,'vg::io::Registry']]],
+ ['register_5fbarrier_10622',['register_barrier',['../classvg_1_1io_1_1StreamMultiplexer.html#acb05844bf345313fc1710db7f3610ac5',1,'vg::io::StreamMultiplexer']]],
+ ['register_5fbreakpoint_10623',['register_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#a562910d0ca3b3fac6b95b0c3ee3c81dd',1,'vg::io::StreamMultiplexer']]],
+ ['register_5fconfigurable_10624',['register_configurable',['../classvg_1_1ConfigurableParser.html#a3c42646beeac7fb48f57c44f1420ec7b',1,'vg::ConfigurableParser']]],
+ ['register_5feverything_10625',['register_everything',['../classvg_1_1io_1_1Registry.html#ad1b4d2c277bdb07c2bf4cc4b60e35745',1,'vg::io::Registry']]],
+ ['register_5ffragment_5flength_10626',['register_fragment_length',['../classvg_1_1FragmentLengthDistribution.html#a888c21e626cb2fd984f9e0ffd39adefc',1,'vg::FragmentLengthDistribution']]],
+ ['register_5fgeneralization_10627',['register_generalization',['../classvg_1_1IndexRegistry.html#a2e1c0e83f49e8719459e644ce143302b',1,'vg::IndexRegistry']]],
+ ['register_5findex_10628',['register_index',['../classvg_1_1IndexRegistry.html#ad8f48075fe06df92c65bc5fd0207f9bc',1,'vg::IndexRegistry']]],
+ ['register_5flibvg_5fio_10629',['register_libvg_io',['../namespacevg_1_1io.html#ad93f27be4f07ab9c6a91a1501b992f70',1,'vg::io']]],
+ ['register_5floader_10630',['register_loader',['../classvg_1_1io_1_1Registry.html#a82c329d405f2dc83880623561a10962f',1,'vg::io::Registry::register_loader(const string &tag, load_function_t loader)'],['../classvg_1_1io_1_1Registry.html#abdbc23294daf5a1f44b34da481929891',1,'vg::io::Registry::register_loader(const std::vector< std::string > &tags, load_function_t loader)']]],
+ ['register_5floader_5fparams_5fjson_10631',['register_loader_params_json',['../namespacevg_1_1io.html#a113c8011c25b00d36f77f49062726bbb',1,'vg::io']]],
+ ['register_5floader_5fsaver_10632',['register_loader_saver',['../classvg_1_1io_1_1Registry.html#a3dfd842b470ff701fb805838e2d7fe61',1,'vg::io::Registry::register_loader_saver(const string &tag, load_function_t loader, save_function_t saver)'],['../classvg_1_1io_1_1Registry.html#a56e76bb9dcab4c47f400d844430536b6',1,'vg::io::Registry::register_loader_saver(const std::vector< std::string > &tags, load_function_t loader, save_function_t saver)']]],
+ ['register_5floader_5fsaver_5fdistance_5findex_10633',['register_loader_saver_distance_index',['../namespacevg_1_1io.html#a45372f8f761a3bce9e7ef6e1422db47b',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbwt_10634',['register_loader_saver_gbwt',['../namespacevg_1_1io.html#a47fc4c5122bf0f0810993822d194eb20',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbwtgraph_10635',['register_loader_saver_gbwtgraph',['../namespacevg_1_1io.html#a6143362abf3060042589f1ffb22ff498',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbz_10636',['register_loader_saver_gbz',['../namespacevg_1_1io.html#adb36b3bf6da822750c5c6c9cd2d987e0',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgbzgraph_10637',['register_loader_saver_gbzgraph',['../namespacevg_1_1io.html#a81649e999e30d305e02187c16b257d07',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgcsa_10638',['register_loader_saver_gcsa',['../namespacevg_1_1io.html#affca170910f12393eb1381c4d72e4e73',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fgfa_10639',['register_loader_saver_gfa',['../namespacevg_1_1io.html#a1fadf5a0f7d91d61c9d2c27d35987c6a',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fhash_5fgraph_10640',['register_loader_saver_hash_graph',['../namespacevg_1_1io.html#a49d41e6f52ad981f96d772396fd4eee5',1,'vg::io']]],
+ ['register_5floader_5fsaver_5flcp_10641',['register_loader_saver_lcp',['../namespacevg_1_1io.html#af7df97a78891ada683647c88c6393eb9',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fminimizer_10642',['register_loader_saver_minimizer',['../namespacevg_1_1io.html#aa69bc026abe7a1db4530704dfc7e7b3f',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fpacked_5fgraph_10643',['register_loader_saver_packed_graph',['../namespacevg_1_1io.html#a776b6490958856d44dc2d962d629440d',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fr_5findex_10644',['register_loader_saver_r_index',['../namespacevg_1_1io.html#a6ce32e4ae1d4f5d244c0d80d3ac09beb',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fsnarl_5fmanager_10645',['register_loader_saver_snarl_manager',['../namespacevg_1_1io.html#a8072168ee8165f81afb2688ef0825ea8',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fvg_10646',['register_loader_saver_vg',['../namespacevg_1_1io.html#ac3485846033fd4accb221b0a866dfeb7',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fxg_10647',['register_loader_saver_xg',['../namespacevg_1_1io.html#a7a23bf45ec66db4b724b7f8a9f223c33',1,'vg::io']]],
+ ['register_5floader_5fsaver_5fzip_5fcodes_10648',['register_loader_saver_zip_codes',['../namespacevg_1_1io.html#ac0521f6b9e5e9e78ab0837548bef8f0e',1,'vg::io']]],
+ ['register_5foption_10649',['register_option',['../classvg_1_1Configurable.html#afa7bba48c6289ea9b9095acd79a5658e',1,'vg::Configurable']]],
+ ['register_5fprotobuf_10650',['register_protobuf',['../classvg_1_1io_1_1Registry.html#ae4880fe254039bfe44b73b9050ce0abc',1,'vg::io::Registry']]],
+ ['register_5frecipe_10651',['register_recipe',['../classvg_1_1IndexRegistry.html#afdda05f4e7f1dfd93ecb33ad3b582aad',1,'vg::IndexRegistry']]],
+ ['register_5fsampled_5fposition_10652',['register_sampled_position',['../classvg_1_1NGSSimulator.html#ab9adc2b15f1d2c31301e5801e773dcbd',1,'vg::NGSSimulator']]],
+ ['register_5fsaver_10653',['register_saver',['../classvg_1_1io_1_1Registry.html#a1bba520da840207b627aface669b80c6',1,'vg::io::Registry']]],
+ ['regress_10654',['regress',['../namespacevg.html#aab16fbb8659a66f16f2004fcc3e8f9db',1,'vg']]],
+ ['regularize_10655',['regularize',['../classvg_1_1SnarlManager.html#ae5015eacc04d12d02ef5196fb23f3075',1,'vg::SnarlManager']]],
+ ['release_10656',['release',['../structjson__autoptr.html#ad3ee76d343667fd42bdbe504f32e7042',1,'json_autoptr']]],
+ ['remaining_5ftree_10657',['remaining_tree',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1f7d072e5054742f4c391b294fe5d839',1,'vg::ZipCodeTree::iterator']]],
+ ['remap_10658',['remap',['../classvg_1_1Filter.html#a66768cd6584270f71d190d525c99a9c4',1,'vg::Filter::remap(Alignment &aln)'],['../classvg_1_1Filter.html#aea9d6813e578a5957131fa6c4c8eff52',1,'vg::Filter::remap(string seq)']]],
+ ['remove_10659',['remove',['../classvg_1_1PhasedGenome.html#a3706e208421ac10d5695ed5d5ec45090',1,'vg::PhasedGenome::remove()'],['../namespacevg_1_1temp__file.html#a9885078330e16129fccc5fb6d8717ec5',1,'vg::temp_file::remove()'],['../namespacexg_1_1temp__file.html#aa4e7fb2251b2ba8f6d054d873eae4988',1,'xg::temp_file::remove()']]],
+ ['remove_5fbonuses_10660',['remove_bonuses',['../classvg_1_1GSSWAligner.html#a35fe72b24fc734d75864275c8cc1257e',1,'vg::GSSWAligner']]],
+ ['remove_5fclipped_5fportion_10661',['remove_clipped_portion',['../classvg_1_1Filter.html#ac246ae985a763a2d10edc92c81639913',1,'vg::Filter']]],
+ ['remove_5fdirectory_10662',['remove_directory',['../structvg_1_1temp__file_1_1Handler.html#acb21b507190287960d50a614ccf611bf',1,'vg::temp_file::Handler']]],
+ ['remove_5fdominated_5fchunks_10663',['remove_dominated_chunks',['../classvg_1_1Surjector.html#aafa4eb4d310ac530ed186170dc34dba9',1,'vg::Surjector']]],
+ ['remove_5fduplicate_5fedges_10664',['remove_duplicate_edges',['../namespacevg.html#add4d3a3d1917566a8df138c80b38e548',1,'vg']]],
+ ['remove_5fduplicate_5fnodes_10665',['remove_duplicate_nodes',['../namespacevg.html#a6dbe8468f2f2bcf8ceb859e6a0f8b4b1',1,'vg']]],
+ ['remove_5fduplicated_5fin_10666',['remove_duplicated_in',['../classvg_1_1VG.html#a33424c3be8c3e088631dfb37c48773d3',1,'vg::VG']]],
+ ['remove_5fduplicates_10667',['remove_duplicates',['../classvg_1_1VG.html#aba9fb73c326ecfab70e35e44dff6a937',1,'vg::VG::remove_duplicates()'],['../namespacevg.html#a5d00fa3c72ac473353496aab96965e60',1,'vg::remove_duplicates(std::vector< GaplessExtension > &result)'],['../namespacevg.html#aecd2e49750e94ed6f9de917dd9c72ac2',1,'vg::remove_duplicates(Graph &graph)']]],
+ ['remove_5fedge_10668',['remove_edge',['../classvg_1_1FlowSort.html#ad5203a8e590cc8e2bdb7038057963aaf',1,'vg::FlowSort']]],
+ ['remove_5fedit_5ftmpfiles_10669',['remove_edit_tmpfiles',['../classvg_1_1Packer.html#a2612eb978cfad2220946fab00cc3360f',1,'vg::Packer']]],
+ ['remove_5fempty_5falignment_5fsections_10670',['remove_empty_alignment_sections',['../namespacevg.html#af3fb034fcd6d50c2b84f40026b40f284',1,'vg']]],
+ ['remove_5ffull_5flength_5fbonuses_10671',['remove_full_length_bonuses',['../classvg_1_1Mapper.html#a2e8194d4eb73fe32467ab37ed9468e09',1,'vg::Mapper']]],
+ ['remove_5fhigh_5fdegree_5fnodes_10672',['remove_high_degree_nodes',['../namespacevg_1_1algorithms.html#a96020f05a81255adfca3821f538c02b9',1,'vg::algorithms']]],
+ ['remove_5finverting_5fedges_10673',['remove_inverting_edges',['../classvg_1_1VG.html#a76005ed499eea217c9f778028751137c',1,'vg::VG']]],
+ ['remove_5flow_5fscoring_5fsections_10674',['remove_low_scoring_sections',['../namespacevg.html#a0ea49989e31a688e22265eb41291c0ae',1,'vg']]],
+ ['remove_5fmapping_10675',['remove_mapping',['../classvg_1_1Paths.html#ad52958174f83ec940328d8610563dc1a',1,'vg::Paths']]],
+ ['remove_5fnode_10676',['remove_node',['../classvg_1_1Paths.html#ab74cefb48d501d96b8dc81e3865770d1',1,'vg::Paths']]],
+ ['remove_5fnode_5fforwarding_5fedges_10677',['remove_node_forwarding_edges',['../classvg_1_1VG.html#ab92694e7fd89275603c967739e60e0d2',1,'vg::VG']]],
+ ['remove_5fnon_5fpath_10678',['remove_non_path',['../classvg_1_1VG.html#ad517da731d2bf9c81cc28e0a1367af33',1,'vg::VG']]],
+ ['remove_5fnon_5ftranscribed_5fnodes_10679',['remove_non_transcribed_nodes',['../classvg_1_1Transcriptome.html#aed6ea709b303bcc0055ea41217b5e1be',1,'vg::Transcriptome']]],
+ ['remove_5fnull_5fnodes_10680',['remove_null_nodes',['../classvg_1_1VG.html#a9b107027697644d771eb529037201f71',1,'vg::VG']]],
+ ['remove_5fnull_5fnodes_5fforwarding_5fedges_10681',['remove_null_nodes_forwarding_edges',['../classvg_1_1VG.html#a0e887a7b2cfc666f2210889a2dec791b',1,'vg::VG']]],
+ ['remove_5forphan_5fedges_10682',['remove_orphan_edges',['../classvg_1_1VG.html#a40dd9bc0458a4948afd676374ae8d1f0',1,'vg::VG::remove_orphan_edges()'],['../namespacevg.html#a0b38f4f0d7e63b1f7f20d2dc985f88c4',1,'vg::remove_orphan_edges()']]],
+ ['remove_5fpath_10683',['remove_path',['../classvg_1_1Paths.html#ad3893e02f5e0429a13621ae333208f9e',1,'vg::Paths::remove_path()'],['../classvg_1_1VG.html#a30c369b4c1b0dfa4e9fbc0d3bce82648',1,'vg::VG::remove_path()']]],
+ ['remove_5fpaths_10684',['remove_paths',['../classvg_1_1Paths.html#a975ff2ed8ee5718aae414cb0cb2fb39b',1,'vg::Paths::remove_paths()'],['../namespacevg.html#ad5e16e94675197650b9d6edb9e7a9081',1,'vg::remove_paths()']]],
+ ['remove_5fredundant_5ftranscript_5fpaths_10685',['remove_redundant_transcript_paths',['../classvg_1_1Transcriptome.html#aa7bf08bef8301bcff774dff1bc92d484',1,'vg::Transcriptome']]],
+ ['remove_5fsamples_10686',['remove_samples',['../gbwt__main_8cpp.html#a9750054dfc43368b363ed04acd832b15',1,'gbwt_main.cpp']]],
+ ['remove_5ftransitive_5fedges_10687',['remove_transitive_edges',['../classvg_1_1MultipathAlignmentGraph.html#aeb9c58b7f20245a4c400dd14e8488069',1,'vg::MultipathAlignmentGraph']]],
+ ['rename_5fpath_10688',['rename_path',['../classhandlegraph_1_1MutablePathHandleGraph.html#a95370bd388b2c113cf0556f266993418',1,'handlegraph::MutablePathHandleGraph']]],
+ ['rend_10689',['rend',['../classvg_1_1ZipCodeTree.html#acb87f941c2eb8bcef3f6008c248f07c4',1,'vg::ZipCodeTree']]],
+ ['reorder_5fadjacency_5flists_10690',['reorder_adjacency_lists',['../classvg_1_1MultipathAlignmentGraph.html#adba05a33bf075eb3eb7260e229245f06',1,'vg::MultipathAlignmentGraph']]],
+ ['reorder_5fexons_10691',['reorder_exons',['../classvg_1_1Transcriptome.html#ae6f600db9b276fe332d4f14919bba983',1,'vg::Transcriptome']]],
+ ['repetitiveness_10692',['repetitiveness',['../structvg_1_1SeqComplexity.html#a192996fb41444e1ccddd6b6e334cf2d3',1,'vg::SeqComplexity']]],
+ ['replace_5fin_5fstring_10693',['replace_in_string',['../namespacevg.html#ab169ac1e2fc6ba662eebc1ede1ffe157',1,'vg']]],
+ ['replace_5flocal_5fhaplotype_10694',['replace_local_haplotype',['../classvg_1_1GenomeState.html#a8048b04c0d1d0b438ec76bdc1c0b5779',1,'vg::GenomeState']]],
+ ['replace_5fmapping_10695',['replace_mapping',['../classvg_1_1Paths.html#a906246385a06c6825aaf9b3c58cbdeac',1,'vg::Paths']]],
+ ['replace_5foccurrence_10696',['replace_occurrence',['../structvg_1_1PathIndex.html#ae8806eb31bcd8b8f9305180fea7b746f',1,'vg::PathIndex']]],
+ ['replace_5fsnarl_5fhaplotype_10697',['replace_snarl_haplotype',['../classvg_1_1GenomeState.html#a83cd070b1d65189fbba77a5bda91d405',1,'vg::GenomeState']]],
+ ['report_5faffinities_10698',['report_affinities',['../classvg_1_1Genotyper.html#abe8c49eaf4799ae7202e19b6e09288a7',1,'vg::Genotyper']]],
+ ['report_5fexception_10699',['report_exception',['../namespacevg.html#a638a54aabac7956dae6fd882468a86fe',1,'vg']]],
+ ['report_5flibrary_10700',['report_library',['../namespacevg.html#a040485dc93c5bf925dc58fe4eaa0bd02',1,'vg']]],
+ ['report_5fsnarl_10701',['report_snarl',['../classvg_1_1Genotyper.html#a6c9c525615b0c453f0685ea2ed987cde',1,'vg::Genotyper']]],
+ ['report_5fsnarl_5ftraversal_10702',['report_snarl_traversal',['../classvg_1_1Genotyper.html#a1a141641a0939e35dc6ee19281001628',1,'vg::Genotyper']]],
+ ['report_5ftime_5fmemory_10703',['report_time_memory',['../gbwt__main_8cpp.html#aa6ba12498251a288731312b850bba212',1,'gbwt_main.cpp']]],
+ ['representativetraversalfinder_10704',['RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html#a5dd3d9602c8056d016d42ba5cb760f11',1,'vg::RepresentativeTraversalFinder']]],
+ ['require_10705',['require',['../classvg_1_1IndexRegistry.html#ac52737ce471d6fb1ea968a2e57dc4b7f',1,'vg::IndexRegistry']]],
+ ['rescue_5fhigh_5fcount_5forder_5flength_5fmems_10706',['rescue_high_count_order_length_mems',['../classvg_1_1BaseMapper.html#aa7a71951ec7acdbf2c31ae9318ceb035',1,'vg::BaseMapper']]],
+ ['resect_5fsnarls_5ffrom_5fpaths_10707',['resect_snarls_from_paths',['../classvg_1_1MultipathAlignmentGraph.html#a9c49582fe16bcb4c87b95e8e3ee93319',1,'vg::MultipathAlignmentGraph']]],
+ ['reset_10708',['reset',['../classvg_1_1IndexRegistry.html#abcba0a09cee5a43096a09d05556353c1',1,'vg::IndexRegistry::reset()'],['../classvg_1_1IndexFile.html#aa16d18589ef1a9944b8e2af8c8ea1232',1,'vg::IndexFile::reset()'],['../structvg_1_1Counts.html#a90e02c9fc99656e6325f5c8fbfccda86',1,'vg::Counts::reset()'],['../classvg_1_1uniform__real__distribution.html#ad9ba8ac53f8a0af213db9d4f8da12617',1,'vg::uniform_real_distribution::reset()'],['../classvg_1_1normal__distribution.html#a7bae578d38533043f42f09413c7c1e32',1,'vg::normal_distribution::reset()'],['../classvg_1_1truncated__normal__distribution.html#ae1ebb560eee14b873305a4b5bf97616e',1,'vg::truncated_normal_distribution::reset()'],['../classvg_1_1uniform__int__distribution.html#a38594c45008dfc36cfbb4f9b9e4193dd',1,'vg::uniform_int_distribution::reset()'],['../classvg_1_1discrete__distribution.html#a5a3ca0751a139bef583b819118188780',1,'vg::discrete_distribution::reset()'],['../structvg_1_1Range.html#a3bf0b390a74ca7ea5f806f6cd98aac2c',1,'vg::Range::reset()']]],
+ ['reset_5falong_5fchain_10709',['reset_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#ade116b41b24892b20ac4fa95a9b5539e',1,'vg::subcommand::TickChainLink::reset_along_chain()'],['../structvg_1_1Range.html#a475da5fc747b64bfa869524e932077df',1,'vg::Range::reset_along_chain()']]],
+ ['reset_5fchain_10710',['reset_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a5a3dd8ac3d8a86fec1d2062e6d864c73',1,'vg::subcommand::TickChainLink::reset_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a05855ac56b836299fc0fc12292555b37',1,'vg::subcommand::OptionGroup::reset_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a73c92bfa80186ac2d64f9b24233aacb8',1,'vg::subcommand::GroupedOptionGroup::reset_chain()']]],
+ ['resize_5findexes_10711',['resize_indexes',['../classvg_1_1VG.html#af8879b1e6aab38b9a246deba0f05ccfe',1,'vg::VG']]],
+ ['restore_5fpaths_10712',['restore_paths',['../classvg_1_1PhaseUnfolder.html#a3cdfb31928c3a4127d9888d543872e1c',1,'vg::PhaseUnfolder']]],
+ ['retry_5fpairing_5fspliced_5falignments_10713',['retry_pairing_spliced_alignments',['../classvg_1_1MultipathMapper.html#ae388023023d7b1a862a77416d9ed1ede',1,'vg::MultipathMapper']]],
+ ['rev_5fcomp_5fmultipath_5falignment_10714',['rev_comp_multipath_alignment',['../namespacevg.html#a785f128b2eeb9aa2a4ee5477e5b9942b',1,'vg']]],
+ ['rev_5fcomp_5fmultipath_5falignment_5fin_5fplace_10715',['rev_comp_multipath_alignment_in_place',['../namespacevg.html#ab9aa92b68bb45684a3b751060508c709',1,'vg']]],
+ ['rev_5fcomp_5fsubpath_10716',['rev_comp_subpath',['../namespacevg.html#a4d802144c81c58c86f814507e1f99e22',1,'vg']]],
+ ['revdna3bit_10717',['revdna3bit',['../namespacexg.html#a09a061b73b78b2ba029940f09ccb6f5b',1,'xg']]],
+ ['reverse_10718',['reverse',['../classvg_1_1NodeTraversal.html#a748acf3ae485ab57fe649e70cad17c5d',1,'vg::NodeTraversal::reverse()'],['../namespacevg.html#a91adfc6327b5709dc73fcc7edbe5da57',1,'vg::reverse(const Position &pos, size_t node_length)'],['../namespacevg.html#a2e300d25fd8281f9453366f68b484196',1,'vg::reverse(const Visit &visit)'],['../namespacevg.html#ac52fd5878b0be1d53de644eea3458663',1,'vg::reverse(const pos_t &pos, size_t node_length)'],['../namespacexg.html#ad11c9145dd19a26ea95db548d7aaac79',1,'xg::reverse()']]],
+ ['reverse_5fadjacencies_10719',['reverse_adjacencies',['../classvg_1_1Surjector.html#a98ca84936638bdcb054e3304b6f959f1',1,'vg::Surjector']]],
+ ['reverse_5falignment_10720',['reverse_alignment',['../classvg_1_1MultipathAlignmentGraph.html#a91aa5268618d2f4c1d7b8665108d455c',1,'vg::MultipathAlignmentGraph']]],
+ ['reverse_5fbase_5fpos_10721',['reverse_base_pos',['../namespacevg.html#ae2f3762e2a8a852c7608d71f030e0345',1,'vg::reverse_base_pos()'],['../namespacexg.html#af6d74fb0781bfeb012e78af79758ab9c',1,'xg::reverse_base_pos()']]],
+ ['reverse_5fcomplement_10722',['reverse_complement',['../namespacevg.html#aa65de7dea52585f07bee6ae7f762eb95',1,'vg::reverse_complement(const char &c)'],['../namespacevg.html#a30732a1a1e8d20d6eaaaeafecc8a50a7',1,'vg::reverse_complement(const string &seq)'],['../namespacexg.html#ac667d522781e3c31d191e4c6db520eaa',1,'xg::reverse_complement(const char &c)'],['../namespacexg.html#ab4f0205fd0abe6aaa4077cd20abcd36f',1,'xg::reverse_complement(const std::string &seq)']]],
+ ['reverse_5fcomplement_5falignment_10723',['reverse_complement_alignment',['../namespacevg.html#a98e512ed0fca2503ccc370435591a6c1',1,'vg']]],
+ ['reverse_5fcomplement_5falignment_5fin_5fplace_10724',['reverse_complement_alignment_in_place',['../namespacevg.html#ab96610ffc81d6207e0b13f675296c234',1,'vg']]],
+ ['reverse_5fcomplement_5falignments_10725',['reverse_complement_alignments',['../namespacevg.html#aed045b02277d7704e997cbede67c2662',1,'vg']]],
+ ['reverse_5fcomplement_5fedit_10726',['reverse_complement_edit',['../namespacevg_1_1io.html#a52a77b52c33c165637fb00be3e9f54e0',1,'vg::io']]],
+ ['reverse_5fcomplement_5fgraph_10727',['reverse_complement_graph',['../classvg_1_1VG.html#a82185028afbc17aaf60b294297507fd2',1,'vg::VG::reverse_complement_graph()'],['../namespacehandlegraph_1_1algorithms.html#a3cb6868def99085050dca0efdd3eb0c9',1,'handlegraph::algorithms::reverse_complement_graph()']]],
+ ['reverse_5fcomplement_5fin_5fplace_10728',['reverse_complement_in_place',['../namespacevg.html#ae6353d47c867f1b4cc7053d82aef42f4',1,'vg::reverse_complement_in_place()'],['../namespacexg.html#a18e172174952ffa498b10715acdc031c',1,'xg::reverse_complement_in_place()']]],
+ ['reverse_5fcomplement_5fmapping_10729',['reverse_complement_mapping',['../namespacevg.html#a3ce6fa1d8f3ba4f8f361fa77a6fd5261',1,'vg::reverse_complement_mapping(const Mapping &m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a798565f048dc7844739ea4913d950d31',1,'vg::reverse_complement_mapping(const path_mapping_t &m, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fcomplement_5fmapping_5fin_5fplace_10730',['reverse_complement_mapping_in_place',['../namespacevg.html#af2dc9d6ee4403027eb5965aa6a71eb4e',1,'vg::reverse_complement_mapping_in_place(Mapping *m, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#abc9bd04ab1099c6d9bd655a2accbe52e',1,'vg::reverse_complement_mapping_in_place(path_mapping_t *m, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fcomplement_5fpath_10731',['reverse_complement_path',['../namespacevg.html#a463d9eaed29cd6d46a8e2afb645c8fda',1,'vg::reverse_complement_path(const Path &path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a3df9f25ec47163ccbfa328673bd28ab5',1,'vg::reverse_complement_path(const path_t &path, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fcomplement_5fpath_5fin_5fplace_10732',['reverse_complement_path_in_place',['../namespacevg.html#af2941a3c80481d02c65d9d72bd835807',1,'vg::reverse_complement_path_in_place(Path *path, const function< int64_t(id_t)> &node_length)'],['../namespacevg.html#a0df8f9c5838119e79ee1f671cd823740',1,'vg::reverse_complement_path_in_place(path_t *path, const function< int64_t(id_t)> &node_length)']]],
+ ['reverse_5fedge_10733',['reverse_edge',['../classvg_1_1FlowSort.html#a237e09746b80c67a96290eac62fbd2c8',1,'vg::FlowSort']]],
+ ['reverse_5ffrom_5fstart_5fto_5fend_5fedge_10734',['reverse_from_start_to_end_edge',['../classvg_1_1FlowSort.html#a095e96bd8ef6f016a600bdbc6af730ee',1,'vg::FlowSort']]],
+ ['reverse_5fiterator_10735',['reverse_iterator',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a58d6dc8114a797ef5fa8b3ef95d3e282',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(vector< tree_item_t >::const_reverse_iterator rbegin, vector< tree_item_t >::const_reverse_iterator rend, size_t distance_limit=std::numeric_limits< size_t >::max())'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa454b7553be8ff9226e7622476de7515',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ac2889d055d75873e7d1d834c758c17ea',1,'vg::ZipCodeTree::reverse_iterator::reverse_iterator(reverse_iterator &&other)']]],
+ ['reversegraph_10736',['ReverseGraph',['../classvg_1_1ReverseGraph.html#a9122b516caa1f30b202ef7ef4cd83d60',1,'vg::ReverseGraph::ReverseGraph(const HandleGraph *forward_graph, bool complement)'],['../classvg_1_1ReverseGraph.html#a4715727accf496a2b7f908688638d873',1,'vg::ReverseGraph::ReverseGraph()=default']]],
+ ['reversing_5ffilter_10737',['reversing_filter',['../classvg_1_1Filter.html#a5ac9ddf9392d973aa726ad6ee4d53b9f',1,'vg::Filter']]],
+ ['rewindplanexception_10738',['RewindPlanException',['../classvg_1_1RewindPlanException.html#ad1b916e8d35f9825b9352045b7e77146',1,'vg::RewindPlanException::RewindPlanException()=delete'],['../classvg_1_1RewindPlanException.html#a28ad0274056215792783b0b3bc8fd258',1,'vg::RewindPlanException::RewindPlanException(const string &msg, const IndexGroup &rewind_to) noexcept']]],
+ ['rewrite_5fsegment_10739',['rewrite_segment',['../classvg_1_1VG.html#abb2dc75f200cfb7480e671fd55207410',1,'vg::VG::rewrite_segment()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#af28f1372aa6dad2654a22eb8463e2a07',1,'handlegraph::MutablePathHandleGraph::rewrite_segment()']]],
+ ['right_5fdegree_10740',['right_degree',['../classvg_1_1VG.html#a23622195177dff4c7c8416edffb7fc93',1,'vg::VG']]],
+ ['right_5fseed_5fnode_10741',['right_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a83d9a8edb6fb9fd1ac20ffa976355155',1,'vg::JoinedSpliceGraph']]],
+ ['right_5fsplice_5fnode_10742',['right_splice_node',['../classvg_1_1JoinedSpliceGraph.html#adf8ca2fd45b0d024bf4b12ea04fbfc79',1,'vg::JoinedSpliceGraph']]],
+ ['ring_5fbuffer_5fempty_10743',['ring_buffer_empty',['../classvg_1_1io_1_1StreamMultiplexer.html#a92c3f4f2de80a840aef85574935758ac',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5ffull_10744',['ring_buffer_full',['../classvg_1_1io_1_1StreamMultiplexer.html#a0d671fb79357a83af6c5becfa890a6f2',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5fpeek_10745',['ring_buffer_peek',['../classvg_1_1io_1_1StreamMultiplexer.html#aa03a8b8e99c728355ade20923bcb4c2f',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5fpop_10746',['ring_buffer_pop',['../classvg_1_1io_1_1StreamMultiplexer.html#ac4f6095e2eb79970075f9b2279e990ce',1,'vg::io::StreamMultiplexer']]],
+ ['ring_5fbuffer_5fpush_10747',['ring_buffer_push',['../classvg_1_1io_1_1StreamMultiplexer.html#a925607e24a8c6e905fc45c4b77bbe62c',1,'vg::io::StreamMultiplexer']]],
+ ['round_5foutward_10748',['round_outward',['../structvg_1_1PathIndex.html#ac02dd3e22c5b29670ef48b6f725a9797',1,'vg::PathIndex']]],
+ ['rrmemo_10749',['RRMemo',['../structhaplo_1_1haploMath_1_1RRMemo.html#a3958ec23ff1fbaac901d909c5f134f27',1,'haplo::haploMath::RRMemo']]],
+ ['run_10750',['run',['../classvg_1_1Genotyper.html#af760be5c99e086b2c41510b3d3a47e5a',1,'vg::Genotyper']]],
+ ['run_5fbenchmark_10751',['run_benchmark',['../namespacevg.html#ac101c453ab2076d74f0324f73d174695',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &under_test)'],['../namespacevg.html#added44ff3bb1c0ce606563a40923c513',1,'vg::run_benchmark(const string &name, size_t iterations, const function< void(void)> &setup, const function< void(void)> &under_test)']]],
+ ['run_5fdp_10752',['run_dp',['../classvg_1_1DeletionAligner.html#a0eb6b38dc11173f5da75c5cafd3053fe',1,'vg::DeletionAligner']]],
+ ['run_5fgenotype_10753',['run_genotype',['../classvg_1_1MCMCGenotyper.html#a3bae6f8b2947e030935d5e9cf46fb324',1,'vg::MCMCGenotyper']]],
+ ['run_5fmultipath_5fdp_10754',['run_multipath_dp',['../namespacevg.html#ae57a78071537c87e2f0f57bfea18ba71',1,'vg']]]
];
diff --git a/search/functions_13.js b/search/functions_13.js
index 5bc90075c4..4b4dc23b59 100644
--- a/search/functions_13.js
+++ b/search/functions_13.js
@@ -1,398 +1,398 @@
var searchData=
[
- ['sa_5fto_5fda_10751',['sa_to_da',['../namespacevg.html#aaac16668663556af1aea74159a73d4ed',1,'vg']]],
- ['sam_5fflag_10752',['sam_flag',['../namespacevg.html#ae37c6d66a01cef6f92707d367ebf4cdb',1,'vg']]],
- ['same_5fcontext_10753',['same_context',['../classvg_1_1VG.html#a96f99984ada5a3a13332ddb2ab0a1c97',1,'vg::VG']]],
- ['sample_5fgam_5fdepth_10754',['sample_gam_depth',['../namespacevg_1_1algorithms.html#a80703607cfe21f1f593f7b2f03c08b40',1,'vg::algorithms']]],
- ['sample_5fhaplotypes_10755',['sample_haplotypes',['../giraffe__main_8cpp.html#a6343c45d56779ead6309ffefbf066fdc',1,'sample_haplotypes(const vector< pair< string, string >> &indexes, string &basename, string &sample_name, string &haplotype_file, string &kff_file, bool progress): giraffe_main.cpp'],['../haplotypes__main_8cpp.html#a13d462ac627c7beb00b431280ac9b0c6',1,'sample_haplotypes(const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, const HaplotypesConfig &config): haplotypes_main.cpp']]],
- ['sample_5fmapping_5fdepth_10756',['sample_mapping_depth',['../namespacevg_1_1algorithms.html#a16bd0de261a829b2d81ec48eed9d6482',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const string &input_filename, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq, const string &format)'],['../namespacevg_1_1algorithms.html#a244822514c71473756cfd5ad87f79e08',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const vector< Alignment > &alignments, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq)']]],
- ['sample_5fminimal_10757',['sample_minimal',['../namespacevg_1_1algorithms.html#a175ee345e226732cb1c37da13a2f045e',1,'vg::algorithms']]],
- ['sample_5fpath_10758',['sample_path',['../classvg_1_1NGSSimulator.html#a57ee602010b5295685556acc30e0355a',1,'vg::NGSSimulator']]],
- ['sample_5fread_10759',['sample_read',['../classvg_1_1ReadFilter.html#aa592c88e758fc257fdf17418b0f189a8',1,'vg::ReadFilter::sample_read()'],['../classvg_1_1Sampler.html#ab48bd0062b357dfe0cf418beb1e18ad4',1,'vg::Sampler::sample_read()'],['../classvg_1_1NGSSimulator.html#a50a20af9dd3edd86233edf1de13a5cda',1,'vg::NGSSimulator::sample_read()']]],
- ['sample_5fread_5finternal_10760',['sample_read_internal',['../classvg_1_1NGSSimulator.html#a957be55e0adcf59449587ccb1f8db9de',1,'vg::NGSSimulator']]],
- ['sample_5fread_5fpair_10761',['sample_read_pair',['../classvg_1_1Sampler.html#a598b41433f5bb9a040749e7a2327b78d',1,'vg::Sampler::sample_read_pair()'],['../classvg_1_1NGSSimulator.html#a5b12189ad9dcf0a4656a321fcf5ff840',1,'vg::NGSSimulator::sample_read_pair()']]],
- ['sample_5fread_5fquality_10762',['sample_read_quality',['../classvg_1_1NGSSimulator.html#a49ad65d878edb1d76518f589aa0bf02c',1,'vg::NGSSimulator']]],
- ['sample_5fread_5fquality_5finternal_10763',['sample_read_quality_internal',['../classvg_1_1NGSSimulator.html#a03fb08f4267424aca8d8892a403b134a',1,'vg::NGSSimulator']]],
- ['sample_5fread_5fquality_5fpair_10764',['sample_read_quality_pair',['../classvg_1_1NGSSimulator.html#a71f6e4ba9442273d4cf1588f24578f55',1,'vg::NGSSimulator']]],
- ['sample_5fstart_5fgraph_5fpos_10765',['sample_start_graph_pos',['../classvg_1_1NGSSimulator.html#ada5f04218c531191b20a8c28cc57d94e',1,'vg::NGSSimulator']]],
- ['sample_5fstart_5fpath_5fpos_10766',['sample_start_path_pos',['../classvg_1_1NGSSimulator.html#ad2f821c685108e8ee6912713f0ced8d3',1,'vg::NGSSimulator']]],
- ['sample_5fstart_5fpos_10767',['sample_start_pos',['../classvg_1_1NGSSimulator.html#a889b49669939bfb7832bad23f02cd02c',1,'vg::NGSSimulator']]],
- ['sample_5ftransition_10768',['sample_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a4434cebe872c32c384c1f916111fc2e1',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['sampler_10769',['Sampler',['../classvg_1_1Sampler.html#ab1d1e96bcf702979dfc86a92dcd8d24b',1,'vg::Sampler']]],
- ['sanitize_5fsequence_5fin_5fplace_10770',['sanitize_sequence_in_place',['../classvg_1_1Constructor.html#a1d90ed36989b851bb3c072f4d67b52dd',1,'vg::Constructor']]],
- ['save_10771',['save',['../classvg_1_1StreamIndexBase.html#a99761d4d917dc5ba1db1e08a36ceb312',1,'vg::StreamIndexBase::save()'],['../classvg_1_1io_1_1VPKG.html#a80551b46351f1e8d47e8b3ebaf028847',1,'vg::io::VPKG::save(const Have &have, ostream &out)'],['../classvg_1_1io_1_1VPKG.html#a0472c51ab91f4b8663a56a150e0e0f12',1,'vg::io::VPKG::save(const Have &have, const string &filename)']]],
- ['save_5fbed_10772',['save_bed',['../classvg_1_1FeatureSet.html#a2914a7c47c085b00a454df2bfc5eda67',1,'vg::FeatureSet']]],
- ['save_5ffrag_5flens_5fto_5falns_10773',['save_frag_lens_to_alns',['../classvg_1_1FragmentLengthStatistics.html#ab9376051edd07e128f52f57ac2b5a410',1,'vg::FragmentLengthStatistics']]],
- ['save_5fgbwt_10774',['save_gbwt',['../namespacevg.html#a790122d8b3f28068aaf09f1eb5b966a9',1,'vg::save_gbwt(const gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a8385d575383b7bae35726e90851a2795',1,'vg::save_gbwt(const gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
- ['save_5fgbwtgraph_10775',['save_gbwtgraph',['../namespacevg.html#aea7640260b1c70795335439f3d6c2eac',1,'vg']]],
- ['save_5fgbz_10776',['save_gbz',['../namespacevg.html#a017e7cda40a98b4b044507ab78a34da9',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a6beaace0e6d90b654dc9c382afb39ce0',1,'vg::save_gbz(const gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#af7669e457f62e6f197f3120086a091e2',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
- ['save_5fgcsa_10777',['save_gcsa',['../namespacevg.html#aa2840fc8dbdb12c000769a3baa39b808',1,'vg']]],
- ['save_5fhandle_5fgraph_10778',['save_handle_graph',['../namespacevg_1_1io.html#af3f5510bd6a0e5514d3083fcd2ffdd32',1,'vg::io::save_handle_graph(HandleGraph *graph, ostream &os)'],['../namespacevg_1_1io.html#a571f402ff74b738d9070a598a41b58da',1,'vg::io::save_handle_graph(HandleGraph *graph, const string &dest_path)']]],
- ['save_5flcp_10779',['save_lcp',['../namespacevg.html#a604f783fb59cb6c3e7fcc783a8286822',1,'vg']]],
- ['save_5fminimizer_10780',['save_minimizer',['../namespacevg.html#af7885143ca20185816afadc669813f12',1,'vg']]],
- ['save_5fr_5findex_10781',['save_r_index',['../namespacevg.html#a50d4b5eef7efd656daeb423af1f6a3c6',1,'vg']]],
- ['save_5frecords_10782',['save_records',['../classvg_1_1HTSWriter.html#a4d3f2772a76d36733f1bb1ccf93f498b',1,'vg::HTSWriter']]],
- ['save_5fto_5ffile_10783',['save_to_file',['../classvg_1_1Packer.html#a936e5283142e2fb3ac089730b217d533',1,'vg::Packer']]],
- ['scan_10784',['scan',['../classvg_1_1DozeuInterface.html#a73d9afd8c6b52ff715ae0606bbae4b63',1,'vg::DozeuInterface::scan()'],['../classvg_1_1XdropAligner.html#a3bf50d433186476abc2f732525bf1377',1,'vg::XdropAligner::scan()'],['../classvg_1_1QualAdjXdropAligner.html#a2e8adea58e74731765b5c7d0eb54386f',1,'vg::QualAdjXdropAligner::scan()'],['../structvg_1_1PositionIDScanner.html#a32743fa0fd2721702fe8fc34d565c64a',1,'vg::PositionIDScanner::scan()'],['../structvg_1_1IDScanner.html#a36577d4a2c2ac0d7a12383ae6e9e999d',1,'vg::IDScanner::scan()'],['../structvg_1_1WrappingPositionScanner.html#ac9e28c724f1361a03b6a07e0f9e29ada',1,'vg::WrappingPositionScanner::scan()'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)']]],
- ['scan_5fbackward_10785',['scan_backward',['../classvg_1_1StreamIndexBase.html#addb451cabccc43915ae629925b3ed3ee',1,'vg::StreamIndexBase']]],
- ['scan_5fcontig_5flengths_10786',['scan_contig_lengths',['../classvg_1_1VCFGenotyper.html#a28f3c05eb4ffefef243a18dc27562b15',1,'vg::VCFGenotyper']]],
- ['scan_5ffor_5fdeletion_10787',['scan_for_deletion',['../classvg_1_1VCFTraversalFinder.html#a7842cce2da7786e41fbd110c78e45ef6',1,'vg::VCFTraversalFinder']]],
- ['scan_5fp_5fvisits_10788',['scan_p_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a04d2b3f11fa053b6d6cdbbcae94b4873',1,'vg::algorithms::GFAParser']]],
- ['scan_5fpath_10789',['scan_path',['../classhandlegraph_1_1PathHandleGraph.html#aa071f31a10a02d8231b029d0a7ddef0b',1,'handlegraph::PathHandleGraph']]],
- ['scan_5fseed_5fposition_10790',['scan_seed_position',['../classvg_1_1DozeuInterface.html#a472afdc993f32bfa38518a9cfbd14dcb',1,'vg::DozeuInterface']]],
- ['scan_5fsnarl_10791',['scan_snarl',['../classvg_1_1VCFOutputCaller.html#ad6cbf084906bc4676fae7715495888b3',1,'vg::VCFOutputCaller']]],
- ['scan_5fvisits_10792',['scan_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a58ceb0c0017e5ea50b35854e5c52f0f4',1,'vg::algorithms::GFAParser']]],
- ['scan_5fw_5fvisits_10793',['scan_w_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a7e83307cfe42aae91205fa7180b802b4',1,'vg::algorithms::GFAParser']]],
- ['scc_5fcopy_5fof_5fhandle_10794',['scc_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a015efe5e782831e59aaa3c2d6f98cbfd',1,'vg::DagifiedGraph']]],
- ['scc_5fcopy_5fof_5fnode_5fid_10795',['scc_copy_of_node_id',['../classvg_1_1DagifiedGraph.html#a26161bf79e0a6385ff8f6fb67a1e907b',1,'vg::DagifiedGraph']]],
- ['score_10796',['score',['../structvg_1_1BenchmarkResult.html#a4baad39dafa27d171b65df225666c887',1,'vg::BenchmarkResult::score()'],['../classvg_1_1MEMChainModel.html#aca053d2a91e4ea7ac440edd670893a84',1,'vg::MEMChainModel::score()'],['../classvg_1_1Funnel.html#a9cdacae4561ece776ba90e293299f930',1,'vg::Funnel::score()'],['../structhaplo_1_1haplo__DP.html#aadc492bf7d73b8d551ed56bb62266baa',1,'haplo::haplo_DP::score(const vg::Path &path, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1haplo__DP.html#a3204316e386c183faa191b9ee6f0b34e',1,'haplo::haplo_DP::score(const gbwt_thread_t &thread, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1linear__haplo__structure.html#a100ae7bbb7fa336e7d273c066f251e29',1,'haplo::linear_haplo_structure::score()'],['../classhaplo_1_1ScoreProvider.html#a4dd1edd0db2c92780af0fce9e62e8a1f',1,'haplo::ScoreProvider::score()'],['../classhaplo_1_1GBWTScoreProvider.html#a9970037ed1e272daa0e0bfdf358c9bce',1,'haplo::GBWTScoreProvider::score()'],['../classhaplo_1_1LinearScoreProvider.html#a0d95fe4eff2760404bce49d3aa50e2f0',1,'haplo::LinearScoreProvider::score()'],['../classvg_1_1AlignmentChainModel.html#a562dbec7e2dc602c82b92ad202620429',1,'vg::AlignmentChainModel::score()'],['../classvg_1_1connection__t.html#a8f34943152ac67f59c15ff776da592e8',1,'vg::connection_t::score()'],['../classvg_1_1subpath__t.html#a9e59579440b9a90f5b0c606dc3cf400a',1,'vg::subpath_t::score()'],['../classvg_1_1algorithms_1_1Anchor.html#aff7b7e2c62b7b7154edd3a9f64b0e5a7',1,'vg::algorithms::Anchor::score()']]],
- ['score_5falignment_10797',['score_alignment',['../classvg_1_1Mapper.html#aa541cae3a3598e10a7baf7d5ed78f644',1,'vg::Mapper']]],
- ['score_5falignment_5fpair_10798',['score_alignment_pair',['../classvg_1_1MinimizerMapper.html#a99ce46a1525f7be9fa393163ca1eac40',1,'vg::MinimizerMapper']]],
- ['score_5fbest_5fchain_10799',['score_best_chain',['../namespacevg_1_1algorithms.html#ad91b7ceb67d3923a4c5cace56a5c4f6e',1,'vg::algorithms']]],
- ['score_5fchain_5fgap_10800',['score_chain_gap',['../namespacevg_1_1algorithms.html#abdc2933db32d78a14a8e439f7e9643ab',1,'vg::algorithms']]],
- ['score_5fcluster_10801',['score_cluster',['../classvg_1_1MinimizerMapper.html#a12e67c2dfdb80db4080d3675ed6a18d4',1,'vg::MinimizerMapper']]],
- ['score_5fcontiguous_5falignment_10802',['score_contiguous_alignment',['../classvg_1_1GSSWAligner.html#a95753239b9d5fa388198ea04ac6c559b',1,'vg::GSSWAligner']]],
- ['score_5fdiscontiguous_5falignment_10803',['score_discontiguous_alignment',['../classvg_1_1GSSWAligner.html#a795072356e28310d80f95bb5f0bb61f3',1,'vg::GSSWAligner']]],
- ['score_5ferror_10804',['score_error',['../structvg_1_1BenchmarkResult.html#a880a443c67063f66623006cd82b5ec9d',1,'vg::BenchmarkResult']]],
- ['score_5fexact_5fmatch_10805',['score_exact_match',['../classvg_1_1GSSWAligner.html#ac33af43d7d8d4a3d94a5ef1582c50cc4',1,'vg::GSSWAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const =0'],['../classvg_1_1GSSWAligner.html#ac8e1b97332df85221c6a2be61cbd1b3d',1,'vg::GSSWAligner::score_exact_match(const string &sequence, const string &base_quality) const =0'],['../classvg_1_1GSSWAligner.html#ac2969d865d7cb4652a7476feabd9c9b5',1,'vg::GSSWAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1Aligner.html#a4e087eea3154fc52fff10cbe14d0cd32',1,'vg::Aligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1Aligner.html#ab18b86459ab4471de6361bce2d8e8459',1,'vg::Aligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1Aligner.html#a86b2a95cc4d4de88a78ab6ce8ccc4b79',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#ae88c5b0e7c75fec448d4ed245cebe9b9',1,'vg::Aligner::score_exact_match(const string &sequence) const'],['../classvg_1_1Aligner.html#a2acc9c763d0b7c16ad69472a148ce75b',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end) const'],['../classvg_1_1QualAdjAligner.html#adf03ac873ae9a9cfbc21e589775111be',1,'vg::QualAdjAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1QualAdjAligner.html#a51941e8914296630f63d303c548cee8d',1,'vg::QualAdjAligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1QualAdjAligner.html#a8348afe2de6738fd4cd26e3fd6358818',1,'vg::QualAdjAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const']]],
- ['score_5fextension_5fgroup_10806',['score_extension_group',['../classvg_1_1MinimizerMapper.html#a2c8ab02743227cb2550fcfd295043253',1,'vg::MinimizerMapper']]],
- ['score_5fextensions_10807',['score_extensions',['../classvg_1_1MinimizerMapper.html#af9ff5e0a1b8c7925ccdb8a23d29872ef',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::vector< GaplessExtension >> &extensions, const Alignment &aln, Funnel &funnel) const'],['../classvg_1_1MinimizerMapper.html#a421cdd65bac59fac39fd3b87cce0f3ae',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::pair< std::vector< GaplessExtension >, size_t >> &extensions, const Alignment &aln, Funnel &funnel) const']]],
- ['score_5ffrom_10808',['score_from',['../classvg_1_1algorithms_1_1TracedScore.html#a999c0829c8c11a2d7478630612b60b74',1,'vg::algorithms::TracedScore']]],
- ['score_5ffull_5flength_5fbonus_10809',['score_full_length_bonus',['../classvg_1_1GSSWAligner.html#ad6bac86acf59cc8edd4969bd671fcf5d',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1GSSWAligner.html#a952bb420992b5e5e4c81388b015caf97',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const =0'],['../classvg_1_1Aligner.html#aaf87ac123c806ef49c509c494b431c9c',1,'vg::Aligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a442d01bf1ed7d011d015d790f0595817',1,'vg::Aligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const'],['../classvg_1_1QualAdjAligner.html#ac4505d206516b2ad51bdc2387309ae9e',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1QualAdjAligner.html#a84b8bacfebeb426d367ec4441800a4e4',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const']]],
- ['score_5fgap_10810',['score_gap',['../classvg_1_1GSSWAligner.html#a4071f79659899761586807411d5ab767',1,'vg::GSSWAligner::score_gap()'],['../namespacevg.html#aea0e7a0965b967bed3ff54e6ff630f91',1,'vg::score_gap()']]],
- ['score_5fmismatch_10811',['score_mismatch',['../classvg_1_1GSSWAligner.html#ab40663f27266555cd2718fca337ac348',1,'vg::GSSWAligner::score_mismatch()'],['../classvg_1_1Aligner.html#a7e359a8a6af31e1fba84a681c751ec23',1,'vg::Aligner::score_mismatch(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a6728bc34b9e4daa49c1045c8ded44553',1,'vg::Aligner::score_mismatch(size_t length) const'],['../classvg_1_1QualAdjAligner.html#ada69f388d291f6c3693812d91c84231a',1,'vg::QualAdjAligner::score_mismatch()']]],
- ['score_5fpartial_5falignment_10812',['score_partial_alignment',['../classvg_1_1GSSWAligner.html#adc950708e8d5ff812a838116c6b50910',1,'vg::GSSWAligner::score_partial_alignment()'],['../classvg_1_1Aligner.html#a4537844a4aa7783f6a41c7cefd758602',1,'vg::Aligner::score_partial_alignment()'],['../classvg_1_1QualAdjAligner.html#aee20bae08e744224825723a878d57bef',1,'vg::QualAdjAligner::score_partial_alignment()']]],
- ['score_5fsort_5fand_5fdeduplicate_5falignments_10813',['score_sort_and_deduplicate_alignments',['../classvg_1_1Mapper.html#ae820fb3edeac9da2ef475cb6b0e0f0e9',1,'vg::Mapper']]],
- ['score_5fto_5funnormalized_5flikelihood_5fln_10814',['score_to_unnormalized_likelihood_ln',['../classvg_1_1GSSWAligner.html#a59623587d4dfb1e0310fb608e9def2f0',1,'vg::GSSWAligner']]],
- ['score_5ftree_10815',['score_tree',['../classvg_1_1MinimizerMapper.html#ad4b6267b5e93d0fb618de0584cf2b213',1,'vg::MinimizerMapper']]],
- ['search_5fleft_10816',['search_left',['../classvg_1_1NestedTraversalFinder.html#a04465d6248557f427e5d35b657292e25',1,'vg::NestedTraversalFinder']]],
- ['search_5fmultipath_5falignment_10817',['search_multipath_alignment',['../namespacevg.html#aa9d71371be6972c8284b267d42fac754',1,'vg']]],
- ['search_5fright_10818',['search_right',['../classvg_1_1NestedTraversalFinder.html#a2b020fead8b7c40b06f9c0e1041b2cb5',1,'vg::NestedTraversalFinder']]],
- ['seed_10819',['Seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#adf405ffb00189f3c469f3fc7e79fde01',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed()=default'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#ad6d85e239a68f94ff5dbf2b0362f3c52',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(pos_t pos, size_t source, ZipCode zipcode)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a7859f190024d96f7182de94f197df881',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(Seed &&other)']]],
- ['seed_5fend_10820',['seed_end',['../classvg_1_1algorithms_1_1Anchor.html#a2db67aba40631bb9e462e2ae744a2ddd',1,'vg::algorithms::Anchor']]],
- ['seed_5fis_5freversed_5fat_5fdepth_10821',['seed_is_reversed_at_depth',['../classvg_1_1ZipCodeTree.html#a984f21c55ccaf7b053ce0e4fe77f91ff',1,'vg::ZipCodeTree']]],
- ['seed_5fstart_10822',['seed_start',['../classvg_1_1algorithms_1_1Anchor.html#af68c4af649ee5dfbf4cfff0e0e4493c8',1,'vg::algorithms::Anchor']]],
- ['seeds_5fin_5fsubgraph_10823',['seeds_in_subgraph',['../classvg_1_1MinimizerMapper.html#a98117858da937a277f445898bcc2d125',1,'vg::MinimizerMapper']]],
- ['seek_10824',['Seek',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa221be19182d88b7caa36ead3e63c829',1,'vg::io::BlockedGzipInputStream']]],
- ['seek_5fgroup_10825',['seek_group',['../classvg_1_1io_1_1MessageIterator.html#a97a1561c82f55827a208b2bea5e8da71',1,'vg::io::MessageIterator::seek_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#aad5921d9a10314f8060b0835225fc3cd',1,'vg::io::ProtobufIterator::seek_group()']]],
- ['select_5fdiploid_10826',['select_diploid',['../namespacevg.html#a5b634a10b029be9c22dccc3ef362f61c',1,'vg']]],
- ['select_5fhaplotypes_10827',['select_haplotypes',['../namespacevg.html#af2de3a2f2b77abef4336df983356fc23',1,'vg']]],
- ['seq_5fchain_5ffor_5fpath_10828',['seq_chain_for_path',['../haplotypes__main_8cpp.html#a462a39ecca4a3d1298196a6f23ef24a5',1,'haplotypes_main.cpp']]],
- ['seq_5ffor_5fchain_10829',['seq_for_chain',['../haplotypes__main_8cpp.html#ace19d06b45cb66b44602157c3bc24916',1,'haplotypes_main.cpp']]],
- ['seqcomplexity_10830',['SeqComplexity',['../structvg_1_1SeqComplexity.html#a18ab1a3d85623f42d1e8848fcf94846d',1,'vg::SeqComplexity::SeqComplexity(string::const_iterator begin, string::const_iterator end)'],['../structvg_1_1SeqComplexity.html#ac7a2e970b541883c812fafa7851d6278',1,'vg::SeqComplexity::SeqComplexity(const string &seq)']]],
- ['sequence_10831',['sequence',['../classvg_1_1MaximalExactMatch.html#a9746bd3ef368dbeae05459381223cebc',1,'vg::MaximalExactMatch::sequence()'],['../classvg_1_1multipath__alignment__t.html#a5637161345c2b1a557a40188b564dd55',1,'vg::multipath_alignment_t::sequence()'],['../classvg_1_1edit__t.html#aca5aef83ea5f5195699732c61c44b86d',1,'vg::edit_t::sequence()'],['../classvg_1_1Sampler.html#a355de4870a71a88834406f3e7f297272',1,'vg::Sampler::sequence()']]],
- ['sequence_5fpositions_10832',['sequence_positions',['../classvg_1_1BaseMapper.html#a1fc5077e5ea4a236ddf8edcf93288eb9',1,'vg::BaseMapper']]],
- ['serialize_10833',['serialize',['../structvg_1_1GBWTHandler.html#aa855690c481cca126734e20f5d126d04',1,'vg::GBWTHandler::serialize()'],['../classvg_1_1Packer.html#a833e1fa21ac3f5f5f6a001c5c5ee0f4c',1,'vg::Packer::serialize()'],['../classvg_1_1SnarlManager.html#afdcb932a1a891671acbdaaf445aee0b2',1,'vg::SnarlManager::serialize()'],['../classvg_1_1VG.html#a0ee4603518e9cd5915a65e65c2d763b2',1,'vg::VG::serialize()'],['../classvg_1_1ZipCodeCollection.html#afb7d15490acd1b076664049072184914',1,'vg::ZipCodeCollection::serialize()'],['../classxg_1_1XGPath.html#a74e7b70ac4829545e7b48c137808d6e4',1,'xg::XGPath::serialize()'],['../classhandlegraph_1_1Serializable.html#adae323cce9552f03774ab71dd5fb07d0',1,'handlegraph::Serializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1Serializable.html#ac6e9dfc830acdf96fbfe53d83d33802e',1,'handlegraph::Serializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1Serializable.html#a050e6c2b6e2fccd85362e908da60d20b',1,'handlegraph::Serializable::serialize(std::ostream &out)'],['../classhandlegraph_1_1Serializable.html#aa97699c9b50235d5f2439eb57c5df653',1,'handlegraph::Serializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#acaec0b472d85de2ff98b8635b5fbf33c',1,'handlegraph::TriviallySerializable::serialize(const std::function< void(const void *, size_t)> &iteratee) const =0'],['../classhandlegraph_1_1TriviallySerializable.html#a2881d2d598bd35cc68008ad3dc4b82d5',1,'handlegraph::TriviallySerializable::serialize(int fd)=0'],['../classhandlegraph_1_1TriviallySerializable.html#ab04c99b94217a13ce598e8fd484b09c1',1,'handlegraph::TriviallySerializable::serialize(int fd) const'],['../classhandlegraph_1_1TriviallySerializable.html#aaeb37dbdd6e221e2c5ddfba9cb226c56',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1TriviallySerializable.html#a6c306e7cce2dfe6079b093aa2fae77a0',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#a674a89ff2072c5e57c7f5f07d915d049',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1TriviallySerializable.html#a89624195e0d24768774e98c61d17c779',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out)']]],
- ['serialize_5fand_5fmeasure_10834',['serialize_and_measure',['../classxg_1_1XG.html#aac0ec5744208c54abfc692bf7ff66536',1,'xg::XG']]],
- ['serialize_5fmembers_10835',['serialize_members',['../classxg_1_1XG.html#a99af109d31808040b7f1819c6a236b05',1,'xg::XG::serialize_members()'],['../classhandlegraph_1_1Serializable.html#a79235728e5f1e8fb1c0e19e275a33fff',1,'handlegraph::Serializable::serialize_members()']]],
- ['serialize_5fmembers_5fand_5fmeasure_10836',['serialize_members_and_measure',['../classxg_1_1XG.html#af7c089f5d1342620dd573b2aa4197ca8',1,'xg::XG']]],
- ['serialize_5fsegment_5ftranslation_10837',['serialize_segment_translation',['../structGraphHandler.html#ad8ffb0dac5a43b9c1dee33eba093d02e',1,'GraphHandler']]],
- ['serialize_5fto_5femitter_10838',['serialize_to_emitter',['../classvg_1_1VG.html#a59121c0226c3fd8c328641490bf2fac6',1,'vg::VG']]],
- ['serialize_5fto_5ffile_10839',['serialize_to_file',['../classvg_1_1VG.html#a3522042a3a00ac802d6738d0bec6269c',1,'vg::VG']]],
- ['serialize_5fto_5ffunction_10840',['serialize_to_function',['../classvg_1_1VG.html#ad3187dd6ce750583f6b1a7c32f278d2a',1,'vg::VG']]],
- ['serialize_5fto_5fostream_10841',['serialize_to_ostream',['../classvg_1_1VG.html#a70e67b525bca0f766d7f0170759ed1d0',1,'vg::VG']]],
- ['set_10842',['set',['../structvg_1_1subcommand_1_1BaseArgSpec.html#ae73224926db6d8d7730212d2714e1dcf',1,'vg::subcommand::BaseArgSpec::set()'],['../structvg_1_1subcommand_1_1ArgSpec.html#afd6266196b810cf1b11c88e5ad3fd2a2',1,'vg::subcommand::ArgSpec::set()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad81d797abdd9ece7dece847ad979f80c',1,'vg::subcommand::BaseOptionGroup::set()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a667b46c883efd1b60966679f31bb03fe',1,'vg::subcommand::OptionGroup::set()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a72309d1c25433c7e3a6e3e7dac0930fd',1,'vg::subcommand::GroupedOptionGroup::set()']]],
- ['set_5falignment_5fscores_10843',['set_alignment_scores',['../classvg_1_1AlignerClient.html#a1fde3e4537147030d153d403fd04ec77',1,'vg::AlignerClient::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#adbdd2fabd7a36353526663aede3cb555',1,'vg::AlignerClient::set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#a79424f53b6e4f588da23ea531a600b84',1,'vg::AlignerClient::set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1BaseMapper.html#addc9b0af15050357598c372e135d6a0e',1,'vg::BaseMapper::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1BaseMapper.html#aed94c577ba8f01eb8098d1be74b8d70a',1,'vg::BaseMapper::set_alignment_scores(istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1MinimizerMapper.html#a98a602ac6b9f20d9da825d8a542ceebd',1,'vg::MinimizerMapper::set_alignment_scores()'],['../classvg_1_1MultipathMapper.html#ad897513b9554b2dabebea47cc3f3da9f',1,'vg::MultipathMapper::set_alignment_scores()']]],
- ['set_5fallele_10844',['set_allele',['../classvg_1_1PhasedGenome.html#ad0fdafbc6cb6fbfb576be92f6f6bc17d',1,'vg::PhasedGenome']]],
- ['set_5fannotation_10845',['set_annotation',['../classvg_1_1multipath__alignment__t.html#aebfe1bbda50606c4feb85bb674698c4e',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name)'],['../classvg_1_1multipath__alignment__t.html#a1927cf1ca631a6efb5ed6c83072e2e2c',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, double value)'],['../classvg_1_1multipath__alignment__t.html#a37e9679383b80b3a5028017155d04296',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, bool value)'],['../classvg_1_1multipath__alignment__t.html#aca07d0a515d16b62eca1f1c9ad44ffc9',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, const string &value)'],['../namespacevg.html#adea29af7b94ac90b1db0eacd908511c0',1,'vg::set_annotation(Annotated *annotated, const string &name, const AnnotationType &annotation)'],['../namespacevg.html#a54bcd5d5fc5318bbdbe784f224b906bd',1,'vg::set_annotation(Annotated &annotated, const string &name, const AnnotationType &annotation)']]],
- ['set_5fautomatic_5fmin_5fclustering_5flength_10846',['set_automatic_min_clustering_length',['../classvg_1_1MultipathMapper.html#ac0a6f15f0273faa48ff52a59a08855e1',1,'vg::MultipathMapper']]],
- ['set_5favg_10847',['set_avg',['../classvg_1_1Filter.html#a3629b0035db72bc575a6f0d440b52288',1,'vg::Filter']]],
- ['set_5fbaseline_5ferror_10848',['set_baseline_error',['../classvg_1_1PoissonSupportSnarlCaller.html#a41964acba3d81c26b01f9b00cd49257a',1,'vg::PoissonSupportSnarlCaller']]],
- ['set_5fchain_5fcomponent_10849',['set_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a6d70e8ff87f9e2a2d47511b9aece4980',1,'vg::ZipCode::node_code_t::set_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a05fecca7e22cfd80595143e5b6fe1b74',1,'vg::ZipCode::snarl_code_t::set_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a969b901d95d609ce1a065278ef6bd7fb',1,'vg::ZipCodeForest::sort_value_t::set_chain_component()']]],
- ['set_5fchain_5forder_10850',['set_chain_order',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a33c2b7d50ccefb836fe376dec56c9c09',1,'vg::ZipCodeForest::sort_value_t']]],
- ['set_5fchain_5fvalues_10851',['set_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae0c994c6c86ccbc4b32689baa6183349',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['set_5fchild_5fcount_10852',['set_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04d8cd3924cd20476f71d21690530ee6',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fcircularity_10853',['set_circularity',['../classvg_1_1VG.html#a73c97ce0157b90f95b888e4b6983f5c8',1,'vg::VG::set_circularity()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a9172694447503e35d50093d55e845eb8',1,'handlegraph::MutablePathHandleGraph::set_circularity()']]],
- ['set_5fcode_5ftype_10854',['set_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aeac2169d6f24e91993e1b8c28b8d5a30',1,'vg::ZipCode::snarl_code_t::set_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ab80c26e62009341686000a010bb0d5c3',1,'vg::ZipCodeForest::sort_value_t::set_code_type()']]],
- ['set_5fcompressed_5fannotation_10855',['set_compressed_annotation',['../namespacevg.html#a3f6c363cc3cb03b7379635741d1b0837',1,'vg::set_compressed_annotation(Annotated *annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)'],['../namespacevg.html#a0efd9e2e5d1ab86647910ccd002109cd',1,'vg::set_compressed_annotation(Annotated &annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)']]],
- ['set_5fconnection_10856',['set_connection',['../classvg_1_1subpath__t.html#ae0073c7a92ebfc9ea0acfe7e17837bd1',1,'vg::subpath_t']]],
- ['set_5fconnectivity_10857',['set_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac59bb21ee878d8f2923ac7f8dc857641',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fcrash_5fcontext_10858',['set_crash_context',['../namespacevg.html#ac801de9444375b2f131d3c21d125e83b',1,'vg']]],
- ['set_5fdir_10859',['set_dir',['../namespacevg_1_1temp__file.html#a13270094cd53cedbd540c7fd4412f0d6',1,'vg::temp_file::set_dir()'],['../namespacexg_1_1temp__file.html#a43d250a4567f29ba269e8a3f4c39dbb6',1,'xg::temp_file::set_dir()']]],
- ['set_5fdistance_5fend_5fleft_10860',['set_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a9b8478c75baaf1a65691dd2d72f4c54d',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fdistance_5fend_5fright_10861',['set_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#acb835fdaed8979f3faa044171bfcbe8f',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fdistance_5fstart_5fleft_10862',['set_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2a611cd876f68bb23d5a62babde8bdf9',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fdistance_5fstart_5fright_10863',['set_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3a6fa5c7c47f14100596b3384d72d51f',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fedge_10864',['set_edge',['../classvg_1_1VG.html#ae1131c1ff0a94ed2ec9ef35cb678801b',1,'vg::VG']]],
- ['set_5ffilter_5fmatches_10865',['set_filter_matches',['../classvg_1_1Filter.html#ad45e46ca49dca65ee8e3d838d28d71b6',1,'vg::Filter']]],
- ['set_5ffragment_5flength_5fdistr_5fparams_10866',['set_fragment_length_distr_params',['../classvg_1_1PairedEndMapper.html#a09e89f6da87d25f0ad66fb9eb3139a98',1,'vg::PairedEndMapper']]],
- ['set_5ffrom_5flength_10867',['set_from_length',['../classvg_1_1edit__t.html#aba75c7882507dcced8ca80081b4b504b',1,'vg::edit_t']]],
- ['set_5fhash_5fcolor_10868',['set_hash_color',['../classvg_1_1Viz.html#ab5559043258bf1e1cd4e3a754342cdde',1,'vg::Viz']]],
- ['set_5fhet_5fbias_10869',['set_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a0cb5e2761e2c2feebc901d54a5891454',1,'vg::RatioSupportSnarlCaller']]],
- ['set_5fid_5fincrement_10870',['set_id_increment',['../classvg_1_1VG.html#aebe71b82645b85e73342366cea0a4549',1,'vg::VG::set_id_increment()'],['../classhandlegraph_1_1MutableHandleGraph.html#ab844ab426cd9f289414aca4d8b892ca9',1,'handlegraph::MutableHandleGraph::set_id_increment()']]],
- ['set_5finsertion_5fbias_10871',['set_insertion_bias',['../classvg_1_1PoissonSupportSnarlCaller.html#abeb1d41aaa26a91cb3319cc5fe6b0af0',1,'vg::PoissonSupportSnarlCaller']]],
- ['set_5fintermediate_5ffile_5fkeeping_10872',['set_intermediate_file_keeping',['../classvg_1_1IndexRegistry.html#a983cdafc1b28ea24def5349f90e415eb',1,'vg::IndexRegistry']]],
- ['set_5fintersection_10873',['set_intersection',['../namespacevg.html#a234b2ca417edb50a3c738991fcfc269a',1,'vg']]],
- ['set_5fintron_5flength_5fdistribution_10874',['set_intron_length_distribution',['../classvg_1_1MultipathMapper.html#a8c6768f5299e424b19d569dd077dbafe',1,'vg::MultipathMapper']]],
- ['set_5finverse_10875',['set_inverse',['../classvg_1_1Filter.html#afb65a7ed6bb059f22196415c631680e9',1,'vg::Filter']]],
- ['set_5fis_5freverse_10876',['set_is_reverse',['../classvg_1_1mapping__t.html#ad248204841f7ba0ce4c3604ec138556d',1,'vg::mapping_t::set_is_reverse()'],['../classvg_1_1position__t.html#a3d78fabe1cda0e0243071a36ccd73996',1,'vg::position_t::set_is_reverse()']]],
- ['set_5fis_5freversed_10877',['set_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#aaab7c0874ce7df9a462009840404e8fb',1,'vg::ZipCode::node_code_t::set_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8836324bf0af9142171328634fba592d',1,'vg::ZipCode::snarl_code_t::set_is_reversed()']]],
- ['set_5flast_5fcomponent_10878',['set_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a98cac9a41d2c53554c96084e35a591b5',1,'vg::ZipCode::chain_code_t']]],
- ['set_5flength_10879',['set_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a2ef78836b286d95e1ad7d0b88c55cbaf',1,'vg::ZipCode::node_code_t::set_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a138235f7ccb84dcc25134cf6f200aecb',1,'vg::ZipCode::chain_code_t::set_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a51cb4c8c5a89e591cede7c9a27d77c8b',1,'vg::ZipCode::snarl_code_t::set_length()']]],
- ['set_5flog_5fodds_5fagainst_5fsplice_10880',['set_log_odds_against_splice',['../classvg_1_1MultipathMapper.html#a8902c35e23b24555f94fd2f7d95ef806',1,'vg::MultipathMapper']]],
- ['set_5fmapping_5fquality_10881',['set_mapping_quality',['../classvg_1_1multipath__alignment__t.html#a492c704bcf2ec27123143b83d8218ad9',1,'vg::multipath_alignment_t']]],
- ['set_5fmax_5fmerge_5fsupression_5flength_10882',['set_max_merge_supression_length',['../classvg_1_1MultipathMapper.html#a3db9d73e2a4b296df8df495c028a615b',1,'vg::MultipathMapper']]],
- ['set_5fmin_5fbp_5fedge_5foverride_10883',['set_min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a920ba7030a3946b9b239b1a7f1abbe44',1,'vg::TraversalSupportFinder']]],
- ['set_5fmin_5fdepth_10884',['set_min_depth',['../classvg_1_1Filter.html#a94d0c4f93831a6faf70411dc6caf0ac3',1,'vg::Filter']]],
- ['set_5fmin_5fpercent_5fidentity_10885',['set_min_percent_identity',['../classvg_1_1Filter.html#ae1837a93c7c3575c52dcba37538070f8',1,'vg::Filter']]],
- ['set_5fmin_5fqual_10886',['set_min_qual',['../classvg_1_1Filter.html#a5c3851f5838da69576fd3e59443bb8d3',1,'vg::Filter']]],
- ['set_5fmin_5fsoftclip_5flength_5ffor_5fsplice_10887',['set_min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#ad3848a9b82e967ca119dd94add068597',1,'vg::MultipathMapper']]],
- ['set_5fmin_5fsplice_5flength_10888',['set_min_splice_length',['../classvg_1_1MultipathAlignmentEmitter.html#aa6e3289654a2ebe8ed2b934a1fcd6d40',1,'vg::MultipathAlignmentEmitter']]],
- ['set_5fmin_5fsupports_10889',['set_min_supports',['../classvg_1_1SupportBasedSnarlCaller.html#a3afbd8d1bc78b6716c587b93424db8cb',1,'vg::SupportBasedSnarlCaller']]],
- ['set_5fmy_5fpath_5fposition_5fgraph_10890',['set_my_path_position_graph',['../classvg_1_1Filter.html#a8986008ebcb92629e17da5ed45a23734',1,'vg::Filter']]],
- ['set_5fmy_5fvg_10891',['set_my_vg',['../classvg_1_1Filter.html#a8742f0354b0e40a55ba2dd7270bd197d',1,'vg::Filter']]],
- ['set_5fnested_10892',['set_nested',['../classvg_1_1VCFOutputCaller.html#a35f5b2f9d93ea764e0d8f5f957ba4c3a',1,'vg::VCFOutputCaller']]],
- ['set_5fnext_10893',['set_next',['../classvg_1_1connection__t.html#adc3fded850671e336763eaa0c6d87e78',1,'vg::connection_t::set_next()'],['../classvg_1_1subpath__t.html#a2f0c0e1b1e509de732a1318919af0177',1,'vg::subpath_t::set_next()']]],
- ['set_5fnode_5fid_10894',['set_node_id',['../classvg_1_1mapping__t.html#a3101ac21e398f36c0367a89b20360cd0',1,'vg::mapping_t::set_node_id()'],['../classvg_1_1position__t.html#a5e2f0de1d8da70bb8b233522597bd02b',1,'vg::position_t::set_node_id()']]],
- ['set_5foffset_10895',['set_offset',['../structhaplo_1_1haplo__DP__rectangle.html#a9ca4ea25d72d1a40b9a0e1a170e88274',1,'haplo::haplo_DP_rectangle::set_offset()'],['../classvg_1_1position__t.html#ad34d5af7aab58a425f33faa2358ef57e',1,'vg::position_t::set_offset()']]],
- ['set_5foption_5fvalue_10896',['set_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abdc58a9c90f9adbcac68d3e18f6c7d36',1,'vg::subcommand::BaseOptionGroup']]],
- ['set_5fpaired_5fall_10897',['set_paired_all',['../structvg_1_1Counts.html#a038f57bbb1cabd1f83b544c22562a0d9',1,'vg::Counts']]],
- ['set_5fpaired_5fany_10898',['set_paired_any',['../structvg_1_1Counts.html#ad4e3e7b118ed1ec1286d933a57bdbf23',1,'vg::Counts']]],
- ['set_5fpath_5fposition_10899',['set_path_position',['../classvg_1_1Surjector.html#ac4e7823cc2ce4b65bb8910ef2c1dcbee',1,'vg::Surjector']]],
- ['set_5fprefix_10900',['set_prefix',['../classvg_1_1IndexRegistry.html#aefc2da48af951d3b300ee0b5c70559c3',1,'vg::IndexRegistry']]],
- ['set_5fprefix_5fsum_5for_5fidentifier_10901',['set_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a0c99221572a9dce4051fa68a79bb540f',1,'vg::ZipCode::node_code_t::set_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8a66d4f3fba23bebe13618b0d45988a4',1,'vg::ZipCode::snarl_code_t::set_prefix_sum_or_identifier()']]],
- ['set_5fprev_5fidx_10902',['set_prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#ad1c78747473f9b8816c459949b8b8e8e',1,'haplo::haplo_DP_rectangle']]],
- ['set_5fquality_10903',['set_quality',['../classvg_1_1multipath__alignment__t.html#a2ff40ca9f44290aeb5406764ccbb5ebf',1,'vg::multipath_alignment_t']]],
- ['set_5fraw_5fchain_5fcomponent_10904',['set_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a32b61e2274b266a217cebace47e2907a',1,'vg::ZipCode::node_code_t::set_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab4c8a0b7d2e5b20bab6ff83558581a4d',1,'vg::ZipCode::snarl_code_t::set_raw_chain_component()']]],
- ['set_5fraw_5fchild_5fcount_10905',['set_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ace304ea5d619189a001274a3c117a97b',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fcode_5ftype_10906',['set_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a4b2441552754d8c09003a86ed412af6e',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fconnectivity_10907',['set_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a7e9fc82b6947464a05b05ad154a706dd',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fraw_5fdistance_5fend_5fleft_10908',['set_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6d9d20da8c7cee397bc621395ebb0595',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fdistance_5fend_5fright_10909',['set_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34782c4f89ca5b5ed549c086d782a49a',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fdistance_5fstart_5fleft_10910',['set_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6ef05afc876f9d157a4a22ece67ec14b',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fdistance_5fstart_5fright_10911',['set_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3c42e8e885b205135c84167f3d0c30f9',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fis_5freversed_10912',['set_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ce29ebd996f8894ed6942633fb387b9',1,'vg::ZipCode::node_code_t::set_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af7cdb5f02946631384bab58c2732c305',1,'vg::ZipCode::snarl_code_t::set_raw_is_reversed()']]],
- ['set_5fraw_5flast_5fcomponent_10913',['set_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a389422a0482e9a0fe88b77bacc88b2fa',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fraw_5flength_10914',['set_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a9eaa33f8ee594c5fe686c4e5e0bfbe30',1,'vg::ZipCode::node_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a373aeb1528f44cf694a7711ab827d088',1,'vg::ZipCode::chain_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6f15f89fa329bcd06088318bb17bbdb2',1,'vg::ZipCode::snarl_code_t::set_raw_length()']]],
- ['set_5fraw_5fprefix_5fsum_5for_5fidentifier_10915',['set_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a02b5011800febaebbef6c517fc08320e',1,'vg::ZipCode::node_code_t::set_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a38cb2f04ee15fc31ec69d5ef06f45ac1',1,'vg::ZipCode::snarl_code_t::set_raw_prefix_sum_or_identifier()']]],
- ['set_5fraw_5frecord_5foffset_10916',['set_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5a5034d3c583b9220450bcc2da59f31f',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fraw_5fsnarl_5frank_5for_5fidentifier_10917',['set_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a214ccf14cf2a287d7756d10036ce9bff',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fread_5f1_5fadapter_10918',['set_read_1_adapter',['../classvg_1_1MultipathMapper.html#aaf7ee8334193018b945900b00cec8826',1,'vg::MultipathMapper']]],
- ['set_5fread_5f2_5fadapter_10919',['set_read_2_adapter',['../classvg_1_1MultipathMapper.html#a1c1674e89e4702168e75bca6fdb4d0bd',1,'vg::MultipathMapper']]],
- ['set_5fread_5fcoverage_10920',['set_read_coverage',['../classvg_1_1MultipathMapper.html#a2ce30f7fe70325b6101356f5eb67df3d',1,'vg::MultipathMapper']]],
- ['set_5fread_5fgroup_10921',['set_read_group',['../classvg_1_1MultipathAlignmentEmitter.html#ad772e7a7315be2a57899c234116de800',1,'vg::MultipathAlignmentEmitter']]],
- ['set_5frecord_5foffset_10922',['set_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a33b431da2b73e995db51480fd2e5385b',1,'vg::ZipCode::snarl_code_t']]],
- ['set_5fregion_10923',['set_region',['../classvg_1_1VcfBuffer.html#a0a636a74fef67c3cfd59730db3ed427c',1,'vg::VcfBuffer::set_region()'],['../classvg_1_1WindowedVcfBuffer.html#ab6c81f821d5ddcace1e67e7081793142',1,'vg::WindowedVcfBuffer::set_region()']]],
- ['set_5fremove_5ffailing_5fedits_10924',['set_remove_failing_edits',['../classvg_1_1Filter.html#ab91fdad4a96917a43f1fed85e11a9645',1,'vg::Filter']]],
- ['set_5fsample_5fname_10925',['set_sample_name',['../classvg_1_1MultipathAlignmentEmitter.html#a398cd239c156944100299fc5babb6194',1,'vg::MultipathAlignmentEmitter']]],
- ['set_5fscore_10926',['set_score',['../classvg_1_1connection__t.html#ab7e71cc31834606883ce7fee437bdd7b',1,'vg::connection_t::set_score()'],['../classvg_1_1subpath__t.html#a7229edbbe9e72084b114bd03079cc105',1,'vg::subpath_t::set_score()'],['../namespacevg.html#a3b05a1318d7be5ecf3547a3eca837618',1,'vg::set_score()']]],
- ['set_5fsequence_10927',['set_sequence',['../classvg_1_1multipath__alignment__t.html#a5cabf8eec673f7aaf7d28add560a7e32',1,'vg::multipath_alignment_t::set_sequence()'],['../classvg_1_1edit__t.html#aa2a77df9db620c8500a3eb4802229f43',1,'vg::edit_t::set_sequence()']]],
- ['set_5fshow_5fprogress_10928',['set_show_progress',['../classvg_1_1GraphCaller.html#a1005b4de9fde3d23adcd1d35f8fece09',1,'vg::GraphCaller']]],
- ['set_5fsnarl_5frank_5for_5fidentifier_10929',['set_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a43ebf63adc3f81a82dd4b9bb77be2772',1,'vg::ZipCode::chain_code_t']]],
- ['set_5fsnarl_5fvalues_10930',['set_snarl_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a858ed22ff1cba852000f4815bd03e20f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['set_5fsoft_5fclip_5flimit_10931',['set_soft_clip_limit',['../classvg_1_1Filter.html#a8e69a6bc40641a3377dd60f44ec52816',1,'vg::Filter']]],
- ['set_5fsort_5fvalue_10932',['set_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aa1ea92740944abf659a9080acc7fa0b3',1,'vg::ZipCodeForest::sort_value_t']]],
- ['set_5fsource_5fpaths_10933',['set_source_paths',['../classvg_1_1Sampler.html#ab217a74d97bc905480c236ab66d30232',1,'vg::Sampler']]],
- ['set_5fsplit_5fread_5flimit_10934',['set_split_read_limit',['../classvg_1_1Filter.html#a377d6661a880d4d3798e8780d61d6db0',1,'vg::Filter']]],
- ['set_5fstart_10935',['set_start',['../classvg_1_1multipath__alignment__t.html#a9230aa70e0c93066e0c8f9f4c4af28fa',1,'vg::multipath_alignment_t']]],
- ['set_5fsupport_5fswitch_5fthreshold_10936',['set_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a53940205edddd5d3bb379b82ede4f74f',1,'vg::TraversalSupportFinder']]],
- ['set_5fsystem_5fdir_10937',['set_system_dir',['../namespacevg_1_1temp__file.html#ac061a6d187921157d4e62930445996e8',1,'vg::temp_file']]],
- ['set_5ftags_10938',['set_tags',['../gbwt__main_8cpp.html#ab3856151a0825f396467961305716704',1,'gbwt_main.cpp']]],
- ['set_5ftarget_5fmemory_5fusage_10939',['set_target_memory_usage',['../classvg_1_1IndexRegistry.html#aee06106e4888a5a17d12fa10f1e87893',1,'vg::IndexRegistry']]],
- ['set_5fto_5flength_10940',['set_to_length',['../classvg_1_1edit__t.html#a9b38a79f561f60c377c35e186c5cfd96',1,'vg::edit_t']]],
- ['set_5ftranslation_10941',['set_translation',['../classvg_1_1VCFOutputCaller.html#a918bfde23f9f6afacec9b10319030414',1,'vg::VCFOutputCaller']]],
- ['set_5fvalue_10942',['set_value',['../structvg_1_1subcommand_1_1ArgSpec.html#a1e31767c05c4a085a3b8087067af70c4',1,'vg::subcommand::ArgSpec::set_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a25817ff171a0199cf4e21fee15261f14',1,'vg::subcommand::ValueArgSpec::set_value()']]],
- ['set_5fwindow_5flength_10943',['set_window_length',['../classvg_1_1Filter.html#adb96fca6a301e45c84b010f5461440a9',1,'vg::Filter']]],
- ['setk_10944',['setK',['../classvg_1_1FlowTraversalFinder.html#adf6216e25b6f61a09aa13816eafcd6e3',1,'vg::FlowTraversalFinder']]],
- ['sha1head_10945',['sha1head',['../namespacevg.html#a6821cd887e206752c50c1a7be764d1f5',1,'vg']]],
- ['sha1sum_10946',['sha1sum',['../namespacevg.html#a0cada7d579d914675f53490e0488ab53',1,'vg']]],
- ['shallow_5fcontents_10947',['shallow_contents',['../classvg_1_1SnarlManager.html#afb7f6b946d3ec05ed619e09491e0a92d',1,'vg::SnarlManager']]],
- ['share_5fterminal_5fpositions_10948',['share_terminal_positions',['../classvg_1_1MultipathMapper.html#aaff4140e7e711a25b1eb284d7c830c2c',1,'vg::MultipathMapper']]],
- ['short_5fmode_5fname_10949',['short_mode_name',['../prune__main_8cpp.html#adf85e917657920f23dce6cefc2ecd2b9',1,'prune_main.cpp']]],
- ['shortest_5fcycle_5flength_10950',['shortest_cycle_length',['../namespacevg_1_1algorithms.html#acfe6f985e8bedbad1b33861c62379772',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph, const handle_t &source)'],['../namespacevg_1_1algorithms.html#a012fced2754c445ec404ff5420018982',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph)']]],
- ['shortest_5fcycle_5flength_5finternal_10951',['shortest_cycle_length_internal',['../namespacevg_1_1algorithms.html#aa87ca8c58307fdb47d448deb2ec43389',1,'vg::algorithms']]],
- ['shortest_5fseq_5fpaths_10952',['shortest_seq_paths',['../classvg_1_1BandedGlobalAligner.html#a7156058732c9d6f40226609f650944a2',1,'vg::BandedGlobalAligner']]],
- ['show_5fstructure_10953',['show_structure',['../classvg_1_1Packer.html#a4aacf109dc6290d39630e5b25020004e',1,'vg::Packer']]],
- ['shuffledpairs_10954',['ShuffledPairs',['../classvg_1_1ShuffledPairs.html#a7143ff811c0359854ac091749b1f5642',1,'vg::ShuffledPairs']]],
- ['sides_5fcontext_10955',['sides_context',['../classvg_1_1VG.html#ad363c6c82e88dcb1b88d05ff55074ed6',1,'vg::VG']]],
- ['sides_5ffrom_10956',['sides_from',['../classvg_1_1VG.html#ac670f3c729f93ebaa7c8bd5063225597',1,'vg::VG::sides_from(NodeSide side)'],['../classvg_1_1VG.html#a95c975ed419a0873c894cef7a2f2d3ba',1,'vg::VG::sides_from(nid_t id)']]],
- ['sides_5fof_10957',['sides_of',['../classvg_1_1VG.html#a030b75d2ad50905cc01fe4b7223cbb83',1,'vg::VG']]],
- ['sides_5fto_10958',['sides_to',['../classvg_1_1VG.html#a1a156ac1e1fde520bae82850105c6c66',1,'vg::VG::sides_to(NodeSide side)'],['../classvg_1_1VG.html#a68733706482bf7b2627be32438160af3',1,'vg::VG::sides_to(nid_t id)']]],
- ['signature_10959',['signature',['../namespacevg.html#a2616dde2763b947a15ac562fd631e688',1,'vg::signature(const Alignment &aln)'],['../namespacevg.html#a134fc6762c4b66dd4847078b0ddbfdd6',1,'vg::signature(const Alignment &aln1, const Alignment &aln2)']]],
- ['simple_5fcomponents_10960',['simple_components',['../namespacehandlegraph_1_1algorithms.html#acc16afc14f0a9dd0a34a4c173b229a4b',1,'handlegraph::algorithms']]],
- ['simple_5foffsets_5fin_5fpaths_10961',['simple_offsets_in_paths',['../namespacevg_1_1algorithms.html#a9ddb73ef3cf5a8891aa82001f272c3c4',1,'vg::algorithms']]],
- ['simple_5fsds_5fload_10962',['simple_sds_load',['../structvg_1_1Haplotypes_1_1Subchain.html#a9dfc087f0bada7635e975b6c8e8479a8',1,'vg::Haplotypes::Subchain::simple_sds_load()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a34163c2bf756a469dd6bba7880836f82',1,'vg::Haplotypes::TopLevelChain::simple_sds_load()'],['../classvg_1_1Haplotypes.html#a908ed1a2f1147a2162051be87e5ba389',1,'vg::Haplotypes::simple_sds_load()']]],
- ['simple_5fsds_5fserialize_10963',['simple_sds_serialize',['../structvg_1_1Haplotypes_1_1Subchain.html#ab30088a7f754d1bfb579773000ac73e0',1,'vg::Haplotypes::Subchain::simple_sds_serialize()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ad5f88539013b3d1c0caed224550e3a06',1,'vg::Haplotypes::TopLevelChain::simple_sds_serialize()'],['../classvg_1_1Haplotypes.html#a3a5a36c107109c893cf382064ad9ea69',1,'vg::Haplotypes::simple_sds_serialize()']]],
- ['simple_5fsds_5fsize_10964',['simple_sds_size',['../structvg_1_1Haplotypes_1_1Subchain.html#a5f1258caf8b13bd3880f2db6e2967908',1,'vg::Haplotypes::Subchain::simple_sds_size()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#afb004505c7fcc83e89b15c229da33a03',1,'vg::Haplotypes::TopLevelChain::simple_sds_size()'],['../classvg_1_1Haplotypes.html#ac0ebaa605235ee2b6f62c084cfdc6126',1,'vg::Haplotypes::simple_sds_size()']]],
- ['simplify_10965',['simplify',['../classvg_1_1RareVariantSimplifier.html#af17e24fe2acb6700bb7b6d39514af7af',1,'vg::RareVariantSimplifier::simplify()'],['../classvg_1_1SmallSnarlSimplifier.html#a9abe74e35298d7e22f13039a4c6ea5ba',1,'vg::SmallSnarlSimplifier::simplify()'],['../namespacevg.html#a486054f13a4dc43e37c0f0131f6a51ad',1,'vg::simplify(const Alignment &a, bool trim_internal_deletions)'],['../namespacevg.html#a86653c665afe3c8932f60cc39163e202',1,'vg::simplify(const Path &p, bool trim_internal_deletions)'],['../namespacevg.html#a9514446da89671007ae40e420c1297d7',1,'vg::simplify(const Mapping &m, bool trim_internal_deletions)']]],
- ['simplify_5fcigar_10966',['simplify_cigar',['../namespacevg.html#a553c3fcfd7de2e51f41a6f174c313947',1,'vg']]],
- ['simplify_5fcomplicated_5fmultipath_5falignment_10967',['simplify_complicated_multipath_alignment',['../classvg_1_1MultipathMapper.html#a92de908372ba0730cfe40638218d815f',1,'vg::MultipathMapper']]],
- ['simplify_5ffiltered_5fedits_10968',['simplify_filtered_edits',['../namespacevg.html#ad6a42e8ba843cd728b9f84738756b30e',1,'vg']]],
- ['simplify_5fonce_10969',['simplify_once',['../classvg_1_1SmallSnarlSimplifier.html#afc5525b90ddf851ee7d43a6476acd99d',1,'vg::SmallSnarlSimplifier']]],
- ['simplify_5fsiblings_10970',['simplify_siblings',['../namespacevg_1_1algorithms.html#a9e4cebdfc1e901db4588c4612653df96',1,'vg::algorithms']]],
- ['single_5fstranded_5forientation_10971',['single_stranded_orientation',['../namespacehandlegraph_1_1algorithms.html#a61255fd1513da53219871ea01283e360',1,'handlegraph::algorithms']]],
- ['size_10972',['size',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#acdf72785ba0579f5985b227ef1ccd48b',1,'vg::DozeuInterface::OrderedGraph::size()'],['../structvg_1_1MatchPos_1_1PathList.html#aee5bea8ee39007b6bf5be7ea72d3695b',1,'vg::MatchPos::PathList::size()'],['../classvg_1_1WFATree.html#ad5da24b01eb588c58e07419dbd5eaca4',1,'vg::WFATree::size()'],['../classvg_1_1SnarlState.html#a02f1d46e384b6617ad43f2390fe0ef98',1,'vg::SnarlState::size()'],['../structhaplo_1_1int__itvl__t.html#acee0f4db1fc8cdfd535e6d181093f01f',1,'haplo::int_itvl_t::size()'],['../structhaplo_1_1gbwt__thread__t.html#a5d4d9e80558ff8e4dbab247cc9782a0c',1,'haplo::gbwt_thread_t::size()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a979f8d5623d9040439803c13e7ebf9b6',1,'haplo::linear_haplo_structure::SNVvector::size()'],['../classvg_1_1HandleGraphNodeSet.html#ae66b372aeb3110162c4d9b5c85e3a28d',1,'vg::HandleGraphNodeSet::size()'],['../classvg_1_1MultipathAlignmentGraph.html#a4ec09c91391cfb06c1c9eea132ce4246',1,'vg::MultipathAlignmentGraph::size()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a028494e0f37785dc8a39de6c4f2876a4',1,'vg::Option< vector< Item >, Parser >::size()'],['../classvg_1_1Paths.html#ac2fb517ea95acdd1eb378bf104c16912',1,'vg::Paths::size()'],['../classvg_1_1SmallBitset.html#a1b3ff28863a53eae0c4b47ff854b4d2d',1,'vg::SmallBitset::size()'],['../classvg_1_1SparseUnionFind.html#a85bfb663efac82a593533bd58890c615',1,'vg::SparseUnionFind::size()'],['../structvg_1_1VectorView.html#a62ec6d3c6520fa2b6d70a23abc473e44',1,'vg::VectorView::size()'],['../classvg_1_1VG.html#a9e3720ce267c8167ce679a015063dab6',1,'vg::VG::size()'],['../classvg_1_1ZipCodeCollection.html#ae1aab3360a759d00d8c43e921dba92f6',1,'vg::ZipCodeCollection::size()']]],
- ['sizelimitexceededexception_10973',['SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html#aeb5d2801f912937112f0e638717156a8',1,'vg::SizeLimitExceededException']]],
- ['skip_10974',['Skip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#af3849b5292df406dec93738920615987',1,'vg::io::BlockedGzipInputStream']]],
- ['slope_10975',['slope',['../namespacevg.html#ad477b45059373004136e69022e802e0b',1,'vg']]],
- ['small_10976',['small',['../classvg_1_1SmallBitset.html#a8e787b217e48311220e91f7fd191fe14',1,'vg::SmallBitset']]],
- ['smallbitset_10977',['SmallBitset',['../classvg_1_1SmallBitset.html#afcefdbe6a3f708ded8d874537ba0616f',1,'vg::SmallBitset::SmallBitset()'],['../classvg_1_1SmallBitset.html#a5c0e06b1e0482ff98adde62fdf9476f2',1,'vg::SmallBitset::SmallBitset(size_t n)'],['../classvg_1_1SmallBitset.html#ae09de51997e95c9c7c85650748e6d9ab',1,'vg::SmallBitset::SmallBitset(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#a59da25f6a4ae99cc7ff12936930ad5e3',1,'vg::SmallBitset::SmallBitset(SmallBitset &&another)']]],
- ['smallsnarlsimplifier_10978',['SmallSnarlSimplifier',['../classvg_1_1SmallSnarlSimplifier.html#ae19c2fcf37820ed9112671fbc7e64033',1,'vg::SmallSnarlSimplifier']]],
- ['smart_5falign_10979',['smart_align',['../classvg_1_1VariantAdder.html#ad3c7e7030142e70f27bc9f0bc42c2cce',1,'vg::VariantAdder']]],
- ['smellslikegzip_10980',['SmellsLikeGzip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa45ae9d5a0c1689efa567d573ad5747c',1,'vg::io::BlockedGzipInputStream']]],
- ['sn_5fdeletion_5fbetween_5fref_10981',['sn_deletion_between_ref',['../structhaplo_1_1linear__haplo__structure.html#aa6e425ddac2acb985a1364dd91a2f948',1,'haplo::linear_haplo_structure']]],
- ['snarl_5fboundary_5findex_10982',['snarl_boundary_index',['../classvg_1_1SnarlManager.html#a77a449f2f85f37760da1a7182cc1e08b',1,'vg::SnarlManager']]],
- ['snarl_5fend_5findex_10983',['snarl_end_index',['../classvg_1_1SnarlManager.html#a1fd57d0de5eec34fc037ad0afbdfcb77',1,'vg::SnarlManager']]],
- ['snarl_5fnumber_10984',['snarl_number',['../classvg_1_1SnarlManager.html#aa779c0eaea2403d9c36761243a7f9262',1,'vg::SnarlManager']]],
- ['snarl_5fsharing_5fend_10985',['snarl_sharing_end',['../classvg_1_1SnarlManager.html#a2ca9eb75908bfcc4cfac8b241236295b',1,'vg::SnarlManager']]],
- ['snarl_5fsharing_5fstart_10986',['snarl_sharing_start',['../classvg_1_1SnarlManager.html#a43ecf19c495295c45ca828d499651481',1,'vg::SnarlManager']]],
- ['snarl_5fstart_5findex_10987',['snarl_start_index',['../classvg_1_1SnarlManager.html#a10a771b6ada139c76e1b435ee301fdb8',1,'vg::SnarlManager']]],
- ['snarldistanceindexclusterer_10988',['SnarlDistanceIndexClusterer',['../classvg_1_1SnarlDistanceIndexClusterer.html#a0333d80b03665df71c7d448b7cfb0b06',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a66a56a78a0500f79258057cd3d688966',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a2275f78a71459c60e56929b106d4ed46',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#ae2d9080f0e9ddf775de34ae3aaab7019',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index)']]],
- ['snarlgraph_10989',['SnarlGraph',['../classvg_1_1SnarlGraph.html#a0a6e447620c3a37ca37345854330ffd3',1,'vg::SnarlGraph']]],
- ['snarlmanager_10990',['SnarlManager',['../classvg_1_1SnarlManager.html#a1037a2341484dc7b54a68cd7207d34b8',1,'vg::SnarlManager::SnarlManager(SnarlIterator begin, SnarlIterator end)'],['../classvg_1_1SnarlManager.html#a61b2b80def0128deea2d2da4886b955e',1,'vg::SnarlManager::SnarlManager(istream &in)'],['../classvg_1_1SnarlManager.html#afe16f481e15e098c885d63f47eceb59c',1,'vg::SnarlManager::SnarlManager(const function< void(const function< void(Snarl &)> &)> &for_each_snarl)'],['../classvg_1_1SnarlManager.html#a43b0ecd9e372556380231f29788948d5',1,'vg::SnarlManager::SnarlManager()=default'],['../classvg_1_1SnarlManager.html#a8e61adc170e3d9241a723ca7593883da',1,'vg::SnarlManager::SnarlManager(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#a7549f1ed7e0e02ae36f172ab5f1d3dbd',1,'vg::SnarlManager::SnarlManager(SnarlManager &&other)=default']]],
- ['snarlmindistance_10991',['SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html#adc8c303e683b90d923c522790355abad',1,'vg::SnarlMinDistance::SnarlMinDistance()=delete'],['../classvg_1_1SnarlMinDistance.html#aa8efbd4c363589a72da76621b5b4330d',1,'vg::SnarlMinDistance::SnarlMinDistance(SnarlDistanceIndex &distance_index)']]],
- ['snarlorienteddistancemeasurer_10992',['SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a81db285adff1ae830dcaf2511652e17a',1,'vg::SnarlOrientedDistanceMeasurer']]],
- ['snarlstate_10993',['SnarlState',['../classvg_1_1SnarlState.html#a14db6ed9f20936f71de90d0d12f92468',1,'vg::SnarlState']]],
- ['snarltreenodeproblem_10994',['SnarlTreeNodeProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a119a5148780cd1bf7dd073e91974f255',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, const SnarlDistanceIndex &distance_index, const SeedCache *seed, size_t zipcode_depth)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a26ebc81ba9dff9a498a2d222ff72291c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, bool is_reversed_in_parent, size_t node_length, size_t prefix_sum, size_t component, const SeedCache *seed, size_t zipcode_depth)']]],
- ['sniff_5fmagic_10995',['sniff_magic',['../classvg_1_1io_1_1Registry.html#aea2d7b2c4852a48417eeac861974b9c1',1,'vg::io::Registry']]],
- ['sniff_5ftag_10996',['sniff_tag',['../classvg_1_1io_1_1MessageIterator.html#ac9b3fff8dbbff744fe1ff60805af1c20',1,'vg::io::MessageIterator::sniff_tag(istream &stream)'],['../classvg_1_1io_1_1MessageIterator.html#aabd024a7358bae988de897aebff39645',1,'vg::io::MessageIterator::sniff_tag(::google::protobuf::io::ZeroCopyInputStream &stream)']]],
- ['snvs_10997',['SNVs',['../structhaplo_1_1linear__haplo__structure.html#acde3b4cb1fc9eae479ee626bb0916992',1,'haplo::linear_haplo_structure']]],
- ['soft_5fclip_5ffilter_10998',['soft_clip_filter',['../classvg_1_1Filter.html#aff62aad43f70cd8de756bdbdf94b962d',1,'vg::Filter']]],
- ['softclip_5fend_10999',['softclip_end',['../namespacevg.html#a05d6d0388148a996d9423524fa4bcc91',1,'vg::softclip_end(const Alignment &alignment)'],['../namespacevg.html#aa84e4c417206a9b3a910dfde0fec3857',1,'vg::softclip_end(const Mapping &mapping)']]],
- ['softclip_5fstart_11000',['softclip_start',['../namespacevg.html#a90f2af92a34fdf5fb4ddfee8f8880b48',1,'vg::softclip_start(const Alignment &alignment)'],['../namespacevg.html#a9fe66eebecbc5017b05c9044413b2b4e',1,'vg::softclip_start(const Mapping &mapping)']]],
- ['softclip_5ftrim_11001',['softclip_trim',['../namespacevg.html#a947760b26fa8669d55f2f420174a578c',1,'vg']]],
- ['sort_11002',['sort',['../classvg_1_1StreamSorter.html#a8372ac35036ca7723bfc90a686115166',1,'vg::StreamSorter::sort()'],['../classvg_1_1VG.html#a902d516631c77d074aa2a11ae70a6957',1,'vg::VG::sort()']]],
- ['sort_5fanchor_5findexes_11003',['sort_anchor_indexes',['../namespacevg_1_1algorithms.html#aaeeaa766337fc50f0a9b4d3214271923',1,'vg::algorithms']]],
- ['sort_5fand_5fcompute_5fmapping_5fquality_11004',['sort_and_compute_mapping_quality',['../classvg_1_1MultipathMapper.html#a2994778198719e960d1a2875fa0815e8',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< multipath_alignment_t > &multipath_alns, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#afcc5ceaad2a3f21c4c38beb05c59f474',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< pair< size_t, size_t >> *duplicate_pairs_out=nullptr, vector< double > *pair_multiplicities=nullptr) const']]],
- ['sort_5fby_5fid_11005',['sort_by_id',['../namespacevg.html#af25c227066a422379ff06d81b5990865',1,'vg']]],
- ['sort_5fby_5fid_5fdedup_5fand_5fclean_11006',['sort_by_id_dedup_and_clean',['../namespacevg.html#a984c1d2199f90f58677096772b870390',1,'vg']]],
- ['sort_5fby_5fmapping_5frank_11007',['sort_by_mapping_rank',['../classvg_1_1Paths.html#a2970302cae3a54ef7f4296dbf49266fd',1,'vg::Paths']]],
- ['sort_5fcompact_5fnodes_11008',['sort_compact_nodes',['../classvg_1_1Transcriptome.html#af7de0784cde3273b344757b81d9bffd5',1,'vg::Transcriptome']]],
- ['sort_5fedges_5fby_5fid_11009',['sort_edges_by_id',['../namespacevg.html#a90cc117e3ac781c77cf8fdaa7802048b',1,'vg']]],
- ['sort_5fminimizers_5fby_5fscore_11010',['sort_minimizers_by_score',['../classvg_1_1MinimizerMapper.html#ad72222c1d644b6f676c91511b4b36789',1,'vg::MinimizerMapper']]],
- ['sort_5fnodes_5fby_5fid_11011',['sort_nodes_by_id',['../namespacevg.html#afb37b16823e6e26cfd8571a1bb621651',1,'vg']]],
- ['sort_5fone_5finterval_11012',['sort_one_interval',['../classvg_1_1ZipCodeForest.html#a499f52fbb75374e2dc06ce7998ad8fd6',1,'vg::ZipCodeForest']]],
- ['sort_5fpair_5fby_5fsecond_11013',['sort_pair_by_second',['../namespacevg.html#a47c7102baf9a07b2c701e9937d53351f',1,'vg']]],
- ['sort_5fpath_5foffsets_11014',['sort_path_offsets',['../namespacevg_1_1algorithms.html#ad8e5913b682c7c14f119543eca7e7548',1,'vg::algorithms']]],
- ['sort_5fpermutation_11015',['sort_permutation',['../namespacevg.html#ae031408254f8c4031ba0b632f5456059',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end, const std::function< bool(const typename Iterator::value_type &, const typename Iterator::value_type &)> &comparator)'],['../namespacevg.html#ab03fad9d3c71a090606afbe1ef22ce71',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end)']]],
- ['sort_5fshuffling_5fties_11016',['sort_shuffling_ties',['../namespacevg.html#afe3de0ca79c815a4eaf63df34805f6d0',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp, LazyRNG &rng)'],['../namespacevg.html#aa071bccfee3a9078930f2c385e8dda20',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp)']]],
- ['sort_5ftranscript_5fpaths_5fby_5fname_11017',['sort_transcript_paths_by_name',['../namespacevg.html#aaddbcf35ad2ff899bf2ae0caf901f778',1,'vg']]],
- ['sort_5ftranscript_5fpaths_5fupdate_5fcopy_5fid_11018',['sort_transcript_paths_update_copy_id',['../classvg_1_1Transcriptome.html#af8caf627ac2480d7439231a2d26162eb',1,'vg::Transcriptome']]],
- ['sort_5fvalue_5ft_11019',['sort_value_t',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ac93c5ff7c1b231cd78122b1e1f009aae',1,'vg::ZipCodeForest::sort_value_t::sort_value_t()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a42776d8b3810278dfb5830307fe8190c',1,'vg::ZipCodeForest::sort_value_t::sort_value_t(size_t sort_value, ZipCode::code_type_t code_type, size_t chain_order)']]],
- ['sorted_5fid_5franges_11020',['sorted_id_ranges',['../namespacevg_1_1algorithms.html#a64bd6b3ff0d2e22bf752e29e3522a98d',1,'vg::algorithms']]],
- ['sourcesinkoverlay_11021',['SourceSinkOverlay',['../classvg_1_1SourceSinkOverlay.html#a6eaf260d8530ba866753bb3bcb612e15',1,'vg::SourceSinkOverlay']]],
- ['sparseunionfind_11022',['SparseUnionFind',['../classvg_1_1SparseUnionFind.html#aabd42adac47a3df51b0dfb55d7cde0f4',1,'vg::SparseUnionFind']]],
- ['spliced_5fcigar_5fagainst_5fpath_11023',['spliced_cigar_against_path',['../classvg_1_1SplicedHTSAlignmentEmitter.html#ac447d6f996b11f12c3b8b2267ff4110e',1,'vg::SplicedHTSAlignmentEmitter']]],
- ['spliced_5fsurject_11024',['spliced_surject',['../classvg_1_1Surjector.html#a8418e7a55b6b53456c80cbcf937406b5',1,'vg::Surjector']]],
- ['splicedhtsalignmentemitter_11025',['SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a8e546a34b4f2155fe6fb916123a0135d',1,'vg::SplicedHTSAlignmentEmitter']]],
- ['spliceregion_11026',['SpliceRegion',['../classvg_1_1SpliceRegion.html#a3ca49fd7bedbe0b97117f87f7a5edba4',1,'vg::SpliceRegion::SpliceRegion(const pos_t &seed_pos, bool search_left, int64_t search_dist, const HandleGraph &graph, const DinucleotideMachine &dinuc_machine, const SpliceStats &splice_stats)'],['../classvg_1_1SpliceRegion.html#a5935bbc5e17cceae08ee9ef0b91b9abe',1,'vg::SpliceRegion::SpliceRegion()=default']]],
- ['splicestats_11027',['SpliceStats',['../classvg_1_1SpliceStats.html#ac508ff2143cf8296531945e7674702bc',1,'vg::SpliceStats::SpliceStats(const GSSWAligner &scorer)'],['../classvg_1_1SpliceStats.html#a1808c3a4e73d0be56de7caca04142b01',1,'vg::SpliceStats::SpliceStats(const vector< tuple< string, string, double >> &motifs, const vector< double > &lognormal_mixture_weights, const vector< pair< double, double >> &lognormal_component_params, const GSSWAligner &scorer)']]],
- ['split_11028',['split',['../classvg_1_1BitString.html#af826e3c7bce1aeada3f989b1b7d1bcc5',1,'vg::BitString']]],
- ['split_5fdelims_11029',['split_delims',['../namespacevg.html#acb2577b9163299f775898c17bcd3f72d',1,'vg::split_delims(const std::string &s, const std::string &delims, std::vector< std::string > &elems, size_t max_cuts)'],['../namespacevg.html#a335fce1edcad06f9840edcfad2c53e34',1,'vg::split_delims(const std::string &s, const std::string &delims, size_t max_cuts)']]],
- ['split_5fext_11030',['split_ext',['../namespacevg.html#a984d142cea24f43a1025bf7bb7b48a53',1,'vg']]],
- ['split_5fmulticomponent_5falignments_11031',['split_multicomponent_alignments',['../classvg_1_1MultipathMapper.html#af91f97b8331648b4df7587a461ca36b2',1,'vg::MultipathMapper::split_multicomponent_alignments(vector< multipath_alignment_t > &multipath_alns_out, const Alignment *alignment=nullptr, vector< clustergraph_t > *cluster_graphs=nullptr, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#a9257a7f9cc75ddd76a8daef803f2d031',1,'vg::MultipathMapper::split_multicomponent_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &multiplicities) const']]],
- ['split_5fread_5ffilter_11032',['split_read_filter',['../classvg_1_1Filter.html#a0bc2a72604a0cb134c1f5bad7889a1bf',1,'vg::Filter']]],
- ['split_5fsplice_5fsegment_11033',['split_splice_segment',['../namespacevg.html#aee945465384e60bdda619684ffca2ece',1,'vg']]],
- ['split_5fstrands_11034',['split_strands',['../namespacehandlegraph_1_1algorithms.html#a1a7504e7155f6f9726c772a4b7c0f2c7',1,'handlegraph::algorithms']]],
- ['ssw_5fto_5fvg_11035',['ssw_to_vg',['../classvg_1_1SSWAligner.html#a8daaaa17b12f1283c006d633d4c9a8fa',1,'vg::SSWAligner']]],
- ['sswaligner_11036',['SSWAligner',['../classvg_1_1SSWAligner.html#ae91911b3a1357b0d3ae9bcecd51a592a',1,'vg::SSWAligner']]],
- ['stack_11037',['stack',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa26ad54b66a37b0f31fa846c48d59882',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['stack_5fpermutations_11038',['stack_permutations',['../namespacevg.html#a5e9c563a243faef4e5357eca9c7c8500',1,'vg']]],
- ['stack_5fup_5fvalid_5fwalks_11039',['stack_up_valid_walks',['../classvg_1_1ExhaustiveTraversalFinder.html#ab37a28d916291506bfe78a6818943585',1,'vg::ExhaustiveTraversalFinder']]],
- ['stacktrace_5fmanually_11040',['stacktrace_manually',['../namespacevg.html#a8d771862cc44504508267240462cb043',1,'vg']]],
- ['stage_11041',['stage',['../classvg_1_1Funnel.html#a21b5f8762aa446a64b5ddb3809e5c8e2',1,'vg::Funnel']]],
- ['stage_5fstop_11042',['stage_stop',['../classvg_1_1Funnel.html#a87e1b8deccb4438d7f71267ee5f12ced',1,'vg::Funnel']]],
- ['standard_5fextend_11043',['standard_extend',['../structhaplo_1_1haplo__DP__column.html#a5364cc0f365e68434e346c2b48eea996',1,'haplo::haplo_DP_column']]],
- ['start_11044',['start',['../classvg_1_1Funnel.html#a4ba2b8db1575820b05d069cd6c802e31',1,'vg::Funnel::start()'],['../classvg_1_1multipath__alignment__t.html#a4cd9b91704e89c799019d9c8962b16bb',1,'vg::multipath_alignment_t::start() const'],['../classvg_1_1multipath__alignment__t.html#ae79344b60aed1577a39391b4b42574f3',1,'vg::multipath_alignment_t::start(size_t i) const']]],
- ['start_5fbackward_11045',['start_backward',['../namespacevg.html#a43f061abac718e0386965aa537398e74',1,'vg']]],
- ['start_5fdegree_11046',['start_degree',['../classvg_1_1VG.html#a1ff00edd627e3445eee7f43927bb1518',1,'vg::VG']]],
- ['start_5fhandle_11047',['start_handle',['../structvg_1_1Haplotypes_1_1Subchain.html#a8b8950af5c76b20ab93ef40dc086da93',1,'vg::Haplotypes::Subchain']]],
- ['start_5fhint_11048',['start_hint',['../classvg_1_1algorithms_1_1Anchor.html#a1be30d40d8252c36c162bfbb568554a1',1,'vg::algorithms::Anchor']]],
- ['start_5fhint_5foffset_11049',['start_hint_offset',['../classvg_1_1algorithms_1_1Anchor.html#afe9a192ac276676633aab322189732b0',1,'vg::algorithms::Anchor']]],
- ['start_5fsize_11050',['start_size',['../classvg_1_1multipath__alignment__t.html#a8155e732811cdcc1e6fcee417b25bf10',1,'vg::multipath_alignment_t']]],
- ['start_5fvcf_11051',['start_vcf',['../classvg_1_1Genotyper.html#a8a5aed6de86a488fe78a223d5e4d6bd6',1,'vg::Genotyper']]],
- ['startfile_11052',['StartFile',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaf788a0a0553f9cc0c531fecb941f228',1,'vg::io::BlockedGzipOutputStream']]],
- ['starting_5fposition_11053',['starting_position',['../structvg_1_1GaplessExtension.html#a2dc9687b1ac33335f593028c981fe494',1,'vg::GaplessExtension']]],
- ['starts_5fat_11054',['starts_at',['../classhandlegraph_1_1SnarlDecomposition.html#ac6bb78bc95acfd353ff8d6c44915e524',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fat_5fend_11055',['starts_at_end',['../classhandlegraph_1_1SnarlDecomposition.html#aab710270e1997f22d1b09a4fd40a3eaf',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fat_5fstart_11056',['starts_at_start',['../classhandlegraph_1_1SnarlDecomposition.html#adb1c7cccea8188c8e24a4e53c34117bb',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fat_5ftip_11057',['starts_at_tip',['../classhandlegraph_1_1SnarlDecomposition.html#ac47bc288b1c0303d3356e953de4878e2',1,'handlegraph::SnarlDecomposition']]],
- ['starts_5fwith_11058',['starts_with',['../namespacevg.html#a7b58d5d004a85a09906301781567970a',1,'vg']]],
- ['state_11059',['state',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4a2a145b0221202c440cca81c0ba89c9',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['std_5fdev_11060',['std_dev',['../classvg_1_1FragmentLengthDistribution.html#a4da22f6209796ad178bd6ae88a995c03',1,'vg::FragmentLengthDistribution']]],
- ['stddev_11061',['stddev',['../classvg_1_1normal__distribution.html#aaf593ce22610d686f290face7b5db895',1,'vg::normal_distribution::stddev()'],['../classvg_1_1truncated__normal__distribution.html#a49f7b71f827df31a5590d120e04dcbcf',1,'vg::truncated_normal_distribution::stddev()']]],
- ['stdev_11062',['stdev',['../namespacevg.html#a11df8bd14dab3c0cfb7ecfa377a362f5',1,'vg']]],
- ['step_5f1_5fbuild_5fgbwts_11063',['step_1_build_gbwts',['../gbwt__main_8cpp.html#a099d84c7e00d3a536ab0c89a42824a67',1,'gbwt_main.cpp']]],
- ['step_5f2_5fmerge_5fgbwts_11064',['step_2_merge_gbwts',['../gbwt__main_8cpp.html#a81911b71bc15131cf9f9cc9652cccf0a',1,'gbwt_main.cpp']]],
- ['step_5f3_5falter_5fgbwt_11065',['step_3_alter_gbwt',['../gbwt__main_8cpp.html#aa89c3d0220f759b0de6756841c3bbfae',1,'gbwt_main.cpp']]],
- ['step_5f4_5fpath_5fcover_11066',['step_4_path_cover',['../gbwt__main_8cpp.html#ac6ed5f1a6fdf7794797be7ab94278897',1,'gbwt_main.cpp']]],
- ['step_5f5_5fgbwtgraph_11067',['step_5_gbwtgraph',['../gbwt__main_8cpp.html#a61f18988124c373bf3aa037ad24719f2',1,'gbwt_main.cpp']]],
- ['step_5f6_5fr_5findex_11068',['step_6_r_index',['../gbwt__main_8cpp.html#a240e0e93804c406946adb930f58c87aa',1,'gbwt_main.cpp']]],
- ['step_5f7_5fmetadata_11069',['step_7_metadata',['../gbwt__main_8cpp.html#a7d810cefdbee01df4d4fe50406806e30',1,'gbwt_main.cpp']]],
- ['step_5f8_5fpaths_11070',['step_8_paths',['../gbwt__main_8cpp.html#a859c16083955e4f1ab36c130fe6cce27',1,'gbwt_main.cpp']]],
- ['step_5fin_5fpath_11071',['step_in_path',['../classvg_1_1VCFTraversalFinder.html#aefa5cf40bc0244f81e52ae2bdb4904d0',1,'vg::VCFTraversalFinder']]],
- ['step_5frank_5fat_5fposition_11072',['step_rank_at_position',['../classxg_1_1XGPath.html#a92b0745ad293f585d5fb20d1bf20f7cc',1,'xg::XGPath']]],
- ['steps_5fof_5fhandle_11073',['steps_of_handle',['../classvg_1_1MemoizingGraph.html#ab96deef5a4149f287541058c256a1115',1,'vg::MemoizingGraph::steps_of_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a015b050f33861cbc8e2a0efaaf771a30',1,'handlegraph::PathHandleGraph::steps_of_handle()']]],
- ['stop_11074',['stop',['../classvg_1_1Funnel.html#adbe0233346c63f1693fa865eca0083b2',1,'vg::Funnel']]],
- ['strandsplitgraph_11075',['StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html#a0e170b8ad07ca370e31497b804932220',1,'vg::StrandSplitGraph::StrandSplitGraph(const HandleGraph *graph)'],['../classvg_1_1StrandSplitGraph.html#aede16e10fc0b17f2527a62861f155c6d',1,'vg::StrandSplitGraph::StrandSplitGraph()=default']]],
- ['stream_5fsort_11076',['stream_sort',['../classvg_1_1StreamSorter.html#a3ef7c0c822f58db91184e6b069c3ce59',1,'vg::StreamSorter']]],
- ['streamcompressstring_11077',['StreamCompressString',['../namespacezstdutil.html#a64155ae3ce93620ea7868913f4c49ab3',1,'zstdutil']]],
- ['streamdecompressstring_11078',['StreamDecompressString',['../namespacezstdutil.html#a2b6cfe0b4f483fea633845a8d912e8dd',1,'zstdutil']]],
- ['streaminbuf_11079',['streaminbuf',['../classvg_1_1io_1_1streaminbuf.html#a611fcbbde05222173c867ea92cf20ed6',1,'vg::io::streaminbuf']]],
- ['streamindex_11080',['StreamIndex',['../classvg_1_1StreamIndex.html#a3508617dbf1b8e8d1df051f4a214fa5e',1,'vg::StreamIndex']]],
- ['streamindexbase_11081',['StreamIndexBase',['../classvg_1_1StreamIndexBase.html#a2df03d2ee53e9f171e4aa519a079901e',1,'vg::StreamIndexBase::StreamIndexBase()=default'],['../classvg_1_1StreamIndexBase.html#a85207efd00788e14df4df717d88233b7',1,'vg::StreamIndexBase::StreamIndexBase(const StreamIndexBase &other)=delete']]],
- ['streaming_5fmerge_11082',['streaming_merge',['../classvg_1_1StreamSorter.html#a1c19cdfb158ff9771e471fbbc2b4ac74',1,'vg::StreamSorter::streaming_merge(list< cursor_t > &cursors, emitter_t &emitter, size_t expected_messages=0)'],['../classvg_1_1StreamSorter.html#a77590f7da1d1418fc00e7bdaec2a76e5',1,'vg::StreamSorter::streaming_merge(const vector< string > &temp_names_in, unordered_map< string, size_t > *messages_per_file=nullptr)']]],
- ['streamistream_11083',['streamistream',['../classvg_1_1io_1_1streamistream.html#a0b87c404670f610d20f49f1e2c166648',1,'vg::io::streamistream']]],
- ['streammultiplexer_11084',['StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html#ae72f4179a6cb14beb1b6460603d88233',1,'vg::io::StreamMultiplexer::StreamMultiplexer(ostream &backing, size_t max_threads)'],['../classvg_1_1io_1_1StreamMultiplexer.html#ad8b06aab5797747b1ce3d544be0cc965',1,'vg::io::StreamMultiplexer::StreamMultiplexer(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#af8352f0fcbb63f162734d48d2ec573ce',1,'vg::io::StreamMultiplexer::StreamMultiplexer(StreamMultiplexer &&other)=delete']]],
- ['streamsorter_11085',['StreamSorter',['../classvg_1_1StreamSorter.html#a9ef0b8a33f5011eaf655b9420d86b0f5',1,'vg::StreamSorter']]],
- ['string_5fquality_5fchar_5fto_5fshort_11086',['string_quality_char_to_short',['../namespacevg_1_1io.html#a4450d95b60550d44cbfe712467e92947',1,'vg::io']]],
- ['string_5fquality_5fshort_5fto_5fchar_11087',['string_quality_short_to_char',['../namespacevg_1_1io.html#a33f3f10cba44d4ab370628c9579f9ca4',1,'vg::io']]],
- ['string_5fto_5fint_11088',['string_to_int',['../namespacegafkluge.html#a35bc1201781dd4bab3581189c777a8af',1,'gafkluge']]],
- ['strip_5ffrom_5fend_11089',['strip_from_end',['../namespacevg.html#adbe45b79675104ebc36691774d4124c4',1,'vg']]],
- ['strip_5ffrom_5fstart_11090',['strip_from_start',['../namespacevg.html#acd6786ea9551b426f95fba325beff138',1,'vg']]],
- ['strip_5ffull_5flength_5fbonuses_11091',['strip_full_length_bonuses',['../classvg_1_1MultipathMapper.html#a1147b64d4c4aeffa84403f5341de52bf',1,'vg::MultipathMapper']]],
- ['strip_5fsubrange_11092',['strip_subrange',['../classvg_1_1Paths.html#aaae6abfe6b12aecfe82457fe8b8b44a8',1,'vg::Paths']]],
- ['strip_5fsuffixes_11093',['strip_suffixes',['../giraffe__main_8cpp.html#ada042c5c5040b9b72848655d3dc5fcf8',1,'giraffe_main.cpp']]],
- ['strongly_5fconnected_5fcomponents_11094',['strongly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a3c63833d51eac5a3141211367935e9e5',1,'handlegraph::algorithms']]],
- ['stubbify_5fref_5fpaths_11095',['stubbify_ref_paths',['../namespacevg.html#a9e14750889892e0d70b8bc18fcc9f905',1,'vg']]],
- ['sub_5foverlaps_5fof_5ffirst_5faln_11096',['sub_overlaps_of_first_aln',['../namespacevg.html#ab63c41956b73af429507b469108d1759',1,'vg']]],
- ['subchain_5fintervals_11097',['subchain_intervals',['../haplotypes__main_8cpp.html#aed90215616b71a8c576afeeb7a137596',1,'haplotypes_main.cpp']]],
- ['subchain_5flength_11098',['subchain_length',['../namespacehaplotypes__defaults.html#af6cc9d47b0c3862d9c0cdea27b55f477',1,'haplotypes_defaults']]],
- ['subchain_5fstatistics_11099',['subchain_statistics',['../haplotypes__main_8cpp.html#a559cad6ab46d0a7dc260987e61ed1175',1,'haplotypes_main.cpp']]],
- ['subchain_5fto_5fstring_11100',['subchain_to_string',['../haplotypes__main_8cpp.html#ae88c7a2ca3744f1826af903b27b2df53',1,'haplotypes_main.cpp']]],
- ['subcommand_11101',['Subcommand',['../classvg_1_1subcommand_1_1Subcommand.html#ad5faf589dd98c3ff0c0d1071fcf90090',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, int priority, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#a38458556194aa9d47b1a49fc8958f345',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#ad2cb9a00761644300914d9ed8439cbe1',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, std::function< int(int, char **)> main_function)']]],
- ['subgraph_11102',['subgraph',['../classvg_1_1SubgraphExplainer.html#a6a8bb147fa3f638f7bc0c2a098475999',1,'vg::SubgraphExplainer']]],
- ['subgraph_5fcontaining_5fpath_5fsnarls_11103',['subgraph_containing_path_snarls',['../namespacevg.html#acc960c295c1e3088dc8e71ab1af5c4d6',1,'vg']]],
- ['subgraph_5fin_5fdistance_5frange_11104',['subgraph_in_distance_range',['../namespacevg.html#aff8a7aca57dd525bc2def1369abae3fe',1,'vg']]],
- ['subgraph_5fin_5fdistance_5frange_5fwalk_5facross_5fchain_11105',['subgraph_in_distance_range_walk_across_chain',['../namespacevg.html#a30f08b56f8c117103357ed4b8ebc08b8',1,'vg']]],
- ['subgraph_5fin_5fdistance_5frange_5fwalk_5fgraph_11106',['subgraph_in_distance_range_walk_graph',['../namespacevg.html#a0312bffc43a4f4176aad1c37073b59df',1,'vg']]],
- ['subgraphexplainer_11107',['SubgraphExplainer',['../classvg_1_1SubgraphExplainer.html#adbcee01cfe7c72e36071da4ed5aa1aec',1,'vg::SubgraphExplainer']]],
- ['subgraphoverlay_11108',['SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html#ac9ffa71f1e615eb30efc626006c11242',1,'vg::SubgraphOverlay']]],
- ['subhandlegraph_11109',['SubHandleGraph',['../classvg_1_1SubHandleGraph.html#ae02101c50fc316637a11ed674637e6a4',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super, HandleIter begin, HandleIter end)'],['../classvg_1_1SubHandleGraph.html#a1426a494a5d412485f5c4959f3b853c8',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super)'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4455c7d0983b1fcce544022a60fa76ab',1,'handlegraph::algorithms::SubHandleGraph::SubHandleGraph()']]],
- ['subpath_11110',['subpath',['../classvg_1_1multipath__alignment__t.html#a87bb864c7cd6e424fe9487cc662cade6',1,'vg::multipath_alignment_t::subpath() const'],['../classvg_1_1multipath__alignment__t.html#a5544e1c157233fda1b528bdd3e426f90',1,'vg::multipath_alignment_t::subpath(size_t i) const']]],
- ['subpath_5fsize_11111',['subpath_size',['../classvg_1_1multipath__alignment__t.html#a3b6820ac77fa5438c55300ba1eb7a97d',1,'vg::multipath_alignment_t']]],
- ['subpath_5ft_11112',['subpath_t',['../classvg_1_1subpath__t.html#a17ac16fd98564bfa3ab34e9b9b20517e',1,'vg::subpath_t::subpath_t()=default'],['../classvg_1_1subpath__t.html#a31254046fc840d936d42012b2c7b23b5',1,'vg::subpath_t::subpath_t(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a096b12ec158dd2cf139dbe38f55ca2f3',1,'vg::subpath_t::subpath_t(subpath_t &&)=default']]],
- ['subpath_5ftopological_5forder_11113',['subpath_topological_order',['../namespacevg.html#ab1dcbe73351c8eaeea745f4b5191b8f0',1,'vg']]],
- ['subpathoverlay_11114',['SubpathOverlay',['../classvg_1_1SubpathOverlay.html#a63691d737697292e0a2fd4233024dfb8',1,'vg::SubpathOverlay::SubpathOverlay(const PathHandleGraph *backing, const step_handle_t &begin, const step_handle_t &end)'],['../classvg_1_1SubpathOverlay.html#aa3cc8559a68870f144d69eb44829c95a',1,'vg::SubpathOverlay::SubpathOverlay()=default']]],
- ['substage_11115',['substage',['../classvg_1_1Funnel.html#a0520d00fd1dcd9fa4af18d715580c900',1,'vg::Funnel']]],
- ['substage_5fstop_11116',['substage_stop',['../classvg_1_1Funnel.html#ab5934891f37d57dc9309e5b0e9f80d9e',1,'vg::Funnel']]],
- ['subtract_5flog_11117',['subtract_log',['../namespacevg.html#a33c8f5153ad0766df2c72bbec623aa19',1,'vg']]],
- ['successor_5foffset_11118',['successor_offset',['../classvg_1_1WFATree.html#a33c5e80cc73d5367a95343deb20d8dac',1,'vg::WFATree']]],
- ['suffix_11119',['suffix',['../classvg_1_1WFAExtender.html#a73ca61152596774e30d6c6f40aeea984',1,'vg::WFAExtender::suffix()'],['../structvg_1_1RecombinatorHaplotype.html#ae22f7c420e3d76d6494f66e817ffb342',1,'vg::RecombinatorHaplotype::suffix()']]],
- ['suggest_5fedge_11120',['suggest_edge',['../classvg_1_1DiagramExplainer.html#a5565fd4595e708faa7f82534b1b87380',1,'vg::DiagramExplainer']]],
- ['sum_11121',['sum',['../namespacevg.html#aa70726366aa31b20debdcac41c89490c',1,'vg']]],
- ['summary_5fstatistics_11122',['summary_statistics',['../namespacevg.html#ae8afe82a05092bbf4bc31c8ead079fe3',1,'vg']]],
- ['support_5fmax_11123',['support_max',['../namespacevg.html#ac3787b0a7fc02bbfe45dc5eb082d5779',1,'vg']]],
- ['support_5fmin_11124',['support_min',['../namespacevg.html#a3c2ae4c37201ebbc6f6d4faaf27fe4de',1,'vg']]],
- ['support_5fval_11125',['support_val',['../classvg_1_1SupportBasedSnarlCaller.html#a84da98787b002a2ed9c8c1da6661cebd',1,'vg::SupportBasedSnarlCaller::support_val()'],['../classvg_1_1TraversalSupportFinder.html#a3a128da202bd6889a2e5fd92ba3227dc',1,'vg::TraversalSupportFinder::support_val()']]],
- ['supportbasedsnarlcaller_11126',['SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html#adff4e7045e950e7caea2858569afec02',1,'vg::SupportBasedSnarlCaller']]],
- ['supportrestrictedtraversalfinder_11127',['SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html#aceeb94d7e05fdbc113557b61448f6b2a',1,'vg::SupportRestrictedTraversalFinder']]],
- ['surject_11128',['surject',['../classvg_1_1Surjector.html#a4e4e4c28b1313850e647f4d258a0ea82',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a265cf90a6fb12021a70b87ec647c0867',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a80afa331fde9e8bcff66c4e87400217a',1,'vg::Surjector::surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
- ['surject_5falignments_5fin_5fplace_11129',['surject_alignments_in_place',['../classvg_1_1SurjectingAlignmentEmitter.html#a5ba8aab649ae5f31c64be2c5461c743c',1,'vg::SurjectingAlignmentEmitter']]],
- ['surject_5finternal_11130',['surject_internal',['../classvg_1_1Surjector.html#a6474f90fe3cf3ea098a553916bd47ae9',1,'vg::Surjector']]],
- ['surjectingalignmentemitter_11131',['SurjectingAlignmentEmitter',['../classvg_1_1SurjectingAlignmentEmitter.html#acf03c9f7eedb8d8dd58d6ffab24f139f',1,'vg::SurjectingAlignmentEmitter']]],
- ['surjector_11132',['Surjector',['../classvg_1_1Surjector.html#a4b083231c3ae02e3e14c3efb2a72eb1d',1,'vg::Surjector']]],
- ['swap_11133',['swap',['../classvg_1_1SnarlState.html#a4e3f0d0c720ea665b3db9542d07f7ec1',1,'vg::SnarlState::swap()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a1466c6e58d54f775b27680dbe5e7fe4d',1,'vg::ZipCodeTree::reverse_iterator::swap()']]],
- ['swap_5falleles_11134',['swap_alleles',['../classvg_1_1PhasedGenome.html#ae325c8488e737b75b980796aacf37246',1,'vg::PhasedGenome']]],
- ['swap_5fendianness_11135',['swap_endianness',['../structvg_1_1endianness.html#a0a3eec44ef047d7771ad9804c5b51c85',1,'vg::endianness']]],
- ['swap_5fhandles_11136',['swap_handles',['../classvg_1_1VG.html#a3d4db6ea2a99bda9a48411491aa6ed4e',1,'vg::VG']]],
- ['swap_5fhaplotypes_11137',['swap_haplotypes',['../classvg_1_1GenomeState.html#aee2aa05cdf5226983f8f25d783da528e',1,'vg::GenomeState']]],
- ['swap_5flabel_11138',['swap_label',['../classvg_1_1PhasedGenome.html#a181b4e71f8debc78ceccf476ce36abcd',1,'vg::PhasedGenome']]],
- ['swap_5fnode_5fid_11139',['swap_node_id',['../classvg_1_1VG.html#afee31880eaf65a1a6d1a250663271b54',1,'vg::VG::swap_node_id(nid_t node_id, nid_t new_id)'],['../classvg_1_1VG.html#a63f2ffa39d84f80e5ab8068a25a03ee9',1,'vg::VG::swap_node_id(Node *node, nid_t new_id)']]],
- ['swap_5fnode_5fids_11140',['swap_node_ids',['../classvg_1_1Paths.html#a3190f22ab39a9039ec9288e1c065ca9c',1,'vg::Paths::swap_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)'],['../classvg_1_1Paths.html#aba01c4d1b1d415622634db97f62b1188',1,'vg::Paths::swap_node_ids(hash_map< id_t, id_t > &id_mapping)']]],
- ['swap_5fnodes_11141',['swap_nodes',['../classvg_1_1VG.html#aa402d1cf817f83ca44f72f6112b6a2e3',1,'vg::VG']]],
- ['swap_5fremove_11142',['swap_remove',['../swap__remove_8hpp.html#a403d9325a22306c4dfefd9202bd3bd00',1,'swap_remove.hpp']]],
- ['sync_5foffsets_11143',['sync_offsets',['../classxg_1_1XGPath.html#af7e2c286ed51c4422b1b615e4f327b9d',1,'xg::XGPath']]],
- ['sync_5fpaths_11144',['sync_paths',['../classvg_1_1VG.html#a124188a9e0cd68c87c2bc009ea7bd799',1,'vg::VG']]],
- ['synthesize_5ftail_5fanchors_11145',['synthesize_tail_anchors',['../classvg_1_1MultipathAlignmentGraph.html#a3c34e5d02c2b81614ccd602351b81ed9',1,'vg::MultipathAlignmentGraph']]]
+ ['sa_5fto_5fda_10755',['sa_to_da',['../namespacevg.html#aaac16668663556af1aea74159a73d4ed',1,'vg']]],
+ ['sam_5fflag_10756',['sam_flag',['../namespacevg.html#ae37c6d66a01cef6f92707d367ebf4cdb',1,'vg']]],
+ ['same_5fcontext_10757',['same_context',['../classvg_1_1VG.html#a96f99984ada5a3a13332ddb2ab0a1c97',1,'vg::VG']]],
+ ['sample_5fgam_5fdepth_10758',['sample_gam_depth',['../namespacevg_1_1algorithms.html#a80703607cfe21f1f593f7b2f03c08b40',1,'vg::algorithms']]],
+ ['sample_5fhaplotypes_10759',['sample_haplotypes',['../giraffe__main_8cpp.html#a6343c45d56779ead6309ffefbf066fdc',1,'sample_haplotypes(const vector< pair< string, string >> &indexes, string &basename, string &sample_name, string &haplotype_file, string &kff_file, bool progress): giraffe_main.cpp'],['../haplotypes__main_8cpp.html#a13d462ac627c7beb00b431280ac9b0c6',1,'sample_haplotypes(const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, const HaplotypesConfig &config): haplotypes_main.cpp']]],
+ ['sample_5fmapping_5fdepth_10760',['sample_mapping_depth',['../namespacevg_1_1algorithms.html#a16bd0de261a829b2d81ec48eed9d6482',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const string &input_filename, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq, const string &format)'],['../namespacevg_1_1algorithms.html#a244822514c71473756cfd5ad87f79e08',1,'vg::algorithms::sample_mapping_depth(const HandleGraph &graph, const vector< Alignment > &alignments, size_t max_nodes, size_t random_seed, size_t min_coverage, size_t min_mapq)']]],
+ ['sample_5fminimal_10761',['sample_minimal',['../namespacevg_1_1algorithms.html#a175ee345e226732cb1c37da13a2f045e',1,'vg::algorithms']]],
+ ['sample_5fpath_10762',['sample_path',['../classvg_1_1NGSSimulator.html#a57ee602010b5295685556acc30e0355a',1,'vg::NGSSimulator']]],
+ ['sample_5fread_10763',['sample_read',['../classvg_1_1ReadFilter.html#aa592c88e758fc257fdf17418b0f189a8',1,'vg::ReadFilter::sample_read()'],['../classvg_1_1Sampler.html#ab48bd0062b357dfe0cf418beb1e18ad4',1,'vg::Sampler::sample_read()'],['../classvg_1_1NGSSimulator.html#a50a20af9dd3edd86233edf1de13a5cda',1,'vg::NGSSimulator::sample_read()']]],
+ ['sample_5fread_5finternal_10764',['sample_read_internal',['../classvg_1_1NGSSimulator.html#a957be55e0adcf59449587ccb1f8db9de',1,'vg::NGSSimulator']]],
+ ['sample_5fread_5fpair_10765',['sample_read_pair',['../classvg_1_1Sampler.html#a598b41433f5bb9a040749e7a2327b78d',1,'vg::Sampler::sample_read_pair()'],['../classvg_1_1NGSSimulator.html#a5b12189ad9dcf0a4656a321fcf5ff840',1,'vg::NGSSimulator::sample_read_pair()']]],
+ ['sample_5fread_5fquality_10766',['sample_read_quality',['../classvg_1_1NGSSimulator.html#a49ad65d878edb1d76518f589aa0bf02c',1,'vg::NGSSimulator']]],
+ ['sample_5fread_5fquality_5finternal_10767',['sample_read_quality_internal',['../classvg_1_1NGSSimulator.html#a03fb08f4267424aca8d8892a403b134a',1,'vg::NGSSimulator']]],
+ ['sample_5fread_5fquality_5fpair_10768',['sample_read_quality_pair',['../classvg_1_1NGSSimulator.html#a71f6e4ba9442273d4cf1588f24578f55',1,'vg::NGSSimulator']]],
+ ['sample_5fstart_5fgraph_5fpos_10769',['sample_start_graph_pos',['../classvg_1_1NGSSimulator.html#ada5f04218c531191b20a8c28cc57d94e',1,'vg::NGSSimulator']]],
+ ['sample_5fstart_5fpath_5fpos_10770',['sample_start_path_pos',['../classvg_1_1NGSSimulator.html#ad2f821c685108e8ee6912713f0ced8d3',1,'vg::NGSSimulator']]],
+ ['sample_5fstart_5fpos_10771',['sample_start_pos',['../classvg_1_1NGSSimulator.html#a889b49669939bfb7832bad23f02cd02c',1,'vg::NGSSimulator']]],
+ ['sample_5ftransition_10772',['sample_transition',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a4434cebe872c32c384c1f916111fc2e1',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['sampler_10773',['Sampler',['../classvg_1_1Sampler.html#ab1d1e96bcf702979dfc86a92dcd8d24b',1,'vg::Sampler']]],
+ ['sanitize_5fsequence_5fin_5fplace_10774',['sanitize_sequence_in_place',['../classvg_1_1Constructor.html#a1d90ed36989b851bb3c072f4d67b52dd',1,'vg::Constructor']]],
+ ['save_10775',['save',['../classvg_1_1StreamIndexBase.html#a99761d4d917dc5ba1db1e08a36ceb312',1,'vg::StreamIndexBase::save()'],['../classvg_1_1io_1_1VPKG.html#a80551b46351f1e8d47e8b3ebaf028847',1,'vg::io::VPKG::save(const Have &have, ostream &out)'],['../classvg_1_1io_1_1VPKG.html#a0472c51ab91f4b8663a56a150e0e0f12',1,'vg::io::VPKG::save(const Have &have, const string &filename)']]],
+ ['save_5fbed_10776',['save_bed',['../classvg_1_1FeatureSet.html#a2914a7c47c085b00a454df2bfc5eda67',1,'vg::FeatureSet']]],
+ ['save_5ffrag_5flens_5fto_5falns_10777',['save_frag_lens_to_alns',['../classvg_1_1FragmentLengthStatistics.html#ab9376051edd07e128f52f57ac2b5a410',1,'vg::FragmentLengthStatistics']]],
+ ['save_5fgbwt_10778',['save_gbwt',['../namespacevg.html#a790122d8b3f28068aaf09f1eb5b966a9',1,'vg::save_gbwt(const gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a8385d575383b7bae35726e90851a2795',1,'vg::save_gbwt(const gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
+ ['save_5fgbwtgraph_10779',['save_gbwtgraph',['../namespacevg.html#aea7640260b1c70795335439f3d6c2eac',1,'vg']]],
+ ['save_5fgbz_10780',['save_gbz',['../namespacevg.html#a017e7cda40a98b4b044507ab78a34da9',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a6beaace0e6d90b654dc9c382afb39ce0',1,'vg::save_gbz(const gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#af7669e457f62e6f197f3120086a091e2',1,'vg::save_gbz(const gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
+ ['save_5fgcsa_10781',['save_gcsa',['../namespacevg.html#aa2840fc8dbdb12c000769a3baa39b808',1,'vg']]],
+ ['save_5fhandle_5fgraph_10782',['save_handle_graph',['../namespacevg_1_1io.html#af3f5510bd6a0e5514d3083fcd2ffdd32',1,'vg::io::save_handle_graph(HandleGraph *graph, ostream &os)'],['../namespacevg_1_1io.html#a571f402ff74b738d9070a598a41b58da',1,'vg::io::save_handle_graph(HandleGraph *graph, const string &dest_path)']]],
+ ['save_5flcp_10783',['save_lcp',['../namespacevg.html#a604f783fb59cb6c3e7fcc783a8286822',1,'vg']]],
+ ['save_5fminimizer_10784',['save_minimizer',['../namespacevg.html#af7885143ca20185816afadc669813f12',1,'vg']]],
+ ['save_5fr_5findex_10785',['save_r_index',['../namespacevg.html#a50d4b5eef7efd656daeb423af1f6a3c6',1,'vg']]],
+ ['save_5frecords_10786',['save_records',['../classvg_1_1HTSWriter.html#a4d3f2772a76d36733f1bb1ccf93f498b',1,'vg::HTSWriter']]],
+ ['save_5fto_5ffile_10787',['save_to_file',['../classvg_1_1Packer.html#a936e5283142e2fb3ac089730b217d533',1,'vg::Packer']]],
+ ['scan_10788',['scan',['../classvg_1_1DozeuInterface.html#a73d9afd8c6b52ff715ae0606bbae4b63',1,'vg::DozeuInterface::scan()'],['../classvg_1_1XdropAligner.html#a3bf50d433186476abc2f732525bf1377',1,'vg::XdropAligner::scan()'],['../classvg_1_1QualAdjXdropAligner.html#a2e8adea58e74731765b5c7d0eb54386f',1,'vg::QualAdjXdropAligner::scan()'],['../structvg_1_1PositionIDScanner.html#a32743fa0fd2721702fe8fc34d565c64a',1,'vg::PositionIDScanner::scan()'],['../structvg_1_1IDScanner.html#a36577d4a2c2ac0d7a12383ae6e9e999d',1,'vg::IDScanner::scan()'],['../structvg_1_1WrappingPositionScanner.html#ac9e28c724f1361a03b6a07e0f9e29ada',1,'vg::WrappingPositionScanner::scan()'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a1f090fe14d731ce588feecd540426bde',1,'vg::PositionIDScanner::scan(const Mapping &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a54073400b300df6e34e3f9060e40787d',1,'vg::PositionIDScanner::scan(const Path &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4bcbbddbe7bfd05b52add552ad4b471d',1,'vg::PositionIDScanner::scan(const Alignment &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#aa519909ec5ee7ad0648f8e302f9b8c4d',1,'vg::PositionIDScanner::scan(const Node &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#a4fce8b2ac2b293e93152c8407e06a02b',1,'vg::PositionIDScanner::scan(const Edge &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)'],['../structvg_1_1PositionIDScanner.html#ae08c1500551856c1884a86e6740ddf85',1,'vg::PositionIDScanner::scan(const Graph &msg, const function< bool(const Position &)> &pos_iteratee, const function< bool(const id_t &)> &id_iteratee)']]],
+ ['scan_5fbackward_10789',['scan_backward',['../classvg_1_1StreamIndexBase.html#addb451cabccc43915ae629925b3ed3ee',1,'vg::StreamIndexBase']]],
+ ['scan_5fcontig_5flengths_10790',['scan_contig_lengths',['../classvg_1_1VCFGenotyper.html#a28f3c05eb4ffefef243a18dc27562b15',1,'vg::VCFGenotyper']]],
+ ['scan_5ffor_5fdeletion_10791',['scan_for_deletion',['../classvg_1_1VCFTraversalFinder.html#a7842cce2da7786e41fbd110c78e45ef6',1,'vg::VCFTraversalFinder']]],
+ ['scan_5fp_5fvisits_10792',['scan_p_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a04d2b3f11fa053b6d6cdbbcae94b4873',1,'vg::algorithms::GFAParser']]],
+ ['scan_5fpath_10793',['scan_path',['../classhandlegraph_1_1PathHandleGraph.html#aa071f31a10a02d8231b029d0a7ddef0b',1,'handlegraph::PathHandleGraph']]],
+ ['scan_5fseed_5fposition_10794',['scan_seed_position',['../classvg_1_1DozeuInterface.html#a472afdc993f32bfa38518a9cfbd14dcb',1,'vg::DozeuInterface']]],
+ ['scan_5fsnarl_10795',['scan_snarl',['../classvg_1_1VCFOutputCaller.html#ad6cbf084906bc4676fae7715495888b3',1,'vg::VCFOutputCaller']]],
+ ['scan_5fvisits_10796',['scan_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a58ceb0c0017e5ea50b35854e5c52f0f4',1,'vg::algorithms::GFAParser']]],
+ ['scan_5fw_5fvisits_10797',['scan_w_visits',['../classvg_1_1algorithms_1_1GFAParser.html#a7e83307cfe42aae91205fa7180b802b4',1,'vg::algorithms::GFAParser']]],
+ ['scc_5fcopy_5fof_5fhandle_10798',['scc_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a015efe5e782831e59aaa3c2d6f98cbfd',1,'vg::DagifiedGraph']]],
+ ['scc_5fcopy_5fof_5fnode_5fid_10799',['scc_copy_of_node_id',['../classvg_1_1DagifiedGraph.html#a26161bf79e0a6385ff8f6fb67a1e907b',1,'vg::DagifiedGraph']]],
+ ['score_10800',['score',['../structvg_1_1BenchmarkResult.html#a4baad39dafa27d171b65df225666c887',1,'vg::BenchmarkResult::score()'],['../classvg_1_1MEMChainModel.html#aca053d2a91e4ea7ac440edd670893a84',1,'vg::MEMChainModel::score()'],['../classvg_1_1Funnel.html#a9cdacae4561ece776ba90e293299f930',1,'vg::Funnel::score()'],['../structhaplo_1_1haplo__DP.html#aadc492bf7d73b8d551ed56bb62266baa',1,'haplo::haplo_DP::score(const vg::Path &path, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1haplo__DP.html#a3204316e386c183faa191b9ee6f0b34e',1,'haplo::haplo_DP::score(const gbwt_thread_t &thread, GBWTType &graph, haploMath::RRMemo &memo)'],['../structhaplo_1_1linear__haplo__structure.html#a100ae7bbb7fa336e7d273c066f251e29',1,'haplo::linear_haplo_structure::score()'],['../classhaplo_1_1ScoreProvider.html#a4dd1edd0db2c92780af0fce9e62e8a1f',1,'haplo::ScoreProvider::score()'],['../classhaplo_1_1GBWTScoreProvider.html#a9970037ed1e272daa0e0bfdf358c9bce',1,'haplo::GBWTScoreProvider::score()'],['../classhaplo_1_1LinearScoreProvider.html#a0d95fe4eff2760404bce49d3aa50e2f0',1,'haplo::LinearScoreProvider::score()'],['../classvg_1_1AlignmentChainModel.html#a562dbec7e2dc602c82b92ad202620429',1,'vg::AlignmentChainModel::score()'],['../classvg_1_1connection__t.html#a8f34943152ac67f59c15ff776da592e8',1,'vg::connection_t::score()'],['../classvg_1_1subpath__t.html#a9e59579440b9a90f5b0c606dc3cf400a',1,'vg::subpath_t::score()'],['../classvg_1_1algorithms_1_1Anchor.html#aff7b7e2c62b7b7154edd3a9f64b0e5a7',1,'vg::algorithms::Anchor::score()']]],
+ ['score_5falignment_10801',['score_alignment',['../classvg_1_1Mapper.html#aa541cae3a3598e10a7baf7d5ed78f644',1,'vg::Mapper']]],
+ ['score_5falignment_5fpair_10802',['score_alignment_pair',['../classvg_1_1MinimizerMapper.html#a99ce46a1525f7be9fa393163ca1eac40',1,'vg::MinimizerMapper']]],
+ ['score_5fbest_5fchain_10803',['score_best_chain',['../namespacevg_1_1algorithms.html#ad91b7ceb67d3923a4c5cace56a5c4f6e',1,'vg::algorithms']]],
+ ['score_5fchain_5fgap_10804',['score_chain_gap',['../namespacevg_1_1algorithms.html#abdc2933db32d78a14a8e439f7e9643ab',1,'vg::algorithms']]],
+ ['score_5fcluster_10805',['score_cluster',['../classvg_1_1MinimizerMapper.html#a12e67c2dfdb80db4080d3675ed6a18d4',1,'vg::MinimizerMapper']]],
+ ['score_5fcontiguous_5falignment_10806',['score_contiguous_alignment',['../classvg_1_1GSSWAligner.html#a95753239b9d5fa388198ea04ac6c559b',1,'vg::GSSWAligner']]],
+ ['score_5fdiscontiguous_5falignment_10807',['score_discontiguous_alignment',['../classvg_1_1GSSWAligner.html#a795072356e28310d80f95bb5f0bb61f3',1,'vg::GSSWAligner']]],
+ ['score_5ferror_10808',['score_error',['../structvg_1_1BenchmarkResult.html#a880a443c67063f66623006cd82b5ec9d',1,'vg::BenchmarkResult']]],
+ ['score_5fexact_5fmatch_10809',['score_exact_match',['../classvg_1_1GSSWAligner.html#ac33af43d7d8d4a3d94a5ef1582c50cc4',1,'vg::GSSWAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const =0'],['../classvg_1_1GSSWAligner.html#ac8e1b97332df85221c6a2be61cbd1b3d',1,'vg::GSSWAligner::score_exact_match(const string &sequence, const string &base_quality) const =0'],['../classvg_1_1GSSWAligner.html#ac2969d865d7cb4652a7476feabd9c9b5',1,'vg::GSSWAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1Aligner.html#a4e087eea3154fc52fff10cbe14d0cd32',1,'vg::Aligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1Aligner.html#ab18b86459ab4471de6361bce2d8e8459',1,'vg::Aligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1Aligner.html#a86b2a95cc4d4de88a78ab6ce8ccc4b79',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#ae88c5b0e7c75fec448d4ed245cebe9b9',1,'vg::Aligner::score_exact_match(const string &sequence) const'],['../classvg_1_1Aligner.html#a2acc9c763d0b7c16ad69472a148ce75b',1,'vg::Aligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end) const'],['../classvg_1_1QualAdjAligner.html#adf03ac873ae9a9cfbc21e589775111be',1,'vg::QualAdjAligner::score_exact_match(const Alignment &aln, size_t read_offset, size_t length) const'],['../classvg_1_1QualAdjAligner.html#a51941e8914296630f63d303c548cee8d',1,'vg::QualAdjAligner::score_exact_match(const string &sequence, const string &base_quality) const'],['../classvg_1_1QualAdjAligner.html#a8348afe2de6738fd4cd26e3fd6358818',1,'vg::QualAdjAligner::score_exact_match(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const']]],
+ ['score_5fextension_5fgroup_10810',['score_extension_group',['../classvg_1_1MinimizerMapper.html#a2c8ab02743227cb2550fcfd295043253',1,'vg::MinimizerMapper']]],
+ ['score_5fextensions_10811',['score_extensions',['../classvg_1_1MinimizerMapper.html#af9ff5e0a1b8c7925ccdb8a23d29872ef',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::vector< GaplessExtension >> &extensions, const Alignment &aln, Funnel &funnel) const'],['../classvg_1_1MinimizerMapper.html#a421cdd65bac59fac39fd3b87cce0f3ae',1,'vg::MinimizerMapper::score_extensions(const std::vector< std::pair< std::vector< GaplessExtension >, size_t >> &extensions, const Alignment &aln, Funnel &funnel) const']]],
+ ['score_5ffrom_10812',['score_from',['../classvg_1_1algorithms_1_1TracedScore.html#a999c0829c8c11a2d7478630612b60b74',1,'vg::algorithms::TracedScore']]],
+ ['score_5ffull_5flength_5fbonus_10813',['score_full_length_bonus',['../classvg_1_1GSSWAligner.html#ad6bac86acf59cc8edd4969bd671fcf5d',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const =0'],['../classvg_1_1GSSWAligner.html#a952bb420992b5e5e4c81388b015caf97',1,'vg::GSSWAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const =0'],['../classvg_1_1Aligner.html#aaf87ac123c806ef49c509c494b431c9c',1,'vg::Aligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a442d01bf1ed7d011d015d790f0595817',1,'vg::Aligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const'],['../classvg_1_1QualAdjAligner.html#ac4505d206516b2ad51bdc2387309ae9e',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1QualAdjAligner.html#a84b8bacfebeb426d367ec4441800a4e4',1,'vg::QualAdjAligner::score_full_length_bonus(bool left_side, const Alignment &alignment) const']]],
+ ['score_5fgap_10814',['score_gap',['../classvg_1_1GSSWAligner.html#a4071f79659899761586807411d5ab767',1,'vg::GSSWAligner::score_gap()'],['../namespacevg.html#aea0e7a0965b967bed3ff54e6ff630f91',1,'vg::score_gap()']]],
+ ['score_5fmismatch_10815',['score_mismatch',['../classvg_1_1GSSWAligner.html#ab40663f27266555cd2718fca337ac348',1,'vg::GSSWAligner::score_mismatch()'],['../classvg_1_1Aligner.html#a7e359a8a6af31e1fba84a681c751ec23',1,'vg::Aligner::score_mismatch(string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const'],['../classvg_1_1Aligner.html#a6728bc34b9e4daa49c1045c8ded44553',1,'vg::Aligner::score_mismatch(size_t length) const'],['../classvg_1_1QualAdjAligner.html#ada69f388d291f6c3693812d91c84231a',1,'vg::QualAdjAligner::score_mismatch()']]],
+ ['score_5fpartial_5falignment_10816',['score_partial_alignment',['../classvg_1_1GSSWAligner.html#adc950708e8d5ff812a838116c6b50910',1,'vg::GSSWAligner::score_partial_alignment()'],['../classvg_1_1Aligner.html#a4537844a4aa7783f6a41c7cefd758602',1,'vg::Aligner::score_partial_alignment()'],['../classvg_1_1QualAdjAligner.html#aee20bae08e744224825723a878d57bef',1,'vg::QualAdjAligner::score_partial_alignment()']]],
+ ['score_5fsort_5fand_5fdeduplicate_5falignments_10817',['score_sort_and_deduplicate_alignments',['../classvg_1_1Mapper.html#ae820fb3edeac9da2ef475cb6b0e0f0e9',1,'vg::Mapper']]],
+ ['score_5fto_5funnormalized_5flikelihood_5fln_10818',['score_to_unnormalized_likelihood_ln',['../classvg_1_1GSSWAligner.html#a59623587d4dfb1e0310fb608e9def2f0',1,'vg::GSSWAligner']]],
+ ['score_5ftree_10819',['score_tree',['../classvg_1_1MinimizerMapper.html#ad4b6267b5e93d0fb618de0584cf2b213',1,'vg::MinimizerMapper']]],
+ ['search_5fleft_10820',['search_left',['../classvg_1_1NestedTraversalFinder.html#a04465d6248557f427e5d35b657292e25',1,'vg::NestedTraversalFinder']]],
+ ['search_5fmultipath_5falignment_10821',['search_multipath_alignment',['../namespacevg.html#aa9d71371be6972c8284b267d42fac754',1,'vg']]],
+ ['search_5fright_10822',['search_right',['../classvg_1_1NestedTraversalFinder.html#a2b020fead8b7c40b06f9c0e1041b2cb5',1,'vg::NestedTraversalFinder']]],
+ ['seed_10823',['Seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#adf405ffb00189f3c469f3fc7e79fde01',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed()=default'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#ad6d85e239a68f94ff5dbf2b0362f3c52',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(pos_t pos, size_t source, ZipCode zipcode)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a7859f190024d96f7182de94f197df881',1,'vg::SnarlDistanceIndexClusterer::Seed::Seed(Seed &&other)']]],
+ ['seed_5fend_10824',['seed_end',['../classvg_1_1algorithms_1_1Anchor.html#a2db67aba40631bb9e462e2ae744a2ddd',1,'vg::algorithms::Anchor']]],
+ ['seed_5fis_5freversed_5fat_5fdepth_10825',['seed_is_reversed_at_depth',['../classvg_1_1ZipCodeTree.html#a984f21c55ccaf7b053ce0e4fe77f91ff',1,'vg::ZipCodeTree']]],
+ ['seed_5fstart_10826',['seed_start',['../classvg_1_1algorithms_1_1Anchor.html#af68c4af649ee5dfbf4cfff0e0e4493c8',1,'vg::algorithms::Anchor']]],
+ ['seeds_5fin_5fsubgraph_10827',['seeds_in_subgraph',['../classvg_1_1MinimizerMapper.html#a98117858da937a277f445898bcc2d125',1,'vg::MinimizerMapper']]],
+ ['seek_10828',['Seek',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa221be19182d88b7caa36ead3e63c829',1,'vg::io::BlockedGzipInputStream']]],
+ ['seek_5fgroup_10829',['seek_group',['../classvg_1_1io_1_1MessageIterator.html#a97a1561c82f55827a208b2bea5e8da71',1,'vg::io::MessageIterator::seek_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#aad5921d9a10314f8060b0835225fc3cd',1,'vg::io::ProtobufIterator::seek_group()']]],
+ ['select_5fdiploid_10830',['select_diploid',['../namespacevg.html#a5b634a10b029be9c22dccc3ef362f61c',1,'vg']]],
+ ['select_5fhaplotypes_10831',['select_haplotypes',['../namespacevg.html#af2de3a2f2b77abef4336df983356fc23',1,'vg']]],
+ ['seq_5fchain_5ffor_5fpath_10832',['seq_chain_for_path',['../haplotypes__main_8cpp.html#a462a39ecca4a3d1298196a6f23ef24a5',1,'haplotypes_main.cpp']]],
+ ['seq_5ffor_5fchain_10833',['seq_for_chain',['../haplotypes__main_8cpp.html#ace19d06b45cb66b44602157c3bc24916',1,'haplotypes_main.cpp']]],
+ ['seqcomplexity_10834',['SeqComplexity',['../structvg_1_1SeqComplexity.html#a18ab1a3d85623f42d1e8848fcf94846d',1,'vg::SeqComplexity::SeqComplexity(string::const_iterator begin, string::const_iterator end)'],['../structvg_1_1SeqComplexity.html#ac7a2e970b541883c812fafa7851d6278',1,'vg::SeqComplexity::SeqComplexity(const string &seq)']]],
+ ['sequence_10835',['sequence',['../classvg_1_1MaximalExactMatch.html#a9746bd3ef368dbeae05459381223cebc',1,'vg::MaximalExactMatch::sequence()'],['../classvg_1_1multipath__alignment__t.html#a5637161345c2b1a557a40188b564dd55',1,'vg::multipath_alignment_t::sequence()'],['../classvg_1_1edit__t.html#aca5aef83ea5f5195699732c61c44b86d',1,'vg::edit_t::sequence()'],['../classvg_1_1Sampler.html#a355de4870a71a88834406f3e7f297272',1,'vg::Sampler::sequence()']]],
+ ['sequence_5fpositions_10836',['sequence_positions',['../classvg_1_1BaseMapper.html#a1fc5077e5ea4a236ddf8edcf93288eb9',1,'vg::BaseMapper']]],
+ ['serialize_10837',['serialize',['../structvg_1_1GBWTHandler.html#aa855690c481cca126734e20f5d126d04',1,'vg::GBWTHandler::serialize()'],['../classvg_1_1Packer.html#a833e1fa21ac3f5f5f6a001c5c5ee0f4c',1,'vg::Packer::serialize()'],['../classvg_1_1SnarlManager.html#afdcb932a1a891671acbdaaf445aee0b2',1,'vg::SnarlManager::serialize()'],['../classvg_1_1VG.html#a0ee4603518e9cd5915a65e65c2d763b2',1,'vg::VG::serialize()'],['../classvg_1_1ZipCodeCollection.html#afb7d15490acd1b076664049072184914',1,'vg::ZipCodeCollection::serialize()'],['../classxg_1_1XGPath.html#a74e7b70ac4829545e7b48c137808d6e4',1,'xg::XGPath::serialize()'],['../classhandlegraph_1_1Serializable.html#adae323cce9552f03774ab71dd5fb07d0',1,'handlegraph::Serializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1Serializable.html#ac6e9dfc830acdf96fbfe53d83d33802e',1,'handlegraph::Serializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1Serializable.html#a050e6c2b6e2fccd85362e908da60d20b',1,'handlegraph::Serializable::serialize(std::ostream &out)'],['../classhandlegraph_1_1Serializable.html#aa97699c9b50235d5f2439eb57c5df653',1,'handlegraph::Serializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#acaec0b472d85de2ff98b8635b5fbf33c',1,'handlegraph::TriviallySerializable::serialize(const std::function< void(const void *, size_t)> &iteratee) const =0'],['../classhandlegraph_1_1TriviallySerializable.html#a2881d2d598bd35cc68008ad3dc4b82d5',1,'handlegraph::TriviallySerializable::serialize(int fd)=0'],['../classhandlegraph_1_1TriviallySerializable.html#ab04c99b94217a13ce598e8fd484b09c1',1,'handlegraph::TriviallySerializable::serialize(int fd) const'],['../classhandlegraph_1_1TriviallySerializable.html#aaeb37dbdd6e221e2c5ddfba9cb226c56',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename) const'],['../classhandlegraph_1_1TriviallySerializable.html#a6c306e7cce2dfe6079b093aa2fae77a0',1,'handlegraph::TriviallySerializable::serialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#a674a89ff2072c5e57c7f5f07d915d049',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out) const'],['../classhandlegraph_1_1TriviallySerializable.html#a89624195e0d24768774e98c61d17c779',1,'handlegraph::TriviallySerializable::serialize(std::ostream &out)']]],
+ ['serialize_5fand_5fmeasure_10838',['serialize_and_measure',['../classxg_1_1XG.html#aac0ec5744208c54abfc692bf7ff66536',1,'xg::XG']]],
+ ['serialize_5fmembers_10839',['serialize_members',['../classxg_1_1XG.html#a99af109d31808040b7f1819c6a236b05',1,'xg::XG::serialize_members()'],['../classhandlegraph_1_1Serializable.html#a79235728e5f1e8fb1c0e19e275a33fff',1,'handlegraph::Serializable::serialize_members()']]],
+ ['serialize_5fmembers_5fand_5fmeasure_10840',['serialize_members_and_measure',['../classxg_1_1XG.html#af7c089f5d1342620dd573b2aa4197ca8',1,'xg::XG']]],
+ ['serialize_5fsegment_5ftranslation_10841',['serialize_segment_translation',['../structGraphHandler.html#ad8ffb0dac5a43b9c1dee33eba093d02e',1,'GraphHandler']]],
+ ['serialize_5fto_5femitter_10842',['serialize_to_emitter',['../classvg_1_1VG.html#a59121c0226c3fd8c328641490bf2fac6',1,'vg::VG']]],
+ ['serialize_5fto_5ffile_10843',['serialize_to_file',['../classvg_1_1VG.html#a3522042a3a00ac802d6738d0bec6269c',1,'vg::VG']]],
+ ['serialize_5fto_5ffunction_10844',['serialize_to_function',['../classvg_1_1VG.html#ad3187dd6ce750583f6b1a7c32f278d2a',1,'vg::VG']]],
+ ['serialize_5fto_5fostream_10845',['serialize_to_ostream',['../classvg_1_1VG.html#a70e67b525bca0f766d7f0170759ed1d0',1,'vg::VG']]],
+ ['set_10846',['set',['../structvg_1_1subcommand_1_1BaseArgSpec.html#ae73224926db6d8d7730212d2714e1dcf',1,'vg::subcommand::BaseArgSpec::set()'],['../structvg_1_1subcommand_1_1ArgSpec.html#afd6266196b810cf1b11c88e5ad3fd2a2',1,'vg::subcommand::ArgSpec::set()'],['../structvg_1_1subcommand_1_1BaseOptionGroup.html#ad81d797abdd9ece7dece847ad979f80c',1,'vg::subcommand::BaseOptionGroup::set()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a667b46c883efd1b60966679f31bb03fe',1,'vg::subcommand::OptionGroup::set()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a72309d1c25433c7e3a6e3e7dac0930fd',1,'vg::subcommand::GroupedOptionGroup::set()']]],
+ ['set_5falignment_5fscores_10847',['set_alignment_scores',['../classvg_1_1AlignerClient.html#a1fde3e4537147030d153d403fd04ec77',1,'vg::AlignerClient::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#adbdd2fabd7a36353526663aede3cb555',1,'vg::AlignerClient::set_alignment_scores(std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1AlignerClient.html#a79424f53b6e4f588da23ea531a600b84',1,'vg::AlignerClient::set_alignment_scores(const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)'],['../classvg_1_1BaseMapper.html#addc9b0af15050357598c372e135d6a0e',1,'vg::BaseMapper::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1BaseMapper.html#aed94c577ba8f01eb8098d1be74b8d70a',1,'vg::BaseMapper::set_alignment_scores(istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, double haplotype_consistency_exponent=1)'],['../classvg_1_1MinimizerMapper.html#a98a602ac6b9f20d9da825d8a542ceebd',1,'vg::MinimizerMapper::set_alignment_scores()'],['../classvg_1_1MultipathMapper.html#ad897513b9554b2dabebea47cc3f3da9f',1,'vg::MultipathMapper::set_alignment_scores()']]],
+ ['set_5fallele_10848',['set_allele',['../classvg_1_1PhasedGenome.html#ad0fdafbc6cb6fbfb576be92f6f6bc17d',1,'vg::PhasedGenome']]],
+ ['set_5fannotation_10849',['set_annotation',['../classvg_1_1multipath__alignment__t.html#aebfe1bbda50606c4feb85bb674698c4e',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name)'],['../classvg_1_1multipath__alignment__t.html#a1927cf1ca631a6efb5ed6c83072e2e2c',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, double value)'],['../classvg_1_1multipath__alignment__t.html#a37e9679383b80b3a5028017155d04296',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, bool value)'],['../classvg_1_1multipath__alignment__t.html#aca07d0a515d16b62eca1f1c9ad44ffc9',1,'vg::multipath_alignment_t::set_annotation(const string &annotation_name, const string &value)'],['../namespacevg.html#adea29af7b94ac90b1db0eacd908511c0',1,'vg::set_annotation(Annotated *annotated, const string &name, const AnnotationType &annotation)'],['../namespacevg.html#a54bcd5d5fc5318bbdbe784f224b906bd',1,'vg::set_annotation(Annotated &annotated, const string &name, const AnnotationType &annotation)']]],
+ ['set_5fautomatic_5fmin_5fclustering_5flength_10850',['set_automatic_min_clustering_length',['../classvg_1_1MultipathMapper.html#ac0a6f15f0273faa48ff52a59a08855e1',1,'vg::MultipathMapper']]],
+ ['set_5favg_10851',['set_avg',['../classvg_1_1Filter.html#a3629b0035db72bc575a6f0d440b52288',1,'vg::Filter']]],
+ ['set_5fbaseline_5ferror_10852',['set_baseline_error',['../classvg_1_1PoissonSupportSnarlCaller.html#a41964acba3d81c26b01f9b00cd49257a',1,'vg::PoissonSupportSnarlCaller']]],
+ ['set_5fchain_5fcomponent_10853',['set_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a6d70e8ff87f9e2a2d47511b9aece4980',1,'vg::ZipCode::node_code_t::set_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a05fecca7e22cfd80595143e5b6fe1b74',1,'vg::ZipCode::snarl_code_t::set_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a969b901d95d609ce1a065278ef6bd7fb',1,'vg::ZipCodeForest::sort_value_t::set_chain_component()']]],
+ ['set_5fchain_5forder_10854',['set_chain_order',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a33c2b7d50ccefb836fe376dec56c9c09',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['set_5fchain_5fvalues_10855',['set_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae0c994c6c86ccbc4b32689baa6183349',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['set_5fchild_5fcount_10856',['set_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04d8cd3924cd20476f71d21690530ee6',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fcircularity_10857',['set_circularity',['../classvg_1_1VG.html#a73c97ce0157b90f95b888e4b6983f5c8',1,'vg::VG::set_circularity()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a9172694447503e35d50093d55e845eb8',1,'handlegraph::MutablePathHandleGraph::set_circularity()']]],
+ ['set_5fcode_5ftype_10858',['set_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aeac2169d6f24e91993e1b8c28b8d5a30',1,'vg::ZipCode::snarl_code_t::set_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ab80c26e62009341686000a010bb0d5c3',1,'vg::ZipCodeForest::sort_value_t::set_code_type()']]],
+ ['set_5fcompressed_5fannotation_10859',['set_compressed_annotation',['../namespacevg.html#a3f6c363cc3cb03b7379635741d1b0837',1,'vg::set_compressed_annotation(Annotated *annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)'],['../namespacevg.html#a0efd9e2e5d1ab86647910ccd002109cd',1,'vg::set_compressed_annotation(Annotated &annotated, const string &base_name, std::vector< AnnotatonValueType > annotation)']]],
+ ['set_5fconnection_10860',['set_connection',['../classvg_1_1subpath__t.html#ae0073c7a92ebfc9ea0acfe7e17837bd1',1,'vg::subpath_t']]],
+ ['set_5fconnectivity_10861',['set_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac59bb21ee878d8f2923ac7f8dc857641',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fcrash_5fcontext_10862',['set_crash_context',['../namespacevg.html#ac801de9444375b2f131d3c21d125e83b',1,'vg']]],
+ ['set_5fdir_10863',['set_dir',['../namespacevg_1_1temp__file.html#a13270094cd53cedbd540c7fd4412f0d6',1,'vg::temp_file::set_dir()'],['../namespacexg_1_1temp__file.html#a43d250a4567f29ba269e8a3f4c39dbb6',1,'xg::temp_file::set_dir()']]],
+ ['set_5fdistance_5fend_5fleft_10864',['set_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a9b8478c75baaf1a65691dd2d72f4c54d',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fdistance_5fend_5fright_10865',['set_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#acb835fdaed8979f3faa044171bfcbe8f',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fdistance_5fstart_5fleft_10866',['set_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2a611cd876f68bb23d5a62babde8bdf9',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fdistance_5fstart_5fright_10867',['set_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3a6fa5c7c47f14100596b3384d72d51f',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fedge_10868',['set_edge',['../classvg_1_1VG.html#ae1131c1ff0a94ed2ec9ef35cb678801b',1,'vg::VG']]],
+ ['set_5ffilter_5fmatches_10869',['set_filter_matches',['../classvg_1_1Filter.html#ad45e46ca49dca65ee8e3d838d28d71b6',1,'vg::Filter']]],
+ ['set_5ffragment_5flength_5fdistr_5fparams_10870',['set_fragment_length_distr_params',['../classvg_1_1PairedEndMapper.html#a09e89f6da87d25f0ad66fb9eb3139a98',1,'vg::PairedEndMapper']]],
+ ['set_5ffrom_5flength_10871',['set_from_length',['../classvg_1_1edit__t.html#aba75c7882507dcced8ca80081b4b504b',1,'vg::edit_t']]],
+ ['set_5fhash_5fcolor_10872',['set_hash_color',['../classvg_1_1Viz.html#ab5559043258bf1e1cd4e3a754342cdde',1,'vg::Viz']]],
+ ['set_5fhet_5fbias_10873',['set_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a0cb5e2761e2c2feebc901d54a5891454',1,'vg::RatioSupportSnarlCaller']]],
+ ['set_5fid_5fincrement_10874',['set_id_increment',['../classvg_1_1VG.html#aebe71b82645b85e73342366cea0a4549',1,'vg::VG::set_id_increment()'],['../classhandlegraph_1_1MutableHandleGraph.html#ab844ab426cd9f289414aca4d8b892ca9',1,'handlegraph::MutableHandleGraph::set_id_increment()']]],
+ ['set_5finsertion_5fbias_10875',['set_insertion_bias',['../classvg_1_1PoissonSupportSnarlCaller.html#abeb1d41aaa26a91cb3319cc5fe6b0af0',1,'vg::PoissonSupportSnarlCaller']]],
+ ['set_5fintermediate_5ffile_5fkeeping_10876',['set_intermediate_file_keeping',['../classvg_1_1IndexRegistry.html#a983cdafc1b28ea24def5349f90e415eb',1,'vg::IndexRegistry']]],
+ ['set_5fintersection_10877',['set_intersection',['../namespacevg.html#a234b2ca417edb50a3c738991fcfc269a',1,'vg']]],
+ ['set_5fintron_5flength_5fdistribution_10878',['set_intron_length_distribution',['../classvg_1_1MultipathMapper.html#a8c6768f5299e424b19d569dd077dbafe',1,'vg::MultipathMapper']]],
+ ['set_5finverse_10879',['set_inverse',['../classvg_1_1Filter.html#afb65a7ed6bb059f22196415c631680e9',1,'vg::Filter']]],
+ ['set_5fis_5freverse_10880',['set_is_reverse',['../classvg_1_1mapping__t.html#ad248204841f7ba0ce4c3604ec138556d',1,'vg::mapping_t::set_is_reverse()'],['../classvg_1_1position__t.html#a3d78fabe1cda0e0243071a36ccd73996',1,'vg::position_t::set_is_reverse()']]],
+ ['set_5fis_5freversed_10881',['set_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#aaab7c0874ce7df9a462009840404e8fb',1,'vg::ZipCode::node_code_t::set_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8836324bf0af9142171328634fba592d',1,'vg::ZipCode::snarl_code_t::set_is_reversed()']]],
+ ['set_5flast_5fcomponent_10882',['set_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a98cac9a41d2c53554c96084e35a591b5',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5flength_10883',['set_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a2ef78836b286d95e1ad7d0b88c55cbaf',1,'vg::ZipCode::node_code_t::set_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a138235f7ccb84dcc25134cf6f200aecb',1,'vg::ZipCode::chain_code_t::set_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a51cb4c8c5a89e591cede7c9a27d77c8b',1,'vg::ZipCode::snarl_code_t::set_length()']]],
+ ['set_5flog_5fodds_5fagainst_5fsplice_10884',['set_log_odds_against_splice',['../classvg_1_1MultipathMapper.html#a8902c35e23b24555f94fd2f7d95ef806',1,'vg::MultipathMapper']]],
+ ['set_5fmapping_5fquality_10885',['set_mapping_quality',['../classvg_1_1multipath__alignment__t.html#a492c704bcf2ec27123143b83d8218ad9',1,'vg::multipath_alignment_t']]],
+ ['set_5fmax_5fmerge_5fsupression_5flength_10886',['set_max_merge_supression_length',['../classvg_1_1MultipathMapper.html#a3db9d73e2a4b296df8df495c028a615b',1,'vg::MultipathMapper']]],
+ ['set_5fmin_5fbp_5fedge_5foverride_10887',['set_min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a920ba7030a3946b9b239b1a7f1abbe44',1,'vg::TraversalSupportFinder']]],
+ ['set_5fmin_5fdepth_10888',['set_min_depth',['../classvg_1_1Filter.html#a94d0c4f93831a6faf70411dc6caf0ac3',1,'vg::Filter']]],
+ ['set_5fmin_5fpercent_5fidentity_10889',['set_min_percent_identity',['../classvg_1_1Filter.html#ae1837a93c7c3575c52dcba37538070f8',1,'vg::Filter']]],
+ ['set_5fmin_5fqual_10890',['set_min_qual',['../classvg_1_1Filter.html#a5c3851f5838da69576fd3e59443bb8d3',1,'vg::Filter']]],
+ ['set_5fmin_5fsoftclip_5flength_5ffor_5fsplice_10891',['set_min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#ad3848a9b82e967ca119dd94add068597',1,'vg::MultipathMapper']]],
+ ['set_5fmin_5fsplice_5flength_10892',['set_min_splice_length',['../classvg_1_1MultipathAlignmentEmitter.html#aa6e3289654a2ebe8ed2b934a1fcd6d40',1,'vg::MultipathAlignmentEmitter']]],
+ ['set_5fmin_5fsupports_10893',['set_min_supports',['../classvg_1_1SupportBasedSnarlCaller.html#a3afbd8d1bc78b6716c587b93424db8cb',1,'vg::SupportBasedSnarlCaller']]],
+ ['set_5fmy_5fpath_5fposition_5fgraph_10894',['set_my_path_position_graph',['../classvg_1_1Filter.html#a8986008ebcb92629e17da5ed45a23734',1,'vg::Filter']]],
+ ['set_5fmy_5fvg_10895',['set_my_vg',['../classvg_1_1Filter.html#a8742f0354b0e40a55ba2dd7270bd197d',1,'vg::Filter']]],
+ ['set_5fnested_10896',['set_nested',['../classvg_1_1VCFOutputCaller.html#a35f5b2f9d93ea764e0d8f5f957ba4c3a',1,'vg::VCFOutputCaller']]],
+ ['set_5fnext_10897',['set_next',['../classvg_1_1connection__t.html#adc3fded850671e336763eaa0c6d87e78',1,'vg::connection_t::set_next()'],['../classvg_1_1subpath__t.html#a2f0c0e1b1e509de732a1318919af0177',1,'vg::subpath_t::set_next()']]],
+ ['set_5fnode_5fid_10898',['set_node_id',['../classvg_1_1mapping__t.html#a3101ac21e398f36c0367a89b20360cd0',1,'vg::mapping_t::set_node_id()'],['../classvg_1_1position__t.html#a5e2f0de1d8da70bb8b233522597bd02b',1,'vg::position_t::set_node_id()']]],
+ ['set_5foffset_10899',['set_offset',['../structhaplo_1_1haplo__DP__rectangle.html#a9ca4ea25d72d1a40b9a0e1a170e88274',1,'haplo::haplo_DP_rectangle::set_offset()'],['../classvg_1_1position__t.html#ad34d5af7aab58a425f33faa2358ef57e',1,'vg::position_t::set_offset()']]],
+ ['set_5foption_5fvalue_10900',['set_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#abdc58a9c90f9adbcac68d3e18f6c7d36',1,'vg::subcommand::BaseOptionGroup']]],
+ ['set_5fpaired_5fall_10901',['set_paired_all',['../structvg_1_1Counts.html#a038f57bbb1cabd1f83b544c22562a0d9',1,'vg::Counts']]],
+ ['set_5fpaired_5fany_10902',['set_paired_any',['../structvg_1_1Counts.html#ad4e3e7b118ed1ec1286d933a57bdbf23',1,'vg::Counts']]],
+ ['set_5fpath_5fposition_10903',['set_path_position',['../classvg_1_1Surjector.html#ac4e7823cc2ce4b65bb8910ef2c1dcbee',1,'vg::Surjector']]],
+ ['set_5fprefix_10904',['set_prefix',['../classvg_1_1IndexRegistry.html#aefc2da48af951d3b300ee0b5c70559c3',1,'vg::IndexRegistry']]],
+ ['set_5fprefix_5fsum_5for_5fidentifier_10905',['set_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a0c99221572a9dce4051fa68a79bb540f',1,'vg::ZipCode::node_code_t::set_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8a66d4f3fba23bebe13618b0d45988a4',1,'vg::ZipCode::snarl_code_t::set_prefix_sum_or_identifier()']]],
+ ['set_5fprev_5fidx_10906',['set_prev_idx',['../structhaplo_1_1haplo__DP__rectangle.html#ad1c78747473f9b8816c459949b8b8e8e',1,'haplo::haplo_DP_rectangle']]],
+ ['set_5fquality_10907',['set_quality',['../classvg_1_1multipath__alignment__t.html#a2ff40ca9f44290aeb5406764ccbb5ebf',1,'vg::multipath_alignment_t']]],
+ ['set_5fraw_5fchain_5fcomponent_10908',['set_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a32b61e2274b266a217cebace47e2907a',1,'vg::ZipCode::node_code_t::set_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab4c8a0b7d2e5b20bab6ff83558581a4d',1,'vg::ZipCode::snarl_code_t::set_raw_chain_component()']]],
+ ['set_5fraw_5fchild_5fcount_10909',['set_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ace304ea5d619189a001274a3c117a97b',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fcode_5ftype_10910',['set_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a4b2441552754d8c09003a86ed412af6e',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fconnectivity_10911',['set_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a7e9fc82b6947464a05b05ad154a706dd',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fraw_5fdistance_5fend_5fleft_10912',['set_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6d9d20da8c7cee397bc621395ebb0595',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fdistance_5fend_5fright_10913',['set_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34782c4f89ca5b5ed549c086d782a49a',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fdistance_5fstart_5fleft_10914',['set_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6ef05afc876f9d157a4a22ece67ec14b',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fdistance_5fstart_5fright_10915',['set_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a3c42e8e885b205135c84167f3d0c30f9',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fis_5freversed_10916',['set_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ce29ebd996f8894ed6942633fb387b9',1,'vg::ZipCode::node_code_t::set_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af7cdb5f02946631384bab58c2732c305',1,'vg::ZipCode::snarl_code_t::set_raw_is_reversed()']]],
+ ['set_5fraw_5flast_5fcomponent_10917',['set_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#a389422a0482e9a0fe88b77bacc88b2fa',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fraw_5flength_10918',['set_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a9eaa33f8ee594c5fe686c4e5e0bfbe30',1,'vg::ZipCode::node_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a373aeb1528f44cf694a7711ab827d088',1,'vg::ZipCode::chain_code_t::set_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a6f15f89fa329bcd06088318bb17bbdb2',1,'vg::ZipCode::snarl_code_t::set_raw_length()']]],
+ ['set_5fraw_5fprefix_5fsum_5for_5fidentifier_10919',['set_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a02b5011800febaebbef6c517fc08320e',1,'vg::ZipCode::node_code_t::set_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a38cb2f04ee15fc31ec69d5ef06f45ac1',1,'vg::ZipCode::snarl_code_t::set_raw_prefix_sum_or_identifier()']]],
+ ['set_5fraw_5frecord_5foffset_10920',['set_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5a5034d3c583b9220450bcc2da59f31f',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fraw_5fsnarl_5frank_5for_5fidentifier_10921',['set_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a214ccf14cf2a287d7756d10036ce9bff',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fread_5f1_5fadapter_10922',['set_read_1_adapter',['../classvg_1_1MultipathMapper.html#aaf7ee8334193018b945900b00cec8826',1,'vg::MultipathMapper']]],
+ ['set_5fread_5f2_5fadapter_10923',['set_read_2_adapter',['../classvg_1_1MultipathMapper.html#a1c1674e89e4702168e75bca6fdb4d0bd',1,'vg::MultipathMapper']]],
+ ['set_5fread_5fcoverage_10924',['set_read_coverage',['../classvg_1_1MultipathMapper.html#a2ce30f7fe70325b6101356f5eb67df3d',1,'vg::MultipathMapper']]],
+ ['set_5fread_5fgroup_10925',['set_read_group',['../classvg_1_1MultipathAlignmentEmitter.html#ad772e7a7315be2a57899c234116de800',1,'vg::MultipathAlignmentEmitter']]],
+ ['set_5frecord_5foffset_10926',['set_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a33b431da2b73e995db51480fd2e5385b',1,'vg::ZipCode::snarl_code_t']]],
+ ['set_5fregion_10927',['set_region',['../classvg_1_1VcfBuffer.html#a0a636a74fef67c3cfd59730db3ed427c',1,'vg::VcfBuffer::set_region()'],['../classvg_1_1WindowedVcfBuffer.html#ab6c81f821d5ddcace1e67e7081793142',1,'vg::WindowedVcfBuffer::set_region()']]],
+ ['set_5fremove_5ffailing_5fedits_10928',['set_remove_failing_edits',['../classvg_1_1Filter.html#ab91fdad4a96917a43f1fed85e11a9645',1,'vg::Filter']]],
+ ['set_5fsample_5fname_10929',['set_sample_name',['../classvg_1_1MultipathAlignmentEmitter.html#a398cd239c156944100299fc5babb6194',1,'vg::MultipathAlignmentEmitter']]],
+ ['set_5fscore_10930',['set_score',['../classvg_1_1connection__t.html#ab7e71cc31834606883ce7fee437bdd7b',1,'vg::connection_t::set_score()'],['../classvg_1_1subpath__t.html#a7229edbbe9e72084b114bd03079cc105',1,'vg::subpath_t::set_score()'],['../namespacevg.html#a3b05a1318d7be5ecf3547a3eca837618',1,'vg::set_score()']]],
+ ['set_5fsequence_10931',['set_sequence',['../classvg_1_1multipath__alignment__t.html#a5cabf8eec673f7aaf7d28add560a7e32',1,'vg::multipath_alignment_t::set_sequence()'],['../classvg_1_1edit__t.html#aa2a77df9db620c8500a3eb4802229f43',1,'vg::edit_t::set_sequence()']]],
+ ['set_5fshow_5fprogress_10932',['set_show_progress',['../classvg_1_1GraphCaller.html#a1005b4de9fde3d23adcd1d35f8fece09',1,'vg::GraphCaller']]],
+ ['set_5fsnarl_5frank_5for_5fidentifier_10933',['set_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a43ebf63adc3f81a82dd4b9bb77be2772',1,'vg::ZipCode::chain_code_t']]],
+ ['set_5fsnarl_5fvalues_10934',['set_snarl_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a858ed22ff1cba852000f4815bd03e20f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['set_5fsoft_5fclip_5flimit_10935',['set_soft_clip_limit',['../classvg_1_1Filter.html#a8e69a6bc40641a3377dd60f44ec52816',1,'vg::Filter']]],
+ ['set_5fsort_5fvalue_10936',['set_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aa1ea92740944abf659a9080acc7fa0b3',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['set_5fsource_5fpaths_10937',['set_source_paths',['../classvg_1_1Sampler.html#ab217a74d97bc905480c236ab66d30232',1,'vg::Sampler']]],
+ ['set_5fsplit_5fread_5flimit_10938',['set_split_read_limit',['../classvg_1_1Filter.html#a377d6661a880d4d3798e8780d61d6db0',1,'vg::Filter']]],
+ ['set_5fstart_10939',['set_start',['../classvg_1_1multipath__alignment__t.html#a9230aa70e0c93066e0c8f9f4c4af28fa',1,'vg::multipath_alignment_t']]],
+ ['set_5fsupport_5fswitch_5fthreshold_10940',['set_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a53940205edddd5d3bb379b82ede4f74f',1,'vg::TraversalSupportFinder']]],
+ ['set_5fsystem_5fdir_10941',['set_system_dir',['../namespacevg_1_1temp__file.html#ac061a6d187921157d4e62930445996e8',1,'vg::temp_file']]],
+ ['set_5ftags_10942',['set_tags',['../gbwt__main_8cpp.html#ab3856151a0825f396467961305716704',1,'gbwt_main.cpp']]],
+ ['set_5ftarget_5fmemory_5fusage_10943',['set_target_memory_usage',['../classvg_1_1IndexRegistry.html#aee06106e4888a5a17d12fa10f1e87893',1,'vg::IndexRegistry']]],
+ ['set_5fto_5flength_10944',['set_to_length',['../classvg_1_1edit__t.html#a9b38a79f561f60c377c35e186c5cfd96',1,'vg::edit_t']]],
+ ['set_5ftranslation_10945',['set_translation',['../classvg_1_1VCFOutputCaller.html#a918bfde23f9f6afacec9b10319030414',1,'vg::VCFOutputCaller']]],
+ ['set_5fvalue_10946',['set_value',['../structvg_1_1subcommand_1_1ArgSpec.html#a1e31767c05c4a085a3b8087067af70c4',1,'vg::subcommand::ArgSpec::set_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a25817ff171a0199cf4e21fee15261f14',1,'vg::subcommand::ValueArgSpec::set_value()']]],
+ ['set_5fwindow_5flength_10947',['set_window_length',['../classvg_1_1Filter.html#adb96fca6a301e45c84b010f5461440a9',1,'vg::Filter']]],
+ ['setk_10948',['setK',['../classvg_1_1FlowTraversalFinder.html#adf6216e25b6f61a09aa13816eafcd6e3',1,'vg::FlowTraversalFinder']]],
+ ['sha1head_10949',['sha1head',['../namespacevg.html#a6821cd887e206752c50c1a7be764d1f5',1,'vg']]],
+ ['sha1sum_10950',['sha1sum',['../namespacevg.html#a0cada7d579d914675f53490e0488ab53',1,'vg']]],
+ ['shallow_5fcontents_10951',['shallow_contents',['../classvg_1_1SnarlManager.html#afb7f6b946d3ec05ed619e09491e0a92d',1,'vg::SnarlManager']]],
+ ['share_5fterminal_5fpositions_10952',['share_terminal_positions',['../classvg_1_1MultipathMapper.html#aaff4140e7e711a25b1eb284d7c830c2c',1,'vg::MultipathMapper']]],
+ ['short_5fmode_5fname_10953',['short_mode_name',['../prune__main_8cpp.html#adf85e917657920f23dce6cefc2ecd2b9',1,'prune_main.cpp']]],
+ ['shortest_5fcycle_5flength_10954',['shortest_cycle_length',['../namespacevg_1_1algorithms.html#acfe6f985e8bedbad1b33861c62379772',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph, const handle_t &source)'],['../namespacevg_1_1algorithms.html#a012fced2754c445ec404ff5420018982',1,'vg::algorithms::shortest_cycle_length(const HandleGraph *graph)']]],
+ ['shortest_5fcycle_5flength_5finternal_10955',['shortest_cycle_length_internal',['../namespacevg_1_1algorithms.html#aa87ca8c58307fdb47d448deb2ec43389',1,'vg::algorithms']]],
+ ['shortest_5fseq_5fpaths_10956',['shortest_seq_paths',['../classvg_1_1BandedGlobalAligner.html#a7156058732c9d6f40226609f650944a2',1,'vg::BandedGlobalAligner']]],
+ ['show_5fstructure_10957',['show_structure',['../classvg_1_1Packer.html#a4aacf109dc6290d39630e5b25020004e',1,'vg::Packer']]],
+ ['shuffledpairs_10958',['ShuffledPairs',['../classvg_1_1ShuffledPairs.html#a7143ff811c0359854ac091749b1f5642',1,'vg::ShuffledPairs']]],
+ ['sides_5fcontext_10959',['sides_context',['../classvg_1_1VG.html#ad363c6c82e88dcb1b88d05ff55074ed6',1,'vg::VG']]],
+ ['sides_5ffrom_10960',['sides_from',['../classvg_1_1VG.html#ac670f3c729f93ebaa7c8bd5063225597',1,'vg::VG::sides_from(NodeSide side)'],['../classvg_1_1VG.html#a95c975ed419a0873c894cef7a2f2d3ba',1,'vg::VG::sides_from(nid_t id)']]],
+ ['sides_5fof_10961',['sides_of',['../classvg_1_1VG.html#a030b75d2ad50905cc01fe4b7223cbb83',1,'vg::VG']]],
+ ['sides_5fto_10962',['sides_to',['../classvg_1_1VG.html#a1a156ac1e1fde520bae82850105c6c66',1,'vg::VG::sides_to(NodeSide side)'],['../classvg_1_1VG.html#a68733706482bf7b2627be32438160af3',1,'vg::VG::sides_to(nid_t id)']]],
+ ['signature_10963',['signature',['../namespacevg.html#a2616dde2763b947a15ac562fd631e688',1,'vg::signature(const Alignment &aln)'],['../namespacevg.html#a134fc6762c4b66dd4847078b0ddbfdd6',1,'vg::signature(const Alignment &aln1, const Alignment &aln2)']]],
+ ['simple_5fcomponents_10964',['simple_components',['../namespacehandlegraph_1_1algorithms.html#acc16afc14f0a9dd0a34a4c173b229a4b',1,'handlegraph::algorithms']]],
+ ['simple_5foffsets_5fin_5fpaths_10965',['simple_offsets_in_paths',['../namespacevg_1_1algorithms.html#a9ddb73ef3cf5a8891aa82001f272c3c4',1,'vg::algorithms']]],
+ ['simple_5fsds_5fload_10966',['simple_sds_load',['../structvg_1_1Haplotypes_1_1Subchain.html#a9dfc087f0bada7635e975b6c8e8479a8',1,'vg::Haplotypes::Subchain::simple_sds_load()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a34163c2bf756a469dd6bba7880836f82',1,'vg::Haplotypes::TopLevelChain::simple_sds_load()'],['../classvg_1_1Haplotypes.html#a908ed1a2f1147a2162051be87e5ba389',1,'vg::Haplotypes::simple_sds_load()']]],
+ ['simple_5fsds_5fserialize_10967',['simple_sds_serialize',['../structvg_1_1Haplotypes_1_1Subchain.html#ab30088a7f754d1bfb579773000ac73e0',1,'vg::Haplotypes::Subchain::simple_sds_serialize()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ad5f88539013b3d1c0caed224550e3a06',1,'vg::Haplotypes::TopLevelChain::simple_sds_serialize()'],['../classvg_1_1Haplotypes.html#a3a5a36c107109c893cf382064ad9ea69',1,'vg::Haplotypes::simple_sds_serialize()']]],
+ ['simple_5fsds_5fsize_10968',['simple_sds_size',['../structvg_1_1Haplotypes_1_1Subchain.html#a5f1258caf8b13bd3880f2db6e2967908',1,'vg::Haplotypes::Subchain::simple_sds_size()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#afb004505c7fcc83e89b15c229da33a03',1,'vg::Haplotypes::TopLevelChain::simple_sds_size()'],['../classvg_1_1Haplotypes.html#ac0ebaa605235ee2b6f62c084cfdc6126',1,'vg::Haplotypes::simple_sds_size()']]],
+ ['simplify_10969',['simplify',['../classvg_1_1RareVariantSimplifier.html#af17e24fe2acb6700bb7b6d39514af7af',1,'vg::RareVariantSimplifier::simplify()'],['../classvg_1_1SmallSnarlSimplifier.html#a9abe74e35298d7e22f13039a4c6ea5ba',1,'vg::SmallSnarlSimplifier::simplify()'],['../namespacevg.html#a486054f13a4dc43e37c0f0131f6a51ad',1,'vg::simplify(const Alignment &a, bool trim_internal_deletions)'],['../namespacevg.html#a86653c665afe3c8932f60cc39163e202',1,'vg::simplify(const Path &p, bool trim_internal_deletions)'],['../namespacevg.html#a9514446da89671007ae40e420c1297d7',1,'vg::simplify(const Mapping &m, bool trim_internal_deletions)']]],
+ ['simplify_5fcigar_10970',['simplify_cigar',['../namespacevg.html#a553c3fcfd7de2e51f41a6f174c313947',1,'vg']]],
+ ['simplify_5fcomplicated_5fmultipath_5falignment_10971',['simplify_complicated_multipath_alignment',['../classvg_1_1MultipathMapper.html#a92de908372ba0730cfe40638218d815f',1,'vg::MultipathMapper']]],
+ ['simplify_5ffiltered_5fedits_10972',['simplify_filtered_edits',['../namespacevg.html#ad6a42e8ba843cd728b9f84738756b30e',1,'vg']]],
+ ['simplify_5fonce_10973',['simplify_once',['../classvg_1_1SmallSnarlSimplifier.html#afc5525b90ddf851ee7d43a6476acd99d',1,'vg::SmallSnarlSimplifier']]],
+ ['simplify_5fsiblings_10974',['simplify_siblings',['../namespacevg_1_1algorithms.html#a9e4cebdfc1e901db4588c4612653df96',1,'vg::algorithms']]],
+ ['single_5fstranded_5forientation_10975',['single_stranded_orientation',['../namespacehandlegraph_1_1algorithms.html#a61255fd1513da53219871ea01283e360',1,'handlegraph::algorithms']]],
+ ['size_10976',['size',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#acdf72785ba0579f5985b227ef1ccd48b',1,'vg::DozeuInterface::OrderedGraph::size()'],['../structvg_1_1MatchPos_1_1PathList.html#aee5bea8ee39007b6bf5be7ea72d3695b',1,'vg::MatchPos::PathList::size()'],['../classvg_1_1WFATree.html#ad5da24b01eb588c58e07419dbd5eaca4',1,'vg::WFATree::size()'],['../classvg_1_1SnarlState.html#a02f1d46e384b6617ad43f2390fe0ef98',1,'vg::SnarlState::size()'],['../structhaplo_1_1int__itvl__t.html#acee0f4db1fc8cdfd535e6d181093f01f',1,'haplo::int_itvl_t::size()'],['../structhaplo_1_1gbwt__thread__t.html#a5d4d9e80558ff8e4dbab247cc9782a0c',1,'haplo::gbwt_thread_t::size()'],['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a979f8d5623d9040439803c13e7ebf9b6',1,'haplo::linear_haplo_structure::SNVvector::size()'],['../classvg_1_1HandleGraphNodeSet.html#ae66b372aeb3110162c4d9b5c85e3a28d',1,'vg::HandleGraphNodeSet::size()'],['../classvg_1_1MultipathAlignmentGraph.html#a4ec09c91391cfb06c1c9eea132ce4246',1,'vg::MultipathAlignmentGraph::size()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a028494e0f37785dc8a39de6c4f2876a4',1,'vg::Option< vector< Item >, Parser >::size()'],['../classvg_1_1Paths.html#ac2fb517ea95acdd1eb378bf104c16912',1,'vg::Paths::size()'],['../classvg_1_1SmallBitset.html#a1b3ff28863a53eae0c4b47ff854b4d2d',1,'vg::SmallBitset::size()'],['../classvg_1_1SparseUnionFind.html#a85bfb663efac82a593533bd58890c615',1,'vg::SparseUnionFind::size()'],['../structvg_1_1VectorView.html#a62ec6d3c6520fa2b6d70a23abc473e44',1,'vg::VectorView::size()'],['../classvg_1_1VG.html#a9e3720ce267c8167ce679a015063dab6',1,'vg::VG::size()'],['../classvg_1_1ZipCodeCollection.html#ae1aab3360a759d00d8c43e921dba92f6',1,'vg::ZipCodeCollection::size()']]],
+ ['sizelimitexceededexception_10977',['SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html#aeb5d2801f912937112f0e638717156a8',1,'vg::SizeLimitExceededException']]],
+ ['skip_10978',['Skip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#af3849b5292df406dec93738920615987',1,'vg::io::BlockedGzipInputStream']]],
+ ['slope_10979',['slope',['../namespacevg.html#ad477b45059373004136e69022e802e0b',1,'vg']]],
+ ['small_10980',['small',['../classvg_1_1SmallBitset.html#a8e787b217e48311220e91f7fd191fe14',1,'vg::SmallBitset']]],
+ ['smallbitset_10981',['SmallBitset',['../classvg_1_1SmallBitset.html#afcefdbe6a3f708ded8d874537ba0616f',1,'vg::SmallBitset::SmallBitset()'],['../classvg_1_1SmallBitset.html#a5c0e06b1e0482ff98adde62fdf9476f2',1,'vg::SmallBitset::SmallBitset(size_t n)'],['../classvg_1_1SmallBitset.html#ae09de51997e95c9c7c85650748e6d9ab',1,'vg::SmallBitset::SmallBitset(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#a59da25f6a4ae99cc7ff12936930ad5e3',1,'vg::SmallBitset::SmallBitset(SmallBitset &&another)']]],
+ ['smallsnarlsimplifier_10982',['SmallSnarlSimplifier',['../classvg_1_1SmallSnarlSimplifier.html#ae19c2fcf37820ed9112671fbc7e64033',1,'vg::SmallSnarlSimplifier']]],
+ ['smart_5falign_10983',['smart_align',['../classvg_1_1VariantAdder.html#ad3c7e7030142e70f27bc9f0bc42c2cce',1,'vg::VariantAdder']]],
+ ['smellslikegzip_10984',['SmellsLikeGzip',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa45ae9d5a0c1689efa567d573ad5747c',1,'vg::io::BlockedGzipInputStream']]],
+ ['sn_5fdeletion_5fbetween_5fref_10985',['sn_deletion_between_ref',['../structhaplo_1_1linear__haplo__structure.html#aa6e425ddac2acb985a1364dd91a2f948',1,'haplo::linear_haplo_structure']]],
+ ['snarl_5fboundary_5findex_10986',['snarl_boundary_index',['../classvg_1_1SnarlManager.html#a77a449f2f85f37760da1a7182cc1e08b',1,'vg::SnarlManager']]],
+ ['snarl_5fend_5findex_10987',['snarl_end_index',['../classvg_1_1SnarlManager.html#a1fd57d0de5eec34fc037ad0afbdfcb77',1,'vg::SnarlManager']]],
+ ['snarl_5fnumber_10988',['snarl_number',['../classvg_1_1SnarlManager.html#aa779c0eaea2403d9c36761243a7f9262',1,'vg::SnarlManager']]],
+ ['snarl_5fsharing_5fend_10989',['snarl_sharing_end',['../classvg_1_1SnarlManager.html#a2ca9eb75908bfcc4cfac8b241236295b',1,'vg::SnarlManager']]],
+ ['snarl_5fsharing_5fstart_10990',['snarl_sharing_start',['../classvg_1_1SnarlManager.html#a43ecf19c495295c45ca828d499651481',1,'vg::SnarlManager']]],
+ ['snarl_5fstart_5findex_10991',['snarl_start_index',['../classvg_1_1SnarlManager.html#a10a771b6ada139c76e1b435ee301fdb8',1,'vg::SnarlManager']]],
+ ['snarldistanceindexclusterer_10992',['SnarlDistanceIndexClusterer',['../classvg_1_1SnarlDistanceIndexClusterer.html#a0333d80b03665df71c7d448b7cfb0b06',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a66a56a78a0500f79258057cd3d688966',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index, const HandleGraph *graph)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a2275f78a71459c60e56929b106d4ed46',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex &distance_index)'],['../classvg_1_1SnarlDistanceIndexClusterer.html#ae2d9080f0e9ddf775de34ae3aaab7019',1,'vg::SnarlDistanceIndexClusterer::SnarlDistanceIndexClusterer(const SnarlDistanceIndex *distance_index)']]],
+ ['snarlgraph_10993',['SnarlGraph',['../classvg_1_1SnarlGraph.html#a0a6e447620c3a37ca37345854330ffd3',1,'vg::SnarlGraph']]],
+ ['snarlmanager_10994',['SnarlManager',['../classvg_1_1SnarlManager.html#a1037a2341484dc7b54a68cd7207d34b8',1,'vg::SnarlManager::SnarlManager(SnarlIterator begin, SnarlIterator end)'],['../classvg_1_1SnarlManager.html#a61b2b80def0128deea2d2da4886b955e',1,'vg::SnarlManager::SnarlManager(istream &in)'],['../classvg_1_1SnarlManager.html#afe16f481e15e098c885d63f47eceb59c',1,'vg::SnarlManager::SnarlManager(const function< void(const function< void(Snarl &)> &)> &for_each_snarl)'],['../classvg_1_1SnarlManager.html#a43b0ecd9e372556380231f29788948d5',1,'vg::SnarlManager::SnarlManager()=default'],['../classvg_1_1SnarlManager.html#a8e61adc170e3d9241a723ca7593883da',1,'vg::SnarlManager::SnarlManager(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#a7549f1ed7e0e02ae36f172ab5f1d3dbd',1,'vg::SnarlManager::SnarlManager(SnarlManager &&other)=default']]],
+ ['snarlmindistance_10995',['SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html#adc8c303e683b90d923c522790355abad',1,'vg::SnarlMinDistance::SnarlMinDistance()=delete'],['../classvg_1_1SnarlMinDistance.html#aa8efbd4c363589a72da76621b5b4330d',1,'vg::SnarlMinDistance::SnarlMinDistance(SnarlDistanceIndex &distance_index)']]],
+ ['snarlorienteddistancemeasurer_10996',['SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a81db285adff1ae830dcaf2511652e17a',1,'vg::SnarlOrientedDistanceMeasurer']]],
+ ['snarlstate_10997',['SnarlState',['../classvg_1_1SnarlState.html#a14db6ed9f20936f71de90d0d12f92468',1,'vg::SnarlState']]],
+ ['snarltreenodeproblem_10998',['SnarlTreeNodeProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a119a5148780cd1bf7dd073e91974f255',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, const SnarlDistanceIndex &distance_index, const SeedCache *seed, size_t zipcode_depth)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a26ebc81ba9dff9a498a2d222ff72291c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem(net_handle_t net, size_t read_count, size_t seed_count, bool is_reversed_in_parent, size_t node_length, size_t prefix_sum, size_t component, const SeedCache *seed, size_t zipcode_depth)']]],
+ ['sniff_5fmagic_10999',['sniff_magic',['../classvg_1_1io_1_1Registry.html#aea2d7b2c4852a48417eeac861974b9c1',1,'vg::io::Registry']]],
+ ['sniff_5ftag_11000',['sniff_tag',['../classvg_1_1io_1_1MessageIterator.html#ac9b3fff8dbbff744fe1ff60805af1c20',1,'vg::io::MessageIterator::sniff_tag(istream &stream)'],['../classvg_1_1io_1_1MessageIterator.html#aabd024a7358bae988de897aebff39645',1,'vg::io::MessageIterator::sniff_tag(::google::protobuf::io::ZeroCopyInputStream &stream)']]],
+ ['snvs_11001',['SNVs',['../structhaplo_1_1linear__haplo__structure.html#acde3b4cb1fc9eae479ee626bb0916992',1,'haplo::linear_haplo_structure']]],
+ ['soft_5fclip_5ffilter_11002',['soft_clip_filter',['../classvg_1_1Filter.html#aff62aad43f70cd8de756bdbdf94b962d',1,'vg::Filter']]],
+ ['softclip_5fend_11003',['softclip_end',['../namespacevg.html#a05d6d0388148a996d9423524fa4bcc91',1,'vg::softclip_end(const Alignment &alignment)'],['../namespacevg.html#aa84e4c417206a9b3a910dfde0fec3857',1,'vg::softclip_end(const Mapping &mapping)']]],
+ ['softclip_5fstart_11004',['softclip_start',['../namespacevg.html#a90f2af92a34fdf5fb4ddfee8f8880b48',1,'vg::softclip_start(const Alignment &alignment)'],['../namespacevg.html#a9fe66eebecbc5017b05c9044413b2b4e',1,'vg::softclip_start(const Mapping &mapping)']]],
+ ['softclip_5ftrim_11005',['softclip_trim',['../namespacevg.html#a947760b26fa8669d55f2f420174a578c',1,'vg']]],
+ ['sort_11006',['sort',['../classvg_1_1StreamSorter.html#a8372ac35036ca7723bfc90a686115166',1,'vg::StreamSorter::sort()'],['../classvg_1_1VG.html#a902d516631c77d074aa2a11ae70a6957',1,'vg::VG::sort()']]],
+ ['sort_5fanchor_5findexes_11007',['sort_anchor_indexes',['../namespacevg_1_1algorithms.html#aaeeaa766337fc50f0a9b4d3214271923',1,'vg::algorithms']]],
+ ['sort_5fand_5fcompute_5fmapping_5fquality_11008',['sort_and_compute_mapping_quality',['../classvg_1_1MultipathMapper.html#a2994778198719e960d1a2875fa0815e8',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< multipath_alignment_t > &multipath_alns, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#afcc5ceaad2a3f21c4c38beb05c59f474',1,'vg::MultipathMapper::sort_and_compute_mapping_quality(vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< pair< size_t, size_t >> *duplicate_pairs_out=nullptr, vector< double > *pair_multiplicities=nullptr) const']]],
+ ['sort_5fby_5fid_11009',['sort_by_id',['../namespacevg.html#af25c227066a422379ff06d81b5990865',1,'vg']]],
+ ['sort_5fby_5fid_5fdedup_5fand_5fclean_11010',['sort_by_id_dedup_and_clean',['../namespacevg.html#a984c1d2199f90f58677096772b870390',1,'vg']]],
+ ['sort_5fby_5fmapping_5frank_11011',['sort_by_mapping_rank',['../classvg_1_1Paths.html#a2970302cae3a54ef7f4296dbf49266fd',1,'vg::Paths']]],
+ ['sort_5fcompact_5fnodes_11012',['sort_compact_nodes',['../classvg_1_1Transcriptome.html#af7de0784cde3273b344757b81d9bffd5',1,'vg::Transcriptome']]],
+ ['sort_5fedges_5fby_5fid_11013',['sort_edges_by_id',['../namespacevg.html#a90cc117e3ac781c77cf8fdaa7802048b',1,'vg']]],
+ ['sort_5fminimizers_5fby_5fscore_11014',['sort_minimizers_by_score',['../classvg_1_1MinimizerMapper.html#ad72222c1d644b6f676c91511b4b36789',1,'vg::MinimizerMapper']]],
+ ['sort_5fnodes_5fby_5fid_11015',['sort_nodes_by_id',['../namespacevg.html#afb37b16823e6e26cfd8571a1bb621651',1,'vg']]],
+ ['sort_5fone_5finterval_11016',['sort_one_interval',['../classvg_1_1ZipCodeForest.html#a499f52fbb75374e2dc06ce7998ad8fd6',1,'vg::ZipCodeForest']]],
+ ['sort_5fpair_5fby_5fsecond_11017',['sort_pair_by_second',['../namespacevg.html#a47c7102baf9a07b2c701e9937d53351f',1,'vg']]],
+ ['sort_5fpath_5foffsets_11018',['sort_path_offsets',['../namespacevg_1_1algorithms.html#ad8e5913b682c7c14f119543eca7e7548',1,'vg::algorithms']]],
+ ['sort_5fpermutation_11019',['sort_permutation',['../namespacevg.html#ae031408254f8c4031ba0b632f5456059',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end, const std::function< bool(const typename Iterator::value_type &, const typename Iterator::value_type &)> &comparator)'],['../namespacevg.html#ab03fad9d3c71a090606afbe1ef22ce71',1,'vg::sort_permutation(const Iterator &begin, const Iterator &end)']]],
+ ['sort_5fshuffling_5fties_11020',['sort_shuffling_ties',['../namespacevg.html#afe3de0ca79c815a4eaf63df34805f6d0',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp, LazyRNG &rng)'],['../namespacevg.html#aa071bccfee3a9078930f2c385e8dda20',1,'vg::sort_shuffling_ties(RandomIt begin, RandomIt end, Compare comp)']]],
+ ['sort_5ftranscript_5fpaths_5fby_5fname_11021',['sort_transcript_paths_by_name',['../namespacevg.html#aaddbcf35ad2ff899bf2ae0caf901f778',1,'vg']]],
+ ['sort_5ftranscript_5fpaths_5fupdate_5fcopy_5fid_11022',['sort_transcript_paths_update_copy_id',['../classvg_1_1Transcriptome.html#af8caf627ac2480d7439231a2d26162eb',1,'vg::Transcriptome']]],
+ ['sort_5fvalue_5ft_11023',['sort_value_t',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#ac93c5ff7c1b231cd78122b1e1f009aae',1,'vg::ZipCodeForest::sort_value_t::sort_value_t()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a42776d8b3810278dfb5830307fe8190c',1,'vg::ZipCodeForest::sort_value_t::sort_value_t(size_t sort_value, ZipCode::code_type_t code_type, size_t chain_order)']]],
+ ['sorted_5fid_5franges_11024',['sorted_id_ranges',['../namespacevg_1_1algorithms.html#a64bd6b3ff0d2e22bf752e29e3522a98d',1,'vg::algorithms']]],
+ ['sourcesinkoverlay_11025',['SourceSinkOverlay',['../classvg_1_1SourceSinkOverlay.html#a6eaf260d8530ba866753bb3bcb612e15',1,'vg::SourceSinkOverlay']]],
+ ['sparseunionfind_11026',['SparseUnionFind',['../classvg_1_1SparseUnionFind.html#aabd42adac47a3df51b0dfb55d7cde0f4',1,'vg::SparseUnionFind']]],
+ ['spliced_5fcigar_5fagainst_5fpath_11027',['spliced_cigar_against_path',['../classvg_1_1SplicedHTSAlignmentEmitter.html#ac447d6f996b11f12c3b8b2267ff4110e',1,'vg::SplicedHTSAlignmentEmitter']]],
+ ['spliced_5fsurject_11028',['spliced_surject',['../classvg_1_1Surjector.html#a8418e7a55b6b53456c80cbcf937406b5',1,'vg::Surjector']]],
+ ['splicedhtsalignmentemitter_11029',['SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a8e546a34b4f2155fe6fb916123a0135d',1,'vg::SplicedHTSAlignmentEmitter']]],
+ ['spliceregion_11030',['SpliceRegion',['../classvg_1_1SpliceRegion.html#a3ca49fd7bedbe0b97117f87f7a5edba4',1,'vg::SpliceRegion::SpliceRegion(const pos_t &seed_pos, bool search_left, int64_t search_dist, const HandleGraph &graph, const DinucleotideMachine &dinuc_machine, const SpliceStats &splice_stats)'],['../classvg_1_1SpliceRegion.html#a5935bbc5e17cceae08ee9ef0b91b9abe',1,'vg::SpliceRegion::SpliceRegion()=default']]],
+ ['splicestats_11031',['SpliceStats',['../classvg_1_1SpliceStats.html#ac508ff2143cf8296531945e7674702bc',1,'vg::SpliceStats::SpliceStats(const GSSWAligner &scorer)'],['../classvg_1_1SpliceStats.html#a1808c3a4e73d0be56de7caca04142b01',1,'vg::SpliceStats::SpliceStats(const vector< tuple< string, string, double >> &motifs, const vector< double > &lognormal_mixture_weights, const vector< pair< double, double >> &lognormal_component_params, const GSSWAligner &scorer)']]],
+ ['split_11032',['split',['../classvg_1_1BitString.html#af826e3c7bce1aeada3f989b1b7d1bcc5',1,'vg::BitString']]],
+ ['split_5fdelims_11033',['split_delims',['../namespacevg.html#acb2577b9163299f775898c17bcd3f72d',1,'vg::split_delims(const std::string &s, const std::string &delims, std::vector< std::string > &elems, size_t max_cuts)'],['../namespacevg.html#a335fce1edcad06f9840edcfad2c53e34',1,'vg::split_delims(const std::string &s, const std::string &delims, size_t max_cuts)']]],
+ ['split_5fext_11034',['split_ext',['../namespacevg.html#a984d142cea24f43a1025bf7bb7b48a53',1,'vg']]],
+ ['split_5fmulticomponent_5falignments_11035',['split_multicomponent_alignments',['../classvg_1_1MultipathMapper.html#af91f97b8331648b4df7587a461ca36b2',1,'vg::MultipathMapper::split_multicomponent_alignments(vector< multipath_alignment_t > &multipath_alns_out, const Alignment *alignment=nullptr, vector< clustergraph_t > *cluster_graphs=nullptr, vector< size_t > *cluster_idxs=nullptr, vector< double > *multiplicities=nullptr) const'],['../classvg_1_1MultipathMapper.html#a9257a7f9cc75ddd76a8daef803f2d031',1,'vg::MultipathMapper::split_multicomponent_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &multiplicities) const']]],
+ ['split_5fread_5ffilter_11036',['split_read_filter',['../classvg_1_1Filter.html#a0bc2a72604a0cb134c1f5bad7889a1bf',1,'vg::Filter']]],
+ ['split_5fsplice_5fsegment_11037',['split_splice_segment',['../namespacevg.html#aee945465384e60bdda619684ffca2ece',1,'vg']]],
+ ['split_5fstrands_11038',['split_strands',['../namespacehandlegraph_1_1algorithms.html#a1a7504e7155f6f9726c772a4b7c0f2c7',1,'handlegraph::algorithms']]],
+ ['ssw_5fto_5fvg_11039',['ssw_to_vg',['../classvg_1_1SSWAligner.html#a8daaaa17b12f1283c006d633d4c9a8fa',1,'vg::SSWAligner']]],
+ ['sswaligner_11040',['SSWAligner',['../classvg_1_1SSWAligner.html#ae91911b3a1357b0d3ae9bcecd51a592a',1,'vg::SSWAligner']]],
+ ['stack_11041',['stack',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa26ad54b66a37b0f31fa846c48d59882',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['stack_5fpermutations_11042',['stack_permutations',['../namespacevg.html#a5e9c563a243faef4e5357eca9c7c8500',1,'vg']]],
+ ['stack_5fup_5fvalid_5fwalks_11043',['stack_up_valid_walks',['../classvg_1_1ExhaustiveTraversalFinder.html#ab37a28d916291506bfe78a6818943585',1,'vg::ExhaustiveTraversalFinder']]],
+ ['stacktrace_5fmanually_11044',['stacktrace_manually',['../namespacevg.html#a8d771862cc44504508267240462cb043',1,'vg']]],
+ ['stage_11045',['stage',['../classvg_1_1Funnel.html#a21b5f8762aa446a64b5ddb3809e5c8e2',1,'vg::Funnel']]],
+ ['stage_5fstop_11046',['stage_stop',['../classvg_1_1Funnel.html#a87e1b8deccb4438d7f71267ee5f12ced',1,'vg::Funnel']]],
+ ['standard_5fextend_11047',['standard_extend',['../structhaplo_1_1haplo__DP__column.html#a5364cc0f365e68434e346c2b48eea996',1,'haplo::haplo_DP_column']]],
+ ['start_11048',['start',['../classvg_1_1Funnel.html#a4ba2b8db1575820b05d069cd6c802e31',1,'vg::Funnel::start()'],['../classvg_1_1multipath__alignment__t.html#a4cd9b91704e89c799019d9c8962b16bb',1,'vg::multipath_alignment_t::start() const'],['../classvg_1_1multipath__alignment__t.html#ae79344b60aed1577a39391b4b42574f3',1,'vg::multipath_alignment_t::start(size_t i) const']]],
+ ['start_5fbackward_11049',['start_backward',['../namespacevg.html#a43f061abac718e0386965aa537398e74',1,'vg']]],
+ ['start_5fdegree_11050',['start_degree',['../classvg_1_1VG.html#a1ff00edd627e3445eee7f43927bb1518',1,'vg::VG']]],
+ ['start_5fhandle_11051',['start_handle',['../structvg_1_1Haplotypes_1_1Subchain.html#a8b8950af5c76b20ab93ef40dc086da93',1,'vg::Haplotypes::Subchain']]],
+ ['start_5fhint_11052',['start_hint',['../classvg_1_1algorithms_1_1Anchor.html#a1be30d40d8252c36c162bfbb568554a1',1,'vg::algorithms::Anchor']]],
+ ['start_5fhint_5foffset_11053',['start_hint_offset',['../classvg_1_1algorithms_1_1Anchor.html#afe9a192ac276676633aab322189732b0',1,'vg::algorithms::Anchor']]],
+ ['start_5fsize_11054',['start_size',['../classvg_1_1multipath__alignment__t.html#a8155e732811cdcc1e6fcee417b25bf10',1,'vg::multipath_alignment_t']]],
+ ['start_5fvcf_11055',['start_vcf',['../classvg_1_1Genotyper.html#a8a5aed6de86a488fe78a223d5e4d6bd6',1,'vg::Genotyper']]],
+ ['startfile_11056',['StartFile',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaf788a0a0553f9cc0c531fecb941f228',1,'vg::io::BlockedGzipOutputStream']]],
+ ['starting_5fposition_11057',['starting_position',['../structvg_1_1GaplessExtension.html#a2dc9687b1ac33335f593028c981fe494',1,'vg::GaplessExtension']]],
+ ['starts_5fat_11058',['starts_at',['../classhandlegraph_1_1SnarlDecomposition.html#ac6bb78bc95acfd353ff8d6c44915e524',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fat_5fend_11059',['starts_at_end',['../classhandlegraph_1_1SnarlDecomposition.html#aab710270e1997f22d1b09a4fd40a3eaf',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fat_5fstart_11060',['starts_at_start',['../classhandlegraph_1_1SnarlDecomposition.html#adb1c7cccea8188c8e24a4e53c34117bb',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fat_5ftip_11061',['starts_at_tip',['../classhandlegraph_1_1SnarlDecomposition.html#ac47bc288b1c0303d3356e953de4878e2',1,'handlegraph::SnarlDecomposition']]],
+ ['starts_5fwith_11062',['starts_with',['../namespacevg.html#a7b58d5d004a85a09906301781567970a',1,'vg']]],
+ ['state_11063',['state',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4a2a145b0221202c440cca81c0ba89c9',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['std_5fdev_11064',['std_dev',['../classvg_1_1FragmentLengthDistribution.html#a4da22f6209796ad178bd6ae88a995c03',1,'vg::FragmentLengthDistribution']]],
+ ['stddev_11065',['stddev',['../classvg_1_1normal__distribution.html#aaf593ce22610d686f290face7b5db895',1,'vg::normal_distribution::stddev()'],['../classvg_1_1truncated__normal__distribution.html#a49f7b71f827df31a5590d120e04dcbcf',1,'vg::truncated_normal_distribution::stddev()']]],
+ ['stdev_11066',['stdev',['../namespacevg.html#a11df8bd14dab3c0cfb7ecfa377a362f5',1,'vg']]],
+ ['step_5f1_5fbuild_5fgbwts_11067',['step_1_build_gbwts',['../gbwt__main_8cpp.html#a099d84c7e00d3a536ab0c89a42824a67',1,'gbwt_main.cpp']]],
+ ['step_5f2_5fmerge_5fgbwts_11068',['step_2_merge_gbwts',['../gbwt__main_8cpp.html#a81911b71bc15131cf9f9cc9652cccf0a',1,'gbwt_main.cpp']]],
+ ['step_5f3_5falter_5fgbwt_11069',['step_3_alter_gbwt',['../gbwt__main_8cpp.html#aa89c3d0220f759b0de6756841c3bbfae',1,'gbwt_main.cpp']]],
+ ['step_5f4_5fpath_5fcover_11070',['step_4_path_cover',['../gbwt__main_8cpp.html#ac6ed5f1a6fdf7794797be7ab94278897',1,'gbwt_main.cpp']]],
+ ['step_5f5_5fgbwtgraph_11071',['step_5_gbwtgraph',['../gbwt__main_8cpp.html#a61f18988124c373bf3aa037ad24719f2',1,'gbwt_main.cpp']]],
+ ['step_5f6_5fr_5findex_11072',['step_6_r_index',['../gbwt__main_8cpp.html#a240e0e93804c406946adb930f58c87aa',1,'gbwt_main.cpp']]],
+ ['step_5f7_5fmetadata_11073',['step_7_metadata',['../gbwt__main_8cpp.html#a7d810cefdbee01df4d4fe50406806e30',1,'gbwt_main.cpp']]],
+ ['step_5f8_5fpaths_11074',['step_8_paths',['../gbwt__main_8cpp.html#a859c16083955e4f1ab36c130fe6cce27',1,'gbwt_main.cpp']]],
+ ['step_5fin_5fpath_11075',['step_in_path',['../classvg_1_1VCFTraversalFinder.html#aefa5cf40bc0244f81e52ae2bdb4904d0',1,'vg::VCFTraversalFinder']]],
+ ['step_5frank_5fat_5fposition_11076',['step_rank_at_position',['../classxg_1_1XGPath.html#a92b0745ad293f585d5fb20d1bf20f7cc',1,'xg::XGPath']]],
+ ['steps_5fof_5fhandle_11077',['steps_of_handle',['../classvg_1_1MemoizingGraph.html#ab96deef5a4149f287541058c256a1115',1,'vg::MemoizingGraph::steps_of_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a015b050f33861cbc8e2a0efaaf771a30',1,'handlegraph::PathHandleGraph::steps_of_handle()']]],
+ ['stop_11078',['stop',['../classvg_1_1Funnel.html#adbe0233346c63f1693fa865eca0083b2',1,'vg::Funnel']]],
+ ['strandsplitgraph_11079',['StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html#a0e170b8ad07ca370e31497b804932220',1,'vg::StrandSplitGraph::StrandSplitGraph(const HandleGraph *graph)'],['../classvg_1_1StrandSplitGraph.html#aede16e10fc0b17f2527a62861f155c6d',1,'vg::StrandSplitGraph::StrandSplitGraph()=default']]],
+ ['stream_5fsort_11080',['stream_sort',['../classvg_1_1StreamSorter.html#a3ef7c0c822f58db91184e6b069c3ce59',1,'vg::StreamSorter']]],
+ ['streamcompressstring_11081',['StreamCompressString',['../namespacezstdutil.html#a64155ae3ce93620ea7868913f4c49ab3',1,'zstdutil']]],
+ ['streamdecompressstring_11082',['StreamDecompressString',['../namespacezstdutil.html#a2b6cfe0b4f483fea633845a8d912e8dd',1,'zstdutil']]],
+ ['streaminbuf_11083',['streaminbuf',['../classvg_1_1io_1_1streaminbuf.html#a611fcbbde05222173c867ea92cf20ed6',1,'vg::io::streaminbuf']]],
+ ['streamindex_11084',['StreamIndex',['../classvg_1_1StreamIndex.html#a3508617dbf1b8e8d1df051f4a214fa5e',1,'vg::StreamIndex']]],
+ ['streamindexbase_11085',['StreamIndexBase',['../classvg_1_1StreamIndexBase.html#a2df03d2ee53e9f171e4aa519a079901e',1,'vg::StreamIndexBase::StreamIndexBase()=default'],['../classvg_1_1StreamIndexBase.html#a85207efd00788e14df4df717d88233b7',1,'vg::StreamIndexBase::StreamIndexBase(const StreamIndexBase &other)=delete']]],
+ ['streaming_5fmerge_11086',['streaming_merge',['../classvg_1_1StreamSorter.html#a1c19cdfb158ff9771e471fbbc2b4ac74',1,'vg::StreamSorter::streaming_merge(list< cursor_t > &cursors, emitter_t &emitter, size_t expected_messages=0)'],['../classvg_1_1StreamSorter.html#a77590f7da1d1418fc00e7bdaec2a76e5',1,'vg::StreamSorter::streaming_merge(const vector< string > &temp_names_in, unordered_map< string, size_t > *messages_per_file=nullptr)']]],
+ ['streamistream_11087',['streamistream',['../classvg_1_1io_1_1streamistream.html#a0b87c404670f610d20f49f1e2c166648',1,'vg::io::streamistream']]],
+ ['streammultiplexer_11088',['StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html#ae72f4179a6cb14beb1b6460603d88233',1,'vg::io::StreamMultiplexer::StreamMultiplexer(ostream &backing, size_t max_threads)'],['../classvg_1_1io_1_1StreamMultiplexer.html#ad8b06aab5797747b1ce3d544be0cc965',1,'vg::io::StreamMultiplexer::StreamMultiplexer(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#af8352f0fcbb63f162734d48d2ec573ce',1,'vg::io::StreamMultiplexer::StreamMultiplexer(StreamMultiplexer &&other)=delete']]],
+ ['streamsorter_11089',['StreamSorter',['../classvg_1_1StreamSorter.html#a9ef0b8a33f5011eaf655b9420d86b0f5',1,'vg::StreamSorter']]],
+ ['string_5fquality_5fchar_5fto_5fshort_11090',['string_quality_char_to_short',['../namespacevg_1_1io.html#a4450d95b60550d44cbfe712467e92947',1,'vg::io']]],
+ ['string_5fquality_5fshort_5fto_5fchar_11091',['string_quality_short_to_char',['../namespacevg_1_1io.html#a33f3f10cba44d4ab370628c9579f9ca4',1,'vg::io']]],
+ ['string_5fto_5fint_11092',['string_to_int',['../namespacegafkluge.html#a35bc1201781dd4bab3581189c777a8af',1,'gafkluge']]],
+ ['strip_5ffrom_5fend_11093',['strip_from_end',['../namespacevg.html#adbe45b79675104ebc36691774d4124c4',1,'vg']]],
+ ['strip_5ffrom_5fstart_11094',['strip_from_start',['../namespacevg.html#acd6786ea9551b426f95fba325beff138',1,'vg']]],
+ ['strip_5ffull_5flength_5fbonuses_11095',['strip_full_length_bonuses',['../classvg_1_1MultipathMapper.html#a1147b64d4c4aeffa84403f5341de52bf',1,'vg::MultipathMapper']]],
+ ['strip_5fsubrange_11096',['strip_subrange',['../classvg_1_1Paths.html#aaae6abfe6b12aecfe82457fe8b8b44a8',1,'vg::Paths']]],
+ ['strip_5fsuffixes_11097',['strip_suffixes',['../giraffe__main_8cpp.html#ada042c5c5040b9b72848655d3dc5fcf8',1,'giraffe_main.cpp']]],
+ ['strongly_5fconnected_5fcomponents_11098',['strongly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a3c63833d51eac5a3141211367935e9e5',1,'handlegraph::algorithms']]],
+ ['stubbify_5fref_5fpaths_11099',['stubbify_ref_paths',['../namespacevg.html#a9e14750889892e0d70b8bc18fcc9f905',1,'vg']]],
+ ['sub_5foverlaps_5fof_5ffirst_5faln_11100',['sub_overlaps_of_first_aln',['../namespacevg.html#ab63c41956b73af429507b469108d1759',1,'vg']]],
+ ['subchain_5fintervals_11101',['subchain_intervals',['../haplotypes__main_8cpp.html#aed90215616b71a8c576afeeb7a137596',1,'haplotypes_main.cpp']]],
+ ['subchain_5flength_11102',['subchain_length',['../namespacehaplotypes__defaults.html#af6cc9d47b0c3862d9c0cdea27b55f477',1,'haplotypes_defaults']]],
+ ['subchain_5fstatistics_11103',['subchain_statistics',['../haplotypes__main_8cpp.html#a559cad6ab46d0a7dc260987e61ed1175',1,'haplotypes_main.cpp']]],
+ ['subchain_5fto_5fstring_11104',['subchain_to_string',['../haplotypes__main_8cpp.html#ae88c7a2ca3744f1826af903b27b2df53',1,'haplotypes_main.cpp']]],
+ ['subcommand_11105',['Subcommand',['../classvg_1_1subcommand_1_1Subcommand.html#ad5faf589dd98c3ff0c0d1071fcf90090',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, int priority, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#a38458556194aa9d47b1a49fc8958f345',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, CommandCategory category, std::function< int(int, char **)> main_function)'],['../classvg_1_1subcommand_1_1Subcommand.html#ad2cb9a00761644300914d9ed8439cbe1',1,'vg::subcommand::Subcommand::Subcommand(std::string name, std::string description, std::function< int(int, char **)> main_function)']]],
+ ['subgraph_11106',['subgraph',['../classvg_1_1SubgraphExplainer.html#a6a8bb147fa3f638f7bc0c2a098475999',1,'vg::SubgraphExplainer']]],
+ ['subgraph_5fcontaining_5fpath_5fsnarls_11107',['subgraph_containing_path_snarls',['../namespacevg.html#acc960c295c1e3088dc8e71ab1af5c4d6',1,'vg']]],
+ ['subgraph_5fin_5fdistance_5frange_11108',['subgraph_in_distance_range',['../namespacevg.html#aff8a7aca57dd525bc2def1369abae3fe',1,'vg']]],
+ ['subgraph_5fin_5fdistance_5frange_5fwalk_5facross_5fchain_11109',['subgraph_in_distance_range_walk_across_chain',['../namespacevg.html#a30f08b56f8c117103357ed4b8ebc08b8',1,'vg']]],
+ ['subgraph_5fin_5fdistance_5frange_5fwalk_5fgraph_11110',['subgraph_in_distance_range_walk_graph',['../namespacevg.html#a0312bffc43a4f4176aad1c37073b59df',1,'vg']]],
+ ['subgraphexplainer_11111',['SubgraphExplainer',['../classvg_1_1SubgraphExplainer.html#adbcee01cfe7c72e36071da4ed5aa1aec',1,'vg::SubgraphExplainer']]],
+ ['subgraphoverlay_11112',['SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html#ac9ffa71f1e615eb30efc626006c11242',1,'vg::SubgraphOverlay']]],
+ ['subhandlegraph_11113',['SubHandleGraph',['../classvg_1_1SubHandleGraph.html#ae02101c50fc316637a11ed674637e6a4',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super, HandleIter begin, HandleIter end)'],['../classvg_1_1SubHandleGraph.html#a1426a494a5d412485f5c4959f3b853c8',1,'vg::SubHandleGraph::SubHandleGraph(const HandleGraph *super)'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4455c7d0983b1fcce544022a60fa76ab',1,'handlegraph::algorithms::SubHandleGraph::SubHandleGraph()']]],
+ ['subpath_11114',['subpath',['../classvg_1_1multipath__alignment__t.html#a87bb864c7cd6e424fe9487cc662cade6',1,'vg::multipath_alignment_t::subpath() const'],['../classvg_1_1multipath__alignment__t.html#a5544e1c157233fda1b528bdd3e426f90',1,'vg::multipath_alignment_t::subpath(size_t i) const']]],
+ ['subpath_5fsize_11115',['subpath_size',['../classvg_1_1multipath__alignment__t.html#a3b6820ac77fa5438c55300ba1eb7a97d',1,'vg::multipath_alignment_t']]],
+ ['subpath_5ft_11116',['subpath_t',['../classvg_1_1subpath__t.html#a17ac16fd98564bfa3ab34e9b9b20517e',1,'vg::subpath_t::subpath_t()=default'],['../classvg_1_1subpath__t.html#a31254046fc840d936d42012b2c7b23b5',1,'vg::subpath_t::subpath_t(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a096b12ec158dd2cf139dbe38f55ca2f3',1,'vg::subpath_t::subpath_t(subpath_t &&)=default']]],
+ ['subpath_5ftopological_5forder_11117',['subpath_topological_order',['../namespacevg.html#ab1dcbe73351c8eaeea745f4b5191b8f0',1,'vg']]],
+ ['subpathoverlay_11118',['SubpathOverlay',['../classvg_1_1SubpathOverlay.html#a63691d737697292e0a2fd4233024dfb8',1,'vg::SubpathOverlay::SubpathOverlay(const PathHandleGraph *backing, const step_handle_t &begin, const step_handle_t &end)'],['../classvg_1_1SubpathOverlay.html#aa3cc8559a68870f144d69eb44829c95a',1,'vg::SubpathOverlay::SubpathOverlay()=default']]],
+ ['substage_11119',['substage',['../classvg_1_1Funnel.html#a0520d00fd1dcd9fa4af18d715580c900',1,'vg::Funnel']]],
+ ['substage_5fstop_11120',['substage_stop',['../classvg_1_1Funnel.html#ab5934891f37d57dc9309e5b0e9f80d9e',1,'vg::Funnel']]],
+ ['subtract_5flog_11121',['subtract_log',['../namespacevg.html#a33c8f5153ad0766df2c72bbec623aa19',1,'vg']]],
+ ['successor_5foffset_11122',['successor_offset',['../classvg_1_1WFATree.html#a33c5e80cc73d5367a95343deb20d8dac',1,'vg::WFATree']]],
+ ['suffix_11123',['suffix',['../classvg_1_1WFAExtender.html#a73ca61152596774e30d6c6f40aeea984',1,'vg::WFAExtender::suffix()'],['../structvg_1_1RecombinatorHaplotype.html#ae22f7c420e3d76d6494f66e817ffb342',1,'vg::RecombinatorHaplotype::suffix()']]],
+ ['suggest_5fedge_11124',['suggest_edge',['../classvg_1_1DiagramExplainer.html#a5565fd4595e708faa7f82534b1b87380',1,'vg::DiagramExplainer']]],
+ ['sum_11125',['sum',['../namespacevg.html#aa70726366aa31b20debdcac41c89490c',1,'vg']]],
+ ['summary_5fstatistics_11126',['summary_statistics',['../namespacevg.html#ae8afe82a05092bbf4bc31c8ead079fe3',1,'vg']]],
+ ['support_5fmax_11127',['support_max',['../namespacevg.html#ac3787b0a7fc02bbfe45dc5eb082d5779',1,'vg']]],
+ ['support_5fmin_11128',['support_min',['../namespacevg.html#a3c2ae4c37201ebbc6f6d4faaf27fe4de',1,'vg']]],
+ ['support_5fval_11129',['support_val',['../classvg_1_1SupportBasedSnarlCaller.html#a84da98787b002a2ed9c8c1da6661cebd',1,'vg::SupportBasedSnarlCaller::support_val()'],['../classvg_1_1TraversalSupportFinder.html#a3a128da202bd6889a2e5fd92ba3227dc',1,'vg::TraversalSupportFinder::support_val()']]],
+ ['supportbasedsnarlcaller_11130',['SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html#adff4e7045e950e7caea2858569afec02',1,'vg::SupportBasedSnarlCaller']]],
+ ['supportrestrictedtraversalfinder_11131',['SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html#aceeb94d7e05fdbc113557b61448f6b2a',1,'vg::SupportRestrictedTraversalFinder']]],
+ ['surject_11132',['surject',['../classvg_1_1Surjector.html#a4e4e4c28b1313850e647f4d258a0ea82',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a265cf90a6fb12021a70b87ec647c0867',1,'vg::Surjector::surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a80afa331fde9e8bcff66c4e87400217a',1,'vg::Surjector::surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, string &path_name_out, int64_t &path_pos_out, bool &path_rev_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
+ ['surject_5falignments_5fin_5fplace_11133',['surject_alignments_in_place',['../classvg_1_1SurjectingAlignmentEmitter.html#a5ba8aab649ae5f31c64be2c5461c743c',1,'vg::SurjectingAlignmentEmitter']]],
+ ['surject_5finternal_11134',['surject_internal',['../classvg_1_1Surjector.html#a6474f90fe3cf3ea098a553916bd47ae9',1,'vg::Surjector']]],
+ ['surjectingalignmentemitter_11135',['SurjectingAlignmentEmitter',['../classvg_1_1SurjectingAlignmentEmitter.html#acf03c9f7eedb8d8dd58d6ffab24f139f',1,'vg::SurjectingAlignmentEmitter']]],
+ ['surjector_11136',['Surjector',['../classvg_1_1Surjector.html#a4b083231c3ae02e3e14c3efb2a72eb1d',1,'vg::Surjector']]],
+ ['swap_11137',['swap',['../classvg_1_1SnarlState.html#a4e3f0d0c720ea665b3db9542d07f7ec1',1,'vg::SnarlState::swap()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a1466c6e58d54f775b27680dbe5e7fe4d',1,'vg::ZipCodeTree::reverse_iterator::swap()']]],
+ ['swap_5falleles_11138',['swap_alleles',['../classvg_1_1PhasedGenome.html#ae325c8488e737b75b980796aacf37246',1,'vg::PhasedGenome']]],
+ ['swap_5fendianness_11139',['swap_endianness',['../structvg_1_1endianness.html#a0a3eec44ef047d7771ad9804c5b51c85',1,'vg::endianness']]],
+ ['swap_5fhandles_11140',['swap_handles',['../classvg_1_1VG.html#a3d4db6ea2a99bda9a48411491aa6ed4e',1,'vg::VG']]],
+ ['swap_5fhaplotypes_11141',['swap_haplotypes',['../classvg_1_1GenomeState.html#aee2aa05cdf5226983f8f25d783da528e',1,'vg::GenomeState']]],
+ ['swap_5flabel_11142',['swap_label',['../classvg_1_1PhasedGenome.html#a181b4e71f8debc78ceccf476ce36abcd',1,'vg::PhasedGenome']]],
+ ['swap_5fnode_5fid_11143',['swap_node_id',['../classvg_1_1VG.html#afee31880eaf65a1a6d1a250663271b54',1,'vg::VG::swap_node_id(nid_t node_id, nid_t new_id)'],['../classvg_1_1VG.html#a63f2ffa39d84f80e5ab8068a25a03ee9',1,'vg::VG::swap_node_id(Node *node, nid_t new_id)']]],
+ ['swap_5fnode_5fids_11144',['swap_node_ids',['../classvg_1_1Paths.html#a3190f22ab39a9039ec9288e1c065ca9c',1,'vg::Paths::swap_node_ids(const std::function< nid_t(const nid_t &)> &get_new_id)'],['../classvg_1_1Paths.html#aba01c4d1b1d415622634db97f62b1188',1,'vg::Paths::swap_node_ids(hash_map< id_t, id_t > &id_mapping)']]],
+ ['swap_5fnodes_11145',['swap_nodes',['../classvg_1_1VG.html#aa402d1cf817f83ca44f72f6112b6a2e3',1,'vg::VG']]],
+ ['swap_5fremove_11146',['swap_remove',['../swap__remove_8hpp.html#a403d9325a22306c4dfefd9202bd3bd00',1,'swap_remove.hpp']]],
+ ['sync_5foffsets_11147',['sync_offsets',['../classxg_1_1XGPath.html#af7e2c286ed51c4422b1b615e4f327b9d',1,'xg::XGPath']]],
+ ['sync_5fpaths_11148',['sync_paths',['../classvg_1_1VG.html#a124188a9e0cd68c87c2bc009ea7bd799',1,'vg::VG']]],
+ ['synthesize_5ftail_5fanchors_11149',['synthesize_tail_anchors',['../classvg_1_1MultipathAlignmentGraph.html#a3c34e5d02c2b81614ccd602351b81ed9',1,'vg::MultipathAlignmentGraph']]]
];
diff --git a/search/functions_14.js b/search/functions_14.js
index 00c144ea02..ae501044b3 100644
--- a/search/functions_14.js
+++ b/search/functions_14.js
@@ -1,163 +1,163 @@
var searchData=
[
- ['tag_11146',['tag',['../classvg_1_1Funnel.html#abd3cf8783612cccf4faf96f25fc4f17c',1,'vg::Funnel']]],
- ['tag_5fcorrect_11147',['tag_correct',['../classvg_1_1Funnel.html#aa725f066e32a967c8d482f50c1606f08',1,'vg::Funnel']]],
- ['tag_5fseeds_11148',['tag_seeds',['../classvg_1_1MinimizerMapper.html#a59d91d716447b3971fd13e7a1920ab8b',1,'vg::MinimizerMapper']]],
- ['tail_5fnodes_11149',['tail_nodes',['../classvg_1_1VG.html#a25bd74b77e139691555c8d48ecf67d9f',1,'vg::VG::tail_nodes(void)'],['../classvg_1_1VG.html#a47fbc525ed5e9f2a7b00c333f03fe6c8',1,'vg::VG::tail_nodes(vector< Node * > &nodes)'],['../namespacehandlegraph_1_1algorithms.html#ad3eb2f190153333cdee10e6624df34c6',1,'handlegraph::algorithms::tail_nodes()']]],
- ['tail_5foffset_11150',['tail_offset',['../structvg_1_1GaplessExtension.html#a94628e41ab7556750c6ab841ca76fafd',1,'vg::GaplessExtension']]],
- ['tail_5fposition_11151',['tail_position',['../structvg_1_1GaplessExtension.html#adb0c7cc3eee2f406d20fde6db08717b1',1,'vg::GaplessExtension']]],
- ['take_11152',['take',['../structvg_1_1RecombinatorHaplotype.html#aec852acffc1ac8250b5c34aada44b980',1,'vg::RecombinatorHaplotype::take()'],['../classvg_1_1io_1_1MessageIterator.html#ab97d50a333e4f27419f0d661e8669774',1,'vg::io::MessageIterator::take()'],['../classvg_1_1io_1_1ProtobufIterator.html#a32bfe2fea01e8bae7759dff71eb64db8',1,'vg::io::ProtobufIterator::take()']]],
- ['take_5funique_5fminimizers_11153',['take_unique_minimizers',['../namespacevg.html#aced59c99c3795653e7d70f176edf9c82',1,'vg']]],
- ['target_5falignment_11154',['target_alignment',['../namespacevg.html#ac712c04180499746dab8cdc6c8795c56',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse, Mapping &cigar_mapping)'],['../namespacevg.html#a08575acb0012ffaabd9859324e404562',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse)']]],
- ['target_5fmemory_5fusage_11155',['target_memory_usage',['../classvg_1_1IndexingPlan.html#a1fd91843fb2c901d9db661e6bc50f07a',1,'vg::IndexingPlan']]],
- ['target_5foffset_11156',['target_offset',['../structvg_1_1WFAPoint.html#a1ffb5ef3c0d0e64eaeeb2290468bb53f',1,'vg::WFAPoint']]],
- ['targetvaluesearch_11157',['TargetValueSearch',['../classvg_1_1TargetValueSearch.html#afaa00740b29b96fd3c0c561898c3330a',1,'vg::TargetValueSearch::TargetValueSearch()=delete'],['../classvg_1_1TargetValueSearch.html#a66c7161857ea38dab47c4da883435ac4',1,'vg::TargetValueSearch::TargetValueSearch(const HandleGraph &handle_graph, DistanceHeuristic *upper_bound_heuristic, DistanceHeuristic *lower_bound_heuristic)']]],
- ['tell_11158',['Tell',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a4b34e76da81d5a09d5ab2634a864d401',1,'vg::io::BlockedGzipInputStream::Tell()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a84bb042b0a5df4ecbdadb3852fa04f91',1,'vg::io::BlockedGzipOutputStream::Tell()']]],
- ['tell_5fgroup_11159',['tell_group',['../classvg_1_1io_1_1MessageIterator.html#afc6ab71583004ebdeb7aa24553817936',1,'vg::io::MessageIterator::tell_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6b51328b5c897e36803b63a7058b6c61',1,'vg::io::ProtobufIterator::tell_group()']]],
- ['test_5fsplice_5fcandidates_11160',['test_splice_candidates',['../classvg_1_1MultipathMapper.html#ac45ca6502977ffa0640b3d5cdf21fae1',1,'vg::MultipathMapper']]],
- ['thread_5fto_5fgraph_5fspanned_11161',['thread_to_graph_spanned',['../namespacevg.html#aa24cc1f72643cab5fa0dfcc551f61d50',1,'vg']]],
- ['threads_11162',['threads',['../namespacehaplotypes__defaults.html#aa204b98aebcd769c098b7842428b94d6',1,'haplotypes_defaults']]],
- ['threads_5ffor_5fcontig_11163',['threads_for_contig',['../namespacevg.html#a5813ee7997572d371f9ff7b45bbe4843',1,'vg']]],
- ['threads_5ffor_5fsample_11164',['threads_for_sample',['../namespacevg.html#a2d4b0a9961f932a8caccb1d0723fd171',1,'vg']]],
- ['threads_5fto_5fjobs_11165',['threads_to_jobs',['../haplotypes__main_8cpp.html#a9f628e188cebb5384d8b2b236a745866',1,'haplotypes_main.cpp']]],
- ['three_5fedge_5fconnected_5fcomponent_5fmerges_11166',['three_edge_connected_component_merges',['../namespacevg_1_1algorithms.html#a7215192f2cc6536b6b3aadef4e95c64a',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponent_5fmerges_5fdense_11167',['three_edge_connected_component_merges_dense',['../namespacevg_1_1algorithms.html#a4d4b7c6814fb1f53a83c2e8355d72efa',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponents_11168',['three_edge_connected_components',['../namespacevg_1_1algorithms.html#ae4677e69f0b8ceb8580bc019cc8fbea8',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponents_5fdense_11169',['three_edge_connected_components_dense',['../namespacevg_1_1algorithms.html#a34c4a74208a88c0f956e697d5e183f5c',1,'vg::algorithms']]],
- ['three_5fedge_5fconnected_5fcomponents_5fdense_5fcactus_11170',['three_edge_connected_components_dense_cactus',['../namespacevg_1_1algorithms.html#a57de725b70b138394479863428f9d2eb',1,'vg::algorithms']]],
- ['tick_11171',['tick',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa1729ac6451d805cfb67301c5aff03b6',1,'vg::ZipCodeTree::reverse_iterator::tick()'],['../structvg_1_1Range.html#a10f700e0447a5a922611122fa1811b61',1,'vg::Range::tick()']]],
- ['tick_5falong_5fchain_11172',['tick_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a1d1a3f2903fbcc9be3d9725b7d27dba8',1,'vg::subcommand::TickChainLink::tick_along_chain()'],['../structvg_1_1Range.html#a66d38c47018ce4cd2589be167588affe',1,'vg::Range::tick_along_chain()']]],
- ['tick_5fchain_11173',['tick_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a90c9bb7ca4ab9e7f91bb246c5949eae4',1,'vg::subcommand::TickChainLink::tick_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aee28025b35a1a448183eb4957d697e62',1,'vg::subcommand::OptionGroup::tick_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ad0a0fc373e9e599842dbf6e1d67b4271',1,'vg::subcommand::GroupedOptionGroup::tick_chain()']]],
- ['tickchainlink_11174',['TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html#a3a814506ba062fcf389d57efa4304d4a',1,'vg::subcommand::TickChainLink::TickChainLink()=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a46213933eb07d96326cdb848f6dcd066',1,'vg::subcommand::TickChainLink::TickChainLink(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#afe9e76f6721953c97baed84957f6c1fe',1,'vg::subcommand::TickChainLink::TickChainLink(TickChainLink &&other)=delete']]],
- ['tipanchoredmaxdistance_11175',['TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html#a7a47ea386b37e4e738f71709184fce75',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance()=delete'],['../classvg_1_1TipAnchoredMaxDistance.html#a2658eecf16503163b9c39c44c7468bcc',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance(SnarlDistanceIndex &distance_index)']]],
- ['to_5falignment_11176',['to_alignment',['../classvg_1_1ReadFilter.html#a21b0bf11e5636b41cf6dfc4a61441c4e',1,'vg::ReadFilter::to_alignment()'],['../namespacevg.html#a10bcb19d45af37e8a58129b939b86f21',1,'vg::to_alignment()']]],
- ['to_5fanchor_11177',['to_anchor',['../classvg_1_1MinimizerMapper.html#ae7509b53b63ffb61b768c80f79f04a4d',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, const VectorView< Minimizer > &minimizers, std::vector< Seed > &seeds, size_t seed_number, const HandleGraph &graph, const Aligner *aligner)'],['../classvg_1_1MinimizerMapper.html#a750d65dcbba1734ca9855225090d0149',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, size_t read_start, size_t read_end, const std::vector< size_t > &sorted_seeds, const std::vector< algorithms::Anchor > &seed_anchors, const std::vector< size_t >::const_iterator &mismatch_begin, const std::vector< size_t >::const_iterator &mismatch_end, const HandleGraph &graph, const Aligner *aligner)']]],
- ['to_5fanchors_11178',['to_anchors',['../classvg_1_1MinimizerMapper.html#aaaabeeaf994436a22232bd59af97ea39',1,'vg::MinimizerMapper']]],
- ['to_5fbacking_11179',['to_backing',['../classvg_1_1ExtraNodeGraph.html#ae3c321717804ea0d0762fb4a8f71a7db',1,'vg::ExtraNodeGraph::to_backing()'],['../classvg_1_1SourceSinkOverlay.html#ada12ceaf3a0ed960ea42cf5a1f5de42a',1,'vg::SourceSinkOverlay::to_backing()']]],
- ['to_5fbig_5fendian_11180',['to_big_endian',['../structvg_1_1endianness.html#a5397898b5e413c0c4d09577952b80984',1,'vg::endianness']]],
- ['to_5fdot_11181',['to_dot',['../classvg_1_1Funnel.html#ad4a9374a423b2b87a15355ffac7a1935',1,'vg::Funnel::to_dot()'],['../classvg_1_1IndexRegistry.html#ad7ff998ac4404629ef683795a9170116',1,'vg::IndexRegistry::to_dot() const'],['../classvg_1_1IndexRegistry.html#a53573d21c79b060ebb0c643b1d395a7f',1,'vg::IndexRegistry::to_dot(const vector< IndexName > &targets) const'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a5eabcd913cf0ba46947d0554eab790fb',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::to_dot()'],['../classvg_1_1MultipathAlignmentGraph.html#a90ff13eb09622a6f5fa9238f6ec4950b',1,'vg::MultipathAlignmentGraph::to_dot()'],['../classvg_1_1VG.html#af502bd29a58e62ff70f8f963d47401a4',1,'vg::VG::to_dot()']]],
- ['to_5fedge_11182',['to_edge',['../namespacevg.html#a1da5277daea16b80ffc4ab75175b1882',1,'vg']]],
- ['to_5fgfa_11183',['to_gfa',['../classxg_1_1XG.html#a7cc1d24330a708afd24e768514c474c6',1,'xg::XG']]],
- ['to_5fgraph_11184',['to_graph',['../classvg_1_1Paths.html#ad215b2c7475b7048a073ce6fa805e709',1,'vg::Paths']]],
- ['to_5fjson_11185',['to_json',['../classvg_1_1Paths.html#ad98bff3b628d499252c7b5fb29191fdc',1,'vg::Paths']]],
- ['to_5fleft_5fside_11186',['to_left_side',['../namespacevg.html#a84d646b72482de0145745a64414ca5df',1,'vg']]],
- ['to_5flength_11187',['to_length',['../classvg_1_1edit__t.html#ad90d417ef77001a113ab3d1912e76954',1,'vg::edit_t::to_length()'],['../namespacevg.html#a5ed83dc32e575ae68b591d142eb38912',1,'vg::to_length()']]],
- ['to_5flength_5fafter_5fpos_11188',['to_length_after_pos',['../namespacevg.html#ad47f373b3433b3190f9f1c0f5f17274d',1,'vg']]],
- ['to_5flength_5fbefore_5fpos_11189',['to_length_before_pos',['../namespacevg.html#aa40f0cfd74a9eeaa7b6ffecbc0926a6d',1,'vg']]],
- ['to_5fmapping_11190',['to_mapping',['../classvg_1_1mapping__t.html#ab60b07378892ab57a661e27d19cef194',1,'vg::mapping_t::to_mapping()'],['../namespacevg.html#a28be7f9898d5ad6e075e25b81df512e8',1,'vg::to_mapping(const Visit &visit, std::function< size_t(id_t)> node_length)'],['../namespacevg.html#a128ffce6142542678bbbdc6e2e0b40cd',1,'vg::to_mapping(const Visit &visit, const HandleGraph &vg)']]],
- ['to_5fmultipath_5falignment_11191',['to_multipath_alignment',['../namespacevg.html#a27656a1e271730b6a62263dc2af8055d',1,'vg']]],
- ['to_5fnode_5ftraversal_11192',['to_node_traversal',['../namespacevg.html#a5a2e772d69c9e45cbc1c1d1a9e6df842',1,'vg::to_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#a2c04918053577c402e4f2cab61abd754',1,'vg::to_node_traversal(const Visit &visit, VG &graph)']]],
- ['to_5fnumber_11193',['to_number',['../classvg_1_1BitString.html#a2d6824816926cd463e586bb32ca3debc',1,'vg::BitString']]],
- ['to_5fpath_11194',['to_path',['../structvg_1_1GaplessExtension.html#ade804b684aa81b0b2f95033ead5930a2',1,'vg::GaplessExtension::to_path()'],['../structvg_1_1WFAAlignment.html#a4d90b156bc529bf52019201f30e12842',1,'vg::WFAAlignment::to_path()'],['../classvg_1_1MinimizerMapper.html#ae1565adcd1bdf28aca55134d7482b1af',1,'vg::MinimizerMapper::to_path()']]],
- ['to_5fproto_5fedit_11195',['to_proto_edit',['../namespacevg.html#a84c5dd6c830450f9100b5e9c11522050',1,'vg']]],
- ['to_5fproto_5fmapping_11196',['to_proto_mapping',['../namespacevg.html#a3da977cb90bf3ffd94166edb2fdb980a',1,'vg']]],
- ['to_5fproto_5fmultipath_5falignment_11197',['to_proto_multipath_alignment',['../namespacevg.html#a8f8f0e54cfa0c3279c18748c503ccbe9',1,'vg']]],
- ['to_5fproto_5fpath_11198',['to_proto_path',['../namespacevg.html#a9473b834c584544cc90c819d6b5bb222',1,'vg']]],
- ['to_5frev_5fnode_5ftraversal_11199',['to_rev_node_traversal',['../namespacevg.html#a0b4a5c32294bf49aa7f0a6d180cc2832',1,'vg::to_rev_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#ae64d7810e64af7119f1b1b3a2d08d797',1,'vg::to_rev_node_traversal(const Visit &visit, VG &graph)']]],
- ['to_5frev_5fvisit_11200',['to_rev_visit',['../namespacevg.html#a7164ae8636d1ca7783d6202c8ce316ca',1,'vg']]],
- ['to_5fright_5fside_11201',['to_right_side',['../namespacevg.html#a74fab09b3ae1d9f799742a31b5206a35',1,'vg']]],
- ['to_5fseed_11202',['to_seed',['../classvg_1_1GaplessExtender.html#a5b141ee05b0f704d29e9f34de8c67a32',1,'vg::GaplessExtender']]],
- ['to_5fsimple_5freverse_11203',['to_simple_reverse',['../classvg_1_1FlowSort.html#ac49c6a1c8605c7e55d532aac7959611c',1,'vg::FlowSort']]],
- ['to_5fsimple_5freverse_5forientation_11204',['to_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a4d4defd602249dfd58abbaea8058ff5a',1,'vg::FlowSort']]],
- ['to_5fstring_11205',['to_string',['../structvg_1_1BREAKPOINT.html#a889fc9b9ff7feec9847c28eaf17ae6ee',1,'vg::BREAKPOINT::to_string()'],['../structvg_1_1Haplotypes_1_1Subchain.html#aa409e312b588c1b48f3855bf8dfbb3c1',1,'vg::Haplotypes::Subchain::to_string()'],['../structReferenceInterval.html#a91983a3892caceab4288482288f76154',1,'ReferenceInterval::to_string()'],['../namespacestd.html#aec6a9d59586ce5d9e0acc951c9c355c8',1,'std::to_string()'],['../namespacevg.html#ae9aadb20454b27a0819f40006556ffe6',1,'vg::to_string(handle_t handle)'],['../namespacevg.html#ad7ec65dd3bb34f37cff811f49c1b9599',1,'vg::to_string(const HandleGraph &graph, handle_t handle)'],['../namespacevg.html#a75bc48248af00118bc7cdacc00e37db1',1,'vg::to_string(const HandleGraph &graph, edge_t edge)'],['../namespacestd.html#af92da72517d799416d58a59067b6afd9',1,'std::to_string(const vg::pos_t &pos)'],['../namespacestd.html#a4d710aefadc1fdcd0988b913096651a8',1,'std::to_string(const vg::ZipCodeTree::tree_item_type_t &type)'],['../namespacestd.html#a0fcc699939402d5652d7dde38fd615fd',1,'std::to_string(const vg::ZipCodeTree::reverse_iterator::State &state)']]],
- ['to_5fstring_5fgbwtgraph_11206',['to_string_gbwtgraph',['../namespacevg.html#adc47f14b546282cf0818ba47826a9110',1,'vg::to_string_gbwtgraph(handle_t handle)'],['../namespacevg.html#a93282dbd7c3a7daaf92b75f77c28dc29',1,'vg::to_string_gbwtgraph(gbwt::node_type node)']]],
- ['to_5fturtle_11207',['to_turtle',['../classvg_1_1VG.html#a582500a3d49fe231faa49a5c2e467cc8',1,'vg::VG']]],
- ['to_5fvcf_5fgenotype_11208',['to_vcf_genotype',['../namespacevg.html#a420f2fd8ef6d04f1a34a08af2a3dee0e',1,'vg']]],
- ['to_5fvector_11209',['to_vector',['../structvg_1_1varint__vector__t.html#a00af7863b11453e9e958375476ff8d4a',1,'vg::varint_vector_t::to_vector()'],['../classvg_1_1ZipCode.html#a43c4b30e62f754722d730d47306e76cd',1,'vg::ZipCode::to_vector()']]],
- ['to_5fvisit_11210',['to_visit',['../classvg_1_1NodeSide.html#af9b1413c4dcef8615892989c6e8b6232',1,'vg::NodeSide::to_visit()'],['../namespacevg.html#a827ce532cdbd4710e86a21ebd986e1cc',1,'vg::to_visit(const NodeTraversal &node_traversal)'],['../namespacevg.html#acd53873bb85623cbf5b797f09bf88dc4',1,'vg::to_visit(const Mapping &mapping, bool make_full_node_match=false)'],['../namespacevg.html#aa76433c3398610bc58b842f2a4b462c7',1,'vg::to_visit(id_t node_id, bool is_reverse)'],['../namespacevg.html#a0a18238f71586af9b3eba2ba1dac2a6e',1,'vg::to_visit(const Snarl &snarl)'],['../namespacevg.html#ae7d774bd39780563236dbf2badfc804b',1,'vg::to_visit(const handlegraph::HandleGraph &graph, const handle_t &handle)']]],
- ['to_5fwfa_5falignment_11211',['to_wfa_alignment',['../classvg_1_1MinimizerMapper.html#a41db60efc7634f542cea078a00f18379',1,'vg::MinimizerMapper']]],
- ['to_5fxg_11212',['to_xg',['../classvg_1_1VGset.html#ab26412de51ff980342dea8aceaca6a6c',1,'vg::VGset::to_xg(xg::XG &index)'],['../classvg_1_1VGset.html#ab7d9649e1ae4cc62b05af39c97cf7b06',1,'vg::VGset::to_xg(xg::XG &index, const function< bool(const string &)> &paths_to_take, map< string, Path > *removed_paths=nullptr)']]],
- ['toggle_5fbit_11213',['toggle_bit',['../structhandlegraph_1_1number__bool__packing.html#a7b54fcfbc7ad7e61d67d637374344a7e',1,'handlegraph::number_bool_packing']]],
- ['top_11214',['top',['../structvg_1_1MatchPos_1_1PathList.html#ac50ec1cafee2fd491fb6d0a10e82835a',1,'vg::MatchPos::PathList::top() const'],['../structvg_1_1MatchPos_1_1PathList.html#a62397e20a1f6c4c50e9e1cec60030685',1,'vg::MatchPos::PathList::top()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa83523c6259341473ec281be15ad2046',1,'vg::ZipCodeTree::reverse_iterator::top()']]],
- ['top_5fdown_5fgenotype_11215',['top_down_genotype',['../classvg_1_1LegacyCaller.html#a01e3b84cc03599fbc8cef1df4fcf43c7',1,'vg::LegacyCaller']]],
- ['top_5flevel_5fsnarls_11216',['top_level_snarls',['../classvg_1_1SnarlManager.html#af31a29d8e7836bca46b389c01c625339',1,'vg::SnarlManager']]],
- ['topological_5forder_11217',['topological_order',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab277385bc0c8b0cd52c850f5368f0339',1,'vg::MEMClusterer::HitGraph::topological_order()'],['../namespacehandlegraph_1_1algorithms.html#a7063506d0cc176b808808147b83d7e33',1,'handlegraph::algorithms::topological_order()']]],
- ['topological_5fsort_11218',['topological_sort',['../classvg_1_1MultipathAlignmentGraph.html#a565b45f37d5be97cd30bce1d29c134fc',1,'vg::MultipathAlignmentGraph']]],
- ['topologically_5forder_5fsubpaths_11219',['topologically_order_subpaths',['../namespacevg.html#a3ca9ccb5a2301ed1ce48f6334b3c4937',1,'vg']]],
- ['total_11220',['total',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#acb07aae84ec439512a012ee80829c357',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::total()'],['../namespacevg.html#a0a064dd8829b2100c6a38780311073f3',1,'vg::total()']]],
- ['total_5fnode_5fquality_11221',['total_node_quality',['../classvg_1_1Packer.html#a67a80245fcdbc4f5788b1062ee6b55f9',1,'vg::Packer']]],
- ['total_5fsupports_11222',['total_supports',['../structvg_1_1BREAKPOINT.html#afc10d66ae6dad31e2086963bc6e34a06',1,'vg::BREAKPOINT']]],
- ['touppercase_11223',['toUppercase',['../namespacevg.html#a00a949105ae94b18ca72452a442b8ddb',1,'vg']]],
- ['touppercaseinplace_11224',['toUppercaseInPlace',['../namespacevg.html#adcf3d4a70f85f067842ccf34a82a4a46',1,'vg']]],
- ['trace_11225',['trace',['../classvg_1_1DozeuInterface.html#a82634289dc80707e1ba8bb1a94503027',1,'vg::DozeuInterface::trace()'],['../classvg_1_1XdropAligner.html#adb3c7fa9b6b7c272ab687e0693a1dc47',1,'vg::XdropAligner::trace()'],['../classvg_1_1QualAdjXdropAligner.html#a8a382e7378bfeb43954a9436cf9d3b09',1,'vg::QualAdjXdropAligner::trace()'],['../classvg_1_1SnarlState.html#a6b13fa6a070139c5d123983265d440bc',1,'vg::SnarlState::trace()']]],
- ['trace_5fhaplotype_11226',['trace_haplotype',['../classvg_1_1GenomeState.html#af167a6237410b8da2c839820e6c804a7',1,'vg::GenomeState']]],
- ['trace_5fhaplotypes_5fand_5fpaths_11227',['trace_haplotypes_and_paths',['../namespacevg.html#a2d9774c4df98285526a427ba54e970ba',1,'vg']]],
- ['trace_5fpath_11228',['trace_path',['../namespacevg.html#a83257be63a821ae991e1b332b62facd4',1,'vg::trace_path()'],['../haplotypes__main_8cpp.html#a8e6fb3993622a6541d6e6beb41ed1c72',1,'trace_path(): haplotypes_main.cpp']]],
- ['trace_5fto_5falignment_11229',['trace_to_alignment',['../classvg_1_1DeletionAligner.html#a1916d488f7ed7e9ad0452a1c6138bc27',1,'vg::DeletionAligner']]],
- ['traceback_11230',['traceback',['../classvg_1_1BandedGlobalAligner.html#a2a2b4909d5eb88633680ea071c5551f4',1,'vg::BandedGlobalAligner::traceback()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a1366942f6ff4eecbebad9b29e9ef2c94',1,'vg::BandedGlobalAligner::BAMatrix::traceback()'],['../classvg_1_1MEMChainModel.html#ae142b05be3a27922e9387108bb052706',1,'vg::MEMChainModel::traceback()'],['../classvg_1_1DeletionAligner.html#aeaa43fcc2267e2aab5ebde031e3852c3',1,'vg::DeletionAligner::traceback()'],['../classvg_1_1AlignmentChainModel.html#ac774ed2018837e64c7ef88ae28c2794a',1,'vg::AlignmentChainModel::traceback()']]],
- ['traceback_5fover_5fedge_11231',['traceback_over_edge',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a0210e1c9a9da04e28e253e2963dd96ad',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['trailing_5fzeros_11232',['trailing_zeros',['../minimizer__main_8cpp.html#a82ed012045f022c7d023ef32c84a9df3',1,'minimizer_main.cpp']]],
- ['transcript_11233',['Transcript',['../structvg_1_1Transcript.html#a151337b8595bb8b0041ed64a325a7650',1,'vg::Transcript']]],
- ['transcript_5ffile_5fnonempty_11234',['transcript_file_nonempty',['../namespacevg.html#aa44c63a293d251b1bffbbeee59d2b7fe',1,'vg']]],
- ['transcript_5fpaths_11235',['transcript_paths',['../classvg_1_1Transcriptome.html#a52ca431b737b92befedebee4e71b0f0c',1,'vg::Transcriptome']]],
- ['transcriptome_11236',['Transcriptome',['../classvg_1_1Transcriptome.html#a041373349b45b5d190316229a5b8c562',1,'vg::Transcriptome']]],
- ['transcriptpath_11237',['TranscriptPath',['../structvg_1_1TranscriptPath.html#ad87c876af2acb7bcbbbb52b33ad25e8d',1,'vg::TranscriptPath::TranscriptPath()'],['../structvg_1_1TranscriptPath.html#aef6b201d9d87a24f2c9e7ed6e9e9e1e7',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const string &embedded_path_name, const bool is_reference_in, const bool is_haplotype_in)'],['../structvg_1_1TranscriptPath.html#a1b9b94ca6d527d0f197d98faf2a6a4b5',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const gbwt::size_type &haplotype_gbwt_id, const bool is_reference_in, const bool is_haplotype_in)']]],
- ['transfer_5fbetween_5fproto_5fannotation_11238',['transfer_between_proto_annotation',['../namespacevg.html#ac0534767a787eae1a5f93444bf21b2a1',1,'vg']]],
- ['transfer_5fboundary_5finfo_11239',['transfer_boundary_info',['../namespacevg.html#a82a83d7c54d733abee06d328f91ef5ee',1,'vg']]],
- ['transfer_5ffrom_5fproto_5fannotation_11240',['transfer_from_proto_annotation',['../namespacevg.html#a57c3f88ce9f85ceae2d77c32fd9de04d',1,'vg']]],
- ['transfer_5fproto_5fmetadata_11241',['transfer_proto_metadata',['../namespacevg.html#a0582a68dfa130c9f0a2bdaa1c7ac5ef5',1,'vg::transfer_proto_metadata(const Alignment &from, MultipathAlignment &to)'],['../namespacevg.html#ad6476e86221a660dda1fa85254e9436d',1,'vg::transfer_proto_metadata(const MultipathAlignment &from, Alignment &to)']]],
- ['transfer_5fread_5fmetadata_11242',['transfer_read_metadata',['../namespacevg.html#a195fc7fa6da6fecfa7e9fa31e5cf6f0c',1,'vg::transfer_read_metadata(const MultipathAlignment &from, multipath_alignment_t &to)'],['../namespacevg.html#acac375591689f0066f6c723dc25fb834',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, MultipathAlignment &to)'],['../namespacevg.html#ad0995c3042ff642b9e8aeaa1727dccb5',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, multipath_alignment_t &to)'],['../namespacevg.html#a54b4f608ad692caffd8fce4df9a1e4ef',1,'vg::transfer_read_metadata(const Alignment &from, multipath_alignment_t &to)'],['../namespacevg.html#a2d8929c8f610705661da889830b0b7b9',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, Alignment &to)'],['../namespacevg.html#af48acb91edce241c75a9a4fd02745620',1,'vg::transfer_read_metadata(const Alignment &from, Alignment &to)']]],
- ['transfer_5fto_5fproto_5fannotation_11243',['transfer_to_proto_annotation',['../namespacevg.html#a90a76dfce70406755151cf45e6990848',1,'vg']]],
- ['transfer_5funiform_5fmetadata_11244',['transfer_uniform_metadata',['../namespacevg.html#adbf827b04e42865ece378b51482df898',1,'vg']]],
- ['transform_11245',['transform',['../classvg_1_1VGset.html#aaa5f1b0e3e71bb00a5ad82f210065e81',1,'vg::VGset']]],
- ['transitive_5freduction_11246',['transitive_reduction',['../classvg_1_1Surjector.html#a2149d1e5e6aba2e07b92030e6afc617d',1,'vg::Surjector']]],
- ['translate_11247',['translate',['../classvg_1_1Translator.html#a3407f68503febdc2bd4366947e96d003',1,'vg::Translator::translate(const Position &position)'],['../classvg_1_1Translator.html#a6e27eb192e227afe777de2dc6488eb26',1,'vg::Translator::translate(const Position &position, const Translation &translation)'],['../classvg_1_1Translator.html#a1a8657e279942f5b4a802aad9e0baab6',1,'vg::Translator::translate(const Edge &edge)'],['../classvg_1_1Translator.html#a9ea3b0a85f25159214b34041b20a5cd3',1,'vg::Translator::translate(const Mapping &mapping)'],['../classvg_1_1Translator.html#a28ee9ca0de37d9d83f24b33639f0893c',1,'vg::Translator::translate(const Path &path)'],['../classvg_1_1Translator.html#af2f3e933feb2e28acf713316840b03c4',1,'vg::Translator::translate(const Alignment &aln)'],['../classvg_1_1Translator.html#ab4dffeb58e1c441c82039c6dd17445f5',1,'vg::Translator::translate(const Locus &locus)']]],
- ['translate_5fback_11248',['translate_back',['../classvg_1_1FlatFileBackTranslation.html#a44128954132be459c4229001b0441add',1,'vg::FlatFileBackTranslation::translate_back()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a762d6c9b1ad1762f3521c3a24cf82f55',1,'vg::algorithms::GFAIDMapInfo::translate_back()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#a4005088073dfdd8d3da33803198ee737',1,'handlegraph::NamedNodeBackTranslation::translate_back()']]],
- ['translate_5fdown_11249',['translate_down',['../classvg_1_1PathSubgraph.html#a7fa974235481756de3a7bb3c04f58ef7',1,'vg::PathSubgraph::translate_down()'],['../classvg_1_1TreeSubgraph.html#a71ab7a4ca370f712cf7c4912ccb5ab25',1,'vg::TreeSubgraph::translate_down()']]],
- ['translate_5fmems_11250',['translate_mems',['../namespacevg.html#a4bc1837d8c1cca33ab223957402b70ba',1,'vg']]],
- ['translate_5fnode_5fids_11251',['translate_node_ids',['../classvg_1_1JoinedSpliceGraph.html#a535cf652e7e39598979b003b7155ae4f',1,'vg::JoinedSpliceGraph::translate_node_ids()'],['../namespacevg.html#af71770196fc31c2e3c9c2a83f3497177',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator)'],['../namespacevg.html#aa49e4506c94e5747c88805e39aa18090',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator, id_t cut_node, size_t bases_removed, bool from_right)'],['../namespacevg.html#a322ec292675d4891ecc265e56a836db7',1,'vg::translate_node_ids(path_t &path, const unordered_map< id_t, id_t > &translator)']]],
- ['translate_5fnodes_11252',['translate_nodes',['../namespacevg.html#a98dcd16f2a4eae4c223a374dd2ab2da4',1,'vg']]],
- ['translate_5foriented_5fnode_5fids_11253',['translate_oriented_node_ids',['../namespacevg.html#a2b0ba7a1d0cf7630b79d03ba0ab65c53',1,'vg::translate_oriented_node_ids(Path &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#acb86c984b743e10c6ddaa57612ca3991',1,'vg::translate_oriented_node_ids(Path &path, const function< pair< id_t, bool >(id_t)> &translator)'],['../namespacevg.html#a449dd4b0d7106c6ee7afceb4f7412d6d',1,'vg::translate_oriented_node_ids(path_t &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#abfebb6e72326ea81b2ed13b4c3b57885',1,'vg::translate_oriented_node_ids(path_t &path, const function< pair< id_t, bool >(id_t)> &translator)']]],
- ['translate_5fsnarl_5fnum_11254',['translate_snarl_num',['../classvg_1_1SnarlManager.html#afdd078898493f277dc1aa5dc3dae5d56',1,'vg::SnarlManager']]],
- ['translator_11255',['Translator',['../classvg_1_1Translator.html#ac23acdcea38566f2e68005eca4afff73',1,'vg::Translator::Translator(void)'],['../classvg_1_1Translator.html#aeab811097e483365bbd273efc4c4445e',1,'vg::Translator::Translator(istream &in)'],['../classvg_1_1Translator.html#a99602b3868ae6f8f1efc6bf7adcde6f6',1,'vg::Translator::Translator(const vector< Translation > &trans)']]],
- ['transpose_11256',['transpose',['../namespacevg.html#a1409ac23ce33abd463dcd46093079023',1,'vg']]],
- ['trav_5fsequence_11257',['trav_sequence',['../classvg_1_1VG.html#a57296ecbcfce10f95b86233e10c35d7d',1,'vg::VG']]],
- ['trav_5fstring_11258',['trav_string',['../classvg_1_1VCFOutputCaller.html#ae4b896a68da613eb2e8e509279e4e1b9',1,'vg::VCFOutputCaller']]],
- ['traversal_5fto_5fstring_11259',['traversal_to_string',['../namespacevg.html#a94385b32246fc81a0a44ea1b47d994ee',1,'vg::traversal_to_string(VG &graph, const SnarlTraversal &path)'],['../namespacevg.html#a6a885124cc3018dc7cd6d2001b6b54f5',1,'vg::traversal_to_string(const PathHandleGraph *graph, const Traversal &traversal, int64_t max_steps)']]],
- ['traversalsupportfinder_11260',['TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html#ab281113b3cdf2992299a2768ce1be832',1,'vg::TraversalSupportFinder']]],
- ['traverse_5fcomponents_11261',['traverse_components',['../namespacevg_1_1algorithms.html#a6341683f1b89495d2ac1558ed2875343',1,'vg::algorithms']]],
- ['traverse_5fcomputed_5fdecomposition_11262',['traverse_computed_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#ab843403935c08e4d1764b693a897c16c',1,'vg::IntegratedSnarlFinder']]],
- ['traverse_5fdecomposition_11263',['traverse_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#a31a75674d1cc7d5f2b6a028161c6038f',1,'vg::IntegratedSnarlFinder::traverse_decomposition()'],['../classvg_1_1HandleGraphSnarlFinder.html#a9cba8688e5dd28b23ed3529af122f308',1,'vg::HandleGraphSnarlFinder::traverse_decomposition()']]],
- ['traverse_5fedge_5fhandle_11264',['traverse_edge_handle',['../classhandlegraph_1_1HandleGraph.html#af167b0664299cfd4eac610f129fa5fee',1,'handlegraph::HandleGraph']]],
- ['traverse_5fin_5forder_11265',['traverse_in_order',['../classvg_1_1BitStringTree.html#a5f825ebeb38c6d1572fa73692810c273',1,'vg::BitStringTree::traverse_in_order()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#aa89c88fbab67819e3f072da4bc82e253',1,'vg::BitStringTree::TreeNode::traverse_in_order()']]],
- ['traverse_5fleft_11266',['traverse_left',['../classvg_1_1Paths.html#a861618af488874863197ad48f17a9ae4',1,'vg::Paths']]],
- ['traverse_5fright_11267',['traverse_right',['../classvg_1_1Paths.html#aabda0fb1288e7681b317cd5b4cfad242',1,'vg::Paths']]],
- ['traverse_5fup_11268',['traverse_up',['../classvg_1_1BitStringTree.html#aefd44d9f67d266cb206724b8516c001c',1,'vg::BitStringTree::traverse_up()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#ae67c2a504203ce10bbc6cc33d94c2e3b',1,'vg::BitStringTree::TreeNode::traverse_up()']]],
- ['travs_5ffrom_11269',['travs_from',['../classvg_1_1VG.html#a34a493a0628857a3bfae181295ba541d',1,'vg::VG']]],
- ['travs_5fof_11270',['travs_of',['../classvg_1_1VG.html#ae065082f817e9bc0e278cf71f31af1e2',1,'vg::VG']]],
- ['travs_5fto_11271',['travs_to',['../classvg_1_1VG.html#a0a962957210c079fa242b383d5c65de3',1,'vg::VG']]],
- ['tree_11272',['Tree',['../structvg_1_1Tree.html#a2583e3d479b8b3fa66e8eb0065417934',1,'vg::Tree']]],
- ['tree_5fitem_5ft_11273',['tree_item_t',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a5740e0956ab1ddcb8148d70702c2000f',1,'vg::ZipCodeTree::tree_item_t::tree_item_t()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a895703befafce6654f476cc86bdc33ed',1,'vg::ZipCodeTree::tree_item_t::tree_item_t(tree_item_type_t type, size_t raw_value, bool is_reversed)']]],
- ['treenode_11274',['TreeNode',['../structvg_1_1TreeNode.html#a386f7b2ec0948165140022155dda8c04',1,'vg::TreeNode']]],
- ['treesubgraph_11275',['TreeSubgraph',['../classvg_1_1TreeSubgraph.html#aa43b054cfbc6f2f96fbc8fcef42887c5',1,'vg::TreeSubgraph']]],
- ['trim_11276',['trim',['../classvg_1_1WFATree.html#aa4c7ff4d5620d1a75545bef9357096f3',1,'vg::WFATree']]],
- ['trim_5falignment_11277',['trim_alignment',['../namespacevg.html#ad83da8607e104967dd51d9230f4b51bb',1,'vg']]],
- ['trim_5fambiguous_5fend_11278',['trim_ambiguous_end',['../classvg_1_1ReadFilter.html#ac5d77581ac1d34661c62f446692217ab',1,'vg::ReadFilter']]],
- ['trim_5fambiguous_5fends_11279',['trim_ambiguous_ends',['../classvg_1_1ReadFilter.html#a265a2c2d5e5af4924c406b97d764d9aa',1,'vg::ReadFilter::trim_ambiguous_ends(Read &read, int k) const'],['../classvg_1_1ReadFilter.html#ac49bf695fadbdaf8b41c972587493630',1,'vg::ReadFilter::trim_ambiguous_ends(Alignment &alignment, int k) const'],['../classvg_1_1ReadFilter.html#a266b5aeeb2081d2bd5f29ae43fdc00f8',1,'vg::ReadFilter::trim_ambiguous_ends(MultipathAlignment &aln, int k) const']]],
- ['trim_5fand_5fcheck_5ffor_5fempty_11280',['trim_and_check_for_empty',['../classvg_1_1MultipathAlignmentGraph.html#a114d073d4422c085a2c5768b6f165001',1,'vg::MultipathAlignmentGraph']]],
- ['trim_5fhanging_5fends_11281',['trim_hanging_ends',['../namespacevg.html#a990f54fb0e09dc439dace1519aff5e9f',1,'vg']]],
- ['trim_5fhanging_5findels_11282',['trim_hanging_indels',['../classvg_1_1MultipathAlignmentGraph.html#aca7bc3f6c3de6fc3df3adabf3161260c',1,'vg::MultipathAlignmentGraph']]],
- ['trim_5fmismatches_11283',['trim_mismatches',['../namespacevg.html#a77211f457b4e1f61915d771faf06cda0',1,'vg']]],
- ['trim_5fpath_11284',['trim_path',['../namespacevg.html#ab8d0345d2d7cea79ffdca38d33ed0c7f',1,'vg']]],
- ['trim_5fto_5fbranch_5fpoints_11285',['trim_to_branch_points',['../classvg_1_1MultipathAlignmentGraph.html#ac3199fb5e097873e2635e3fb34a8eafe',1,'vg::MultipathAlignmentGraph']]],
- ['trim_5fto_5fvariable_11286',['trim_to_variable',['../classvg_1_1Constructor.html#a428cf1b27e402a304c18e40f87e9dc02',1,'vg::Constructor']]],
- ['trimmed_5fend_11287',['trimmed_end',['../namespacevg.html#a9e61398cd459bb9ba3a1ced205491712',1,'vg']]],
- ['triviallyserializable_11288',['TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html#a209a7ede82e8ad286a8a3fb1e51c3604',1,'handlegraph::TriviallySerializable']]],
- ['trivialtraversalfinder_11289',['TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html#a46403401b7efaec8d99b63b2013f7e60',1,'vg::TrivialTraversalFinder']]],
- ['truncate_5fhandle_11290',['truncate_handle',['../classhandlegraph_1_1DeletableHandleGraph.html#aa65cef3b3261f8d1bc2057c5f2ee100a',1,'handlegraph::DeletableHandleGraph']]],
- ['truncated_5fnormal_5fdistribution_11291',['truncated_normal_distribution',['../classvg_1_1truncated__normal__distribution.html#aa48544711e2d4a11ffe876366898e463',1,'vg::truncated_normal_distribution']]],
- ['try_5fload_5fbare_11292',['try_load_bare',['../classvg_1_1io_1_1VPKG.html#ad5d2bad9c95479a3f1520c5fadcba1b2',1,'vg::io::VPKG']]],
- ['try_5fload_5fencapsulated_11293',['try_load_encapsulated',['../classvg_1_1io_1_1VPKG.html#a695e5a53bfbc9a5b36c5ea2306f253db',1,'vg::io::VPKG::try_load_encapsulated(istream &in)'],['../classvg_1_1io_1_1VPKG.html#a860f50291f4b5a6be232e5312eb884ab',1,'vg::io::VPKG::try_load_encapsulated(MessageIterator &it)']]],
- ['try_5fload_5ffirst_11294',['try_load_first',['../classvg_1_1io_1_1VPKG.html#a58ed1c37748fed4b15d4e611659ce4c3',1,'vg::io::VPKG::try_load_first(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a504e965a2a019ce27267ea85c106a91b',1,'vg::io::VPKG::try_load_first(const string &filename)']]],
- ['try_5fload_5ffirst_5fbare_11295',['try_load_first_bare',['../classvg_1_1io_1_1VPKG.html#acfc929254f523522f369c4a17c8f0941',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a2707edbb6b28a6623ea8ae11e607c861',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)']]],
- ['try_5fload_5ffirst_5fencapsulated_11296',['try_load_first_encapsulated',['../classvg_1_1io_1_1VPKG.html#a12f9922d4b17194d248dc3f19a449f60',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a186f277ebf475632f1b4d1eac4c48139',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)']]],
- ['try_5fload_5fone_11297',['try_load_one',['../classvg_1_1io_1_1VPKG.html#a0d7f96d4dd7fe5b1fe47b330ca617623',1,'vg::io::VPKG::try_load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#ab3a2026ac79ee1539271ba1791108c66',1,'vg::io::VPKG::try_load_one(const string &filename)']]],
- ['tsvalignmentemitter_11298',['TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html#aa8778347f51972fcb03f74565c5e3117',1,'vg::io::TSVAlignmentEmitter']]],
- ['tsvexplainer_11299',['TSVExplainer',['../classvg_1_1TSVExplainer.html#a3a9d31e471d1808b30dfdc6c995660b4',1,'vg::TSVExplainer']]],
- ['tv_5fpath_11300',['tv_path',['../classvg_1_1TargetValueSearch.html#a9ab66a82967803031203885c18291c6f',1,'vg::TargetValueSearch']]],
- ['tv_5fpath_5fexists_11301',['tv_path_exists',['../classvg_1_1TargetValueSearch.html#a407607bcab4cfd14e283386bac418636',1,'vg::TargetValueSearch']]],
- ['tv_5fpath_5flength_11302',['tv_path_length',['../classvg_1_1TargetValueSearch.html#a7dc599c6d4a317999890c81634d9ddf5',1,'vg::TargetValueSearch']]],
- ['tv_5fphase2_11303',['tv_phase2',['../classvg_1_1TargetValueSearch.html#a794b8271df6bcf349db5e6d605402744',1,'vg::TargetValueSearch']]],
- ['tvsclusterer_11304',['TVSClusterer',['../classvg_1_1TVSClusterer.html#a5b8fdb6006095094e85e6f760b8d0e3d',1,'vg::TVSClusterer']]],
- ['type_5fas_5fchar_11305',['type_as_char',['../structReferenceInterval.html#a9ae0102fab5146105642e388d6bef997',1,'ReferenceInterval']]]
+ ['tag_11150',['tag',['../classvg_1_1Funnel.html#abd3cf8783612cccf4faf96f25fc4f17c',1,'vg::Funnel']]],
+ ['tag_5fcorrect_11151',['tag_correct',['../classvg_1_1Funnel.html#aa725f066e32a967c8d482f50c1606f08',1,'vg::Funnel']]],
+ ['tag_5fseeds_11152',['tag_seeds',['../classvg_1_1MinimizerMapper.html#a59d91d716447b3971fd13e7a1920ab8b',1,'vg::MinimizerMapper']]],
+ ['tail_5fnodes_11153',['tail_nodes',['../classvg_1_1VG.html#a25bd74b77e139691555c8d48ecf67d9f',1,'vg::VG::tail_nodes(void)'],['../classvg_1_1VG.html#a47fbc525ed5e9f2a7b00c333f03fe6c8',1,'vg::VG::tail_nodes(vector< Node * > &nodes)'],['../namespacehandlegraph_1_1algorithms.html#ad3eb2f190153333cdee10e6624df34c6',1,'handlegraph::algorithms::tail_nodes()']]],
+ ['tail_5foffset_11154',['tail_offset',['../structvg_1_1GaplessExtension.html#a94628e41ab7556750c6ab841ca76fafd',1,'vg::GaplessExtension']]],
+ ['tail_5fposition_11155',['tail_position',['../structvg_1_1GaplessExtension.html#adb0c7cc3eee2f406d20fde6db08717b1',1,'vg::GaplessExtension']]],
+ ['take_11156',['take',['../structvg_1_1RecombinatorHaplotype.html#aec852acffc1ac8250b5c34aada44b980',1,'vg::RecombinatorHaplotype::take()'],['../classvg_1_1io_1_1MessageIterator.html#ab97d50a333e4f27419f0d661e8669774',1,'vg::io::MessageIterator::take()'],['../classvg_1_1io_1_1ProtobufIterator.html#a32bfe2fea01e8bae7759dff71eb64db8',1,'vg::io::ProtobufIterator::take()']]],
+ ['take_5funique_5fminimizers_11157',['take_unique_minimizers',['../namespacevg.html#aced59c99c3795653e7d70f176edf9c82',1,'vg']]],
+ ['target_5falignment_11158',['target_alignment',['../namespacevg.html#ac712c04180499746dab8cdc6c8795c56',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse, Mapping &cigar_mapping)'],['../namespacevg.html#a08575acb0012ffaabd9859324e404562',1,'vg::target_alignment(const PathPositionHandleGraph *graph, const path_handle_t &path, size_t pos1, size_t pos2, const string &feature, bool is_reverse)']]],
+ ['target_5fmemory_5fusage_11159',['target_memory_usage',['../classvg_1_1IndexingPlan.html#a1fd91843fb2c901d9db661e6bc50f07a',1,'vg::IndexingPlan']]],
+ ['target_5foffset_11160',['target_offset',['../structvg_1_1WFAPoint.html#a1ffb5ef3c0d0e64eaeeb2290468bb53f',1,'vg::WFAPoint']]],
+ ['targetvaluesearch_11161',['TargetValueSearch',['../classvg_1_1TargetValueSearch.html#afaa00740b29b96fd3c0c561898c3330a',1,'vg::TargetValueSearch::TargetValueSearch()=delete'],['../classvg_1_1TargetValueSearch.html#a66c7161857ea38dab47c4da883435ac4',1,'vg::TargetValueSearch::TargetValueSearch(const HandleGraph &handle_graph, DistanceHeuristic *upper_bound_heuristic, DistanceHeuristic *lower_bound_heuristic)']]],
+ ['tell_11162',['Tell',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a4b34e76da81d5a09d5ab2634a864d401',1,'vg::io::BlockedGzipInputStream::Tell()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a84bb042b0a5df4ecbdadb3852fa04f91',1,'vg::io::BlockedGzipOutputStream::Tell()']]],
+ ['tell_5fgroup_11163',['tell_group',['../classvg_1_1io_1_1MessageIterator.html#afc6ab71583004ebdeb7aa24553817936',1,'vg::io::MessageIterator::tell_group()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6b51328b5c897e36803b63a7058b6c61',1,'vg::io::ProtobufIterator::tell_group()']]],
+ ['test_5fsplice_5fcandidates_11164',['test_splice_candidates',['../classvg_1_1MultipathMapper.html#ac45ca6502977ffa0640b3d5cdf21fae1',1,'vg::MultipathMapper']]],
+ ['thread_5fto_5fgraph_5fspanned_11165',['thread_to_graph_spanned',['../namespacevg.html#aa24cc1f72643cab5fa0dfcc551f61d50',1,'vg']]],
+ ['threads_11166',['threads',['../namespacehaplotypes__defaults.html#aa204b98aebcd769c098b7842428b94d6',1,'haplotypes_defaults']]],
+ ['threads_5ffor_5fcontig_11167',['threads_for_contig',['../namespacevg.html#a5813ee7997572d371f9ff7b45bbe4843',1,'vg']]],
+ ['threads_5ffor_5fsample_11168',['threads_for_sample',['../namespacevg.html#a2d4b0a9961f932a8caccb1d0723fd171',1,'vg']]],
+ ['threads_5fto_5fjobs_11169',['threads_to_jobs',['../haplotypes__main_8cpp.html#a9f628e188cebb5384d8b2b236a745866',1,'haplotypes_main.cpp']]],
+ ['three_5fedge_5fconnected_5fcomponent_5fmerges_11170',['three_edge_connected_component_merges',['../namespacevg_1_1algorithms.html#a7215192f2cc6536b6b3aadef4e95c64a',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponent_5fmerges_5fdense_11171',['three_edge_connected_component_merges_dense',['../namespacevg_1_1algorithms.html#a4d4b7c6814fb1f53a83c2e8355d72efa',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponents_11172',['three_edge_connected_components',['../namespacevg_1_1algorithms.html#ae4677e69f0b8ceb8580bc019cc8fbea8',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponents_5fdense_11173',['three_edge_connected_components_dense',['../namespacevg_1_1algorithms.html#a34c4a74208a88c0f956e697d5e183f5c',1,'vg::algorithms']]],
+ ['three_5fedge_5fconnected_5fcomponents_5fdense_5fcactus_11174',['three_edge_connected_components_dense_cactus',['../namespacevg_1_1algorithms.html#a57de725b70b138394479863428f9d2eb',1,'vg::algorithms']]],
+ ['tick_11175',['tick',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa1729ac6451d805cfb67301c5aff03b6',1,'vg::ZipCodeTree::reverse_iterator::tick()'],['../structvg_1_1Range.html#a10f700e0447a5a922611122fa1811b61',1,'vg::Range::tick()']]],
+ ['tick_5falong_5fchain_11176',['tick_along_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a1d1a3f2903fbcc9be3d9725b7d27dba8',1,'vg::subcommand::TickChainLink::tick_along_chain()'],['../structvg_1_1Range.html#a66d38c47018ce4cd2589be167588affe',1,'vg::Range::tick_along_chain()']]],
+ ['tick_5fchain_11177',['tick_chain',['../structvg_1_1subcommand_1_1TickChainLink.html#a90c9bb7ca4ab9e7f91bb246c5949eae4',1,'vg::subcommand::TickChainLink::tick_chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#aee28025b35a1a448183eb4957d697e62',1,'vg::subcommand::OptionGroup::tick_chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ad0a0fc373e9e599842dbf6e1d67b4271',1,'vg::subcommand::GroupedOptionGroup::tick_chain()']]],
+ ['tickchainlink_11178',['TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html#a3a814506ba062fcf389d57efa4304d4a',1,'vg::subcommand::TickChainLink::TickChainLink()=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a46213933eb07d96326cdb848f6dcd066',1,'vg::subcommand::TickChainLink::TickChainLink(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#afe9e76f6721953c97baed84957f6c1fe',1,'vg::subcommand::TickChainLink::TickChainLink(TickChainLink &&other)=delete']]],
+ ['tipanchoredmaxdistance_11179',['TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html#a7a47ea386b37e4e738f71709184fce75',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance()=delete'],['../classvg_1_1TipAnchoredMaxDistance.html#a2658eecf16503163b9c39c44c7468bcc',1,'vg::TipAnchoredMaxDistance::TipAnchoredMaxDistance(SnarlDistanceIndex &distance_index)']]],
+ ['to_5falignment_11180',['to_alignment',['../classvg_1_1ReadFilter.html#a21b0bf11e5636b41cf6dfc4a61441c4e',1,'vg::ReadFilter::to_alignment()'],['../namespacevg.html#a10bcb19d45af37e8a58129b939b86f21',1,'vg::to_alignment()']]],
+ ['to_5fanchor_11181',['to_anchor',['../classvg_1_1MinimizerMapper.html#ae7509b53b63ffb61b768c80f79f04a4d',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, const VectorView< Minimizer > &minimizers, std::vector< Seed > &seeds, size_t seed_number, const HandleGraph &graph, const Aligner *aligner)'],['../classvg_1_1MinimizerMapper.html#a750d65dcbba1734ca9855225090d0149',1,'vg::MinimizerMapper::to_anchor(const Alignment &aln, size_t read_start, size_t read_end, const std::vector< size_t > &sorted_seeds, const std::vector< algorithms::Anchor > &seed_anchors, const std::vector< size_t >::const_iterator &mismatch_begin, const std::vector< size_t >::const_iterator &mismatch_end, const HandleGraph &graph, const Aligner *aligner)']]],
+ ['to_5fanchors_11182',['to_anchors',['../classvg_1_1MinimizerMapper.html#aaaabeeaf994436a22232bd59af97ea39',1,'vg::MinimizerMapper']]],
+ ['to_5fbacking_11183',['to_backing',['../classvg_1_1ExtraNodeGraph.html#ae3c321717804ea0d0762fb4a8f71a7db',1,'vg::ExtraNodeGraph::to_backing()'],['../classvg_1_1SourceSinkOverlay.html#ada12ceaf3a0ed960ea42cf5a1f5de42a',1,'vg::SourceSinkOverlay::to_backing()']]],
+ ['to_5fbig_5fendian_11184',['to_big_endian',['../structvg_1_1endianness.html#a5397898b5e413c0c4d09577952b80984',1,'vg::endianness']]],
+ ['to_5fdot_11185',['to_dot',['../classvg_1_1Funnel.html#ad4a9374a423b2b87a15355ffac7a1935',1,'vg::Funnel::to_dot()'],['../classvg_1_1IndexRegistry.html#ad7ff998ac4404629ef683795a9170116',1,'vg::IndexRegistry::to_dot() const'],['../classvg_1_1IndexRegistry.html#a53573d21c79b060ebb0c643b1d395a7f',1,'vg::IndexRegistry::to_dot(const vector< IndexName > &targets) const'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a5eabcd913cf0ba46947d0554eab790fb',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::to_dot()'],['../classvg_1_1MultipathAlignmentGraph.html#a90ff13eb09622a6f5fa9238f6ec4950b',1,'vg::MultipathAlignmentGraph::to_dot()'],['../classvg_1_1VG.html#af502bd29a58e62ff70f8f963d47401a4',1,'vg::VG::to_dot()']]],
+ ['to_5fedge_11186',['to_edge',['../namespacevg.html#a1da5277daea16b80ffc4ab75175b1882',1,'vg']]],
+ ['to_5fgfa_11187',['to_gfa',['../classxg_1_1XG.html#a7cc1d24330a708afd24e768514c474c6',1,'xg::XG']]],
+ ['to_5fgraph_11188',['to_graph',['../classvg_1_1Paths.html#ad215b2c7475b7048a073ce6fa805e709',1,'vg::Paths']]],
+ ['to_5fjson_11189',['to_json',['../classvg_1_1Paths.html#ad98bff3b628d499252c7b5fb29191fdc',1,'vg::Paths']]],
+ ['to_5fleft_5fside_11190',['to_left_side',['../namespacevg.html#a84d646b72482de0145745a64414ca5df',1,'vg']]],
+ ['to_5flength_11191',['to_length',['../classvg_1_1edit__t.html#ad90d417ef77001a113ab3d1912e76954',1,'vg::edit_t::to_length()'],['../namespacevg.html#a5ed83dc32e575ae68b591d142eb38912',1,'vg::to_length()']]],
+ ['to_5flength_5fafter_5fpos_11192',['to_length_after_pos',['../namespacevg.html#ad47f373b3433b3190f9f1c0f5f17274d',1,'vg']]],
+ ['to_5flength_5fbefore_5fpos_11193',['to_length_before_pos',['../namespacevg.html#aa40f0cfd74a9eeaa7b6ffecbc0926a6d',1,'vg']]],
+ ['to_5fmapping_11194',['to_mapping',['../classvg_1_1mapping__t.html#ab60b07378892ab57a661e27d19cef194',1,'vg::mapping_t::to_mapping()'],['../namespacevg.html#a28be7f9898d5ad6e075e25b81df512e8',1,'vg::to_mapping(const Visit &visit, std::function< size_t(id_t)> node_length)'],['../namespacevg.html#a128ffce6142542678bbbdc6e2e0b40cd',1,'vg::to_mapping(const Visit &visit, const HandleGraph &vg)']]],
+ ['to_5fmultipath_5falignment_11195',['to_multipath_alignment',['../namespacevg.html#a27656a1e271730b6a62263dc2af8055d',1,'vg']]],
+ ['to_5fnode_5ftraversal_11196',['to_node_traversal',['../namespacevg.html#a5a2e772d69c9e45cbc1c1d1a9e6df842',1,'vg::to_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#a2c04918053577c402e4f2cab61abd754',1,'vg::to_node_traversal(const Visit &visit, VG &graph)']]],
+ ['to_5fnumber_11197',['to_number',['../classvg_1_1BitString.html#a2d6824816926cd463e586bb32ca3debc',1,'vg::BitString']]],
+ ['to_5fpath_11198',['to_path',['../structvg_1_1GaplessExtension.html#ade804b684aa81b0b2f95033ead5930a2',1,'vg::GaplessExtension::to_path()'],['../structvg_1_1WFAAlignment.html#a4d90b156bc529bf52019201f30e12842',1,'vg::WFAAlignment::to_path()'],['../classvg_1_1MinimizerMapper.html#ae1565adcd1bdf28aca55134d7482b1af',1,'vg::MinimizerMapper::to_path()']]],
+ ['to_5fproto_5fedit_11199',['to_proto_edit',['../namespacevg.html#a84c5dd6c830450f9100b5e9c11522050',1,'vg']]],
+ ['to_5fproto_5fmapping_11200',['to_proto_mapping',['../namespacevg.html#a3da977cb90bf3ffd94166edb2fdb980a',1,'vg']]],
+ ['to_5fproto_5fmultipath_5falignment_11201',['to_proto_multipath_alignment',['../namespacevg.html#a8f8f0e54cfa0c3279c18748c503ccbe9',1,'vg']]],
+ ['to_5fproto_5fpath_11202',['to_proto_path',['../namespacevg.html#a9473b834c584544cc90c819d6b5bb222',1,'vg']]],
+ ['to_5frev_5fnode_5ftraversal_11203',['to_rev_node_traversal',['../namespacevg.html#a0b4a5c32294bf49aa7f0a6d180cc2832',1,'vg::to_rev_node_traversal(const Visit &visit, const VG &graph)'],['../namespacevg.html#ae64d7810e64af7119f1b1b3a2d08d797',1,'vg::to_rev_node_traversal(const Visit &visit, VG &graph)']]],
+ ['to_5frev_5fvisit_11204',['to_rev_visit',['../namespacevg.html#a7164ae8636d1ca7783d6202c8ce316ca',1,'vg']]],
+ ['to_5fright_5fside_11205',['to_right_side',['../namespacevg.html#a74fab09b3ae1d9f799742a31b5206a35',1,'vg']]],
+ ['to_5fseed_11206',['to_seed',['../classvg_1_1GaplessExtender.html#a5b141ee05b0f704d29e9f34de8c67a32',1,'vg::GaplessExtender']]],
+ ['to_5fsimple_5freverse_11207',['to_simple_reverse',['../classvg_1_1FlowSort.html#ac49c6a1c8605c7e55d532aac7959611c',1,'vg::FlowSort']]],
+ ['to_5fsimple_5freverse_5forientation_11208',['to_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a4d4defd602249dfd58abbaea8058ff5a',1,'vg::FlowSort']]],
+ ['to_5fstring_11209',['to_string',['../structvg_1_1BREAKPOINT.html#a889fc9b9ff7feec9847c28eaf17ae6ee',1,'vg::BREAKPOINT::to_string()'],['../structvg_1_1Haplotypes_1_1Subchain.html#aa409e312b588c1b48f3855bf8dfbb3c1',1,'vg::Haplotypes::Subchain::to_string()'],['../structReferenceInterval.html#a91983a3892caceab4288482288f76154',1,'ReferenceInterval::to_string()'],['../namespacestd.html#aec6a9d59586ce5d9e0acc951c9c355c8',1,'std::to_string()'],['../namespacevg.html#ae9aadb20454b27a0819f40006556ffe6',1,'vg::to_string(handle_t handle)'],['../namespacevg.html#ad7ec65dd3bb34f37cff811f49c1b9599',1,'vg::to_string(const HandleGraph &graph, handle_t handle)'],['../namespacevg.html#a75bc48248af00118bc7cdacc00e37db1',1,'vg::to_string(const HandleGraph &graph, edge_t edge)'],['../namespacestd.html#af92da72517d799416d58a59067b6afd9',1,'std::to_string(const vg::pos_t &pos)'],['../namespacestd.html#a4d710aefadc1fdcd0988b913096651a8',1,'std::to_string(const vg::ZipCodeTree::tree_item_type_t &type)'],['../namespacestd.html#a0fcc699939402d5652d7dde38fd615fd',1,'std::to_string(const vg::ZipCodeTree::reverse_iterator::State &state)']]],
+ ['to_5fstring_5fgbwtgraph_11210',['to_string_gbwtgraph',['../namespacevg.html#adc47f14b546282cf0818ba47826a9110',1,'vg::to_string_gbwtgraph(handle_t handle)'],['../namespacevg.html#a93282dbd7c3a7daaf92b75f77c28dc29',1,'vg::to_string_gbwtgraph(gbwt::node_type node)']]],
+ ['to_5fturtle_11211',['to_turtle',['../classvg_1_1VG.html#a582500a3d49fe231faa49a5c2e467cc8',1,'vg::VG']]],
+ ['to_5fvcf_5fgenotype_11212',['to_vcf_genotype',['../namespacevg.html#a420f2fd8ef6d04f1a34a08af2a3dee0e',1,'vg']]],
+ ['to_5fvector_11213',['to_vector',['../structvg_1_1varint__vector__t.html#a00af7863b11453e9e958375476ff8d4a',1,'vg::varint_vector_t::to_vector()'],['../classvg_1_1ZipCode.html#a43c4b30e62f754722d730d47306e76cd',1,'vg::ZipCode::to_vector()']]],
+ ['to_5fvisit_11214',['to_visit',['../classvg_1_1NodeSide.html#af9b1413c4dcef8615892989c6e8b6232',1,'vg::NodeSide::to_visit()'],['../namespacevg.html#a827ce532cdbd4710e86a21ebd986e1cc',1,'vg::to_visit(const NodeTraversal &node_traversal)'],['../namespacevg.html#acd53873bb85623cbf5b797f09bf88dc4',1,'vg::to_visit(const Mapping &mapping, bool make_full_node_match=false)'],['../namespacevg.html#aa76433c3398610bc58b842f2a4b462c7',1,'vg::to_visit(id_t node_id, bool is_reverse)'],['../namespacevg.html#a0a18238f71586af9b3eba2ba1dac2a6e',1,'vg::to_visit(const Snarl &snarl)'],['../namespacevg.html#ae7d774bd39780563236dbf2badfc804b',1,'vg::to_visit(const handlegraph::HandleGraph &graph, const handle_t &handle)']]],
+ ['to_5fwfa_5falignment_11215',['to_wfa_alignment',['../classvg_1_1MinimizerMapper.html#a41db60efc7634f542cea078a00f18379',1,'vg::MinimizerMapper']]],
+ ['to_5fxg_11216',['to_xg',['../classvg_1_1VGset.html#ab26412de51ff980342dea8aceaca6a6c',1,'vg::VGset::to_xg(xg::XG &index)'],['../classvg_1_1VGset.html#ab7d9649e1ae4cc62b05af39c97cf7b06',1,'vg::VGset::to_xg(xg::XG &index, const function< bool(const string &)> &paths_to_take, map< string, Path > *removed_paths=nullptr)']]],
+ ['toggle_5fbit_11217',['toggle_bit',['../structhandlegraph_1_1number__bool__packing.html#a7b54fcfbc7ad7e61d67d637374344a7e',1,'handlegraph::number_bool_packing']]],
+ ['top_11218',['top',['../structvg_1_1MatchPos_1_1PathList.html#ac50ec1cafee2fd491fb6d0a10e82835a',1,'vg::MatchPos::PathList::top() const'],['../structvg_1_1MatchPos_1_1PathList.html#a62397e20a1f6c4c50e9e1cec60030685',1,'vg::MatchPos::PathList::top()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa83523c6259341473ec281be15ad2046',1,'vg::ZipCodeTree::reverse_iterator::top()']]],
+ ['top_5fdown_5fgenotype_11219',['top_down_genotype',['../classvg_1_1LegacyCaller.html#a01e3b84cc03599fbc8cef1df4fcf43c7',1,'vg::LegacyCaller']]],
+ ['top_5flevel_5fsnarls_11220',['top_level_snarls',['../classvg_1_1SnarlManager.html#af31a29d8e7836bca46b389c01c625339',1,'vg::SnarlManager']]],
+ ['topological_5forder_11221',['topological_order',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab277385bc0c8b0cd52c850f5368f0339',1,'vg::MEMClusterer::HitGraph::topological_order()'],['../namespacehandlegraph_1_1algorithms.html#a7063506d0cc176b808808147b83d7e33',1,'handlegraph::algorithms::topological_order()']]],
+ ['topological_5fsort_11222',['topological_sort',['../classvg_1_1MultipathAlignmentGraph.html#a565b45f37d5be97cd30bce1d29c134fc',1,'vg::MultipathAlignmentGraph']]],
+ ['topologically_5forder_5fsubpaths_11223',['topologically_order_subpaths',['../namespacevg.html#a3ca9ccb5a2301ed1ce48f6334b3c4937',1,'vg']]],
+ ['total_11224',['total',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#acb07aae84ec439512a012ee80829c357',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::total()'],['../namespacevg.html#a0a064dd8829b2100c6a38780311073f3',1,'vg::total()']]],
+ ['total_5fnode_5fquality_11225',['total_node_quality',['../classvg_1_1Packer.html#a67a80245fcdbc4f5788b1062ee6b55f9',1,'vg::Packer']]],
+ ['total_5fsupports_11226',['total_supports',['../structvg_1_1BREAKPOINT.html#afc10d66ae6dad31e2086963bc6e34a06',1,'vg::BREAKPOINT']]],
+ ['touppercase_11227',['toUppercase',['../namespacevg.html#a00a949105ae94b18ca72452a442b8ddb',1,'vg']]],
+ ['touppercaseinplace_11228',['toUppercaseInPlace',['../namespacevg.html#adcf3d4a70f85f067842ccf34a82a4a46',1,'vg']]],
+ ['trace_11229',['trace',['../classvg_1_1DozeuInterface.html#a82634289dc80707e1ba8bb1a94503027',1,'vg::DozeuInterface::trace()'],['../classvg_1_1XdropAligner.html#adb3c7fa9b6b7c272ab687e0693a1dc47',1,'vg::XdropAligner::trace()'],['../classvg_1_1QualAdjXdropAligner.html#a8a382e7378bfeb43954a9436cf9d3b09',1,'vg::QualAdjXdropAligner::trace()'],['../classvg_1_1SnarlState.html#a6b13fa6a070139c5d123983265d440bc',1,'vg::SnarlState::trace()']]],
+ ['trace_5fhaplotype_11230',['trace_haplotype',['../classvg_1_1GenomeState.html#af167a6237410b8da2c839820e6c804a7',1,'vg::GenomeState']]],
+ ['trace_5fhaplotypes_5fand_5fpaths_11231',['trace_haplotypes_and_paths',['../namespacevg.html#a2d9774c4df98285526a427ba54e970ba',1,'vg']]],
+ ['trace_5fpath_11232',['trace_path',['../namespacevg.html#a83257be63a821ae991e1b332b62facd4',1,'vg::trace_path()'],['../haplotypes__main_8cpp.html#a8e6fb3993622a6541d6e6beb41ed1c72',1,'trace_path(): haplotypes_main.cpp']]],
+ ['trace_5fto_5falignment_11233',['trace_to_alignment',['../classvg_1_1DeletionAligner.html#a1916d488f7ed7e9ad0452a1c6138bc27',1,'vg::DeletionAligner']]],
+ ['traceback_11234',['traceback',['../classvg_1_1BandedGlobalAligner.html#a2a2b4909d5eb88633680ea071c5551f4',1,'vg::BandedGlobalAligner::traceback()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a1366942f6ff4eecbebad9b29e9ef2c94',1,'vg::BandedGlobalAligner::BAMatrix::traceback()'],['../classvg_1_1MEMChainModel.html#ae142b05be3a27922e9387108bb052706',1,'vg::MEMChainModel::traceback()'],['../classvg_1_1DeletionAligner.html#aeaa43fcc2267e2aab5ebde031e3852c3',1,'vg::DeletionAligner::traceback()'],['../classvg_1_1AlignmentChainModel.html#ac774ed2018837e64c7ef88ae28c2794a',1,'vg::AlignmentChainModel::traceback()']]],
+ ['traceback_5fover_5fedge_11235',['traceback_over_edge',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a0210e1c9a9da04e28e253e2963dd96ad',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['trailing_5fzeros_11236',['trailing_zeros',['../minimizer__main_8cpp.html#a82ed012045f022c7d023ef32c84a9df3',1,'minimizer_main.cpp']]],
+ ['transcript_11237',['Transcript',['../structvg_1_1Transcript.html#a151337b8595bb8b0041ed64a325a7650',1,'vg::Transcript']]],
+ ['transcript_5ffile_5fnonempty_11238',['transcript_file_nonempty',['../namespacevg.html#aa44c63a293d251b1bffbbeee59d2b7fe',1,'vg']]],
+ ['transcript_5fpaths_11239',['transcript_paths',['../classvg_1_1Transcriptome.html#a52ca431b737b92befedebee4e71b0f0c',1,'vg::Transcriptome']]],
+ ['transcriptome_11240',['Transcriptome',['../classvg_1_1Transcriptome.html#a041373349b45b5d190316229a5b8c562',1,'vg::Transcriptome']]],
+ ['transcriptpath_11241',['TranscriptPath',['../structvg_1_1TranscriptPath.html#ad87c876af2acb7bcbbbb52b33ad25e8d',1,'vg::TranscriptPath::TranscriptPath()'],['../structvg_1_1TranscriptPath.html#aef6b201d9d87a24f2c9e7ed6e9e9e1e7',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const string &embedded_path_name, const bool is_reference_in, const bool is_haplotype_in)'],['../structvg_1_1TranscriptPath.html#a1b9b94ca6d527d0f197d98faf2a6a4b5',1,'vg::TranscriptPath::TranscriptPath(const string &transcript_name, const gbwt::size_type &haplotype_gbwt_id, const bool is_reference_in, const bool is_haplotype_in)']]],
+ ['transfer_5fbetween_5fproto_5fannotation_11242',['transfer_between_proto_annotation',['../namespacevg.html#ac0534767a787eae1a5f93444bf21b2a1',1,'vg']]],
+ ['transfer_5fboundary_5finfo_11243',['transfer_boundary_info',['../namespacevg.html#a82a83d7c54d733abee06d328f91ef5ee',1,'vg']]],
+ ['transfer_5ffrom_5fproto_5fannotation_11244',['transfer_from_proto_annotation',['../namespacevg.html#a57c3f88ce9f85ceae2d77c32fd9de04d',1,'vg']]],
+ ['transfer_5fproto_5fmetadata_11245',['transfer_proto_metadata',['../namespacevg.html#a0582a68dfa130c9f0a2bdaa1c7ac5ef5',1,'vg::transfer_proto_metadata(const Alignment &from, MultipathAlignment &to)'],['../namespacevg.html#ad6476e86221a660dda1fa85254e9436d',1,'vg::transfer_proto_metadata(const MultipathAlignment &from, Alignment &to)']]],
+ ['transfer_5fread_5fmetadata_11246',['transfer_read_metadata',['../namespacevg.html#a195fc7fa6da6fecfa7e9fa31e5cf6f0c',1,'vg::transfer_read_metadata(const MultipathAlignment &from, multipath_alignment_t &to)'],['../namespacevg.html#acac375591689f0066f6c723dc25fb834',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, MultipathAlignment &to)'],['../namespacevg.html#ad0995c3042ff642b9e8aeaa1727dccb5',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, multipath_alignment_t &to)'],['../namespacevg.html#a54b4f608ad692caffd8fce4df9a1e4ef',1,'vg::transfer_read_metadata(const Alignment &from, multipath_alignment_t &to)'],['../namespacevg.html#a2d8929c8f610705661da889830b0b7b9',1,'vg::transfer_read_metadata(const multipath_alignment_t &from, Alignment &to)'],['../namespacevg.html#af48acb91edce241c75a9a4fd02745620',1,'vg::transfer_read_metadata(const Alignment &from, Alignment &to)']]],
+ ['transfer_5fto_5fproto_5fannotation_11247',['transfer_to_proto_annotation',['../namespacevg.html#a90a76dfce70406755151cf45e6990848',1,'vg']]],
+ ['transfer_5funiform_5fmetadata_11248',['transfer_uniform_metadata',['../namespacevg.html#adbf827b04e42865ece378b51482df898',1,'vg']]],
+ ['transform_11249',['transform',['../classvg_1_1VGset.html#aaa5f1b0e3e71bb00a5ad82f210065e81',1,'vg::VGset']]],
+ ['transitive_5freduction_11250',['transitive_reduction',['../classvg_1_1Surjector.html#a2149d1e5e6aba2e07b92030e6afc617d',1,'vg::Surjector']]],
+ ['translate_11251',['translate',['../classvg_1_1Translator.html#a3407f68503febdc2bd4366947e96d003',1,'vg::Translator::translate(const Position &position)'],['../classvg_1_1Translator.html#a6e27eb192e227afe777de2dc6488eb26',1,'vg::Translator::translate(const Position &position, const Translation &translation)'],['../classvg_1_1Translator.html#a1a8657e279942f5b4a802aad9e0baab6',1,'vg::Translator::translate(const Edge &edge)'],['../classvg_1_1Translator.html#a9ea3b0a85f25159214b34041b20a5cd3',1,'vg::Translator::translate(const Mapping &mapping)'],['../classvg_1_1Translator.html#a28ee9ca0de37d9d83f24b33639f0893c',1,'vg::Translator::translate(const Path &path)'],['../classvg_1_1Translator.html#af2f3e933feb2e28acf713316840b03c4',1,'vg::Translator::translate(const Alignment &aln)'],['../classvg_1_1Translator.html#ab4dffeb58e1c441c82039c6dd17445f5',1,'vg::Translator::translate(const Locus &locus)']]],
+ ['translate_5fback_11252',['translate_back',['../classvg_1_1FlatFileBackTranslation.html#a44128954132be459c4229001b0441add',1,'vg::FlatFileBackTranslation::translate_back()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a762d6c9b1ad1762f3521c3a24cf82f55',1,'vg::algorithms::GFAIDMapInfo::translate_back()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#a4005088073dfdd8d3da33803198ee737',1,'handlegraph::NamedNodeBackTranslation::translate_back()']]],
+ ['translate_5fdown_11253',['translate_down',['../classvg_1_1PathSubgraph.html#a7fa974235481756de3a7bb3c04f58ef7',1,'vg::PathSubgraph::translate_down()'],['../classvg_1_1TreeSubgraph.html#a71ab7a4ca370f712cf7c4912ccb5ab25',1,'vg::TreeSubgraph::translate_down()']]],
+ ['translate_5fmems_11254',['translate_mems',['../namespacevg.html#a4bc1837d8c1cca33ab223957402b70ba',1,'vg']]],
+ ['translate_5fnode_5fids_11255',['translate_node_ids',['../classvg_1_1JoinedSpliceGraph.html#a535cf652e7e39598979b003b7155ae4f',1,'vg::JoinedSpliceGraph::translate_node_ids()'],['../namespacevg.html#af71770196fc31c2e3c9c2a83f3497177',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator)'],['../namespacevg.html#aa49e4506c94e5747c88805e39aa18090',1,'vg::translate_node_ids(Path &path, const unordered_map< id_t, id_t > &translator, id_t cut_node, size_t bases_removed, bool from_right)'],['../namespacevg.html#a322ec292675d4891ecc265e56a836db7',1,'vg::translate_node_ids(path_t &path, const unordered_map< id_t, id_t > &translator)']]],
+ ['translate_5fnodes_11256',['translate_nodes',['../namespacevg.html#a98dcd16f2a4eae4c223a374dd2ab2da4',1,'vg']]],
+ ['translate_5foriented_5fnode_5fids_11257',['translate_oriented_node_ids',['../namespacevg.html#a2b0ba7a1d0cf7630b79d03ba0ab65c53',1,'vg::translate_oriented_node_ids(Path &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#acb86c984b743e10c6ddaa57612ca3991',1,'vg::translate_oriented_node_ids(Path &path, const function< pair< id_t, bool >(id_t)> &translator)'],['../namespacevg.html#a449dd4b0d7106c6ee7afceb4f7412d6d',1,'vg::translate_oriented_node_ids(path_t &path, const unordered_map< id_t, pair< id_t, bool >> &translator)'],['../namespacevg.html#abfebb6e72326ea81b2ed13b4c3b57885',1,'vg::translate_oriented_node_ids(path_t &path, const function< pair< id_t, bool >(id_t)> &translator)']]],
+ ['translate_5fsnarl_5fnum_11258',['translate_snarl_num',['../classvg_1_1SnarlManager.html#afdd078898493f277dc1aa5dc3dae5d56',1,'vg::SnarlManager']]],
+ ['translator_11259',['Translator',['../classvg_1_1Translator.html#ac23acdcea38566f2e68005eca4afff73',1,'vg::Translator::Translator(void)'],['../classvg_1_1Translator.html#aeab811097e483365bbd273efc4c4445e',1,'vg::Translator::Translator(istream &in)'],['../classvg_1_1Translator.html#a99602b3868ae6f8f1efc6bf7adcde6f6',1,'vg::Translator::Translator(const vector< Translation > &trans)']]],
+ ['transpose_11260',['transpose',['../namespacevg.html#a1409ac23ce33abd463dcd46093079023',1,'vg']]],
+ ['trav_5fsequence_11261',['trav_sequence',['../classvg_1_1VG.html#a57296ecbcfce10f95b86233e10c35d7d',1,'vg::VG']]],
+ ['trav_5fstring_11262',['trav_string',['../classvg_1_1VCFOutputCaller.html#ae4b896a68da613eb2e8e509279e4e1b9',1,'vg::VCFOutputCaller']]],
+ ['traversal_5fto_5fstring_11263',['traversal_to_string',['../namespacevg.html#a94385b32246fc81a0a44ea1b47d994ee',1,'vg::traversal_to_string(VG &graph, const SnarlTraversal &path)'],['../namespacevg.html#a6a885124cc3018dc7cd6d2001b6b54f5',1,'vg::traversal_to_string(const PathHandleGraph *graph, const Traversal &traversal, int64_t max_steps)']]],
+ ['traversalsupportfinder_11264',['TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html#ab281113b3cdf2992299a2768ce1be832',1,'vg::TraversalSupportFinder']]],
+ ['traverse_5fcomponents_11265',['traverse_components',['../namespacevg_1_1algorithms.html#a6341683f1b89495d2ac1558ed2875343',1,'vg::algorithms']]],
+ ['traverse_5fcomputed_5fdecomposition_11266',['traverse_computed_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#ab843403935c08e4d1764b693a897c16c',1,'vg::IntegratedSnarlFinder']]],
+ ['traverse_5fdecomposition_11267',['traverse_decomposition',['../classvg_1_1IntegratedSnarlFinder.html#a31a75674d1cc7d5f2b6a028161c6038f',1,'vg::IntegratedSnarlFinder::traverse_decomposition()'],['../classvg_1_1HandleGraphSnarlFinder.html#a9cba8688e5dd28b23ed3529af122f308',1,'vg::HandleGraphSnarlFinder::traverse_decomposition()']]],
+ ['traverse_5fedge_5fhandle_11268',['traverse_edge_handle',['../classhandlegraph_1_1HandleGraph.html#af167b0664299cfd4eac610f129fa5fee',1,'handlegraph::HandleGraph']]],
+ ['traverse_5fin_5forder_11269',['traverse_in_order',['../classvg_1_1BitStringTree.html#a5f825ebeb38c6d1572fa73692810c273',1,'vg::BitStringTree::traverse_in_order()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#aa89c88fbab67819e3f072da4bc82e253',1,'vg::BitStringTree::TreeNode::traverse_in_order()']]],
+ ['traverse_5fleft_11270',['traverse_left',['../classvg_1_1Paths.html#a861618af488874863197ad48f17a9ae4',1,'vg::Paths']]],
+ ['traverse_5fright_11271',['traverse_right',['../classvg_1_1Paths.html#aabda0fb1288e7681b317cd5b4cfad242',1,'vg::Paths']]],
+ ['traverse_5fup_11272',['traverse_up',['../classvg_1_1BitStringTree.html#aefd44d9f67d266cb206724b8516c001c',1,'vg::BitStringTree::traverse_up()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#ae67c2a504203ce10bbc6cc33d94c2e3b',1,'vg::BitStringTree::TreeNode::traverse_up()']]],
+ ['travs_5ffrom_11273',['travs_from',['../classvg_1_1VG.html#a34a493a0628857a3bfae181295ba541d',1,'vg::VG']]],
+ ['travs_5fof_11274',['travs_of',['../classvg_1_1VG.html#ae065082f817e9bc0e278cf71f31af1e2',1,'vg::VG']]],
+ ['travs_5fto_11275',['travs_to',['../classvg_1_1VG.html#a0a962957210c079fa242b383d5c65de3',1,'vg::VG']]],
+ ['tree_11276',['Tree',['../structvg_1_1Tree.html#a2583e3d479b8b3fa66e8eb0065417934',1,'vg::Tree']]],
+ ['tree_5fitem_5ft_11277',['tree_item_t',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a5740e0956ab1ddcb8148d70702c2000f',1,'vg::ZipCodeTree::tree_item_t::tree_item_t()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a895703befafce6654f476cc86bdc33ed',1,'vg::ZipCodeTree::tree_item_t::tree_item_t(tree_item_type_t type, size_t raw_value, bool is_reversed)']]],
+ ['treenode_11278',['TreeNode',['../structvg_1_1TreeNode.html#a386f7b2ec0948165140022155dda8c04',1,'vg::TreeNode']]],
+ ['treesubgraph_11279',['TreeSubgraph',['../classvg_1_1TreeSubgraph.html#aa43b054cfbc6f2f96fbc8fcef42887c5',1,'vg::TreeSubgraph']]],
+ ['trim_11280',['trim',['../classvg_1_1WFATree.html#aa4c7ff4d5620d1a75545bef9357096f3',1,'vg::WFATree']]],
+ ['trim_5falignment_11281',['trim_alignment',['../namespacevg.html#ad83da8607e104967dd51d9230f4b51bb',1,'vg']]],
+ ['trim_5fambiguous_5fend_11282',['trim_ambiguous_end',['../classvg_1_1ReadFilter.html#ac5d77581ac1d34661c62f446692217ab',1,'vg::ReadFilter']]],
+ ['trim_5fambiguous_5fends_11283',['trim_ambiguous_ends',['../classvg_1_1ReadFilter.html#a265a2c2d5e5af4924c406b97d764d9aa',1,'vg::ReadFilter::trim_ambiguous_ends(Read &read, int k) const'],['../classvg_1_1ReadFilter.html#ac49bf695fadbdaf8b41c972587493630',1,'vg::ReadFilter::trim_ambiguous_ends(Alignment &alignment, int k) const'],['../classvg_1_1ReadFilter.html#a266b5aeeb2081d2bd5f29ae43fdc00f8',1,'vg::ReadFilter::trim_ambiguous_ends(MultipathAlignment &aln, int k) const']]],
+ ['trim_5fand_5fcheck_5ffor_5fempty_11284',['trim_and_check_for_empty',['../classvg_1_1MultipathAlignmentGraph.html#a114d073d4422c085a2c5768b6f165001',1,'vg::MultipathAlignmentGraph']]],
+ ['trim_5fhanging_5fends_11285',['trim_hanging_ends',['../namespacevg.html#a990f54fb0e09dc439dace1519aff5e9f',1,'vg']]],
+ ['trim_5fhanging_5findels_11286',['trim_hanging_indels',['../classvg_1_1MultipathAlignmentGraph.html#aca7bc3f6c3de6fc3df3adabf3161260c',1,'vg::MultipathAlignmentGraph']]],
+ ['trim_5fmismatches_11287',['trim_mismatches',['../namespacevg.html#a77211f457b4e1f61915d771faf06cda0',1,'vg']]],
+ ['trim_5fpath_11288',['trim_path',['../namespacevg.html#ab8d0345d2d7cea79ffdca38d33ed0c7f',1,'vg']]],
+ ['trim_5fto_5fbranch_5fpoints_11289',['trim_to_branch_points',['../classvg_1_1MultipathAlignmentGraph.html#ac3199fb5e097873e2635e3fb34a8eafe',1,'vg::MultipathAlignmentGraph']]],
+ ['trim_5fto_5fvariable_11290',['trim_to_variable',['../classvg_1_1Constructor.html#a428cf1b27e402a304c18e40f87e9dc02',1,'vg::Constructor']]],
+ ['trimmed_5fend_11291',['trimmed_end',['../namespacevg.html#a9e61398cd459bb9ba3a1ced205491712',1,'vg']]],
+ ['triviallyserializable_11292',['TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html#a209a7ede82e8ad286a8a3fb1e51c3604',1,'handlegraph::TriviallySerializable']]],
+ ['trivialtraversalfinder_11293',['TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html#a46403401b7efaec8d99b63b2013f7e60',1,'vg::TrivialTraversalFinder']]],
+ ['truncate_5fhandle_11294',['truncate_handle',['../classhandlegraph_1_1DeletableHandleGraph.html#aa65cef3b3261f8d1bc2057c5f2ee100a',1,'handlegraph::DeletableHandleGraph']]],
+ ['truncated_5fnormal_5fdistribution_11295',['truncated_normal_distribution',['../classvg_1_1truncated__normal__distribution.html#aa48544711e2d4a11ffe876366898e463',1,'vg::truncated_normal_distribution']]],
+ ['try_5fload_5fbare_11296',['try_load_bare',['../classvg_1_1io_1_1VPKG.html#ad5d2bad9c95479a3f1520c5fadcba1b2',1,'vg::io::VPKG']]],
+ ['try_5fload_5fencapsulated_11297',['try_load_encapsulated',['../classvg_1_1io_1_1VPKG.html#a695e5a53bfbc9a5b36c5ea2306f253db',1,'vg::io::VPKG::try_load_encapsulated(istream &in)'],['../classvg_1_1io_1_1VPKG.html#a860f50291f4b5a6be232e5312eb884ab',1,'vg::io::VPKG::try_load_encapsulated(MessageIterator &it)']]],
+ ['try_5fload_5ffirst_11298',['try_load_first',['../classvg_1_1io_1_1VPKG.html#a58ed1c37748fed4b15d4e611659ce4c3',1,'vg::io::VPKG::try_load_first(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a504e965a2a019ce27267ea85c106a91b',1,'vg::io::VPKG::try_load_first(const string &filename)']]],
+ ['try_5fload_5ffirst_5fbare_11299',['try_load_first_bare',['../classvg_1_1io_1_1VPKG.html#acfc929254f523522f369c4a17c8f0941',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a2707edbb6b28a6623ea8ae11e607c861',1,'vg::io::VPKG::try_load_first_bare(istream &in, const string &filename, bool &found)']]],
+ ['try_5fload_5ffirst_5fencapsulated_11300',['try_load_first_encapsulated',['../classvg_1_1io_1_1VPKG.html#a12f9922d4b17194d248dc3f19a449f60',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)'],['../classvg_1_1io_1_1VPKG.html#a186f277ebf475632f1b4d1eac4c48139',1,'vg::io::VPKG::try_load_first_encapsulated(MessageIterator &it, bool &found)']]],
+ ['try_5fload_5fone_11301',['try_load_one',['../classvg_1_1io_1_1VPKG.html#a0d7f96d4dd7fe5b1fe47b330ca617623',1,'vg::io::VPKG::try_load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#ab3a2026ac79ee1539271ba1791108c66',1,'vg::io::VPKG::try_load_one(const string &filename)']]],
+ ['tsvalignmentemitter_11302',['TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html#aa8778347f51972fcb03f74565c5e3117',1,'vg::io::TSVAlignmentEmitter']]],
+ ['tsvexplainer_11303',['TSVExplainer',['../classvg_1_1TSVExplainer.html#a3a9d31e471d1808b30dfdc6c995660b4',1,'vg::TSVExplainer']]],
+ ['tv_5fpath_11304',['tv_path',['../classvg_1_1TargetValueSearch.html#a9ab66a82967803031203885c18291c6f',1,'vg::TargetValueSearch']]],
+ ['tv_5fpath_5fexists_11305',['tv_path_exists',['../classvg_1_1TargetValueSearch.html#a407607bcab4cfd14e283386bac418636',1,'vg::TargetValueSearch']]],
+ ['tv_5fpath_5flength_11306',['tv_path_length',['../classvg_1_1TargetValueSearch.html#a7dc599c6d4a317999890c81634d9ddf5',1,'vg::TargetValueSearch']]],
+ ['tv_5fphase2_11307',['tv_phase2',['../classvg_1_1TargetValueSearch.html#a794b8271df6bcf349db5e6d605402744',1,'vg::TargetValueSearch']]],
+ ['tvsclusterer_11308',['TVSClusterer',['../classvg_1_1TVSClusterer.html#a5b8fdb6006095094e85e6f760b8d0e3d',1,'vg::TVSClusterer']]],
+ ['type_5fas_5fchar_11309',['type_as_char',['../structReferenceInterval.html#a9ae0102fab5146105642e388d6bef997',1,'ReferenceInterval']]]
];
diff --git a/search/functions_15.js b/search/functions_15.js
index c5ca888944..66a72c858b 100644
--- a/search/functions_15.js
+++ b/search/functions_15.js
@@ -1,58 +1,58 @@
var searchData=
[
- ['uf_5fhandle_11306',['uf_handle',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a84a5d20d03e165edd89bdddf7ccfa25f',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['uf_5frank_11307',['uf_rank',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a7d285e6a4baec754e89edd5338589f3e',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['unbacked_11308',['unbacked',['../structvg_1_1GBWTHandler.html#aed5e6775de6c9c96c78a752903a5a3ac',1,'vg::GBWTHandler']]],
- ['unchop_11309',['unchop',['../namespacehandlegraph_1_1algorithms.html#a407196811333767aa7f89b7ecc231564',1,'handlegraph::algorithms']]],
- ['underflow_11310',['underflow',['../classvg_1_1io_1_1fdinbuf.html#a67ea7aab3e21cacec9fb836d4a70673e',1,'vg::io::fdinbuf::underflow()'],['../classvg_1_1io_1_1streaminbuf.html#afa7f9b8f4f3159d819b2c9a2eb6a05cb',1,'vg::io::streaminbuf::underflow()']]],
- ['underlying_5finterval_11311',['underlying_interval',['../classvg_1_1IncrementalSubgraph.html#ab6537f375ee27409fee46bd4dfdcb1a3',1,'vg::IncrementalSubgraph::underlying_interval()'],['../classvg_1_1JoinedSpliceGraph.html#ad9a0c6d572cb5052efa79e66d8cd29ab',1,'vg::JoinedSpliceGraph::underlying_interval()']]],
- ['unescape_5fdelim_11312',['unescape_delim',['../classvg_1_1Packer.html#a32f8697cf4c222f5e207a4b15a1f0883',1,'vg::Packer']]],
- ['unescape_5fdelims_11313',['unescape_delims',['../classvg_1_1Packer.html#a92b44e965dd5da9da72e1a9196290d94',1,'vg::Packer']]],
- ['unfold_11314',['unfold',['../classvg_1_1PhaseUnfolder.html#a39a286ab3746a9a175a898bead3d2612',1,'vg::PhaseUnfolder::unfold()'],['../classvg_1_1VG.html#a6552b9da8cff82802ee24090064eb3a8',1,'vg::VG::unfold()']]],
- ['unfold_5fcomponent_11315',['unfold_component',['../classvg_1_1PhaseUnfolder.html#a84543fbc3521c9da70838339613ac3b9',1,'vg::PhaseUnfolder']]],
- ['uniform_5fint_5fdistribution_11316',['uniform_int_distribution',['../classvg_1_1uniform__int__distribution.html#ab8d23ee7f2beacc01804f3206c3bc663',1,'vg::uniform_int_distribution']]],
- ['uniform_5freal_5fdistribution_11317',['uniform_real_distribution',['../classvg_1_1uniform__real__distribution.html#aaa8046adecf3b01e7e702df2e4fe3abd',1,'vg::uniform_real_distribution']]],
- ['unindex_5fedge_5fby_5fnode_5fsides_11318',['unindex_edge_by_node_sides',['../classvg_1_1VG.html#a1c0b7db8d3043747e8b9a44cba4eaac9',1,'vg::VG::unindex_edge_by_node_sides(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a5677da9ff22052f6c6a85bfe66e1256d',1,'vg::VG::unindex_edge_by_node_sides(Edge *edge)']]],
- ['union_5fgroups_11319',['union_groups',['../classvg_1_1SparseUnionFind.html#ac3fdf36c05a3145bc8c309d4ec3bd2d6',1,'vg::SparseUnionFind']]],
- ['unique_5fminimizers_11320',['unique_minimizers',['../classvg_1_1HaplotypePartitioner.html#a16638525e7b8ceca27c326af457519b6',1,'vg::HaplotypePartitioner::unique_minimizers(gbwt::size_type sequence_id) const'],['../classvg_1_1HaplotypePartitioner.html#aa846481b6e9014761d65a430179e5d80',1,'vg::HaplotypePartitioner::unique_minimizers(sequence_type sequence, Subchain subchain) const']]],
- ['unlocalized_5finsertion_11321',['unlocalized_insertion',['../structvg_1_1WFAAlignment.html#a5f48d4dc6b6001b37549054ad20b9b47',1,'vg::WFAAlignment']]],
- ['unlock_11322',['unlock',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1cfc8d66ced1ef3d435f99579ac44ca6',1,'vg::GraphSynchronizer::Lock']]],
- ['unmapped_5ffilter_11323',['unmapped_filter',['../classvg_1_1Filter.html#a3a02d37cb7cf0b042aa5933186a76061',1,'vg::Filter']]],
- ['unoriented_5fdistance_5fbetween_11324',['unoriented_distance_between',['../classvg_1_1MinimizerMapper.html#a6fc70b73ed8c2aa3505a483b074671b8',1,'vg::MinimizerMapper']]],
- ['unoriented_5fmotif_11325',['unoriented_motif',['../classvg_1_1SpliceStats.html#aaeeab4dee70e8e231fa92646267ccbff',1,'vg::SpliceStats']]],
- ['unpack_5fbit_11326',['unpack_bit',['../structhandlegraph_1_1number__bool__packing.html#a52f57c83e66ad6f09b519dff55be71d9',1,'handlegraph::number_bool_packing']]],
- ['unpack_5fchain_5fcode_11327',['unpack_chain_code',['../classvg_1_1ZipCode.html#a66e91c21e0b8a818b6de6a620ee0bdf5',1,'vg::ZipCode']]],
- ['unpack_5fnode_5fcode_11328',['unpack_node_code',['../classvg_1_1ZipCode.html#a7e7cd0b16ad1b9ac447b6eb0458f289d',1,'vg::ZipCode']]],
- ['unpack_5fnumber_11329',['unpack_number',['../structhandlegraph_1_1number__bool__packing.html#a5f2f610bc0e6819ff0ae3d91d2aff9fc',1,'handlegraph::number_bool_packing']]],
- ['unpack_5fsnarl_5fcode_11330',['unpack_snarl_code',['../classvg_1_1ZipCode.html#a4b76c5d63d72f9938352327e6d7b06c0',1,'vg::ZipCode']]],
- ['unpaired_5ffor_5feach_5fparallel_11331',['unpaired_for_each_parallel',['../namespacevg_1_1io.html#ac3daebbee97f2451b25aec3c642c06c8',1,'vg::io']]],
- ['unparse_11332',['unparse',['../classvg_1_1OptionValueParser.html#a816cf0ccd1d8b95f6f8f47434e1af376',1,'vg::OptionValueParser::unparse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a57f771079219ffb85ea0cebc6b024045',1,'vg::OptionValueParser< vector< Item > >::unparse()'],['../classvg_1_1OptionValueParser.html#aa72adfa088347d83a7019da414c4b8a7',1,'vg::OptionValueParser::unparse()']]],
- ['unrecord_11333',['unrecord',['../classvg_1_1SnarlManager.html#a40be4db13bf881c882f3be70c067c111',1,'vg::SnarlManager::unrecord(const SnarlRecord *record) const'],['../classvg_1_1SnarlManager.html#aeeb8bf1eb342004f69b33caadad5a713',1,'vg::SnarlManager::unrecord(SnarlRecord *record)']]],
- ['unreverse_5fgraph_11334',['unreverse_graph',['../classvg_1_1GSSWAligner.html#aeb2785609201c50f8e7addde7eeddb0a',1,'vg::GSSWAligner']]],
- ['unreverse_5fgraph_5fmapping_11335',['unreverse_graph_mapping',['../classvg_1_1GSSWAligner.html#aa00b750624c67e2cfa4d98193acf8dd9',1,'vg::GSSWAligner']]],
- ['unset_11336',['unset',['../classvg_1_1algorithms_1_1TracedScore.html#a5ba55d94d11446319300052e02df1b23',1,'vg::algorithms::TracedScore']]],
- ['update_11337',['update',['../structvg_1_1WFANode.html#a3ca9cee0c921c093c9c9b88506f1e58a',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, const MatchPos &pos)'],['../structvg_1_1WFANode.html#a8577faa0410e723fa6c5a2de7f4e452c',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, uint32_t seq_offset, uint32_t node_offset)']]],
- ['update_5fdiagonal_5frange_11338',['update_diagonal_range',['../classvg_1_1WFATree.html#a923bbbd53962ce4121989e66291afa5a',1,'vg::WFATree']]],
- ['update_5fhaplotype_5findex_11339',['update_haplotype_index',['../classvg_1_1Transcriptome.html#a5b33f790ea79988af1d05ba0b1fd1cea',1,'vg::Transcriptome']]],
- ['update_5fin_5fout_5fedges_11340',['update_in_out_edges',['../classvg_1_1FlowSort.html#a09b6782a1ab4d5c5ed7fa23cf83083d8',1,'vg::FlowSort']]],
- ['update_5finner_5fvalues_11341',['update_inner_values',['../structhaplo_1_1haplo__DP__column.html#ae5860a155f8e49360b2fb2289e2555b8',1,'haplo::haplo_DP_column']]],
- ['update_5fintron_5flength_5fdistribution_11342',['update_intron_length_distribution',['../classvg_1_1SpliceStats.html#a984c94dae240b73a92d40f4d36d39fb6',1,'vg::SpliceStats']]],
- ['update_5fmapping_5fpositions_11343',['update_mapping_positions',['../structvg_1_1PathIndex.html#a783b7aafb86a509a3434c10b5ae9355f',1,'vg::PathIndex']]],
- ['update_5fmotifs_11344',['update_motifs',['../classvg_1_1SpliceStats.html#a26085c886cc27966f45c239fb13e0136',1,'vg::SpliceStats']]],
- ['update_5fnesting_5finfo_5ftags_11345',['update_nesting_info_tags',['../classvg_1_1VCFOutputCaller.html#a131c6d35d0722a64bd18b4a646efac5a',1,'vg::VCFOutputCaller']]],
- ['update_5fpath_5findexes_11346',['update_path_indexes',['../classvg_1_1GraphSynchronizer.html#a056cd54145b467de24d6ce128749af27',1,'vg::GraphSynchronizer']]],
- ['update_5fprogress_11347',['update_progress',['../classvg_1_1Progressive.html#a0d64e6aa69bc094c163f4827602a302c',1,'vg::Progressive']]],
- ['update_5fscore_5fvector_11348',['update_score_vector',['../structhaplo_1_1haplo__DP__column.html#a40859e4ede0d3829b5e7dca9a89af660',1,'haplo::haplo_DP_column']]],
- ['update_5fscoring_11349',['update_scoring',['../classvg_1_1SpliceStats.html#a23dd768b9e57750de42c5f88a2b2d8d4',1,'vg::SpliceStats']]],
- ['update_5fstate_11350',['update_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#afb76a0ce92c750ae8cb12eaf2c0ae7fd',1,'vg::BandedGlobalAligner::BABuilder::update_state()'],['../classvg_1_1DinucleotideMachine.html#a9b246cec10b2a7e45ed7f3a3261427e5',1,'vg::DinucleotideMachine::update_state()']]],
- ['update_5ftranscript_5fpaths_11351',['update_transcript_paths',['../classvg_1_1Transcriptome.html#a9f55d0f16470ee2750fe09986c85b464',1,'vg::Transcriptome']]],
- ['update_5fvcf_5fheader_11352',['update_vcf_header',['../classvg_1_1SnarlCaller.html#a7fb3205d6e94505aadf0c9944fac7eb4',1,'vg::SnarlCaller::update_vcf_header()'],['../classvg_1_1RatioSupportSnarlCaller.html#ac7a153c3c35bc7d314f69f8ccbc30ae1',1,'vg::RatioSupportSnarlCaller::update_vcf_header()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a2872f6728e288de01d5403fcdb76a05b',1,'vg::PoissonSupportSnarlCaller::update_vcf_header()']]],
- ['update_5fvcf_5finfo_11353',['update_vcf_info',['../classvg_1_1MCMCCaller.html#a8deeb18605436556136403261715155e',1,'vg::MCMCCaller::update_vcf_info()'],['../classvg_1_1SnarlCaller.html#a5098383d371e037c79e4c278e3fbbea1',1,'vg::SnarlCaller::update_vcf_info()'],['../classvg_1_1SupportBasedSnarlCaller.html#a3ddd1e17537734b984fa0befe9f0d7f6',1,'vg::SupportBasedSnarlCaller::update_vcf_info()'],['../classvg_1_1RatioSupportSnarlCaller.html#a3dc6a3524e755fba03211f0f0dd3483f',1,'vg::RatioSupportSnarlCaller::update_vcf_info()'],['../classvg_1_1PoissonSupportSnarlCaller.html#abe1990823417defcd0c6f68132680db1',1,'vg::PoissonSupportSnarlCaller::update_vcf_info()']]],
- ['use_11354',['use',['../structvg_1_1GBWTHandler.html#a8062238f984f4c521cef46cfc2961626',1,'vg::GBWTHandler::use(gbwt::GBWT &new_index)'],['../structvg_1_1GBWTHandler.html#a574972e799a708837a0e2e481926f87a',1,'vg::GBWTHandler::use(gbwt::DynamicGBWT &new_index)'],['../structGraphHandler.html#a4ccfddaf318c987155ab13de16dcfc2c',1,'GraphHandler::use()']]],
- ['use_5fcompressed_11355',['use_compressed',['../structvg_1_1GBWTHandler.html#a40007a32d020290a72aaef0e830454c4',1,'vg::GBWTHandler']]],
- ['use_5fdynamic_11356',['use_dynamic',['../structvg_1_1GBWTHandler.html#a88de75253b3b9b54e844d0a20ff9a5c7',1,'vg::GBWTHandler']]],
- ['use_5for_5fsave_11357',['use_or_save',['../gbwt__main_8cpp.html#ab82463d53fb85eaec6c4e581e009d9e6',1,'gbwt_main.cpp']]],
- ['use_5fpreset_11358',['use_preset',['../gbwt__main_8cpp.html#ad246795d44cf23172412ae1c6a7a86e6',1,'gbwt_main.cpp']]],
- ['used_5fbins_5fof_5frange_11359',['used_bins_of_range',['../classvg_1_1StreamIndexBase.html#a94777b19236dfb74d66ba8c484bf663f',1,'vg::StreamIndexBase']]],
- ['uses_5fus_11360',['uses_Us',['../namespacevg.html#acd966c42f332957a1b9317faa3d26407',1,'vg']]]
+ ['uf_5fhandle_11310',['uf_handle',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a84a5d20d03e165edd89bdddf7ccfa25f',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['uf_5frank_11311',['uf_rank',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a7d285e6a4baec754e89edd5338589f3e',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['unbacked_11312',['unbacked',['../structvg_1_1GBWTHandler.html#aed5e6775de6c9c96c78a752903a5a3ac',1,'vg::GBWTHandler']]],
+ ['unchop_11313',['unchop',['../namespacehandlegraph_1_1algorithms.html#a407196811333767aa7f89b7ecc231564',1,'handlegraph::algorithms']]],
+ ['underflow_11314',['underflow',['../classvg_1_1io_1_1fdinbuf.html#a67ea7aab3e21cacec9fb836d4a70673e',1,'vg::io::fdinbuf::underflow()'],['../classvg_1_1io_1_1streaminbuf.html#afa7f9b8f4f3159d819b2c9a2eb6a05cb',1,'vg::io::streaminbuf::underflow()']]],
+ ['underlying_5finterval_11315',['underlying_interval',['../classvg_1_1IncrementalSubgraph.html#ab6537f375ee27409fee46bd4dfdcb1a3',1,'vg::IncrementalSubgraph::underlying_interval()'],['../classvg_1_1JoinedSpliceGraph.html#ad9a0c6d572cb5052efa79e66d8cd29ab',1,'vg::JoinedSpliceGraph::underlying_interval()']]],
+ ['unescape_5fdelim_11316',['unescape_delim',['../classvg_1_1Packer.html#a32f8697cf4c222f5e207a4b15a1f0883',1,'vg::Packer']]],
+ ['unescape_5fdelims_11317',['unescape_delims',['../classvg_1_1Packer.html#a92b44e965dd5da9da72e1a9196290d94',1,'vg::Packer']]],
+ ['unfold_11318',['unfold',['../classvg_1_1PhaseUnfolder.html#a39a286ab3746a9a175a898bead3d2612',1,'vg::PhaseUnfolder::unfold()'],['../classvg_1_1VG.html#a6552b9da8cff82802ee24090064eb3a8',1,'vg::VG::unfold()']]],
+ ['unfold_5fcomponent_11319',['unfold_component',['../classvg_1_1PhaseUnfolder.html#a84543fbc3521c9da70838339613ac3b9',1,'vg::PhaseUnfolder']]],
+ ['uniform_5fint_5fdistribution_11320',['uniform_int_distribution',['../classvg_1_1uniform__int__distribution.html#ab8d23ee7f2beacc01804f3206c3bc663',1,'vg::uniform_int_distribution']]],
+ ['uniform_5freal_5fdistribution_11321',['uniform_real_distribution',['../classvg_1_1uniform__real__distribution.html#aaa8046adecf3b01e7e702df2e4fe3abd',1,'vg::uniform_real_distribution']]],
+ ['unindex_5fedge_5fby_5fnode_5fsides_11322',['unindex_edge_by_node_sides',['../classvg_1_1VG.html#a1c0b7db8d3043747e8b9a44cba4eaac9',1,'vg::VG::unindex_edge_by_node_sides(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a5677da9ff22052f6c6a85bfe66e1256d',1,'vg::VG::unindex_edge_by_node_sides(Edge *edge)']]],
+ ['union_5fgroups_11323',['union_groups',['../classvg_1_1SparseUnionFind.html#ac3fdf36c05a3145bc8c309d4ec3bd2d6',1,'vg::SparseUnionFind']]],
+ ['unique_5fminimizers_11324',['unique_minimizers',['../classvg_1_1HaplotypePartitioner.html#a16638525e7b8ceca27c326af457519b6',1,'vg::HaplotypePartitioner::unique_minimizers(gbwt::size_type sequence_id) const'],['../classvg_1_1HaplotypePartitioner.html#aa846481b6e9014761d65a430179e5d80',1,'vg::HaplotypePartitioner::unique_minimizers(sequence_type sequence, Subchain subchain) const']]],
+ ['unlocalized_5finsertion_11325',['unlocalized_insertion',['../structvg_1_1WFAAlignment.html#a5f48d4dc6b6001b37549054ad20b9b47',1,'vg::WFAAlignment']]],
+ ['unlock_11326',['unlock',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1cfc8d66ced1ef3d435f99579ac44ca6',1,'vg::GraphSynchronizer::Lock']]],
+ ['unmapped_5ffilter_11327',['unmapped_filter',['../classvg_1_1Filter.html#a3a02d37cb7cf0b042aa5933186a76061',1,'vg::Filter']]],
+ ['unoriented_5fdistance_5fbetween_11328',['unoriented_distance_between',['../classvg_1_1MinimizerMapper.html#a6fc70b73ed8c2aa3505a483b074671b8',1,'vg::MinimizerMapper']]],
+ ['unoriented_5fmotif_11329',['unoriented_motif',['../classvg_1_1SpliceStats.html#aaeeab4dee70e8e231fa92646267ccbff',1,'vg::SpliceStats']]],
+ ['unpack_5fbit_11330',['unpack_bit',['../structhandlegraph_1_1number__bool__packing.html#a52f57c83e66ad6f09b519dff55be71d9',1,'handlegraph::number_bool_packing']]],
+ ['unpack_5fchain_5fcode_11331',['unpack_chain_code',['../classvg_1_1ZipCode.html#a66e91c21e0b8a818b6de6a620ee0bdf5',1,'vg::ZipCode']]],
+ ['unpack_5fnode_5fcode_11332',['unpack_node_code',['../classvg_1_1ZipCode.html#a7e7cd0b16ad1b9ac447b6eb0458f289d',1,'vg::ZipCode']]],
+ ['unpack_5fnumber_11333',['unpack_number',['../structhandlegraph_1_1number__bool__packing.html#a5f2f610bc0e6819ff0ae3d91d2aff9fc',1,'handlegraph::number_bool_packing']]],
+ ['unpack_5fsnarl_5fcode_11334',['unpack_snarl_code',['../classvg_1_1ZipCode.html#a4b76c5d63d72f9938352327e6d7b06c0',1,'vg::ZipCode']]],
+ ['unpaired_5ffor_5feach_5fparallel_11335',['unpaired_for_each_parallel',['../namespacevg_1_1io.html#ac3daebbee97f2451b25aec3c642c06c8',1,'vg::io']]],
+ ['unparse_11336',['unparse',['../classvg_1_1OptionValueParser.html#a816cf0ccd1d8b95f6f8f47434e1af376',1,'vg::OptionValueParser::unparse()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a57f771079219ffb85ea0cebc6b024045',1,'vg::OptionValueParser< vector< Item > >::unparse()'],['../classvg_1_1OptionValueParser.html#aa72adfa088347d83a7019da414c4b8a7',1,'vg::OptionValueParser::unparse()']]],
+ ['unrecord_11337',['unrecord',['../classvg_1_1SnarlManager.html#a40be4db13bf881c882f3be70c067c111',1,'vg::SnarlManager::unrecord(const SnarlRecord *record) const'],['../classvg_1_1SnarlManager.html#aeeb8bf1eb342004f69b33caadad5a713',1,'vg::SnarlManager::unrecord(SnarlRecord *record)']]],
+ ['unreverse_5fgraph_11338',['unreverse_graph',['../classvg_1_1GSSWAligner.html#aeb2785609201c50f8e7addde7eeddb0a',1,'vg::GSSWAligner']]],
+ ['unreverse_5fgraph_5fmapping_11339',['unreverse_graph_mapping',['../classvg_1_1GSSWAligner.html#aa00b750624c67e2cfa4d98193acf8dd9',1,'vg::GSSWAligner']]],
+ ['unset_11340',['unset',['../classvg_1_1algorithms_1_1TracedScore.html#a5ba55d94d11446319300052e02df1b23',1,'vg::algorithms::TracedScore']]],
+ ['update_11341',['update',['../structvg_1_1WFANode.html#a3ca9cee0c921c093c9c9b88506f1e58a',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, const MatchPos &pos)'],['../structvg_1_1WFANode.html#a8577faa0410e723fa6c5a2de7f4e452c',1,'vg::WFANode::update(size_t type, int32_t score, int32_t diagonal, uint32_t seq_offset, uint32_t node_offset)']]],
+ ['update_5fdiagonal_5frange_11342',['update_diagonal_range',['../classvg_1_1WFATree.html#a923bbbd53962ce4121989e66291afa5a',1,'vg::WFATree']]],
+ ['update_5fhaplotype_5findex_11343',['update_haplotype_index',['../classvg_1_1Transcriptome.html#a5b33f790ea79988af1d05ba0b1fd1cea',1,'vg::Transcriptome']]],
+ ['update_5fin_5fout_5fedges_11344',['update_in_out_edges',['../classvg_1_1FlowSort.html#a09b6782a1ab4d5c5ed7fa23cf83083d8',1,'vg::FlowSort']]],
+ ['update_5finner_5fvalues_11345',['update_inner_values',['../structhaplo_1_1haplo__DP__column.html#ae5860a155f8e49360b2fb2289e2555b8',1,'haplo::haplo_DP_column']]],
+ ['update_5fintron_5flength_5fdistribution_11346',['update_intron_length_distribution',['../classvg_1_1SpliceStats.html#a984c94dae240b73a92d40f4d36d39fb6',1,'vg::SpliceStats']]],
+ ['update_5fmapping_5fpositions_11347',['update_mapping_positions',['../structvg_1_1PathIndex.html#a783b7aafb86a509a3434c10b5ae9355f',1,'vg::PathIndex']]],
+ ['update_5fmotifs_11348',['update_motifs',['../classvg_1_1SpliceStats.html#a26085c886cc27966f45c239fb13e0136',1,'vg::SpliceStats']]],
+ ['update_5fnesting_5finfo_5ftags_11349',['update_nesting_info_tags',['../classvg_1_1VCFOutputCaller.html#a131c6d35d0722a64bd18b4a646efac5a',1,'vg::VCFOutputCaller']]],
+ ['update_5fpath_5findexes_11350',['update_path_indexes',['../classvg_1_1GraphSynchronizer.html#a056cd54145b467de24d6ce128749af27',1,'vg::GraphSynchronizer']]],
+ ['update_5fprogress_11351',['update_progress',['../classvg_1_1Progressive.html#a0d64e6aa69bc094c163f4827602a302c',1,'vg::Progressive']]],
+ ['update_5fscore_5fvector_11352',['update_score_vector',['../structhaplo_1_1haplo__DP__column.html#a40859e4ede0d3829b5e7dca9a89af660',1,'haplo::haplo_DP_column']]],
+ ['update_5fscoring_11353',['update_scoring',['../classvg_1_1SpliceStats.html#a23dd768b9e57750de42c5f88a2b2d8d4',1,'vg::SpliceStats']]],
+ ['update_5fstate_11354',['update_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#afb76a0ce92c750ae8cb12eaf2c0ae7fd',1,'vg::BandedGlobalAligner::BABuilder::update_state()'],['../classvg_1_1DinucleotideMachine.html#a9b246cec10b2a7e45ed7f3a3261427e5',1,'vg::DinucleotideMachine::update_state()']]],
+ ['update_5ftranscript_5fpaths_11355',['update_transcript_paths',['../classvg_1_1Transcriptome.html#a9f55d0f16470ee2750fe09986c85b464',1,'vg::Transcriptome']]],
+ ['update_5fvcf_5fheader_11356',['update_vcf_header',['../classvg_1_1SnarlCaller.html#a7fb3205d6e94505aadf0c9944fac7eb4',1,'vg::SnarlCaller::update_vcf_header()'],['../classvg_1_1RatioSupportSnarlCaller.html#ac7a153c3c35bc7d314f69f8ccbc30ae1',1,'vg::RatioSupportSnarlCaller::update_vcf_header()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a2872f6728e288de01d5403fcdb76a05b',1,'vg::PoissonSupportSnarlCaller::update_vcf_header()']]],
+ ['update_5fvcf_5finfo_11357',['update_vcf_info',['../classvg_1_1MCMCCaller.html#a8deeb18605436556136403261715155e',1,'vg::MCMCCaller::update_vcf_info()'],['../classvg_1_1SnarlCaller.html#a5098383d371e037c79e4c278e3fbbea1',1,'vg::SnarlCaller::update_vcf_info()'],['../classvg_1_1SupportBasedSnarlCaller.html#a3ddd1e17537734b984fa0befe9f0d7f6',1,'vg::SupportBasedSnarlCaller::update_vcf_info()'],['../classvg_1_1RatioSupportSnarlCaller.html#a3dc6a3524e755fba03211f0f0dd3483f',1,'vg::RatioSupportSnarlCaller::update_vcf_info()'],['../classvg_1_1PoissonSupportSnarlCaller.html#abe1990823417defcd0c6f68132680db1',1,'vg::PoissonSupportSnarlCaller::update_vcf_info()']]],
+ ['use_11358',['use',['../structvg_1_1GBWTHandler.html#a8062238f984f4c521cef46cfc2961626',1,'vg::GBWTHandler::use(gbwt::GBWT &new_index)'],['../structvg_1_1GBWTHandler.html#a574972e799a708837a0e2e481926f87a',1,'vg::GBWTHandler::use(gbwt::DynamicGBWT &new_index)'],['../structGraphHandler.html#a4ccfddaf318c987155ab13de16dcfc2c',1,'GraphHandler::use()']]],
+ ['use_5fcompressed_11359',['use_compressed',['../structvg_1_1GBWTHandler.html#a40007a32d020290a72aaef0e830454c4',1,'vg::GBWTHandler']]],
+ ['use_5fdynamic_11360',['use_dynamic',['../structvg_1_1GBWTHandler.html#a88de75253b3b9b54e844d0a20ff9a5c7',1,'vg::GBWTHandler']]],
+ ['use_5for_5fsave_11361',['use_or_save',['../gbwt__main_8cpp.html#ab82463d53fb85eaec6c4e581e009d9e6',1,'gbwt_main.cpp']]],
+ ['use_5fpreset_11362',['use_preset',['../gbwt__main_8cpp.html#ad246795d44cf23172412ae1c6a7a86e6',1,'gbwt_main.cpp']]],
+ ['used_5fbins_5fof_5frange_11363',['used_bins_of_range',['../classvg_1_1StreamIndexBase.html#a94777b19236dfb74d66ba8c484bf663f',1,'vg::StreamIndexBase']]],
+ ['uses_5fus_11364',['uses_Us',['../namespacevg.html#acd966c42f332957a1b9317faa3d26407',1,'vg']]]
];
diff --git a/search/functions_16.js b/search/functions_16.js
index 366c2069ec..1cbf7d539f 100644
--- a/search/functions_16.js
+++ b/search/functions_16.js
@@ -1,62 +1,62 @@
var searchData=
[
- ['valid_5foutput_5fformat_11361',['valid_output_format',['../namespacevg_1_1io.html#accd0bfdce54ff793cf2fae6b1122ec54',1,'vg::io']]],
- ['validate_5fchain_11362',['validate_chain',['../haplotypes__main_8cpp.html#a3a45e87bba0a989b6090009d4625b7be',1,'haplotypes_main.cpp']]],
- ['validate_5fclusters_11363',['validate_clusters',['../classvg_1_1MinimizerMapper.html#a6570c2ad670d859a7968185b9ca4766b',1,'vg::MinimizerMapper']]],
- ['validate_5fedges_11364',['validate_edges',['../haplotypes__main_8cpp.html#a999c98d1ee58048171f7dcecf358d2d3',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_11365',['validate_error',['../haplotypes__main_8cpp.html#a0ea019c2395c52022f514fa4f82cf160',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_5fchain_11366',['validate_error_chain',['../haplotypes__main_8cpp.html#afdc6618a23f46fd617c11c59dc002c49',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_5fsequence_11367',['validate_error_sequence',['../haplotypes__main_8cpp.html#a2d43c126781548ac00da14e8e01adcb2',1,'haplotypes_main.cpp']]],
- ['validate_5ferror_5fsubchain_11368',['validate_error_subchain',['../haplotypes__main_8cpp.html#a89350da9375f069d78273ad1f90779f7',1,'haplotypes_main.cpp']]],
- ['validate_5fgbwt_5fconfig_11369',['validate_gbwt_config',['../gbwt__main_8cpp.html#af5ed19bfdb99fb96253ad3871e87fe21',1,'gbwt_main.cpp']]],
- ['validate_5fhaplotypes_11370',['validate_haplotypes',['../haplotypes__main_8cpp.html#a32b60c224f945b606e8ad835badd30e0',1,'haplotypes_main.cpp']]],
- ['validate_5fmultipath_5falignment_11371',['validate_multipath_alignment',['../namespacevg.html#a026842b7758f60f2be6a474cf41d3fe1',1,'vg']]],
- ['validate_5fnodes_11372',['validate_nodes',['../haplotypes__main_8cpp.html#aacf025eb707a93ff8273d2030a917941',1,'haplotypes_main.cpp']]],
- ['validate_5fsnarl_11373',['validate_snarl',['../classvg_1_1ZipCodeTree.html#a8650ce6bcf5e49fe2cdcda115907a6a4',1,'vg::ZipCodeTree']]],
- ['validate_5fsubgraph_11374',['validate_subgraph',['../haplotypes__main_8cpp.html#a34f1931e5c2978decef6f1b46cfe5808',1,'haplotypes_main.cpp']]],
- ['validate_5funary_5fpath_11375',['validate_unary_path',['../haplotypes__main_8cpp.html#a5ec83acb4aef7e3600194a474bf7503c',1,'haplotypes_main.cpp']]],
- ['validate_5fzip_5fforest_11376',['validate_zip_forest',['../classvg_1_1ZipCodeForest.html#a61e851b424a075f606092a97d0106845',1,'vg::ZipCodeForest']]],
- ['validate_5fzip_5ftree_11377',['validate_zip_tree',['../classvg_1_1ZipCodeTree.html#aae99837c7693b5ee6bdc2a2b0dd053ec',1,'vg::ZipCodeTree']]],
- ['valuation_11378',['Valuation',['../structvg_1_1subcommand_1_1Valuation.html#aa6eadc2e42b34b522bfd972d37ffec72',1,'vg::subcommand::Valuation']]],
- ['value_11379',['value',['../classvg_1_1ProblemDumpExplainer.html#a27164f7c9d1bd3f25bafed94b745444c',1,'vg::ProblemDumpExplainer::value(const std::string &v)'],['../classvg_1_1ProblemDumpExplainer.html#a6b948ca538c47cc4042d039fcb6381d7',1,'vg::ProblemDumpExplainer::value(double v)'],['../classvg_1_1ProblemDumpExplainer.html#a97c2e3c2f810e01cf79d3e4c0cf4ae47',1,'vg::ProblemDumpExplainer::value(size_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a9847ed10905a3633101e1c71f36abc7a',1,'vg::ProblemDumpExplainer::value(int v)'],['../classvg_1_1ProblemDumpExplainer.html#aca748cde7cbb1763ef518d5715a9855b',1,'vg::ProblemDumpExplainer::value(bool v)'],['../classvg_1_1ProblemDumpExplainer.html#a5617b0887736bf19ffbc177f43f3807f',1,'vg::ProblemDumpExplainer::value(vg::id_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a327bd602828aca8f102f1ca46f1e6115',1,'vg::ProblemDumpExplainer::value(const pos_t &v)'],['../classvg_1_1ProblemDumpExplainer.html#aad49d76e8e8442d74b8b987906dd0bc3',1,'vg::ProblemDumpExplainer::value(const HandleGraph &v)'],['../classvg_1_1ProblemDumpExplainer.html#a2c21785e31b448b21733c4dc53729823',1,'vg::ProblemDumpExplainer::value(const handle_t &v, const HandleGraph &context)'],['../structvg_1_1WFAPoint.html#aeae29642d758fc5ca9c308b094ff3c53',1,'vg::WFAPoint::value()']]],
- ['value_5fcast_11380',['value_cast',['../namespacevg.html#a76fc86953f8c080621c080cd35bc9ae0',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#ac84a9621d5108f53976d51f1188e7214',1,'vg::value_cast(const T &wrap)'],['../namespacevg.html#a12109d27c9801031e32a408e75af2bd1',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#aca53457219a2ced000f439df5bd0d71f',1,'vg::value_cast(const Container &wrap)']]],
- ['value_5fcast_3c_20bool_20_3e_11381',['value_cast< bool >',['../namespacevg.html#ac90d23f22ad3ec78da4e03dc011cabf8',1,'vg::value_cast< bool >(const google::protobuf::Value &value)'],['../namespacevg.html#ab572dfa4b65db43984f1572d74a94036',1,'vg::value_cast< bool >(const bool &wrap)']]],
- ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3astruct_20_2a_20_3e_11382',['value_cast< const google::protobuf::Struct * >',['../namespacevg.html#a2683b1d5f38a8b34051fec41d7c011f0',1,'vg']]],
- ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3avalue_20_2a_20_3e_11383',['value_cast< const google::protobuf::Value * >',['../namespacevg.html#a248b5f3265dbbdde641fee26c075842a',1,'vg']]],
- ['value_5fcast_3c_20double_20_3e_11384',['value_cast< double >',['../namespacevg.html#a13a0cc45e4277281efeedb821c1444f6',1,'vg::value_cast< double >(const google::protobuf::Value &value)'],['../namespacevg.html#ac16fdb4078f95e252450a80a1e9e14f2',1,'vg::value_cast< double >(const double &wrap)']]],
- ['value_5fcast_3c_20int_20_3e_11385',['value_cast< int >',['../namespacevg.html#ad1ca627c13de536f96efbc08934edb62',1,'vg']]],
- ['value_5fcast_3c_20size_5ft_20_3e_11386',['value_cast< size_t >',['../namespacevg.html#a2a12578ee636d9d929a9c1205e7c8525',1,'vg']]],
- ['value_5fcast_3c_20string_20_3e_11387',['value_cast< string >',['../namespacevg.html#a16575a017d153499fe4a0976e801be61',1,'vg::value_cast< string >(const google::protobuf::Value &value)'],['../namespacevg.html#a51e6a112ff1115272420d46ca4316f63',1,'vg::value_cast< string >(const string &wrap)']]],
- ['valueargspec_11388',['ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html#af9860ac96dc38b06b5de9b00ae31ffbe',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, char short_option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a10b4640232a0e4ece857459d903c3809',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)']]],
- ['variant_5frecall_11389',['variant_recall',['../namespacevg.html#a96096594534e59d12b7a2cff3c400ef0',1,'vg']]],
- ['variantadder_11390',['VariantAdder',['../classvg_1_1VariantAdder.html#a267056ae90838d3aef2ddfe992a045ff',1,'vg::VariantAdder']]],
- ['vcf_5fcontigs_11391',['vcf_contigs',['../namespacevg.html#a691144860bc63559aaf088d2e052af62',1,'vg']]],
- ['vcf_5ffixup_11392',['vcf_fixup',['../classvg_1_1VCFOutputCaller.html#ab063824a02c65e499cac3d2ca96ca504',1,'vg::VCFOutputCaller']]],
- ['vcf_5fheader_11393',['vcf_header',['../classvg_1_1VCFOutputCaller.html#aeb9a75eed0ba2a369439abddf1ac3f65',1,'vg::VCFOutputCaller::vcf_header()'],['../classvg_1_1VCFGenotyper.html#a8dae0df9c45f88aadca9fcaa8d0e7214',1,'vg::VCFGenotyper::vcf_header()'],['../classvg_1_1LegacyCaller.html#a4536625fdb753727a7d8321cadc6946b',1,'vg::LegacyCaller::vcf_header()'],['../classvg_1_1FlowCaller.html#a2c4e7365e43593313a30d7d4ea03c4a9',1,'vg::FlowCaller::vcf_header()'],['../classvg_1_1NestedFlowCaller.html#a38c3758ea8fd04852eb62c40ec9be010',1,'vg::NestedFlowCaller::vcf_header()'],['../classvg_1_1MCMCCaller.html#af67e8bf51b99831bd5b9f67c2581d084',1,'vg::MCMCCaller::vcf_header()']]],
- ['vcf_5fis_5fphased_11394',['vcf_is_phased',['../classvg_1_1IndexRegistry.html#abeceb0062997804e84372c7bca76c8ae',1,'vg::IndexRegistry']]],
- ['vcf_5fto_5ffasta_11395',['vcf_to_fasta',['../classvg_1_1NameMapper.html#a6e8c36e6207dbc905170bde6a5c396b3',1,'vg::NameMapper']]],
- ['vcfbuffer_11396',['VcfBuffer',['../classvg_1_1VcfBuffer.html#a402d5cadd95f5725876b22b8c9bd830b',1,'vg::VcfBuffer::VcfBuffer(vcflib::VariantCallFile *file=nullptr)'],['../classvg_1_1VcfBuffer.html#ad388f47df62ebab69ab9188efd37be1e',1,'vg::VcfBuffer::VcfBuffer(const VcfBuffer &other)=delete']]],
- ['vcfgenotyper_11397',['VCFGenotyper',['../classvg_1_1VCFGenotyper.html#a8c65e87515bd32e6f90bba45712175bf',1,'vg::VCFGenotyper']]],
- ['vcfoutputcaller_11398',['VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html#ad758f9180a51784374ef044b54883f87',1,'vg::VCFOutputCaller']]],
- ['vcftraversalfinder_11399',['VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html#aaa8aa0b5cbe8a0e2ff664b6b385339da',1,'vg::VCFTraversalFinder']]],
- ['vectorizer_11400',['Vectorizer',['../classVectorizer.html#ac6f2b56806bc2e8444492cb3d32f42be',1,'Vectorizer']]],
- ['vectorview_11401',['VectorView',['../structvg_1_1VectorView.html#aefb5d25c5ced8c23549c605abb29c09f',1,'vg::VectorView::VectorView()'],['../structvg_1_1VectorView.html#adaf1a835fd36e7c4194d4ee53adc4528',1,'vg::VectorView::VectorView(const VectorView &other)=default'],['../structvg_1_1VectorView.html#ac6ad816ef159fe1b9dad8c9539a5b8de',1,'vg::VectorView::VectorView(VectorView &&other)=default'],['../structvg_1_1VectorView.html#ace693cb938bdc8545ff2d00faf2c9136',1,'vg::VectorView::VectorView(const vector< Item > &items)'],['../structvg_1_1VectorView.html#a5e4711cb47476cfe22eccef4823d4fa8',1,'vg::VectorView::VectorView(const vector< Item > &items, const vector< size_t > &indexes)']]],
- ['vectorviewinverse_11402',['VectorViewInverse',['../classvg_1_1VectorViewInverse.html#a6f4c737e0dc739eca4f09a472e520335',1,'vg::VectorViewInverse::VectorViewInverse()'],['../classvg_1_1VectorViewInverse.html#ab87205a1d88681364f2768e778e87c8d',1,'vg::VectorViewInverse::VectorViewInverse(const VectorView< Item > &view)']]],
- ['verify_5fpath_11403',['verify_path',['../namespacevg.html#a3ed0a4f26673002b2081832a7602e9bd',1,'vg']]],
- ['verify_5fpaths_11404',['verify_paths',['../classvg_1_1PhaseUnfolder.html#a910deba7dd5b5f9bce7a1da4e53cfeb1',1,'vg::PhaseUnfolder']]],
- ['verify_5fvalid_5flog_5fodds_5fscore_5fmatrix_11405',['verify_valid_log_odds_score_matrix',['../classvg_1_1GSSWAligner.html#acc5d3a8c0c22cbd966e96a42eb095cd8',1,'vg::GSSWAligner']]],
- ['version_11406',['Version',['../classvg_1_1Version.html#a05bb9f14c7597bf90a2981db7e59b058',1,'vg::Version']]],
- ['vg_11407',['VG',['../classvg_1_1VG.html#ac2399de59931e282fb1f4d3da9a8dcb1',1,'vg::VG::VG(void)'],['../classvg_1_1VG.html#a2dc9648985454d3aedd9a477ff0c52b2',1,'vg::VG::VG(istream &in, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#a0fbb777fd8ab6050124a6eaf9eca9133',1,'vg::VG::VG(const function< void(const function< void(Graph &)> &)> &send_graphs, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#af4d321b31b873153431c261090d052af',1,'vg::VG::VG(const Graph &from, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#abeafee2d3bc6e0039e99fccdea10f4f9',1,'vg::VG::VG(set< Node * > &nodes, set< Edge * > &edges)'],['../classvg_1_1VG.html#a3148455330df9ac055c6bd1eb7da3167',1,'vg::VG::VG(const VG &other)'],['../classvg_1_1VG.html#ab8365ccd6a093ec50f7d54b1c7a7c672',1,'vg::VG::VG(VG &&other) noexcept']]],
- ['vg_5fhelp_11408',['vg_help',['../main_8cpp.html#aae3a18cc6fba2e4bf97e9a01f4734f4f',1,'main.cpp']]],
- ['vg_5fmain_11409',['vg_main',['../main_8cpp.html#a8b9f48d3aed7bbfe82cdc4f092867c50',1,'main.cpp']]],
- ['vgalignmentemitter_11410',['VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html#af278878b244808a182eae17640f23a45',1,'vg::io::VGAlignmentEmitter']]],
- ['vgset_11411',['VGset',['../classvg_1_1VGset.html#a5ff9a6c4fa0223bcee7072f86a657751',1,'vg::VGset::VGset()'],['../classvg_1_1VGset.html#a6adbb25be82de20911fd901da4e9fe41',1,'vg::VGset::VGset(vector< string > &files)']]],
- ['view_5fmultipath_5falignment_11412',['view_multipath_alignment',['../namespacevg.html#a411a023efbe439f069829603a2775673',1,'vg']]],
- ['view_5fmultipath_5falignment_5fas_5fdot_11413',['view_multipath_alignment_as_dot',['../namespacevg.html#a716909fc23ddaab59e0d2bf89fdd1ae3',1,'vg']]],
- ['visit_5fcontained_5fsnarls_11414',['visit_contained_snarls',['../namespacevg.html#ae3a49e3aea82c8e552e4cf9fd8396ad4',1,'vg']]],
- ['visit_5fnext_5fnode_11415',['visit_next_node',['../classvg_1_1ExhaustiveTraversalFinder.html#a2cec9de94838e3575a20271db01a1a4f',1,'vg::ExhaustiveTraversalFinder::visit_next_node()'],['../classvg_1_1SupportRestrictedTraversalFinder.html#a9cdb3b8f554e58cba6fea9c2ccb40e14',1,'vg::SupportRestrictedTraversalFinder::visit_next_node()']]],
- ['visits_5fleft_11416',['visits_left',['../classvg_1_1SnarlManager.html#a27e95077ab5c9a7288f2833d5e66433e',1,'vg::SnarlManager']]],
- ['visits_5fright_11417',['visits_right',['../classvg_1_1SnarlManager.html#a567554948e5dc03604a46972eb42d295',1,'vg::SnarlManager']]],
- ['viz_11418',['Viz',['../classvg_1_1Viz.html#a8e9440d6c67fde7f10fe9c0366759041',1,'vg::Viz::Viz(void)'],['../classvg_1_1Viz.html#a5d343eb2d20b2db1eb66def4b8d3081c',1,'vg::Viz::Viz(PathHandleGraph *x, vector< Packer > *p, const vector< string > &n, const string &o, int w, int h, bool c, bool d, bool t)']]],
- ['vpmax_11419',['vpmax',['../namespacevg.html#aec4813274fc2af3d83679e128fdeb32f',1,'vg']]]
+ ['valid_5foutput_5fformat_11365',['valid_output_format',['../namespacevg_1_1io.html#accd0bfdce54ff793cf2fae6b1122ec54',1,'vg::io']]],
+ ['validate_5fchain_11366',['validate_chain',['../haplotypes__main_8cpp.html#a3a45e87bba0a989b6090009d4625b7be',1,'haplotypes_main.cpp']]],
+ ['validate_5fclusters_11367',['validate_clusters',['../classvg_1_1MinimizerMapper.html#a6570c2ad670d859a7968185b9ca4766b',1,'vg::MinimizerMapper']]],
+ ['validate_5fedges_11368',['validate_edges',['../haplotypes__main_8cpp.html#a999c98d1ee58048171f7dcecf358d2d3',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_11369',['validate_error',['../haplotypes__main_8cpp.html#a0ea019c2395c52022f514fa4f82cf160',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_5fchain_11370',['validate_error_chain',['../haplotypes__main_8cpp.html#afdc6618a23f46fd617c11c59dc002c49',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_5fsequence_11371',['validate_error_sequence',['../haplotypes__main_8cpp.html#a2d43c126781548ac00da14e8e01adcb2',1,'haplotypes_main.cpp']]],
+ ['validate_5ferror_5fsubchain_11372',['validate_error_subchain',['../haplotypes__main_8cpp.html#a89350da9375f069d78273ad1f90779f7',1,'haplotypes_main.cpp']]],
+ ['validate_5fgbwt_5fconfig_11373',['validate_gbwt_config',['../gbwt__main_8cpp.html#af5ed19bfdb99fb96253ad3871e87fe21',1,'gbwt_main.cpp']]],
+ ['validate_5fhaplotypes_11374',['validate_haplotypes',['../haplotypes__main_8cpp.html#a32b60c224f945b606e8ad835badd30e0',1,'haplotypes_main.cpp']]],
+ ['validate_5fmultipath_5falignment_11375',['validate_multipath_alignment',['../namespacevg.html#a026842b7758f60f2be6a474cf41d3fe1',1,'vg']]],
+ ['validate_5fnodes_11376',['validate_nodes',['../haplotypes__main_8cpp.html#aacf025eb707a93ff8273d2030a917941',1,'haplotypes_main.cpp']]],
+ ['validate_5fsnarl_11377',['validate_snarl',['../classvg_1_1ZipCodeTree.html#a8650ce6bcf5e49fe2cdcda115907a6a4',1,'vg::ZipCodeTree']]],
+ ['validate_5fsubgraph_11378',['validate_subgraph',['../haplotypes__main_8cpp.html#a34f1931e5c2978decef6f1b46cfe5808',1,'haplotypes_main.cpp']]],
+ ['validate_5funary_5fpath_11379',['validate_unary_path',['../haplotypes__main_8cpp.html#a5ec83acb4aef7e3600194a474bf7503c',1,'haplotypes_main.cpp']]],
+ ['validate_5fzip_5fforest_11380',['validate_zip_forest',['../classvg_1_1ZipCodeForest.html#a61e851b424a075f606092a97d0106845',1,'vg::ZipCodeForest']]],
+ ['validate_5fzip_5ftree_11381',['validate_zip_tree',['../classvg_1_1ZipCodeTree.html#aae99837c7693b5ee6bdc2a2b0dd053ec',1,'vg::ZipCodeTree']]],
+ ['valuation_11382',['Valuation',['../structvg_1_1subcommand_1_1Valuation.html#aa6eadc2e42b34b522bfd972d37ffec72',1,'vg::subcommand::Valuation']]],
+ ['value_11383',['value',['../classvg_1_1ProblemDumpExplainer.html#a27164f7c9d1bd3f25bafed94b745444c',1,'vg::ProblemDumpExplainer::value(const std::string &v)'],['../classvg_1_1ProblemDumpExplainer.html#a6b948ca538c47cc4042d039fcb6381d7',1,'vg::ProblemDumpExplainer::value(double v)'],['../classvg_1_1ProblemDumpExplainer.html#a97c2e3c2f810e01cf79d3e4c0cf4ae47',1,'vg::ProblemDumpExplainer::value(size_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a9847ed10905a3633101e1c71f36abc7a',1,'vg::ProblemDumpExplainer::value(int v)'],['../classvg_1_1ProblemDumpExplainer.html#aca748cde7cbb1763ef518d5715a9855b',1,'vg::ProblemDumpExplainer::value(bool v)'],['../classvg_1_1ProblemDumpExplainer.html#a5617b0887736bf19ffbc177f43f3807f',1,'vg::ProblemDumpExplainer::value(vg::id_t v)'],['../classvg_1_1ProblemDumpExplainer.html#a327bd602828aca8f102f1ca46f1e6115',1,'vg::ProblemDumpExplainer::value(const pos_t &v)'],['../classvg_1_1ProblemDumpExplainer.html#aad49d76e8e8442d74b8b987906dd0bc3',1,'vg::ProblemDumpExplainer::value(const HandleGraph &v)'],['../classvg_1_1ProblemDumpExplainer.html#a2c21785e31b448b21733c4dc53729823',1,'vg::ProblemDumpExplainer::value(const handle_t &v, const HandleGraph &context)'],['../structvg_1_1WFAPoint.html#aeae29642d758fc5ca9c308b094ff3c53',1,'vg::WFAPoint::value()']]],
+ ['value_5fcast_11384',['value_cast',['../namespacevg.html#a76fc86953f8c080621c080cd35bc9ae0',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#ac84a9621d5108f53976d51f1188e7214',1,'vg::value_cast(const T &wrap)'],['../namespacevg.html#a12109d27c9801031e32a408e75af2bd1',1,'vg::value_cast(const google::protobuf::Value &value)'],['../namespacevg.html#aca53457219a2ced000f439df5bd0d71f',1,'vg::value_cast(const Container &wrap)']]],
+ ['value_5fcast_3c_20bool_20_3e_11385',['value_cast< bool >',['../namespacevg.html#ac90d23f22ad3ec78da4e03dc011cabf8',1,'vg::value_cast< bool >(const google::protobuf::Value &value)'],['../namespacevg.html#ab572dfa4b65db43984f1572d74a94036',1,'vg::value_cast< bool >(const bool &wrap)']]],
+ ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3astruct_20_2a_20_3e_11386',['value_cast< const google::protobuf::Struct * >',['../namespacevg.html#a2683b1d5f38a8b34051fec41d7c011f0',1,'vg']]],
+ ['value_5fcast_3c_20const_20google_3a_3aprotobuf_3a_3avalue_20_2a_20_3e_11387',['value_cast< const google::protobuf::Value * >',['../namespacevg.html#a248b5f3265dbbdde641fee26c075842a',1,'vg']]],
+ ['value_5fcast_3c_20double_20_3e_11388',['value_cast< double >',['../namespacevg.html#a13a0cc45e4277281efeedb821c1444f6',1,'vg::value_cast< double >(const google::protobuf::Value &value)'],['../namespacevg.html#ac16fdb4078f95e252450a80a1e9e14f2',1,'vg::value_cast< double >(const double &wrap)']]],
+ ['value_5fcast_3c_20int_20_3e_11389',['value_cast< int >',['../namespacevg.html#ad1ca627c13de536f96efbc08934edb62',1,'vg']]],
+ ['value_5fcast_3c_20size_5ft_20_3e_11390',['value_cast< size_t >',['../namespacevg.html#a2a12578ee636d9d929a9c1205e7c8525',1,'vg']]],
+ ['value_5fcast_3c_20string_20_3e_11391',['value_cast< string >',['../namespacevg.html#a16575a017d153499fe4a0976e801be61',1,'vg::value_cast< string >(const google::protobuf::Value &value)'],['../namespacevg.html#a51e6a112ff1115272420d46ca4316f63',1,'vg::value_cast< string >(const string &wrap)']]],
+ ['valueargspec_11392',['ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html#af9860ac96dc38b06b5de9b00ae31ffbe',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, char short_option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a10b4640232a0e4ece857459d903c3809',1,'vg::subcommand::ValueArgSpec::ValueArgSpec(const std::string &option, T Receiver::*dest, const T &default_value, const std::string &help, const ValidatorFunction< T > &validator)']]],
+ ['variant_5frecall_11393',['variant_recall',['../namespacevg.html#a96096594534e59d12b7a2cff3c400ef0',1,'vg']]],
+ ['variantadder_11394',['VariantAdder',['../classvg_1_1VariantAdder.html#a267056ae90838d3aef2ddfe992a045ff',1,'vg::VariantAdder']]],
+ ['vcf_5fcontigs_11395',['vcf_contigs',['../namespacevg.html#a691144860bc63559aaf088d2e052af62',1,'vg']]],
+ ['vcf_5ffixup_11396',['vcf_fixup',['../classvg_1_1VCFOutputCaller.html#ab063824a02c65e499cac3d2ca96ca504',1,'vg::VCFOutputCaller']]],
+ ['vcf_5fheader_11397',['vcf_header',['../classvg_1_1VCFOutputCaller.html#aeb9a75eed0ba2a369439abddf1ac3f65',1,'vg::VCFOutputCaller::vcf_header()'],['../classvg_1_1VCFGenotyper.html#a8dae0df9c45f88aadca9fcaa8d0e7214',1,'vg::VCFGenotyper::vcf_header()'],['../classvg_1_1LegacyCaller.html#a4536625fdb753727a7d8321cadc6946b',1,'vg::LegacyCaller::vcf_header()'],['../classvg_1_1FlowCaller.html#a2c4e7365e43593313a30d7d4ea03c4a9',1,'vg::FlowCaller::vcf_header()'],['../classvg_1_1NestedFlowCaller.html#a38c3758ea8fd04852eb62c40ec9be010',1,'vg::NestedFlowCaller::vcf_header()'],['../classvg_1_1MCMCCaller.html#af67e8bf51b99831bd5b9f67c2581d084',1,'vg::MCMCCaller::vcf_header()']]],
+ ['vcf_5fis_5fphased_11398',['vcf_is_phased',['../classvg_1_1IndexRegistry.html#abeceb0062997804e84372c7bca76c8ae',1,'vg::IndexRegistry']]],
+ ['vcf_5fto_5ffasta_11399',['vcf_to_fasta',['../classvg_1_1NameMapper.html#a6e8c36e6207dbc905170bde6a5c396b3',1,'vg::NameMapper']]],
+ ['vcfbuffer_11400',['VcfBuffer',['../classvg_1_1VcfBuffer.html#a402d5cadd95f5725876b22b8c9bd830b',1,'vg::VcfBuffer::VcfBuffer(vcflib::VariantCallFile *file=nullptr)'],['../classvg_1_1VcfBuffer.html#ad388f47df62ebab69ab9188efd37be1e',1,'vg::VcfBuffer::VcfBuffer(const VcfBuffer &other)=delete']]],
+ ['vcfgenotyper_11401',['VCFGenotyper',['../classvg_1_1VCFGenotyper.html#a8c65e87515bd32e6f90bba45712175bf',1,'vg::VCFGenotyper']]],
+ ['vcfoutputcaller_11402',['VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html#ad758f9180a51784374ef044b54883f87',1,'vg::VCFOutputCaller']]],
+ ['vcftraversalfinder_11403',['VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html#aaa8aa0b5cbe8a0e2ff664b6b385339da',1,'vg::VCFTraversalFinder']]],
+ ['vectorizer_11404',['Vectorizer',['../classVectorizer.html#ac6f2b56806bc2e8444492cb3d32f42be',1,'Vectorizer']]],
+ ['vectorview_11405',['VectorView',['../structvg_1_1VectorView.html#aefb5d25c5ced8c23549c605abb29c09f',1,'vg::VectorView::VectorView()'],['../structvg_1_1VectorView.html#adaf1a835fd36e7c4194d4ee53adc4528',1,'vg::VectorView::VectorView(const VectorView &other)=default'],['../structvg_1_1VectorView.html#ac6ad816ef159fe1b9dad8c9539a5b8de',1,'vg::VectorView::VectorView(VectorView &&other)=default'],['../structvg_1_1VectorView.html#ace693cb938bdc8545ff2d00faf2c9136',1,'vg::VectorView::VectorView(const vector< Item > &items)'],['../structvg_1_1VectorView.html#a5e4711cb47476cfe22eccef4823d4fa8',1,'vg::VectorView::VectorView(const vector< Item > &items, const vector< size_t > &indexes)']]],
+ ['vectorviewinverse_11406',['VectorViewInverse',['../classvg_1_1VectorViewInverse.html#a6f4c737e0dc739eca4f09a472e520335',1,'vg::VectorViewInverse::VectorViewInverse()'],['../classvg_1_1VectorViewInverse.html#ab87205a1d88681364f2768e778e87c8d',1,'vg::VectorViewInverse::VectorViewInverse(const VectorView< Item > &view)']]],
+ ['verify_5fpath_11407',['verify_path',['../namespacevg.html#a3ed0a4f26673002b2081832a7602e9bd',1,'vg']]],
+ ['verify_5fpaths_11408',['verify_paths',['../classvg_1_1PhaseUnfolder.html#a910deba7dd5b5f9bce7a1da4e53cfeb1',1,'vg::PhaseUnfolder']]],
+ ['verify_5fvalid_5flog_5fodds_5fscore_5fmatrix_11409',['verify_valid_log_odds_score_matrix',['../classvg_1_1GSSWAligner.html#acc5d3a8c0c22cbd966e96a42eb095cd8',1,'vg::GSSWAligner']]],
+ ['version_11410',['Version',['../classvg_1_1Version.html#a05bb9f14c7597bf90a2981db7e59b058',1,'vg::Version']]],
+ ['vg_11411',['VG',['../classvg_1_1VG.html#ac2399de59931e282fb1f4d3da9a8dcb1',1,'vg::VG::VG(void)'],['../classvg_1_1VG.html#a2dc9648985454d3aedd9a477ff0c52b2',1,'vg::VG::VG(istream &in, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#a0fbb777fd8ab6050124a6eaf9eca9133',1,'vg::VG::VG(const function< void(const function< void(Graph &)> &)> &send_graphs, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#af4d321b31b873153431c261090d052af',1,'vg::VG::VG(const Graph &from, bool showp=false, bool warn_on_duplicates=true)'],['../classvg_1_1VG.html#abeafee2d3bc6e0039e99fccdea10f4f9',1,'vg::VG::VG(set< Node * > &nodes, set< Edge * > &edges)'],['../classvg_1_1VG.html#a3148455330df9ac055c6bd1eb7da3167',1,'vg::VG::VG(const VG &other)'],['../classvg_1_1VG.html#ab8365ccd6a093ec50f7d54b1c7a7c672',1,'vg::VG::VG(VG &&other) noexcept']]],
+ ['vg_5fhelp_11412',['vg_help',['../main_8cpp.html#aae3a18cc6fba2e4bf97e9a01f4734f4f',1,'main.cpp']]],
+ ['vg_5fmain_11413',['vg_main',['../main_8cpp.html#a8b9f48d3aed7bbfe82cdc4f092867c50',1,'main.cpp']]],
+ ['vgalignmentemitter_11414',['VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html#af278878b244808a182eae17640f23a45',1,'vg::io::VGAlignmentEmitter']]],
+ ['vgset_11415',['VGset',['../classvg_1_1VGset.html#a5ff9a6c4fa0223bcee7072f86a657751',1,'vg::VGset::VGset()'],['../classvg_1_1VGset.html#a6adbb25be82de20911fd901da4e9fe41',1,'vg::VGset::VGset(vector< string > &files)']]],
+ ['view_5fmultipath_5falignment_11416',['view_multipath_alignment',['../namespacevg.html#a411a023efbe439f069829603a2775673',1,'vg']]],
+ ['view_5fmultipath_5falignment_5fas_5fdot_11417',['view_multipath_alignment_as_dot',['../namespacevg.html#a716909fc23ddaab59e0d2bf89fdd1ae3',1,'vg']]],
+ ['visit_5fcontained_5fsnarls_11418',['visit_contained_snarls',['../namespacevg.html#ae3a49e3aea82c8e552e4cf9fd8396ad4',1,'vg']]],
+ ['visit_5fnext_5fnode_11419',['visit_next_node',['../classvg_1_1ExhaustiveTraversalFinder.html#a2cec9de94838e3575a20271db01a1a4f',1,'vg::ExhaustiveTraversalFinder::visit_next_node()'],['../classvg_1_1SupportRestrictedTraversalFinder.html#a9cdb3b8f554e58cba6fea9c2ccb40e14',1,'vg::SupportRestrictedTraversalFinder::visit_next_node()']]],
+ ['visits_5fleft_11420',['visits_left',['../classvg_1_1SnarlManager.html#a27e95077ab5c9a7288f2833d5e66433e',1,'vg::SnarlManager']]],
+ ['visits_5fright_11421',['visits_right',['../classvg_1_1SnarlManager.html#a567554948e5dc03604a46972eb42d295',1,'vg::SnarlManager']]],
+ ['viz_11422',['Viz',['../classvg_1_1Viz.html#a8e9440d6c67fde7f10fe9c0366759041',1,'vg::Viz::Viz(void)'],['../classvg_1_1Viz.html#a5d343eb2d20b2db1eb66def4b8d3081c',1,'vg::Viz::Viz(PathHandleGraph *x, vector< Packer > *p, const vector< string > &n, const string &o, int w, int h, bool c, bool d, bool t)']]],
+ ['vpmax_11423',['vpmax',['../namespacevg.html#aec4813274fc2af3d83679e128fdeb32f',1,'vg']]]
];
diff --git a/search/functions_17.js b/search/functions_17.js
index 5089efefe7..8b9d5b9b4c 100644
--- a/search/functions_17.js
+++ b/search/functions_17.js
@@ -1,83 +1,83 @@
var searchData=
[
- ['w_11420',['w',['../namespacehaplotypes__defaults.html#a9e7cea9525076e8d069877c9f1a08552',1,'haplotypes_defaults']]],
- ['wabbitize_11421',['wabbitize',['../classVectorizer.html#ae4c3627b5c8ec7b066f5735ca6dfb3f1',1,'Vectorizer']]],
- ['walk_5fbackwards_11422',['walk_backwards',['../classvg_1_1NGSSimulator.html#a3b87398480be75b240a98d270bfc843c',1,'vg::NGSSimulator']]],
- ['walk_5fbackwards_5falong_5falignment_11423',['walk_backwards_along_alignment',['../classvg_1_1NGSSimulator.html#af033e5bc63e8407c917f151a4311b64d',1,'vg::NGSSimulator']]],
- ['walk_5ffanout_5fpath_11424',['walk_fanout_path',['../classvg_1_1BaseMapper.html#ad52deed127976201bd63b32929b71491',1,'vg::BaseMapper']]],
- ['walk_5fhaplotype_5ffrequency_11425',['walk_haplotype_frequency',['../namespacevg_1_1algorithms.html#a4af5e9c480c0dc7d0843cf981cd52c32',1,'vg::algorithms']]],
- ['walk_5fhaplotype_5fnames_11426',['walk_haplotype_names',['../namespacevg_1_1algorithms.html#abe9cb62b2ae1c6eb08b10f172980788d',1,'vg::algorithms']]],
- ['walk_5ft_11427',['walk_t',['../structvg_1_1algorithms_1_1walk__t.html#a5a5ed7ca0dac4f9e742ddeeb28e317e1',1,'vg::algorithms::walk_t::walk_t(uint16_t l, const pos_t &b, const pos_t &e, const handle_t &c, uint16_t f)'],['../structvg_1_1algorithms_1_1walk__t.html#af8c4463befc5bb6cec73b3e493acf545',1,'vg::algorithms::walk_t::walk_t(const std::string &s, const pos_t &b, const pos_t &e, const handle_t &c)']]],
- ['wang_5fhash_5f64_11428',['wang_hash_64',['../namespacevg.html#a38d35bca25e8a6d5fe10f603cb9048c3',1,'vg']]],
- ['want_5fbreakpoint_11429',['want_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#ac0698f3b6387ce47f4e9d5b2929d6cf4',1,'vg::io::StreamMultiplexer']]],
- ['was_5fcorrect_11430',['was_correct',['../classvg_1_1Funnel.html#aac71f37530afee1b7e49770aff8cc53b',1,'vg::Funnel::was_correct(size_t prev_stage_item) const'],['../classvg_1_1Funnel.html#a5f0037505a9df13b92e381f5ff108d72',1,'vg::Funnel::was_correct(size_t prev_stage_index, const string &prev_stage_name, size_t prev_stage_item) const']]],
- ['was_5fprovided_5fdirectly_11431',['was_provided_directly',['../classvg_1_1IndexFile.html#afabf00d9034342540b3614dfc7055715',1,'vg::IndexFile']]],
- ['was_5fset_11432',['was_set',['../structvg_1_1subcommand_1_1ArgSpec.html#acfb22902f7ebf4d8053ec39999dd2821',1,'vg::subcommand::ArgSpec::was_set()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aac6bd613601f636c187b684a69fa25ce',1,'vg::subcommand::ValueArgSpec::was_set()']]],
- ['watchdog_11433',['Watchdog',['../classvg_1_1Watchdog.html#a87e679ecbb8461ae6a26a1958216629b',1,'vg::Watchdog::Watchdog(size_t thread_count, const duration &timeout)'],['../classvg_1_1Watchdog.html#a2934cc5c1fc3b7d0ab20343e6bde1a56',1,'vg::Watchdog::Watchdog(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a73aa9888b0017ed46053c75c085f2748',1,'vg::Watchdog::Watchdog(Watchdog &&other)=delete']]],
- ['watcher_5floop_11434',['watcher_loop',['../classvg_1_1Watchdog.html#ad2e2c831258c42fdba7f2d0fa8625cc9',1,'vg::Watchdog']]],
- ['weakly_5fconnected_5fcomponents_11435',['weakly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a96c80b09388c6d079754c66d2f7362e5',1,'handlegraph::algorithms']]],
- ['weakly_5fconnected_5fcomponents_5fwith_5ftips_11436',['weakly_connected_components_with_tips',['../namespacehandlegraph_1_1algorithms.html#aa5ff9ed76bd82438b3af0c3112437ccd',1,'handlegraph::algorithms']]],
- ['weibull_5fcdf_11437',['weibull_cdf',['../namespacevg.html#a100efe5dfc5bfe434b53416f93d2a0e1',1,'vg']]],
- ['weibull_5flog_5flikelihood_11438',['weibull_log_likelihood',['../namespacevg.html#ad93405cf370e6d92396691fc3320be1c',1,'vg']]],
- ['weighted_5fjaccard_5fcoefficient_11439',['weighted_jaccard_coefficient',['../namespacevg.html#aa0b9062cb7b053e7823169d589e113d1',1,'vg']]],
- ['wellford_5fmean_5fvar_11440',['wellford_mean_var',['../namespacevg.html#a4b96cd801bc780d426db346f80ab2172',1,'vg']]],
- ['wellford_5fupdate_11441',['wellford_update',['../namespacevg.html#a614c672ed69c280b699a278ce0f34ade',1,'vg']]],
- ['wfa_5falignment_5fto_5falignment_11442',['wfa_alignment_to_alignment',['../classvg_1_1MinimizerMapper.html#a597914c2167ca2b06a3dccbb23e21340',1,'vg::MinimizerMapper']]],
- ['wfaextender_11443',['WFAExtender',['../classvg_1_1WFAExtender.html#a7d7324769e3d80c6acdd68de034c5830',1,'vg::WFAExtender::WFAExtender()'],['../classvg_1_1WFAExtender.html#a9cc09b85da35171c971868e80cfe2938',1,'vg::WFAExtender::WFAExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner, const ErrorModel &error_model=default_error_model)']]],
- ['wfanode_11444',['WFANode',['../structvg_1_1WFANode.html#a93d02d2b8f73a4cdcbe5a356258cb5e8',1,'vg::WFANode']]],
- ['wfatree_11445',['WFATree',['../classvg_1_1WFATree.html#ad9880bb173f2bd8e2cdc3708cbb8005f',1,'vg::WFATree']]],
- ['what_11446',['what',['../classvg_1_1NoAlignmentInBandException.html#a006dddb79b9d1c6035c2466c35dbcacf',1,'vg::NoAlignmentInBandException::what()'],['../classvg_1_1InsufficientInputException.html#ae9fd64e80e950783955ff7d875138469',1,'vg::InsufficientInputException::what()'],['../classvg_1_1RewindPlanException.html#a5d3526ac6c26a49f65a962f12c246615',1,'vg::RewindPlanException::what()'],['../classvg_1_1SizeLimitExceededException.html#acb8fbb8940007b68bede049fcf19b046',1,'vg::SizeLimitExceededException::what()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#a7fdc5893f8439a8c8c6169865a8c6e0d',1,'vg::algorithms::GFAFormatError::what()'],['../classj2pb__error.html#a4ac3313fff0e2721ca9480b61ebe6a8b',1,'j2pb_error::what()']]],
- ['which_5fhaplotype_11447',['which_haplotype',['../classvg_1_1PhasedGenome_1_1iterator.html#a02b60bd3c0ec6d86a8bec582e717ea15',1,'vg::PhasedGenome::iterator']]],
- ['wideningprng_11448',['WideningPRNG',['../classvg_1_1WideningPRNG.html#a5437179a5230df00551a618df6bc4c53',1,'vg::WideningPRNG']]],
- ['widest_5fdijkstra_11449',['widest_dijkstra',['../namespacevg_1_1algorithms.html#a08c6d85f2dc09c22c5d14ed81808769e',1,'vg::algorithms']]],
- ['window_5fbreaking_5fquality_11450',['window_breaking_quality',['../classvg_1_1MinimizerMapper.html#a7999b2f0a931930bfa9eddec4065b51b',1,'vg::MinimizerMapper']]],
- ['window_5fof_5fid_11451',['window_of_id',['../classvg_1_1StreamIndexBase.html#a320b27d89fbc1a74574cc00befe1e7fe',1,'vg::StreamIndexBase']]],
- ['window_5fsize_11452',['window_size',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a7fb1665349757422a2868159d2b66437',1,'vg::MinimizerMapper::Minimizer']]],
- ['windowedvcfbuffer_11453',['WindowedVcfBuffer',['../classvg_1_1WindowedVcfBuffer.html#a7d7af1d1441bab6c687bdf1be7fc4675',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(vcflib::VariantCallFile *file, size_t window_size)'],['../classvg_1_1WindowedVcfBuffer.html#aa57da13990d5983d5e8aa787dfe56995',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(const WindowedVcfBuffer &other)=delete']]],
- ['with_5fcache_5fentry_11454',['with_cache_entry',['../classvg_1_1IndexedVG.html#ac14226d9ccd03cb99af9a08cef31d6ff',1,'vg::IndexedVG']]],
- ['with_5fcursor_11455',['with_cursor',['../classvg_1_1IndexedVG.html#af380961c8e8b342ba8f688c2f073de2e',1,'vg::IndexedVG']]],
- ['with_5fdagified_5flocal_5fgraph_11456',['with_dagified_local_graph',['../classvg_1_1MinimizerMapper.html#a96b3c359c5f86557ddccfdedd67af570',1,'vg::MinimizerMapper']]],
- ['with_5fexception_5fhandling_11457',['with_exception_handling',['../namespacevg.html#a1d2cbe5fe5e1b8a33b7d707f7059b3c6',1,'vg']]],
- ['with_5ffunction_5fcalling_5fstream_11458',['with_function_calling_stream',['../namespacevg_1_1io.html#a8b1a63276edf814575b7afb3b2b9844d',1,'vg::io']]],
- ['with_5fpath_5findex_11459',['with_path_index',['../classvg_1_1GraphSynchronizer.html#a336f5828883adce86ee5e536f8c299ea',1,'vg::GraphSynchronizer']]],
- ['with_5fprogress_11460',['with_progress',['../classvg_1_1Progressive.html#ab44ff020fc951b95dfcd1252c015a020',1,'vg::Progressive']]],
- ['with_5fputback_11461',['with_putback',['../classvg_1_1io_1_1VPKG.html#a0bcbb5a28413d3599a642cd5f22d93be',1,'vg::io::VPKG']]],
- ['with_5fsave_5fstream_11462',['with_save_stream',['../classvg_1_1io_1_1VPKG.html#a030910ec652e742dbf98a845b95943a5',1,'vg::io::VPKG']]],
- ['with_5fvector_11463',['with_vector',['../structvg_1_1VectorView.html#af21c3547b8588e6c20f10f5dc67620bf',1,'vg::VectorView::with_vector(const std::function< void(const vector< Item > &)> &callback) const'],['../structvg_1_1VectorView.html#a2e2e6494c350a37135b9c77cd6320f05',1,'vg::VectorView::with_vector(const std::function< void(vector< Item > &)> &callback)']]],
- ['without_5fread_11464',['without_read',['../structvg_1_1alignment__index__t.html#a3df9895a83da6114ae22d5981a83f9a5',1,'vg::alignment_index_t']]],
- ['worst_5falignment_5fscore_11465',['worst_alignment_score',['../namespacevg.html#a8e2c6fbf0d030acabb7dd6b8d428e143',1,'vg']]],
- ['wrap_11466',['wrap',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01true_01_4.html#afdb8a7b86ca03dafaa44a27b573c0c7d',1,'handlegraph::BoolReturningWrapper< Iteratee, true >::wrap()'],['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01false_01_4.html#a2dc122df61cb917d075af250c16931de',1,'handlegraph::BoolReturningWrapper< Iteratee, false >::wrap()']]],
- ['wrap_5fbare_5floader_11467',['wrap_bare_loader',['../namespacevg_1_1io.html#a36870772d6af0c6fbc0a099f6bed2caf',1,'vg::io']]],
- ['wrap_5fbare_5fsaver_11468',['wrap_bare_saver',['../namespacevg_1_1io.html#ae0cd97ec5478403a25e02c9805f3d286',1,'vg::io']]],
- ['wrap_5ftext_11469',['wrap_text',['../namespacevg.html#a57f111dda471f40192704110bae04a0f',1,'vg']]],
- ['wrap_5fwith_5fnull_5fnodes_11470',['wrap_with_null_nodes',['../classvg_1_1VG.html#a2239c89d6ac7e9dec0d76325c2a68f97',1,'vg::VG']]],
- ['write_11471',['write',['../classvg_1_1Paths.html#a8a520b4d648c566f4297418025051784',1,'vg::Paths::write()'],['../classvg_1_1io_1_1JSONStreamHelper.html#ad024636dddd28df4afcd78671598203f',1,'vg::io::JSONStreamHelper::write()'],['../classvg_1_1io_1_1MessageEmitter.html#a58bdb39f127ad810b8dc3b5288bf61df',1,'vg::io::MessageEmitter::write(const string &tag)'],['../classvg_1_1io_1_1MessageEmitter.html#afe12ded46a9500d7b51192ce8cbff596',1,'vg::io::MessageEmitter::write(const string &tag, string &&message)'],['../classvg_1_1io_1_1ProtobufEmitter.html#af2956417dd81044bd5134794693942fd',1,'vg::io::ProtobufEmitter::write()'],['../namespacevg_1_1io.html#a1b6b275aeefcf193d8d25a6b3b7b8f11',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T &(size_t)> &lambda, bool compressed=true)'],['../namespacevg_1_1io.html#aa4c230c8fd256d7a5dfd16aa2014a51f',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T(size_t)> &lambda, bool compressed=true)']]],
- ['write_5falignment_5fto_5ffile_11472',['write_alignment_to_file',['../namespacevg.html#a81c8bc6d3b973fd1a34c3457a9d2e401',1,'vg']]],
- ['write_5fannotations_11473',['write_annotations',['../classvg_1_1DiagramExplainer.html#a173f7e3fbc63ca644ed8f540fef7d41c',1,'vg::DiagramExplainer']]],
- ['write_5farray_5fto_5faux_11474',['write_array_to_aux',['../namespacevg.html#ab55dcc8a50b26b55f7fc142678b7ce63',1,'vg']]],
- ['write_5fbuffered_11475',['write_buffered',['../namespacevg_1_1io.html#a482c50dd5f56410de4988931f2510f57',1,'vg::io']]],
- ['write_5fconnected_5fcomponents_11476',['write_connected_components',['../classvg_1_1DiagramExplainer.html#a5a93fe3708e127f400324b3f6abc1afb',1,'vg::DiagramExplainer']]],
- ['write_5fcopy_11477',['write_copy',['../classvg_1_1io_1_1MessageEmitter.html#af50b05f458e958c26ac55f7994d1f573',1,'vg::io::MessageEmitter::write_copy()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a8ded624b6ba6d5dddf1abe668214ce7e',1,'vg::io::ProtobufEmitter::write_copy()']]],
- ['write_5fedge_11478',['write_edge',['../classvg_1_1DiagramExplainer.html#a36ea9fc4006dda44b55ef17696a53ffe',1,'vg::DiagramExplainer']]],
- ['write_5fedits_11479',['write_edits',['../classvg_1_1Packer.html#af63b2387c9139d25cf7084de15fc4b27',1,'vg::Packer::write_edits(vector< ofstream * > &out) const'],['../classvg_1_1Packer.html#adab10cdf7d5776fb59da650f9b469a24',1,'vg::Packer::write_edits(ostream &out, size_t bin) const']]],
- ['write_5ffasta_5fsequence_11480',['write_fasta_sequence',['../namespacevg.html#a239160a6fee7d0af8914c4ebc7275c78',1,'vg']]],
- ['write_5fgcsa_5fkmers_11481',['write_gcsa_kmers',['../namespacevg.html#a6d8c71ff9f77ddd4a366119e83122771',1,'vg']]],
- ['write_5fgcsa_5fkmers_5fascii_11482',['write_gcsa_kmers_ascii',['../classvg_1_1VGset.html#a8f9d1a671c39aa51a768d0733bccecb9',1,'vg::VGset']]],
- ['write_5fgcsa_5fkmers_5fbinary_11483',['write_gcsa_kmers_binary',['../classvg_1_1VGset.html#a7de0f3cd0ccccd60dc0ef4c29840fe0b',1,'vg::VGset::write_gcsa_kmers_binary(ostream &out, int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)'],['../classvg_1_1VGset.html#a0c1615ae5874cbcc4f77d0b224f2e12e',1,'vg::VGset::write_gcsa_kmers_binary(int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)']]],
- ['write_5fgcsa_5fkmers_5fto_5ftmpfile_11484',['write_gcsa_kmers_to_tmpfile',['../namespacevg.html#a38d9326cbc013aed614bc052c8c224e6',1,'vg']]],
- ['write_5fglobals_11485',['write_globals',['../classvg_1_1DiagramExplainer.html#a47b4615506be1350c648a34fe52fcecd',1,'vg::DiagramExplainer']]],
- ['write_5fgraph_11486',['write_graph',['../classvg_1_1Transcriptome.html#a2b11042d0caef33a18a10e5be784e15c',1,'vg::Transcriptome']]],
- ['write_5fmany_11487',['write_many',['../classvg_1_1io_1_1ProtobufEmitter.html#a05abdc0c51cc62b21c849c2ef13e81e0',1,'vg::io::ProtobufEmitter']]],
- ['write_5fmapping_11488',['write_mapping',['../classvg_1_1PhaseUnfolder.html#a708fb760e358eedc63c624c617885548',1,'vg::PhaseUnfolder']]],
- ['write_5fnode_11489',['write_node',['../classvg_1_1DiagramExplainer.html#adcf77caa4c9627dd25c97f1080888291',1,'vg::DiagramExplainer']]],
- ['write_5fsupports_11490',['write_supports',['../structvg_1_1SupportAugmentedGraph.html#a4f08f8c78bf0ffbfe7e364d4404b97a9',1,'vg::SupportAugmentedGraph']]],
- ['write_5fto_5ffile_11491',['write_to_file',['../namespacevg_1_1io.html#a88cb8e7bbebb78a2ef3bdce1c64ba077',1,'vg::io']]],
- ['write_5ftranscript_5finfo_11492',['write_transcript_info',['../classvg_1_1Transcriptome.html#ada48319a8370ad45364d9bc8241b275a',1,'vg::Transcriptome']]],
- ['write_5ftranscript_5fsequences_11493',['write_transcript_sequences',['../classvg_1_1Transcriptome.html#a4ce90a0e2556b51c62e4a3e550108750',1,'vg::Transcriptome']]],
- ['write_5ftranslations_11494',['write_translations',['../structvg_1_1AugmentedGraph.html#a70ffd6eb24e80cfa265ae48cdde15a45',1,'vg::AugmentedGraph']]],
- ['write_5fvariant_11495',['write_variant',['../classvg_1_1Genotyper.html#af5b580b6db4e727934f964d00b058038',1,'vg::Genotyper']]],
- ['write_5fvariants_11496',['write_variants',['../classvg_1_1VCFOutputCaller.html#afff7887f0111aae8ae3103b990ff54dd',1,'vg::VCFOutputCaller']]],
- ['write_5fvcf_5fheader_11497',['write_vcf_header',['../classvg_1_1Genotyper.html#ad2beb83f750d1deec75b16a60c2ea805',1,'vg::Genotyper']]],
- ['writealiasedraw_11498',['WriteAliasedRaw',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a85d9e1ca69d7bad9e2941b7ecec08a42',1,'vg::io::BlockedGzipOutputStream']]],
- ['writer_5fthread_5ffunction_11499',['writer_thread_function',['../classvg_1_1io_1_1StreamMultiplexer.html#a29ba6b97591887c453b0cc112cae41e4',1,'vg::io::StreamMultiplexer']]]
+ ['w_11424',['w',['../namespacehaplotypes__defaults.html#a9e7cea9525076e8d069877c9f1a08552',1,'haplotypes_defaults']]],
+ ['wabbitize_11425',['wabbitize',['../classVectorizer.html#ae4c3627b5c8ec7b066f5735ca6dfb3f1',1,'Vectorizer']]],
+ ['walk_5fbackwards_11426',['walk_backwards',['../classvg_1_1NGSSimulator.html#a3b87398480be75b240a98d270bfc843c',1,'vg::NGSSimulator']]],
+ ['walk_5fbackwards_5falong_5falignment_11427',['walk_backwards_along_alignment',['../classvg_1_1NGSSimulator.html#af033e5bc63e8407c917f151a4311b64d',1,'vg::NGSSimulator']]],
+ ['walk_5ffanout_5fpath_11428',['walk_fanout_path',['../classvg_1_1BaseMapper.html#ad52deed127976201bd63b32929b71491',1,'vg::BaseMapper']]],
+ ['walk_5fhaplotype_5ffrequency_11429',['walk_haplotype_frequency',['../namespacevg_1_1algorithms.html#a4af5e9c480c0dc7d0843cf981cd52c32',1,'vg::algorithms']]],
+ ['walk_5fhaplotype_5fnames_11430',['walk_haplotype_names',['../namespacevg_1_1algorithms.html#abe9cb62b2ae1c6eb08b10f172980788d',1,'vg::algorithms']]],
+ ['walk_5ft_11431',['walk_t',['../structvg_1_1algorithms_1_1walk__t.html#a5a5ed7ca0dac4f9e742ddeeb28e317e1',1,'vg::algorithms::walk_t::walk_t(uint16_t l, const pos_t &b, const pos_t &e, const handle_t &c, uint16_t f)'],['../structvg_1_1algorithms_1_1walk__t.html#af8c4463befc5bb6cec73b3e493acf545',1,'vg::algorithms::walk_t::walk_t(const std::string &s, const pos_t &b, const pos_t &e, const handle_t &c)']]],
+ ['wang_5fhash_5f64_11432',['wang_hash_64',['../namespacevg.html#a38d35bca25e8a6d5fe10f603cb9048c3',1,'vg']]],
+ ['want_5fbreakpoint_11433',['want_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#ac0698f3b6387ce47f4e9d5b2929d6cf4',1,'vg::io::StreamMultiplexer']]],
+ ['was_5fcorrect_11434',['was_correct',['../classvg_1_1Funnel.html#aac71f37530afee1b7e49770aff8cc53b',1,'vg::Funnel::was_correct(size_t prev_stage_item) const'],['../classvg_1_1Funnel.html#a5f0037505a9df13b92e381f5ff108d72',1,'vg::Funnel::was_correct(size_t prev_stage_index, const string &prev_stage_name, size_t prev_stage_item) const']]],
+ ['was_5fprovided_5fdirectly_11435',['was_provided_directly',['../classvg_1_1IndexFile.html#afabf00d9034342540b3614dfc7055715',1,'vg::IndexFile']]],
+ ['was_5fset_11436',['was_set',['../structvg_1_1subcommand_1_1ArgSpec.html#acfb22902f7ebf4d8053ec39999dd2821',1,'vg::subcommand::ArgSpec::was_set()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aac6bd613601f636c187b684a69fa25ce',1,'vg::subcommand::ValueArgSpec::was_set()']]],
+ ['watchdog_11437',['Watchdog',['../classvg_1_1Watchdog.html#a87e679ecbb8461ae6a26a1958216629b',1,'vg::Watchdog::Watchdog(size_t thread_count, const duration &timeout)'],['../classvg_1_1Watchdog.html#a2934cc5c1fc3b7d0ab20343e6bde1a56',1,'vg::Watchdog::Watchdog(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a73aa9888b0017ed46053c75c085f2748',1,'vg::Watchdog::Watchdog(Watchdog &&other)=delete']]],
+ ['watcher_5floop_11438',['watcher_loop',['../classvg_1_1Watchdog.html#ad2e2c831258c42fdba7f2d0fa8625cc9',1,'vg::Watchdog']]],
+ ['weakly_5fconnected_5fcomponents_11439',['weakly_connected_components',['../namespacehandlegraph_1_1algorithms.html#a96c80b09388c6d079754c66d2f7362e5',1,'handlegraph::algorithms']]],
+ ['weakly_5fconnected_5fcomponents_5fwith_5ftips_11440',['weakly_connected_components_with_tips',['../namespacehandlegraph_1_1algorithms.html#aa5ff9ed76bd82438b3af0c3112437ccd',1,'handlegraph::algorithms']]],
+ ['weibull_5fcdf_11441',['weibull_cdf',['../namespacevg.html#a100efe5dfc5bfe434b53416f93d2a0e1',1,'vg']]],
+ ['weibull_5flog_5flikelihood_11442',['weibull_log_likelihood',['../namespacevg.html#ad93405cf370e6d92396691fc3320be1c',1,'vg']]],
+ ['weighted_5fjaccard_5fcoefficient_11443',['weighted_jaccard_coefficient',['../namespacevg.html#aa0b9062cb7b053e7823169d589e113d1',1,'vg']]],
+ ['wellford_5fmean_5fvar_11444',['wellford_mean_var',['../namespacevg.html#a4b96cd801bc780d426db346f80ab2172',1,'vg']]],
+ ['wellford_5fupdate_11445',['wellford_update',['../namespacevg.html#a614c672ed69c280b699a278ce0f34ade',1,'vg']]],
+ ['wfa_5falignment_5fto_5falignment_11446',['wfa_alignment_to_alignment',['../classvg_1_1MinimizerMapper.html#a597914c2167ca2b06a3dccbb23e21340',1,'vg::MinimizerMapper']]],
+ ['wfaextender_11447',['WFAExtender',['../classvg_1_1WFAExtender.html#a7d7324769e3d80c6acdd68de034c5830',1,'vg::WFAExtender::WFAExtender()'],['../classvg_1_1WFAExtender.html#a9cc09b85da35171c971868e80cfe2938',1,'vg::WFAExtender::WFAExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner, const ErrorModel &error_model=default_error_model)']]],
+ ['wfanode_11448',['WFANode',['../structvg_1_1WFANode.html#a93d02d2b8f73a4cdcbe5a356258cb5e8',1,'vg::WFANode']]],
+ ['wfatree_11449',['WFATree',['../classvg_1_1WFATree.html#ad9880bb173f2bd8e2cdc3708cbb8005f',1,'vg::WFATree']]],
+ ['what_11450',['what',['../classvg_1_1NoAlignmentInBandException.html#a006dddb79b9d1c6035c2466c35dbcacf',1,'vg::NoAlignmentInBandException::what()'],['../classvg_1_1InsufficientInputException.html#ae9fd64e80e950783955ff7d875138469',1,'vg::InsufficientInputException::what()'],['../classvg_1_1RewindPlanException.html#a5d3526ac6c26a49f65a962f12c246615',1,'vg::RewindPlanException::what()'],['../classvg_1_1SizeLimitExceededException.html#acb8fbb8940007b68bede049fcf19b046',1,'vg::SizeLimitExceededException::what()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#a7fdc5893f8439a8c8c6169865a8c6e0d',1,'vg::algorithms::GFAFormatError::what()'],['../classj2pb__error.html#a4ac3313fff0e2721ca9480b61ebe6a8b',1,'j2pb_error::what()']]],
+ ['which_5fhaplotype_11451',['which_haplotype',['../classvg_1_1PhasedGenome_1_1iterator.html#a02b60bd3c0ec6d86a8bec582e717ea15',1,'vg::PhasedGenome::iterator']]],
+ ['wideningprng_11452',['WideningPRNG',['../classvg_1_1WideningPRNG.html#a5437179a5230df00551a618df6bc4c53',1,'vg::WideningPRNG']]],
+ ['widest_5fdijkstra_11453',['widest_dijkstra',['../namespacevg_1_1algorithms.html#a08c6d85f2dc09c22c5d14ed81808769e',1,'vg::algorithms']]],
+ ['window_5fbreaking_5fquality_11454',['window_breaking_quality',['../classvg_1_1MinimizerMapper.html#a7999b2f0a931930bfa9eddec4065b51b',1,'vg::MinimizerMapper']]],
+ ['window_5fof_5fid_11455',['window_of_id',['../classvg_1_1StreamIndexBase.html#a320b27d89fbc1a74574cc00befe1e7fe',1,'vg::StreamIndexBase']]],
+ ['window_5fsize_11456',['window_size',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a7fb1665349757422a2868159d2b66437',1,'vg::MinimizerMapper::Minimizer']]],
+ ['windowedvcfbuffer_11457',['WindowedVcfBuffer',['../classvg_1_1WindowedVcfBuffer.html#a7d7af1d1441bab6c687bdf1be7fc4675',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(vcflib::VariantCallFile *file, size_t window_size)'],['../classvg_1_1WindowedVcfBuffer.html#aa57da13990d5983d5e8aa787dfe56995',1,'vg::WindowedVcfBuffer::WindowedVcfBuffer(const WindowedVcfBuffer &other)=delete']]],
+ ['with_5fcache_5fentry_11458',['with_cache_entry',['../classvg_1_1IndexedVG.html#ac14226d9ccd03cb99af9a08cef31d6ff',1,'vg::IndexedVG']]],
+ ['with_5fcursor_11459',['with_cursor',['../classvg_1_1IndexedVG.html#af380961c8e8b342ba8f688c2f073de2e',1,'vg::IndexedVG']]],
+ ['with_5fdagified_5flocal_5fgraph_11460',['with_dagified_local_graph',['../classvg_1_1MinimizerMapper.html#a96b3c359c5f86557ddccfdedd67af570',1,'vg::MinimizerMapper']]],
+ ['with_5fexception_5fhandling_11461',['with_exception_handling',['../namespacevg.html#a1d2cbe5fe5e1b8a33b7d707f7059b3c6',1,'vg']]],
+ ['with_5ffunction_5fcalling_5fstream_11462',['with_function_calling_stream',['../namespacevg_1_1io.html#a8b1a63276edf814575b7afb3b2b9844d',1,'vg::io']]],
+ ['with_5fpath_5findex_11463',['with_path_index',['../classvg_1_1GraphSynchronizer.html#a336f5828883adce86ee5e536f8c299ea',1,'vg::GraphSynchronizer']]],
+ ['with_5fprogress_11464',['with_progress',['../classvg_1_1Progressive.html#ab44ff020fc951b95dfcd1252c015a020',1,'vg::Progressive']]],
+ ['with_5fputback_11465',['with_putback',['../classvg_1_1io_1_1VPKG.html#a0bcbb5a28413d3599a642cd5f22d93be',1,'vg::io::VPKG']]],
+ ['with_5fsave_5fstream_11466',['with_save_stream',['../classvg_1_1io_1_1VPKG.html#a030910ec652e742dbf98a845b95943a5',1,'vg::io::VPKG']]],
+ ['with_5fvector_11467',['with_vector',['../structvg_1_1VectorView.html#af21c3547b8588e6c20f10f5dc67620bf',1,'vg::VectorView::with_vector(const std::function< void(const vector< Item > &)> &callback) const'],['../structvg_1_1VectorView.html#a2e2e6494c350a37135b9c77cd6320f05',1,'vg::VectorView::with_vector(const std::function< void(vector< Item > &)> &callback)']]],
+ ['without_5fread_11468',['without_read',['../structvg_1_1alignment__index__t.html#a3df9895a83da6114ae22d5981a83f9a5',1,'vg::alignment_index_t']]],
+ ['worst_5falignment_5fscore_11469',['worst_alignment_score',['../namespacevg.html#a8e2c6fbf0d030acabb7dd6b8d428e143',1,'vg']]],
+ ['wrap_11470',['wrap',['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01true_01_4.html#afdb8a7b86ca03dafaa44a27b573c0c7d',1,'handlegraph::BoolReturningWrapper< Iteratee, true >::wrap()'],['../structhandlegraph_1_1BoolReturningWrapper_3_01Iteratee_00_01false_01_4.html#a2dc122df61cb917d075af250c16931de',1,'handlegraph::BoolReturningWrapper< Iteratee, false >::wrap()']]],
+ ['wrap_5fbare_5floader_11471',['wrap_bare_loader',['../namespacevg_1_1io.html#a36870772d6af0c6fbc0a099f6bed2caf',1,'vg::io']]],
+ ['wrap_5fbare_5fsaver_11472',['wrap_bare_saver',['../namespacevg_1_1io.html#ae0cd97ec5478403a25e02c9805f3d286',1,'vg::io']]],
+ ['wrap_5ftext_11473',['wrap_text',['../namespacevg.html#a57f111dda471f40192704110bae04a0f',1,'vg']]],
+ ['wrap_5fwith_5fnull_5fnodes_11474',['wrap_with_null_nodes',['../classvg_1_1VG.html#a2239c89d6ac7e9dec0d76325c2a68f97',1,'vg::VG']]],
+ ['write_11475',['write',['../classvg_1_1Paths.html#a8a520b4d648c566f4297418025051784',1,'vg::Paths::write()'],['../classvg_1_1io_1_1JSONStreamHelper.html#ad024636dddd28df4afcd78671598203f',1,'vg::io::JSONStreamHelper::write()'],['../classvg_1_1io_1_1MessageEmitter.html#a58bdb39f127ad810b8dc3b5288bf61df',1,'vg::io::MessageEmitter::write(const string &tag)'],['../classvg_1_1io_1_1MessageEmitter.html#afe12ded46a9500d7b51192ce8cbff596',1,'vg::io::MessageEmitter::write(const string &tag, string &&message)'],['../classvg_1_1io_1_1ProtobufEmitter.html#af2956417dd81044bd5134794693942fd',1,'vg::io::ProtobufEmitter::write()'],['../namespacevg_1_1io.html#a1b6b275aeefcf193d8d25a6b3b7b8f11',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T &(size_t)> &lambda, bool compressed=true)'],['../namespacevg_1_1io.html#aa4c230c8fd256d7a5dfd16aa2014a51f',1,'vg::io::write(std::ostream &out, size_t count, const std::function< T(size_t)> &lambda, bool compressed=true)']]],
+ ['write_5falignment_5fto_5ffile_11476',['write_alignment_to_file',['../namespacevg.html#a81c8bc6d3b973fd1a34c3457a9d2e401',1,'vg']]],
+ ['write_5fannotations_11477',['write_annotations',['../classvg_1_1DiagramExplainer.html#a173f7e3fbc63ca644ed8f540fef7d41c',1,'vg::DiagramExplainer']]],
+ ['write_5farray_5fto_5faux_11478',['write_array_to_aux',['../namespacevg.html#ab55dcc8a50b26b55f7fc142678b7ce63',1,'vg']]],
+ ['write_5fbuffered_11479',['write_buffered',['../namespacevg_1_1io.html#a482c50dd5f56410de4988931f2510f57',1,'vg::io']]],
+ ['write_5fconnected_5fcomponents_11480',['write_connected_components',['../classvg_1_1DiagramExplainer.html#a5a93fe3708e127f400324b3f6abc1afb',1,'vg::DiagramExplainer']]],
+ ['write_5fcopy_11481',['write_copy',['../classvg_1_1io_1_1MessageEmitter.html#af50b05f458e958c26ac55f7994d1f573',1,'vg::io::MessageEmitter::write_copy()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a8ded624b6ba6d5dddf1abe668214ce7e',1,'vg::io::ProtobufEmitter::write_copy()']]],
+ ['write_5fedge_11482',['write_edge',['../classvg_1_1DiagramExplainer.html#a36ea9fc4006dda44b55ef17696a53ffe',1,'vg::DiagramExplainer']]],
+ ['write_5fedits_11483',['write_edits',['../classvg_1_1Packer.html#af63b2387c9139d25cf7084de15fc4b27',1,'vg::Packer::write_edits(vector< ofstream * > &out) const'],['../classvg_1_1Packer.html#adab10cdf7d5776fb59da650f9b469a24',1,'vg::Packer::write_edits(ostream &out, size_t bin) const']]],
+ ['write_5ffasta_5fsequence_11484',['write_fasta_sequence',['../namespacevg.html#a239160a6fee7d0af8914c4ebc7275c78',1,'vg']]],
+ ['write_5fgcsa_5fkmers_11485',['write_gcsa_kmers',['../namespacevg.html#a6d8c71ff9f77ddd4a366119e83122771',1,'vg']]],
+ ['write_5fgcsa_5fkmers_5fascii_11486',['write_gcsa_kmers_ascii',['../classvg_1_1VGset.html#a8f9d1a671c39aa51a768d0733bccecb9',1,'vg::VGset']]],
+ ['write_5fgcsa_5fkmers_5fbinary_11487',['write_gcsa_kmers_binary',['../classvg_1_1VGset.html#a7de0f3cd0ccccd60dc0ef4c29840fe0b',1,'vg::VGset::write_gcsa_kmers_binary(ostream &out, int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)'],['../classvg_1_1VGset.html#a0c1615ae5874cbcc4f77d0b224f2e12e',1,'vg::VGset::write_gcsa_kmers_binary(int kmer_size, size_t &size_limit, nid_t head_id=0, nid_t tail_id=0)']]],
+ ['write_5fgcsa_5fkmers_5fto_5ftmpfile_11488',['write_gcsa_kmers_to_tmpfile',['../namespacevg.html#a38d9326cbc013aed614bc052c8c224e6',1,'vg']]],
+ ['write_5fglobals_11489',['write_globals',['../classvg_1_1DiagramExplainer.html#a47b4615506be1350c648a34fe52fcecd',1,'vg::DiagramExplainer']]],
+ ['write_5fgraph_11490',['write_graph',['../classvg_1_1Transcriptome.html#a2b11042d0caef33a18a10e5be784e15c',1,'vg::Transcriptome']]],
+ ['write_5fmany_11491',['write_many',['../classvg_1_1io_1_1ProtobufEmitter.html#a05abdc0c51cc62b21c849c2ef13e81e0',1,'vg::io::ProtobufEmitter']]],
+ ['write_5fmapping_11492',['write_mapping',['../classvg_1_1PhaseUnfolder.html#a708fb760e358eedc63c624c617885548',1,'vg::PhaseUnfolder']]],
+ ['write_5fnode_11493',['write_node',['../classvg_1_1DiagramExplainer.html#adcf77caa4c9627dd25c97f1080888291',1,'vg::DiagramExplainer']]],
+ ['write_5fsupports_11494',['write_supports',['../structvg_1_1SupportAugmentedGraph.html#a4f08f8c78bf0ffbfe7e364d4404b97a9',1,'vg::SupportAugmentedGraph']]],
+ ['write_5fto_5ffile_11495',['write_to_file',['../namespacevg_1_1io.html#a88cb8e7bbebb78a2ef3bdce1c64ba077',1,'vg::io']]],
+ ['write_5ftranscript_5finfo_11496',['write_transcript_info',['../classvg_1_1Transcriptome.html#ada48319a8370ad45364d9bc8241b275a',1,'vg::Transcriptome']]],
+ ['write_5ftranscript_5fsequences_11497',['write_transcript_sequences',['../classvg_1_1Transcriptome.html#a4ce90a0e2556b51c62e4a3e550108750',1,'vg::Transcriptome']]],
+ ['write_5ftranslations_11498',['write_translations',['../structvg_1_1AugmentedGraph.html#a70ffd6eb24e80cfa265ae48cdde15a45',1,'vg::AugmentedGraph']]],
+ ['write_5fvariant_11499',['write_variant',['../classvg_1_1Genotyper.html#af5b580b6db4e727934f964d00b058038',1,'vg::Genotyper']]],
+ ['write_5fvariants_11500',['write_variants',['../classvg_1_1VCFOutputCaller.html#afff7887f0111aae8ae3103b990ff54dd',1,'vg::VCFOutputCaller']]],
+ ['write_5fvcf_5fheader_11501',['write_vcf_header',['../classvg_1_1Genotyper.html#ad2beb83f750d1deec75b16a60c2ea805',1,'vg::Genotyper']]],
+ ['writealiasedraw_11502',['WriteAliasedRaw',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a85d9e1ca69d7bad9e2941b7ecec08a42',1,'vg::io::BlockedGzipOutputStream']]],
+ ['writer_5fthread_5ffunction_11503',['writer_thread_function',['../classvg_1_1io_1_1StreamMultiplexer.html#a29ba6b97591887c453b0cc112cae41e4',1,'vg::io::StreamMultiplexer']]]
];
diff --git a/search/functions_18.js b/search/functions_18.js
index 77b0bd2094..a50c865418 100644
--- a/search/functions_18.js
+++ b/search/functions_18.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['xdropaligner_11500',['XdropAligner',['../classvg_1_1XdropAligner.html#ae707a0f10732b011cea8aab49913a142',1,'vg::XdropAligner::XdropAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1XdropAligner.html#a553d87ce9c62f404b01490ad0619164a',1,'vg::XdropAligner::XdropAligner()=default'],['../classvg_1_1XdropAligner.html#af42a02f900600c3c375fa0b6644c97a9',1,'vg::XdropAligner::XdropAligner(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a2eb9135c8b9e7534b90124968e4d3f48',1,'vg::XdropAligner::XdropAligner(XdropAligner &&other)']]],
- ['xg_11501',['XG',['../classxg_1_1XG.html#ab71253786ed61320ec3101a06df3f369',1,'xg::XG::XG(void)=default'],['../classxg_1_1XG.html#a16821ba9ad761dac00ef46a1d9bc7424',1,'xg::XG::XG(const XG &other)=delete'],['../classxg_1_1XG.html#a4bcac3042196387b5c04b6833de7a035',1,'xg::XG::XG(XG &&other)=delete']]],
- ['xg_5findex_5fsize_11502',['xg_index_size',['../namespacevg.html#a07b713793f27ae9eb7f96617e97549f1',1,'vg']]],
- ['xgpath_11503',['XGPath',['../classxg_1_1XGPath.html#af623a612337301ad98ed9c45108b9616',1,'xg::XGPath::XGPath(void)=default'],['../classxg_1_1XGPath.html#a7a3d21f2e1ad0f36c25897591b6e31da',1,'xg::XGPath::XGPath(const std::string &path_name, const std::vector< handle_t > &path, bool is_circular, XG &graph)'],['../classxg_1_1XGPath.html#aeb3f65f6d78a0fa02486f0c9c51c97a8',1,'xg::XGPath::XGPath(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a010789a1a74731505b2b8a570f4e7547',1,'xg::XGPath::XGPath(XGPath &&other)=delete']]],
- ['xsputn_11504',['xsputn',['../classvg_1_1io_1_1fdoutbuf.html#a1eba1fc19d1c9100bc5eb98259cc914b',1,'vg::io::fdoutbuf']]]
+ ['xdropaligner_11504',['XdropAligner',['../classvg_1_1XdropAligner.html#ae707a0f10732b011cea8aab49913a142',1,'vg::XdropAligner::XdropAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension)'],['../classvg_1_1XdropAligner.html#a553d87ce9c62f404b01490ad0619164a',1,'vg::XdropAligner::XdropAligner()=default'],['../classvg_1_1XdropAligner.html#af42a02f900600c3c375fa0b6644c97a9',1,'vg::XdropAligner::XdropAligner(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a2eb9135c8b9e7534b90124968e4d3f48',1,'vg::XdropAligner::XdropAligner(XdropAligner &&other)']]],
+ ['xg_11505',['XG',['../classxg_1_1XG.html#ab71253786ed61320ec3101a06df3f369',1,'xg::XG::XG(void)=default'],['../classxg_1_1XG.html#a16821ba9ad761dac00ef46a1d9bc7424',1,'xg::XG::XG(const XG &other)=delete'],['../classxg_1_1XG.html#a4bcac3042196387b5c04b6833de7a035',1,'xg::XG::XG(XG &&other)=delete']]],
+ ['xg_5findex_5fsize_11506',['xg_index_size',['../namespacevg.html#a07b713793f27ae9eb7f96617e97549f1',1,'vg']]],
+ ['xgpath_11507',['XGPath',['../classxg_1_1XGPath.html#af623a612337301ad98ed9c45108b9616',1,'xg::XGPath::XGPath(void)=default'],['../classxg_1_1XGPath.html#a7a3d21f2e1ad0f36c25897591b6e31da',1,'xg::XGPath::XGPath(const std::string &path_name, const std::vector< handle_t > &path, bool is_circular, XG &graph)'],['../classxg_1_1XGPath.html#aeb3f65f6d78a0fa02486f0c9c51c97a8',1,'xg::XGPath::XGPath(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a010789a1a74731505b2b8a570f4e7547',1,'xg::XGPath::XGPath(XGPath &&other)=delete']]],
+ ['xsputn_11508',['xsputn',['../classvg_1_1io_1_1fdoutbuf.html#a1eba1fc19d1c9100bc5eb98259cc914b',1,'vg::io::fdoutbuf']]]
];
diff --git a/search/functions_19.js b/search/functions_19.js
index 0ca470cf84..5139484110 100644
--- a/search/functions_19.js
+++ b/search/functions_19.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['yens_5fk_5fwidest_5fpaths_11505',['yens_k_widest_paths',['../namespacevg_1_1algorithms.html#ad9a715606bdd30499dc9db88583c6573',1,'vg::algorithms']]]
+ ['yens_5fk_5fwidest_5fpaths_11509',['yens_k_widest_paths',['../namespacevg_1_1algorithms.html#ad9a715606bdd30499dc9db88583c6573',1,'vg::algorithms']]]
];
diff --git a/search/functions_1a.js b/search/functions_1a.js
index 0e021ddedf..f645c89097 100644
--- a/search/functions_1a.js
+++ b/search/functions_1a.js
@@ -1,12 +1,12 @@
var searchData=
[
- ['fill_5fin_5fforest_3c_20minimizermapper_3a_3aminimizer_20_3e_11506',['fill_in_forest< MinimizerMapper::Minimizer >',['../namespacevg.html#ad4f0e6958b0bfd7c256ee10291a95925',1,'vg']]],
- ['get_5fcyclic_5fsnarl_5fintervals_3c_20minimizermapper_3a_3aminimizer_20_3e_11507',['get_cyclic_snarl_intervals< MinimizerMapper::Minimizer >',['../namespacevg.html#a279d0eb09ed478cc7c6c98e3cbcd9864',1,'vg']]],
- ['print_5fself_3c_20minimizermapper_3a_3aminimizer_20_3e_11508',['print_self< MinimizerMapper::Minimizer >',['../namespacevg.html#a48dec55a9705e1b2a636a90c7c9d9e9d',1,'vg']]],
- ['z_11509',['Z',['../classvg_1_1truncated__normal__distribution.html#aeef658109dfa3a3d4904aea92a93b93d',1,'vg::truncated_normal_distribution']]],
- ['zip_5falignments_11510',['zip_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a96a24f6cbdc09cf0098251f8b61baf4a',1,'vg::MultipathAlignmentGraph']]],
- ['zip_5ftree_5ftransition_5fiterator_11511',['zip_tree_transition_iterator',['../namespacevg_1_1algorithms.html#a73608f2f497e40cc514deaa74a00cb52',1,'vg::algorithms']]],
- ['zipcodecollection_11512',['ZipCodeCollection',['../classvg_1_1ZipCodeCollection.html#aef34ada27f78937e260e90fb1fe8a1d0',1,'vg::ZipCodeCollection']]],
- ['zipcodeforest_11513',['ZipCodeForest',['../classvg_1_1ZipCodeForest.html#ab6f83d5af9f5ab490040e469f38b68df',1,'vg::ZipCodeForest']]],
- ['zipcodetree_11514',['ZipCodeTree',['../classvg_1_1ZipCodeTree.html#a891b100128d123066ee70e97d1374f41',1,'vg::ZipCodeTree']]]
+ ['fill_5fin_5fforest_3c_20minimizermapper_3a_3aminimizer_20_3e_11510',['fill_in_forest< MinimizerMapper::Minimizer >',['../namespacevg.html#ad4f0e6958b0bfd7c256ee10291a95925',1,'vg']]],
+ ['get_5fcyclic_5fsnarl_5fintervals_3c_20minimizermapper_3a_3aminimizer_20_3e_11511',['get_cyclic_snarl_intervals< MinimizerMapper::Minimizer >',['../namespacevg.html#a279d0eb09ed478cc7c6c98e3cbcd9864',1,'vg']]],
+ ['print_5fself_3c_20minimizermapper_3a_3aminimizer_20_3e_11512',['print_self< MinimizerMapper::Minimizer >',['../namespacevg.html#a48dec55a9705e1b2a636a90c7c9d9e9d',1,'vg']]],
+ ['z_11513',['Z',['../classvg_1_1truncated__normal__distribution.html#aeef658109dfa3a3d4904aea92a93b93d',1,'vg::truncated_normal_distribution']]],
+ ['zip_5falignments_11514',['zip_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a96a24f6cbdc09cf0098251f8b61baf4a',1,'vg::MultipathAlignmentGraph']]],
+ ['zip_5ftree_5ftransition_5fiterator_11515',['zip_tree_transition_iterator',['../namespacevg_1_1algorithms.html#a73608f2f497e40cc514deaa74a00cb52',1,'vg::algorithms']]],
+ ['zipcodecollection_11516',['ZipCodeCollection',['../classvg_1_1ZipCodeCollection.html#aef34ada27f78937e260e90fb1fe8a1d0',1,'vg::ZipCodeCollection']]],
+ ['zipcodeforest_11517',['ZipCodeForest',['../classvg_1_1ZipCodeForest.html#ab6f83d5af9f5ab490040e469f38b68df',1,'vg::ZipCodeForest']]],
+ ['zipcodetree_11518',['ZipCodeTree',['../classvg_1_1ZipCodeTree.html#a891b100128d123066ee70e97d1374f41',1,'vg::ZipCodeTree']]]
];
diff --git a/search/functions_1b.js b/search/functions_1b.js
index fd19087818..c2a1197fb7 100644
--- a/search/functions_1b.js
+++ b/search/functions_1b.js
@@ -1,201 +1,201 @@
var searchData=
[
- ['_7eabstractreadsampler_11515',['~AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html#aab2237075e873b1fac2b9d927835dd5d',1,'vg::AbstractReadSampler']]],
- ['_7ealiasgraph_11516',['~AliasGraph',['../classvg_1_1AliasGraph.html#aa6557ac096d2a238b4bde66341fa4bbf',1,'vg::AliasGraph']]],
- ['_7ealigner_11517',['~Aligner',['../classvg_1_1Aligner.html#ab652846ac99c793321f513e80b3567e7',1,'vg::Aligner']]],
- ['_7ealignmentchainmodelvertex_11518',['~AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html#a2956b8c27f6438dda8d392c47c29da59',1,'vg::AlignmentChainModelVertex']]],
- ['_7ealignmentemitter_11519',['~AlignmentEmitter',['../classvg_1_1io_1_1AlignmentEmitter.html#a8a2ed8eecf9bc49b0c82e0276a8c3ecf',1,'vg::io::AlignmentEmitter']]],
- ['_7ealttracebackstack_11520',['~AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a7271beafb4fd9d7d993e7225d0289ee8',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['_7eappendhaplotypecommand_11521',['~AppendHaplotypeCommand',['../structvg_1_1AppendHaplotypeCommand.html#a5890b1f7b3374109bb8326372f3dcd18',1,'vg::AppendHaplotypeCommand']]],
- ['_7eargspec_11522',['~ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html#a85d84f459627dc7d5d476ef600cd4eaa',1,'vg::subcommand::ArgSpec']]],
- ['_7ebabuilder_11523',['~BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#af4852751e6f009ed647f81926b8c6ac0',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['_7ebamatrix_11524',['~BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac174727f3eb7d040f75bbb638e3ef585',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['_7ebandedglobalaligner_11525',['~BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html#ac211fadde52f8cc1312fddb585c021b0',1,'vg::BandedGlobalAligner']]],
- ['_7ebaseargspec_11526',['~BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a6324c7d0c79aece0d2cf73a9bb385377',1,'vg::subcommand::BaseArgSpec']]],
- ['_7ebaseoption_11527',['~BaseOption',['../classvg_1_1BaseOption.html#a877daeaa51e8978827609c35bffa6f7d',1,'vg::BaseOption']]],
- ['_7ebaseoptiongroup_11528',['~BaseOptionGroup',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a65cfafee0415b04533cece4cde5c9b8a',1,'vg::subcommand::BaseOptionGroup']]],
- ['_7ebasevaluation_11529',['~BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html#af8bbcfd7d30f6c358ba91db3be2a7084',1,'vg::subcommand::BaseValuation']]],
- ['_7eblockedgzipinputstream_11530',['~BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a56990712e743be20a39e760309a8934c',1,'vg::io::BlockedGzipInputStream']]],
- ['_7eblockedgzipoutputstream_11531',['~BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaac9002de6d983cb46a36b44620448bb',1,'vg::io::BlockedGzipOutputStream']]],
- ['_7ebuildablesnarldecomposition_11532',['~BuildableSnarlDecomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a04eec535a4ad69c3d57a7733cbb56f23',1,'handlegraph::BuildableSnarlDecomposition']]],
- ['_7ecachedpackedtraversalsupportfinder_11533',['~CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html#ae90902c6346948c1b2ab45dd389b4014',1,'vg::CachedPackedTraversalSupportFinder']]],
- ['_7ecallinfo_11534',['~CallInfo',['../structvg_1_1SnarlCaller_1_1CallInfo.html#a596d13cd23b7d5dd9a24bdea876a286d',1,'vg::SnarlCaller::CallInfo']]],
- ['_7ecolors_11535',['~Colors',['../classvg_1_1Colors.html#ac08aaa9a815d639d327c3ea80b97ed2b',1,'vg::Colors']]],
- ['_7ecompletedtranscriptpath_11536',['~CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html#a885c00ed2c371cddfe7a9a78c00dcd94',1,'vg::CompletedTranscriptPath']]],
- ['_7ecomponentmindistanceclusterer_11537',['~ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html#aa13390387862e6477651a627db8b36b3',1,'vg::ComponentMinDistanceClusterer']]],
- ['_7econnection_5ft_11538',['~connection_t',['../classvg_1_1connection__t.html#ac3664dfd1f422b7a88b2760e9a4ee83d',1,'vg::connection_t']]],
- ['_7econsistencycalculator_11539',['~ConsistencyCalculator',['../classvg_1_1ConsistencyCalculator.html#afb05d4ab7a962df47c62c408d0154ba0',1,'vg::ConsistencyCalculator']]],
- ['_7edagifiedgraph_11540',['~DagifiedGraph',['../classvg_1_1DagifiedGraph.html#acb7989cf7dcc34da6fd11228d36321f7',1,'vg::DagifiedGraph']]],
- ['_7edeconstructor_11541',['~Deconstructor',['../classvg_1_1Deconstructor.html#a875c8006f289ad46470c05c8808bdd73',1,'vg::Deconstructor']]],
- ['_7edeflection_11542',['~Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#af4deb014af190975b2e7fe3540f6f461',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['_7edeletablehandlegraph_11543',['~DeletableHandleGraph',['../classhandlegraph_1_1DeletableHandleGraph.html#a62ed805e124ceb05cfa98d4e631a9ebd',1,'handlegraph::DeletableHandleGraph']]],
- ['_7edeletehaplotypecommand_11544',['~DeleteHaplotypeCommand',['../structvg_1_1DeleteHaplotypeCommand.html#a2049b0eb4e4cf76d42b26fb9b0ecb659',1,'vg::DeleteHaplotypeCommand']]],
- ['_7edeletionaligner_11545',['~DeletionAligner',['../classvg_1_1DeletionAligner.html#a797ac3036e59d5086c0822b90302dd14',1,'vg::DeletionAligner']]],
- ['_7ediagramexplainer_11546',['~DiagramExplainer',['../classvg_1_1DiagramExplainer.html#aacac728ac8712e2d1f803c0735c34990',1,'vg::DiagramExplainer']]],
- ['_7edinucleotidemachine_11547',['~DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html#a927431a787e6f77549850cea55d883b0',1,'vg::DinucleotideMachine']]],
- ['_7edistanceheuristic_11548',['~DistanceHeuristic',['../classvg_1_1DistanceHeuristic.html#abca20b0fc239abad09fabb6d6bad0b50',1,'vg::DistanceHeuristic']]],
- ['_7edozeuinterface_11549',['~DozeuInterface',['../classvg_1_1DozeuInterface.html#a0ac4d30c781e2a2278986ecbb84a34a6',1,'vg::DozeuInterface']]],
- ['_7edozeupinningoverlay_11550',['~DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html#a6fe397bf132beeabd0ed7f830b1f9994',1,'vg::DozeuPinningOverlay']]],
- ['_7edpscorecomparator_11551',['~DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a02c3e3552497f6425a1f3d14682c1d06',1,'vg::MEMClusterer::DPScoreComparator']]],
- ['_7eedit_5ft_11552',['~edit_t',['../classvg_1_1edit__t.html#a43201af48ee260fa83a5bde0ed75a978',1,'vg::edit_t']]],
- ['_7eeditedtranscriptpath_11553',['~EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html#aba2f28b19414c8c3795e60e76a07f807',1,'vg::EditedTranscriptPath']]],
- ['_7eexhaustivetraversalfinder_11554',['~ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html#a7586c1b256f63d9e4295a9f1011b921a',1,'vg::ExhaustiveTraversalFinder']]],
- ['_7eexpandingoverlaygraph_11555',['~ExpandingOverlayGraph',['../classhandlegraph_1_1ExpandingOverlayGraph.html#a9d7cac3cf3b289fe1980d0575e70be72',1,'handlegraph::ExpandingOverlayGraph']]],
- ['_7eexplainer_11556',['~Explainer',['../classvg_1_1Explainer.html#a68991032a4a7fed25227a884f7f76a2a',1,'vg::Explainer']]],
- ['_7efilter_11557',['~Filter',['../classvg_1_1Filter.html#a09073f3ae2d26bc61cf639dfc4072745',1,'vg::Filter']]],
- ['_7efixedgenotypepriorcalculator_11558',['~FixedGenotypePriorCalculator',['../classvg_1_1FixedGenotypePriorCalculator.html#a4adc4bf44587b687076826dffc91ccf0',1,'vg::FixedGenotypePriorCalculator']]],
- ['_7eflagargspec_11559',['~FlagArgSpec',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a7988d073aa24da829c03c9d68ae651f9',1,'vg::subcommand::FlagArgSpec']]],
- ['_7eflatfilebacktranslation_11560',['~FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html#a4330bd5f76951158a1ea50755b43293d',1,'vg::FlatFileBackTranslation']]],
- ['_7eflowcaller_11561',['~FlowCaller',['../classvg_1_1FlowCaller.html#a6fc652c91844cba402eb9e143883eefa',1,'vg::FlowCaller']]],
- ['_7efragmentlengthdistribution_11562',['~FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html#a5ca105be9aca035e59985092d1a6aa79',1,'vg::FragmentLengthDistribution']]],
- ['_7egafalignmentemitter_11563',['~GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html#ab8c76602efdaadba7319ca5103bc9107',1,'vg::io::GafAlignmentEmitter']]],
- ['_7egafoutputcaller_11564',['~GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html#af275fa29f22a94c9c4180280675a160e',1,'vg::GAFOutputCaller']]],
- ['_7egbwttraversalfinder_11565',['~GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html#aaf4b52f7a7807922daa514df94235a3a',1,'vg::GBWTTraversalFinder']]],
- ['_7egenomestatecommand_11566',['~GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html#a951ebc208c74b7ec323de6f517d02527',1,'vg::GenomeStateCommand']]],
- ['_7egenotypelikelihoodcalculator_11567',['~GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html#a295ae8723775d0481023badde359d44c',1,'vg::GenotypeLikelihoodCalculator']]],
- ['_7egenotypepriorcalculator_11568',['~GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html#a63a28c3dff800ddc5ee37efcd836ba4d',1,'vg::GenotypePriorCalculator']]],
- ['_7egfahandlegraph_11569',['~GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html#aeaa72881401798c61af748a47bc4746e',1,'vg::GFAHandleGraph']]],
- ['_7egffreader_11570',['~GFFReader',['../classvg_1_1GFFReader.html#ac13f3d71875c489d9cc9a400d04d6e8e',1,'vg::GFFReader']]],
- ['_7egffrecord_11571',['~GFFRecord',['../structvg_1_1GFFRecord.html#af031304f06fc3a9bdb1f4e7b81695f1a',1,'vg::GFFRecord']]],
- ['_7egraphcaller_11572',['~GraphCaller',['../classvg_1_1GraphCaller.html#a443486cd8ab78a5392b5ed47506ca4c4',1,'vg::GraphCaller']]],
- ['_7egreedymindistanceclusterer_11573',['~GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html#a9d51c4982f45dda3d6da98f182969c6b',1,'vg::GreedyMinDistanceClusterer']]],
- ['_7egroupedoptiongroup_11574',['~GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a03413226481dddd57ccb32b1aa4ef94c',1,'vg::subcommand::GroupedOptionGroup']]],
- ['_7egsswaligner_11575',['~GSSWAligner',['../classvg_1_1GSSWAligner.html#a7a80ce643da0316c9151fab19e8e8581',1,'vg::GSSWAligner']]],
- ['_7ehandlegraph_11576',['~HandleGraph',['../classhandlegraph_1_1HandleGraph.html#a24fb796441c9ad8c870fdb716a82b305',1,'handlegraph::HandleGraph']]],
- ['_7ehandlegraphsnarlfinder_11577',['~HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html#a01f84699fe59b5d360df0ef4a671edb2',1,'vg::HandleGraphSnarlFinder']]],
- ['_7ehandler_11578',['~Handler',['../structvg_1_1temp__file_1_1Handler.html#abefd598acc672c960d80c70fa53c5476',1,'vg::temp_file::Handler::~Handler()'],['../structxg_1_1temp__file_1_1Handler.html#a6a4006456b42c1507d5d3505a8aa93a2',1,'xg::temp_file::Handler::~Handler()']]],
- ['_7ehaplo_5fdp_5fcolumn_11579',['~haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html#a179bfa823f2329b2500fb948bfff30ca',1,'haplo::haplo_DP_column']]],
- ['_7ehaplotype_11580',['~Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a29c3049eebafef23e3ec539093ffe9ce',1,'vg::PhasedGenome::Haplotype']]],
- ['_7ehaplotypenode_11581',['~HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a4e012749eab6e610da87b54036717ec5',1,'vg::PhasedGenome::HaplotypeNode']]],
- ['_7ehitedge_11582',['~HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html#ae1edc6409a97d72b9ae873d4e74d6721',1,'vg::MEMClusterer::HitEdge']]],
- ['_7ehitnode_11583',['~HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html#af253bd2d33cba3d97a13a9a4159c4f41',1,'vg::MEMClusterer::HitNode']]],
- ['_7ehtsalignmentemitter_11584',['~HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html#ab2914f2bdd3ecf8cd230e30479675304',1,'vg::HTSAlignmentEmitter']]],
- ['_7ehtswriter_11585',['~HTSWriter',['../classvg_1_1HTSWriter.html#a8be4096c91ac54b168828071b814104d',1,'vg::HTSWriter']]],
- ['_7eidentityoverlay_11586',['~IdentityOverlay',['../classvg_1_1IdentityOverlay.html#a15e797a8861789f9d2f0ec0f0ca57032',1,'vg::IdentityOverlay']]],
- ['_7eincrementalsubgraph_11587',['~IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html#a330ad1c9229ac053777528cb79efad3e',1,'vg::IncrementalSubgraph']]],
- ['_7eindexingplan_11588',['~IndexingPlan',['../classvg_1_1IndexingPlan.html#adf7d45d963ee4dc8a4ca8c3c3d3ca3ee',1,'vg::IndexingPlan']]],
- ['_7eindexregistry_11589',['~IndexRegistry',['../classvg_1_1IndexRegistry.html#a95e5aa1a57680dd60b599d3735145ac4',1,'vg::IndexRegistry']]],
- ['_7einserthaplotypecommand_11590',['~InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html#a173157b02306f85eb55291107367602e',1,'vg::InsertHaplotypeCommand']]],
- ['_7eiterator_11591',['~iterator',['../classvg_1_1PhasedGenome_1_1iterator.html#a49c0df47c5f5eb7afc45a2978f5dc497',1,'vg::PhasedGenome::iterator::~iterator()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a578e1ae4eb29377b05133e390ad1d4c3',1,'handlegraph::PathForEachSocket::iterator::~iterator()']]],
- ['_7ej2pb_5ferror_11592',['~j2pb_error',['../classj2pb__error.html#a4bf7997e2520c68a3861f9f105132510',1,'j2pb_error']]],
- ['_7ejobschedule_11593',['~JobSchedule',['../classvg_1_1JobSchedule.html#a2c08f9b4c3db46f28c2a44d23524b9aa',1,'vg::JobSchedule']]],
- ['_7ejoinedsplicegraph_11594',['~JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html#a1998a6854f0f56b1fc69476f09ebb5c7',1,'vg::JoinedSpliceGraph']]],
- ['_7ejson_5fautoptr_11595',['~json_autoptr',['../structjson__autoptr.html#a90ed076495793f454cea2f2e8ba3738b',1,'json_autoptr']]],
- ['_7ejsonstreamhelper_11596',['~JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html#a0cb9dd04575adfdb70b5a454a65871a7',1,'vg::io::JSONStreamHelper']]],
- ['_7elegacycaller_11597',['~LegacyCaller',['../classvg_1_1LegacyCaller.html#a10147f341d558b896d91c2180f0361d8',1,'vg::LegacyCaller']]],
- ['_7elinear_5fhaplo_5fstructure_11598',['~linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html#a11b487a3f7b503ed282cd1cfee5ae2f3',1,'haplo::linear_haplo_structure']]],
- ['_7emapper_11599',['~Mapper',['../classvg_1_1Mapper.html#a285dd133a8540553f671b7eac33f6ca0',1,'vg::Mapper']]],
- ['_7emasker_11600',['~Masker',['../classvg_1_1Masker.html#ab8ef1024fde833626e6ef18fbb6fdb9d',1,'vg::Masker']]],
- ['_7emcmccaller_11601',['~MCMCCaller',['../classvg_1_1MCMCCaller.html#a1bd5d1d33ec02a9b5dabcb882996d964',1,'vg::MCMCCaller']]],
- ['_7ememchainmodelvertex_11602',['~MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html#accc20533b5065e34208355797f373a04',1,'vg::MEMChainModelVertex']]],
- ['_7ememclusterer_11603',['~MEMClusterer',['../classvg_1_1MEMClusterer.html#a86a3a3ccd7e416a727118f7aa763db18',1,'vg::MEMClusterer']]],
- ['_7ememoizinggraph_11604',['~MemoizingGraph',['../classvg_1_1MemoizingGraph.html#a7b70d3665f07afcce593013fd4d27170',1,'vg::MemoizingGraph']]],
- ['_7emessageemitter_11605',['~MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html#ae9fa66759101257b58f38ec4f54dabfa',1,'vg::io::MessageEmitter']]],
- ['_7emindistanceclusterer_11606',['~MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html#a92349c1915d207de2c5d3b01df53ce37',1,'vg::MinDistanceClusterer']]],
- ['_7emsaconverter_11607',['~MSAConverter',['../classvg_1_1MSAConverter.html#a3b731a1e51d01aecae26e789fe06b788',1,'vg::MSAConverter']]],
- ['_7emultipath_5falignment_5ft_11608',['~multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html#a732686b480b69ea1a261004c308510e0',1,'vg::multipath_alignment_t']]],
- ['_7emultipathalignmentemitter_11609',['~MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html#a18c81d0a9a77020adca05f0bc5b7fbcb',1,'vg::MultipathAlignmentEmitter']]],
- ['_7emultipathalignmentgraph_11610',['~MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html#a85e2932360f805d5c6353cd25e377e5d',1,'vg::MultipathAlignmentGraph']]],
- ['_7emultipathmapper_11611',['~MultipathMapper',['../classvg_1_1MultipathMapper.html#aae4b40b1c3c0668b884ae3247779f188',1,'vg::MultipathMapper']]],
- ['_7emutablehandlegraph_11612',['~MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html#ace50b9ed07cbbe94f7da963ff02d4141',1,'handlegraph::MutableHandleGraph']]],
- ['_7emutablepathdeletablehandlegraph_11613',['~MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html#a2d936ce540af42363619ebb77c60a4ff',1,'handlegraph::MutablePathDeletableHandleGraph']]],
- ['_7emutablepathhandlegraph_11614',['~MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html#a3b9b032ce45f87e1abd5c175db6f5275',1,'handlegraph::MutablePathHandleGraph']]],
- ['_7emutablepathmetadata_11615',['~MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html#a8be356ab572a35e496b6306a17db4a7e',1,'handlegraph::MutablePathMetadata']]],
- ['_7emutablepathmutablehandlegraph_11616',['~MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html#a55379ced0e4f2952ca3353c558affc44',1,'handlegraph::MutablePathMutableHandleGraph']]],
- ['_7enamednodebacktranslation_11617',['~NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html#ae9fb216bd267d21bf3879b4be822a855',1,'handlegraph::NamedNodeBackTranslation']]],
- ['_7enestedcachedpackedtraversalsupportfinder_11618',['~NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af533ff7a6df4501eedfb085e29ca58d6',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
- ['_7enestedflowcaller_11619',['~NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html#a715d0c0f7ccdca4c4162910ecd75e62e',1,'vg::NestedFlowCaller']]],
- ['_7enestedtraversalfinder_11620',['~NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html#a8ce9c736ca873d86fb63b84c7039dd70',1,'vg::NestedTraversalFinder']]],
- ['_7enullclusterer_11621',['~NullClusterer',['../classvg_1_1NullClusterer.html#a76fedb932d24bd5691d2b8c990abf221',1,'vg::NullClusterer']]],
- ['_7enullmaskinggraph_11622',['~NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html#a2423b2f9fd83988f10edcc70f9df4d51',1,'vg::NullMaskingGraph']]],
- ['_7eoption_11623',['~Option',['../classvg_1_1Option.html#a5e003513f76f5555d0c51b9e61389c22',1,'vg::Option::~Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#acce49922cb0d364a1d3ff4b2db78379a',1,'vg::Option< vector< Item >, Parser >::~Option()']]],
- ['_7eoptiongroup_11624',['~OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html#a8bcbcd0c78cef9c4837dbf77be4f5ad2',1,'vg::subcommand::OptionGroup']]],
- ['_7eoptioninterface_11625',['~OptionInterface',['../classvg_1_1OptionInterface.html#a064598bb6752f1e24c95a91e472448fe',1,'vg::OptionInterface']]],
- ['_7eorienteddistancemeasurer_11626',['~OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html#a5352a20621ca5018d567728fac12a44f',1,'vg::OrientedDistanceMeasurer']]],
- ['_7epackedtraversalsupportfinder_11627',['~PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html#ab5d69efb780653096e7ab6b810db3dcb',1,'vg::PackedTraversalSupportFinder']]],
- ['_7epacker_11628',['~Packer',['../classvg_1_1Packer.html#a771083c86ded80dc5076bc9112a463d7',1,'vg::Packer']]],
- ['_7epath_5fmapping_5ft_11629',['~path_mapping_t',['../classvg_1_1path__mapping__t.html#aa7a0aa3c177f2dff3cf364b78013deac',1,'vg::path_mapping_t']]],
- ['_7epath_5ft_11630',['~path_t',['../classvg_1_1path__t.html#a91a944b05194ede0711911b9235e88d4',1,'vg::path_t']]],
- ['_7epathbasedtraversalfinder_11631',['~PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html#ad60a772a43a10e819d2b2655f1602762',1,'vg::PathBasedTraversalFinder']]],
- ['_7epathchunker_11632',['~PathChunker',['../classvg_1_1PathChunker.html#a49b9500998c8e6faace1206d587ac67d',1,'vg::PathChunker']]],
- ['_7epathforeachsocket_11633',['~PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html#a982a69f458a874ddd5e5feaf61d950f8',1,'handlegraph::PathForEachSocket']]],
- ['_7epathhandlegraph_11634',['~PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html#a49fe5658c5ef27e1d7aba69cd3d7159b',1,'handlegraph::PathHandleGraph']]],
- ['_7epathmetadata_11635',['~PathMetadata',['../classhandlegraph_1_1PathMetadata.html#aee403b8c1269b11877df67ff42b759f3',1,'handlegraph::PathMetadata']]],
- ['_7epathorienteddistancemeasurer_11636',['~PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6ae7fe802887b8e9c1dbd4ab0106a2e3',1,'vg::PathOrientedDistanceMeasurer']]],
- ['_7epathpositionhandlegraph_11637',['~PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html#a2352c6463ffe0b4a279c05a223d8da24',1,'handlegraph::PathPositionHandleGraph']]],
- ['_7epathrestrictedtraversalfinder_11638',['~PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html#a63b53f979b357845cb6a73a9008f4614',1,'vg::PathRestrictedTraversalFinder']]],
- ['_7epathsubgraphoverlay_11639',['~PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html#a2e4550c165f6d744146feff76a7aad89',1,'vg::PathSubgraphOverlay']]],
- ['_7ephasedgenome_11640',['~PhasedGenome',['../classvg_1_1PhasedGenome.html#a08609371573b24264b5f5e14af6d0139',1,'vg::PhasedGenome']]],
- ['_7epictographs_11641',['~Pictographs',['../classvg_1_1Pictographs.html#a0889bee7fb20ed90c52442a614a1648b',1,'vg::Pictographs']]],
- ['_7epoissoncallinfo_11642',['~PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a066ee903413c3c1959ff3de6feeecf5e',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['_7epoissonsupportsnarlcaller_11643',['~PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html#a5bef85e69a8ae047888c4fb72356f215',1,'vg::PoissonSupportSnarlCaller']]],
- ['_7eposition_5ft_11644',['~position_t',['../classvg_1_1position__t.html#a5746bca2e97a32c1f6e941c4775a511f',1,'vg::position_t']]],
- ['_7eproblemdumpexplainer_11645',['~ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html#a649d96d5df14e3276d0b5ef389281fdb',1,'vg::ProblemDumpExplainer']]],
- ['_7eprotobufemitter_11646',['~ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html#ab1994a31484b9a52710a38315adb2bcc',1,'vg::io::ProtobufEmitter']]],
- ['_7equaladjaligner_11647',['~QualAdjAligner',['../classvg_1_1QualAdjAligner.html#a2fb50e162cf507b6feca91f4294c4e1a',1,'vg::QualAdjAligner']]],
- ['_7equaladjxdropaligner_11648',['~QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html#adcaec532a190e022823a64ea56c47d3a',1,'vg::QualAdjXdropAligner']]],
- ['_7erangeargspec_11649',['~RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html#a80afea8df9e2fb8f5b29996e361752f5',1,'vg::subcommand::RangeArgSpec']]],
- ['_7eratiosupportsnarlcaller_11650',['~RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html#a791e985fb18b5fdd13056d609d793eff',1,'vg::RatioSupportSnarlCaller']]],
- ['_7ereadrestrictedtraversalfinder_11651',['~ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html#a8753fffb0d164d41a61de388a148448f',1,'vg::ReadRestrictedTraversalFinder']]],
- ['_7eregionexpander_11652',['~RegionExpander',['../classvg_1_1RegionExpander.html#abf8aece5a42cfe0d0225d04e0fc7836f',1,'vg::RegionExpander']]],
- ['_7ereplacelocalhaplotypecommand_11653',['~ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html#aecd5ab146c17e1e5146cbf6e57c2d3a7',1,'vg::ReplaceLocalHaplotypeCommand']]],
- ['_7ereplacesnarlhaplotypecommand_11654',['~ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a91ce2448ef86a1e7fcb78995b39cbf1a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
- ['_7erepresentativetraversalfinder_11655',['~RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html#ae0f2414849b616e9a027ac675caf462c',1,'vg::RepresentativeTraversalFinder']]],
- ['_7ereversegraph_11656',['~ReverseGraph',['../classvg_1_1ReverseGraph.html#a202906f97f8aa781ed4a7c6ef41cbe85',1,'vg::ReverseGraph']]],
- ['_7erewindplanexception_11657',['~RewindPlanException',['../classvg_1_1RewindPlanException.html#a86b60f1af33c65e62f3cf8f6edffaf67',1,'vg::RewindPlanException']]],
- ['_7escoreprovider_11658',['~ScoreProvider',['../classhaplo_1_1ScoreProvider.html#adc52c96c8d122268f57187010a3eef7f',1,'haplo::ScoreProvider']]],
- ['_7eserializable_11659',['~Serializable',['../classhandlegraph_1_1Serializable.html#ade5618a9c7a93b72550fdbb06ca41518',1,'handlegraph::Serializable']]],
- ['_7esimpleconsistencycalculator_11660',['~SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html#a1b254ae9c4be5dc930b1593bd65fe2a9',1,'vg::SimpleConsistencyCalculator']]],
- ['_7esimpletraversalsupportcalculator_11661',['~SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html#a8b886a386884b9dd13ef5eaeb7eee2fc',1,'vg::SimpleTraversalSupportCalculator']]],
- ['_7esizelimitexceededexception_11662',['~SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html#aeedf0b21d4c09460fb4926ac98fae907',1,'vg::SizeLimitExceededException']]],
- ['_7esmallbitset_11663',['~SmallBitset',['../classvg_1_1SmallBitset.html#ab480cbcce093b352a39bba8404d6ea27',1,'vg::SmallBitset']]],
- ['_7esnarlcaller_11664',['~SnarlCaller',['../classvg_1_1SnarlCaller.html#abda61a55c21f1473db0443293144c96d',1,'vg::SnarlCaller']]],
- ['_7esnarldecomposition_11665',['~SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html#ad5055e48b8816d5785052da55e6da996',1,'handlegraph::SnarlDecomposition']]],
- ['_7esnarlfinder_11666',['~SnarlFinder',['../classvg_1_1SnarlFinder.html#aa2511b024b03f3902ac149f3d6a055d5',1,'vg::SnarlFinder']]],
- ['_7esnarlmanager_11667',['~SnarlManager',['../classvg_1_1SnarlManager.html#a3a6eb9b943f3e1b090e21f23dae5f8ea',1,'vg::SnarlManager']]],
- ['_7esnarlmindistance_11668',['~SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html#af2b84f7d4327621d3def1da80b2853e2',1,'vg::SnarlMinDistance']]],
- ['_7esnarlorienteddistancemeasurer_11669',['~SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#afba648bfa8f3712d2ed3fb698c36cdca',1,'vg::SnarlOrientedDistanceMeasurer']]],
- ['_7esparseunionfind_11670',['~SparseUnionFind',['../classvg_1_1SparseUnionFind.html#a1804e9081d4b8fb2ef37f61a119804aa',1,'vg::SparseUnionFind']]],
- ['_7esplicedhtsalignmentemitter_11671',['~SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a4ecdb4b35322bff73f961e934f4c53f5',1,'vg::SplicedHTSAlignmentEmitter']]],
- ['_7espliceregion_11672',['~SpliceRegion',['../classvg_1_1SpliceRegion.html#a8f4f2d7679069899606445ae1604f9c0',1,'vg::SpliceRegion']]],
- ['_7esswaligner_11673',['~SSWAligner',['../classvg_1_1SSWAligner.html#afccac3a7c1be69feb1602c30749b1b84',1,'vg::SSWAligner']]],
- ['_7estrandsplitgraph_11674',['~StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html#a4ab1bab60dfb53a4e6fd6f2f7efe7e58',1,'vg::StrandSplitGraph']]],
- ['_7estreammultiplexer_11675',['~StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html#ab59b05564e82666f5213863cb2d0af19',1,'vg::io::StreamMultiplexer']]],
- ['_7esubgraphoverlay_11676',['~SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html#ac39107fbe2937cefee3d7a97ba27278b',1,'vg::SubgraphOverlay']]],
- ['_7esubpath_5ft_11677',['~subpath_t',['../classvg_1_1subpath__t.html#a5b759f0b9b9eb1c91cc958ea7f217d73',1,'vg::subpath_t']]],
- ['_7esubpathoverlay_11678',['~SubpathOverlay',['../classvg_1_1SubpathOverlay.html#addf877952378e0897622236387dc4823',1,'vg::SubpathOverlay']]],
- ['_7esupportbasedsnarlcaller_11679',['~SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html#a1bc8a2019ce7e220dbee5b26c4b27211',1,'vg::SupportBasedSnarlCaller']]],
- ['_7esupportrestrictedtraversalfinder_11680',['~SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html#afc63ce9daf884e00c5946d0d133273bd',1,'vg::SupportRestrictedTraversalFinder']]],
- ['_7eswaphaplotypescommand_11681',['~SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html#a1c95200d197a7635ebd54facdf1b2257',1,'vg::SwapHaplotypesCommand']]],
- ['_7etargetvaluesearch_11682',['~TargetValueSearch',['../classvg_1_1TargetValueSearch.html#a11e6bc6d502a87f0bab3ef5cfa012eb6',1,'vg::TargetValueSearch']]],
- ['_7etickchainlink_11683',['~TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html#abe6fcaa01ec5b6b71aa6f956d6c968fd',1,'vg::subcommand::TickChainLink']]],
- ['_7etipanchoredmaxdistance_11684',['~TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html#a7a02421438454a8639035fdecbead5e6',1,'vg::TipAnchoredMaxDistance']]],
- ['_7etranscriptpath_11685',['~TranscriptPath',['../structvg_1_1TranscriptPath.html#a7684fbec1bec3a02319ff8d112f894ff',1,'vg::TranscriptPath']]],
- ['_7etraversalfinder_11686',['~TraversalFinder',['../classvg_1_1TraversalFinder.html#aa42ea2599b925f21244928ad5b997168',1,'vg::TraversalFinder']]],
- ['_7etraversalsupportcalculator_11687',['~TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html#acd55c7b07d365ae00206ac88bf1e3ff9',1,'vg::TraversalSupportCalculator']]],
- ['_7etraversalsupportfinder_11688',['~TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html#a86fe98aaabf74546462d2d52017f69a5',1,'vg::TraversalSupportFinder']]],
- ['_7etree_11689',['~Tree',['../structvg_1_1Tree.html#aa29f56c135efd59c283721181db4f27a',1,'vg::Tree']]],
- ['_7etreenode_11690',['~TreeNode',['../structvg_1_1TreeNode.html#abe3058472100249948412715677d2644',1,'vg::TreeNode']]],
- ['_7etriviallyserializable_11691',['~TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html#ae6c6c81c7b722686ed51bfbff3a2e442',1,'handlegraph::TriviallySerializable']]],
- ['_7etrivialtraversalfinder_11692',['~TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html#a95f1dc0e83e536f4ded43f35982420f3',1,'vg::TrivialTraversalFinder']]],
- ['_7etsvalignmentemitter_11693',['~TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a69a2f7650e4271c33985c5754f6b6f53',1,'vg::io::TSVAlignmentEmitter']]],
- ['_7etsvexplainer_11694',['~TSVExplainer',['../classvg_1_1TSVExplainer.html#ac7c5964711efd7f58c22d6aa9f07884c',1,'vg::TSVExplainer']]],
- ['_7etvsclusterer_11695',['~TVSClusterer',['../classvg_1_1TVSClusterer.html#ad0bd55ec4d0141dbd6b22cab86e2af85',1,'vg::TVSClusterer']]],
- ['_7evaluation_11696',['~Valuation',['../structvg_1_1subcommand_1_1Valuation.html#a299acc17034d0fc8b6107bca001ba49e',1,'vg::subcommand::Valuation']]],
- ['_7evalueargspec_11697',['~ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a97f01678f8355598db5bc6a34a8515af',1,'vg::subcommand::ValueArgSpec']]],
- ['_7evcfgenotyper_11698',['~VCFGenotyper',['../classvg_1_1VCFGenotyper.html#a91aad8f951949331a1753f7e07588381',1,'vg::VCFGenotyper']]],
- ['_7evcfoutputcaller_11699',['~VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html#a61c1441b882dbaaed73154aeae8109d6',1,'vg::VCFOutputCaller']]],
- ['_7evcfrecordconverter_11700',['~VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html#a49013729b000b0fd7c4a380c7ca79da6',1,'vg::VcfRecordConverter']]],
- ['_7evcfrecordfilter_11701',['~VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html#a11f60090fa5e3185bb42ece601457889',1,'vg::VcfRecordFilter']]],
- ['_7evcftraversalfinder_11702',['~VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html#a574fb1c2bdcf2752e75626f4c21bc90c',1,'vg::VCFTraversalFinder']]],
- ['_7evectorizablehandlegraph_11703',['~VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html#ae5986cf718d8f9d98b20f7e819db43f3',1,'handlegraph::VectorizableHandleGraph']]],
- ['_7evectorizer_11704',['~Vectorizer',['../classVectorizer.html#a9e7ee4e6f8a517a85b6e9ed785958104',1,'Vectorizer']]],
- ['_7evectorview_11705',['~VectorView',['../structvg_1_1VectorView.html#af9ec1a56ae0a3d357ccdc67f0958da0c',1,'vg::VectorView']]],
- ['_7evg_11706',['~VG',['../classvg_1_1VG.html#a7513ddb88aeb58bd85a810c2a2ccdf67',1,'vg::VG']]],
- ['_7evgalignmentemitter_11707',['~VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a55e34fab0faf2988c90105e10b33c727',1,'vg::io::VGAlignmentEmitter']]],
- ['_7eviz_11708',['~Viz',['../classvg_1_1Viz.html#ab63af6e73d13224a8a96f0d776cfd248',1,'vg::Viz']]],
- ['_7ewatchdog_11709',['~Watchdog',['../classvg_1_1Watchdog.html#a58772622205b1e7c103612e518a6c995',1,'vg::Watchdog']]],
- ['_7exdropaligner_11710',['~XdropAligner',['../classvg_1_1XdropAligner.html#aaa342dfcc4afb1448b98857fd216044a',1,'vg::XdropAligner']]],
- ['_7exg_11711',['~XG',['../classxg_1_1XG.html#a1670ddfeb5c9c5f04cd14fe725eb0cfd',1,'xg::XG']]],
- ['_7exgpath_11712',['~XGPath',['../classxg_1_1XGPath.html#a831bd85ed9f0db9154a1a8e3b0ad69fd',1,'xg::XGPath']]]
+ ['_7eabstractreadsampler_11519',['~AbstractReadSampler',['../classvg_1_1AbstractReadSampler.html#aab2237075e873b1fac2b9d927835dd5d',1,'vg::AbstractReadSampler']]],
+ ['_7ealiasgraph_11520',['~AliasGraph',['../classvg_1_1AliasGraph.html#aa6557ac096d2a238b4bde66341fa4bbf',1,'vg::AliasGraph']]],
+ ['_7ealigner_11521',['~Aligner',['../classvg_1_1Aligner.html#ab652846ac99c793321f513e80b3567e7',1,'vg::Aligner']]],
+ ['_7ealignmentchainmodelvertex_11522',['~AlignmentChainModelVertex',['../classvg_1_1AlignmentChainModelVertex.html#a2956b8c27f6438dda8d392c47c29da59',1,'vg::AlignmentChainModelVertex']]],
+ ['_7ealignmentemitter_11523',['~AlignmentEmitter',['../classvg_1_1io_1_1AlignmentEmitter.html#a8a2ed8eecf9bc49b0c82e0276a8c3ecf',1,'vg::io::AlignmentEmitter']]],
+ ['_7ealttracebackstack_11524',['~AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a7271beafb4fd9d7d993e7225d0289ee8',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['_7eappendhaplotypecommand_11525',['~AppendHaplotypeCommand',['../structvg_1_1AppendHaplotypeCommand.html#a5890b1f7b3374109bb8326372f3dcd18',1,'vg::AppendHaplotypeCommand']]],
+ ['_7eargspec_11526',['~ArgSpec',['../structvg_1_1subcommand_1_1ArgSpec.html#a85d84f459627dc7d5d476ef600cd4eaa',1,'vg::subcommand::ArgSpec']]],
+ ['_7ebabuilder_11527',['~BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#af4852751e6f009ed647f81926b8c6ac0',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['_7ebamatrix_11528',['~BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac174727f3eb7d040f75bbb638e3ef585',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['_7ebandedglobalaligner_11529',['~BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html#ac211fadde52f8cc1312fddb585c021b0',1,'vg::BandedGlobalAligner']]],
+ ['_7ebaseargspec_11530',['~BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a6324c7d0c79aece0d2cf73a9bb385377',1,'vg::subcommand::BaseArgSpec']]],
+ ['_7ebaseoption_11531',['~BaseOption',['../classvg_1_1BaseOption.html#a877daeaa51e8978827609c35bffa6f7d',1,'vg::BaseOption']]],
+ ['_7ebaseoptiongroup_11532',['~BaseOptionGroup',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a65cfafee0415b04533cece4cde5c9b8a',1,'vg::subcommand::BaseOptionGroup']]],
+ ['_7ebasevaluation_11533',['~BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html#af8bbcfd7d30f6c358ba91db3be2a7084',1,'vg::subcommand::BaseValuation']]],
+ ['_7eblockedgzipinputstream_11534',['~BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a56990712e743be20a39e760309a8934c',1,'vg::io::BlockedGzipInputStream']]],
+ ['_7eblockedgzipoutputstream_11535',['~BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aaac9002de6d983cb46a36b44620448bb',1,'vg::io::BlockedGzipOutputStream']]],
+ ['_7ebuildablesnarldecomposition_11536',['~BuildableSnarlDecomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a04eec535a4ad69c3d57a7733cbb56f23',1,'handlegraph::BuildableSnarlDecomposition']]],
+ ['_7ecachedpackedtraversalsupportfinder_11537',['~CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html#ae90902c6346948c1b2ab45dd389b4014',1,'vg::CachedPackedTraversalSupportFinder']]],
+ ['_7ecallinfo_11538',['~CallInfo',['../structvg_1_1SnarlCaller_1_1CallInfo.html#a596d13cd23b7d5dd9a24bdea876a286d',1,'vg::SnarlCaller::CallInfo']]],
+ ['_7ecolors_11539',['~Colors',['../classvg_1_1Colors.html#ac08aaa9a815d639d327c3ea80b97ed2b',1,'vg::Colors']]],
+ ['_7ecompletedtranscriptpath_11540',['~CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html#a885c00ed2c371cddfe7a9a78c00dcd94',1,'vg::CompletedTranscriptPath']]],
+ ['_7ecomponentmindistanceclusterer_11541',['~ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html#aa13390387862e6477651a627db8b36b3',1,'vg::ComponentMinDistanceClusterer']]],
+ ['_7econnection_5ft_11542',['~connection_t',['../classvg_1_1connection__t.html#ac3664dfd1f422b7a88b2760e9a4ee83d',1,'vg::connection_t']]],
+ ['_7econsistencycalculator_11543',['~ConsistencyCalculator',['../classvg_1_1ConsistencyCalculator.html#afb05d4ab7a962df47c62c408d0154ba0',1,'vg::ConsistencyCalculator']]],
+ ['_7edagifiedgraph_11544',['~DagifiedGraph',['../classvg_1_1DagifiedGraph.html#acb7989cf7dcc34da6fd11228d36321f7',1,'vg::DagifiedGraph']]],
+ ['_7edeconstructor_11545',['~Deconstructor',['../classvg_1_1Deconstructor.html#a875c8006f289ad46470c05c8808bdd73',1,'vg::Deconstructor']]],
+ ['_7edeflection_11546',['~Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#af4deb014af190975b2e7fe3540f6f461',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['_7edeletablehandlegraph_11547',['~DeletableHandleGraph',['../classhandlegraph_1_1DeletableHandleGraph.html#a62ed805e124ceb05cfa98d4e631a9ebd',1,'handlegraph::DeletableHandleGraph']]],
+ ['_7edeletehaplotypecommand_11548',['~DeleteHaplotypeCommand',['../structvg_1_1DeleteHaplotypeCommand.html#a2049b0eb4e4cf76d42b26fb9b0ecb659',1,'vg::DeleteHaplotypeCommand']]],
+ ['_7edeletionaligner_11549',['~DeletionAligner',['../classvg_1_1DeletionAligner.html#a797ac3036e59d5086c0822b90302dd14',1,'vg::DeletionAligner']]],
+ ['_7ediagramexplainer_11550',['~DiagramExplainer',['../classvg_1_1DiagramExplainer.html#aacac728ac8712e2d1f803c0735c34990',1,'vg::DiagramExplainer']]],
+ ['_7edinucleotidemachine_11551',['~DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html#a927431a787e6f77549850cea55d883b0',1,'vg::DinucleotideMachine']]],
+ ['_7edistanceheuristic_11552',['~DistanceHeuristic',['../classvg_1_1DistanceHeuristic.html#abca20b0fc239abad09fabb6d6bad0b50',1,'vg::DistanceHeuristic']]],
+ ['_7edozeuinterface_11553',['~DozeuInterface',['../classvg_1_1DozeuInterface.html#a0ac4d30c781e2a2278986ecbb84a34a6',1,'vg::DozeuInterface']]],
+ ['_7edozeupinningoverlay_11554',['~DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html#a6fe397bf132beeabd0ed7f830b1f9994',1,'vg::DozeuPinningOverlay']]],
+ ['_7edpscorecomparator_11555',['~DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a02c3e3552497f6425a1f3d14682c1d06',1,'vg::MEMClusterer::DPScoreComparator']]],
+ ['_7eedit_5ft_11556',['~edit_t',['../classvg_1_1edit__t.html#a43201af48ee260fa83a5bde0ed75a978',1,'vg::edit_t']]],
+ ['_7eeditedtranscriptpath_11557',['~EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html#aba2f28b19414c8c3795e60e76a07f807',1,'vg::EditedTranscriptPath']]],
+ ['_7eexhaustivetraversalfinder_11558',['~ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html#a7586c1b256f63d9e4295a9f1011b921a',1,'vg::ExhaustiveTraversalFinder']]],
+ ['_7eexpandingoverlaygraph_11559',['~ExpandingOverlayGraph',['../classhandlegraph_1_1ExpandingOverlayGraph.html#a9d7cac3cf3b289fe1980d0575e70be72',1,'handlegraph::ExpandingOverlayGraph']]],
+ ['_7eexplainer_11560',['~Explainer',['../classvg_1_1Explainer.html#a68991032a4a7fed25227a884f7f76a2a',1,'vg::Explainer']]],
+ ['_7efilter_11561',['~Filter',['../classvg_1_1Filter.html#a09073f3ae2d26bc61cf639dfc4072745',1,'vg::Filter']]],
+ ['_7efixedgenotypepriorcalculator_11562',['~FixedGenotypePriorCalculator',['../classvg_1_1FixedGenotypePriorCalculator.html#a4adc4bf44587b687076826dffc91ccf0',1,'vg::FixedGenotypePriorCalculator']]],
+ ['_7eflagargspec_11563',['~FlagArgSpec',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a7988d073aa24da829c03c9d68ae651f9',1,'vg::subcommand::FlagArgSpec']]],
+ ['_7eflatfilebacktranslation_11564',['~FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html#a4330bd5f76951158a1ea50755b43293d',1,'vg::FlatFileBackTranslation']]],
+ ['_7eflowcaller_11565',['~FlowCaller',['../classvg_1_1FlowCaller.html#a6fc652c91844cba402eb9e143883eefa',1,'vg::FlowCaller']]],
+ ['_7efragmentlengthdistribution_11566',['~FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html#a5ca105be9aca035e59985092d1a6aa79',1,'vg::FragmentLengthDistribution']]],
+ ['_7egafalignmentemitter_11567',['~GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html#ab8c76602efdaadba7319ca5103bc9107',1,'vg::io::GafAlignmentEmitter']]],
+ ['_7egafoutputcaller_11568',['~GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html#af275fa29f22a94c9c4180280675a160e',1,'vg::GAFOutputCaller']]],
+ ['_7egbwttraversalfinder_11569',['~GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html#aaf4b52f7a7807922daa514df94235a3a',1,'vg::GBWTTraversalFinder']]],
+ ['_7egenomestatecommand_11570',['~GenomeStateCommand',['../structvg_1_1GenomeStateCommand.html#a951ebc208c74b7ec323de6f517d02527',1,'vg::GenomeStateCommand']]],
+ ['_7egenotypelikelihoodcalculator_11571',['~GenotypeLikelihoodCalculator',['../classvg_1_1GenotypeLikelihoodCalculator.html#a295ae8723775d0481023badde359d44c',1,'vg::GenotypeLikelihoodCalculator']]],
+ ['_7egenotypepriorcalculator_11572',['~GenotypePriorCalculator',['../classvg_1_1GenotypePriorCalculator.html#a63a28c3dff800ddc5ee37efcd836ba4d',1,'vg::GenotypePriorCalculator']]],
+ ['_7egfahandlegraph_11573',['~GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html#aeaa72881401798c61af748a47bc4746e',1,'vg::GFAHandleGraph']]],
+ ['_7egffreader_11574',['~GFFReader',['../classvg_1_1GFFReader.html#ac13f3d71875c489d9cc9a400d04d6e8e',1,'vg::GFFReader']]],
+ ['_7egffrecord_11575',['~GFFRecord',['../structvg_1_1GFFRecord.html#af031304f06fc3a9bdb1f4e7b81695f1a',1,'vg::GFFRecord']]],
+ ['_7egraphcaller_11576',['~GraphCaller',['../classvg_1_1GraphCaller.html#a443486cd8ab78a5392b5ed47506ca4c4',1,'vg::GraphCaller']]],
+ ['_7egreedymindistanceclusterer_11577',['~GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html#a9d51c4982f45dda3d6da98f182969c6b',1,'vg::GreedyMinDistanceClusterer']]],
+ ['_7egroupedoptiongroup_11578',['~GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a03413226481dddd57ccb32b1aa4ef94c',1,'vg::subcommand::GroupedOptionGroup']]],
+ ['_7egsswaligner_11579',['~GSSWAligner',['../classvg_1_1GSSWAligner.html#a7a80ce643da0316c9151fab19e8e8581',1,'vg::GSSWAligner']]],
+ ['_7ehandlegraph_11580',['~HandleGraph',['../classhandlegraph_1_1HandleGraph.html#a24fb796441c9ad8c870fdb716a82b305',1,'handlegraph::HandleGraph']]],
+ ['_7ehandlegraphsnarlfinder_11581',['~HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html#a01f84699fe59b5d360df0ef4a671edb2',1,'vg::HandleGraphSnarlFinder']]],
+ ['_7ehandler_11582',['~Handler',['../structvg_1_1temp__file_1_1Handler.html#abefd598acc672c960d80c70fa53c5476',1,'vg::temp_file::Handler::~Handler()'],['../structxg_1_1temp__file_1_1Handler.html#a6a4006456b42c1507d5d3505a8aa93a2',1,'xg::temp_file::Handler::~Handler()']]],
+ ['_7ehaplo_5fdp_5fcolumn_11583',['~haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html#a179bfa823f2329b2500fb948bfff30ca',1,'haplo::haplo_DP_column']]],
+ ['_7ehaplotype_11584',['~Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a29c3049eebafef23e3ec539093ffe9ce',1,'vg::PhasedGenome::Haplotype']]],
+ ['_7ehaplotypenode_11585',['~HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a4e012749eab6e610da87b54036717ec5',1,'vg::PhasedGenome::HaplotypeNode']]],
+ ['_7ehitedge_11586',['~HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html#ae1edc6409a97d72b9ae873d4e74d6721',1,'vg::MEMClusterer::HitEdge']]],
+ ['_7ehitnode_11587',['~HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html#af253bd2d33cba3d97a13a9a4159c4f41',1,'vg::MEMClusterer::HitNode']]],
+ ['_7ehtsalignmentemitter_11588',['~HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html#ab2914f2bdd3ecf8cd230e30479675304',1,'vg::HTSAlignmentEmitter']]],
+ ['_7ehtswriter_11589',['~HTSWriter',['../classvg_1_1HTSWriter.html#a8be4096c91ac54b168828071b814104d',1,'vg::HTSWriter']]],
+ ['_7eidentityoverlay_11590',['~IdentityOverlay',['../classvg_1_1IdentityOverlay.html#a15e797a8861789f9d2f0ec0f0ca57032',1,'vg::IdentityOverlay']]],
+ ['_7eincrementalsubgraph_11591',['~IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html#a330ad1c9229ac053777528cb79efad3e',1,'vg::IncrementalSubgraph']]],
+ ['_7eindexingplan_11592',['~IndexingPlan',['../classvg_1_1IndexingPlan.html#adf7d45d963ee4dc8a4ca8c3c3d3ca3ee',1,'vg::IndexingPlan']]],
+ ['_7eindexregistry_11593',['~IndexRegistry',['../classvg_1_1IndexRegistry.html#a95e5aa1a57680dd60b599d3735145ac4',1,'vg::IndexRegistry']]],
+ ['_7einserthaplotypecommand_11594',['~InsertHaplotypeCommand',['../structvg_1_1InsertHaplotypeCommand.html#a173157b02306f85eb55291107367602e',1,'vg::InsertHaplotypeCommand']]],
+ ['_7eiterator_11595',['~iterator',['../classvg_1_1PhasedGenome_1_1iterator.html#a49c0df47c5f5eb7afc45a2978f5dc497',1,'vg::PhasedGenome::iterator::~iterator()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a578e1ae4eb29377b05133e390ad1d4c3',1,'handlegraph::PathForEachSocket::iterator::~iterator()']]],
+ ['_7ej2pb_5ferror_11596',['~j2pb_error',['../classj2pb__error.html#a4bf7997e2520c68a3861f9f105132510',1,'j2pb_error']]],
+ ['_7ejobschedule_11597',['~JobSchedule',['../classvg_1_1JobSchedule.html#a2c08f9b4c3db46f28c2a44d23524b9aa',1,'vg::JobSchedule']]],
+ ['_7ejoinedsplicegraph_11598',['~JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html#a1998a6854f0f56b1fc69476f09ebb5c7',1,'vg::JoinedSpliceGraph']]],
+ ['_7ejson_5fautoptr_11599',['~json_autoptr',['../structjson__autoptr.html#a90ed076495793f454cea2f2e8ba3738b',1,'json_autoptr']]],
+ ['_7ejsonstreamhelper_11600',['~JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html#a0cb9dd04575adfdb70b5a454a65871a7',1,'vg::io::JSONStreamHelper']]],
+ ['_7elegacycaller_11601',['~LegacyCaller',['../classvg_1_1LegacyCaller.html#a10147f341d558b896d91c2180f0361d8',1,'vg::LegacyCaller']]],
+ ['_7elinear_5fhaplo_5fstructure_11602',['~linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html#a11b487a3f7b503ed282cd1cfee5ae2f3',1,'haplo::linear_haplo_structure']]],
+ ['_7emapper_11603',['~Mapper',['../classvg_1_1Mapper.html#a285dd133a8540553f671b7eac33f6ca0',1,'vg::Mapper']]],
+ ['_7emasker_11604',['~Masker',['../classvg_1_1Masker.html#ab8ef1024fde833626e6ef18fbb6fdb9d',1,'vg::Masker']]],
+ ['_7emcmccaller_11605',['~MCMCCaller',['../classvg_1_1MCMCCaller.html#a1bd5d1d33ec02a9b5dabcb882996d964',1,'vg::MCMCCaller']]],
+ ['_7ememchainmodelvertex_11606',['~MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html#accc20533b5065e34208355797f373a04',1,'vg::MEMChainModelVertex']]],
+ ['_7ememclusterer_11607',['~MEMClusterer',['../classvg_1_1MEMClusterer.html#a86a3a3ccd7e416a727118f7aa763db18',1,'vg::MEMClusterer']]],
+ ['_7ememoizinggraph_11608',['~MemoizingGraph',['../classvg_1_1MemoizingGraph.html#a7b70d3665f07afcce593013fd4d27170',1,'vg::MemoizingGraph']]],
+ ['_7emessageemitter_11609',['~MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html#ae9fa66759101257b58f38ec4f54dabfa',1,'vg::io::MessageEmitter']]],
+ ['_7emindistanceclusterer_11610',['~MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html#a92349c1915d207de2c5d3b01df53ce37',1,'vg::MinDistanceClusterer']]],
+ ['_7emsaconverter_11611',['~MSAConverter',['../classvg_1_1MSAConverter.html#a3b731a1e51d01aecae26e789fe06b788',1,'vg::MSAConverter']]],
+ ['_7emultipath_5falignment_5ft_11612',['~multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html#a732686b480b69ea1a261004c308510e0',1,'vg::multipath_alignment_t']]],
+ ['_7emultipathalignmentemitter_11613',['~MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html#a18c81d0a9a77020adca05f0bc5b7fbcb',1,'vg::MultipathAlignmentEmitter']]],
+ ['_7emultipathalignmentgraph_11614',['~MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html#a85e2932360f805d5c6353cd25e377e5d',1,'vg::MultipathAlignmentGraph']]],
+ ['_7emultipathmapper_11615',['~MultipathMapper',['../classvg_1_1MultipathMapper.html#aae4b40b1c3c0668b884ae3247779f188',1,'vg::MultipathMapper']]],
+ ['_7emutablehandlegraph_11616',['~MutableHandleGraph',['../classhandlegraph_1_1MutableHandleGraph.html#ace50b9ed07cbbe94f7da963ff02d4141',1,'handlegraph::MutableHandleGraph']]],
+ ['_7emutablepathdeletablehandlegraph_11617',['~MutablePathDeletableHandleGraph',['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html#a2d936ce540af42363619ebb77c60a4ff',1,'handlegraph::MutablePathDeletableHandleGraph']]],
+ ['_7emutablepathhandlegraph_11618',['~MutablePathHandleGraph',['../classhandlegraph_1_1MutablePathHandleGraph.html#a3b9b032ce45f87e1abd5c175db6f5275',1,'handlegraph::MutablePathHandleGraph']]],
+ ['_7emutablepathmetadata_11619',['~MutablePathMetadata',['../classhandlegraph_1_1MutablePathMetadata.html#a8be356ab572a35e496b6306a17db4a7e',1,'handlegraph::MutablePathMetadata']]],
+ ['_7emutablepathmutablehandlegraph_11620',['~MutablePathMutableHandleGraph',['../classhandlegraph_1_1MutablePathMutableHandleGraph.html#a55379ced0e4f2952ca3353c558affc44',1,'handlegraph::MutablePathMutableHandleGraph']]],
+ ['_7enamednodebacktranslation_11621',['~NamedNodeBackTranslation',['../classhandlegraph_1_1NamedNodeBackTranslation.html#ae9fb216bd267d21bf3879b4be822a855',1,'handlegraph::NamedNodeBackTranslation']]],
+ ['_7enestedcachedpackedtraversalsupportfinder_11622',['~NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af533ff7a6df4501eedfb085e29ca58d6',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
+ ['_7enestedflowcaller_11623',['~NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html#a715d0c0f7ccdca4c4162910ecd75e62e',1,'vg::NestedFlowCaller']]],
+ ['_7enestedtraversalfinder_11624',['~NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html#a8ce9c736ca873d86fb63b84c7039dd70',1,'vg::NestedTraversalFinder']]],
+ ['_7enullclusterer_11625',['~NullClusterer',['../classvg_1_1NullClusterer.html#a76fedb932d24bd5691d2b8c990abf221',1,'vg::NullClusterer']]],
+ ['_7enullmaskinggraph_11626',['~NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html#a2423b2f9fd83988f10edcc70f9df4d51',1,'vg::NullMaskingGraph']]],
+ ['_7eoption_11627',['~Option',['../classvg_1_1Option.html#a5e003513f76f5555d0c51b9e61389c22',1,'vg::Option::~Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#acce49922cb0d364a1d3ff4b2db78379a',1,'vg::Option< vector< Item >, Parser >::~Option()']]],
+ ['_7eoptiongroup_11628',['~OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html#a8bcbcd0c78cef9c4837dbf77be4f5ad2',1,'vg::subcommand::OptionGroup']]],
+ ['_7eoptioninterface_11629',['~OptionInterface',['../classvg_1_1OptionInterface.html#a064598bb6752f1e24c95a91e472448fe',1,'vg::OptionInterface']]],
+ ['_7eorienteddistancemeasurer_11630',['~OrientedDistanceMeasurer',['../classvg_1_1OrientedDistanceMeasurer.html#a5352a20621ca5018d567728fac12a44f',1,'vg::OrientedDistanceMeasurer']]],
+ ['_7epackedtraversalsupportfinder_11631',['~PackedTraversalSupportFinder',['../classvg_1_1PackedTraversalSupportFinder.html#ab5d69efb780653096e7ab6b810db3dcb',1,'vg::PackedTraversalSupportFinder']]],
+ ['_7epacker_11632',['~Packer',['../classvg_1_1Packer.html#a771083c86ded80dc5076bc9112a463d7',1,'vg::Packer']]],
+ ['_7epath_5fmapping_5ft_11633',['~path_mapping_t',['../classvg_1_1path__mapping__t.html#aa7a0aa3c177f2dff3cf364b78013deac',1,'vg::path_mapping_t']]],
+ ['_7epath_5ft_11634',['~path_t',['../classvg_1_1path__t.html#a91a944b05194ede0711911b9235e88d4',1,'vg::path_t']]],
+ ['_7epathbasedtraversalfinder_11635',['~PathBasedTraversalFinder',['../classvg_1_1PathBasedTraversalFinder.html#ad60a772a43a10e819d2b2655f1602762',1,'vg::PathBasedTraversalFinder']]],
+ ['_7epathchunker_11636',['~PathChunker',['../classvg_1_1PathChunker.html#a49b9500998c8e6faace1206d587ac67d',1,'vg::PathChunker']]],
+ ['_7epathforeachsocket_11637',['~PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket.html#a982a69f458a874ddd5e5feaf61d950f8',1,'handlegraph::PathForEachSocket']]],
+ ['_7epathhandlegraph_11638',['~PathHandleGraph',['../classhandlegraph_1_1PathHandleGraph.html#a49fe5658c5ef27e1d7aba69cd3d7159b',1,'handlegraph::PathHandleGraph']]],
+ ['_7epathmetadata_11639',['~PathMetadata',['../classhandlegraph_1_1PathMetadata.html#aee403b8c1269b11877df67ff42b759f3',1,'handlegraph::PathMetadata']]],
+ ['_7epathorienteddistancemeasurer_11640',['~PathOrientedDistanceMeasurer',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6ae7fe802887b8e9c1dbd4ab0106a2e3',1,'vg::PathOrientedDistanceMeasurer']]],
+ ['_7epathpositionhandlegraph_11641',['~PathPositionHandleGraph',['../classhandlegraph_1_1PathPositionHandleGraph.html#a2352c6463ffe0b4a279c05a223d8da24',1,'handlegraph::PathPositionHandleGraph']]],
+ ['_7epathrestrictedtraversalfinder_11642',['~PathRestrictedTraversalFinder',['../classvg_1_1PathRestrictedTraversalFinder.html#a63b53f979b357845cb6a73a9008f4614',1,'vg::PathRestrictedTraversalFinder']]],
+ ['_7epathsubgraphoverlay_11643',['~PathSubgraphOverlay',['../classvg_1_1PathSubgraphOverlay.html#a2e4550c165f6d744146feff76a7aad89',1,'vg::PathSubgraphOverlay']]],
+ ['_7ephasedgenome_11644',['~PhasedGenome',['../classvg_1_1PhasedGenome.html#a08609371573b24264b5f5e14af6d0139',1,'vg::PhasedGenome']]],
+ ['_7epictographs_11645',['~Pictographs',['../classvg_1_1Pictographs.html#a0889bee7fb20ed90c52442a614a1648b',1,'vg::Pictographs']]],
+ ['_7epoissoncallinfo_11646',['~PoissonCallInfo',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a066ee903413c3c1959ff3de6feeecf5e',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['_7epoissonsupportsnarlcaller_11647',['~PoissonSupportSnarlCaller',['../classvg_1_1PoissonSupportSnarlCaller.html#a5bef85e69a8ae047888c4fb72356f215',1,'vg::PoissonSupportSnarlCaller']]],
+ ['_7eposition_5ft_11648',['~position_t',['../classvg_1_1position__t.html#a5746bca2e97a32c1f6e941c4775a511f',1,'vg::position_t']]],
+ ['_7eproblemdumpexplainer_11649',['~ProblemDumpExplainer',['../classvg_1_1ProblemDumpExplainer.html#a649d96d5df14e3276d0b5ef389281fdb',1,'vg::ProblemDumpExplainer']]],
+ ['_7eprotobufemitter_11650',['~ProtobufEmitter',['../classvg_1_1io_1_1ProtobufEmitter.html#ab1994a31484b9a52710a38315adb2bcc',1,'vg::io::ProtobufEmitter']]],
+ ['_7equaladjaligner_11651',['~QualAdjAligner',['../classvg_1_1QualAdjAligner.html#a2fb50e162cf507b6feca91f4294c4e1a',1,'vg::QualAdjAligner']]],
+ ['_7equaladjxdropaligner_11652',['~QualAdjXdropAligner',['../classvg_1_1QualAdjXdropAligner.html#adcaec532a190e022823a64ea56c47d3a',1,'vg::QualAdjXdropAligner']]],
+ ['_7erangeargspec_11653',['~RangeArgSpec',['../structvg_1_1subcommand_1_1RangeArgSpec.html#a80afea8df9e2fb8f5b29996e361752f5',1,'vg::subcommand::RangeArgSpec']]],
+ ['_7eratiosupportsnarlcaller_11654',['~RatioSupportSnarlCaller',['../classvg_1_1RatioSupportSnarlCaller.html#a791e985fb18b5fdd13056d609d793eff',1,'vg::RatioSupportSnarlCaller']]],
+ ['_7ereadrestrictedtraversalfinder_11655',['~ReadRestrictedTraversalFinder',['../classvg_1_1ReadRestrictedTraversalFinder.html#a8753fffb0d164d41a61de388a148448f',1,'vg::ReadRestrictedTraversalFinder']]],
+ ['_7eregionexpander_11656',['~RegionExpander',['../classvg_1_1RegionExpander.html#abf8aece5a42cfe0d0225d04e0fc7836f',1,'vg::RegionExpander']]],
+ ['_7ereplacelocalhaplotypecommand_11657',['~ReplaceLocalHaplotypeCommand',['../structvg_1_1ReplaceLocalHaplotypeCommand.html#aecd5ab146c17e1e5146cbf6e57c2d3a7',1,'vg::ReplaceLocalHaplotypeCommand']]],
+ ['_7ereplacesnarlhaplotypecommand_11658',['~ReplaceSnarlHaplotypeCommand',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a91ce2448ef86a1e7fcb78995b39cbf1a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
+ ['_7erepresentativetraversalfinder_11659',['~RepresentativeTraversalFinder',['../classvg_1_1RepresentativeTraversalFinder.html#ae0f2414849b616e9a027ac675caf462c',1,'vg::RepresentativeTraversalFinder']]],
+ ['_7ereversegraph_11660',['~ReverseGraph',['../classvg_1_1ReverseGraph.html#a202906f97f8aa781ed4a7c6ef41cbe85',1,'vg::ReverseGraph']]],
+ ['_7erewindplanexception_11661',['~RewindPlanException',['../classvg_1_1RewindPlanException.html#a86b60f1af33c65e62f3cf8f6edffaf67',1,'vg::RewindPlanException']]],
+ ['_7escoreprovider_11662',['~ScoreProvider',['../classhaplo_1_1ScoreProvider.html#adc52c96c8d122268f57187010a3eef7f',1,'haplo::ScoreProvider']]],
+ ['_7eserializable_11663',['~Serializable',['../classhandlegraph_1_1Serializable.html#ade5618a9c7a93b72550fdbb06ca41518',1,'handlegraph::Serializable']]],
+ ['_7esimpleconsistencycalculator_11664',['~SimpleConsistencyCalculator',['../classvg_1_1SimpleConsistencyCalculator.html#a1b254ae9c4be5dc930b1593bd65fe2a9',1,'vg::SimpleConsistencyCalculator']]],
+ ['_7esimpletraversalsupportcalculator_11665',['~SimpleTraversalSupportCalculator',['../classvg_1_1SimpleTraversalSupportCalculator.html#a8b886a386884b9dd13ef5eaeb7eee2fc',1,'vg::SimpleTraversalSupportCalculator']]],
+ ['_7esizelimitexceededexception_11666',['~SizeLimitExceededException',['../classvg_1_1SizeLimitExceededException.html#aeedf0b21d4c09460fb4926ac98fae907',1,'vg::SizeLimitExceededException']]],
+ ['_7esmallbitset_11667',['~SmallBitset',['../classvg_1_1SmallBitset.html#ab480cbcce093b352a39bba8404d6ea27',1,'vg::SmallBitset']]],
+ ['_7esnarlcaller_11668',['~SnarlCaller',['../classvg_1_1SnarlCaller.html#abda61a55c21f1473db0443293144c96d',1,'vg::SnarlCaller']]],
+ ['_7esnarldecomposition_11669',['~SnarlDecomposition',['../classhandlegraph_1_1SnarlDecomposition.html#ad5055e48b8816d5785052da55e6da996',1,'handlegraph::SnarlDecomposition']]],
+ ['_7esnarlfinder_11670',['~SnarlFinder',['../classvg_1_1SnarlFinder.html#aa2511b024b03f3902ac149f3d6a055d5',1,'vg::SnarlFinder']]],
+ ['_7esnarlmanager_11671',['~SnarlManager',['../classvg_1_1SnarlManager.html#a3a6eb9b943f3e1b090e21f23dae5f8ea',1,'vg::SnarlManager']]],
+ ['_7esnarlmindistance_11672',['~SnarlMinDistance',['../classvg_1_1SnarlMinDistance.html#af2b84f7d4327621d3def1da80b2853e2',1,'vg::SnarlMinDistance']]],
+ ['_7esnarlorienteddistancemeasurer_11673',['~SnarlOrientedDistanceMeasurer',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#afba648bfa8f3712d2ed3fb698c36cdca',1,'vg::SnarlOrientedDistanceMeasurer']]],
+ ['_7esparseunionfind_11674',['~SparseUnionFind',['../classvg_1_1SparseUnionFind.html#a1804e9081d4b8fb2ef37f61a119804aa',1,'vg::SparseUnionFind']]],
+ ['_7esplicedhtsalignmentemitter_11675',['~SplicedHTSAlignmentEmitter',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a4ecdb4b35322bff73f961e934f4c53f5',1,'vg::SplicedHTSAlignmentEmitter']]],
+ ['_7espliceregion_11676',['~SpliceRegion',['../classvg_1_1SpliceRegion.html#a8f4f2d7679069899606445ae1604f9c0',1,'vg::SpliceRegion']]],
+ ['_7esswaligner_11677',['~SSWAligner',['../classvg_1_1SSWAligner.html#afccac3a7c1be69feb1602c30749b1b84',1,'vg::SSWAligner']]],
+ ['_7estrandsplitgraph_11678',['~StrandSplitGraph',['../classvg_1_1StrandSplitGraph.html#a4ab1bab60dfb53a4e6fd6f2f7efe7e58',1,'vg::StrandSplitGraph']]],
+ ['_7estreammultiplexer_11679',['~StreamMultiplexer',['../classvg_1_1io_1_1StreamMultiplexer.html#ab59b05564e82666f5213863cb2d0af19',1,'vg::io::StreamMultiplexer']]],
+ ['_7esubgraphoverlay_11680',['~SubgraphOverlay',['../classvg_1_1SubgraphOverlay.html#ac39107fbe2937cefee3d7a97ba27278b',1,'vg::SubgraphOverlay']]],
+ ['_7esubpath_5ft_11681',['~subpath_t',['../classvg_1_1subpath__t.html#a5b759f0b9b9eb1c91cc958ea7f217d73',1,'vg::subpath_t']]],
+ ['_7esubpathoverlay_11682',['~SubpathOverlay',['../classvg_1_1SubpathOverlay.html#addf877952378e0897622236387dc4823',1,'vg::SubpathOverlay']]],
+ ['_7esupportbasedsnarlcaller_11683',['~SupportBasedSnarlCaller',['../classvg_1_1SupportBasedSnarlCaller.html#a1bc8a2019ce7e220dbee5b26c4b27211',1,'vg::SupportBasedSnarlCaller']]],
+ ['_7esupportrestrictedtraversalfinder_11684',['~SupportRestrictedTraversalFinder',['../classvg_1_1SupportRestrictedTraversalFinder.html#afc63ce9daf884e00c5946d0d133273bd',1,'vg::SupportRestrictedTraversalFinder']]],
+ ['_7eswaphaplotypescommand_11685',['~SwapHaplotypesCommand',['../structvg_1_1SwapHaplotypesCommand.html#a1c95200d197a7635ebd54facdf1b2257',1,'vg::SwapHaplotypesCommand']]],
+ ['_7etargetvaluesearch_11686',['~TargetValueSearch',['../classvg_1_1TargetValueSearch.html#a11e6bc6d502a87f0bab3ef5cfa012eb6',1,'vg::TargetValueSearch']]],
+ ['_7etickchainlink_11687',['~TickChainLink',['../structvg_1_1subcommand_1_1TickChainLink.html#abe6fcaa01ec5b6b71aa6f956d6c968fd',1,'vg::subcommand::TickChainLink']]],
+ ['_7etipanchoredmaxdistance_11688',['~TipAnchoredMaxDistance',['../classvg_1_1TipAnchoredMaxDistance.html#a7a02421438454a8639035fdecbead5e6',1,'vg::TipAnchoredMaxDistance']]],
+ ['_7etranscriptpath_11689',['~TranscriptPath',['../structvg_1_1TranscriptPath.html#a7684fbec1bec3a02319ff8d112f894ff',1,'vg::TranscriptPath']]],
+ ['_7etraversalfinder_11690',['~TraversalFinder',['../classvg_1_1TraversalFinder.html#aa42ea2599b925f21244928ad5b997168',1,'vg::TraversalFinder']]],
+ ['_7etraversalsupportcalculator_11691',['~TraversalSupportCalculator',['../classvg_1_1TraversalSupportCalculator.html#acd55c7b07d365ae00206ac88bf1e3ff9',1,'vg::TraversalSupportCalculator']]],
+ ['_7etraversalsupportfinder_11692',['~TraversalSupportFinder',['../classvg_1_1TraversalSupportFinder.html#a86fe98aaabf74546462d2d52017f69a5',1,'vg::TraversalSupportFinder']]],
+ ['_7etree_11693',['~Tree',['../structvg_1_1Tree.html#aa29f56c135efd59c283721181db4f27a',1,'vg::Tree']]],
+ ['_7etreenode_11694',['~TreeNode',['../structvg_1_1TreeNode.html#abe3058472100249948412715677d2644',1,'vg::TreeNode']]],
+ ['_7etriviallyserializable_11695',['~TriviallySerializable',['../classhandlegraph_1_1TriviallySerializable.html#ae6c6c81c7b722686ed51bfbff3a2e442',1,'handlegraph::TriviallySerializable']]],
+ ['_7etrivialtraversalfinder_11696',['~TrivialTraversalFinder',['../classvg_1_1TrivialTraversalFinder.html#a95f1dc0e83e536f4ded43f35982420f3',1,'vg::TrivialTraversalFinder']]],
+ ['_7etsvalignmentemitter_11697',['~TSVAlignmentEmitter',['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a69a2f7650e4271c33985c5754f6b6f53',1,'vg::io::TSVAlignmentEmitter']]],
+ ['_7etsvexplainer_11698',['~TSVExplainer',['../classvg_1_1TSVExplainer.html#ac7c5964711efd7f58c22d6aa9f07884c',1,'vg::TSVExplainer']]],
+ ['_7etvsclusterer_11699',['~TVSClusterer',['../classvg_1_1TVSClusterer.html#ad0bd55ec4d0141dbd6b22cab86e2af85',1,'vg::TVSClusterer']]],
+ ['_7evaluation_11700',['~Valuation',['../structvg_1_1subcommand_1_1Valuation.html#a299acc17034d0fc8b6107bca001ba49e',1,'vg::subcommand::Valuation']]],
+ ['_7evalueargspec_11701',['~ValueArgSpec',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a97f01678f8355598db5bc6a34a8515af',1,'vg::subcommand::ValueArgSpec']]],
+ ['_7evcfgenotyper_11702',['~VCFGenotyper',['../classvg_1_1VCFGenotyper.html#a91aad8f951949331a1753f7e07588381',1,'vg::VCFGenotyper']]],
+ ['_7evcfoutputcaller_11703',['~VCFOutputCaller',['../classvg_1_1VCFOutputCaller.html#a61c1441b882dbaaed73154aeae8109d6',1,'vg::VCFOutputCaller']]],
+ ['_7evcfrecordconverter_11704',['~VcfRecordConverter',['../classvg_1_1VcfRecordConverter.html#a49013729b000b0fd7c4a380c7ca79da6',1,'vg::VcfRecordConverter']]],
+ ['_7evcfrecordfilter_11705',['~VcfRecordFilter',['../classvg_1_1VcfRecordFilter.html#a11f60090fa5e3185bb42ece601457889',1,'vg::VcfRecordFilter']]],
+ ['_7evcftraversalfinder_11706',['~VCFTraversalFinder',['../classvg_1_1VCFTraversalFinder.html#a574fb1c2bdcf2752e75626f4c21bc90c',1,'vg::VCFTraversalFinder']]],
+ ['_7evectorizablehandlegraph_11707',['~VectorizableHandleGraph',['../classhandlegraph_1_1VectorizableHandleGraph.html#ae5986cf718d8f9d98b20f7e819db43f3',1,'handlegraph::VectorizableHandleGraph']]],
+ ['_7evectorizer_11708',['~Vectorizer',['../classVectorizer.html#a9e7ee4e6f8a517a85b6e9ed785958104',1,'Vectorizer']]],
+ ['_7evectorview_11709',['~VectorView',['../structvg_1_1VectorView.html#af9ec1a56ae0a3d357ccdc67f0958da0c',1,'vg::VectorView']]],
+ ['_7evg_11710',['~VG',['../classvg_1_1VG.html#a7513ddb88aeb58bd85a810c2a2ccdf67',1,'vg::VG']]],
+ ['_7evgalignmentemitter_11711',['~VGAlignmentEmitter',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a55e34fab0faf2988c90105e10b33c727',1,'vg::io::VGAlignmentEmitter']]],
+ ['_7eviz_11712',['~Viz',['../classvg_1_1Viz.html#ab63af6e73d13224a8a96f0d776cfd248',1,'vg::Viz']]],
+ ['_7ewatchdog_11713',['~Watchdog',['../classvg_1_1Watchdog.html#a58772622205b1e7c103612e518a6c995',1,'vg::Watchdog']]],
+ ['_7exdropaligner_11714',['~XdropAligner',['../classvg_1_1XdropAligner.html#aaa342dfcc4afb1448b98857fd216044a',1,'vg::XdropAligner']]],
+ ['_7exg_11715',['~XG',['../classxg_1_1XG.html#a1670ddfeb5c9c5f04cd14fe725eb0cfd',1,'xg::XG']]],
+ ['_7exgpath_11716',['~XGPath',['../classxg_1_1XGPath.html#a831bd85ed9f0db9154a1a8e3b0ad69fd',1,'xg::XGPath']]]
];
diff --git a/search/functions_2.js b/search/functions_2.js
index 4a0a76cea4..790b5be126 100644
--- a/search/functions_2.js
+++ b/search/functions_2.js
@@ -1,64 +1,64 @@
var searchData=
[
- ['b_8221',['b',['../classvg_1_1uniform__real__distribution.html#a6583cca9d3b8133ecd853c48c37f2256',1,'vg::uniform_real_distribution::b()'],['../classvg_1_1uniform__int__distribution.html#a56282403defd710bacffb1326a146a4f',1,'vg::uniform_int_distribution::b()']]],
- ['b64_5fdecode_8222',['b64_decode',['../bin2ascii_8h.html#ac9c3e26b958b172011908ac99df520c9',1,'bin2ascii.h']]],
- ['b64_5fencode_8223',['b64_encode',['../bin2ascii_8h.html#accfad92fa2269e4d4c9a161fa5d64b29',1,'bin2ascii.h']]],
- ['babuilder_8224',['BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a5b3be9bb6e0b7962713791917206cf88',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['back_8225',['back',['../structhaplo_1_1gbwt__thread__t.html#a5df1f6bd0fd29b353a813312d54d3f00',1,'haplo::gbwt_thread_t::back()'],['../structhaplo_1_1gbwt__thread__t.html#a077fbd98ab93393731eec9b4a6bd3151',1,'haplo::gbwt_thread_t::back() const']]],
- ['back_5ftranslate_5falignments_5fin_5fplace_8226',['back_translate_alignments_in_place',['../classvg_1_1BackTranslatingAlignmentEmitter.html#ab703e494d4452bab6eccabe47b7f1f71',1,'vg::BackTranslatingAlignmentEmitter']]],
- ['back_5ftranslate_5fin_5fplace_8227',['back_translate_in_place',['../namespacevg_1_1algorithms.html#a0d0e29a34fb2e1f712751a8a8fda6f03',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, Path &path)'],['../namespacevg_1_1algorithms.html#a0fb0b1f6ca5892b532032ecddd8fde19',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, Snarl &snarl)'],['../namespacevg_1_1algorithms.html#a0efe72c9db6dd4c1828dae311795e9b0',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, SnarlTraversal &traversal)'],['../namespacevg_1_1algorithms.html#a0e04f69397f1d7e1f33b99f0ff145af5',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, Visit &visit)']]],
- ['backing_5findex_8228',['backing_index',['../structvg_1_1VectorView.html#acd4b6eaf8079236c2b33e7de9f1a0ef5',1,'vg::VectorView']]],
- ['backtranslatingalignmentemitter_8229',['BackTranslatingAlignmentEmitter',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a9a3658c043e979e9c10ab86b41b9fc05',1,'vg::BackTranslatingAlignmentEmitter']]],
- ['backup_8230',['BackUp',['../classvg_1_1io_1_1BlockedGzipInputStream.html#afae170aec0e88c42956c48fdce82d068',1,'vg::io::BlockedGzipInputStream::BackUp()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a2a333a1aed4a53ff6d1619f2a48be0de',1,'vg::io::BlockedGzipOutputStream::BackUp()']]],
- ['badness_8231',['badness',['../structvg_1_1Haplotypes_1_1Subchain.html#a70d92ad6f8e97487395fc6548f053e30',1,'vg::Haplotypes::Subchain::badness()'],['../namespacehaplotypes__defaults.html#a17e78ca2607ec749a88124e297543301',1,'haplotypes_defaults::badness()']]],
- ['balanced_5fkmers_8232',['balanced_kmers',['../namespacevg.html#ab7caa49b187d9fc25833daa572cdf770',1,'vg']]],
- ['balanced_5fstride_8233',['balanced_stride',['../namespacevg.html#a7211eb89509ce3ca625333936c08ec9b',1,'vg']]],
- ['bam_5ftag_5fstrings_8234',['bam_tag_strings',['../namespacevg.html#a53e18f8d54689906de9c3e0cfe0761f3',1,'vg']]],
- ['bam_5fto_5falignment_8235',['bam_to_alignment',['../namespacevg.html#a461b5385c79e073ab10d8fe860ff9428',1,'vg::bam_to_alignment(const bam1_t *b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle, const bam_hdr_t *bh, const PathPositionHandleGraph *graph)'],['../namespacevg.html#a1f8705957c0972a6b4778efb5036c6aa',1,'vg::bam_to_alignment(const bam1_t *b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle)']]],
- ['bamatrix_8236',['BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a5cbc56500929e0097ddc365901e5e628',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['bandedglobalaligner_8237',['BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html#ad6ad604436c8a0aedf63c73f4d8b7f58',1,'vg::BandedGlobalAligner::BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, uint64_t max_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1BandedGlobalAligner.html#a8709982741375d04d1ca85155958be08',1,'vg::BandedGlobalAligner::BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > &alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, uint64_t max_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1BandedGlobalAligner.html#a36463b98552e45ab373b756625413f77',1,'vg::BandedGlobalAligner::BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, uint64_t max_cells=std::numeric_limits< uint64_t >::max())']]],
- ['base_5fedge_8238',['base_edge',['../structvg_1_1AugmentedGraph.html#acfd8bc29f1837a8a9bd87a8d2d36d757',1,'vg::AugmentedGraph']]],
- ['base_5fmappings_8239',['base_mappings',['../gamcompare__main_8cpp.html#a26d7af1f9ed3dbaf18a1a7f1bf09995e',1,'gamcompare_main.cpp']]],
- ['base_5fseed_5flength_8240',['base_seed_length',['../classvg_1_1algorithms_1_1Anchor.html#ad4b06c8a50ada7e74cb7a5fd3bedd186',1,'vg::algorithms::Anchor']]],
- ['baseargspec_8241',['BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a3f0488ffa39f25e9cb34c99669a5976b',1,'vg::subcommand::BaseArgSpec::BaseArgSpec(const std::string &option, char short_option, const std::string &help)'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a429ce67ad4ce117a20f5bc7c1ba328c2',1,'vg::subcommand::BaseArgSpec::BaseArgSpec(const std::string &option, const std::string &help)']]],
- ['basemapper_8242',['BaseMapper',['../classvg_1_1BaseMapper.html#a9a924463193888114237a20617f9485e',1,'vg::BaseMapper::BaseMapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr)'],['../classvg_1_1BaseMapper.html#a895c239d974f084e7a0a83025e104fd8',1,'vg::BaseMapper::BaseMapper(void)']]],
- ['baseoption_8243',['BaseOption',['../classvg_1_1BaseOption.html#a368247286ff1adae58018b7d16598d17',1,'vg::BaseOption::BaseOption()=delete'],['../classvg_1_1BaseOption.html#a2cad5b14f958dd4e71a4f21debe2c0a0',1,'vg::BaseOption::BaseOption(Configurable *owner, const string &long_opt, const string &short_opts, const Value &default_value, const string &description)']]],
- ['basevaluation_8244',['BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html#a677dfea8a32ef151bc80c63a101cd61b',1,'vg::subcommand::BaseValuation']]],
- ['begin_8245',['begin',['../classvg_1_1ShuffledPairs.html#adb49843f1fd59a0c592b88d85ae4e8f0',1,'vg::ShuffledPairs::begin()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a5d420005a03d913545a2c28527aeae1b',1,'vg::Option< vector< Item >, Parser >::begin()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a63060a85a3d8e92246fa4d91daefda53',1,'vg::Option< vector< Item >, Parser >::begin() const'],['../structvg_1_1PathIndex.html#ad239d0a2fb9bbbddce753a6c3cf639ed',1,'vg::PathIndex::begin()'],['../classvg_1_1PhasedGenome.html#a5ec1fda02f9b639fa315337290dca80f',1,'vg::PhasedGenome::begin()'],['../structvg_1_1VectorView.html#a89bb660be2b09d42f6840400a6a44784',1,'vg::VectorView::begin()'],['../classvg_1_1ZipCodeTree.html#a22e815e1b43a9c18518a42127f30a570',1,'vg::ZipCodeTree::begin()'],['../classhandlegraph_1_1PathForEachSocket.html#a0b82e3b3b8674d484cb181fb47e16b31',1,'handlegraph::PathForEachSocket::begin()']]],
- ['bellman_5fford_5fshortest_5fcycle_5flength_8246',['bellman_ford_shortest_cycle_length',['../namespacevg_1_1algorithms.html#af51e5eafc2c18f33dd6a120c753247a3',1,'vg::algorithms']]],
- ['benchmark_5fcontrol_8247',['benchmark_control',['../namespacevg.html#a71046fb34dc43f0a3e102e1394ce8697',1,'vg']]],
- ['bfs_8248',['bfs',['../classvg_1_1FlowSort.html#a7aec281b9414097e6d80fcb2f59727dd',1,'vg::FlowSort']]],
- ['bfs_5fleft_8249',['bfs_left',['../classvg_1_1RepresentativeTraversalFinder.html#a2d9526f7512a88d8ed9caa4518ceb2be',1,'vg::RepresentativeTraversalFinder']]],
- ['bfs_5fright_8250',['bfs_right',['../classvg_1_1RepresentativeTraversalFinder.html#a527da8cefe9c920e3da0dc34e6f9020f',1,'vg::RepresentativeTraversalFinder']]],
- ['bin2hex_8251',['bin2hex',['../bin2ascii_8h.html#a2c15dd2c8ce03c39b72aacba126d8a80',1,'bin2ascii.h']]],
- ['bin_5ffor_5fposition_8252',['bin_for_position',['../classvg_1_1Packer.html#a51d95763b8d110e0ac4406eee7573a77',1,'vg::Packer']]],
- ['bin_5fto_5fprefix_8253',['bin_to_prefix',['../classvg_1_1StreamIndexBase.html#ac4e243c64474f83800e3f9baa9894eea',1,'vg::StreamIndexBase']]],
- ['binary_5fextend_5fintervals_8254',['binary_extend_intervals',['../structhaplo_1_1haplo__DP__column.html#a69b9396f9bc9534432d89c411c60c8c5',1,'haplo::haplo_DP_column']]],
- ['binned_5fpacked_5fdepth_8255',['binned_packed_depth',['../namespacevg_1_1algorithms.html#a8fb3df22b1d7955546bbcc8c438f6efc',1,'vg::algorithms']]],
- ['binned_5fpacked_5fdepth_5findex_8256',['binned_packed_depth_index',['../namespacevg_1_1algorithms.html#af05e00ad1e6a7b34cde8c37aa9dbbdbc',1,'vg::algorithms']]],
- ['binned_5fpath_5fdepth_8257',['binned_path_depth',['../namespacevg_1_1algorithms.html#a1d48562b230a318ee15820aa508867fc',1,'vg::algorithms']]],
- ['binomial_5fcmf_5fln_8258',['binomial_cmf_ln',['../namespacevg.html#a038ccb26c0c9c0a87601edc7b8b5df70',1,'vg']]],
- ['bitstring_8259',['BitString',['../classvg_1_1BitString.html#af4fe4f4f6514d38a1c232dd08c0c6e07',1,'vg::BitString::BitString(uint64_t bits, size_t length)'],['../classvg_1_1BitString.html#afadfcba9fa4a1589646174bb71a97823',1,'vg::BitString::BitString()'],['../classvg_1_1BitString.html#a6210ace31bcc1718b5c5bb3f2b7f5f05',1,'vg::BitString::BitString(const BitString &other)=default'],['../classvg_1_1BitString.html#a67b6548484b23ab6423d894f4e23efea',1,'vg::BitString::BitString(BitString &&other)=default']]],
- ['blockedgzipinputstream_8260',['BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a68ce515c9bee3c71da952dfe5db7ecac',1,'vg::io::BlockedGzipInputStream::BlockedGzipInputStream(std::istream &stream, size_t thread_count=0)'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#a986e73fd3903582d1ab4110b73345d75',1,'vg::io::BlockedGzipInputStream::BlockedGzipInputStream(const BlockedGzipInputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#ae2bcf77f6592aa95ac9ee599d9816e84',1,'vg::io::BlockedGzipInputStream::BlockedGzipInputStream(BlockedGzipInputStream &&other)=delete']]],
- ['blockedgzipoutputstream_8261',['BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a2277edf73df28a4da63b44157ef4a904',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(BGZF *bgzf_handle)'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a861f784237f0656f67956acd6e55022b',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(std::ostream &stream)'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a2c69ba0487ee2cd5e6da92b7225d01f0',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(const BlockedGzipOutputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae68648f5c06ce291e3daafb993c9b71c',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(BlockedGzipOutputStream &&other)=delete']]],
- ['bp_5flength_8262',['bp_length',['../classvg_1_1NestedTraversalFinder.html#af86694400e6610dbf5ac59725d7122d4',1,'vg::NestedTraversalFinder::bp_length()'],['../classvg_1_1RepresentativeTraversalFinder.html#a46f34cb373ca08864f0149bde93d880a',1,'vg::RepresentativeTraversalFinder::bp_length()']]],
- ['break_5fchain_8263',['break_chain',['../classvg_1_1GraphCaller.html#ab68875a5e1aa9028dc4442f8ee827571',1,'vg::GraphCaller']]],
- ['break_5fcycles_8264',['break_cycles',['../classvg_1_1VG.html#a93cb2d6686e0bb92d7f0b632fc813702',1,'vg::VG']]],
- ['breakend_5ffilter_8265',['breakend_filter',['../classvg_1_1Filter.html#ab590f8b51e20860f1af0e40ca22932be',1,'vg::Filter']]],
- ['brute_5fforce_5falt_5ftraversals_8266',['brute_force_alt_traversals',['../classvg_1_1VCFTraversalFinder.html#a31598f482dd2d5dbdc06e273ffc18204',1,'vg::VCFTraversalFinder']]],
- ['build_5fedge_5findexes_8267',['build_edge_indexes',['../classvg_1_1VG.html#a3fb2cb59474393ac822847033f185d17',1,'vg::VG']]],
- ['build_5fedge_5findexes_5fno_5finit_5fsize_8268',['build_edge_indexes_no_init_size',['../classvg_1_1VG.html#af63d4a22a3baa5b21623128b81a14872',1,'vg::VG']]],
- ['build_5fgbwt_8269',['build_gbwt',['../classvg_1_1HaplotypeIndexer.html#a0389ee96c5ce8a6d9c158fda39aca9d9',1,'vg::HaplotypeIndexer::build_gbwt(const std::vector< std::string > &vcf_parse_files, const std::string &job_name="GBWT", const PathHandleGraph *graph=nullptr, const std::unordered_set< path_handle_t > *paths=nullptr, bool skip_unvisited_paths=false) const'],['../classvg_1_1HaplotypeIndexer.html#ae92d109c2e7baf0b7ddded8df80a6f70',1,'vg::HaplotypeIndexer::build_gbwt(const PathHandleGraph &graph) const'],['../classvg_1_1HaplotypeIndexer.html#a34fc36c5ba77f4cedd32073dda118b84',1,'vg::HaplotypeIndexer::build_gbwt(const HandleGraph &graph, const std::vector< std::string > &aln_filenames, const std::string &aln_format, size_t parallel_jobs=1) const']]],
- ['build_5fgcsa_5flcp_8270',['build_gcsa_lcp',['../namespacevg.html#a34b89433618346e971606020965b10ed',1,'vg']]],
- ['build_5findexes_8271',['build_indexes',['../classvg_1_1SnarlManager.html#a962ce88320136f82a1f5f58a036698c2',1,'vg::SnarlManager::build_indexes()'],['../classvg_1_1VG.html#a7f71911fe2c652dc11aec0a0d705b1e4',1,'vg::VG::build_indexes()']]],
- ['build_5findexes_5fno_5finit_5fsize_8272',['build_indexes_no_init_size',['../classvg_1_1VG.html#aa78095fb5d27e182c5cc4d5c10d3da39',1,'vg::VG']]],
- ['build_5findices_8273',['build_indices',['../classvg_1_1PhasedGenome.html#a72e27ed72d346717ce196d5b2081365b',1,'vg::PhasedGenome']]],
- ['build_5fnode_5findexes_8274',['build_node_indexes',['../classvg_1_1VG.html#a5156da43d4175597d7a8b1d88b5179af',1,'vg::VG']]],
- ['build_5fnode_5findexes_5fno_5finit_5fsize_8275',['build_node_indexes_no_init_size',['../classvg_1_1VG.html#a0ca442744267b08609887cd842ca543d',1,'vg::VG']]],
- ['build_5fposition_5ftable_8276',['build_position_table',['../classvg_1_1Translator.html#a1199f5152e05a5a52d6d00cc00ab0ea1',1,'vg::Translator']]],
- ['build_5fsite_5findices_5finternal_8277',['build_site_indices_internal',['../classvg_1_1PhasedGenome.html#ab7badd2e4e135f118fc14f7e0aad1b5a',1,'vg::PhasedGenome']]],
- ['build_5fsnarl_5fdecomposition_8278',['build_snarl_decomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a75213fa82b64e8dadc24df8fad7a1e5c',1,'handlegraph::BuildableSnarlDecomposition']]],
- ['build_5fsubchains_8279',['build_subchains',['../classvg_1_1HaplotypePartitioner.html#a74a37ea177a421b5581d3ed6c4e1d09a',1,'vg::HaplotypePartitioner']]],
- ['byte_5fcount_8280',['byte_count',['../structvg_1_1varint__vector__t.html#af5bad24493a4f813eeca62cd706a04c3',1,'vg::varint_vector_t::byte_count()'],['../classvg_1_1ZipCode.html#a36fb166e87c595d4e513b5e6a7676958',1,'vg::ZipCode::byte_count()']]],
- ['bytecount_8281',['ByteCount',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa90daab17c2449563e96bbca827c8ccf',1,'vg::io::BlockedGzipInputStream::ByteCount()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a35058523e5b100a0c55af4f4371544a7',1,'vg::io::BlockedGzipOutputStream::ByteCount()']]]
+ ['b_8223',['b',['../classvg_1_1uniform__real__distribution.html#a6583cca9d3b8133ecd853c48c37f2256',1,'vg::uniform_real_distribution::b()'],['../classvg_1_1uniform__int__distribution.html#a56282403defd710bacffb1326a146a4f',1,'vg::uniform_int_distribution::b()']]],
+ ['b64_5fdecode_8224',['b64_decode',['../bin2ascii_8h.html#ac9c3e26b958b172011908ac99df520c9',1,'bin2ascii.h']]],
+ ['b64_5fencode_8225',['b64_encode',['../bin2ascii_8h.html#accfad92fa2269e4d4c9a161fa5d64b29',1,'bin2ascii.h']]],
+ ['babuilder_8226',['BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a5b3be9bb6e0b7962713791917206cf88',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['back_8227',['back',['../structhaplo_1_1gbwt__thread__t.html#a5df1f6bd0fd29b353a813312d54d3f00',1,'haplo::gbwt_thread_t::back()'],['../structhaplo_1_1gbwt__thread__t.html#a077fbd98ab93393731eec9b4a6bd3151',1,'haplo::gbwt_thread_t::back() const']]],
+ ['back_5ftranslate_5falignments_5fin_5fplace_8228',['back_translate_alignments_in_place',['../classvg_1_1BackTranslatingAlignmentEmitter.html#ab703e494d4452bab6eccabe47b7f1f71',1,'vg::BackTranslatingAlignmentEmitter']]],
+ ['back_5ftranslate_5fin_5fplace_8229',['back_translate_in_place',['../namespacevg_1_1algorithms.html#a0d0e29a34fb2e1f712751a8a8fda6f03',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, Path &path)'],['../namespacevg_1_1algorithms.html#a0fb0b1f6ca5892b532032ecddd8fde19',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, Snarl &snarl)'],['../namespacevg_1_1algorithms.html#a0efe72c9db6dd4c1828dae311795e9b0',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, SnarlTraversal &traversal)'],['../namespacevg_1_1algorithms.html#a0e04f69397f1d7e1f33b99f0ff145af5',1,'vg::algorithms::back_translate_in_place(const NamedNodeBackTranslation *translation, Visit &visit)']]],
+ ['backing_5findex_8230',['backing_index',['../structvg_1_1VectorView.html#acd4b6eaf8079236c2b33e7de9f1a0ef5',1,'vg::VectorView']]],
+ ['backtranslatingalignmentemitter_8231',['BackTranslatingAlignmentEmitter',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a9a3658c043e979e9c10ab86b41b9fc05',1,'vg::BackTranslatingAlignmentEmitter']]],
+ ['backup_8232',['BackUp',['../classvg_1_1io_1_1BlockedGzipInputStream.html#afae170aec0e88c42956c48fdce82d068',1,'vg::io::BlockedGzipInputStream::BackUp()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a2a333a1aed4a53ff6d1619f2a48be0de',1,'vg::io::BlockedGzipOutputStream::BackUp()']]],
+ ['badness_8233',['badness',['../structvg_1_1Haplotypes_1_1Subchain.html#a70d92ad6f8e97487395fc6548f053e30',1,'vg::Haplotypes::Subchain::badness()'],['../namespacehaplotypes__defaults.html#a17e78ca2607ec749a88124e297543301',1,'haplotypes_defaults::badness()']]],
+ ['balanced_5fkmers_8234',['balanced_kmers',['../namespacevg.html#ab7caa49b187d9fc25833daa572cdf770',1,'vg']]],
+ ['balanced_5fstride_8235',['balanced_stride',['../namespacevg.html#a7211eb89509ce3ca625333936c08ec9b',1,'vg']]],
+ ['bam_5ftag_5fstrings_8236',['bam_tag_strings',['../namespacevg.html#a53e18f8d54689906de9c3e0cfe0761f3',1,'vg']]],
+ ['bam_5fto_5falignment_8237',['bam_to_alignment',['../namespacevg.html#a461b5385c79e073ab10d8fe860ff9428',1,'vg::bam_to_alignment(const bam1_t *b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle, const bam_hdr_t *bh, const PathPositionHandleGraph *graph)'],['../namespacevg.html#a1f8705957c0972a6b4778efb5036c6aa',1,'vg::bam_to_alignment(const bam1_t *b, const map< string, string > &rg_sample, const map< int, path_handle_t > &tid_path_handle)']]],
+ ['bamatrix_8238',['BAMatrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a5cbc56500929e0097ddc365901e5e628',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['bandedglobalaligner_8239',['BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner.html#ad6ad604436c8a0aedf63c73f4d8b7f58',1,'vg::BandedGlobalAligner::BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, uint64_t max_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1BandedGlobalAligner.html#a8709982741375d04d1ca85155958be08',1,'vg::BandedGlobalAligner::BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > &alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, uint64_t max_cells=std::numeric_limits< uint64_t >::max())'],['../classvg_1_1BandedGlobalAligner.html#a36463b98552e45ab373b756625413f77',1,'vg::BandedGlobalAligner::BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, uint64_t max_cells=std::numeric_limits< uint64_t >::max())']]],
+ ['base_5fedge_8240',['base_edge',['../structvg_1_1AugmentedGraph.html#acfd8bc29f1837a8a9bd87a8d2d36d757',1,'vg::AugmentedGraph']]],
+ ['base_5fmappings_8241',['base_mappings',['../gamcompare__main_8cpp.html#a26d7af1f9ed3dbaf18a1a7f1bf09995e',1,'gamcompare_main.cpp']]],
+ ['base_5fseed_5flength_8242',['base_seed_length',['../classvg_1_1algorithms_1_1Anchor.html#ad4b06c8a50ada7e74cb7a5fd3bedd186',1,'vg::algorithms::Anchor']]],
+ ['baseargspec_8243',['BaseArgSpec',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a3f0488ffa39f25e9cb34c99669a5976b',1,'vg::subcommand::BaseArgSpec::BaseArgSpec(const std::string &option, char short_option, const std::string &help)'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#a429ce67ad4ce117a20f5bc7c1ba328c2',1,'vg::subcommand::BaseArgSpec::BaseArgSpec(const std::string &option, const std::string &help)']]],
+ ['basemapper_8244',['BaseMapper',['../classvg_1_1BaseMapper.html#a9a924463193888114237a20617f9485e',1,'vg::BaseMapper::BaseMapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr)'],['../classvg_1_1BaseMapper.html#a895c239d974f084e7a0a83025e104fd8',1,'vg::BaseMapper::BaseMapper(void)']]],
+ ['baseoption_8245',['BaseOption',['../classvg_1_1BaseOption.html#a368247286ff1adae58018b7d16598d17',1,'vg::BaseOption::BaseOption()=delete'],['../classvg_1_1BaseOption.html#a2cad5b14f958dd4e71a4f21debe2c0a0',1,'vg::BaseOption::BaseOption(Configurable *owner, const string &long_opt, const string &short_opts, const Value &default_value, const string &description)']]],
+ ['basevaluation_8246',['BaseValuation',['../structvg_1_1subcommand_1_1BaseValuation.html#a677dfea8a32ef151bc80c63a101cd61b',1,'vg::subcommand::BaseValuation']]],
+ ['begin_8247',['begin',['../classvg_1_1ShuffledPairs.html#adb49843f1fd59a0c592b88d85ae4e8f0',1,'vg::ShuffledPairs::begin()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a5d420005a03d913545a2c28527aeae1b',1,'vg::Option< vector< Item >, Parser >::begin()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a63060a85a3d8e92246fa4d91daefda53',1,'vg::Option< vector< Item >, Parser >::begin() const'],['../structvg_1_1PathIndex.html#ad239d0a2fb9bbbddce753a6c3cf639ed',1,'vg::PathIndex::begin()'],['../classvg_1_1PhasedGenome.html#a5ec1fda02f9b639fa315337290dca80f',1,'vg::PhasedGenome::begin()'],['../structvg_1_1VectorView.html#a89bb660be2b09d42f6840400a6a44784',1,'vg::VectorView::begin()'],['../classvg_1_1ZipCodeTree.html#a22e815e1b43a9c18518a42127f30a570',1,'vg::ZipCodeTree::begin()'],['../classhandlegraph_1_1PathForEachSocket.html#a0b82e3b3b8674d484cb181fb47e16b31',1,'handlegraph::PathForEachSocket::begin()']]],
+ ['bellman_5fford_5fshortest_5fcycle_5flength_8248',['bellman_ford_shortest_cycle_length',['../namespacevg_1_1algorithms.html#af51e5eafc2c18f33dd6a120c753247a3',1,'vg::algorithms']]],
+ ['benchmark_5fcontrol_8249',['benchmark_control',['../namespacevg.html#a71046fb34dc43f0a3e102e1394ce8697',1,'vg']]],
+ ['bfs_8250',['bfs',['../classvg_1_1FlowSort.html#a7aec281b9414097e6d80fcb2f59727dd',1,'vg::FlowSort']]],
+ ['bfs_5fleft_8251',['bfs_left',['../classvg_1_1RepresentativeTraversalFinder.html#a2d9526f7512a88d8ed9caa4518ceb2be',1,'vg::RepresentativeTraversalFinder']]],
+ ['bfs_5fright_8252',['bfs_right',['../classvg_1_1RepresentativeTraversalFinder.html#a527da8cefe9c920e3da0dc34e6f9020f',1,'vg::RepresentativeTraversalFinder']]],
+ ['bin2hex_8253',['bin2hex',['../bin2ascii_8h.html#a2c15dd2c8ce03c39b72aacba126d8a80',1,'bin2ascii.h']]],
+ ['bin_5ffor_5fposition_8254',['bin_for_position',['../classvg_1_1Packer.html#a51d95763b8d110e0ac4406eee7573a77',1,'vg::Packer']]],
+ ['bin_5fto_5fprefix_8255',['bin_to_prefix',['../classvg_1_1StreamIndexBase.html#ac4e243c64474f83800e3f9baa9894eea',1,'vg::StreamIndexBase']]],
+ ['binary_5fextend_5fintervals_8256',['binary_extend_intervals',['../structhaplo_1_1haplo__DP__column.html#a69b9396f9bc9534432d89c411c60c8c5',1,'haplo::haplo_DP_column']]],
+ ['binned_5fpacked_5fdepth_8257',['binned_packed_depth',['../namespacevg_1_1algorithms.html#a8fb3df22b1d7955546bbcc8c438f6efc',1,'vg::algorithms']]],
+ ['binned_5fpacked_5fdepth_5findex_8258',['binned_packed_depth_index',['../namespacevg_1_1algorithms.html#af05e00ad1e6a7b34cde8c37aa9dbbdbc',1,'vg::algorithms']]],
+ ['binned_5fpath_5fdepth_8259',['binned_path_depth',['../namespacevg_1_1algorithms.html#a1d48562b230a318ee15820aa508867fc',1,'vg::algorithms']]],
+ ['binomial_5fcmf_5fln_8260',['binomial_cmf_ln',['../namespacevg.html#a038ccb26c0c9c0a87601edc7b8b5df70',1,'vg']]],
+ ['bitstring_8261',['BitString',['../classvg_1_1BitString.html#af4fe4f4f6514d38a1c232dd08c0c6e07',1,'vg::BitString::BitString(uint64_t bits, size_t length)'],['../classvg_1_1BitString.html#afadfcba9fa4a1589646174bb71a97823',1,'vg::BitString::BitString()'],['../classvg_1_1BitString.html#a6210ace31bcc1718b5c5bb3f2b7f5f05',1,'vg::BitString::BitString(const BitString &other)=default'],['../classvg_1_1BitString.html#a67b6548484b23ab6423d894f4e23efea',1,'vg::BitString::BitString(BitString &&other)=default']]],
+ ['blockedgzipinputstream_8262',['BlockedGzipInputStream',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a68ce515c9bee3c71da952dfe5db7ecac',1,'vg::io::BlockedGzipInputStream::BlockedGzipInputStream(std::istream &stream, size_t thread_count=0)'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#a986e73fd3903582d1ab4110b73345d75',1,'vg::io::BlockedGzipInputStream::BlockedGzipInputStream(const BlockedGzipInputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#ae2bcf77f6592aa95ac9ee599d9816e84',1,'vg::io::BlockedGzipInputStream::BlockedGzipInputStream(BlockedGzipInputStream &&other)=delete']]],
+ ['blockedgzipoutputstream_8263',['BlockedGzipOutputStream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a2277edf73df28a4da63b44157ef4a904',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(BGZF *bgzf_handle)'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a861f784237f0656f67956acd6e55022b',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(std::ostream &stream)'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a2c69ba0487ee2cd5e6da92b7225d01f0',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(const BlockedGzipOutputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae68648f5c06ce291e3daafb993c9b71c',1,'vg::io::BlockedGzipOutputStream::BlockedGzipOutputStream(BlockedGzipOutputStream &&other)=delete']]],
+ ['bp_5flength_8264',['bp_length',['../classvg_1_1NestedTraversalFinder.html#af86694400e6610dbf5ac59725d7122d4',1,'vg::NestedTraversalFinder::bp_length()'],['../classvg_1_1RepresentativeTraversalFinder.html#a46f34cb373ca08864f0149bde93d880a',1,'vg::RepresentativeTraversalFinder::bp_length()']]],
+ ['break_5fchain_8265',['break_chain',['../classvg_1_1GraphCaller.html#ab68875a5e1aa9028dc4442f8ee827571',1,'vg::GraphCaller']]],
+ ['break_5fcycles_8266',['break_cycles',['../classvg_1_1VG.html#a93cb2d6686e0bb92d7f0b632fc813702',1,'vg::VG']]],
+ ['breakend_5ffilter_8267',['breakend_filter',['../classvg_1_1Filter.html#ab590f8b51e20860f1af0e40ca22932be',1,'vg::Filter']]],
+ ['brute_5fforce_5falt_5ftraversals_8268',['brute_force_alt_traversals',['../classvg_1_1VCFTraversalFinder.html#a31598f482dd2d5dbdc06e273ffc18204',1,'vg::VCFTraversalFinder']]],
+ ['build_5fedge_5findexes_8269',['build_edge_indexes',['../classvg_1_1VG.html#a3fb2cb59474393ac822847033f185d17',1,'vg::VG']]],
+ ['build_5fedge_5findexes_5fno_5finit_5fsize_8270',['build_edge_indexes_no_init_size',['../classvg_1_1VG.html#af63d4a22a3baa5b21623128b81a14872',1,'vg::VG']]],
+ ['build_5fgbwt_8271',['build_gbwt',['../classvg_1_1HaplotypeIndexer.html#a0389ee96c5ce8a6d9c158fda39aca9d9',1,'vg::HaplotypeIndexer::build_gbwt(const std::vector< std::string > &vcf_parse_files, const std::string &job_name="GBWT", const PathHandleGraph *graph=nullptr, const std::unordered_set< path_handle_t > *paths=nullptr, bool skip_unvisited_paths=false) const'],['../classvg_1_1HaplotypeIndexer.html#ae92d109c2e7baf0b7ddded8df80a6f70',1,'vg::HaplotypeIndexer::build_gbwt(const PathHandleGraph &graph) const'],['../classvg_1_1HaplotypeIndexer.html#a34fc36c5ba77f4cedd32073dda118b84',1,'vg::HaplotypeIndexer::build_gbwt(const HandleGraph &graph, const std::vector< std::string > &aln_filenames, const std::string &aln_format, size_t parallel_jobs=1) const']]],
+ ['build_5fgcsa_5flcp_8272',['build_gcsa_lcp',['../namespacevg.html#a34b89433618346e971606020965b10ed',1,'vg']]],
+ ['build_5findexes_8273',['build_indexes',['../classvg_1_1SnarlManager.html#a962ce88320136f82a1f5f58a036698c2',1,'vg::SnarlManager::build_indexes()'],['../classvg_1_1VG.html#a7f71911fe2c652dc11aec0a0d705b1e4',1,'vg::VG::build_indexes()']]],
+ ['build_5findexes_5fno_5finit_5fsize_8274',['build_indexes_no_init_size',['../classvg_1_1VG.html#aa78095fb5d27e182c5cc4d5c10d3da39',1,'vg::VG']]],
+ ['build_5findices_8275',['build_indices',['../classvg_1_1PhasedGenome.html#a72e27ed72d346717ce196d5b2081365b',1,'vg::PhasedGenome']]],
+ ['build_5fnode_5findexes_8276',['build_node_indexes',['../classvg_1_1VG.html#a5156da43d4175597d7a8b1d88b5179af',1,'vg::VG']]],
+ ['build_5fnode_5findexes_5fno_5finit_5fsize_8277',['build_node_indexes_no_init_size',['../classvg_1_1VG.html#a0ca442744267b08609887cd842ca543d',1,'vg::VG']]],
+ ['build_5fposition_5ftable_8278',['build_position_table',['../classvg_1_1Translator.html#a1199f5152e05a5a52d6d00cc00ab0ea1',1,'vg::Translator']]],
+ ['build_5fsite_5findices_5finternal_8279',['build_site_indices_internal',['../classvg_1_1PhasedGenome.html#ab7badd2e4e135f118fc14f7e0aad1b5a',1,'vg::PhasedGenome']]],
+ ['build_5fsnarl_5fdecomposition_8280',['build_snarl_decomposition',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a75213fa82b64e8dadc24df8fad7a1e5c',1,'handlegraph::BuildableSnarlDecomposition']]],
+ ['build_5fsubchains_8281',['build_subchains',['../classvg_1_1HaplotypePartitioner.html#a74a37ea177a421b5581d3ed6c4e1d09a',1,'vg::HaplotypePartitioner']]],
+ ['byte_5fcount_8282',['byte_count',['../structvg_1_1varint__vector__t.html#af5bad24493a4f813eeca62cd706a04c3',1,'vg::varint_vector_t::byte_count()'],['../classvg_1_1ZipCode.html#a36fb166e87c595d4e513b5e6a7676958',1,'vg::ZipCode::byte_count()']]],
+ ['bytecount_8283',['ByteCount',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aa90daab17c2449563e96bbca827c8ccf',1,'vg::io::BlockedGzipInputStream::ByteCount()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a35058523e5b100a0c55af4f4371544a7',1,'vg::io::BlockedGzipOutputStream::ByteCount()']]]
];
diff --git a/search/functions_3.js b/search/functions_3.js
index 6dd84c5d65..4213177341 100644
--- a/search/functions_3.js
+++ b/search/functions_3.js
@@ -1,273 +1,273 @@
var searchData=
[
- ['cachedpackedtraversalsupportfinder_8282',['CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html#acf3672c8fe5fcdd91afd44d5c1eec12f',1,'vg::CachedPackedTraversalSupportFinder']]],
- ['cacheentry_8283',['CacheEntry',['../structvg_1_1IndexedVG_1_1CacheEntry.html#aab15096460395eb73cf757068bd33b11',1,'vg::IndexedVG::CacheEntry::CacheEntry(cursor_t &to_read)'],['../structvg_1_1IndexedVG_1_1CacheEntry.html#ad0d6214f5d1f91aee27e67788f203e97',1,'vg::IndexedVG::CacheEntry::CacheEntry(CacheEntry &&other)=default']]],
- ['cactus_5fto_5fvg_8284',['cactus_to_vg',['../namespacevg.html#adf53e86632a6d1d4b54370e6d948d08c',1,'vg']]],
- ['cactusify_8285',['cactusify',['../namespacevg.html#aa4d05bc207717708d48e1da09f83eec6',1,'vg']]],
- ['cactussnarlfinder_8286',['CactusSnarlFinder',['../classvg_1_1CactusSnarlFinder.html#a523de5b05cbb527b87940258eed03e9b',1,'vg::CactusSnarlFinder']]],
- ['calculate_5fand_5fsave_5falignment_8287',['calculate_and_save_alignment',['../classvg_1_1DozeuInterface.html#aa8e98b63ac97d3d4c60ca93708973302',1,'vg::DozeuInterface']]],
- ['calculate_5fconsistency_8288',['calculate_consistency',['../classvg_1_1ConsistencyCalculator.html#a208c36e5e95ab3c538f2c16175275c39',1,'vg::ConsistencyCalculator::calculate_consistency()'],['../classvg_1_1SimpleConsistencyCalculator.html#a391f08cf329583daf0c2a58cd5e20473',1,'vg::SimpleConsistencyCalculator::calculate_consistency()']]],
- ['calculate_5fi_8289',['calculate_I',['../structhaplo_1_1haplo__DP__rectangle.html#ab2680796767cbf6721c326e5b0273e61',1,'haplo::haplo_DP_rectangle']]],
- ['calculate_5flog_5flikelihood_8290',['calculate_log_likelihood',['../classvg_1_1GenotypeLikelihoodCalculator.html#af7ced3cd97277cd6a1201d8c06b67e72',1,'vg::GenotypeLikelihoodCalculator']]],
- ['calculate_5flog_5fprior_8291',['calculate_log_prior',['../classvg_1_1GenotypePriorCalculator.html#a892b1d833c73f5a81b484269641c5d5c',1,'vg::GenotypePriorCalculator::calculate_log_prior()'],['../classvg_1_1FixedGenotypePriorCalculator.html#a3cbc25b27cb2831b172bb30e0809e58c',1,'vg::FixedGenotypePriorCalculator::calculate_log_prior()']]],
- ['calculate_5fmax_5fposition_8292',['calculate_max_position',['../classvg_1_1DozeuInterface.html#aa863b61f59ea128a5e17e97538405d9b',1,'vg::DozeuInterface']]],
- ['calculate_5fseed_5fposition_8293',['calculate_seed_position',['../classvg_1_1DozeuInterface.html#a397c817ed543794a609d32fb21063790',1,'vg::DozeuInterface']]],
- ['calculate_5fsupports_8294',['calculate_supports',['../classvg_1_1TraversalSupportCalculator.html#a799e376d809e07eec89161d25dd3f3e7',1,'vg::TraversalSupportCalculator::calculate_supports()'],['../classvg_1_1SimpleTraversalSupportCalculator.html#a7950181bdbfc5f4db0583b7f92bdfe17',1,'vg::SimpleTraversalSupportCalculator::calculate_supports()']]],
- ['calibrate_5fmismapping_5fdetection_8295',['calibrate_mismapping_detection',['../classvg_1_1MultipathMapper.html#aa4307bce23fe2a909f96273dbca7b126',1,'vg::MultipathMapper']]],
- ['call_5fsnarl_8296',['call_snarl',['../classvg_1_1GraphCaller.html#a6064d47ccef10174fab1037764a3cf29',1,'vg::GraphCaller::call_snarl()'],['../classvg_1_1VCFGenotyper.html#a1e3a89bae885b463272873e538815151',1,'vg::VCFGenotyper::call_snarl()'],['../classvg_1_1LegacyCaller.html#a732a1385c9846d9605db70139d8e275b',1,'vg::LegacyCaller::call_snarl()'],['../classvg_1_1FlowCaller.html#abe755bb8027b80711002dc229fe3399a',1,'vg::FlowCaller::call_snarl()'],['../classvg_1_1NestedFlowCaller.html#a519712fdd96921a721be77a5f7d12638',1,'vg::NestedFlowCaller::call_snarl()'],['../classvg_1_1MCMCCaller.html#a82a9f6d69f5168582d19ff1d2484ea70',1,'vg::MCMCCaller::call_snarl()']]],
- ['call_5fsnarl_5frecursive_8297',['call_snarl_recursive',['../classvg_1_1NestedFlowCaller.html#ad35a296c010962d699d2e613d8f7bfc9',1,'vg::NestedFlowCaller']]],
- ['call_5ftop_5flevel_5fchains_8298',['call_top_level_chains',['../classvg_1_1GraphCaller.html#ae39e4d55f2c5599a941957a080f3cd10',1,'vg::GraphCaller']]],
- ['call_5ftop_5flevel_5fsnarls_8299',['call_top_level_snarls',['../classvg_1_1GraphCaller.html#a905253c21cb1a94605587ac7759d4aa6',1,'vg::GraphCaller::call_top_level_snarls()'],['../classvg_1_1MCMCCaller.html#aa4acabff49b9dee265127563d9424cbd',1,'vg::MCMCCaller::call_top_level_snarls()']]],
- ['candidate_5fsplice_5fsites_8300',['candidate_splice_sites',['../classvg_1_1SpliceRegion.html#acf682cf55a977a23d54ff5c55ce1b4b9',1,'vg::SpliceRegion']]],
- ['candidates_8301',['candidates',['../namespacehaplotypes__defaults.html#aa492bd09d6c7d4877e2a54b851185a92',1,'haplotypes_defaults']]],
- ['canonical_8302',['canonical',['../classhandlegraph_1_1SnarlDecomposition.html#ac26d4f14c1803734517afe18ec68a53a',1,'handlegraph::SnarlDecomposition']]],
- ['canonical_5fhuffman_8303',['canonical_huffman',['../namespacevg.html#a208dee68429b2d4b0ee0b02cea090d9b',1,'vg']]],
- ['canonical_5forientation_8304',['canonical_orientation',['../namespacevg.html#a74563bc5f9f3268b9a933688ad1a5edb',1,'vg']]],
- ['chain_8305',['chain',['../structvg_1_1subcommand_1_1TickChainLink.html#aa5742ab455378cdb60f18cafba2ce01d',1,'vg::subcommand::TickChainLink::chain()'],['../structvg_1_1subcommand_1_1RangeArgSpec.html#a005c03f54977a58a1c81967750f7d2c9',1,'vg::subcommand::RangeArgSpec::chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a4540cc78899ade0b653dbb46e698784e',1,'vg::subcommand::OptionGroup::chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a54298aca1a143832c3d0f2d26cc729ed',1,'vg::subcommand::GroupedOptionGroup::chain()']]],
- ['chain_5fbegin_8306',['chain_begin',['../namespacevg.html#ac3b14246f4fe83e3fbdadb1ba838faeb',1,'vg']]],
- ['chain_5fbegin_5ffrom_8307',['chain_begin_from',['../namespacevg.html#aefacc656d2c444dfd6e0e445218265cc',1,'vg']]],
- ['chain_5fend_8308',['chain_end',['../namespacevg.html#a0612d7af2f7366ff81c89824f43a5865',1,'vg']]],
- ['chain_5fend_5ffrom_8309',['chain_end_from',['../namespacevg.html#a0627b5d536b881a355d8b419b6f329c6',1,'vg']]],
- ['chain_5finfo_5fto_5fseed_8310',['chain_info_to_seed',['../classvg_1_1MinimizerMapper.html#ae0c70429455b4170120c4f1364449e99',1,'vg::MinimizerMapper']]],
- ['chain_5fitems_5fdp_8311',['chain_items_dp',['../namespacevg_1_1algorithms.html#a2fda86d465d26d7f101e00f3431564e8',1,'vg::algorithms']]],
- ['chain_5fitems_5ftraceback_8312',['chain_items_traceback',['../namespacevg_1_1algorithms.html#a7a9239fd23ed6838263f4dd05828d18c',1,'vg::algorithms']]],
- ['chain_5fof_8313',['chain_of',['../classvg_1_1SnarlManager.html#a411e51927a6f65513e55b8efc02237a8',1,'vg::SnarlManager']]],
- ['chain_5forientation_5fof_8314',['chain_orientation_of',['../classvg_1_1SnarlManager.html#a3227a00cc5b9ba1484a35be22eea1927',1,'vg::SnarlManager']]],
- ['chain_5frank_5fof_8315',['chain_rank_of',['../classvg_1_1SnarlManager.html#a7fcb9d66d4de93aa61ceb6d01e2efd4e',1,'vg::SnarlManager']]],
- ['chain_5frbegin_8316',['chain_rbegin',['../namespacevg.html#aa24387fbb4606765c23a280316bfcb65',1,'vg']]],
- ['chain_5frcbegin_8317',['chain_rcbegin',['../namespacevg.html#a7aed054b974860f2cc4d5be4b7615de0',1,'vg']]],
- ['chain_5frcend_8318',['chain_rcend',['../namespacevg.html#ae1369d5e29159750fd14482f73421660',1,'vg']]],
- ['chain_5frend_8319',['chain_rend',['../namespacevg.html#a2c65134c67609a001a61291b22337f8d',1,'vg']]],
- ['chains_5fof_8320',['chains_of',['../classvg_1_1SnarlManager.html#a237e4dae871d0555ccb855285364ab8a',1,'vg::SnarlManager']]],
- ['change_5fsequence_8321',['change_sequence',['../classhandlegraph_1_1DeletableHandleGraph.html#a074aa4e0604e7b89e111c3bb71864f4c',1,'handlegraph::DeletableHandleGraph::change_sequence()'],['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html#a496296d7be48b5d6de5635002b1c0226',1,'handlegraph::MutablePathDeletableHandleGraph::change_sequence()']]],
- ['check_5falignment_8322',['check_alignment',['../classvg_1_1Mapper.html#a0750e1ca5a4eff47c148b176081c5333',1,'vg::Mapper']]],
- ['check_5fduplicate_5fpath_5fnames_8323',['check_duplicate_path_names',['../convert__main_8cpp.html#a4355d9c8b84855c02d82983d0cd8eb2f',1,'convert_main.cpp']]],
- ['check_5ffor_5fread_5fin_8324',['check_for_read_in',['../structvg_1_1read__alignment__index__t.html#acabc585a1b0aba09a1c8f03b4a9ce740',1,'vg::read_alignment_index_t']]],
- ['check_5fin_8325',['check_in',['../classvg_1_1Watchdog.html#a73fff63eede4aaf60f04ca41f2373cdc',1,'vg::Watchdog']]],
- ['check_5flengths_8326',['check_lengths',['../structvg_1_1WFAAlignment.html#aa0af12c84438f056d94bae26dcd52697',1,'vg::WFAAlignment']]],
- ['check_5fmax_5ftrav_5fcutoff_8327',['check_max_trav_cutoff',['../classvg_1_1VCFTraversalFinder.html#aab82f66226266e3adcfc7076f158ff23',1,'vg::VCFTraversalFinder']]],
- ['check_5fout_8328',['check_out',['../classvg_1_1Watchdog.html#abef59fb95cd3cb40a103d6e73e4c8031',1,'vg::Watchdog']]],
- ['check_5fprotobuf_5ftag_8329',['check_protobuf_tag',['../classvg_1_1io_1_1Registry.html#a0600b489129e1f4090172fccb7863f2b',1,'vg::io::Registry']]],
- ['check_5fquality_5flength_8330',['check_quality_length',['../namespacevg.html#a5de2cc2253344ecabb528c2aa7fd5c1d',1,'vg']]],
- ['check_5fstatus_8331',['check_status',['../classvg_1_1Viz.html#a8dea2be732160c29b1892e76b9dfeeaa',1,'vg::Viz']]],
- ['check_5ftag_5fvalidity_8332',['check_tag_validity',['../gbwt__main_8cpp.html#a4a6504bbdeed67c591fe5b36192a79d7',1,'gbwt_main.cpp']]],
- ['child_5finfo_5ft_8333',['child_info_t',['../structvg_1_1ZipCodeForest_1_1child__info__t.html#aa03360bbe51a60b6da4dfe63e3f1acba',1,'vg::ZipCodeForest::child_info_t']]],
- ['children_5fof_8334',['children_of',['../classvg_1_1SnarlManager.html#abeae275f106a85cca72817c02fd132b2',1,'vg::SnarlManager']]],
- ['choose_5fgood_5fthread_5fcount_8335',['choose_good_thread_count',['../namespacevg.html#acfe23dc452245bf901fee2ed698afe7d',1,'vg']]],
- ['choose_5fln_8336',['choose_ln',['../namespacevg.html#abf777e701e331bb422d91135a13408d2',1,'vg']]],
- ['choose_5ftraversals_8337',['choose_traversals',['../classvg_1_1Deconstructor.html#aedfa437974ff91e1e374cdd0dc786187',1,'vg::Deconstructor']]],
- ['chop_8338',['chop',['../namespacehandlegraph_1_1algorithms.html#a1ff065056c27de74f802ab3e902efc63',1,'handlegraph::algorithms::chop(MutablePathDeletableHandleGraph &graph, size_t max_node_length, const std::function< void(nid_t, size_t, size_t, handle_t)> &record_change)'],['../namespacehandlegraph_1_1algorithms.html#a56d58f1abfff84945de95e7fc6c72a12',1,'handlegraph::algorithms::chop(MutablePathDeletableHandleGraph &graph, size_t max_node_length)']]],
- ['chop_5fnodes_8339',['chop_nodes',['../classvg_1_1Transcriptome.html#ab283e741b49bb9099335fc76c93e6fc7',1,'vg::Transcriptome']]],
- ['chunk_5fto_5femitter_8340',['chunk_to_emitter',['../paths__main_8cpp.html#a94d4a4abb97cdbaf3e5564d60d4ce07c',1,'paths_main.cpp']]],
- ['cigar_5fagainst_5fpath_8341',['cigar_against_path',['../namespacevg.html#a43ac2d1903fa51a20a2366a865f5f0a4',1,'vg::cigar_against_path(const Alignment &alignment, bool on_reverse_strand, int64_t &pos, size_t path_len, size_t softclip_suppress)'],['../namespacevg.html#aaa223d83f7bc78267d7c7a522c909231',1,'vg::cigar_against_path(const multipath_alignment_t &multipath_aln, const string &path_name, bool rev, int64_t path_pos, const PathPositionHandleGraph &graph, int64_t min_splice_length)']]],
- ['cigar_5fmapping_8342',['cigar_mapping',['../namespacevg.html#a81755bb87928f81a864e4a752973bd69',1,'vg::cigar_mapping(const bam1_t *b, Mapping *mapping)'],['../namespacevg.html#a598379872a84d4be8ff74df6242abf10',1,'vg::cigar_mapping(const bam1_t *b, Mapping &mapping)']]],
- ['cigar_5fstring_8343',['cigar_string',['../namespacevg.html#a022b99db4260a7fd77a248bf27c50041',1,'vg']]],
- ['circularize_8344',['circularize',['../classvg_1_1VG.html#a1e2649b8ef5de75db451146c7ac92e92',1,'vg::VG::circularize(nid_t head, nid_t tail)'],['../classvg_1_1VG.html#ad96ff883534a13b28b18cd84dd094e72',1,'vg::VG::circularize(vector< string > pathnames)']]],
- ['classify_5fkmers_8345',['classify_kmers',['../classvg_1_1Recombinator.html#aa7fd2b3cd41b3a1b8ddb04ee7cbfb671',1,'vg::Recombinator::classify_kmers()'],['../namespacevg.html#ab79dc273687fd5360cc145ce18aed912',1,'vg::classify_kmers()'],['../haplotypes__main_8cpp.html#abd40ce33a846ef256ca3b375d9cbb288',1,'classify_kmers(): haplotypes_main.cpp']]],
- ['clear_8346',['clear',['../structvg_1_1Annotation.html#a02cfdb97e80a91c1b108bef79bc4b3af',1,'vg::Annotation::clear()'],['../structvg_1_1GBWTHandler.html#a4563b4f645ab0f48f11d579953410308',1,'vg::GBWTHandler::clear()'],['../structvg_1_1AugmentedGraph.html#ad394712ba7a2480a7c811e8bde56253b',1,'vg::AugmentedGraph::clear()'],['../structvg_1_1SupportAugmentedGraph.html#a02bf17acd1d5deb6e3044f9807756e81',1,'vg::SupportAugmentedGraph::clear()'],['../classvg_1_1Packer.html#a0680bd0b5bbe74029e94b33e2f1ea666',1,'vg::Packer::clear()'],['../classvg_1_1Paths.html#a8ddaaebbbe22105029887baddf9cbdf7',1,'vg::Paths::clear()'],['../classvg_1_1SmallBitset.html#a22c6afec220aa75244da08ca04f5825d',1,'vg::SmallBitset::clear()'],['../classvg_1_1VG.html#aa1eb3332c0a99a25c75681da485297e5',1,'vg::VG::clear()'],['../structGraphHandler.html#aafe821b2ce9cab8ae340e685154bff87',1,'GraphHandler::clear()'],['../classhandlegraph_1_1DeletableHandleGraph.html#a6e1a83e72b47643e43c6176f39d8db5e',1,'handlegraph::DeletableHandleGraph::clear()']]],
- ['clear_5falignment_8347',['clear_alignment',['../namespacevg.html#a0406641335bb841c51b0c103219a29da',1,'vg']]],
- ['clear_5fannotation_8348',['clear_annotation',['../classvg_1_1multipath__alignment__t.html#a9d1c72d4a76dff3ac93f3185bcd3e981',1,'vg::multipath_alignment_t::clear_annotation()'],['../namespacevg.html#ad970d2836c53996c21e5c5d9d3e0a6d8',1,'vg::clear_annotation(Annotated *annotated, const string &name)'],['../namespacevg.html#ae414970cfc37049b4dc9b308d9ed5f59',1,'vg::clear_annotation(Annotated &annotated, const string &name)']]],
- ['clear_5fconnection_8349',['clear_connection',['../classvg_1_1subpath__t.html#a6584b9a093baa1a3edf9e690cc232b2d',1,'vg::subpath_t']]],
- ['clear_5fcrash_5fcontext_8350',['clear_crash_context',['../namespacevg.html#af64359d12f27f1035ce70e4ff1622f9c',1,'vg']]],
- ['clear_5fedge_5findexes_8351',['clear_edge_indexes',['../classvg_1_1VG.html#a10d4b49633db2aef463e0070e0af64a0',1,'vg::VG']]],
- ['clear_5fedge_5findexes_5fno_5fresize_8352',['clear_edge_indexes_no_resize',['../classvg_1_1VG.html#a5195712f8aa650417d93324ff1c89ecf',1,'vg::VG']]],
- ['clear_5findexes_8353',['clear_indexes',['../classvg_1_1VG.html#aae960ce1d640fadc4772795f6d0ff5b5',1,'vg::VG']]],
- ['clear_5findexes_5fno_5fresize_8354',['clear_indexes_no_resize',['../classvg_1_1VG.html#a103c69bad02121590779530338861374',1,'vg::VG']]],
- ['clear_5fmapping_8355',['clear_mapping',['../classvg_1_1path__t.html#a4c03d698f5c00f0d4545fa78f1c615f3',1,'vg::path_t']]],
- ['clear_5fmapping_5franks_8356',['clear_mapping_ranks',['../classvg_1_1Paths.html#a599d6b0652ff6f3c9bbe731136ad910a',1,'vg::Paths']]],
- ['clear_5fnext_8357',['clear_next',['../classvg_1_1subpath__t.html#a691d6adfa24ab6970ba1736212e2f276',1,'vg::subpath_t']]],
- ['clear_5fnode_5findexes_8358',['clear_node_indexes',['../classvg_1_1VG.html#a212a2d1028f28046088a86e128b40559',1,'vg::VG']]],
- ['clear_5fnode_5findexes_5fno_5fresize_8359',['clear_node_indexes_no_resize',['../classvg_1_1VG.html#af51220e88887adf92d7cff25dad5cd91',1,'vg::VG']]],
- ['clear_5fpaths_8360',['clear_paths',['../classvg_1_1VG.html#aa4e534461834b2937b7f0b0c2420b899',1,'vg::VG']]],
- ['clear_5freachability_5fedges_8361',['clear_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#af112f1a5af47cf079a163eec1c2e31f4',1,'vg::MultipathAlignmentGraph']]],
- ['clear_5fscores_8362',['clear_scores',['../classvg_1_1MEMChainModel.html#aef30eacf1dfd97658fbdc85ce175fad1',1,'vg::MEMChainModel::clear_scores()'],['../classvg_1_1AlignmentChainModel.html#a0357717699cc97b6c5a8a164dfd424fb',1,'vg::AlignmentChainModel::clear_scores()']]],
- ['clear_5fstart_8363',['clear_start',['../classvg_1_1multipath__alignment__t.html#a9436c421aa0550bb65c55bd557ad97c4',1,'vg::multipath_alignment_t']]],
- ['clear_5fsubpath_8364',['clear_subpath',['../classvg_1_1multipath__alignment__t.html#af72f755d9dd5b4b11b379ee227997a2b',1,'vg::multipath_alignment_t']]],
- ['clip_5fcontained_5flow_5fdepth_5fnodes_5fand_5fedges_8365',['clip_contained_low_depth_nodes_and_edges',['../namespacevg.html#afca0783176bbca00f50e9c8f4b53515c',1,'vg']]],
- ['clip_5fcontained_5fsnarls_8366',['clip_contained_snarls',['../namespacevg.html#affb16bab122c9abe8aa4282992b8fe12',1,'vg']]],
- ['clip_5fcontained_5fstubs_8367',['clip_contained_stubs',['../namespacevg.html#afc1766ad15ac6853f074a743d19873fc',1,'vg']]],
- ['clip_5fdeletion_5fedges_8368',['clip_deletion_edges',['../namespacevg.html#a4f58b3aa775dcde39a1d511a9d838b97',1,'vg']]],
- ['clip_5flow_5fdepth_5fnodes_5fand_5fedges_8369',['clip_low_depth_nodes_and_edges',['../namespacevg.html#aeaa0f9143fd06ff6948f2b548e4dde12',1,'vg']]],
- ['clip_5flow_5fdepth_5fnodes_5fand_5fedges_5fgeneric_8370',['clip_low_depth_nodes_and_edges_generic',['../namespacevg.html#a1c4eb49afa34726115d01e380372669a',1,'vg']]],
- ['clip_5fstubs_8371',['clip_stubs',['../namespacevg.html#ae596e7d9757cad372b5aaeb5e8a5146e',1,'vg']]],
- ['clip_5fstubs_5fgeneric_8372',['clip_stubs_generic',['../namespacevg.html#aba796b34b1f89333758ff6cb4271f708',1,'vg']]],
- ['close_8373',['close',['../classvg_1_1Viz.html#a80cd5bc578f48ea2279e298405e71393',1,'vg::Viz']]],
- ['close_5fchain_8374',['close_chain',['../classvg_1_1ZipCodeForest.html#a2307457a70762459688446395338b3f8',1,'vg::ZipCodeForest']]],
- ['close_5fedit_5ftmpfiles_8375',['close_edit_tmpfiles',['../classvg_1_1Packer.html#afd2c25becb15d4780d62673b11b2bce9',1,'vg::Packer']]],
- ['close_5ffd_8376',['close_fd',['../classhandlegraph_1_1TriviallySerializable.html#afc178fcc343f3447429904192127ce5e',1,'handlegraph::TriviallySerializable']]],
- ['close_5fsnarl_8377',['close_snarl',['../classvg_1_1ZipCodeForest.html#a5579f467bd35b2e13a753af31baf5bf6',1,'vg::ZipCodeForest']]],
- ['cluster_5fchain_5flevel_8378',['cluster_chain_level',['../classvg_1_1SnarlDistanceIndexClusterer.html#a92faf3de4024dcb284ae3b0487f6b1f2',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5fcover_8379',['cluster_cover',['../namespacevg.html#afe3e65f9aafb5ab9ce5455cc72fa0b56',1,'vg']]],
- ['cluster_5fcoverage_8380',['cluster_coverage',['../namespacevg.html#a3380e0f81fc879601afe493949814a4d',1,'vg']]],
- ['cluster_5fmultiplicity_8381',['cluster_multiplicity',['../classvg_1_1MultipathMapper.html#a773dfb92a782fc5bc46d371aaeee5d7e',1,'vg::MultipathMapper']]],
- ['cluster_5fnodes_8382',['cluster_nodes',['../namespacevg.html#af6c60d6eb4cafd02a45384cf71a12bfe',1,'vg']]],
- ['cluster_5fone_5fchain_8383',['cluster_one_chain',['../classvg_1_1SnarlDistanceIndexClusterer.html#ad5f6b8a6201ce57b88b2d7bf772e1da6',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5fone_5fnode_8384',['cluster_one_node',['../classvg_1_1SnarlDistanceIndexClusterer.html#a1b3707a4eac66610e37faaf4f6ff9eff',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5fone_5fsnarl_8385',['cluster_one_snarl',['../classvg_1_1SnarlDistanceIndexClusterer.html#a0f1a2986c932dfe614d11707cef49bd8',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5froot_8386',['cluster_root',['../classvg_1_1SnarlDistanceIndexClusterer.html#afed897fb0affc471c0800137a5ff9872',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5fseeds_8387',['cluster_seeds',['../classvg_1_1SnarlDistanceIndexClusterer.html#a210ee5c625ead0e415f2276d1d20bb05',1,'vg::SnarlDistanceIndexClusterer::cluster_seeds(const vector< Seed > &seeds, size_t read_distance_limit) const'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a37e825d3d82904c3bda0598ac1093326',1,'vg::SnarlDistanceIndexClusterer::cluster_seeds(const vector< vector< Seed >> &all_seeds, size_t read_distance_limit, size_t fragment_distance_limit=0) const']]],
- ['cluster_5fseeds_5finternal_8388',['cluster_seeds_internal',['../classvg_1_1SnarlDistanceIndexClusterer.html#a1c7c1aee0a7019289ca94234fe604075',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5fseeds_5fon_5flinear_5fstructure_8389',['cluster_seeds_on_linear_structure',['../classvg_1_1SnarlDistanceIndexClusterer.html#a31a2fd3cf7ce67590b86c45bb4f2b91e',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5fsnarl_5flevel_8390',['cluster_snarl_level',['../classvg_1_1SnarlDistanceIndexClusterer.html#ac823b12963123338ac75a24f930dd93e',1,'vg::SnarlDistanceIndexClusterer']]],
- ['cluster_5fsubgraph_5fcontaining_8391',['cluster_subgraph_containing',['../namespacevg.html#ae9f1bd05c1d67c074797eded33151e88',1,'vg']]],
- ['cluster_5fsubgraph_5fwalk_8392',['cluster_subgraph_walk',['../namespacevg.html#ac20a47954c6352afbd98da5b7d4f2d95',1,'vg']]],
- ['cluster_5ftraversals_8393',['cluster_traversals',['../namespacevg.html#a392e3bc708a380e7a3d9b3a669aaf2a9',1,'vg']]],
- ['clusterhead_8394',['ClusterHead',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a87d8ac85cefd70275dc55c20bc49ee5b',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::ClusterHead()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a621a8a6363f9a729a95232eed4f7411e',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::ClusterHead(const size_t &read_num, const size_t &cluster_num, const size_t &distance_left, const size_t &distance_right)']]],
- ['clusteringproblem_8395',['ClusteringProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a1b2df3785e61d5e89573a07384226e30',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['clusters_8396',['clusters',['../classvg_1_1MEMClusterer.html#ad3b20603d24524f93534cc72a15abc22',1,'vg::MEMClusterer::clusters()'],['../classvg_1_1MEMClusterer_1_1HitGraph.html#a3ee3c0afa42fc839555bdbac8d4a8876',1,'vg::MEMClusterer::HitGraph::clusters()']]],
- ['clusters_5foverlap_5fin_5fgraph_8397',['clusters_overlap_in_graph',['../namespacevg.html#a9d8947e51da3156529e12ae131c25a47',1,'vg']]],
- ['clusters_5foverlap_5fin_5fread_8398',['clusters_overlap_in_read',['../namespacevg.html#af67eb440256877ac857d6649052d7db1',1,'vg']]],
- ['clusters_5foverlap_5flength_8399',['clusters_overlap_length',['../namespacevg.html#a50260b7d42777dd7f352a5ba40ac655e',1,'vg']]],
- ['clusters_5fto_5fdrop_8400',['clusters_to_drop',['../classvg_1_1Mapper.html#acb02353297bd88867df48edcac91cf9d',1,'vg::Mapper']]],
- ['collapse_5forder_5flength_5fruns_8401',['collapse_order_length_runs',['../classvg_1_1MultipathAlignmentGraph.html#a8f309bbf60941b009379bd9661cb9060',1,'vg::MultipathAlignmentGraph']]],
- ['collect_5fcoverage_8402',['collect_coverage',['../classvg_1_1Packer.html#a84a402c1da28b53f120ee11ff6bf0f44',1,'vg::Packer']]],
- ['collect_5fsubgraph_8403',['collect_subgraph',['../classvg_1_1VG.html#a688cbe42750d98695114ad4ad640c1d3',1,'vg::VG']]],
- ['collect_5ftranscribed_5fnodes_8404',['collect_transcribed_nodes',['../classvg_1_1Transcriptome.html#a3f7a516340769783dda7a5556049916b',1,'vg::Transcriptome']]],
- ['colors_8405',['Colors',['../classvg_1_1Colors.html#a8bef9f7ce8512f3e800dded6a8470ac1',1,'vg::Colors::Colors(void)'],['../classvg_1_1Colors.html#a89032e6156425d236bcd721e3f1343d4',1,'vg::Colors::Colors(int seed_val)']]],
- ['combine_8406',['combine',['../structvg_1_1Recombinator_1_1Statistics.html#a9f4b13079e31ae50f127b4f05cdc5ce9',1,'vg::Recombinator::Statistics::combine()'],['../classvg_1_1VG.html#a7d06218f137184c366de80df755ae001',1,'vg::VG::combine()']]],
- ['combine_5fhandles_8407',['combine_handles',['../namespacehandlegraph_1_1algorithms.html#a843ff1c62aa75e4c3ec1b7a5d0ea88d3',1,'handlegraph::algorithms']]],
- ['combine_5fhashes_8408',['combine_hashes',['../namespacestd.html#abae1208746caacfaebe7e9493549ae0b',1,'std']]],
- ['combine_5fqualities_8409',['combine_qualities',['../classvg_1_1Packer.html#a2ae7de0ddbcb2e930a313e2881f6a988',1,'vg::Packer']]],
- ['comma_8410',['comma',['../classvg_1_1ProblemDumpExplainer.html#a4f372e8fa0273774608ef668584a1b42',1,'vg::ProblemDumpExplainer']]],
- ['common_5fancestor_5fnext_8411',['common_ancestor_next',['../classvg_1_1VG.html#a2e1708efaeceace87615bb67715d60fa',1,'vg::VG']]],
- ['common_5fancestor_5fprev_8412',['common_ancestor_prev',['../classvg_1_1VG.html#ab3ba20713228cb76fa4b982d967654aa',1,'vg::VG']]],
- ['common_5fbin_8413',['common_bin',['../classvg_1_1StreamIndexBase.html#a8486253e2bf627ef07fbb2eec5614bd3',1,'vg::StreamIndexBase']]],
- ['common_5fprefix_5flength_8414',['common_prefix_length',['../classvg_1_1BitString.html#ab455acfc92e349b674bcc865446f13bf',1,'vg::BitString']]],
- ['compact_5fids_8415',['compact_ids',['../classvg_1_1VG.html#a161ef56bd0eeee937602f60b8617f24d',1,'vg::VG::compact_ids(void)'],['../classvg_1_1VG.html#ae931543bdeed5e60edcf6225489e3ceb',1,'vg::VG::compact_ids(hash_map< nid_t, nid_t > &new_id)']]],
- ['compact_5franks_8416',['compact_ranks',['../classvg_1_1Paths.html#aaf065b12a8a942c96f6d88a2c6db7c8e',1,'vg::Paths']]],
- ['compare_8417',['compare',['../structReferenceInterval.html#a192a091b5ecee1d80e18143a9ea6d909',1,'ReferenceInterval']]],
- ['compare_5fand_5fcombine_5fcluster_5fon_5fchild_5fstructures_8418',['compare_and_combine_cluster_on_child_structures',['../classvg_1_1SnarlDistanceIndexClusterer.html#a0d03992071ee1f20ad833992e145b305',1,'vg::SnarlDistanceIndexClusterer']]],
- ['compare_5fand_5fcombine_5fcluster_5fon_5fone_5fchild_8419',['compare_and_combine_cluster_on_one_child',['../classvg_1_1SnarlDistanceIndexClusterer.html#a98757d1cd5e82dd67e9056890cc1077d',1,'vg::SnarlDistanceIndexClusterer']]],
- ['complement_5fcomponents_8420',['complement_components',['../classvg_1_1PhaseUnfolder.html#a09b845f1fd318a70f5f9e9aa50e5d435',1,'vg::PhaseUnfolder']]],
- ['completed_5findexes_8421',['completed_indexes',['../classvg_1_1IndexRegistry.html#a1a39419b55745505a20ee70bfdc43f48',1,'vg::IndexRegistry']]],
- ['completedtranscriptpath_8422',['CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html#a159b9e750c37a9bbe1b1509e3ebca344',1,'vg::CompletedTranscriptPath::CompletedTranscriptPath(const EditedTranscriptPath &edited_transcript_path)'],['../structvg_1_1CompletedTranscriptPath.html#a2ccd3feaa958a813a2121d99cc7283f3',1,'vg::CompletedTranscriptPath::CompletedTranscriptPath(const EditedTranscriptPath &edited_transcript_path, const HandleGraph &graph)']]],
- ['component_5fpaths_8423',['component_paths',['../namespacevg_1_1algorithms.html#a51f810108840ab4014eb58b2bfe19ac1',1,'vg::algorithms']]],
- ['component_5fpaths_5fparallel_8424',['component_paths_parallel',['../namespacevg_1_1algorithms.html#a10b07f6f41f8dd36c5d3b1ff9a03ce93',1,'vg::algorithms']]],
- ['component_5fsizes_8425',['component_sizes',['../namespacevg_1_1algorithms.html#a8e5fdb03a21f88395e1d69f53821ae59',1,'vg::algorithms']]],
- ['component_5ftopological_5forder_8426',['component_topological_order',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a44c8d49fb946c427aca7584dcd28746a',1,'vg::MEMClusterer::HitGraph']]],
- ['componentmindistanceclusterer_8427',['ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html#a9d544da8f5ad8699bc359d0b3407f1d4',1,'vg::ComponentMinDistanceClusterer']]],
- ['components_8428',['components',['../classvg_1_1Haplotypes.html#a1617e9b0fbd01fc77fd87c527e5dbd24',1,'vg::Haplotypes']]],
- ['compose_5fshort_5fpath_5fname_8429',['compose_short_path_name',['../namespacevg.html#a04bb552d73f5ed9ca37d1227acacee4a',1,'vg']]],
- ['compressstring_8430',['CompressString',['../namespacezstdutil.html#a2ae66a8ffc0bbea2444ff59fc0421033',1,'zstdutil']]],
- ['compute_5fall_5fmapping_5fqualities_8431',['compute_all_mapping_qualities',['../classvg_1_1GSSWAligner.html#af5f906f0628c45c3507524da99754d93',1,'vg::GSSWAligner']]],
- ['compute_5fborders_5fand_5fdimensions_8432',['compute_borders_and_dimensions',['../classvg_1_1Viz.html#a8a9eb721a92953e9a3e84f45f1952a9c',1,'vg::Viz']]],
- ['compute_5fchains_8433',['compute_chains',['../classvg_1_1SnarlManager.html#a50fd20deea9859d27991e276b224d7d5',1,'vg::SnarlManager']]],
- ['compute_5fcluster_5fmapping_5fquality_8434',['compute_cluster_mapping_quality',['../classvg_1_1Mapper.html#a3c546df7f298da47127ca6dbaf3462b7',1,'vg::Mapper']]],
- ['compute_5ffirst_5fmapping_5fquality_8435',['compute_first_mapping_quality',['../classvg_1_1GSSWAligner.html#ad39d942f83d8d168daf96142a1fecd2b',1,'vg::GSSWAligner']]],
- ['compute_5fgroup_5fmapping_5fquality_8436',['compute_group_mapping_quality',['../classvg_1_1GSSWAligner.html#a84bcb00f3e4cb834cdbc62beaec8f894',1,'vg::GSSWAligner']]],
- ['compute_5fmapping_5fqualities_8437',['compute_mapping_qualities',['../classvg_1_1Mapper.html#ad062cafbbb49bc4960e59b3ffd499ca8',1,'vg::Mapper::compute_mapping_qualities(vector< Alignment > &alns, double cluster_mq, double mq_estimate, double mq_cap)'],['../classvg_1_1Mapper.html#af4905e4355e1132811a974cb5cb42e95',1,'vg::Mapper::compute_mapping_qualities(pair< vector< Alignment >, vector< Alignment >> &pair_alns, double cluster_mq, double mq_estmate1, double mq_estimate2, double mq_cap1, double mq_cap2)']]],
- ['compute_5fmapping_5fquality_8438',['compute_mapping_quality',['../classvg_1_1GSSWAligner.html#a627256abe48089a54509400db8916ff3',1,'vg::GSSWAligner']]],
- ['compute_5fmapq_5fcaps_8439',['compute_mapq_caps',['../classvg_1_1MinimizerMapper.html#ad0a9d591551601ea3699b8a1b2347e81',1,'vg::MinimizerMapper']]],
- ['compute_5fmax_5fmapping_5fquality_8440',['compute_max_mapping_quality',['../classvg_1_1GSSWAligner.html#ae2f5d5343d90ef6778d8c634bfc76c06',1,'vg::GSSWAligner']]],
- ['compute_5fmin_5fcut_8441',['compute_min_cut',['../namespacevg_1_1algorithms.html#a7ae1eba2313c3ce068851c85b8d019e2',1,'vg::algorithms']]],
- ['compute_5fpaired_5fmapping_5fquality_8442',['compute_paired_mapping_quality',['../classvg_1_1GSSWAligner.html#ad896b2b0b1956da5f57bc3abbbd65701',1,'vg::GSSWAligner']]],
- ['compute_5fpath_5finterval_8443',['compute_path_interval',['../classvg_1_1Surjector.html#adf6d3d9d2bec77f147192b05fc4df18b',1,'vg::Surjector']]],
- ['compute_5fquality_8444',['compute_quality',['../classvg_1_1Packer.html#aedce0118963e5d735a2e70e29b70fe62',1,'vg::Packer']]],
- ['compute_5fraw_5fmapping_5fqualities_5ffrom_5fscores_8445',['compute_raw_mapping_qualities_from_scores',['../classvg_1_1MultipathMapper.html#a114346585956311ff3db920e34573501',1,'vg::MultipathMapper']]],
- ['compute_5ftail_5fmem_5fcoverage_8446',['compute_tail_mem_coverage',['../classvg_1_1OrientedDistanceClusterer.html#a5fad154b1267d5d3861870a51b482d9b',1,'vg::OrientedDistanceClusterer']]],
- ['compute_5ftemplate_5flengths_8447',['compute_template_lengths',['../namespacevg.html#ad3824b96906cc229f270166a06a7a625',1,'vg']]],
- ['compute_5funiqueness_8448',['compute_uniqueness',['../classvg_1_1Mapper.html#a4f13155eaeae93ca9ad6ec8095e2335c',1,'vg::Mapper']]],
- ['concat_5fmappings_8449',['concat_mappings',['../namespacevg.html#a8fc7225da088d27cd1201422ba011f51',1,'vg']]],
- ['concat_5fmappings_5ffor_5fnode_5fpair_8450',['concat_mappings_for_node_pair',['../classvg_1_1VG.html#a150341270e41f42db2578a2897e48c1b',1,'vg::VG']]],
- ['concat_5fnodes_8451',['concat_nodes',['../namespacehandlegraph_1_1algorithms.html#a9c46c9dde150b8a2e2bbe785b1889534',1,'handlegraph::algorithms']]],
- ['concat_5fpaths_8452',['concat_paths',['../namespacevg.html#ac7d43d119d665bda802489b3309e0bce',1,'vg']]],
- ['condense_5fedits_8453',['condense_edits',['../classvg_1_1Constructor.html#a1b13ae925876f9f7617850ab4e2ad355',1,'vg::Constructor']]],
- ['configurableparser_8454',['ConfigurableParser',['../classvg_1_1ConfigurableParser.html#ad04ba6f1c85aa2ab15b93e51c4a093f7',1,'vg::ConfigurableParser']]],
- ['connect_8455',['connect',['../classvg_1_1WFAExtender.html#afa5938e94fc17adb3df680632ff97601',1,'vg::WFAExtender::connect()'],['../structvg_1_1RecombinatorHaplotype.html#ac449ff9fef162a7f627df68bcc9b1007',1,'vg::RecombinatorHaplotype::connect()']]],
- ['connect_5fconsistently_8456',['connect_consistently',['../classvg_1_1MinimizerMapper.html#a2bba608ac7474700ace2ac9a071198f1',1,'vg::MinimizerMapper']]],
- ['connect_5fnode_5fto_5fnodes_8457',['connect_node_to_nodes',['../classvg_1_1VG.html#ad68d2bfaa6627686967add4ca7fb5f4c',1,'vg::VG::connect_node_to_nodes(NodeTraversal node, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#ab8189716ecbb9eeeefec8be64e34a9e3',1,'vg::VG::connect_node_to_nodes(Node *node, vector< Node * > &nodes, bool from_start=false)']]],
- ['connect_5fnodes_5fto_5fnode_8458',['connect_nodes_to_node',['../classvg_1_1VG.html#a7ee6066424793dfcda9097419f03b568',1,'vg::VG::connect_nodes_to_node(vector< NodeTraversal > &nodes, NodeTraversal node)'],['../classvg_1_1VG.html#acc4db5878a40e8dc7d2d2b25ff62ff1e',1,'vg::VG::connect_nodes_to_node(vector< Node * > &nodes, Node *node, bool to_end=false)']]],
- ['connect_5fto_5fposition_5ffile_8459',['connect_to_position_file',['../classvg_1_1NGSSimulator.html#aceec560b267d4a2d4a1c37fb3691dde5',1,'vg::NGSSimulator']]],
- ['connected_5fcomponents_8460',['connected_components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ad18510c8be7b8b21bc0cce8b33bf54e3',1,'vg::MEMClusterer::HitGraph::connected_components()'],['../classvg_1_1Surjector.html#af7bc3c25f2466322fd6ffd67d66c6dfa',1,'vg::Surjector::connected_components()'],['../namespacevg.html#a68859b86cb7465d17ca9cb68553a8e4c',1,'vg::connected_components()']]],
- ['connected_5fcomps_5fdo_8461',['connected_comps_do',['../namespacevg.html#a37c256d47f5d50349766d6f8085b017f',1,'vg']]],
- ['connection_8462',['connection',['../classvg_1_1subpath__t.html#ab0f42733d3f01f36292bd20368e169e7',1,'vg::subpath_t::connection() const'],['../classvg_1_1subpath__t.html#adb07c26e5a8a06dad0f64cf68f7a5e26',1,'vg::subpath_t::connection(size_t i) const']]],
- ['connection_5fsize_8463',['connection_size',['../classvg_1_1subpath__t.html#ac69a45141f2de5117178e2b000ec9507',1,'vg::subpath_t']]],
- ['connection_5ft_8464',['connection_t',['../classvg_1_1connection__t.html#ae8ba824a4323fa99471a02d908df41c0',1,'vg::connection_t::connection_t()=default'],['../classvg_1_1connection__t.html#abd98927a5c23d95159667eba540b4646',1,'vg::connection_t::connection_t(const connection_t &)=default'],['../classvg_1_1connection__t.html#ad940cca19833570b242f00d57f817a97',1,'vg::connection_t::connection_t(connection_t &&)=default']]],
- ['construct_8465',['construct',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a7ce1ec0bba000de1600ce2beb70acc47',1,'vg::FlowSort::WeightedGraph']]],
- ['construct_5fchunk_8466',['construct_chunk',['../classvg_1_1Constructor.html#aab2b25c3b99fabdb0f382e2698ca3a52',1,'vg::Constructor']]],
- ['construct_5fcompleted_5ftranscript_5fpaths_8467',['construct_completed_transcript_paths',['../classvg_1_1Transcriptome.html#ade5704f06f63770a2871b92d48efdabd',1,'vg::Transcriptome']]],
- ['construct_5fgraph_8468',['construct_graph',['../classvg_1_1Constructor.html#a0a87f468f65b2cacc3a47060378de7a3',1,'vg::Constructor::construct_graph(string vcf_contig, FastaReference &reference, VcfBuffer &variant_source, const vector< FastaReference * > &insertion, const function< void(Graph &)> &callback)'],['../classvg_1_1Constructor.html#a2d69f28be35ff23ef4d0f80e645bdbc2',1,'vg::Constructor::construct_graph(const vector< FastaReference * > &references, const vector< vcflib::VariantCallFile * > &variant_files, const vector< FastaReference * > &insertions, const function< void(Graph &)> &callback)'],['../classvg_1_1Constructor.html#a100345d3fca726262c98ab83768f0f0c',1,'vg::Constructor::construct_graph(const vector< string > &reference_filenames, const vector< string > &variant_filenames, const vector< string > &insertion_filenames, const function< void(Graph &)> &callback)'],['../classvg_1_1Constructor.html#a5dbf56a3eee98b1f678dafc69bb35e97',1,'vg::Constructor::construct_graph(const vector< FastaReference * > &references, const vector< vcflib::VariantCallFile * > &variant_files, const vector< FastaReference * > &insertions, MutablePathMutableHandleGraph *destination)'],['../classvg_1_1Constructor.html#a5c9a9c3adb2ddafc4d4434c689bb42ad',1,'vg::Constructor::construct_graph(const vector< string > &reference_filenames, const vector< string > &variant_filenames, const vector< string > &insertion_filenames, MutablePathMutableHandleGraph *destination)']]],
- ['construct_5fgraph_5ffrom_5fnodes_5fand_5fedges_8469',['construct_graph_from_nodes_and_edges',['../namespacevg.html#a5b7416f4636f53c22bcb1fab81d63de8',1,'vg']]],
- ['construct_5freference_5ftranscript_5fpaths_5fembedded_8470',['construct_reference_transcript_paths_embedded',['../classvg_1_1Transcriptome.html#aab8e9e4cf0cf855de888086388577d56',1,'vg::Transcriptome']]],
- ['construct_5freference_5ftranscript_5fpaths_5fembedded_5fcallback_8471',['construct_reference_transcript_paths_embedded_callback',['../classvg_1_1Transcriptome.html#a342c0573251aa2839b7ea1ebbdd44db9',1,'vg::Transcriptome']]],
- ['construct_5freference_5ftranscript_5fpaths_5fgbwt_8472',['construct_reference_transcript_paths_gbwt',['../classvg_1_1Transcriptome.html#a1a74c22fd6c47986e1dc4e7a68dad42d',1,'vg::Transcriptome']]],
- ['construct_5freference_5ftranscript_5fpaths_5fgbwt_5fcallback_8473',['construct_reference_transcript_paths_gbwt_callback',['../classvg_1_1Transcriptome.html#a162034e99f2ee027816af34776a9b3d6',1,'vg::Transcriptome']]],
- ['contains_8474',['contains',['../structvg_1_1GaplessExtension.html#a019486c5f7e5aab04d9e5b78aac3d069',1,'vg::GaplessExtension::contains()'],['../classvg_1_1SmallBitset.html#a58b8cbb133801d25d76785eb54bf6247',1,'vg::SmallBitset::contains()']]],
- ['contains_5fconnection_8475',['contains_connection',['../namespacevg.html#a3f65013661cfc322222585843c30773a',1,'vg']]],
- ['contains_5fmatch_8476',['contains_match',['../namespacevg.html#accfb6f4fc450e420c5b147cff9e6ae31',1,'vg']]],
- ['contains_5freversals_8477',['contains_reversals',['../classvg_1_1HaplotypePartitioner.html#a4c032fa5d7fcb5c2d52bba8604c1d0d7',1,'vg::HaplotypePartitioner']]],
- ['contains_5fsubsequence_8478',['contains_subsequence',['../classvg_1_1ReadFilter.html#a553af1f5f52e24334fb2dd22928ac86a',1,'vg::ReadFilter']]],
- ['contract_8479',['contract',['../classvg_1_1ContractingGraph.html#afd959435308c7c6afdd041519ed71cda',1,'vg::ContractingGraph']]],
- ['contractinggraph_8480',['ContractingGraph',['../classvg_1_1ContractingGraph.html#acc9acc04ee74d97808d811d77252afc3',1,'vg::ContractingGraph']]],
- ['convert_8481',['convert',['../classvg_1_1VcfRecordConverter.html#a30aaab305cfc665f6f9588997fdd2297',1,'vg::VcfRecordConverter::convert()'],['../namespacevg.html#a5674e45f23020370046d49c674fd691f',1,'vg::convert(const std::string &s, T &r)'],['../namespacevg.html#ad7b1ca8b13ad1732d0679723bb206f18',1,'vg::convert(const T &r)']]],
- ['convert_5falignment_8482',['convert_alignment',['../classvg_1_1HTSAlignmentEmitter.html#a5cfe9918348db19fc8b8a153a953715b',1,'vg::HTSAlignmentEmitter::convert_alignment()'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#ac837e6ec08c270afb4f6d231e4f58473',1,'vg::SplicedHTSAlignmentEmitter::convert_alignment()']]],
- ['convert_5falignment_5fchar_8483',['convert_alignment_char',['../namespacevg.html#a256962a964ea02f3d4ec54c5c48d72a8',1,'vg']]],
- ['convert_5fmultipath_5falignment_5fchar_8484',['convert_multipath_alignment_char',['../namespacevg.html#a1f29020dbd628bd21a9a039ee718b29b',1,'vg']]],
- ['convert_5fpaired_8485',['convert_paired',['../classvg_1_1HTSAlignmentEmitter.html#a8a9025992d59e3425495bb39d97846d9',1,'vg::HTSAlignmentEmitter']]],
- ['convert_5fto_5falignment_8486',['convert_to_alignment',['../classvg_1_1MultipathAlignmentEmitter.html#a968d8ce848da6dfda8ef0493f6044625',1,'vg::MultipathAlignmentEmitter']]],
- ['convert_5fto_5fhts_5fpaired_8487',['convert_to_hts_paired',['../classvg_1_1MultipathAlignmentEmitter.html#aff86d0fed6f025e037468c9f94dc47d7',1,'vg::MultipathAlignmentEmitter']]],
- ['convert_5fto_5fhts_5funpaired_8488',['convert_to_hts_unpaired',['../classvg_1_1MultipathAlignmentEmitter.html#a47ac4acd24f69e0d8427a136e29b872f',1,'vg::MultipathAlignmentEmitter']]],
- ['convert_5fts_5fto_5fus_8489',['convert_Ts_to_Us',['../namespacevg.html#add9a4cf274b29df3caf222d0360805f3',1,'vg::convert_Ts_to_Us(Alignment &alignment)'],['../namespacevg.html#a92c7d384c096b813501b23730e308796',1,'vg::convert_Ts_to_Us(multipath_alignment_t &multipath_aln)']]],
- ['convert_5funpaired_8490',['convert_unpaired',['../classvg_1_1HTSAlignmentEmitter.html#a8813a78822ccd54b41dc4fbe944f9d65',1,'vg::HTSAlignmentEmitter']]],
- ['convert_5fus_5fto_5fts_8491',['convert_Us_to_Ts',['../namespacevg.html#abdc8589575aed95e82c0bb70828ab036',1,'vg::convert_Us_to_Ts(Alignment &alignment)'],['../namespacevg.html#a5a6e3cc99aac92404ec33126dbbd9192',1,'vg::convert_Us_to_Ts(multipath_alignment_t &multipath_aln)']]],
- ['copy_8492',['copy',['../classvg_1_1SmallBitset.html#aac805c827da15890d9b237643fc49b1f',1,'vg::SmallBitset']]],
- ['copy_5ffile_8493',['copy_file',['../namespacevg.html#a1c2f1e37da37dda61d25e9d8bb6552d6',1,'vg']]],
- ['copy_5fhandle_5fgraph_8494',['copy_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a3031a57a4bd2e9e4f65a1130fe4eb148',1,'handlegraph::algorithms']]],
- ['copy_5fmetadata_8495',['copy_metadata',['../namespacevg.html#ab2237df8adff809619083730f10d0e2e',1,'vg']]],
- ['copy_5fpath_8496',['copy_path',['../namespacehandlegraph_1_1algorithms.html#a57d9936f8b98983f3121d074c62583bd',1,'handlegraph::algorithms::copy_path(const PathHandleGraph *from, const path_handle_t &from_path, MutablePathHandleGraph *into)'],['../namespacehandlegraph_1_1algorithms.html#a8ec649327e4580fc65bad976f04f6e1c',1,'handlegraph::algorithms::copy_path(const PathHandleGraph *from, const path_handle_t &from_path, MutablePathHandleGraph *into, const path_handle_t &into_path)']]],
- ['copy_5fpath_5fhandle_5fgraph_8497',['copy_path_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a1a253b430ffee65ce08f3a7508306550',1,'handlegraph::algorithms']]],
- ['copy_5freference_5fsamples_8498',['copy_reference_samples',['../namespacevg.html#a03a4b946e48b89b3ec8857b04ded59db',1,'vg::copy_reference_samples(const gbwt::GBWT &source, gbwt::GBWT &destination)'],['../namespacevg.html#a2422b98737c90954afcd957a8566857d',1,'vg::copy_reference_samples(const PathHandleGraph &source, gbwt::GBWT &destination)']]],
- ['corresponding_5ffrom_5flength_8499',['corresponding_from_length',['../namespacevg.html#a84d3002d98148b82b4f395c7b625b892',1,'vg']]],
- ['corresponding_5flength_5finternal_8500',['corresponding_length_internal',['../namespacevg.html#a9dffafa4fdd05242ff4b73f5aafedd95',1,'vg']]],
- ['corresponding_5fto_5flength_8501',['corresponding_to_length',['../namespacevg.html#a1fa02fa34866aee06ca1e3cead896b8d',1,'vg']]],
- ['count_8502',['count',['../classvg_1_1HandleGraphNodeSet.html#ab39b3c91e81b50028a4b7cef88b2a772',1,'vg::HandleGraphNodeSet::count()'],['../classvg_1_1SmallBitset.html#af834de5870b38cc53768eb8ba9c60025',1,'vg::SmallBitset::count()']]],
- ['count_5fback_5finserter_8503',['count_back_inserter',['../classvg_1_1count__back__inserter.html#afa63b1cd14eba57e2e437709495ce388',1,'vg::count_back_inserter']]],
- ['count_5fcovered_8504',['count_covered',['../namespacevg_1_1algorithms.html#a2b477c1e232c9d4f1e689a95dd55861d',1,'vg::algorithms']]],
- ['count_5fhaplotypes_8505',['count_haplotypes',['../classvg_1_1GenomeState.html#ab400687776bac0a85c3eab173354a48f',1,'vg::GenomeState::count_haplotypes(const pair< const Snarl *, const Snarl * > &telomere_pair) const'],['../classvg_1_1GenomeState.html#a07dc4168e8469c98227847c4f168cc78',1,'vg::GenomeState::count_haplotypes(const Snarl *snarl) const']]],
- ['count_5fns_8506',['count_Ns',['../classvg_1_1MaximalExactMatch.html#a63fc8de6080c763b6fd0639d1f4f8941',1,'vg::MaximalExactMatch']]],
- ['count_5freachability_5fedges_8507',['count_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#ae053f01b2505d284a43a5d0c2046c82b',1,'vg::MultipathAlignmentGraph']]],
- ['count_5fwalks_8508',['count_walks',['../namespacehandlegraph_1_1algorithms.html#a735c13fd9a1fb84b477ac45d6d81f005',1,'handlegraph::algorithms']]],
- ['count_5fwalks_5fthrough_5fnodes_8509',['count_walks_through_nodes',['../namespacehandlegraph_1_1algorithms.html#a873fe0ce03bbac9de36e28618799031d',1,'handlegraph::algorithms']]],
- ['counts_8510',['Counts',['../structvg_1_1Counts.html#a87773870a3b04302bec59e41e5bdbc2e',1,'vg::Counts']]],
- ['coverage_8511',['coverage',['../namespacehaplotypes__defaults.html#a2056acf86c1a81a966790b30eaa62dbb',1,'haplotypes_defaults']]],
- ['coverage_5fat_5fposition_8512',['coverage_at_position',['../classvg_1_1Packer.html#a40c607faa60ebbd6bf6723744461dddf',1,'vg::Packer']]],
- ['coverage_5fbin_5foffset_8513',['coverage_bin_offset',['../classvg_1_1Packer.html#a22b05709f04be8c616f52ff0d600b171',1,'vg::Packer']]],
- ['coverage_5fbin_5fsize_8514',['coverage_bin_size',['../classvg_1_1Packer.html#a18a02dddbc6787823cd4e01d92047af1',1,'vg::Packer']]],
- ['coverage_5ffilter_8515',['coverage_filter',['../classvg_1_1Filter.html#a663ae4f690064447baa5ed353e31e10f',1,'vg::Filter']]],
- ['coverage_5fsize_8516',['coverage_size',['../classvg_1_1Packer.html#a58e12b20148d88c47d9fbf504bb9918b',1,'vg::Packer']]],
- ['covered_5fintervals_8517',['covered_intervals',['../classvg_1_1MultipathMapper.html#a3de527ec7d32fd23f7b36a87fea0ac21',1,'vg::MultipathMapper']]],
- ['crash_5funless_5ffailed_8518',['crash_unless_failed',['../namespacevg.html#a4373c1c1d20b8b00d1bb9b3e80986333',1,'vg']]],
- ['create_8519',['create',['../namespacevg_1_1temp__file.html#a84ef71efd10b4010f206ae8510545f40',1,'vg::temp_file::create(const string &base)'],['../namespacevg_1_1temp__file.html#a24d977ff5083290a0ed89afac03d4810',1,'vg::temp_file::create()'],['../namespacexg_1_1temp__file.html#ac0e87efd95eba6015352e631772e47f3',1,'xg::temp_file::create(const std::string &base)'],['../namespacexg_1_1temp__file.html#ab3ce11a32b3f4601c0291f4814f74ff2',1,'xg::temp_file::create()']]],
- ['create_5falignment_5fmetadata_8520',['create_alignment_metadata',['../namespacevg.html#a15fce4efa9b96ccf185504825d3b39cf',1,'vg']]],
- ['create_5falignment_5fshim_8521',['create_alignment_shim',['../classvg_1_1MultipathAlignmentEmitter.html#a3316b8a1a84bdc728bdfe9cf2064f727',1,'vg::MultipathAlignmentEmitter']]],
- ['create_5fdirectory_8522',['create_directory',['../namespacevg_1_1temp__file.html#a0f3d35f494b316980ad8ceab4992747e',1,'vg::temp_file']]],
- ['create_5fedge_8523',['create_edge',['../classvg_1_1VG.html#a8922810d5228ab5c4619eb2ddc16e78b',1,'vg::VG::create_edge(const handle_t &left, const handle_t &right)'],['../classvg_1_1VG.html#a8ecb9833a1b3e7d5ca41fcaa96000976',1,'vg::VG::create_edge(Node *from, Node *to, bool from_start=false, bool to_end=false)'],['../classvg_1_1VG.html#abf766c692dc78334d6b7568f1a9d972b',1,'vg::VG::create_edge(nid_t from, nid_t to, bool from_start=false, bool to_end=false)'],['../classvg_1_1VG.html#a8fd0565d5133a239856444049783edcd',1,'vg::VG::create_edge(NodeTraversal left, NodeTraversal right)'],['../classvg_1_1VG.html#ac2cd4705aa5b919f349d02089c97cbc2',1,'vg::VG::create_edge(NodeSide side1, NodeSide side2)'],['../classhandlegraph_1_1MutableHandleGraph.html#a34a5e01f270713ba856a93c55039faf0',1,'handlegraph::MutableHandleGraph::create_edge(const handle_t &left, const handle_t &right)=0'],['../classhandlegraph_1_1MutableHandleGraph.html#a3ff0a0f9497da3498170fdfc2ce97797',1,'handlegraph::MutableHandleGraph::create_edge(const edge_t &edge)']]],
- ['create_5fgssw_5fgraph_8524',['create_gssw_graph',['../classvg_1_1GSSWAligner.html#a46733f8704aeffeca98904240c774823',1,'vg::GSSWAligner']]],
- ['create_5fhandle_8525',['create_handle',['../classvg_1_1VG.html#a54ad97e46dc1297b1a65a32697e2d37e',1,'vg::VG::create_handle(const string &sequence)'],['../classvg_1_1VG.html#a292614805cec28a1d863bbdb494d1c04',1,'vg::VG::create_handle(const string &sequence, const nid_t &id)'],['../classhandlegraph_1_1MutableHandleGraph.html#a8c9d8ca8160a9b94a57000eab3e97aaa',1,'handlegraph::MutableHandleGraph::create_handle(const std::string &sequence)=0'],['../classhandlegraph_1_1MutableHandleGraph.html#ae844fce457858cd2dc54dde786f79e5c',1,'handlegraph::MutableHandleGraph::create_handle(const std::string &sequence, const nid_t &id)=0']]],
- ['create_5fidentity_5fprojection_5ftrans_8526',['create_identity_projection_trans',['../classvg_1_1MultipathAlignmentGraph.html#af626a9a7a96800aa13aa257a5781fffe',1,'vg::MultipathAlignmentGraph']]],
- ['create_5finjection_5ftrans_8527',['create_injection_trans',['../classvg_1_1MultipathAlignmentGraph.html#a8cbd1429036d9f365bd361ffbc8aa855',1,'vg::MultipathAlignmentGraph::create_injection_trans(const unordered_map< id_t, pair< id_t, bool >> &projection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a00d9d6f3a0995aabf9d09204dd6a4ac9',1,'vg::MultipathAlignmentGraph::create_injection_trans(const HandleGraph &graph, const function< pair< id_t, bool >(id_t)> &project)']]],
- ['create_5fitem_8528',['create_item',['../classvg_1_1Funnel.html#a9d28d3fee3f8658d59a63c52338644e2',1,'vg::Funnel']]],
- ['create_5fmatch_5fnodes_8529',['create_match_nodes',['../classvg_1_1MultipathAlignmentGraph.html#ad8f0e93b7dd5db8e92e7889629784c70',1,'vg::MultipathAlignmentGraph']]],
- ['create_5fnode_8530',['create_node',['../classvg_1_1VG.html#a8cb95ac1c24c5263a962c13f3d6bc0c3',1,'vg::VG::create_node(const string &seq)'],['../classvg_1_1VG.html#aefa25ac8acfa9407e8489b402f6317dc',1,'vg::VG::create_node(const string &seq, nid_t id)']]],
- ['create_5fpath_8531',['create_path',['../classvg_1_1Paths.html#a55306d115aee9abbf3166505bacdb35a',1,'vg::Paths::create_path()'],['../classvg_1_1VG.html#a3195bfadb7e65e4952c4b98d51e862f1',1,'vg::VG::create_path(const list< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#adc07ec73a57485a700e621517c962b8b',1,'vg::VG::create_path(const vector< NodeTraversal > &nodes)'],['../classhandlegraph_1_1MutablePathMetadata.html#a8c430d07cbfe89f05b374bb818ce0885',1,'handlegraph::MutablePathMetadata::create_path()']]],
- ['create_5fpath_5fchunk_5fnodes_8532',['create_path_chunk_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a4b53be595c1409ee4041167ec9ac9211',1,'vg::MultipathAlignmentGraph']]],
- ['create_5fpath_5fhandle_8533',['create_path_handle',['../classvg_1_1VG.html#af7c99e48723b360eb2b1315b2c5af7cc',1,'vg::VG::create_path_handle()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a0873a6eb776bb2557a5b8453dbf13824',1,'handlegraph::MutablePathHandleGraph::create_path_handle()'],['../classhandlegraph_1_1MutablePathMetadata.html#aac0d9fcc3f20d952a581157ff5027a17',1,'handlegraph::MutablePathMetadata::create_path_handle()']]],
- ['create_5fpath_5fname_8534',['create_path_name',['../classhandlegraph_1_1PathMetadata.html#aab22165da25ce2036f708203039760c4',1,'handlegraph::PathMetadata']]],
- ['create_5fprogress_8535',['create_progress',['../classvg_1_1Progressive.html#a1cce3f715516ed2bbb4ce3a312b01e02',1,'vg::Progressive::create_progress(const string &message, long count)'],['../classvg_1_1Progressive.html#a75d4e92a36a277be5bc0cee5d01f5ca1',1,'vg::Progressive::create_progress(long count)']]],
- ['create_5fprojector_8536',['create_projector',['../classvg_1_1MultipathAlignmentGraph.html#a4f4f566eaf695fac8c08dc6e5c2083a7',1,'vg::MultipathAlignmentGraph']]],
- ['create_5fref_5fallele_8537',['create_ref_allele',['../namespacevg.html#ae9e16eec9e4a4120718eba7d5711a7df',1,'vg']]],
- ['create_5fstate_8538',['create_state',['../classvg_1_1PhaseUnfolder.html#ad02d721a40368b2da3a34909399c82d2',1,'vg::PhaseUnfolder']]],
- ['create_5fvariant_5findex_8539',['create_variant_index',['../classvg_1_1VCFTraversalFinder.html#a130dc99a1c006ef64569279631f97d60',1,'vg::VCFTraversalFinder']]],
- ['cumul_8540',['cumul',['../classvg_1_1truncated__normal__distribution.html#afbf1a66222a8631e628ae9cb4582aa42',1,'vg::truncated_normal_distribution']]],
- ['curr_5fsample_5fsize_8541',['curr_sample_size',['../classvg_1_1FragmentLengthDistribution.html#ad1efcd79538c4dab52d617cea238a689',1,'vg::FragmentLengthDistribution']]],
- ['current_5fempty_5fprefix_8542',['current_empty_prefix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a34e7aba20c216d4f3f3fbe391b622254',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['current_5fsum_8543',['current_sum',['../structhaplo_1_1haplo__DP__column.html#aa2318a6ff42c8d3ff97eda99841cd83e',1,'haplo::haplo_DP_column']]],
- ['current_5ftraceback_5fscore_8544',['current_traceback_score',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#ad2e6a57a6066af01004aaa01700a9a66',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['cut_5fanchors_8545',['cut_anchors',['../classvg_1_1Surjector.html#ac59182d764335c01e1d6ce301179f039',1,'vg::Surjector']]],
- ['cut_5fedit_5fat_5ffrom_8546',['cut_edit_at_from',['../namespacevg_1_1io.html#af7bca02992262d43640a5c1793a1a4e0',1,'vg::io']]],
- ['cut_5fedit_5fat_5fto_8547',['cut_edit_at_to',['../namespacevg_1_1io.html#a98eb54b93dec04564efd8645db7ea0fc',1,'vg::io']]],
- ['cut_5fmapping_8548',['cut_mapping',['../namespacevg.html#a4f45a0764dcd0711bb37067151c78d6a',1,'vg::cut_mapping(const Mapping &m, const Position &pos)'],['../namespacevg.html#a1cb07d52156c2d1a3e13c566bf629760',1,'vg::cut_mapping(const mapping_t &m, const Position &pos)'],['../namespacevg.html#a86cd2447c52bf50d938b0142bf98dc57',1,'vg::cut_mapping(const Mapping &m, size_t offset)'],['../namespacevg.html#af98f355163fd3a01d1d23c978fa1dbd3',1,'vg::cut_mapping(const mapping_t &m, size_t offset)']]],
- ['cut_5fmapping_5foffset_8549',['cut_mapping_offset',['../namespacevg.html#a9e9091c8bf2f73d219522420a705dc1f',1,'vg::cut_mapping_offset(const Mapping &m, size_t offset)'],['../namespacevg.html#a455dd0d543b21690c3e71e67ff45e57d',1,'vg::cut_mapping_offset(const mapping_t &m, size_t offset)']]],
- ['cut_5fpath_8550',['cut_path',['../namespacevg.html#a0456e049dd685a689886372f4b0a354d',1,'vg::cut_path(const Path &path, const Position &pos)'],['../namespacevg.html#a1dbdbb650e0a076cd3890c2a74515260',1,'vg::cut_path(const Path &path, size_t offset)']]],
- ['cycles_5fin_5fcactus_8551',['cycles_in_cactus',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a8ef2897eef1a33c4dd97306058f379e6',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]]
+ ['cachedpackedtraversalsupportfinder_8284',['CachedPackedTraversalSupportFinder',['../classvg_1_1CachedPackedTraversalSupportFinder.html#acf3672c8fe5fcdd91afd44d5c1eec12f',1,'vg::CachedPackedTraversalSupportFinder']]],
+ ['cacheentry_8285',['CacheEntry',['../structvg_1_1IndexedVG_1_1CacheEntry.html#aab15096460395eb73cf757068bd33b11',1,'vg::IndexedVG::CacheEntry::CacheEntry(cursor_t &to_read)'],['../structvg_1_1IndexedVG_1_1CacheEntry.html#ad0d6214f5d1f91aee27e67788f203e97',1,'vg::IndexedVG::CacheEntry::CacheEntry(CacheEntry &&other)=default']]],
+ ['cactus_5fto_5fvg_8286',['cactus_to_vg',['../namespacevg.html#adf53e86632a6d1d4b54370e6d948d08c',1,'vg']]],
+ ['cactusify_8287',['cactusify',['../namespacevg.html#aa4d05bc207717708d48e1da09f83eec6',1,'vg']]],
+ ['cactussnarlfinder_8288',['CactusSnarlFinder',['../classvg_1_1CactusSnarlFinder.html#a523de5b05cbb527b87940258eed03e9b',1,'vg::CactusSnarlFinder']]],
+ ['calculate_5fand_5fsave_5falignment_8289',['calculate_and_save_alignment',['../classvg_1_1DozeuInterface.html#aa8e98b63ac97d3d4c60ca93708973302',1,'vg::DozeuInterface']]],
+ ['calculate_5fconsistency_8290',['calculate_consistency',['../classvg_1_1ConsistencyCalculator.html#a208c36e5e95ab3c538f2c16175275c39',1,'vg::ConsistencyCalculator::calculate_consistency()'],['../classvg_1_1SimpleConsistencyCalculator.html#a391f08cf329583daf0c2a58cd5e20473',1,'vg::SimpleConsistencyCalculator::calculate_consistency()']]],
+ ['calculate_5fi_8291',['calculate_I',['../structhaplo_1_1haplo__DP__rectangle.html#ab2680796767cbf6721c326e5b0273e61',1,'haplo::haplo_DP_rectangle']]],
+ ['calculate_5flog_5flikelihood_8292',['calculate_log_likelihood',['../classvg_1_1GenotypeLikelihoodCalculator.html#af7ced3cd97277cd6a1201d8c06b67e72',1,'vg::GenotypeLikelihoodCalculator']]],
+ ['calculate_5flog_5fprior_8293',['calculate_log_prior',['../classvg_1_1GenotypePriorCalculator.html#a892b1d833c73f5a81b484269641c5d5c',1,'vg::GenotypePriorCalculator::calculate_log_prior()'],['../classvg_1_1FixedGenotypePriorCalculator.html#a3cbc25b27cb2831b172bb30e0809e58c',1,'vg::FixedGenotypePriorCalculator::calculate_log_prior()']]],
+ ['calculate_5fmax_5fposition_8294',['calculate_max_position',['../classvg_1_1DozeuInterface.html#aa863b61f59ea128a5e17e97538405d9b',1,'vg::DozeuInterface']]],
+ ['calculate_5fseed_5fposition_8295',['calculate_seed_position',['../classvg_1_1DozeuInterface.html#a397c817ed543794a609d32fb21063790',1,'vg::DozeuInterface']]],
+ ['calculate_5fsupports_8296',['calculate_supports',['../classvg_1_1TraversalSupportCalculator.html#a799e376d809e07eec89161d25dd3f3e7',1,'vg::TraversalSupportCalculator::calculate_supports()'],['../classvg_1_1SimpleTraversalSupportCalculator.html#a7950181bdbfc5f4db0583b7f92bdfe17',1,'vg::SimpleTraversalSupportCalculator::calculate_supports()']]],
+ ['calibrate_5fmismapping_5fdetection_8297',['calibrate_mismapping_detection',['../classvg_1_1MultipathMapper.html#aa4307bce23fe2a909f96273dbca7b126',1,'vg::MultipathMapper']]],
+ ['call_5fsnarl_8298',['call_snarl',['../classvg_1_1GraphCaller.html#a6064d47ccef10174fab1037764a3cf29',1,'vg::GraphCaller::call_snarl()'],['../classvg_1_1VCFGenotyper.html#a1e3a89bae885b463272873e538815151',1,'vg::VCFGenotyper::call_snarl()'],['../classvg_1_1LegacyCaller.html#a732a1385c9846d9605db70139d8e275b',1,'vg::LegacyCaller::call_snarl()'],['../classvg_1_1FlowCaller.html#abe755bb8027b80711002dc229fe3399a',1,'vg::FlowCaller::call_snarl()'],['../classvg_1_1NestedFlowCaller.html#a519712fdd96921a721be77a5f7d12638',1,'vg::NestedFlowCaller::call_snarl()'],['../classvg_1_1MCMCCaller.html#a82a9f6d69f5168582d19ff1d2484ea70',1,'vg::MCMCCaller::call_snarl()']]],
+ ['call_5fsnarl_5frecursive_8299',['call_snarl_recursive',['../classvg_1_1NestedFlowCaller.html#ad35a296c010962d699d2e613d8f7bfc9',1,'vg::NestedFlowCaller']]],
+ ['call_5ftop_5flevel_5fchains_8300',['call_top_level_chains',['../classvg_1_1GraphCaller.html#ae39e4d55f2c5599a941957a080f3cd10',1,'vg::GraphCaller']]],
+ ['call_5ftop_5flevel_5fsnarls_8301',['call_top_level_snarls',['../classvg_1_1GraphCaller.html#a905253c21cb1a94605587ac7759d4aa6',1,'vg::GraphCaller::call_top_level_snarls()'],['../classvg_1_1MCMCCaller.html#aa4acabff49b9dee265127563d9424cbd',1,'vg::MCMCCaller::call_top_level_snarls()']]],
+ ['candidate_5fsplice_5fsites_8302',['candidate_splice_sites',['../classvg_1_1SpliceRegion.html#acf682cf55a977a23d54ff5c55ce1b4b9',1,'vg::SpliceRegion']]],
+ ['candidates_8303',['candidates',['../namespacehaplotypes__defaults.html#aa492bd09d6c7d4877e2a54b851185a92',1,'haplotypes_defaults']]],
+ ['canonical_8304',['canonical',['../classhandlegraph_1_1SnarlDecomposition.html#ac26d4f14c1803734517afe18ec68a53a',1,'handlegraph::SnarlDecomposition']]],
+ ['canonical_5fhuffman_8305',['canonical_huffman',['../namespacevg.html#a208dee68429b2d4b0ee0b02cea090d9b',1,'vg']]],
+ ['canonical_5forientation_8306',['canonical_orientation',['../namespacevg.html#a74563bc5f9f3268b9a933688ad1a5edb',1,'vg']]],
+ ['chain_8307',['chain',['../structvg_1_1subcommand_1_1TickChainLink.html#aa5742ab455378cdb60f18cafba2ce01d',1,'vg::subcommand::TickChainLink::chain()'],['../structvg_1_1subcommand_1_1RangeArgSpec.html#a005c03f54977a58a1c81967750f7d2c9',1,'vg::subcommand::RangeArgSpec::chain()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a4540cc78899ade0b653dbb46e698784e',1,'vg::subcommand::OptionGroup::chain()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a54298aca1a143832c3d0f2d26cc729ed',1,'vg::subcommand::GroupedOptionGroup::chain()']]],
+ ['chain_5fbegin_8308',['chain_begin',['../namespacevg.html#ac3b14246f4fe83e3fbdadb1ba838faeb',1,'vg']]],
+ ['chain_5fbegin_5ffrom_8309',['chain_begin_from',['../namespacevg.html#aefacc656d2c444dfd6e0e445218265cc',1,'vg']]],
+ ['chain_5fend_8310',['chain_end',['../namespacevg.html#a0612d7af2f7366ff81c89824f43a5865',1,'vg']]],
+ ['chain_5fend_5ffrom_8311',['chain_end_from',['../namespacevg.html#a0627b5d536b881a355d8b419b6f329c6',1,'vg']]],
+ ['chain_5finfo_5fto_5fseed_8312',['chain_info_to_seed',['../classvg_1_1MinimizerMapper.html#ae0c70429455b4170120c4f1364449e99',1,'vg::MinimizerMapper']]],
+ ['chain_5fitems_5fdp_8313',['chain_items_dp',['../namespacevg_1_1algorithms.html#a2fda86d465d26d7f101e00f3431564e8',1,'vg::algorithms']]],
+ ['chain_5fitems_5ftraceback_8314',['chain_items_traceback',['../namespacevg_1_1algorithms.html#a7a9239fd23ed6838263f4dd05828d18c',1,'vg::algorithms']]],
+ ['chain_5fof_8315',['chain_of',['../classvg_1_1SnarlManager.html#a411e51927a6f65513e55b8efc02237a8',1,'vg::SnarlManager']]],
+ ['chain_5forientation_5fof_8316',['chain_orientation_of',['../classvg_1_1SnarlManager.html#a3227a00cc5b9ba1484a35be22eea1927',1,'vg::SnarlManager']]],
+ ['chain_5frank_5fof_8317',['chain_rank_of',['../classvg_1_1SnarlManager.html#a7fcb9d66d4de93aa61ceb6d01e2efd4e',1,'vg::SnarlManager']]],
+ ['chain_5frbegin_8318',['chain_rbegin',['../namespacevg.html#aa24387fbb4606765c23a280316bfcb65',1,'vg']]],
+ ['chain_5frcbegin_8319',['chain_rcbegin',['../namespacevg.html#a7aed054b974860f2cc4d5be4b7615de0',1,'vg']]],
+ ['chain_5frcend_8320',['chain_rcend',['../namespacevg.html#ae1369d5e29159750fd14482f73421660',1,'vg']]],
+ ['chain_5frend_8321',['chain_rend',['../namespacevg.html#a2c65134c67609a001a61291b22337f8d',1,'vg']]],
+ ['chains_5fof_8322',['chains_of',['../classvg_1_1SnarlManager.html#a237e4dae871d0555ccb855285364ab8a',1,'vg::SnarlManager']]],
+ ['change_5fsequence_8323',['change_sequence',['../classhandlegraph_1_1DeletableHandleGraph.html#a074aa4e0604e7b89e111c3bb71864f4c',1,'handlegraph::DeletableHandleGraph::change_sequence()'],['../classhandlegraph_1_1MutablePathDeletableHandleGraph.html#a496296d7be48b5d6de5635002b1c0226',1,'handlegraph::MutablePathDeletableHandleGraph::change_sequence()']]],
+ ['check_5falignment_8324',['check_alignment',['../classvg_1_1Mapper.html#a0750e1ca5a4eff47c148b176081c5333',1,'vg::Mapper']]],
+ ['check_5fduplicate_5fpath_5fnames_8325',['check_duplicate_path_names',['../convert__main_8cpp.html#a4355d9c8b84855c02d82983d0cd8eb2f',1,'convert_main.cpp']]],
+ ['check_5ffor_5fread_5fin_8326',['check_for_read_in',['../structvg_1_1read__alignment__index__t.html#acabc585a1b0aba09a1c8f03b4a9ce740',1,'vg::read_alignment_index_t']]],
+ ['check_5fin_8327',['check_in',['../classvg_1_1Watchdog.html#a73fff63eede4aaf60f04ca41f2373cdc',1,'vg::Watchdog']]],
+ ['check_5flengths_8328',['check_lengths',['../structvg_1_1WFAAlignment.html#aa0af12c84438f056d94bae26dcd52697',1,'vg::WFAAlignment']]],
+ ['check_5fmax_5ftrav_5fcutoff_8329',['check_max_trav_cutoff',['../classvg_1_1VCFTraversalFinder.html#aab82f66226266e3adcfc7076f158ff23',1,'vg::VCFTraversalFinder']]],
+ ['check_5fout_8330',['check_out',['../classvg_1_1Watchdog.html#abef59fb95cd3cb40a103d6e73e4c8031',1,'vg::Watchdog']]],
+ ['check_5fprotobuf_5ftag_8331',['check_protobuf_tag',['../classvg_1_1io_1_1Registry.html#a0600b489129e1f4090172fccb7863f2b',1,'vg::io::Registry']]],
+ ['check_5fquality_5flength_8332',['check_quality_length',['../namespacevg.html#a5de2cc2253344ecabb528c2aa7fd5c1d',1,'vg']]],
+ ['check_5fstatus_8333',['check_status',['../classvg_1_1Viz.html#a8dea2be732160c29b1892e76b9dfeeaa',1,'vg::Viz']]],
+ ['check_5ftag_5fvalidity_8334',['check_tag_validity',['../gbwt__main_8cpp.html#a4a6504bbdeed67c591fe5b36192a79d7',1,'gbwt_main.cpp']]],
+ ['child_5finfo_5ft_8335',['child_info_t',['../structvg_1_1ZipCodeForest_1_1child__info__t.html#aa03360bbe51a60b6da4dfe63e3f1acba',1,'vg::ZipCodeForest::child_info_t']]],
+ ['children_5fof_8336',['children_of',['../classvg_1_1SnarlManager.html#abeae275f106a85cca72817c02fd132b2',1,'vg::SnarlManager']]],
+ ['choose_5fgood_5fthread_5fcount_8337',['choose_good_thread_count',['../namespacevg.html#acfe23dc452245bf901fee2ed698afe7d',1,'vg']]],
+ ['choose_5fln_8338',['choose_ln',['../namespacevg.html#abf777e701e331bb422d91135a13408d2',1,'vg']]],
+ ['choose_5ftraversals_8339',['choose_traversals',['../classvg_1_1Deconstructor.html#aedfa437974ff91e1e374cdd0dc786187',1,'vg::Deconstructor']]],
+ ['chop_8340',['chop',['../namespacehandlegraph_1_1algorithms.html#a1ff065056c27de74f802ab3e902efc63',1,'handlegraph::algorithms::chop(MutablePathDeletableHandleGraph &graph, size_t max_node_length, const std::function< void(nid_t, size_t, size_t, handle_t)> &record_change)'],['../namespacehandlegraph_1_1algorithms.html#a56d58f1abfff84945de95e7fc6c72a12',1,'handlegraph::algorithms::chop(MutablePathDeletableHandleGraph &graph, size_t max_node_length)']]],
+ ['chop_5fnodes_8341',['chop_nodes',['../classvg_1_1Transcriptome.html#ab283e741b49bb9099335fc76c93e6fc7',1,'vg::Transcriptome']]],
+ ['chunk_5fto_5femitter_8342',['chunk_to_emitter',['../paths__main_8cpp.html#a94d4a4abb97cdbaf3e5564d60d4ce07c',1,'paths_main.cpp']]],
+ ['cigar_5fagainst_5fpath_8343',['cigar_against_path',['../namespacevg.html#a43ac2d1903fa51a20a2366a865f5f0a4',1,'vg::cigar_against_path(const Alignment &alignment, bool on_reverse_strand, int64_t &pos, size_t path_len, size_t softclip_suppress)'],['../namespacevg.html#aaa223d83f7bc78267d7c7a522c909231',1,'vg::cigar_against_path(const multipath_alignment_t &multipath_aln, const string &path_name, bool rev, int64_t path_pos, const PathPositionHandleGraph &graph, int64_t min_splice_length)']]],
+ ['cigar_5fmapping_8344',['cigar_mapping',['../namespacevg.html#a81755bb87928f81a864e4a752973bd69',1,'vg::cigar_mapping(const bam1_t *b, Mapping *mapping)'],['../namespacevg.html#a598379872a84d4be8ff74df6242abf10',1,'vg::cigar_mapping(const bam1_t *b, Mapping &mapping)']]],
+ ['cigar_5fstring_8345',['cigar_string',['../namespacevg.html#a022b99db4260a7fd77a248bf27c50041',1,'vg']]],
+ ['circularize_8346',['circularize',['../classvg_1_1VG.html#a1e2649b8ef5de75db451146c7ac92e92',1,'vg::VG::circularize(nid_t head, nid_t tail)'],['../classvg_1_1VG.html#ad96ff883534a13b28b18cd84dd094e72',1,'vg::VG::circularize(vector< string > pathnames)']]],
+ ['classify_5fkmers_8347',['classify_kmers',['../classvg_1_1Recombinator.html#aa7fd2b3cd41b3a1b8ddb04ee7cbfb671',1,'vg::Recombinator::classify_kmers()'],['../namespacevg.html#ab79dc273687fd5360cc145ce18aed912',1,'vg::classify_kmers()'],['../haplotypes__main_8cpp.html#abd40ce33a846ef256ca3b375d9cbb288',1,'classify_kmers(): haplotypes_main.cpp']]],
+ ['clear_8348',['clear',['../structvg_1_1Annotation.html#a02cfdb97e80a91c1b108bef79bc4b3af',1,'vg::Annotation::clear()'],['../structvg_1_1GBWTHandler.html#a4563b4f645ab0f48f11d579953410308',1,'vg::GBWTHandler::clear()'],['../structvg_1_1AugmentedGraph.html#ad394712ba7a2480a7c811e8bde56253b',1,'vg::AugmentedGraph::clear()'],['../structvg_1_1SupportAugmentedGraph.html#a02bf17acd1d5deb6e3044f9807756e81',1,'vg::SupportAugmentedGraph::clear()'],['../classvg_1_1Packer.html#a0680bd0b5bbe74029e94b33e2f1ea666',1,'vg::Packer::clear()'],['../classvg_1_1Paths.html#a8ddaaebbbe22105029887baddf9cbdf7',1,'vg::Paths::clear()'],['../classvg_1_1SmallBitset.html#a22c6afec220aa75244da08ca04f5825d',1,'vg::SmallBitset::clear()'],['../classvg_1_1VG.html#aa1eb3332c0a99a25c75681da485297e5',1,'vg::VG::clear()'],['../structGraphHandler.html#aafe821b2ce9cab8ae340e685154bff87',1,'GraphHandler::clear()'],['../classhandlegraph_1_1DeletableHandleGraph.html#a6e1a83e72b47643e43c6176f39d8db5e',1,'handlegraph::DeletableHandleGraph::clear()']]],
+ ['clear_5falignment_8349',['clear_alignment',['../namespacevg.html#a0406641335bb841c51b0c103219a29da',1,'vg']]],
+ ['clear_5fannotation_8350',['clear_annotation',['../classvg_1_1multipath__alignment__t.html#a9d1c72d4a76dff3ac93f3185bcd3e981',1,'vg::multipath_alignment_t::clear_annotation()'],['../namespacevg.html#ad970d2836c53996c21e5c5d9d3e0a6d8',1,'vg::clear_annotation(Annotated *annotated, const string &name)'],['../namespacevg.html#ae414970cfc37049b4dc9b308d9ed5f59',1,'vg::clear_annotation(Annotated &annotated, const string &name)']]],
+ ['clear_5fconnection_8351',['clear_connection',['../classvg_1_1subpath__t.html#a6584b9a093baa1a3edf9e690cc232b2d',1,'vg::subpath_t']]],
+ ['clear_5fcrash_5fcontext_8352',['clear_crash_context',['../namespacevg.html#af64359d12f27f1035ce70e4ff1622f9c',1,'vg']]],
+ ['clear_5fedge_5findexes_8353',['clear_edge_indexes',['../classvg_1_1VG.html#a10d4b49633db2aef463e0070e0af64a0',1,'vg::VG']]],
+ ['clear_5fedge_5findexes_5fno_5fresize_8354',['clear_edge_indexes_no_resize',['../classvg_1_1VG.html#a5195712f8aa650417d93324ff1c89ecf',1,'vg::VG']]],
+ ['clear_5findexes_8355',['clear_indexes',['../classvg_1_1VG.html#aae960ce1d640fadc4772795f6d0ff5b5',1,'vg::VG']]],
+ ['clear_5findexes_5fno_5fresize_8356',['clear_indexes_no_resize',['../classvg_1_1VG.html#a103c69bad02121590779530338861374',1,'vg::VG']]],
+ ['clear_5fmapping_8357',['clear_mapping',['../classvg_1_1path__t.html#a4c03d698f5c00f0d4545fa78f1c615f3',1,'vg::path_t']]],
+ ['clear_5fmapping_5franks_8358',['clear_mapping_ranks',['../classvg_1_1Paths.html#a599d6b0652ff6f3c9bbe731136ad910a',1,'vg::Paths']]],
+ ['clear_5fnext_8359',['clear_next',['../classvg_1_1subpath__t.html#a691d6adfa24ab6970ba1736212e2f276',1,'vg::subpath_t']]],
+ ['clear_5fnode_5findexes_8360',['clear_node_indexes',['../classvg_1_1VG.html#a212a2d1028f28046088a86e128b40559',1,'vg::VG']]],
+ ['clear_5fnode_5findexes_5fno_5fresize_8361',['clear_node_indexes_no_resize',['../classvg_1_1VG.html#af51220e88887adf92d7cff25dad5cd91',1,'vg::VG']]],
+ ['clear_5fpaths_8362',['clear_paths',['../classvg_1_1VG.html#aa4e534461834b2937b7f0b0c2420b899',1,'vg::VG']]],
+ ['clear_5freachability_5fedges_8363',['clear_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#af112f1a5af47cf079a163eec1c2e31f4',1,'vg::MultipathAlignmentGraph']]],
+ ['clear_5fscores_8364',['clear_scores',['../classvg_1_1MEMChainModel.html#aef30eacf1dfd97658fbdc85ce175fad1',1,'vg::MEMChainModel::clear_scores()'],['../classvg_1_1AlignmentChainModel.html#a0357717699cc97b6c5a8a164dfd424fb',1,'vg::AlignmentChainModel::clear_scores()']]],
+ ['clear_5fstart_8365',['clear_start',['../classvg_1_1multipath__alignment__t.html#a9436c421aa0550bb65c55bd557ad97c4',1,'vg::multipath_alignment_t']]],
+ ['clear_5fsubpath_8366',['clear_subpath',['../classvg_1_1multipath__alignment__t.html#af72f755d9dd5b4b11b379ee227997a2b',1,'vg::multipath_alignment_t']]],
+ ['clip_5fcontained_5flow_5fdepth_5fnodes_5fand_5fedges_8367',['clip_contained_low_depth_nodes_and_edges',['../namespacevg.html#afca0783176bbca00f50e9c8f4b53515c',1,'vg']]],
+ ['clip_5fcontained_5fsnarls_8368',['clip_contained_snarls',['../namespacevg.html#affb16bab122c9abe8aa4282992b8fe12',1,'vg']]],
+ ['clip_5fcontained_5fstubs_8369',['clip_contained_stubs',['../namespacevg.html#afc1766ad15ac6853f074a743d19873fc',1,'vg']]],
+ ['clip_5fdeletion_5fedges_8370',['clip_deletion_edges',['../namespacevg.html#a4f58b3aa775dcde39a1d511a9d838b97',1,'vg']]],
+ ['clip_5flow_5fdepth_5fnodes_5fand_5fedges_8371',['clip_low_depth_nodes_and_edges',['../namespacevg.html#aeaa0f9143fd06ff6948f2b548e4dde12',1,'vg']]],
+ ['clip_5flow_5fdepth_5fnodes_5fand_5fedges_5fgeneric_8372',['clip_low_depth_nodes_and_edges_generic',['../namespacevg.html#a1c4eb49afa34726115d01e380372669a',1,'vg']]],
+ ['clip_5fstubs_8373',['clip_stubs',['../namespacevg.html#ae596e7d9757cad372b5aaeb5e8a5146e',1,'vg']]],
+ ['clip_5fstubs_5fgeneric_8374',['clip_stubs_generic',['../namespacevg.html#aba796b34b1f89333758ff6cb4271f708',1,'vg']]],
+ ['close_8375',['close',['../classvg_1_1Viz.html#a80cd5bc578f48ea2279e298405e71393',1,'vg::Viz']]],
+ ['close_5fchain_8376',['close_chain',['../classvg_1_1ZipCodeForest.html#a2307457a70762459688446395338b3f8',1,'vg::ZipCodeForest']]],
+ ['close_5fedit_5ftmpfiles_8377',['close_edit_tmpfiles',['../classvg_1_1Packer.html#afd2c25becb15d4780d62673b11b2bce9',1,'vg::Packer']]],
+ ['close_5ffd_8378',['close_fd',['../classhandlegraph_1_1TriviallySerializable.html#afc178fcc343f3447429904192127ce5e',1,'handlegraph::TriviallySerializable']]],
+ ['close_5fsnarl_8379',['close_snarl',['../classvg_1_1ZipCodeForest.html#a5579f467bd35b2e13a753af31baf5bf6',1,'vg::ZipCodeForest']]],
+ ['cluster_5fchain_5flevel_8380',['cluster_chain_level',['../classvg_1_1SnarlDistanceIndexClusterer.html#a92faf3de4024dcb284ae3b0487f6b1f2',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5fcover_8381',['cluster_cover',['../namespacevg.html#afe3e65f9aafb5ab9ce5455cc72fa0b56',1,'vg']]],
+ ['cluster_5fcoverage_8382',['cluster_coverage',['../namespacevg.html#a3380e0f81fc879601afe493949814a4d',1,'vg']]],
+ ['cluster_5fmultiplicity_8383',['cluster_multiplicity',['../classvg_1_1MultipathMapper.html#a773dfb92a782fc5bc46d371aaeee5d7e',1,'vg::MultipathMapper']]],
+ ['cluster_5fnodes_8384',['cluster_nodes',['../namespacevg.html#af6c60d6eb4cafd02a45384cf71a12bfe',1,'vg']]],
+ ['cluster_5fone_5fchain_8385',['cluster_one_chain',['../classvg_1_1SnarlDistanceIndexClusterer.html#ad5f6b8a6201ce57b88b2d7bf772e1da6',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5fone_5fnode_8386',['cluster_one_node',['../classvg_1_1SnarlDistanceIndexClusterer.html#a1b3707a4eac66610e37faaf4f6ff9eff',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5fone_5fsnarl_8387',['cluster_one_snarl',['../classvg_1_1SnarlDistanceIndexClusterer.html#a0f1a2986c932dfe614d11707cef49bd8',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5froot_8388',['cluster_root',['../classvg_1_1SnarlDistanceIndexClusterer.html#afed897fb0affc471c0800137a5ff9872',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5fseeds_8389',['cluster_seeds',['../classvg_1_1SnarlDistanceIndexClusterer.html#a210ee5c625ead0e415f2276d1d20bb05',1,'vg::SnarlDistanceIndexClusterer::cluster_seeds(const vector< Seed > &seeds, size_t read_distance_limit) const'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a37e825d3d82904c3bda0598ac1093326',1,'vg::SnarlDistanceIndexClusterer::cluster_seeds(const vector< vector< Seed >> &all_seeds, size_t read_distance_limit, size_t fragment_distance_limit=0) const']]],
+ ['cluster_5fseeds_5finternal_8390',['cluster_seeds_internal',['../classvg_1_1SnarlDistanceIndexClusterer.html#a1c7c1aee0a7019289ca94234fe604075',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5fseeds_5fon_5flinear_5fstructure_8391',['cluster_seeds_on_linear_structure',['../classvg_1_1SnarlDistanceIndexClusterer.html#a31a2fd3cf7ce67590b86c45bb4f2b91e',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5fsnarl_5flevel_8392',['cluster_snarl_level',['../classvg_1_1SnarlDistanceIndexClusterer.html#ac823b12963123338ac75a24f930dd93e',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['cluster_5fsubgraph_5fcontaining_8393',['cluster_subgraph_containing',['../namespacevg.html#ae9f1bd05c1d67c074797eded33151e88',1,'vg']]],
+ ['cluster_5fsubgraph_5fwalk_8394',['cluster_subgraph_walk',['../namespacevg.html#ac20a47954c6352afbd98da5b7d4f2d95',1,'vg']]],
+ ['cluster_5ftraversals_8395',['cluster_traversals',['../namespacevg.html#a392e3bc708a380e7a3d9b3a669aaf2a9',1,'vg']]],
+ ['clusterhead_8396',['ClusterHead',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a87d8ac85cefd70275dc55c20bc49ee5b',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::ClusterHead()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a621a8a6363f9a729a95232eed4f7411e',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::ClusterHead(const size_t &read_num, const size_t &cluster_num, const size_t &distance_left, const size_t &distance_right)']]],
+ ['clusteringproblem_8397',['ClusteringProblem',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a1b2df3785e61d5e89573a07384226e30',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['clusters_8398',['clusters',['../classvg_1_1MEMClusterer.html#ad3b20603d24524f93534cc72a15abc22',1,'vg::MEMClusterer::clusters()'],['../classvg_1_1MEMClusterer_1_1HitGraph.html#a3ee3c0afa42fc839555bdbac8d4a8876',1,'vg::MEMClusterer::HitGraph::clusters()']]],
+ ['clusters_5foverlap_5fin_5fgraph_8399',['clusters_overlap_in_graph',['../namespacevg.html#a9d8947e51da3156529e12ae131c25a47',1,'vg']]],
+ ['clusters_5foverlap_5fin_5fread_8400',['clusters_overlap_in_read',['../namespacevg.html#af67eb440256877ac857d6649052d7db1',1,'vg']]],
+ ['clusters_5foverlap_5flength_8401',['clusters_overlap_length',['../namespacevg.html#a50260b7d42777dd7f352a5ba40ac655e',1,'vg']]],
+ ['clusters_5fto_5fdrop_8402',['clusters_to_drop',['../classvg_1_1Mapper.html#acb02353297bd88867df48edcac91cf9d',1,'vg::Mapper']]],
+ ['collapse_5forder_5flength_5fruns_8403',['collapse_order_length_runs',['../classvg_1_1MultipathAlignmentGraph.html#a8f309bbf60941b009379bd9661cb9060',1,'vg::MultipathAlignmentGraph']]],
+ ['collect_5fcoverage_8404',['collect_coverage',['../classvg_1_1Packer.html#a84a402c1da28b53f120ee11ff6bf0f44',1,'vg::Packer']]],
+ ['collect_5fsubgraph_8405',['collect_subgraph',['../classvg_1_1VG.html#a688cbe42750d98695114ad4ad640c1d3',1,'vg::VG']]],
+ ['collect_5ftranscribed_5fnodes_8406',['collect_transcribed_nodes',['../classvg_1_1Transcriptome.html#a3f7a516340769783dda7a5556049916b',1,'vg::Transcriptome']]],
+ ['colors_8407',['Colors',['../classvg_1_1Colors.html#a8bef9f7ce8512f3e800dded6a8470ac1',1,'vg::Colors::Colors(void)'],['../classvg_1_1Colors.html#a89032e6156425d236bcd721e3f1343d4',1,'vg::Colors::Colors(int seed_val)']]],
+ ['combine_8408',['combine',['../structvg_1_1Recombinator_1_1Statistics.html#a9f4b13079e31ae50f127b4f05cdc5ce9',1,'vg::Recombinator::Statistics::combine()'],['../classvg_1_1VG.html#a7d06218f137184c366de80df755ae001',1,'vg::VG::combine()']]],
+ ['combine_5fhandles_8409',['combine_handles',['../namespacehandlegraph_1_1algorithms.html#a843ff1c62aa75e4c3ec1b7a5d0ea88d3',1,'handlegraph::algorithms']]],
+ ['combine_5fhashes_8410',['combine_hashes',['../namespacestd.html#abae1208746caacfaebe7e9493549ae0b',1,'std']]],
+ ['combine_5fqualities_8411',['combine_qualities',['../classvg_1_1Packer.html#a2ae7de0ddbcb2e930a313e2881f6a988',1,'vg::Packer']]],
+ ['comma_8412',['comma',['../classvg_1_1ProblemDumpExplainer.html#a4f372e8fa0273774608ef668584a1b42',1,'vg::ProblemDumpExplainer']]],
+ ['common_5fancestor_5fnext_8413',['common_ancestor_next',['../classvg_1_1VG.html#a2e1708efaeceace87615bb67715d60fa',1,'vg::VG']]],
+ ['common_5fancestor_5fprev_8414',['common_ancestor_prev',['../classvg_1_1VG.html#ab3ba20713228cb76fa4b982d967654aa',1,'vg::VG']]],
+ ['common_5fbin_8415',['common_bin',['../classvg_1_1StreamIndexBase.html#a8486253e2bf627ef07fbb2eec5614bd3',1,'vg::StreamIndexBase']]],
+ ['common_5fprefix_5flength_8416',['common_prefix_length',['../classvg_1_1BitString.html#ab455acfc92e349b674bcc865446f13bf',1,'vg::BitString']]],
+ ['compact_5fids_8417',['compact_ids',['../classvg_1_1VG.html#a161ef56bd0eeee937602f60b8617f24d',1,'vg::VG::compact_ids(void)'],['../classvg_1_1VG.html#ae931543bdeed5e60edcf6225489e3ceb',1,'vg::VG::compact_ids(hash_map< nid_t, nid_t > &new_id)']]],
+ ['compact_5franks_8418',['compact_ranks',['../classvg_1_1Paths.html#aaf065b12a8a942c96f6d88a2c6db7c8e',1,'vg::Paths']]],
+ ['compare_8419',['compare',['../structReferenceInterval.html#a192a091b5ecee1d80e18143a9ea6d909',1,'ReferenceInterval']]],
+ ['compare_5fand_5fcombine_5fcluster_5fon_5fchild_5fstructures_8420',['compare_and_combine_cluster_on_child_structures',['../classvg_1_1SnarlDistanceIndexClusterer.html#a0d03992071ee1f20ad833992e145b305',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['compare_5fand_5fcombine_5fcluster_5fon_5fone_5fchild_8421',['compare_and_combine_cluster_on_one_child',['../classvg_1_1SnarlDistanceIndexClusterer.html#a98757d1cd5e82dd67e9056890cc1077d',1,'vg::SnarlDistanceIndexClusterer']]],
+ ['complement_5fcomponents_8422',['complement_components',['../classvg_1_1PhaseUnfolder.html#a09b845f1fd318a70f5f9e9aa50e5d435',1,'vg::PhaseUnfolder']]],
+ ['completed_5findexes_8423',['completed_indexes',['../classvg_1_1IndexRegistry.html#a1a39419b55745505a20ee70bfdc43f48',1,'vg::IndexRegistry']]],
+ ['completedtranscriptpath_8424',['CompletedTranscriptPath',['../structvg_1_1CompletedTranscriptPath.html#a159b9e750c37a9bbe1b1509e3ebca344',1,'vg::CompletedTranscriptPath::CompletedTranscriptPath(const EditedTranscriptPath &edited_transcript_path)'],['../structvg_1_1CompletedTranscriptPath.html#a2ccd3feaa958a813a2121d99cc7283f3',1,'vg::CompletedTranscriptPath::CompletedTranscriptPath(const EditedTranscriptPath &edited_transcript_path, const HandleGraph &graph)']]],
+ ['component_5fpaths_8425',['component_paths',['../namespacevg_1_1algorithms.html#a51f810108840ab4014eb58b2bfe19ac1',1,'vg::algorithms']]],
+ ['component_5fpaths_5fparallel_8426',['component_paths_parallel',['../namespacevg_1_1algorithms.html#a10b07f6f41f8dd36c5d3b1ff9a03ce93',1,'vg::algorithms']]],
+ ['component_5fsizes_8427',['component_sizes',['../namespacevg_1_1algorithms.html#a8e5fdb03a21f88395e1d69f53821ae59',1,'vg::algorithms']]],
+ ['component_5ftopological_5forder_8428',['component_topological_order',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a44c8d49fb946c427aca7584dcd28746a',1,'vg::MEMClusterer::HitGraph']]],
+ ['componentmindistanceclusterer_8429',['ComponentMinDistanceClusterer',['../classvg_1_1ComponentMinDistanceClusterer.html#a9d544da8f5ad8699bc359d0b3407f1d4',1,'vg::ComponentMinDistanceClusterer']]],
+ ['components_8430',['components',['../classvg_1_1Haplotypes.html#a1617e9b0fbd01fc77fd87c527e5dbd24',1,'vg::Haplotypes']]],
+ ['compose_5fshort_5fpath_5fname_8431',['compose_short_path_name',['../namespacevg.html#a04bb552d73f5ed9ca37d1227acacee4a',1,'vg']]],
+ ['compressstring_8432',['CompressString',['../namespacezstdutil.html#a2ae66a8ffc0bbea2444ff59fc0421033',1,'zstdutil']]],
+ ['compute_5fall_5fmapping_5fqualities_8433',['compute_all_mapping_qualities',['../classvg_1_1GSSWAligner.html#af5f906f0628c45c3507524da99754d93',1,'vg::GSSWAligner']]],
+ ['compute_5fborders_5fand_5fdimensions_8434',['compute_borders_and_dimensions',['../classvg_1_1Viz.html#a8a9eb721a92953e9a3e84f45f1952a9c',1,'vg::Viz']]],
+ ['compute_5fchains_8435',['compute_chains',['../classvg_1_1SnarlManager.html#a50fd20deea9859d27991e276b224d7d5',1,'vg::SnarlManager']]],
+ ['compute_5fcluster_5fmapping_5fquality_8436',['compute_cluster_mapping_quality',['../classvg_1_1Mapper.html#a3c546df7f298da47127ca6dbaf3462b7',1,'vg::Mapper']]],
+ ['compute_5ffirst_5fmapping_5fquality_8437',['compute_first_mapping_quality',['../classvg_1_1GSSWAligner.html#ad39d942f83d8d168daf96142a1fecd2b',1,'vg::GSSWAligner']]],
+ ['compute_5fgroup_5fmapping_5fquality_8438',['compute_group_mapping_quality',['../classvg_1_1GSSWAligner.html#a84bcb00f3e4cb834cdbc62beaec8f894',1,'vg::GSSWAligner']]],
+ ['compute_5fmapping_5fqualities_8439',['compute_mapping_qualities',['../classvg_1_1Mapper.html#ad062cafbbb49bc4960e59b3ffd499ca8',1,'vg::Mapper::compute_mapping_qualities(vector< Alignment > &alns, double cluster_mq, double mq_estimate, double mq_cap)'],['../classvg_1_1Mapper.html#af4905e4355e1132811a974cb5cb42e95',1,'vg::Mapper::compute_mapping_qualities(pair< vector< Alignment >, vector< Alignment >> &pair_alns, double cluster_mq, double mq_estmate1, double mq_estimate2, double mq_cap1, double mq_cap2)']]],
+ ['compute_5fmapping_5fquality_8440',['compute_mapping_quality',['../classvg_1_1GSSWAligner.html#a627256abe48089a54509400db8916ff3',1,'vg::GSSWAligner']]],
+ ['compute_5fmapq_5fcaps_8441',['compute_mapq_caps',['../classvg_1_1MinimizerMapper.html#ad0a9d591551601ea3699b8a1b2347e81',1,'vg::MinimizerMapper']]],
+ ['compute_5fmax_5fmapping_5fquality_8442',['compute_max_mapping_quality',['../classvg_1_1GSSWAligner.html#ae2f5d5343d90ef6778d8c634bfc76c06',1,'vg::GSSWAligner']]],
+ ['compute_5fmin_5fcut_8443',['compute_min_cut',['../namespacevg_1_1algorithms.html#a7ae1eba2313c3ce068851c85b8d019e2',1,'vg::algorithms']]],
+ ['compute_5fpaired_5fmapping_5fquality_8444',['compute_paired_mapping_quality',['../classvg_1_1GSSWAligner.html#ad896b2b0b1956da5f57bc3abbbd65701',1,'vg::GSSWAligner']]],
+ ['compute_5fpath_5finterval_8445',['compute_path_interval',['../classvg_1_1Surjector.html#adf6d3d9d2bec77f147192b05fc4df18b',1,'vg::Surjector']]],
+ ['compute_5fquality_8446',['compute_quality',['../classvg_1_1Packer.html#aedce0118963e5d735a2e70e29b70fe62',1,'vg::Packer']]],
+ ['compute_5fraw_5fmapping_5fqualities_5ffrom_5fscores_8447',['compute_raw_mapping_qualities_from_scores',['../classvg_1_1MultipathMapper.html#a114346585956311ff3db920e34573501',1,'vg::MultipathMapper']]],
+ ['compute_5ftail_5fmem_5fcoverage_8448',['compute_tail_mem_coverage',['../classvg_1_1OrientedDistanceClusterer.html#a5fad154b1267d5d3861870a51b482d9b',1,'vg::OrientedDistanceClusterer']]],
+ ['compute_5ftemplate_5flengths_8449',['compute_template_lengths',['../namespacevg.html#ad3824b96906cc229f270166a06a7a625',1,'vg']]],
+ ['compute_5funiqueness_8450',['compute_uniqueness',['../classvg_1_1Mapper.html#a4f13155eaeae93ca9ad6ec8095e2335c',1,'vg::Mapper']]],
+ ['concat_5fmappings_8451',['concat_mappings',['../namespacevg.html#a8fc7225da088d27cd1201422ba011f51',1,'vg']]],
+ ['concat_5fmappings_5ffor_5fnode_5fpair_8452',['concat_mappings_for_node_pair',['../classvg_1_1VG.html#a150341270e41f42db2578a2897e48c1b',1,'vg::VG']]],
+ ['concat_5fnodes_8453',['concat_nodes',['../namespacehandlegraph_1_1algorithms.html#a9c46c9dde150b8a2e2bbe785b1889534',1,'handlegraph::algorithms']]],
+ ['concat_5fpaths_8454',['concat_paths',['../namespacevg.html#ac7d43d119d665bda802489b3309e0bce',1,'vg']]],
+ ['condense_5fedits_8455',['condense_edits',['../classvg_1_1Constructor.html#a1b13ae925876f9f7617850ab4e2ad355',1,'vg::Constructor']]],
+ ['configurableparser_8456',['ConfigurableParser',['../classvg_1_1ConfigurableParser.html#ad04ba6f1c85aa2ab15b93e51c4a093f7',1,'vg::ConfigurableParser']]],
+ ['connect_8457',['connect',['../classvg_1_1WFAExtender.html#afa5938e94fc17adb3df680632ff97601',1,'vg::WFAExtender::connect()'],['../structvg_1_1RecombinatorHaplotype.html#ac449ff9fef162a7f627df68bcc9b1007',1,'vg::RecombinatorHaplotype::connect()']]],
+ ['connect_5fconsistently_8458',['connect_consistently',['../classvg_1_1MinimizerMapper.html#a2bba608ac7474700ace2ac9a071198f1',1,'vg::MinimizerMapper']]],
+ ['connect_5fnode_5fto_5fnodes_8459',['connect_node_to_nodes',['../classvg_1_1VG.html#ad68d2bfaa6627686967add4ca7fb5f4c',1,'vg::VG::connect_node_to_nodes(NodeTraversal node, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#ab8189716ecbb9eeeefec8be64e34a9e3',1,'vg::VG::connect_node_to_nodes(Node *node, vector< Node * > &nodes, bool from_start=false)']]],
+ ['connect_5fnodes_5fto_5fnode_8460',['connect_nodes_to_node',['../classvg_1_1VG.html#a7ee6066424793dfcda9097419f03b568',1,'vg::VG::connect_nodes_to_node(vector< NodeTraversal > &nodes, NodeTraversal node)'],['../classvg_1_1VG.html#acc4db5878a40e8dc7d2d2b25ff62ff1e',1,'vg::VG::connect_nodes_to_node(vector< Node * > &nodes, Node *node, bool to_end=false)']]],
+ ['connect_5fto_5fposition_5ffile_8461',['connect_to_position_file',['../classvg_1_1NGSSimulator.html#aceec560b267d4a2d4a1c37fb3691dde5',1,'vg::NGSSimulator']]],
+ ['connected_5fcomponents_8462',['connected_components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ad18510c8be7b8b21bc0cce8b33bf54e3',1,'vg::MEMClusterer::HitGraph::connected_components()'],['../classvg_1_1Surjector.html#af7bc3c25f2466322fd6ffd67d66c6dfa',1,'vg::Surjector::connected_components()'],['../namespacevg.html#a68859b86cb7465d17ca9cb68553a8e4c',1,'vg::connected_components()']]],
+ ['connected_5fcomps_5fdo_8463',['connected_comps_do',['../namespacevg.html#a37c256d47f5d50349766d6f8085b017f',1,'vg']]],
+ ['connection_8464',['connection',['../classvg_1_1subpath__t.html#ab0f42733d3f01f36292bd20368e169e7',1,'vg::subpath_t::connection() const'],['../classvg_1_1subpath__t.html#adb07c26e5a8a06dad0f64cf68f7a5e26',1,'vg::subpath_t::connection(size_t i) const']]],
+ ['connection_5fsize_8465',['connection_size',['../classvg_1_1subpath__t.html#ac69a45141f2de5117178e2b000ec9507',1,'vg::subpath_t']]],
+ ['connection_5ft_8466',['connection_t',['../classvg_1_1connection__t.html#ae8ba824a4323fa99471a02d908df41c0',1,'vg::connection_t::connection_t()=default'],['../classvg_1_1connection__t.html#abd98927a5c23d95159667eba540b4646',1,'vg::connection_t::connection_t(const connection_t &)=default'],['../classvg_1_1connection__t.html#ad940cca19833570b242f00d57f817a97',1,'vg::connection_t::connection_t(connection_t &&)=default']]],
+ ['construct_8467',['construct',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a7ce1ec0bba000de1600ce2beb70acc47',1,'vg::FlowSort::WeightedGraph']]],
+ ['construct_5fchunk_8468',['construct_chunk',['../classvg_1_1Constructor.html#aab2b25c3b99fabdb0f382e2698ca3a52',1,'vg::Constructor']]],
+ ['construct_5fcompleted_5ftranscript_5fpaths_8469',['construct_completed_transcript_paths',['../classvg_1_1Transcriptome.html#ade5704f06f63770a2871b92d48efdabd',1,'vg::Transcriptome']]],
+ ['construct_5fgraph_8470',['construct_graph',['../classvg_1_1Constructor.html#a0a87f468f65b2cacc3a47060378de7a3',1,'vg::Constructor::construct_graph(string vcf_contig, FastaReference &reference, VcfBuffer &variant_source, const vector< FastaReference * > &insertion, const function< void(Graph &)> &callback)'],['../classvg_1_1Constructor.html#a2d69f28be35ff23ef4d0f80e645bdbc2',1,'vg::Constructor::construct_graph(const vector< FastaReference * > &references, const vector< vcflib::VariantCallFile * > &variant_files, const vector< FastaReference * > &insertions, const function< void(Graph &)> &callback)'],['../classvg_1_1Constructor.html#a100345d3fca726262c98ab83768f0f0c',1,'vg::Constructor::construct_graph(const vector< string > &reference_filenames, const vector< string > &variant_filenames, const vector< string > &insertion_filenames, const function< void(Graph &)> &callback)'],['../classvg_1_1Constructor.html#a5dbf56a3eee98b1f678dafc69bb35e97',1,'vg::Constructor::construct_graph(const vector< FastaReference * > &references, const vector< vcflib::VariantCallFile * > &variant_files, const vector< FastaReference * > &insertions, MutablePathMutableHandleGraph *destination)'],['../classvg_1_1Constructor.html#a5c9a9c3adb2ddafc4d4434c689bb42ad',1,'vg::Constructor::construct_graph(const vector< string > &reference_filenames, const vector< string > &variant_filenames, const vector< string > &insertion_filenames, MutablePathMutableHandleGraph *destination)']]],
+ ['construct_5fgraph_5ffrom_5fnodes_5fand_5fedges_8471',['construct_graph_from_nodes_and_edges',['../namespacevg.html#a5b7416f4636f53c22bcb1fab81d63de8',1,'vg']]],
+ ['construct_5freference_5ftranscript_5fpaths_5fembedded_8472',['construct_reference_transcript_paths_embedded',['../classvg_1_1Transcriptome.html#aab8e9e4cf0cf855de888086388577d56',1,'vg::Transcriptome']]],
+ ['construct_5freference_5ftranscript_5fpaths_5fembedded_5fcallback_8473',['construct_reference_transcript_paths_embedded_callback',['../classvg_1_1Transcriptome.html#a342c0573251aa2839b7ea1ebbdd44db9',1,'vg::Transcriptome']]],
+ ['construct_5freference_5ftranscript_5fpaths_5fgbwt_8474',['construct_reference_transcript_paths_gbwt',['../classvg_1_1Transcriptome.html#a1a74c22fd6c47986e1dc4e7a68dad42d',1,'vg::Transcriptome']]],
+ ['construct_5freference_5ftranscript_5fpaths_5fgbwt_5fcallback_8475',['construct_reference_transcript_paths_gbwt_callback',['../classvg_1_1Transcriptome.html#a162034e99f2ee027816af34776a9b3d6',1,'vg::Transcriptome']]],
+ ['contains_8476',['contains',['../structvg_1_1GaplessExtension.html#a019486c5f7e5aab04d9e5b78aac3d069',1,'vg::GaplessExtension::contains()'],['../classvg_1_1SmallBitset.html#a58b8cbb133801d25d76785eb54bf6247',1,'vg::SmallBitset::contains()']]],
+ ['contains_5fconnection_8477',['contains_connection',['../namespacevg.html#a3f65013661cfc322222585843c30773a',1,'vg']]],
+ ['contains_5fmatch_8478',['contains_match',['../namespacevg.html#accfb6f4fc450e420c5b147cff9e6ae31',1,'vg']]],
+ ['contains_5freversals_8479',['contains_reversals',['../classvg_1_1HaplotypePartitioner.html#a4c032fa5d7fcb5c2d52bba8604c1d0d7',1,'vg::HaplotypePartitioner']]],
+ ['contains_5fsubsequence_8480',['contains_subsequence',['../classvg_1_1ReadFilter.html#a553af1f5f52e24334fb2dd22928ac86a',1,'vg::ReadFilter']]],
+ ['contract_8481',['contract',['../classvg_1_1ContractingGraph.html#afd959435308c7c6afdd041519ed71cda',1,'vg::ContractingGraph']]],
+ ['contractinggraph_8482',['ContractingGraph',['../classvg_1_1ContractingGraph.html#acc9acc04ee74d97808d811d77252afc3',1,'vg::ContractingGraph']]],
+ ['convert_8483',['convert',['../classvg_1_1VcfRecordConverter.html#a30aaab305cfc665f6f9588997fdd2297',1,'vg::VcfRecordConverter::convert()'],['../namespacevg.html#a5674e45f23020370046d49c674fd691f',1,'vg::convert(const std::string &s, T &r)'],['../namespacevg.html#ad7b1ca8b13ad1732d0679723bb206f18',1,'vg::convert(const T &r)']]],
+ ['convert_5falignment_8484',['convert_alignment',['../classvg_1_1HTSAlignmentEmitter.html#a5cfe9918348db19fc8b8a153a953715b',1,'vg::HTSAlignmentEmitter::convert_alignment()'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#ac837e6ec08c270afb4f6d231e4f58473',1,'vg::SplicedHTSAlignmentEmitter::convert_alignment()']]],
+ ['convert_5falignment_5fchar_8485',['convert_alignment_char',['../namespacevg.html#a256962a964ea02f3d4ec54c5c48d72a8',1,'vg']]],
+ ['convert_5fmultipath_5falignment_5fchar_8486',['convert_multipath_alignment_char',['../namespacevg.html#a1f29020dbd628bd21a9a039ee718b29b',1,'vg']]],
+ ['convert_5fpaired_8487',['convert_paired',['../classvg_1_1HTSAlignmentEmitter.html#a8a9025992d59e3425495bb39d97846d9',1,'vg::HTSAlignmentEmitter']]],
+ ['convert_5fto_5falignment_8488',['convert_to_alignment',['../classvg_1_1MultipathAlignmentEmitter.html#a968d8ce848da6dfda8ef0493f6044625',1,'vg::MultipathAlignmentEmitter']]],
+ ['convert_5fto_5fhts_5fpaired_8489',['convert_to_hts_paired',['../classvg_1_1MultipathAlignmentEmitter.html#aff86d0fed6f025e037468c9f94dc47d7',1,'vg::MultipathAlignmentEmitter']]],
+ ['convert_5fto_5fhts_5funpaired_8490',['convert_to_hts_unpaired',['../classvg_1_1MultipathAlignmentEmitter.html#a47ac4acd24f69e0d8427a136e29b872f',1,'vg::MultipathAlignmentEmitter']]],
+ ['convert_5fts_5fto_5fus_8491',['convert_Ts_to_Us',['../namespacevg.html#add9a4cf274b29df3caf222d0360805f3',1,'vg::convert_Ts_to_Us(Alignment &alignment)'],['../namespacevg.html#a92c7d384c096b813501b23730e308796',1,'vg::convert_Ts_to_Us(multipath_alignment_t &multipath_aln)']]],
+ ['convert_5funpaired_8492',['convert_unpaired',['../classvg_1_1HTSAlignmentEmitter.html#a8813a78822ccd54b41dc4fbe944f9d65',1,'vg::HTSAlignmentEmitter']]],
+ ['convert_5fus_5fto_5fts_8493',['convert_Us_to_Ts',['../namespacevg.html#abdc8589575aed95e82c0bb70828ab036',1,'vg::convert_Us_to_Ts(Alignment &alignment)'],['../namespacevg.html#a5a6e3cc99aac92404ec33126dbbd9192',1,'vg::convert_Us_to_Ts(multipath_alignment_t &multipath_aln)']]],
+ ['copy_8494',['copy',['../classvg_1_1SmallBitset.html#aac805c827da15890d9b237643fc49b1f',1,'vg::SmallBitset']]],
+ ['copy_5ffile_8495',['copy_file',['../namespacevg.html#a1c2f1e37da37dda61d25e9d8bb6552d6',1,'vg']]],
+ ['copy_5fhandle_5fgraph_8496',['copy_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a3031a57a4bd2e9e4f65a1130fe4eb148',1,'handlegraph::algorithms']]],
+ ['copy_5fmetadata_8497',['copy_metadata',['../namespacevg.html#ab2237df8adff809619083730f10d0e2e',1,'vg']]],
+ ['copy_5fpath_8498',['copy_path',['../namespacehandlegraph_1_1algorithms.html#a57d9936f8b98983f3121d074c62583bd',1,'handlegraph::algorithms::copy_path(const PathHandleGraph *from, const path_handle_t &from_path, MutablePathHandleGraph *into)'],['../namespacehandlegraph_1_1algorithms.html#a8ec649327e4580fc65bad976f04f6e1c',1,'handlegraph::algorithms::copy_path(const PathHandleGraph *from, const path_handle_t &from_path, MutablePathHandleGraph *into, const path_handle_t &into_path)']]],
+ ['copy_5fpath_5fhandle_5fgraph_8499',['copy_path_handle_graph',['../namespacehandlegraph_1_1algorithms.html#a1a253b430ffee65ce08f3a7508306550',1,'handlegraph::algorithms']]],
+ ['copy_5freference_5fsamples_8500',['copy_reference_samples',['../namespacevg.html#a03a4b946e48b89b3ec8857b04ded59db',1,'vg::copy_reference_samples(const gbwt::GBWT &source, gbwt::GBWT &destination)'],['../namespacevg.html#a2422b98737c90954afcd957a8566857d',1,'vg::copy_reference_samples(const PathHandleGraph &source, gbwt::GBWT &destination)']]],
+ ['corresponding_5ffrom_5flength_8501',['corresponding_from_length',['../namespacevg.html#a84d3002d98148b82b4f395c7b625b892',1,'vg']]],
+ ['corresponding_5flength_5finternal_8502',['corresponding_length_internal',['../namespacevg.html#a9dffafa4fdd05242ff4b73f5aafedd95',1,'vg']]],
+ ['corresponding_5fto_5flength_8503',['corresponding_to_length',['../namespacevg.html#a1fa02fa34866aee06ca1e3cead896b8d',1,'vg']]],
+ ['count_8504',['count',['../classvg_1_1HandleGraphNodeSet.html#ab39b3c91e81b50028a4b7cef88b2a772',1,'vg::HandleGraphNodeSet::count()'],['../classvg_1_1SmallBitset.html#af834de5870b38cc53768eb8ba9c60025',1,'vg::SmallBitset::count()']]],
+ ['count_5fback_5finserter_8505',['count_back_inserter',['../classvg_1_1count__back__inserter.html#afa63b1cd14eba57e2e437709495ce388',1,'vg::count_back_inserter']]],
+ ['count_5fcovered_8506',['count_covered',['../namespacevg_1_1algorithms.html#a2b477c1e232c9d4f1e689a95dd55861d',1,'vg::algorithms']]],
+ ['count_5fhaplotypes_8507',['count_haplotypes',['../classvg_1_1GenomeState.html#ab400687776bac0a85c3eab173354a48f',1,'vg::GenomeState::count_haplotypes(const pair< const Snarl *, const Snarl * > &telomere_pair) const'],['../classvg_1_1GenomeState.html#a07dc4168e8469c98227847c4f168cc78',1,'vg::GenomeState::count_haplotypes(const Snarl *snarl) const']]],
+ ['count_5fns_8508',['count_Ns',['../classvg_1_1MaximalExactMatch.html#a63fc8de6080c763b6fd0639d1f4f8941',1,'vg::MaximalExactMatch']]],
+ ['count_5freachability_5fedges_8509',['count_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#ae053f01b2505d284a43a5d0c2046c82b',1,'vg::MultipathAlignmentGraph']]],
+ ['count_5fwalks_8510',['count_walks',['../namespacehandlegraph_1_1algorithms.html#a735c13fd9a1fb84b477ac45d6d81f005',1,'handlegraph::algorithms']]],
+ ['count_5fwalks_5fthrough_5fnodes_8511',['count_walks_through_nodes',['../namespacehandlegraph_1_1algorithms.html#a873fe0ce03bbac9de36e28618799031d',1,'handlegraph::algorithms']]],
+ ['counts_8512',['Counts',['../structvg_1_1Counts.html#a87773870a3b04302bec59e41e5bdbc2e',1,'vg::Counts']]],
+ ['coverage_8513',['coverage',['../namespacehaplotypes__defaults.html#a2056acf86c1a81a966790b30eaa62dbb',1,'haplotypes_defaults']]],
+ ['coverage_5fat_5fposition_8514',['coverage_at_position',['../classvg_1_1Packer.html#a40c607faa60ebbd6bf6723744461dddf',1,'vg::Packer']]],
+ ['coverage_5fbin_5foffset_8515',['coverage_bin_offset',['../classvg_1_1Packer.html#a22b05709f04be8c616f52ff0d600b171',1,'vg::Packer']]],
+ ['coverage_5fbin_5fsize_8516',['coverage_bin_size',['../classvg_1_1Packer.html#a18a02dddbc6787823cd4e01d92047af1',1,'vg::Packer']]],
+ ['coverage_5ffilter_8517',['coverage_filter',['../classvg_1_1Filter.html#a663ae4f690064447baa5ed353e31e10f',1,'vg::Filter']]],
+ ['coverage_5fsize_8518',['coverage_size',['../classvg_1_1Packer.html#a58e12b20148d88c47d9fbf504bb9918b',1,'vg::Packer']]],
+ ['covered_5fintervals_8519',['covered_intervals',['../classvg_1_1MultipathMapper.html#a3de527ec7d32fd23f7b36a87fea0ac21',1,'vg::MultipathMapper']]],
+ ['crash_5funless_5ffailed_8520',['crash_unless_failed',['../namespacevg.html#a4373c1c1d20b8b00d1bb9b3e80986333',1,'vg']]],
+ ['create_8521',['create',['../namespacevg_1_1temp__file.html#a84ef71efd10b4010f206ae8510545f40',1,'vg::temp_file::create(const string &base)'],['../namespacevg_1_1temp__file.html#a24d977ff5083290a0ed89afac03d4810',1,'vg::temp_file::create()'],['../namespacexg_1_1temp__file.html#ac0e87efd95eba6015352e631772e47f3',1,'xg::temp_file::create(const std::string &base)'],['../namespacexg_1_1temp__file.html#ab3ce11a32b3f4601c0291f4814f74ff2',1,'xg::temp_file::create()']]],
+ ['create_5falignment_5fmetadata_8522',['create_alignment_metadata',['../namespacevg.html#a15fce4efa9b96ccf185504825d3b39cf',1,'vg']]],
+ ['create_5falignment_5fshim_8523',['create_alignment_shim',['../classvg_1_1MultipathAlignmentEmitter.html#a3316b8a1a84bdc728bdfe9cf2064f727',1,'vg::MultipathAlignmentEmitter']]],
+ ['create_5fdirectory_8524',['create_directory',['../namespacevg_1_1temp__file.html#a0f3d35f494b316980ad8ceab4992747e',1,'vg::temp_file']]],
+ ['create_5fedge_8525',['create_edge',['../classvg_1_1VG.html#a8922810d5228ab5c4619eb2ddc16e78b',1,'vg::VG::create_edge(const handle_t &left, const handle_t &right)'],['../classvg_1_1VG.html#a8ecb9833a1b3e7d5ca41fcaa96000976',1,'vg::VG::create_edge(Node *from, Node *to, bool from_start=false, bool to_end=false)'],['../classvg_1_1VG.html#abf766c692dc78334d6b7568f1a9d972b',1,'vg::VG::create_edge(nid_t from, nid_t to, bool from_start=false, bool to_end=false)'],['../classvg_1_1VG.html#a8fd0565d5133a239856444049783edcd',1,'vg::VG::create_edge(NodeTraversal left, NodeTraversal right)'],['../classvg_1_1VG.html#ac2cd4705aa5b919f349d02089c97cbc2',1,'vg::VG::create_edge(NodeSide side1, NodeSide side2)'],['../classhandlegraph_1_1MutableHandleGraph.html#a34a5e01f270713ba856a93c55039faf0',1,'handlegraph::MutableHandleGraph::create_edge(const handle_t &left, const handle_t &right)=0'],['../classhandlegraph_1_1MutableHandleGraph.html#a3ff0a0f9497da3498170fdfc2ce97797',1,'handlegraph::MutableHandleGraph::create_edge(const edge_t &edge)']]],
+ ['create_5fgssw_5fgraph_8526',['create_gssw_graph',['../classvg_1_1GSSWAligner.html#a46733f8704aeffeca98904240c774823',1,'vg::GSSWAligner']]],
+ ['create_5fhandle_8527',['create_handle',['../classvg_1_1VG.html#a54ad97e46dc1297b1a65a32697e2d37e',1,'vg::VG::create_handle(const string &sequence)'],['../classvg_1_1VG.html#a292614805cec28a1d863bbdb494d1c04',1,'vg::VG::create_handle(const string &sequence, const nid_t &id)'],['../classhandlegraph_1_1MutableHandleGraph.html#a8c9d8ca8160a9b94a57000eab3e97aaa',1,'handlegraph::MutableHandleGraph::create_handle(const std::string &sequence)=0'],['../classhandlegraph_1_1MutableHandleGraph.html#ae844fce457858cd2dc54dde786f79e5c',1,'handlegraph::MutableHandleGraph::create_handle(const std::string &sequence, const nid_t &id)=0']]],
+ ['create_5fidentity_5fprojection_5ftrans_8528',['create_identity_projection_trans',['../classvg_1_1MultipathAlignmentGraph.html#af626a9a7a96800aa13aa257a5781fffe',1,'vg::MultipathAlignmentGraph']]],
+ ['create_5finjection_5ftrans_8529',['create_injection_trans',['../classvg_1_1MultipathAlignmentGraph.html#a8cbd1429036d9f365bd361ffbc8aa855',1,'vg::MultipathAlignmentGraph::create_injection_trans(const unordered_map< id_t, pair< id_t, bool >> &projection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a00d9d6f3a0995aabf9d09204dd6a4ac9',1,'vg::MultipathAlignmentGraph::create_injection_trans(const HandleGraph &graph, const function< pair< id_t, bool >(id_t)> &project)']]],
+ ['create_5fitem_8530',['create_item',['../classvg_1_1Funnel.html#a9d28d3fee3f8658d59a63c52338644e2',1,'vg::Funnel']]],
+ ['create_5fmatch_5fnodes_8531',['create_match_nodes',['../classvg_1_1MultipathAlignmentGraph.html#ad8f0e93b7dd5db8e92e7889629784c70',1,'vg::MultipathAlignmentGraph']]],
+ ['create_5fnode_8532',['create_node',['../classvg_1_1VG.html#a8cb95ac1c24c5263a962c13f3d6bc0c3',1,'vg::VG::create_node(const string &seq)'],['../classvg_1_1VG.html#aefa25ac8acfa9407e8489b402f6317dc',1,'vg::VG::create_node(const string &seq, nid_t id)']]],
+ ['create_5fpath_8533',['create_path',['../classvg_1_1Paths.html#a55306d115aee9abbf3166505bacdb35a',1,'vg::Paths::create_path()'],['../classvg_1_1VG.html#a3195bfadb7e65e4952c4b98d51e862f1',1,'vg::VG::create_path(const list< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#adc07ec73a57485a700e621517c962b8b',1,'vg::VG::create_path(const vector< NodeTraversal > &nodes)'],['../classhandlegraph_1_1MutablePathMetadata.html#a8c430d07cbfe89f05b374bb818ce0885',1,'handlegraph::MutablePathMetadata::create_path()']]],
+ ['create_5fpath_5fchunk_5fnodes_8534',['create_path_chunk_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a4b53be595c1409ee4041167ec9ac9211',1,'vg::MultipathAlignmentGraph']]],
+ ['create_5fpath_5fhandle_8535',['create_path_handle',['../classvg_1_1VG.html#af7c99e48723b360eb2b1315b2c5af7cc',1,'vg::VG::create_path_handle()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a0873a6eb776bb2557a5b8453dbf13824',1,'handlegraph::MutablePathHandleGraph::create_path_handle()'],['../classhandlegraph_1_1MutablePathMetadata.html#aac0d9fcc3f20d952a581157ff5027a17',1,'handlegraph::MutablePathMetadata::create_path_handle()']]],
+ ['create_5fpath_5fname_8536',['create_path_name',['../classhandlegraph_1_1PathMetadata.html#aab22165da25ce2036f708203039760c4',1,'handlegraph::PathMetadata']]],
+ ['create_5fprogress_8537',['create_progress',['../classvg_1_1Progressive.html#a1cce3f715516ed2bbb4ce3a312b01e02',1,'vg::Progressive::create_progress(const string &message, long count)'],['../classvg_1_1Progressive.html#a75d4e92a36a277be5bc0cee5d01f5ca1',1,'vg::Progressive::create_progress(long count)']]],
+ ['create_5fprojector_8538',['create_projector',['../classvg_1_1MultipathAlignmentGraph.html#a4f4f566eaf695fac8c08dc6e5c2083a7',1,'vg::MultipathAlignmentGraph']]],
+ ['create_5fref_5fallele_8539',['create_ref_allele',['../namespacevg.html#ae9e16eec9e4a4120718eba7d5711a7df',1,'vg']]],
+ ['create_5fstate_8540',['create_state',['../classvg_1_1PhaseUnfolder.html#ad02d721a40368b2da3a34909399c82d2',1,'vg::PhaseUnfolder']]],
+ ['create_5fvariant_5findex_8541',['create_variant_index',['../classvg_1_1VCFTraversalFinder.html#a130dc99a1c006ef64569279631f97d60',1,'vg::VCFTraversalFinder']]],
+ ['cumul_8542',['cumul',['../classvg_1_1truncated__normal__distribution.html#afbf1a66222a8631e628ae9cb4582aa42',1,'vg::truncated_normal_distribution']]],
+ ['curr_5fsample_5fsize_8543',['curr_sample_size',['../classvg_1_1FragmentLengthDistribution.html#ad1efcd79538c4dab52d617cea238a689',1,'vg::FragmentLengthDistribution']]],
+ ['current_5fempty_5fprefix_8544',['current_empty_prefix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a34e7aba20c216d4f3f3fbe391b622254',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['current_5fsum_8545',['current_sum',['../structhaplo_1_1haplo__DP__column.html#aa2318a6ff42c8d3ff97eda99841cd83e',1,'haplo::haplo_DP_column']]],
+ ['current_5ftraceback_5fscore_8546',['current_traceback_score',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#ad2e6a57a6066af01004aaa01700a9a66',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['cut_5fanchors_8547',['cut_anchors',['../classvg_1_1Surjector.html#ac59182d764335c01e1d6ce301179f039',1,'vg::Surjector']]],
+ ['cut_5fedit_5fat_5ffrom_8548',['cut_edit_at_from',['../namespacevg_1_1io.html#af7bca02992262d43640a5c1793a1a4e0',1,'vg::io']]],
+ ['cut_5fedit_5fat_5fto_8549',['cut_edit_at_to',['../namespacevg_1_1io.html#a98eb54b93dec04564efd8645db7ea0fc',1,'vg::io']]],
+ ['cut_5fmapping_8550',['cut_mapping',['../namespacevg.html#a4f45a0764dcd0711bb37067151c78d6a',1,'vg::cut_mapping(const Mapping &m, const Position &pos)'],['../namespacevg.html#a1cb07d52156c2d1a3e13c566bf629760',1,'vg::cut_mapping(const mapping_t &m, const Position &pos)'],['../namespacevg.html#a86cd2447c52bf50d938b0142bf98dc57',1,'vg::cut_mapping(const Mapping &m, size_t offset)'],['../namespacevg.html#af98f355163fd3a01d1d23c978fa1dbd3',1,'vg::cut_mapping(const mapping_t &m, size_t offset)']]],
+ ['cut_5fmapping_5foffset_8551',['cut_mapping_offset',['../namespacevg.html#a9e9091c8bf2f73d219522420a705dc1f',1,'vg::cut_mapping_offset(const Mapping &m, size_t offset)'],['../namespacevg.html#a455dd0d543b21690c3e71e67ff45e57d',1,'vg::cut_mapping_offset(const mapping_t &m, size_t offset)']]],
+ ['cut_5fpath_8552',['cut_path',['../namespacevg.html#a0456e049dd685a689886372f4b0a354d',1,'vg::cut_path(const Path &path, const Position &pos)'],['../namespacevg.html#a1dbdbb650e0a076cd3890c2a74515260',1,'vg::cut_path(const Path &path, size_t offset)']]],
+ ['cycles_5fin_5fcactus_8553',['cycles_in_cactus',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a8ef2897eef1a33c4dd97306058f379e6',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]]
];
diff --git a/search/functions_4.js b/search/functions_4.js
index 70b03da7ce..59a2d1b42f 100644
--- a/search/functions_4.js
+++ b/search/functions_4.js
@@ -1,116 +1,116 @@
var searchData=
[
- ['dag_5fand_5fnon_5fdag_5fsnarl_5fcount_8552',['dag_and_non_dag_snarl_count',['../classvg_1_1ZipCodeTree.html#a0651e6fb7447bfd47181226c264bd45d',1,'vg::ZipCodeTree']]],
- ['dagifiedgraph_8553',['DagifiedGraph',['../classvg_1_1DagifiedGraph.html#a39faa4602acdc54d568410dda0d1ae35',1,'vg::DagifiedGraph::DagifiedGraph(const HandleGraph *graph, size_t min_preserved_path_length, size_t max_num_duplications=std::numeric_limits< size_t >::max())'],['../classvg_1_1DagifiedGraph.html#ada562ce53bd2fc9a59aeef495eafa6c8',1,'vg::DagifiedGraph::DagifiedGraph()=default']]],
- ['dagify_8554',['dagify',['../classvg_1_1VG.html#a2c8890bbc32c99bba8ca17f24a11d343',1,'vg::VG::dagify()'],['../namespacehandlegraph_1_1algorithms.html#a64feaa655343996c7d233d938a5f35d8',1,'handlegraph::algorithms::dagify()']]],
- ['dagify_5ffrom_8555',['dagify_from',['../namespacehandlegraph_1_1algorithms.html#a1922a67cde14a6cc4e30d2fd62728df1',1,'handlegraph::algorithms']]],
- ['data_5fsize_8556',['data_size',['../classvg_1_1SmallBitset.html#ad0e138252408f61ed254f45bb641bee8',1,'vg::SmallBitset']]],
- ['debug_5fstring_8557',['debug_string',['../namespacevg.html#ae72a83063f59506e0fcd76304b85d842',1,'vg::debug_string(const connection_t &connection)'],['../namespacevg.html#a8401a5ba093820ee017f9db390058087',1,'vg::debug_string(const subpath_t &subpath)'],['../namespacevg.html#a3a723cb7c4957a689cb7de6812237dea',1,'vg::debug_string(const multipath_alignment_t &multipath_aln)'],['../namespacevg.html#a472702e0931449cfaa10a337d7119d63',1,'vg::debug_string(const path_t &path)'],['../namespacevg.html#a11592884d28d3865ea95f76232e2fed4',1,'vg::debug_string(const path_mapping_t &mapping)'],['../namespacevg.html#a51469d56a6d4e55660c15af135c92b46',1,'vg::debug_string(const edit_t &edit)'],['../namespacevg.html#a99864b7ad9781d2c41c424ae69187e2e',1,'vg::debug_string(const position_t &pos)']]],
- ['decode_5frgfa_5ftags_8558',['decode_rgfa_tags',['../classvg_1_1algorithms_1_1GFAParser.html#abca93aab4d7a7375deca9a970808005d',1,'vg::algorithms::GFAParser']]],
- ['decoder_5flength_8559',['decoder_length',['../classvg_1_1ZipCode.html#ab5cc414a3fa14b68799c93fa61486a31',1,'vg::ZipCode']]],
- ['decoder_5ft_8560',['decoder_t',['../structvg_1_1ZipCode_1_1decoder__t.html#a075168865b66d94ce93b852c7fb7e4d6',1,'vg::ZipCode::decoder_t']]],
- ['decompose_8561',['decompose',['../namespacevg.html#a90fe8f4de1196dd902ac05f7567b9b7b',1,'vg']]],
- ['decompose_5falignments_8562',['decompose_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a8e7fa26541aea68ea2c456d79c950377',1,'vg::MultipathAlignmentGraph']]],
- ['decompose_5fgenotype_5ffast_8563',['decompose_genotype_fast',['../classvg_1_1WindowedVcfBuffer.html#ae05d4861f68f92b5c11e293f1a34618b',1,'vg::WindowedVcfBuffer']]],
- ['decompressstring_8564',['DecompressString',['../namespacezstdutil.html#a96bc1e7d01552bb8397ffd2a8dbc0167',1,'zstdutil']]],
- ['deconstruct_8565',['deconstruct',['../classvg_1_1Deconstructor.html#a65c57f3f6e3b4504ceb8bb6b3a96925c',1,'vg::Deconstructor']]],
- ['deconstruct_5fgraph_8566',['deconstruct_graph',['../classvg_1_1Deconstructor.html#a2b35a006fe649bbd6e2ee8c7ca0fefd8',1,'vg::Deconstructor']]],
- ['deconstruct_5fgraph_5ftop_5fdown_8567',['deconstruct_graph_top_down',['../classvg_1_1Deconstructor.html#a1ec4ade6a850ee9e5b6debfe07e2b31a',1,'vg::Deconstructor']]],
- ['deconstruct_5fsite_8568',['deconstruct_site',['../classvg_1_1Deconstructor.html#ae39b201fb62f77c2309a3230d8bfd5bb',1,'vg::Deconstructor']]],
- ['deconstructor_8569',['Deconstructor',['../classvg_1_1Deconstructor.html#ac164fa41d5d207dec36a99b891d405be',1,'vg::Deconstructor']]],
- ['decrement_5fnode_5fids_8570',['decrement_node_ids',['../classvg_1_1VG.html#aae60b30eaa432d73f91dc28283679a18',1,'vg::VG']]],
- ['deduplicate_5falt_5falns_8571',['deduplicate_alt_alns',['../classvg_1_1MultipathAlignmentGraph.html#acf97e6e2b5f03198f3087d7746e19b85',1,'vg::MultipathAlignmentGraph']]],
- ['deduplicate_5fcluster_5fpairs_8572',['deduplicate_cluster_pairs',['../classvg_1_1MEMClusterer.html#ae99c87e944c8c1056abb8efc7da5786e',1,'vg::MEMClusterer']]],
- ['deep_5fcontents_8573',['deep_contents',['../classvg_1_1SnarlManager.html#a88dbb1a06fa24de3459f62ecdbc7d962',1,'vg::SnarlManager']]],
- ['default_5fbuild_5fjobs_8574',['default_build_jobs',['../structGBWTConfig.html#aae95569c118992c2d9f0c70ee0115034',1,'GBWTConfig']]],
- ['default_5fcontext_5flength_8575',['default_context_length',['../structGBWTConfig.html#ac7920a61ea6e371b8d91754c757e4644',1,'GBWTConfig']]],
- ['default_5fdistance_8576',['default_distance',['../structvg_1_1WFAExtender_1_1ErrorModel.html#aa2ddef59dceb81bd45cc7a485ff3fb6f',1,'vg::WFAExtender::ErrorModel']]],
- ['default_5fgap_5flength_8577',['default_gap_length',['../structvg_1_1WFAExtender_1_1ErrorModel.html#a542b1c4afc94ad305ab098e3a226075c',1,'vg::WFAExtender::ErrorModel']]],
- ['default_5fgaps_8578',['default_gaps',['../structvg_1_1WFAExtender_1_1ErrorModel.html#affe4519ada47143c048385a6eb9caf88',1,'vg::WFAExtender::ErrorModel']]],
- ['default_5fmerge_5fjobs_8579',['default_merge_jobs',['../structGBWTConfig.html#a19a35e22dd696babede6279a85859742',1,'GBWTConfig']]],
- ['default_5fmismatches_8580',['default_mismatches',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ab68d1f72fc508682dafd052bab6d268c',1,'vg::WFAExtender::ErrorModel']]],
- ['default_5fnum_5fpaths_8581',['default_num_paths',['../structGBWTConfig.html#aae283e22db9032f46239d1e06deaa459',1,'GBWTConfig']]],
- ['default_5fnum_5fpaths_5flocal_8582',['default_num_paths_local',['../structGBWTConfig.html#a28b0e3eb72d2c6ba04301f4e27460714',1,'GBWTConfig']]],
- ['default_5fsort_5fzipcodes_8583',['default_sort_zipcodes',['../classvg_1_1ZipCodeForest.html#a5eed49e06827ec7883f8abe8da3d548e',1,'vg::ZipCodeForest']]],
- ['deflect_5fto_5fmatrix_8584',['deflect_to_matrix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a6abbf28540a3e93c039ee2ec6ccf26be',1,'vg::BandedGlobalAligner::AltTracebackStack::deflect_to_matrix()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a5c24b2c60ef30f7ff29f3b28534496c2',1,'vg::BandedGlobalAligner::AltTracebackStack::deflect_to_matrix(int64_t &to_node_id)']]],
- ['deflection_8585',['Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a44389670dc49e1dadf64104423dd064f',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['del_5fpredecessor_8586',['del_predecessor',['../classvg_1_1WFATree.html#a14b76054dbd37a01db3065bbe453cf4c',1,'vg::WFATree']]],
- ['delete_5fhaplotype_8587',['delete_haplotype',['../classvg_1_1GenomeState.html#a3abfa8020eb5f6f6229e7b59924dad30',1,'vg::GenomeState']]],
- ['delete_5fnodes_5fand_5fchop_5fpaths_8588',['delete_nodes_and_chop_paths',['../namespacevg.html#ab273ea17c855b1b0a32fc4e98405519e',1,'vg']]],
- ['delete_5fvariant_5findex_8589',['delete_variant_index',['../classvg_1_1VCFTraversalFinder.html#a45b91ad0f95daad0ce2610953873f867',1,'vg::VCFTraversalFinder']]],
- ['deletion_5ffilter_8590',['deletion_filter',['../classvg_1_1Filter.html#a8b867ca7572a1f8687b96cba2687f749',1,'vg::Filter']]],
- ['deletionaligner_8591',['DeletionAligner',['../classvg_1_1DeletionAligner.html#ae118f6eccda2b49e39aed57e6c1a6950',1,'vg::DeletionAligner::DeletionAligner(int8_t gap_open, int8_t gap_extension)'],['../classvg_1_1DeletionAligner.html#a7c942c5a7530fd098f0771956a245862',1,'vg::DeletionAligner::DeletionAligner()=default']]],
- ['density_8592',['density',['../classvg_1_1truncated__normal__distribution.html#a9cfc0bed97ccf33b216fdbaf8fced235',1,'vg::truncated_normal_distribution']]],
- ['dependency_5forder_8593',['dependency_order',['../classvg_1_1IndexRegistry.html#a2c133bd3842c61cb885868de26c51fe6',1,'vg::IndexRegistry']]],
- ['dependents_8594',['dependents',['../classvg_1_1IndexingPlan.html#ad8dc425414eec61802c17ef877d9483d',1,'vg::IndexingPlan']]],
- ['depth_8595',['depth',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aefb003f914686b6564f144dccad77f4c',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['depth_5ffilter_8596',['depth_filter',['../classvg_1_1Filter.html#a554d7fd6bc98d2c7e720e3edcb98c7d0',1,'vg::Filter']]],
- ['describe_8597',['describe',['../classvg_1_1io_1_1VPKG.html#af08bb9c650bfbbf15521ca1a215d0939',1,'vg::io::VPKG']]],
- ['deserialize_8598',['deserialize',['../classvg_1_1VG.html#a24359ba8e4ecbbd692bba5a517456659',1,'vg::VG::deserialize()'],['../classvg_1_1ZipCodeCollection.html#a9adaac607e3d9c8b46f9ae1e3a45e37e',1,'vg::ZipCodeCollection::deserialize()'],['../classhandlegraph_1_1Serializable.html#a2e101879c6d02c4d189248c9bc340319',1,'handlegraph::Serializable::deserialize(std::istream &in)'],['../classhandlegraph_1_1Serializable.html#ad3b89e4a5c2a4724fe8748c586dd8ccf',1,'handlegraph::Serializable::deserialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#ab675ab02cad114960ea7cbdf8b751ada',1,'handlegraph::TriviallySerializable::deserialize(int fd)=0'],['../classhandlegraph_1_1TriviallySerializable.html#a8851ae4c53082c72dd9d5eee60f2ba93',1,'handlegraph::TriviallySerializable::deserialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#a71a1e9bda6b28669c8c406ec1762c8d7',1,'handlegraph::TriviallySerializable::deserialize(std::istream &in)']]],
- ['deserialize_5fmembers_8599',['deserialize_members',['../classxg_1_1XG.html#a43717eb175308f40c9303257b30366bb',1,'xg::XG::deserialize_members()'],['../classhandlegraph_1_1Serializable.html#a33651ea0e5d56a7a1471f8f0ce10b95d',1,'handlegraph::Serializable::deserialize_members()']]],
- ['destroy_5fedge_8600',['destroy_edge',['../classvg_1_1VG.html#a9d4264e39e3826ded714992361ab879e',1,'vg::VG::destroy_edge(const handle_t &left, const handle_t &right)'],['../classvg_1_1VG.html#a284327157f9d4b82224fc856179a668d',1,'vg::VG::destroy_edge(Edge *edge)'],['../classvg_1_1VG.html#abe6b91020abf39815d28995eceac4e2d',1,'vg::VG::destroy_edge(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a7fd2744b37b62862df68e82cbe7b6b59',1,'vg::VG::destroy_edge(const pair< NodeSide, NodeSide > &sides)'],['../classhandlegraph_1_1DeletableHandleGraph.html#a285ac35e805eab548c4106ee534d79f2',1,'handlegraph::DeletableHandleGraph::destroy_edge(const handle_t &left, const handle_t &right)=0'],['../classhandlegraph_1_1DeletableHandleGraph.html#aec2b397c1b4ec7f9c75ccc5b9ce06564',1,'handlegraph::DeletableHandleGraph::destroy_edge(const edge_t &edge)']]],
- ['destroy_5fhandle_8601',['destroy_handle',['../classvg_1_1VG.html#a3e52875d37f046daeaf9e7b301ad59ff',1,'vg::VG::destroy_handle()'],['../classhandlegraph_1_1DeletableHandleGraph.html#a06d4d3ecda0694d5045c457f3eecd8e3',1,'handlegraph::DeletableHandleGraph::destroy_handle()']]],
- ['destroy_5fnode_8602',['destroy_node',['../classvg_1_1VG.html#ab9cd34f3c968f90370c42e8692222619',1,'vg::VG::destroy_node(Node *node)'],['../classvg_1_1VG.html#a983041950b8dc25a77bd828dd6c05a1b',1,'vg::VG::destroy_node(nid_t id)']]],
- ['destroy_5fpath_8603',['destroy_path',['../classvg_1_1VG.html#adb25bd1fdb9e36c55157c5be864ca403',1,'vg::VG::destroy_path()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a421fe49069d9a533db9ab682d4bec754',1,'handlegraph::MutablePathHandleGraph::destroy_path()']]],
- ['destroy_5fpaths_8604',['destroy_paths',['../classhandlegraph_1_1MutablePathHandleGraph.html#a9c87d426fc5c9f4606faf11caa557e92',1,'handlegraph::MutablePathHandleGraph']]],
- ['destroy_5fprogress_8605',['destroy_progress',['../classvg_1_1Progressive.html#aaab8c6ae92870077bb59f86a15c8d18f',1,'vg::Progressive']]],
- ['determine_5fdistance_5fcorrelation_8606',['determine_distance_correlation',['../classvg_1_1MultipathMapper.html#ad25f505dc4d7fbca4040b483d2eb11a2',1,'vg::MultipathMapper']]],
- ['determine_5fflag_8607',['determine_flag',['../namespacevg.html#afa3eeb1e344417323232103c7e38747f',1,'vg']]],
- ['determine_5fjobs_8608',['determine_jobs',['../gbwt__main_8cpp.html#a561987b9179ef0c4d1e0cfa0c0cde254',1,'gbwt_main.cpp']]],
- ['deterministic_5fbeats_8609',['deterministic_beats',['../namespacevg.html#a1f573d1f1f474086cbe0a8933fe29988',1,'vg']]],
- ['deterministic_5fflip_8610',['deterministic_flip',['../namespacevg.html#a73b5e48235129c3583b5b3942ff4d44d',1,'vg']]],
- ['deterministic_5fshuffle_8611',['deterministic_shuffle',['../namespacevg.html#a2a2c2b828b3943b33f2b0b12f756ed9a',1,'vg::deterministic_shuffle(RandomIt begin, RandomIt end, LazyRNG &rng)'],['../namespacevg.html#ae74e428a09df726b5c2f4998b9d0a442',1,'vg::deterministic_shuffle(RandomIt begin, RandomIt end)']]],
- ['dfs_8612',['dfs',['../classvg_1_1FlowSort.html#ab2154c68fe44aa6cf33aa7dba294fc7a',1,'vg::FlowSort::dfs()'],['../classvg_1_1VG.html#aec0db609d022b3c3183403600970238f',1,'vg::VG::dfs(const function< void(NodeTraversal)> &node_begin_fn, const function< void(NodeTraversal)> &node_end_fn, const function< bool(void)> &break_fn, const function< void(Edge *)> &edge_fn, const function< void(Edge *)> &tree_fn, const function< void(Edge *)> &edge_curr_fn, const function< void(Edge *)> &edge_cross_fn, const vector< NodeTraversal > *sources, const unordered_set< NodeTraversal > *sinks)'],['../classvg_1_1VG.html#a287e5d12ba0bc0823d1b6e0fa56af3d6',1,'vg::VG::dfs(const function< void(NodeTraversal)> &node_begin_fn, const function< void(NodeTraversal)> &node_end_fn, const vector< NodeTraversal > *sources=NULL, const unordered_set< NodeTraversal > *sinks=NULL)'],['../classvg_1_1VG.html#a8ee80f3ce939643d59157e1a1d707068',1,'vg::VG::dfs(const function< void(NodeTraversal)> &node_begin_fn, const function< void(NodeTraversal)> &node_end_fn, const function< bool(void)> &break_fn)'],['../namespacevg_1_1algorithms.html#a2a2ca7e29cbf4769c5f6432499a45e23',1,'vg::algorithms::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn, const function< void(const edge_t &)> &edge_fn, const function< void(const edge_t &)> &tree_fn, const function< void(const edge_t &)> &edge_curr_fn, const function< void(const edge_t &)> &edge_cross_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacevg_1_1algorithms.html#ade95900b3f3715ae3ecf9b3aee79961f',1,'vg::algorithms::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacevg_1_1algorithms.html#ac89d8d2356483ef348082609dc310b80',1,'vg::algorithms::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn)'],['../namespacehandlegraph_1_1algorithms_1_1internal.html#a09003b82c452cbd09b41aea19352196f',1,'handlegraph::algorithms::internal::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn, const function< void(const edge_t &)> &edge_fn, const function< void(const edge_t &)> &tree_fn, const function< void(const edge_t &)> &edge_curr_fn, const function< void(const edge_t &)> &edge_cross_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacehandlegraph_1_1algorithms_1_1internal.html#afeb7e14a45b41d2b3d8743cd0e4988ed',1,'handlegraph::algorithms::internal::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacehandlegraph_1_1algorithms_1_1internal.html#a6e401edc92d22fe914e9744431731457',1,'handlegraph::algorithms::internal::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn)']]],
- ['dfs_5fgbwt_8613',['dfs_gbwt',['../classvg_1_1MinimizerMapper.html#a4355a2ecfe99c02410f92093efc77ce4',1,'vg::MinimizerMapper::dfs_gbwt(const Position &from, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const'],['../classvg_1_1MinimizerMapper.html#a657e584de6e57a3f6f15616f245e39ef',1,'vg::MinimizerMapper::dfs_gbwt(handle_t from_handle, size_t from_offset, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const'],['../classvg_1_1MinimizerMapper.html#a759504362bfa77a4eb8428e1b2be1ccf',1,'vg::MinimizerMapper::dfs_gbwt(const gbwt::SearchState &start_state, size_t from_offset, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const']]],
- ['diagramexplainer_8614',['DiagramExplainer',['../classvg_1_1DiagramExplainer.html#a0b8ae8fd0309f7d23f591d5680eea251',1,'vg::DiagramExplainer']]],
- ['dijkstra_8615',['dijkstra',['../namespacehandlegraph_1_1algorithms.html#a8e7bda18174c291a0d991002c2f56a4d',1,'handlegraph::algorithms::dijkstra(const HandleGraph *g, handle_t start, function< bool(const handle_t &, size_t)> reached_callback, bool traverse_leftward, bool prune, bool cycle_to_start)'],['../namespacehandlegraph_1_1algorithms.html#a236138ba6f70d430d3a401251372ff74',1,'handlegraph::algorithms::dijkstra(const HandleGraph *g, const unordered_set< handle_t > &starts, function< bool(const handle_t &, size_t)> reached_callback, bool traverse_leftward, bool prune, bool cycle_to_start)']]],
- ['dijkstra_5fshortest_5fcycle_5flength_8616',['dijkstra_shortest_cycle_length',['../namespacevg_1_1algorithms.html#a40d6162a9f0dba28306c836d07d7d6e3',1,'vg::algorithms']]],
- ['dinucleotidemachine_8617',['DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html#ad34ca2eea941b95d73d401c9abbe65a1',1,'vg::DinucleotideMachine']]],
- ['discard_5fbytes_8618',['discard_bytes',['../classvg_1_1io_1_1StreamMultiplexer.html#af25792444fb888296deead30a520f7b3',1,'vg::io::StreamMultiplexer']]],
- ['discard_5fto_5fbreakpoint_8619',['discard_to_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#a6107af83d4ce5347df10459d0f57e399',1,'vg::io::StreamMultiplexer']]],
- ['discount_8620',['discount',['../namespacehaplotypes__defaults.html#ac06fc8c64358ce5d9e9e5b26df84a7be',1,'haplotypes_defaults']]],
- ['discrete_5fdistribution_8621',['discrete_distribution',['../classvg_1_1discrete__distribution.html#af776d23ad1fa743df24837bd31e32665',1,'vg::discrete_distribution::discrete_distribution(InputIt first, InputIt last)'],['../classvg_1_1discrete__distribution.html#a038d37d1df2526016be0119d7d5feea6',1,'vg::discrete_distribution::discrete_distribution(initializer_list< double > weights={1})']]],
- ['discrete_5funiform_5fsample_8622',['discrete_uniform_sample',['../classvg_1_1SnarlManager.html#aff971d38975386cfc73d44560027110a',1,'vg::SnarlManager']]],
- ['disjoint_8623',['disjoint',['../structhaplo_1_1int__itvl__t.html#ae0a7468e2fc96d6a68c0d6226344a38b',1,'haplo::int_itvl_t']]],
- ['disjoint_5fcomponents_8624',['disjoint_components',['../namespacevg_1_1algorithms.html#a38ba5a6719f9f5496130c72a047ad890',1,'vg::algorithms']]],
- ['display_8625',['display',['../classvg_1_1MEMChainModel.html#ab02e84fb2d25c2ff7f19941b78e458ba',1,'vg::MEMChainModel::display()'],['../classvg_1_1AlignmentChainModel.html#a142994d7c623a99007811acb547e6112',1,'vg::AlignmentChainModel::display()']]],
- ['display_5fdot_8626',['display_dot',['../classvg_1_1MEMChainModel.html#acfdb6531ee913ada6b21fa375ae35724',1,'vg::MEMChainModel::display_dot()'],['../classvg_1_1AlignmentChainModel.html#a16e9e8fc71345d31f1e58827e665a43c',1,'vg::AlignmentChainModel::display_dot()']]],
- ['dissociate_8627',['dissociate',['../classhandlegraph_1_1TriviallySerializable.html#acb05cd688a0b14471e3995aa60d9103c',1,'handlegraph::TriviallySerializable']]],
- ['distance_8628',['distance',['../structvg_1_1MatchPos.html#a3adf7aecb3aaf7dd92bd4e7b515c9cf4',1,'vg::MatchPos::distance()'],['../classvg_1_1MultipathMapper.html#ac3de928a00a38f13fe42009ea5185a7a',1,'vg::MultipathMapper::distance()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a7ad6324e922cb42e58a7406a33ea30bd',1,'vg::Haplotypes::Subchain::distance()']]],
- ['distance_5fbetween_8629',['distance_between',['../classvg_1_1MinimizerMapper.html#af68c4bd9915413525c9c66b668779331',1,'vg::MinimizerMapper::distance_between(const pos_t &pos1, const pos_t &pos2)'],['../classvg_1_1MinimizerMapper.html#ae68add551501e3b58c9329d9297d620d',1,'vg::MinimizerMapper::distance_between(const Alignment &aln1, const Alignment &aln2)'],['../classvg_1_1MultipathMapper.html#aa948917259866a65c3ca0c2d711a9187',1,'vg::MultipathMapper::distance_between()']]],
- ['distance_5fbetween_5fpositions_8630',['distance_between_positions',['../classvg_1_1Filter.html#a9f3ede63fb8518a85f966c3aececb4a6',1,'vg::Filter']]],
- ['distance_5fto_5fannotation_8631',['distance_to_annotation',['../classvg_1_1MinimizerMapper.html#af629f2b0730c6f38794d4193740317cc',1,'vg::MinimizerMapper']]],
- ['distance_5fto_5fhead_8632',['distance_to_head',['../namespacevg_1_1algorithms.html#a187fd628ac942c540a1a5fde0e27b0ef',1,'vg::algorithms::distance_to_head(handle_t h, int32_t limit, const HandleGraph *graph)'],['../namespacevg_1_1algorithms.html#a33aca5bac60aa4d0a4c402ed607b06a3',1,'vg::algorithms::distance_to_head(handle_t h, int32_t limit, int32_t dist, unordered_set< handle_t > &seen, const HandleGraph *graph)']]],
- ['distance_5fto_5ftail_8633',['distance_to_tail',['../namespacevg_1_1algorithms.html#a458c768a87a1182eae38b362aa7b5ad7',1,'vg::algorithms::distance_to_tail(handle_t h, int32_t limit, const HandleGraph *graph)'],['../namespacevg_1_1algorithms.html#ac8fb0ce9a4ccbb1505e661a1caa266f8',1,'vg::algorithms::distance_to_tail(handle_t h, int32_t limit, int32_t dist, unordered_set< handle_t > &seen, const HandleGraph *graph)']]],
- ['divergence_8634',['divergence',['../namespacevg.html#ad3b0a534daaa4c4eb7204b139fbbe3b7',1,'vg']]],
- ['divide_5fhandle_8635',['divide_handle',['../classvg_1_1VG.html#a7a5dbc95fa80e7fe3dc04d62ac6d7b3c',1,'vg::VG::divide_handle()'],['../classhandlegraph_1_1MutableHandleGraph.html#aca166406fa2000778552ed77c41a5e4c',1,'handlegraph::MutableHandleGraph::divide_handle(const handle_t &handle, const std::vector< size_t > &offsets)=0'],['../classhandlegraph_1_1MutableHandleGraph.html#a05c38787f0ff4a2695e61d98cb402175',1,'handlegraph::MutableHandleGraph::divide_handle(const handle_t &handle, size_t offset)']]],
- ['divide_5fmapping_8636',['divide_mapping',['../classvg_1_1Paths.html#ab307239574344cac532dd2df6e4bc6f9',1,'vg::Paths::divide_mapping(mapping_t *m, const Position &pos)'],['../classvg_1_1Paths.html#a98161e70365341b3522a198b4c199556',1,'vg::Paths::divide_mapping(mapping_t *m, size_t offset)']]],
- ['divide_5fnode_8637',['divide_node',['../classvg_1_1VG.html#ad06f0fcad4bf5b1c29cf937a870a58b4',1,'vg::VG::divide_node(Node *node, int pos, Node *&left, Node *&right)'],['../classvg_1_1VG.html#a7bee7317e4f7e42d85d8e7ef8d07273a',1,'vg::VG::divide_node(Node *node, vector< int > &positions, vector< Node * > &parts)']]],
- ['divide_5fpath_8638',['divide_path',['../classvg_1_1VG.html#a0466bd1a92042266f6a99aa306d387c9',1,'vg::VG']]],
- ['dna3bit_8639',['dna3bit',['../namespacexg.html#a0b632a6673e7464eced03fe8bb491f97',1,'xg']]],
- ['do_5falignment_5fon_5fchains_8640',['do_alignment_on_chains',['../classvg_1_1MinimizerMapper.html#ae369fba07da94be9dea486d79f251d59',1,'vg::MinimizerMapper']]],
- ['do_5fchaining_5fon_5ffragments_8641',['do_chaining_on_fragments',['../classvg_1_1MinimizerMapper.html#a895936ea103ac0db5c8b9860cc898c4d',1,'vg::MinimizerMapper']]],
- ['do_5ffragmenting_5fon_5ftrees_8642',['do_fragmenting_on_trees',['../classvg_1_1MinimizerMapper.html#ae5ab30eddb294c77922940b3ab5b1880',1,'vg::MinimizerMapper']]],
- ['do_5fpoa_8643',['do_poa',['../classvg_1_1DozeuInterface.html#a4f8194b77acf4e94604b5b0759231c62',1,'vg::DozeuInterface']]],
- ['do_5frescue_5falignment_8644',['do_rescue_alignment',['../classvg_1_1MultipathMapper.html#acc6d405f8349b1c5ae932e50a8e4cc47',1,'vg::MultipathMapper']]],
- ['dotdumpexplainer_8645',['DotDumpExplainer',['../classvg_1_1DotDumpExplainer.html#aff9bc2f478a7a2c71b95f03b8e84e47c',1,'vg::DotDumpExplainer']]],
- ['downsample_5fchunks_8646',['downsample_chunks',['../classvg_1_1Surjector.html#a2dac1e9d5af63b0fe7c9513afa4909e1',1,'vg::Surjector']]],
- ['dozeupinningoverlay_8647',['DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html#a2a71927eb2c877e8bad8208d804f028e',1,'vg::DozeuPinningOverlay::DozeuPinningOverlay(const HandleGraph *graph, bool preserve_sinks)'],['../classvg_1_1DozeuPinningOverlay.html#a5b86da6db2f137450aba39f1807640a1',1,'vg::DozeuPinningOverlay::DozeuPinningOverlay()=default']]],
- ['dpscorecomparator_8648',['DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#aac5cf15234c5137ca426604d910340c8',1,'vg::MEMClusterer::DPScoreComparator::DPScoreComparator()=delete'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a1c6be54ddf88de294dd910d8f39427aa',1,'vg::MEMClusterer::DPScoreComparator::DPScoreComparator(const vector< HitNode > &nodes)']]],
- ['draw_8649',['draw',['../classvg_1_1Viz.html#aed21697f1ddd4fb1b9c5ea2fcaa831b3',1,'vg::Viz']]],
- ['draw_5fgraph_8650',['draw_graph',['../classvg_1_1Viz.html#ad8b787e3208a261c77e12d8cd70e0d08',1,'vg::Viz']]],
- ['drop_5fprefix_8651',['drop_prefix',['../classvg_1_1BitString.html#a2200dc1668821c7aa772f87fe9239ff3',1,'vg::BitString']]],
- ['dump_8652',['dump',['../classvg_1_1SnarlState.html#a73e89359341e01d66fbb28f110a6c24a',1,'vg::SnarlState::dump()'],['../classvg_1_1GenomeState.html#a96f209015d1816d0b7cdefc8f10c25b3',1,'vg::GenomeState::dump()'],['../classvg_1_1ZipCode.html#aae9095d31b64aa151d6d30e246ee4561',1,'vg::ZipCode::dump()']]],
- ['dump_5fchaining_5fproblem_8653',['dump_chaining_problem',['../classvg_1_1MinimizerMapper.html#ade827ad4371daa0bf40a48f136be39ce',1,'vg::MinimizerMapper']]],
- ['dump_5fdebug_5fclustering_8654',['dump_debug_clustering',['../classvg_1_1MinimizerMapper.html#a1b466bf5f7a58e3d229073beba810131',1,'vg::MinimizerMapper']]],
- ['dump_5fdebug_5fdotplot_8655',['dump_debug_dotplot',['../classvg_1_1MinimizerMapper.html#ab6b793e4d06e9b58195a49a86a9ec152',1,'vg::MinimizerMapper']]],
- ['dump_5fdebug_5fextension_5fset_8656',['dump_debug_extension_set',['../classvg_1_1MinimizerMapper.html#a2a9803373db4106b6362c97333a850fb',1,'vg::MinimizerMapper']]],
- ['dump_5fdebug_5fgraph_8657',['dump_debug_graph',['../classvg_1_1MinimizerMapper.html#af667c12a73803c136e79fe22c3fc6cb7',1,'vg::MinimizerMapper']]],
- ['dump_5fdebug_5fminimizers_8658',['dump_debug_minimizers',['../classvg_1_1MinimizerMapper.html#aa5ad810a56c4188ac65a4d00ef882583',1,'vg::MinimizerMapper']]],
- ['dump_5fdebug_5fquery_8659',['dump_debug_query',['../classvg_1_1MinimizerMapper.html#a14d4ea0c3d2e6c82acdba6db0afb0fc5',1,'vg::MinimizerMapper::dump_debug_query(const Alignment &aln)'],['../classvg_1_1MinimizerMapper.html#a79654a1638227197fd75f33ab24b1276',1,'vg::MinimizerMapper::dump_debug_query(const Alignment &aln1, const Alignment &aln2)']]],
- ['dump_5fdebug_5fseeds_8660',['dump_debug_seeds',['../classvg_1_1MinimizerMapper.html#a1f1a80614f3a36b6c14b46590619027b',1,'vg::MinimizerMapper']]],
- ['dump_5fdebug_5fsequence_8661',['dump_debug_sequence',['../classvg_1_1MinimizerMapper.html#a1b7705ed18be207fc6b18f8bc3012296',1,'vg::MinimizerMapper']]],
- ['dump_5fto_5fstream_8662',['dump_to_stream',['../classxg_1_1XG.html#a676a88d58aa3a9cc1cbe580472e3e083',1,'xg::XG']]],
- ['dup_8663',['dup',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ac98b43745a7cbaaae5f164852d3d8460',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['duplication_5ffilter_8664',['duplication_filter',['../classvg_1_1Filter.html#a55d17dd60e541900c814c3fe5cef9338',1,'vg::Filter']]]
+ ['dag_5fand_5fnon_5fdag_5fsnarl_5fcount_8554',['dag_and_non_dag_snarl_count',['../classvg_1_1ZipCodeTree.html#a0651e6fb7447bfd47181226c264bd45d',1,'vg::ZipCodeTree']]],
+ ['dagifiedgraph_8555',['DagifiedGraph',['../classvg_1_1DagifiedGraph.html#a39faa4602acdc54d568410dda0d1ae35',1,'vg::DagifiedGraph::DagifiedGraph(const HandleGraph *graph, size_t min_preserved_path_length, size_t max_num_duplications=std::numeric_limits< size_t >::max())'],['../classvg_1_1DagifiedGraph.html#ada562ce53bd2fc9a59aeef495eafa6c8',1,'vg::DagifiedGraph::DagifiedGraph()=default']]],
+ ['dagify_8556',['dagify',['../classvg_1_1VG.html#a2c8890bbc32c99bba8ca17f24a11d343',1,'vg::VG::dagify()'],['../namespacehandlegraph_1_1algorithms.html#a64feaa655343996c7d233d938a5f35d8',1,'handlegraph::algorithms::dagify()']]],
+ ['dagify_5ffrom_8557',['dagify_from',['../namespacehandlegraph_1_1algorithms.html#a1922a67cde14a6cc4e30d2fd62728df1',1,'handlegraph::algorithms']]],
+ ['data_5fsize_8558',['data_size',['../classvg_1_1SmallBitset.html#ad0e138252408f61ed254f45bb641bee8',1,'vg::SmallBitset']]],
+ ['debug_5fstring_8559',['debug_string',['../namespacevg.html#ae72a83063f59506e0fcd76304b85d842',1,'vg::debug_string(const connection_t &connection)'],['../namespacevg.html#a8401a5ba093820ee017f9db390058087',1,'vg::debug_string(const subpath_t &subpath)'],['../namespacevg.html#a3a723cb7c4957a689cb7de6812237dea',1,'vg::debug_string(const multipath_alignment_t &multipath_aln)'],['../namespacevg.html#a472702e0931449cfaa10a337d7119d63',1,'vg::debug_string(const path_t &path)'],['../namespacevg.html#a11592884d28d3865ea95f76232e2fed4',1,'vg::debug_string(const path_mapping_t &mapping)'],['../namespacevg.html#a51469d56a6d4e55660c15af135c92b46',1,'vg::debug_string(const edit_t &edit)'],['../namespacevg.html#a99864b7ad9781d2c41c424ae69187e2e',1,'vg::debug_string(const position_t &pos)']]],
+ ['decode_5frgfa_5ftags_8560',['decode_rgfa_tags',['../classvg_1_1algorithms_1_1GFAParser.html#abca93aab4d7a7375deca9a970808005d',1,'vg::algorithms::GFAParser']]],
+ ['decoder_5flength_8561',['decoder_length',['../classvg_1_1ZipCode.html#ab5cc414a3fa14b68799c93fa61486a31',1,'vg::ZipCode']]],
+ ['decoder_5ft_8562',['decoder_t',['../structvg_1_1ZipCode_1_1decoder__t.html#a075168865b66d94ce93b852c7fb7e4d6',1,'vg::ZipCode::decoder_t']]],
+ ['decompose_8563',['decompose',['../namespacevg.html#a90fe8f4de1196dd902ac05f7567b9b7b',1,'vg']]],
+ ['decompose_5falignments_8564',['decompose_alignments',['../classvg_1_1MultipathAlignmentGraph.html#a8e7fa26541aea68ea2c456d79c950377',1,'vg::MultipathAlignmentGraph']]],
+ ['decompose_5fgenotype_5ffast_8565',['decompose_genotype_fast',['../classvg_1_1WindowedVcfBuffer.html#ae05d4861f68f92b5c11e293f1a34618b',1,'vg::WindowedVcfBuffer']]],
+ ['decompressstring_8566',['DecompressString',['../namespacezstdutil.html#a96bc1e7d01552bb8397ffd2a8dbc0167',1,'zstdutil']]],
+ ['deconstruct_8567',['deconstruct',['../classvg_1_1Deconstructor.html#a65c57f3f6e3b4504ceb8bb6b3a96925c',1,'vg::Deconstructor']]],
+ ['deconstruct_5fgraph_8568',['deconstruct_graph',['../classvg_1_1Deconstructor.html#a2b35a006fe649bbd6e2ee8c7ca0fefd8',1,'vg::Deconstructor']]],
+ ['deconstruct_5fgraph_5ftop_5fdown_8569',['deconstruct_graph_top_down',['../classvg_1_1Deconstructor.html#a1ec4ade6a850ee9e5b6debfe07e2b31a',1,'vg::Deconstructor']]],
+ ['deconstruct_5fsite_8570',['deconstruct_site',['../classvg_1_1Deconstructor.html#ae39b201fb62f77c2309a3230d8bfd5bb',1,'vg::Deconstructor']]],
+ ['deconstructor_8571',['Deconstructor',['../classvg_1_1Deconstructor.html#ac164fa41d5d207dec36a99b891d405be',1,'vg::Deconstructor']]],
+ ['decrement_5fnode_5fids_8572',['decrement_node_ids',['../classvg_1_1VG.html#aae60b30eaa432d73f91dc28283679a18',1,'vg::VG']]],
+ ['deduplicate_5falt_5falns_8573',['deduplicate_alt_alns',['../classvg_1_1MultipathAlignmentGraph.html#acf97e6e2b5f03198f3087d7746e19b85',1,'vg::MultipathAlignmentGraph']]],
+ ['deduplicate_5fcluster_5fpairs_8574',['deduplicate_cluster_pairs',['../classvg_1_1MEMClusterer.html#ae99c87e944c8c1056abb8efc7da5786e',1,'vg::MEMClusterer']]],
+ ['deep_5fcontents_8575',['deep_contents',['../classvg_1_1SnarlManager.html#a88dbb1a06fa24de3459f62ecdbc7d962',1,'vg::SnarlManager']]],
+ ['default_5fbuild_5fjobs_8576',['default_build_jobs',['../structGBWTConfig.html#aae95569c118992c2d9f0c70ee0115034',1,'GBWTConfig']]],
+ ['default_5fcontext_5flength_8577',['default_context_length',['../structGBWTConfig.html#ac7920a61ea6e371b8d91754c757e4644',1,'GBWTConfig']]],
+ ['default_5fdistance_8578',['default_distance',['../structvg_1_1WFAExtender_1_1ErrorModel.html#aa2ddef59dceb81bd45cc7a485ff3fb6f',1,'vg::WFAExtender::ErrorModel']]],
+ ['default_5fgap_5flength_8579',['default_gap_length',['../structvg_1_1WFAExtender_1_1ErrorModel.html#a542b1c4afc94ad305ab098e3a226075c',1,'vg::WFAExtender::ErrorModel']]],
+ ['default_5fgaps_8580',['default_gaps',['../structvg_1_1WFAExtender_1_1ErrorModel.html#affe4519ada47143c048385a6eb9caf88',1,'vg::WFAExtender::ErrorModel']]],
+ ['default_5fmerge_5fjobs_8581',['default_merge_jobs',['../structGBWTConfig.html#a19a35e22dd696babede6279a85859742',1,'GBWTConfig']]],
+ ['default_5fmismatches_8582',['default_mismatches',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ab68d1f72fc508682dafd052bab6d268c',1,'vg::WFAExtender::ErrorModel']]],
+ ['default_5fnum_5fpaths_8583',['default_num_paths',['../structGBWTConfig.html#aae283e22db9032f46239d1e06deaa459',1,'GBWTConfig']]],
+ ['default_5fnum_5fpaths_5flocal_8584',['default_num_paths_local',['../structGBWTConfig.html#a28b0e3eb72d2c6ba04301f4e27460714',1,'GBWTConfig']]],
+ ['default_5fsort_5fzipcodes_8585',['default_sort_zipcodes',['../classvg_1_1ZipCodeForest.html#a5eed49e06827ec7883f8abe8da3d548e',1,'vg::ZipCodeForest']]],
+ ['deflect_5fto_5fmatrix_8586',['deflect_to_matrix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a6abbf28540a3e93c039ee2ec6ccf26be',1,'vg::BandedGlobalAligner::AltTracebackStack::deflect_to_matrix()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a5c24b2c60ef30f7ff29f3b28534496c2',1,'vg::BandedGlobalAligner::AltTracebackStack::deflect_to_matrix(int64_t &to_node_id)']]],
+ ['deflection_8587',['Deflection',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a44389670dc49e1dadf64104423dd064f',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['del_5fpredecessor_8588',['del_predecessor',['../classvg_1_1WFATree.html#a14b76054dbd37a01db3065bbe453cf4c',1,'vg::WFATree']]],
+ ['delete_5fhaplotype_8589',['delete_haplotype',['../classvg_1_1GenomeState.html#a3abfa8020eb5f6f6229e7b59924dad30',1,'vg::GenomeState']]],
+ ['delete_5fnodes_5fand_5fchop_5fpaths_8590',['delete_nodes_and_chop_paths',['../namespacevg.html#ab273ea17c855b1b0a32fc4e98405519e',1,'vg']]],
+ ['delete_5fvariant_5findex_8591',['delete_variant_index',['../classvg_1_1VCFTraversalFinder.html#a45b91ad0f95daad0ce2610953873f867',1,'vg::VCFTraversalFinder']]],
+ ['deletion_5ffilter_8592',['deletion_filter',['../classvg_1_1Filter.html#a8b867ca7572a1f8687b96cba2687f749',1,'vg::Filter']]],
+ ['deletionaligner_8593',['DeletionAligner',['../classvg_1_1DeletionAligner.html#ae118f6eccda2b49e39aed57e6c1a6950',1,'vg::DeletionAligner::DeletionAligner(int8_t gap_open, int8_t gap_extension)'],['../classvg_1_1DeletionAligner.html#a7c942c5a7530fd098f0771956a245862',1,'vg::DeletionAligner::DeletionAligner()=default']]],
+ ['density_8594',['density',['../classvg_1_1truncated__normal__distribution.html#a9cfc0bed97ccf33b216fdbaf8fced235',1,'vg::truncated_normal_distribution']]],
+ ['dependency_5forder_8595',['dependency_order',['../classvg_1_1IndexRegistry.html#a2c133bd3842c61cb885868de26c51fe6',1,'vg::IndexRegistry']]],
+ ['dependents_8596',['dependents',['../classvg_1_1IndexingPlan.html#ad8dc425414eec61802c17ef877d9483d',1,'vg::IndexingPlan']]],
+ ['depth_8597',['depth',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aefb003f914686b6564f144dccad77f4c',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['depth_5ffilter_8598',['depth_filter',['../classvg_1_1Filter.html#a554d7fd6bc98d2c7e720e3edcb98c7d0',1,'vg::Filter']]],
+ ['describe_8599',['describe',['../classvg_1_1io_1_1VPKG.html#af08bb9c650bfbbf15521ca1a215d0939',1,'vg::io::VPKG']]],
+ ['deserialize_8600',['deserialize',['../classvg_1_1VG.html#a24359ba8e4ecbbd692bba5a517456659',1,'vg::VG::deserialize()'],['../classvg_1_1ZipCodeCollection.html#a9adaac607e3d9c8b46f9ae1e3a45e37e',1,'vg::ZipCodeCollection::deserialize()'],['../classhandlegraph_1_1Serializable.html#a2e101879c6d02c4d189248c9bc340319',1,'handlegraph::Serializable::deserialize(std::istream &in)'],['../classhandlegraph_1_1Serializable.html#ad3b89e4a5c2a4724fe8748c586dd8ccf',1,'handlegraph::Serializable::deserialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#ab675ab02cad114960ea7cbdf8b751ada',1,'handlegraph::TriviallySerializable::deserialize(int fd)=0'],['../classhandlegraph_1_1TriviallySerializable.html#a8851ae4c53082c72dd9d5eee60f2ba93',1,'handlegraph::TriviallySerializable::deserialize(const std::string &filename)'],['../classhandlegraph_1_1TriviallySerializable.html#a71a1e9bda6b28669c8c406ec1762c8d7',1,'handlegraph::TriviallySerializable::deserialize(std::istream &in)']]],
+ ['deserialize_5fmembers_8601',['deserialize_members',['../classxg_1_1XG.html#a43717eb175308f40c9303257b30366bb',1,'xg::XG::deserialize_members()'],['../classhandlegraph_1_1Serializable.html#a33651ea0e5d56a7a1471f8f0ce10b95d',1,'handlegraph::Serializable::deserialize_members()']]],
+ ['destroy_5fedge_8602',['destroy_edge',['../classvg_1_1VG.html#a9d4264e39e3826ded714992361ab879e',1,'vg::VG::destroy_edge(const handle_t &left, const handle_t &right)'],['../classvg_1_1VG.html#a284327157f9d4b82224fc856179a668d',1,'vg::VG::destroy_edge(Edge *edge)'],['../classvg_1_1VG.html#abe6b91020abf39815d28995eceac4e2d',1,'vg::VG::destroy_edge(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a7fd2744b37b62862df68e82cbe7b6b59',1,'vg::VG::destroy_edge(const pair< NodeSide, NodeSide > &sides)'],['../classhandlegraph_1_1DeletableHandleGraph.html#a285ac35e805eab548c4106ee534d79f2',1,'handlegraph::DeletableHandleGraph::destroy_edge(const handle_t &left, const handle_t &right)=0'],['../classhandlegraph_1_1DeletableHandleGraph.html#aec2b397c1b4ec7f9c75ccc5b9ce06564',1,'handlegraph::DeletableHandleGraph::destroy_edge(const edge_t &edge)']]],
+ ['destroy_5fhandle_8603',['destroy_handle',['../classvg_1_1VG.html#a3e52875d37f046daeaf9e7b301ad59ff',1,'vg::VG::destroy_handle()'],['../classhandlegraph_1_1DeletableHandleGraph.html#a06d4d3ecda0694d5045c457f3eecd8e3',1,'handlegraph::DeletableHandleGraph::destroy_handle()']]],
+ ['destroy_5fnode_8604',['destroy_node',['../classvg_1_1VG.html#ab9cd34f3c968f90370c42e8692222619',1,'vg::VG::destroy_node(Node *node)'],['../classvg_1_1VG.html#a983041950b8dc25a77bd828dd6c05a1b',1,'vg::VG::destroy_node(nid_t id)']]],
+ ['destroy_5fpath_8605',['destroy_path',['../classvg_1_1VG.html#adb25bd1fdb9e36c55157c5be864ca403',1,'vg::VG::destroy_path()'],['../classhandlegraph_1_1MutablePathHandleGraph.html#a421fe49069d9a533db9ab682d4bec754',1,'handlegraph::MutablePathHandleGraph::destroy_path()']]],
+ ['destroy_5fpaths_8606',['destroy_paths',['../classhandlegraph_1_1MutablePathHandleGraph.html#a9c87d426fc5c9f4606faf11caa557e92',1,'handlegraph::MutablePathHandleGraph']]],
+ ['destroy_5fprogress_8607',['destroy_progress',['../classvg_1_1Progressive.html#aaab8c6ae92870077bb59f86a15c8d18f',1,'vg::Progressive']]],
+ ['determine_5fdistance_5fcorrelation_8608',['determine_distance_correlation',['../classvg_1_1MultipathMapper.html#ad25f505dc4d7fbca4040b483d2eb11a2',1,'vg::MultipathMapper']]],
+ ['determine_5fflag_8609',['determine_flag',['../namespacevg.html#afa3eeb1e344417323232103c7e38747f',1,'vg']]],
+ ['determine_5fjobs_8610',['determine_jobs',['../gbwt__main_8cpp.html#a561987b9179ef0c4d1e0cfa0c0cde254',1,'gbwt_main.cpp']]],
+ ['deterministic_5fbeats_8611',['deterministic_beats',['../namespacevg.html#a1f573d1f1f474086cbe0a8933fe29988',1,'vg']]],
+ ['deterministic_5fflip_8612',['deterministic_flip',['../namespacevg.html#a73b5e48235129c3583b5b3942ff4d44d',1,'vg']]],
+ ['deterministic_5fshuffle_8613',['deterministic_shuffle',['../namespacevg.html#a2a2c2b828b3943b33f2b0b12f756ed9a',1,'vg::deterministic_shuffle(RandomIt begin, RandomIt end, LazyRNG &rng)'],['../namespacevg.html#ae74e428a09df726b5c2f4998b9d0a442',1,'vg::deterministic_shuffle(RandomIt begin, RandomIt end)']]],
+ ['dfs_8614',['dfs',['../classvg_1_1FlowSort.html#ab2154c68fe44aa6cf33aa7dba294fc7a',1,'vg::FlowSort::dfs()'],['../classvg_1_1VG.html#aec0db609d022b3c3183403600970238f',1,'vg::VG::dfs(const function< void(NodeTraversal)> &node_begin_fn, const function< void(NodeTraversal)> &node_end_fn, const function< bool(void)> &break_fn, const function< void(Edge *)> &edge_fn, const function< void(Edge *)> &tree_fn, const function< void(Edge *)> &edge_curr_fn, const function< void(Edge *)> &edge_cross_fn, const vector< NodeTraversal > *sources, const unordered_set< NodeTraversal > *sinks)'],['../classvg_1_1VG.html#a287e5d12ba0bc0823d1b6e0fa56af3d6',1,'vg::VG::dfs(const function< void(NodeTraversal)> &node_begin_fn, const function< void(NodeTraversal)> &node_end_fn, const vector< NodeTraversal > *sources=NULL, const unordered_set< NodeTraversal > *sinks=NULL)'],['../classvg_1_1VG.html#a8ee80f3ce939643d59157e1a1d707068',1,'vg::VG::dfs(const function< void(NodeTraversal)> &node_begin_fn, const function< void(NodeTraversal)> &node_end_fn, const function< bool(void)> &break_fn)'],['../namespacevg_1_1algorithms.html#a2a2ca7e29cbf4769c5f6432499a45e23',1,'vg::algorithms::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn, const function< void(const edge_t &)> &edge_fn, const function< void(const edge_t &)> &tree_fn, const function< void(const edge_t &)> &edge_curr_fn, const function< void(const edge_t &)> &edge_cross_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacevg_1_1algorithms.html#ade95900b3f3715ae3ecf9b3aee79961f',1,'vg::algorithms::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacevg_1_1algorithms.html#ac89d8d2356483ef348082609dc310b80',1,'vg::algorithms::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn)'],['../namespacehandlegraph_1_1algorithms_1_1internal.html#a09003b82c452cbd09b41aea19352196f',1,'handlegraph::algorithms::internal::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn, const function< void(const edge_t &)> &edge_fn, const function< void(const edge_t &)> &tree_fn, const function< void(const edge_t &)> &edge_curr_fn, const function< void(const edge_t &)> &edge_cross_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacehandlegraph_1_1algorithms_1_1internal.html#afeb7e14a45b41d2b3d8743cd0e4988ed',1,'handlegraph::algorithms::internal::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const vector< handle_t > &sources, const unordered_set< handle_t > &sinks)'],['../namespacehandlegraph_1_1algorithms_1_1internal.html#a6e401edc92d22fe914e9744431731457',1,'handlegraph::algorithms::internal::dfs(const HandleGraph &graph, const function< void(const handle_t &)> &handle_begin_fn, const function< void(const handle_t &)> &handle_end_fn, const function< bool(void)> &break_fn)']]],
+ ['dfs_5fgbwt_8615',['dfs_gbwt',['../classvg_1_1MinimizerMapper.html#a4355a2ecfe99c02410f92093efc77ce4',1,'vg::MinimizerMapper::dfs_gbwt(const Position &from, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const'],['../classvg_1_1MinimizerMapper.html#a657e584de6e57a3f6f15616f245e39ef',1,'vg::MinimizerMapper::dfs_gbwt(handle_t from_handle, size_t from_offset, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const'],['../classvg_1_1MinimizerMapper.html#a759504362bfa77a4eb8428e1b2be1ccf',1,'vg::MinimizerMapper::dfs_gbwt(const gbwt::SearchState &start_state, size_t from_offset, size_t walk_distance, const function< void(const handle_t &)> &enter_handle, const function< void(void)> exit_handle) const']]],
+ ['diagramexplainer_8616',['DiagramExplainer',['../classvg_1_1DiagramExplainer.html#a0b8ae8fd0309f7d23f591d5680eea251',1,'vg::DiagramExplainer']]],
+ ['dijkstra_8617',['dijkstra',['../namespacehandlegraph_1_1algorithms.html#a8e7bda18174c291a0d991002c2f56a4d',1,'handlegraph::algorithms::dijkstra(const HandleGraph *g, handle_t start, function< bool(const handle_t &, size_t)> reached_callback, bool traverse_leftward, bool prune, bool cycle_to_start)'],['../namespacehandlegraph_1_1algorithms.html#a236138ba6f70d430d3a401251372ff74',1,'handlegraph::algorithms::dijkstra(const HandleGraph *g, const unordered_set< handle_t > &starts, function< bool(const handle_t &, size_t)> reached_callback, bool traverse_leftward, bool prune, bool cycle_to_start)']]],
+ ['dijkstra_5fshortest_5fcycle_5flength_8618',['dijkstra_shortest_cycle_length',['../namespacevg_1_1algorithms.html#a40d6162a9f0dba28306c836d07d7d6e3',1,'vg::algorithms']]],
+ ['dinucleotidemachine_8619',['DinucleotideMachine',['../classvg_1_1DinucleotideMachine.html#ad34ca2eea941b95d73d401c9abbe65a1',1,'vg::DinucleotideMachine']]],
+ ['discard_5fbytes_8620',['discard_bytes',['../classvg_1_1io_1_1StreamMultiplexer.html#af25792444fb888296deead30a520f7b3',1,'vg::io::StreamMultiplexer']]],
+ ['discard_5fto_5fbreakpoint_8621',['discard_to_breakpoint',['../classvg_1_1io_1_1StreamMultiplexer.html#a6107af83d4ce5347df10459d0f57e399',1,'vg::io::StreamMultiplexer']]],
+ ['discount_8622',['discount',['../namespacehaplotypes__defaults.html#ac06fc8c64358ce5d9e9e5b26df84a7be',1,'haplotypes_defaults']]],
+ ['discrete_5fdistribution_8623',['discrete_distribution',['../classvg_1_1discrete__distribution.html#af776d23ad1fa743df24837bd31e32665',1,'vg::discrete_distribution::discrete_distribution(InputIt first, InputIt last)'],['../classvg_1_1discrete__distribution.html#a038d37d1df2526016be0119d7d5feea6',1,'vg::discrete_distribution::discrete_distribution(initializer_list< double > weights={1})']]],
+ ['discrete_5funiform_5fsample_8624',['discrete_uniform_sample',['../classvg_1_1SnarlManager.html#aff971d38975386cfc73d44560027110a',1,'vg::SnarlManager']]],
+ ['disjoint_8625',['disjoint',['../structhaplo_1_1int__itvl__t.html#ae0a7468e2fc96d6a68c0d6226344a38b',1,'haplo::int_itvl_t']]],
+ ['disjoint_5fcomponents_8626',['disjoint_components',['../namespacevg_1_1algorithms.html#a38ba5a6719f9f5496130c72a047ad890',1,'vg::algorithms']]],
+ ['display_8627',['display',['../classvg_1_1MEMChainModel.html#ab02e84fb2d25c2ff7f19941b78e458ba',1,'vg::MEMChainModel::display()'],['../classvg_1_1AlignmentChainModel.html#a142994d7c623a99007811acb547e6112',1,'vg::AlignmentChainModel::display()']]],
+ ['display_5fdot_8628',['display_dot',['../classvg_1_1MEMChainModel.html#acfdb6531ee913ada6b21fa375ae35724',1,'vg::MEMChainModel::display_dot()'],['../classvg_1_1AlignmentChainModel.html#a16e9e8fc71345d31f1e58827e665a43c',1,'vg::AlignmentChainModel::display_dot()']]],
+ ['dissociate_8629',['dissociate',['../classhandlegraph_1_1TriviallySerializable.html#acb05cd688a0b14471e3995aa60d9103c',1,'handlegraph::TriviallySerializable']]],
+ ['distance_8630',['distance',['../structvg_1_1MatchPos.html#a3adf7aecb3aaf7dd92bd4e7b515c9cf4',1,'vg::MatchPos::distance()'],['../classvg_1_1MultipathMapper.html#ac3de928a00a38f13fe42009ea5185a7a',1,'vg::MultipathMapper::distance()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a7ad6324e922cb42e58a7406a33ea30bd',1,'vg::Haplotypes::Subchain::distance()']]],
+ ['distance_5fbetween_8631',['distance_between',['../classvg_1_1MinimizerMapper.html#af68c4bd9915413525c9c66b668779331',1,'vg::MinimizerMapper::distance_between(const pos_t &pos1, const pos_t &pos2)'],['../classvg_1_1MinimizerMapper.html#ae68add551501e3b58c9329d9297d620d',1,'vg::MinimizerMapper::distance_between(const Alignment &aln1, const Alignment &aln2)'],['../classvg_1_1MultipathMapper.html#aa948917259866a65c3ca0c2d711a9187',1,'vg::MultipathMapper::distance_between()']]],
+ ['distance_5fbetween_5fpositions_8632',['distance_between_positions',['../classvg_1_1Filter.html#a9f3ede63fb8518a85f966c3aececb4a6',1,'vg::Filter']]],
+ ['distance_5fto_5fannotation_8633',['distance_to_annotation',['../classvg_1_1MinimizerMapper.html#af629f2b0730c6f38794d4193740317cc',1,'vg::MinimizerMapper']]],
+ ['distance_5fto_5fhead_8634',['distance_to_head',['../namespacevg_1_1algorithms.html#a187fd628ac942c540a1a5fde0e27b0ef',1,'vg::algorithms::distance_to_head(handle_t h, int32_t limit, const HandleGraph *graph)'],['../namespacevg_1_1algorithms.html#a33aca5bac60aa4d0a4c402ed607b06a3',1,'vg::algorithms::distance_to_head(handle_t h, int32_t limit, int32_t dist, unordered_set< handle_t > &seen, const HandleGraph *graph)']]],
+ ['distance_5fto_5ftail_8635',['distance_to_tail',['../namespacevg_1_1algorithms.html#a458c768a87a1182eae38b362aa7b5ad7',1,'vg::algorithms::distance_to_tail(handle_t h, int32_t limit, const HandleGraph *graph)'],['../namespacevg_1_1algorithms.html#ac8fb0ce9a4ccbb1505e661a1caa266f8',1,'vg::algorithms::distance_to_tail(handle_t h, int32_t limit, int32_t dist, unordered_set< handle_t > &seen, const HandleGraph *graph)']]],
+ ['divergence_8636',['divergence',['../namespacevg.html#ad3b0a534daaa4c4eb7204b139fbbe3b7',1,'vg']]],
+ ['divide_5fhandle_8637',['divide_handle',['../classvg_1_1VG.html#a7a5dbc95fa80e7fe3dc04d62ac6d7b3c',1,'vg::VG::divide_handle()'],['../classhandlegraph_1_1MutableHandleGraph.html#aca166406fa2000778552ed77c41a5e4c',1,'handlegraph::MutableHandleGraph::divide_handle(const handle_t &handle, const std::vector< size_t > &offsets)=0'],['../classhandlegraph_1_1MutableHandleGraph.html#a05c38787f0ff4a2695e61d98cb402175',1,'handlegraph::MutableHandleGraph::divide_handle(const handle_t &handle, size_t offset)']]],
+ ['divide_5fmapping_8638',['divide_mapping',['../classvg_1_1Paths.html#ab307239574344cac532dd2df6e4bc6f9',1,'vg::Paths::divide_mapping(mapping_t *m, const Position &pos)'],['../classvg_1_1Paths.html#a98161e70365341b3522a198b4c199556',1,'vg::Paths::divide_mapping(mapping_t *m, size_t offset)']]],
+ ['divide_5fnode_8639',['divide_node',['../classvg_1_1VG.html#ad06f0fcad4bf5b1c29cf937a870a58b4',1,'vg::VG::divide_node(Node *node, int pos, Node *&left, Node *&right)'],['../classvg_1_1VG.html#a7bee7317e4f7e42d85d8e7ef8d07273a',1,'vg::VG::divide_node(Node *node, vector< int > &positions, vector< Node * > &parts)']]],
+ ['divide_5fpath_8640',['divide_path',['../classvg_1_1VG.html#a0466bd1a92042266f6a99aa306d387c9',1,'vg::VG']]],
+ ['dna3bit_8641',['dna3bit',['../namespacexg.html#a0b632a6673e7464eced03fe8bb491f97',1,'xg']]],
+ ['do_5falignment_5fon_5fchains_8642',['do_alignment_on_chains',['../classvg_1_1MinimizerMapper.html#ae369fba07da94be9dea486d79f251d59',1,'vg::MinimizerMapper']]],
+ ['do_5fchaining_5fon_5ffragments_8643',['do_chaining_on_fragments',['../classvg_1_1MinimizerMapper.html#a895936ea103ac0db5c8b9860cc898c4d',1,'vg::MinimizerMapper']]],
+ ['do_5ffragmenting_5fon_5ftrees_8644',['do_fragmenting_on_trees',['../classvg_1_1MinimizerMapper.html#ae5ab30eddb294c77922940b3ab5b1880',1,'vg::MinimizerMapper']]],
+ ['do_5fpoa_8645',['do_poa',['../classvg_1_1DozeuInterface.html#a4f8194b77acf4e94604b5b0759231c62',1,'vg::DozeuInterface']]],
+ ['do_5frescue_5falignment_8646',['do_rescue_alignment',['../classvg_1_1MultipathMapper.html#acc6d405f8349b1c5ae932e50a8e4cc47',1,'vg::MultipathMapper']]],
+ ['dotdumpexplainer_8647',['DotDumpExplainer',['../classvg_1_1DotDumpExplainer.html#aff9bc2f478a7a2c71b95f03b8e84e47c',1,'vg::DotDumpExplainer']]],
+ ['downsample_5fchunks_8648',['downsample_chunks',['../classvg_1_1Surjector.html#a2dac1e9d5af63b0fe7c9513afa4909e1',1,'vg::Surjector']]],
+ ['dozeupinningoverlay_8649',['DozeuPinningOverlay',['../classvg_1_1DozeuPinningOverlay.html#a2a71927eb2c877e8bad8208d804f028e',1,'vg::DozeuPinningOverlay::DozeuPinningOverlay(const HandleGraph *graph, bool preserve_sinks)'],['../classvg_1_1DozeuPinningOverlay.html#a5b86da6db2f137450aba39f1807640a1',1,'vg::DozeuPinningOverlay::DozeuPinningOverlay()=default']]],
+ ['dpscorecomparator_8650',['DPScoreComparator',['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#aac5cf15234c5137ca426604d910340c8',1,'vg::MEMClusterer::DPScoreComparator::DPScoreComparator()=delete'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a1c6be54ddf88de294dd910d8f39427aa',1,'vg::MEMClusterer::DPScoreComparator::DPScoreComparator(const vector< HitNode > &nodes)']]],
+ ['draw_8651',['draw',['../classvg_1_1Viz.html#aed21697f1ddd4fb1b9c5ea2fcaa831b3',1,'vg::Viz']]],
+ ['draw_5fgraph_8652',['draw_graph',['../classvg_1_1Viz.html#ad8b787e3208a261c77e12d8cd70e0d08',1,'vg::Viz']]],
+ ['drop_5fprefix_8653',['drop_prefix',['../classvg_1_1BitString.html#a2200dc1668821c7aa772f87fe9239ff3',1,'vg::BitString']]],
+ ['dump_8654',['dump',['../classvg_1_1SnarlState.html#a73e89359341e01d66fbb28f110a6c24a',1,'vg::SnarlState::dump()'],['../classvg_1_1GenomeState.html#a96f209015d1816d0b7cdefc8f10c25b3',1,'vg::GenomeState::dump()'],['../classvg_1_1ZipCode.html#aae9095d31b64aa151d6d30e246ee4561',1,'vg::ZipCode::dump()']]],
+ ['dump_5fchaining_5fproblem_8655',['dump_chaining_problem',['../classvg_1_1MinimizerMapper.html#ade827ad4371daa0bf40a48f136be39ce',1,'vg::MinimizerMapper']]],
+ ['dump_5fdebug_5fclustering_8656',['dump_debug_clustering',['../classvg_1_1MinimizerMapper.html#a1b466bf5f7a58e3d229073beba810131',1,'vg::MinimizerMapper']]],
+ ['dump_5fdebug_5fdotplot_8657',['dump_debug_dotplot',['../classvg_1_1MinimizerMapper.html#ab6b793e4d06e9b58195a49a86a9ec152',1,'vg::MinimizerMapper']]],
+ ['dump_5fdebug_5fextension_5fset_8658',['dump_debug_extension_set',['../classvg_1_1MinimizerMapper.html#a2a9803373db4106b6362c97333a850fb',1,'vg::MinimizerMapper']]],
+ ['dump_5fdebug_5fgraph_8659',['dump_debug_graph',['../classvg_1_1MinimizerMapper.html#af667c12a73803c136e79fe22c3fc6cb7',1,'vg::MinimizerMapper']]],
+ ['dump_5fdebug_5fminimizers_8660',['dump_debug_minimizers',['../classvg_1_1MinimizerMapper.html#aa5ad810a56c4188ac65a4d00ef882583',1,'vg::MinimizerMapper']]],
+ ['dump_5fdebug_5fquery_8661',['dump_debug_query',['../classvg_1_1MinimizerMapper.html#a14d4ea0c3d2e6c82acdba6db0afb0fc5',1,'vg::MinimizerMapper::dump_debug_query(const Alignment &aln)'],['../classvg_1_1MinimizerMapper.html#a79654a1638227197fd75f33ab24b1276',1,'vg::MinimizerMapper::dump_debug_query(const Alignment &aln1, const Alignment &aln2)']]],
+ ['dump_5fdebug_5fseeds_8662',['dump_debug_seeds',['../classvg_1_1MinimizerMapper.html#a1f1a80614f3a36b6c14b46590619027b',1,'vg::MinimizerMapper']]],
+ ['dump_5fdebug_5fsequence_8663',['dump_debug_sequence',['../classvg_1_1MinimizerMapper.html#a1b7705ed18be207fc6b18f8bc3012296',1,'vg::MinimizerMapper']]],
+ ['dump_5fto_5fstream_8664',['dump_to_stream',['../classxg_1_1XG.html#a676a88d58aa3a9cc1cbe580472e3e083',1,'xg::XG']]],
+ ['dup_8665',['dup',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ac98b43745a7cbaaae5f164852d3d8460',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['duplication_5ffilter_8666',['duplication_filter',['../classvg_1_1Filter.html#a55d17dd60e541900c814c3fe5cef9338',1,'vg::Filter']]]
];
diff --git a/search/functions_5.js b/search/functions_5.js
index 04d6f858e5..f74a29c3e4 100644
--- a/search/functions_5.js
+++ b/search/functions_5.js
@@ -1,164 +1,164 @@
var searchData=
[
- ['each_5fapprox_5fgraph_5fmemory_8665',['each_approx_graph_memory',['../namespacevg.html#a104aaf42bb3f44518626b9417a4db2d5',1,'vg']]],
- ['eades_5falgorithm_8666',['eades_algorithm',['../namespacehandlegraph_1_1algorithms.html#a2dad089a8ba50413b0737bf6ceb52f80',1,'handlegraph::algorithms']]],
- ['easy_5fsort_8667',['easy_sort',['../classvg_1_1StreamSorter.html#ab01d2165ebd3f76b7c036c5428f4b2bc',1,'vg::StreamSorter']]],
- ['edge_5fallele_5flabels_8668',['edge_allele_labels',['../classvg_1_1Genotyper.html#aae52b974044843aed34fc31152ccda77',1,'vg::Genotyper']]],
- ['edge_5fcount_8669',['edge_count',['../classvg_1_1VG.html#a25ef81b910a6fc47c9a6ba4c1636cf83',1,'vg::VG']]],
- ['edge_5fcoverage_8670',['edge_coverage',['../classvg_1_1Packer.html#a5ff601ec8eace2559df20c9b1b11e030',1,'vg::Packer::edge_coverage(Edge &e) const'],['../classvg_1_1Packer.html#a241eceae29b5f183b876586e0e504a76',1,'vg::Packer::edge_coverage(size_t i) const']]],
- ['edge_5fcoverage_5fbin_5foffset_8671',['edge_coverage_bin_offset',['../classvg_1_1Packer.html#ab2f586cd7d0443b6ab3de98d321db4ac',1,'vg::Packer']]],
- ['edge_5fcoverage_5fbin_5fsize_8672',['edge_coverage_bin_size',['../classvg_1_1Packer.html#a8d35d0868d13a974e038425f02c97b10',1,'vg::Packer']]],
- ['edge_5fhandle_8673',['edge_handle',['../classhandlegraph_1_1HandleGraph.html#a3766f1aca1cbdbf827f2a12aaf2078ec',1,'handlegraph::HandleGraph']]],
- ['edge_5findex_8674',['edge_index',['../classvg_1_1Packer.html#aaac9a172415e1e7fbc419e5a7e13e985',1,'vg::Packer::edge_index()'],['../classxg_1_1XG.html#a184f3b8960859cee3ef5d929a4391e0b',1,'xg::XG::edge_index()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a5aa85bce7358af90d1e63d2060a50a39',1,'handlegraph::VectorizableHandleGraph::edge_index()']]],
- ['edge_5forientation_8675',['edge_orientation',['../classxg_1_1XG.html#a8b60df344ef1f990d0d6e0ed4eb77b92',1,'xg::XG']]],
- ['edge_5frelative_5foffset_8676',['edge_relative_offset',['../classxg_1_1XG.html#a3bbffb5a6cc0d70f7d20919c53af9520',1,'xg::XG']]],
- ['edge_5fto_5fsnarl_5fedge_8677',['edge_to_snarl_edge',['../classvg_1_1SnarlGraph.html#a607672055416281719361bdc35830567',1,'vg::SnarlGraph']]],
- ['edge_5fvector_5fsize_8678',['edge_vector_size',['../classvg_1_1Packer.html#a34b7060f8b021857f88bfbd598c207d0',1,'vg::Packer']]],
- ['edges_5fend_8679',['edges_end',['../classvg_1_1VG.html#a9a37e4df96356dbf4f7e78da9eb8fd89',1,'vg::VG::edges_end(Node *node)'],['../classvg_1_1VG.html#aaaae0ba5428a83ece038f506c9c5df54',1,'vg::VG::edges_end(nid_t id)']]],
- ['edges_5ffrom_8680',['edges_from',['../classvg_1_1VG.html#ae1a7e0aa663eadc0ebdaaf13b667323e',1,'vg::VG']]],
- ['edges_5fof_8681',['edges_of',['../classvg_1_1VG.html#aa1bf5492e5c6d586cd266d2a48f792df',1,'vg::VG']]],
- ['edges_5fof_5fnode_8682',['edges_of_node',['../classvg_1_1VG.html#a5b6a5e92afb1a70d9c63a1848a01f241',1,'vg::VG']]],
- ['edges_5fof_5fnodes_8683',['edges_of_nodes',['../classvg_1_1VG.html#a3b2d900fc42cffe079c3ba3897717eae',1,'vg::VG']]],
- ['edges_5fstart_8684',['edges_start',['../classvg_1_1VG.html#a3032de0eb7258c9e2db4a27f16a8604c',1,'vg::VG::edges_start(Node *node)'],['../classvg_1_1VG.html#aee2439ec8f0d8ee87becac3f6fbf13bb',1,'vg::VG::edges_start(nid_t id)']]],
- ['edges_5fto_8685',['edges_to',['../classvg_1_1VG.html#a3789cf6561f2d3da5ef85f23b5c6454f',1,'vg::VG']]],
- ['edit_8686',['edit',['../classvg_1_1path__mapping__t.html#ab8f590be7d2d5dc9f847b315d48b4d9a',1,'vg::path_mapping_t::edit() const'],['../classvg_1_1path__mapping__t.html#a98a2810ae03cc5bc9ca241a3a1cbd7e2',1,'vg::path_mapping_t::edit(size_t i) const'],['../classvg_1_1VG.html#a5962aa939727f27cb7c62b2ce2706fe9',1,'vg::VG::edit(vector< Path > &paths_to_add, vector< Translation > *out_translations=nullptr, bool save_paths=false, bool update_paths=false, bool break_at_ends=false)'],['../classvg_1_1VG.html#aa800d382b361f1bdad0e5855dd4c05ca',1,'vg::VG::edit(const string &paths_to_add_path, vector< Translation > *out_translations=nullptr, bool save_paths=false, const string &out_gam_path="", bool break_at_ends=false, bool remove_softclips=false)']]],
- ['edit_5fcount_8687',['edit_count',['../namespacevg.html#a2610da8a8fbe723e13519d79ac2d0afe',1,'vg']]],
- ['edit_5ffast_8688',['edit_fast',['../classvg_1_1VG.html#a78f70eb7eddb0245be7cdfc048616638',1,'vg::VG']]],
- ['edit_5fis_5fdeletion_8689',['edit_is_deletion',['../namespacevg_1_1io.html#af23faba545c4d2714c1c86c15db79433',1,'vg::io']]],
- ['edit_5fis_5fempty_8690',['edit_is_empty',['../namespacevg_1_1io.html#a738f411081a82bfb4a1cb0d12bafc9bc',1,'vg::io']]],
- ['edit_5fis_5finsertion_8691',['edit_is_insertion',['../namespacevg_1_1io.html#a26c4d6dee35ff3ed8365a87e0125813e',1,'vg::io']]],
- ['edit_5fis_5fmatch_8692',['edit_is_match',['../namespacevg_1_1io.html#a5af2def0a0ebdab4130882eab0f0851d',1,'vg::io']]],
- ['edit_5fis_5fsub_8693',['edit_is_sub',['../namespacevg_1_1io.html#a77d59f64a316fdbc91577079af83fbc4',1,'vg::io']]],
- ['edit_5fsize_8694',['edit_size',['../classvg_1_1path__mapping__t.html#a03c9f7be25a6af86cb073f9bbc8fd310',1,'vg::path_mapping_t']]],
- ['edit_5ft_8695',['edit_t',['../classvg_1_1edit__t.html#a4987eba1f565f0b9ad0ac035d324290c',1,'vg::edit_t::edit_t() noexcept'],['../classvg_1_1edit__t.html#a0b3a99d70c0f3ec050ad81a81e6afd06',1,'vg::edit_t::edit_t(const edit_t &other)=default'],['../classvg_1_1edit__t.html#a9369c96a6763e648e8aaec848623da25',1,'vg::edit_t::edit_t(edit_t &&other)=default']]],
- ['edit_5fvalue_8696',['edit_value',['../classvg_1_1Packer.html#aff566a3e094a0e28bbc51a468d60b800',1,'vg::Packer']]],
- ['editedtranscriptpath_8697',['EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html#a8235f7b3dc4e3fac60234c849fecb2fb',1,'vg::EditedTranscriptPath::EditedTranscriptPath(const string &transcript_name, const string &embedded_path_name, const bool is_reference_in, const bool is_haplotype_in)'],['../structvg_1_1EditedTranscriptPath.html#af70d348a2aaf1ab702b4abe2106d95b8',1,'vg::EditedTranscriptPath::EditedTranscriptPath(const string &transcript_name, const gbwt::size_type &haplotype_gbwt_id, const bool is_reference_in, const bool is_haplotype_in)']]],
- ['edits_5fare_5fcompatible_8698',['edits_are_compatible',['../namespacevg.html#abfba7a19cbb794cd210116be91c62d96',1,'vg']]],
- ['edits_5fat_5fposition_8699',['edits_at_position',['../classvg_1_1Packer.html#a8b632f64e269417895cbc84d0e377a8a',1,'vg::Packer']]],
- ['effective_5fposition_5funion_8700',['effective_position_union',['../classvg_1_1Funnel.html#a5195231cc0b426406133439d5a7d6026',1,'vg::Funnel']]],
- ['embed_5fref_5fpath_5fsnarls_8701',['embed_ref_path_snarls',['../classvg_1_1SnarlGraph.html#a80d4241e20274286f95bbe35fa916481',1,'vg::SnarlGraph']]],
- ['embed_5fsnarl_8702',['embed_snarl',['../classvg_1_1SnarlGraph.html#af1dc28423f51b60f019e08f716e9b082',1,'vg::SnarlGraph']]],
- ['embed_5fsnarls_8703',['embed_snarls',['../classvg_1_1SnarlGraph.html#a30a11c3b13a39e23394731d982ce7f75',1,'vg::SnarlGraph']]],
- ['embed_5ftranscript_5fpaths_8704',['embed_transcript_paths',['../classvg_1_1Transcriptome.html#a0f729698bd8dca0fdcd3f78a56f708cc',1,'vg::Transcriptome']]],
- ['emit_8705',['emit',['../classvg_1_1ReadFilter.html#a50fce1e4c1159834e6371156040c6cbe',1,'vg::ReadFilter::emit(Read &read)'],['../classvg_1_1ReadFilter.html#a5beda5e781b3a4b1b6ec139b280785d9',1,'vg::ReadFilter::emit(Read &read1, Read &read2)'],['../classVectorizer.html#a086dc2c83d1627780103d9367b7d3191',1,'Vectorizer::emit()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a020229bc89c799a2d16ebcbb7a349b94',1,'vg::io::TSVAlignmentEmitter::emit()'],['../classvg_1_1ReadFilter.html#a4436cd59a7d2ed18c4a315ef157239ed',1,'vg::ReadFilter::emit(Alignment &aln)'],['../classvg_1_1ReadFilter.html#ae811413740325799e12d313149f2b15a',1,'vg::ReadFilter::emit(Alignment &aln1, Alignment &aln2)'],['../classvg_1_1ReadFilter.html#a95b5ca4213c6da0a174e53c2f91fb36b',1,'vg::ReadFilter::emit(MultipathAlignment &mp_aln)'],['../classvg_1_1ReadFilter.html#a3864d427682af9b6e0a67a157fddcfa2',1,'vg::ReadFilter::emit(MultipathAlignment &mp_aln1, MultipathAlignment &mp_aln2)']]],
- ['emit_5fextra_5fmessage_8706',['emit_extra_message',['../classvg_1_1BackTranslatingAlignmentEmitter.html#aed2fce246283ef5280a9219229f1e6e1',1,'vg::BackTranslatingAlignmentEmitter::emit_extra_message()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a72579ae4d3ac98e946b9bef7c147ed81',1,'vg::SurjectingAlignmentEmitter::emit_extra_message()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a4eb6186a8322603353d123295e0558f1',1,'vg::io::AlignmentEmitter::emit_extra_message()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a5c128b83d74f99f7c7951a4d2f5fb27d',1,'vg::io::VGAlignmentEmitter::emit_extra_message()']]],
- ['emit_5fgaf_5ftraversals_8707',['emit_gaf_traversals',['../classvg_1_1GAFOutputCaller.html#ac3ece689949d9d3d7c0078ab753532e7',1,'vg::GAFOutputCaller']]],
- ['emit_5fgaf_5fvariant_8708',['emit_gaf_variant',['../classvg_1_1GAFOutputCaller.html#ac5a6e77d30c33cd4087bac27b9dc780f',1,'vg::GAFOutputCaller']]],
- ['emit_5fgroup_8709',['emit_group',['../classvg_1_1io_1_1MessageEmitter.html#a1f37b89141a12819675b1d2a9dccdb10',1,'vg::io::MessageEmitter::emit_group()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a55b19615de43ba7ef0fc38487fe7e811',1,'vg::io::ProtobufEmitter::emit_group()']]],
- ['emit_5fmapped_5fpair_8710',['emit_mapped_pair',['../classvg_1_1io_1_1AlignmentEmitter.html#a9fd17a6201b33a32f2bbb133952c0d26',1,'vg::io::AlignmentEmitter']]],
- ['emit_5fmapped_5fpairs_8711',['emit_mapped_pairs',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a2e0b48b26e6563de0728055ee80947f4',1,'vg::BackTranslatingAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1HTSAlignmentEmitter.html#a144167b8b9b973a113beb3950d8f64e7',1,'vg::HTSAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a5f3a358a96878a701407a648dd925b28',1,'vg::SurjectingAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a430ea0461fdb40d7df836b92fc529a55',1,'vg::io::AlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#a9cf86d953fb199dc1be11a4a18020299',1,'vg::io::NullAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#ab2ead89927010b48bcc8788f6dc71445',1,'vg::io::TSVAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a16ef4e377610cdf7678faa0564aa83fa',1,'vg::io::VGAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a7f9275cb4115e8ea629a8c58f468ac66',1,'vg::io::GafAlignmentEmitter::emit_mapped_pairs()']]],
- ['emit_5fmapped_5fsingle_8712',['emit_mapped_single',['../classvg_1_1io_1_1AlignmentEmitter.html#a424cb81bfd87685b3be4823e95a023eb',1,'vg::io::AlignmentEmitter']]],
- ['emit_5fmapped_5fsingles_8713',['emit_mapped_singles',['../classvg_1_1BackTranslatingAlignmentEmitter.html#abe1c7762c88dd018e0e949afdfce33b1',1,'vg::BackTranslatingAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1HTSAlignmentEmitter.html#a3137223a14396af5a6284830c716b943',1,'vg::HTSAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a96d4bea40f617e8083c732ce3ce6d9f8',1,'vg::SurjectingAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a3314c504ff0d278f5f44a316ec573b30',1,'vg::io::AlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#ab4da7694c104089d8f25b715aedb76bc',1,'vg::io::NullAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#adcda781ada60a6d3116f5a7bc57ae513',1,'vg::io::TSVAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a6e54f94f8e7e772b3d98aa51deb8723e',1,'vg::io::VGAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a4762f418851fc7aac06333590e51ade2',1,'vg::io::GafAlignmentEmitter::emit_mapped_singles()']]],
- ['emit_5fpair_8714',['emit_pair',['../classvg_1_1io_1_1AlignmentEmitter.html#a719d2cbafa6160bf55e724be1ef9d6f9',1,'vg::io::AlignmentEmitter']]],
- ['emit_5fpairs_8715',['emit_pairs',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a37bb7f41cd3d94ee37b837e5254d2122',1,'vg::BackTranslatingAlignmentEmitter::emit_pairs()'],['../classvg_1_1HTSAlignmentEmitter.html#a6c2dbcf61c25fe6646b6753d51b73771',1,'vg::HTSAlignmentEmitter::emit_pairs()'],['../classvg_1_1MultipathAlignmentEmitter.html#a7467c3e0ce1525f32e27f4f99d00c8b5',1,'vg::MultipathAlignmentEmitter::emit_pairs()'],['../classvg_1_1SurjectingAlignmentEmitter.html#ac053805811c71dfffc31eb3decab4279',1,'vg::SurjectingAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1AlignmentEmitter.html#aae5f5e6108e47d0a481d656abd4a8075',1,'vg::io::AlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#a2313d024a104c2771531a6e2a725b0e1',1,'vg::io::NullAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a57c0cd7c8a5bd41a358de2430ca40e5f',1,'vg::io::TSVAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a72a72eef5e85e422acdfacb788bee8d0',1,'vg::io::VGAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#affa85e71afb3d28d219a0cce2703e45e',1,'vg::io::GafAlignmentEmitter::emit_pairs()']]],
- ['emit_5fsingle_8716',['emit_single',['../classvg_1_1io_1_1AlignmentEmitter.html#a9c09a54a452278ec02084ca498105b8d',1,'vg::io::AlignmentEmitter']]],
- ['emit_5fsingles_8717',['emit_singles',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a7a9bacd81bff0b873c4449e2fe698305',1,'vg::BackTranslatingAlignmentEmitter::emit_singles()'],['../classvg_1_1HTSAlignmentEmitter.html#a90e671da1b62eebf423f95c01a865fdd',1,'vg::HTSAlignmentEmitter::emit_singles()'],['../classvg_1_1MultipathAlignmentEmitter.html#a923124cdc8bdc96e95db68281bb79fcd',1,'vg::MultipathAlignmentEmitter::emit_singles()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a60e0c7fa81a98961a04bfaa42dc8e3af',1,'vg::SurjectingAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a132fc9cf3a53a99f1ac61538d6433760',1,'vg::io::AlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#a83b9c08b6d394dccbd7321f0b75294fe',1,'vg::io::NullAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#aef4194a290204811292491db459d49d1',1,'vg::io::TSVAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#ac8b4fed94e74172899ba065cc3f8ce5d',1,'vg::io::VGAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a2b4af0175e6a6b928d77bc2ab9085e17',1,'vg::io::GafAlignmentEmitter::emit_singles()']]],
- ['emit_5fsnarl_5frecursive_8718',['emit_snarl_recursive',['../classvg_1_1NestedFlowCaller.html#afa870673ddc9fbcc7a1f321a5aaa0746',1,'vg::NestedFlowCaller']]],
- ['emit_5fstacktrace_8719',['emit_stacktrace',['../namespacevg.html#a40556998a17c0f59c8ecc682af3a99a3',1,'vg']]],
- ['emit_5fto_8720',['emit_to',['../namespacevg_1_1io.html#ae5ab0e97965e5b5e461a997ed374423e',1,'vg::io']]],
- ['emit_5ftsv_8721',['emit_tsv',['../classvg_1_1ReadFilter.html#a02ed848e6d5395a8b966f883bd318a8e',1,'vg::ReadFilter::emit_tsv(Read &read, std::ostream &out)'],['../classvg_1_1ReadFilter.html#a8ee0191017a8bf8b6c09ea5ef01e9517',1,'vg::ReadFilter::emit_tsv(MultipathAlignment &read, std::ostream &out)'],['../classvg_1_1ReadFilter.html#a7ce4a34cb9883643cfc277ac0c213f64',1,'vg::ReadFilter::emit_tsv(Alignment &read, std::ostream &out)']]],
- ['emit_5fvariant_8722',['emit_variant',['../classvg_1_1VCFOutputCaller.html#a3ed9068c446bfd72f912184421c3d7ce',1,'vg::VCFOutputCaller::emit_variant()'],['../classvg_1_1MCMCCaller.html#ac5c178b336cdc31a491a2166137805ea',1,'vg::MCMCCaller::emit_variant()']]],
- ['emplace_5fback_8723',['emplace_back',['../classvg_1_1ZipCodeCollection.html#ad7cf238df94a2d6016a499f4a66a40bc',1,'vg::ZipCodeCollection']]],
- ['empty_8724',['empty',['../structvg_1_1MatchPos_1_1PathList.html#a2782600d1fa18f7f6ec09b52c6dae0d6',1,'vg::MatchPos::PathList::empty()'],['../structvg_1_1MatchPos.html#a3cfc20cb1d5f87a78aa4cf0187ea109b',1,'vg::MatchPos::empty()'],['../structvg_1_1GaplessExtension.html#a72542968a383c49ac29cc4f939cb3d9d',1,'vg::GaplessExtension::empty()'],['../structvg_1_1WFAAlignment.html#a3dd26de023774ab65b2c7e115e0aa88a',1,'vg::WFAAlignment::empty()'],['../structhaplo_1_1int__itvl__t.html#ad491ab3b9181c1601580d0458d4017eb',1,'haplo::int_itvl_t::empty()'],['../classvg_1_1MultipathAlignmentGraph.html#a91dd7a4bc802e510067ae6bcb0fc5b74',1,'vg::MultipathAlignmentGraph::empty()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a2916bfc8fc45ebb3160f4cdab7c67eab',1,'vg::Option< vector< Item >, Parser >::empty()'],['../classvg_1_1Paths.html#a6488500dc1c44646ad3003ce29816b08',1,'vg::Paths::empty()'],['../classvg_1_1BitString.html#a82ccba78adaa516a8223a74d53886b0b',1,'vg::BitString::empty()'],['../structvg_1_1VectorView.html#a468cbc6d153bdc27f394a4bd81d8bffe',1,'vg::VectorView::empty()'],['../classvg_1_1VG.html#a42d7f84de5d99fe0ce51186fcbea420c',1,'vg::VG::empty()'],['../classvg_1_1ZipCodeCollection.html#a89ed6fc02819ba84907ee24ff1daa98c',1,'vg::ZipCodeCollection::empty()'],['../classvg_1_1algorithms_1_1GFAParser.html#a3b8240590446e1ee287c9c05a74e2a9e',1,'vg::algorithms::GFAParser::empty()']]],
- ['empty_5fdiagonal_5frange_8725',['empty_diagonal_range',['../classvg_1_1WFATree.html#a599b32ec4cbb624705c893caa34c6561',1,'vg::WFATree']]],
- ['empty_5fgbwtgraph_5fhandle_8726',['empty_gbwtgraph_handle',['../namespacevg.html#a8811548042613f9e65545d1ed377643e',1,'vg']]],
- ['empty_5fpos_5ft_8727',['empty_pos_t',['../namespacevg.html#ad0576520eed494787a895b6ce862e1f0',1,'vg']]],
- ['enable_5fcrash_5fhandling_8728',['enable_crash_handling',['../namespacevg.html#a1f4461f901aba4b67353768ee25e23d7',1,'vg']]],
- ['encode_8729',['encode',['../classvg_1_1MEMAccelerator.html#a5e9b9dd9f3b1f278675404da99c37166',1,'vg::MEMAccelerator']]],
- ['encode_5fchars_8730',['encode_chars',['../namespacevg.html#aa25419c15b3dcae6b217f893c243c487',1,'vg']]],
- ['encode_5fedge_8731',['encode_edge',['../classxg_1_1XG.html#a9aaeb0232bdc092f1097704b8595b50a',1,'xg::XG']]],
- ['end_8732',['end',['../classvg_1_1ShuffledPairs.html#ad670dd24e999776922243cf7d212764e',1,'vg::ShuffledPairs::end()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a8392b88a5dc4781f64868bfaafbffb3d',1,'vg::Option< vector< Item >, Parser >::end()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a4bae8cab0824d37275f78170e9e3a319',1,'vg::Option< vector< Item >, Parser >::end() const'],['../structvg_1_1PathIndex.html#ada3ccf7b77f16b46373ff5bb19fdbc11',1,'vg::PathIndex::end()'],['../classvg_1_1PhasedGenome.html#a621ecd8fc372256aa037a8beb9ea4c39',1,'vg::PhasedGenome::end()'],['../structvg_1_1VectorView.html#ac7d28343b9bc2318a35ed2b029a7c052',1,'vg::VectorView::end()'],['../classvg_1_1ZipCodeTree.html#a952f6619fc095e7ab40e839ac0189692',1,'vg::ZipCodeTree::end()'],['../classhandlegraph_1_1PathForEachSocket.html#ae4a2081511b675e49566d335bdbe4945',1,'handlegraph::PathForEachSocket::end()']]],
- ['end_5fbackward_8733',['end_backward',['../namespacevg.html#acab8d2ef076a0e866c7849aace290124',1,'vg']]],
- ['end_5fdegree_8734',['end_degree',['../classvg_1_1VG.html#af3cf82dca43799a03d93b199133f1d4b',1,'vg::VG']]],
- ['end_5fhandle_8735',['end_handle',['../structvg_1_1Haplotypes_1_1Subchain.html#a7cee546f2ab356b0ed2920209011c2e5',1,'vg::Haplotypes::Subchain']]],
- ['end_5fhint_8736',['end_hint',['../classvg_1_1algorithms_1_1Anchor.html#a4911502b781ce9d07369a4e2ccb5d27a',1,'vg::algorithms::Anchor']]],
- ['end_5fhint_5foffset_8737',['end_hint_offset',['../classvg_1_1algorithms_1_1Anchor.html#afea64615714994d6e170242e1c4b17fc',1,'vg::algorithms::Anchor']]],
- ['endfile_8738',['EndFile',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aa6cf204591880e126bacc2d01799f3e6',1,'vg::io::BlockedGzipOutputStream']]],
- ['ends_5fat_8739',['ends_at',['../classhandlegraph_1_1SnarlDecomposition.html#a4f345867fbee2cbcd283e5c0ed4f5920',1,'handlegraph::SnarlDecomposition']]],
- ['ends_5fat_5fend_8740',['ends_at_end',['../classhandlegraph_1_1SnarlDecomposition.html#a5f13d153fedcd2e24575fb69672650cd',1,'handlegraph::SnarlDecomposition']]],
- ['ends_5fat_5fstart_8741',['ends_at_start',['../classhandlegraph_1_1SnarlDecomposition.html#a63e795bd9764b2b793472d46069cecab',1,'handlegraph::SnarlDecomposition']]],
- ['ends_5fat_5ftip_8742',['ends_at_tip',['../classhandlegraph_1_1SnarlDecomposition.html#ae397ce26e9c979cf64c18f56546e490c',1,'handlegraph::SnarlDecomposition']]],
- ['ends_5fwith_8743',['ends_with',['../haplotypes__main_8cpp.html#a1ffaf31343dd95074c3237bf89b38a33',1,'haplotypes_main.cpp']]],
- ['ensure_5fbreakpoints_8744',['ensure_breakpoints',['../namespacevg.html#a35bec7a1758e5eb88a359da78174d8d9',1,'vg']]],
- ['ensure_5fedge_8745',['ensure_edge',['../classvg_1_1DiagramExplainer.html#a4e632e8785e76ea1b2e3e27ef9315465',1,'vg::DiagramExplainer']]],
- ['ensure_5fedit_5ftmpfiles_5fopen_8746',['ensure_edit_tmpfiles_open',['../classvg_1_1Packer.html#a3120b075177c3ca1916d20557b175733',1,'vg::Packer']]],
- ['ensure_5fheader_8747',['ensure_header',['../classvg_1_1HTSWriter.html#a5eff59af09a0169f3da8510b8359b098',1,'vg::HTSWriter']]],
- ['ensure_5fnode_8748',['ensure_node',['../classvg_1_1DiagramExplainer.html#a72d8b7ba51d152e410146ccad7afcaed',1,'vg::DiagramExplainer']]],
- ['ensure_5fparent_5fdirectory_8749',['ensure_parent_directory',['../structvg_1_1temp__file_1_1Handler.html#a150465560cdc7dc8ffdab2a4b0cbbcc1',1,'vg::temp_file::Handler']]],
- ['entropy_8750',['entropy',['../namespacevg.html#ac3165438256db24864e88601839197df',1,'vg::entropy(const string &st)'],['../namespacevg.html#a77c1cb6069f865239d0365b55649bc8a',1,'vg::entropy(const char *st, size_t len)']]],
- ['erase_8751',['erase',['../classvg_1_1SnarlState.html#a92e53694dd3b0169ad55103076997660',1,'vg::SnarlState']]],
- ['erase_5fin_5fout_5fedges_8752',['erase_in_out_edges',['../classvg_1_1FlowSort.html#a8c021f7aad3257d61f531d1084484f23',1,'vg::FlowSort']]],
- ['escape_5fdelim_8753',['escape_delim',['../classvg_1_1Packer.html#aed800a1a6084d971951240a7791282bb',1,'vg::Packer']]],
- ['escape_5fdelims_8754',['escape_delims',['../classvg_1_1Packer.html#a6b86be5851966fc9da0c793b70496564',1,'vg::Packer']]],
- ['establish_5fstrand_5fconsistency_8755',['establish_strand_consistency',['../classvg_1_1MultipathMapper.html#a362ad957c6634b60317158966c3e02f7',1,'vg::MultipathMapper']]],
- ['estimate_5fbatch_5fsize_8756',['estimate_batch_size',['../classvg_1_1Packer.html#ad155cc551af3e3f306c35c36ec3d048f',1,'vg::Packer']]],
- ['estimate_5fbin_5fcount_8757',['estimate_bin_count',['../classvg_1_1Packer.html#ad88597461d2fdf1eb998a609c91bda0d',1,'vg::Packer']]],
- ['estimate_5fdata_5fwidth_8758',['estimate_data_width',['../classvg_1_1Packer.html#adda3242dea599a49f281fc56c66e5965',1,'vg::Packer']]],
- ['estimate_5fdistribution_8759',['estimate_distribution',['../classvg_1_1FragmentLengthDistribution.html#a87a5794f706a81748136f0890f2168cd',1,'vg::FragmentLengthDistribution']]],
- ['estimate_5fedge_5fscore_8760',['estimate_edge_score',['../classvg_1_1MEMClusterer.html#a941476ae17420e703a8ef743232643ab',1,'vg::MEMClusterer']]],
- ['estimate_5fgc_5fcontent_8761',['estimate_gc_content',['../classvg_1_1BaseMapper.html#aa08b00e5a349252d013d76651f754f8d',1,'vg::BaseMapper']]],
- ['estimate_5fhash_5ftable_5fsize_8762',['estimate_hash_table_size',['../minimizer__main_8cpp.html#a2f3588cd2c21ddbe85727345718e9ca3',1,'minimizer_main.cpp']]],
- ['estimate_5fmax_5fpossible_5fmapping_5fquality_8763',['estimate_max_possible_mapping_quality',['../classvg_1_1GSSWAligner.html#a0dc19c58a3f70a67a4b2a1ad475af79d',1,'vg::GSSWAligner::estimate_max_possible_mapping_quality()'],['../classvg_1_1Mapper.html#ac8613c49c8390b280aef7323151a4fd8',1,'vg::Mapper::estimate_max_possible_mapping_quality()']]],
- ['estimate_5fmissed_5frescue_5fmultiplicity_8764',['estimate_missed_rescue_multiplicity',['../classvg_1_1MultipathMapper.html#a46edc0708ffa290b067a937c1876904c',1,'vg::MultipathMapper']]],
- ['estimate_5fnext_5fbest_5fscore_8765',['estimate_next_best_score',['../classvg_1_1GSSWAligner.html#a439ed0a50959b73b99d08d5ec0af4bc6',1,'vg::GSSWAligner']]],
- ['evaluate_8766',['evaluate',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a10e095ce1c007e526ac2506808aec71c',1,'vg::WFAExtender::ErrorModel::Event']]],
- ['ewens_5faf_5fprob_5fln_8767',['ewens_af_prob_ln',['../namespacevg.html#a59d4b5d91539506f52c32664fc1c0ddd',1,'vg']]],
- ['exact_8768',['exact',['../structvg_1_1GaplessExtension.html#aad05249efda81ed89bc782040bc3ba33',1,'vg::GaplessExtension']]],
- ['exclude_5fdist_5ftree_5fmerges_8769',['exclude_dist_tree_merges',['../classvg_1_1OrientedDistanceClusterer.html#af55b22c582dd1fdeb6a62061830c52ad',1,'vg::OrientedDistanceClusterer']]],
- ['exclude_5fmerges_8770',['exclude_merges',['../classvg_1_1OrientedDistanceMeasurer.html#a738f242df59c42bc9da14b07071b7ea3',1,'vg::OrientedDistanceMeasurer::exclude_merges()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a1791e7bf9d420b6303c16de3a1d7305e',1,'vg::PathOrientedDistanceMeasurer::exclude_merges()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a77a7d291ff3ea117e59861914ee84998',1,'vg::SnarlOrientedDistanceMeasurer::exclude_merges()']]],
- ['execute_8771',['execute',['../structvg_1_1GenomeStateCommand.html#a6ab4d8d0b53557324a094eba903ac74e',1,'vg::GenomeStateCommand::execute()'],['../structvg_1_1InsertHaplotypeCommand.html#a37b0c787712d1d3f9b0c0c64f0ab39c6',1,'vg::InsertHaplotypeCommand::execute()'],['../structvg_1_1DeleteHaplotypeCommand.html#af187726ffac73739f1a88552f12ae508',1,'vg::DeleteHaplotypeCommand::execute()'],['../structvg_1_1SwapHaplotypesCommand.html#afaccc42cb694c2b393955a39d7f0bd8f',1,'vg::SwapHaplotypesCommand::execute()'],['../structvg_1_1AppendHaplotypeCommand.html#a32ff3ddd9ff5bfbd6aef198d56ad07b6',1,'vg::AppendHaplotypeCommand::execute()'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#adc46192413e975507c86df1cda095e62',1,'vg::ReplaceSnarlHaplotypeCommand::execute()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a50908d3a7dc5da9f81a8c1c77be6ead0',1,'vg::ReplaceLocalHaplotypeCommand::execute()'],['../classvg_1_1GenomeState.html#a4150ec08000ac81447d631bcc5801543',1,'vg::GenomeState::execute()'],['../structvg_1_1IndexRecipe.html#a086051f9a92e58402095aa174274345c',1,'vg::IndexRecipe::execute()'],['../classvg_1_1JobSchedule.html#a048bac48af4bb855daf57e8738f981e4',1,'vg::JobSchedule::execute()']]],
- ['execute_5fin_5ffork_8772',['execute_in_fork',['../namespacevg.html#ae09739a5bb4d6d49b5c3a44264103606',1,'vg']]],
- ['execute_5frecipe_8773',['execute_recipe',['../classvg_1_1IndexRegistry.html#ab22b81a5248cf4b12a8be5fb424c9bd4',1,'vg::IndexRegistry']]],
- ['exhaustivetraversalfinder_8774',['ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html#a4c35877fcb69aefe449943a4646bd469',1,'vg::ExhaustiveTraversalFinder']]],
- ['expand_8775',['expand',['../classvg_1_1Funnel.html#a9440c3268e8c60b664a37283d9fc5cff',1,'vg::Funnel']]],
- ['expand_5fcontext_8776',['expand_context',['../classvg_1_1VG.html#a6a525e3290d6968c79314c2500f13cc3',1,'vg::VG::expand_context()'],['../namespacevg_1_1algorithms.html#aec7fcd701af4fdcbb87e83f0ea5b420a',1,'vg::algorithms::expand_context()']]],
- ['expand_5fcontext_5fby_5flength_8777',['expand_context_by_length',['../classvg_1_1VG.html#a5ba5a5416ee9eaf67c7ae5607fc7ae1f',1,'vg::VG::expand_context_by_length()'],['../namespacevg_1_1algorithms.html#a238775e0e0ecf0b7576f7c2265dfd5e0',1,'vg::algorithms::expand_context_by_length()']]],
- ['expand_5fcontext_5fby_5fsteps_8778',['expand_context_by_steps',['../classvg_1_1VG.html#aca4ead561b46cd1cde77ada1f611befa',1,'vg::VG::expand_context_by_steps()'],['../namespacevg_1_1algorithms.html#a354ea4a2a6aed208945fc0994ec50d9d',1,'vg::algorithms::expand_context_by_steps()']]],
- ['expand_5fcontext_5fwith_5fpaths_8779',['expand_context_with_paths',['../namespacevg_1_1algorithms.html#a8a0c0c6d333cb438f96e5df6faec3621',1,'vg::algorithms']]],
- ['expand_5ffor_5fsoftclips_8780',['expand_for_softclips',['../classvg_1_1MultipathMapper.html#af2e4bfb6634ee5d318cc5a84d35cb1ef',1,'vg::MultipathMapper']]],
- ['expand_5fif_5fnecessary_8781',['expand_if_necessary',['../classvg_1_1WFATree.html#a2e014cad6e29600bc11b82855a74dd6b',1,'vg::WFATree']]],
- ['expand_5fpath_8782',['expand_path',['../classvg_1_1VG.html#aa9273361525befc57536dc96a762c29d',1,'vg::VG::expand_path(const list< NodeTraversal > &path, vector< NodeTraversal > &expanded)'],['../classvg_1_1VG.html#ae151983cac753c02ce3852274798f8d5',1,'vg::VG::expand_path(list< NodeTraversal > &path, vector< list< NodeTraversal >::iterator > &expanded)']]],
- ['expand_5fsubgraph_5fby_5flength_8783',['expand_subgraph_by_length',['../namespacevg_1_1algorithms.html#a5b57bed3b0fc8427419ccddc077fe20c',1,'vg::algorithms']]],
- ['expand_5fsubgraph_5fby_5fsteps_8784',['expand_subgraph_by_steps',['../namespacevg_1_1algorithms.html#ac8ff68675a6735fbd34ce736e67a9d52',1,'vg::algorithms']]],
- ['expand_5fsubgraph_5fto_5flength_8785',['expand_subgraph_to_length',['../namespacevg_1_1algorithms.html#aa93f6a90a43d95f7340318a0d9ac4fe6',1,'vg::algorithms']]],
- ['expand_5fsubgraph_5fto_5fnode_5fcount_8786',['expand_subgraph_to_node_count',['../namespacevg_1_1algorithms.html#ae1998da7905d222d25839ca3b9b6c52c',1,'vg::algorithms']]],
- ['expanded_8787',['expanded',['../structvg_1_1WFANode.html#a80571c88f088ee4b4267f2548d57cda2',1,'vg::WFANode']]],
- ['expanded_5fsubgraph_8788',['expanded_subgraph',['../classvg_1_1RegionExpander.html#ab814b5c541d4d651791fda99d380133b',1,'vg::RegionExpander']]],
- ['expected_5fgot_8789',['expected_got',['../haplotypes__main_8cpp.html#aa2d607487bc2383196fd7f59936075b1',1,'haplotypes_main.cpp']]],
- ['explainer_8790',['Explainer',['../classvg_1_1Explainer.html#a6731729e992afae0857c09c646df3418',1,'vg::Explainer']]],
- ['explaining_8791',['explaining',['../classvg_1_1Explainer.html#a9cc8dab32c3fb040cf2b6da4d0bdef49',1,'vg::Explainer']]],
- ['extend_8792',['extend',['../classvg_1_1DozeuInterface.html#ab8102472215beaaa523c33e34be6c849',1,'vg::DozeuInterface::extend()'],['../classvg_1_1XdropAligner.html#a9c65c36083d9f587665bf1fbcf4ba208',1,'vg::XdropAligner::extend()'],['../classvg_1_1QualAdjXdropAligner.html#a3f2fec934929a0dacc2f2870755e117f',1,'vg::QualAdjXdropAligner::extend()'],['../classvg_1_1WFATree.html#aea8b15c95221c9d56bc545b2a4b66719',1,'vg::WFATree::extend()'],['../classvg_1_1GaplessExtender.html#a0bc61b755c3d208a07bac12fea248ff4',1,'vg::GaplessExtender::extend()'],['../structhaplo_1_1haplo__DP__rectangle.html#a46ffe0af953ecd6abf889315d50153a4',1,'haplo::haplo_DP_rectangle::extend()'],['../structhaplo_1_1haplo__DP__column.html#af2d28d03a6d456b0f17453e4ae0a8c16',1,'haplo::haplo_DP_column::extend()'],['../classvg_1_1IncrementalSubgraph.html#a35e5051258b792c91da00cc0810ed178',1,'vg::IncrementalSubgraph::extend()'],['../classvg_1_1Paths.html#a1b630067f63b3e4e1ef143902bbdcca1',1,'vg::Paths::extend(const Paths &paths, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1Paths.html#a36f713f6d40d4c42a0426b7cb932da1d',1,'vg::Paths::extend(const Path &p, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1Paths.html#a83e61d4adfdb931c93a06dbc119a6963',1,'vg::Paths::extend(const vector< Path > &paths, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../structvg_1_1RecombinatorHaplotype.html#a5b69c19b38c982602eb05c759bfa82eb',1,'vg::RecombinatorHaplotype::extend()'],['../classvg_1_1VG.html#a2519c3b939f48bca226e6fdea4c91f9d',1,'vg::VG::extend(const VG &g, bool warn_on_duplicates=false)'],['../classvg_1_1VG.html#a5e517214b33812b16f195a1f87841c0d',1,'vg::VG::extend(const Graph &graph, bool warn_on_duplicates=false)'],['../namespacehandlegraph_1_1algorithms.html#ab9dd25807e2edab1a0b14462dacfadcf',1,'handlegraph::algorithms::extend()']]],
- ['extend_5falignment_8793',['extend_alignment',['../namespacevg.html#a491e9c11712ae965b8c6745ab33aba21',1,'vg']]],
- ['extend_5fdist_5ftree_5fby_5fbuckets_8794',['extend_dist_tree_by_buckets',['../classvg_1_1OrientedDistanceClusterer.html#ac18b00f6a4f810b76f05aa6c3dfb35cf',1,'vg::OrientedDistanceClusterer']]],
- ['extend_5fdist_5ftree_5fby_5fpermutations_8795',['extend_dist_tree_by_permutations',['../classvg_1_1OrientedDistanceClusterer.html#acb079f0634a19d2d8185a3e338443819',1,'vg::OrientedDistanceClusterer']]],
- ['extend_5fover_8796',['extend_over',['../classvg_1_1WFATree.html#af4370990b94837e5d873ba2c5a65ca59',1,'vg::WFATree']]],
- ['extend_5fpath_8797',['extend_path',['../classvg_1_1PhaseUnfolder.html#a40a20697627b7742f98776111b8dbc66',1,'vg::PhaseUnfolder::extend_path()'],['../namespacevg.html#afcc55b3037b4e078c4268f08dda7cf4b',1,'vg::extend_path()']]],
- ['extend_5fseed_5fgroup_8798',['extend_seed_group',['../classvg_1_1MinimizerMapper.html#adf57055010f3109518838b251663cc20',1,'vg::MinimizerMapper']]],
- ['extend_5fstate_8799',['extend_state',['../classvg_1_1PhaseUnfolder.html#a610d8256b9dc58fe6d04b1ff7aaafebb',1,'vg::PhaseUnfolder']]],
- ['extension_5fto_5falignment_8800',['extension_to_alignment',['../classvg_1_1MinimizerMapper.html#a33fac2713ca1929fc6f870f4bb9e82b8',1,'vg::MinimizerMapper']]],
- ['external_5fhandle_8801',['external_handle',['../classxg_1_1XGPath.html#a002267f235e618bb59e28cad12bb02a3',1,'xg::XGPath']]],
- ['extract_8802',['extract',['../classvg_1_1algorithms_1_1GFAParser.html#af845e3a9176f98ccbb7c04b31f4f6dc0',1,'vg::algorithms::GFAParser']]],
- ['extract_5fas_5fgbwt_5fpath_8803',['extract_as_gbwt_path',['../namespacevg.html#a0d1c00a44e9aeb5c4294edd60fcbaa61',1,'vg']]],
- ['extract_5fcluster_5fgraph_8804',['extract_cluster_graph',['../classvg_1_1MultipathMapper.html#a411882d1f1f4908582333944ac346443',1,'vg::MultipathMapper']]],
- ['extract_5fcomponent_8805',['extract_component',['../classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54',1,'vg::PathChunker']]],
- ['extract_5fconnecting_5fgraph_8806',['extract_connecting_graph',['../namespacevg_1_1algorithms.html#ac0d0446bde00e10bd77816c968ae97b0',1,'vg::algorithms']]],
- ['extract_5fcontaining_5fgraph_8807',['extract_containing_graph',['../namespacevg_1_1algorithms.html#a4270da794ad0185dacef1874a1e4d3c2',1,'vg::algorithms::extract_containing_graph(const HandleGraph *source, MutableHandleGraph *into, const vector< pos_t > &positions, const vector< size_t > &forward_search_lengths, const vector< size_t > &backward_search_lengths, size_t reversing_walk_length)'],['../namespacevg_1_1algorithms.html#a0ecd79b7d4b622b583a8e08df594e45c',1,'vg::algorithms::extract_containing_graph(const HandleGraph *source, MutableHandleGraph *into, const vector< pos_t > &positions, size_t max_dist, size_t reversing_walk_length)'],['../namespacevg_1_1algorithms.html#ab31b1b707c93f96d6f013e579c4d8783',1,'vg::algorithms::extract_containing_graph(const HandleGraph *source, MutableHandleGraph *into, const vector< pos_t > &positions, const vector< size_t > &position_max_dist, size_t reversing_walk_length)']]],
- ['extract_5fcontext_8808',['extract_context',['../namespacevg_1_1algorithms.html#a38ea20ebc7800702ec0cdb96920c6184',1,'vg::algorithms']]],
- ['extract_5fextending_5fgraph_8809',['extract_extending_graph',['../namespacevg_1_1algorithms.html#a1f600eb589d48607c2616bed69ff2e27',1,'vg::algorithms']]],
- ['extract_5fgbwt_5fpath_8810',['extract_gbwt_path',['../namespacevg.html#a768828fcd9f2ecf7661e7d873f23bc58',1,'vg']]],
- ['extract_5fhaplotypes_8811',['extract_haplotypes',['../haplotypes__main_8cpp.html#a56be3686d2a011df59c271f092f6f40c',1,'haplotypes_main.cpp']]],
- ['extract_5fid_5frange_8812',['extract_id_range',['../classvg_1_1PathChunker.html#a140b4a86b4f8ea18d29a39c7b1aab66f',1,'vg::PathChunker::extract_id_range()'],['../namespacevg_1_1algorithms.html#ac53dd7f2ff1b53bec309f368a79db951',1,'vg::algorithms::extract_id_range()']]],
- ['extract_5fmaximal_5fgraph_8813',['extract_maximal_graph',['../classvg_1_1MultipathMapper.html#a2688faa30ec227f9c9266ce37ce5ca6b',1,'vg::MultipathMapper']]],
- ['extract_5foverlapping_5fpaths_8814',['extract_overlapping_paths',['../classvg_1_1Surjector.html#af4b7099431a6a5334141760cc8922281',1,'vg::Surjector::extract_overlapping_paths(const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) const'],['../classvg_1_1Surjector.html#adc4dbb4ce6f48d755c91e4931028c6d8',1,'vg::Surjector::extract_overlapping_paths(const PathPositionHandleGraph *graph, const multipath_alignment_t &source, const unordered_set< path_handle_t > &surjection_paths, unordered_map< pair< path_handle_t, bool >, vector< tuple< size_t, size_t, int32_t >>> &connections_out) const']]],
- ['extract_5fpath_5fcomponent_8815',['extract_path_component',['../classvg_1_1PathChunker.html#aca0d2bec2834fdc534d42238a0a53b46',1,'vg::PathChunker']]],
- ['extract_5fpath_5fmetadata_8816',['extract_path_metadata',['../namespacevg.html#aa381cdc7f966379fc7cc9ea11257f632',1,'vg']]],
- ['extract_5fpath_5frange_8817',['extract_path_range',['../namespacevg_1_1algorithms.html#a6da60961fae57a5568354ef5b541bcf7',1,'vg::algorithms']]],
- ['extract_5frescue_5fgraph_8818',['extract_rescue_graph',['../classvg_1_1MultipathMapper.html#a6cecbd08d03efe5b248cf2e93e5f619c',1,'vg::MultipathMapper']]],
- ['extract_5frestrained_5fgraph_8819',['extract_restrained_graph',['../classvg_1_1MultipathMapper.html#a282d59b6aa693b4f454ab25c5f7f328c',1,'vg::MultipathMapper']]],
- ['extract_5fsequences_8820',['extract_sequences',['../classvg_1_1Recombinator.html#a5267a1c51ed0caf5e78834e1b6221e0a',1,'vg::Recombinator']]],
- ['extract_5fsnarls_8821',['extract_snarls',['../classvg_1_1PathChunker.html#a20d6a2e56df993a7420e5b1c62df5154',1,'vg::PathChunker']]],
- ['extract_5fsub_5fmultipath_5falignment_8822',['extract_sub_multipath_alignment',['../namespacevg.html#a2b9703408d4c7160e8d9e83303c4d1c7',1,'vg']]],
- ['extract_5fsubgraph_8823',['extract_subgraph',['../classvg_1_1PathChunker.html#a90aac076d1669b467ca5ca5868c7ed2e',1,'vg::PathChunker']]],
- ['extracting_5fleft_8824',['extracting_left',['../classvg_1_1IncrementalSubgraph.html#a91bb045370337f4f91aea10c14fdca95',1,'vg::IncrementalSubgraph']]],
- ['extranodegraph_8825',['ExtraNodeGraph',['../classvg_1_1ExtraNodeGraph.html#aafddbd22f8123df59e0bbdb634f5ba0a',1,'vg::ExtraNodeGraph']]]
+ ['each_5fapprox_5fgraph_5fmemory_8667',['each_approx_graph_memory',['../namespacevg.html#a104aaf42bb3f44518626b9417a4db2d5',1,'vg']]],
+ ['eades_5falgorithm_8668',['eades_algorithm',['../namespacehandlegraph_1_1algorithms.html#a2dad089a8ba50413b0737bf6ceb52f80',1,'handlegraph::algorithms']]],
+ ['easy_5fsort_8669',['easy_sort',['../classvg_1_1StreamSorter.html#ab01d2165ebd3f76b7c036c5428f4b2bc',1,'vg::StreamSorter']]],
+ ['edge_5fallele_5flabels_8670',['edge_allele_labels',['../classvg_1_1Genotyper.html#aae52b974044843aed34fc31152ccda77',1,'vg::Genotyper']]],
+ ['edge_5fcount_8671',['edge_count',['../classvg_1_1VG.html#a25ef81b910a6fc47c9a6ba4c1636cf83',1,'vg::VG']]],
+ ['edge_5fcoverage_8672',['edge_coverage',['../classvg_1_1Packer.html#a5ff601ec8eace2559df20c9b1b11e030',1,'vg::Packer::edge_coverage(Edge &e) const'],['../classvg_1_1Packer.html#a241eceae29b5f183b876586e0e504a76',1,'vg::Packer::edge_coverage(size_t i) const']]],
+ ['edge_5fcoverage_5fbin_5foffset_8673',['edge_coverage_bin_offset',['../classvg_1_1Packer.html#ab2f586cd7d0443b6ab3de98d321db4ac',1,'vg::Packer']]],
+ ['edge_5fcoverage_5fbin_5fsize_8674',['edge_coverage_bin_size',['../classvg_1_1Packer.html#a8d35d0868d13a974e038425f02c97b10',1,'vg::Packer']]],
+ ['edge_5fhandle_8675',['edge_handle',['../classhandlegraph_1_1HandleGraph.html#a3766f1aca1cbdbf827f2a12aaf2078ec',1,'handlegraph::HandleGraph']]],
+ ['edge_5findex_8676',['edge_index',['../classvg_1_1Packer.html#aaac9a172415e1e7fbc419e5a7e13e985',1,'vg::Packer::edge_index()'],['../classxg_1_1XG.html#a184f3b8960859cee3ef5d929a4391e0b',1,'xg::XG::edge_index()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a5aa85bce7358af90d1e63d2060a50a39',1,'handlegraph::VectorizableHandleGraph::edge_index()']]],
+ ['edge_5forientation_8677',['edge_orientation',['../classxg_1_1XG.html#a8b60df344ef1f990d0d6e0ed4eb77b92',1,'xg::XG']]],
+ ['edge_5frelative_5foffset_8678',['edge_relative_offset',['../classxg_1_1XG.html#a3bbffb5a6cc0d70f7d20919c53af9520',1,'xg::XG']]],
+ ['edge_5fto_5fsnarl_5fedge_8679',['edge_to_snarl_edge',['../classvg_1_1SnarlGraph.html#a607672055416281719361bdc35830567',1,'vg::SnarlGraph']]],
+ ['edge_5fvector_5fsize_8680',['edge_vector_size',['../classvg_1_1Packer.html#a34b7060f8b021857f88bfbd598c207d0',1,'vg::Packer']]],
+ ['edges_5fend_8681',['edges_end',['../classvg_1_1VG.html#a9a37e4df96356dbf4f7e78da9eb8fd89',1,'vg::VG::edges_end(Node *node)'],['../classvg_1_1VG.html#aaaae0ba5428a83ece038f506c9c5df54',1,'vg::VG::edges_end(nid_t id)']]],
+ ['edges_5ffrom_8682',['edges_from',['../classvg_1_1VG.html#ae1a7e0aa663eadc0ebdaaf13b667323e',1,'vg::VG']]],
+ ['edges_5fof_8683',['edges_of',['../classvg_1_1VG.html#aa1bf5492e5c6d586cd266d2a48f792df',1,'vg::VG']]],
+ ['edges_5fof_5fnode_8684',['edges_of_node',['../classvg_1_1VG.html#a5b6a5e92afb1a70d9c63a1848a01f241',1,'vg::VG']]],
+ ['edges_5fof_5fnodes_8685',['edges_of_nodes',['../classvg_1_1VG.html#a3b2d900fc42cffe079c3ba3897717eae',1,'vg::VG']]],
+ ['edges_5fstart_8686',['edges_start',['../classvg_1_1VG.html#a3032de0eb7258c9e2db4a27f16a8604c',1,'vg::VG::edges_start(Node *node)'],['../classvg_1_1VG.html#aee2439ec8f0d8ee87becac3f6fbf13bb',1,'vg::VG::edges_start(nid_t id)']]],
+ ['edges_5fto_8687',['edges_to',['../classvg_1_1VG.html#a3789cf6561f2d3da5ef85f23b5c6454f',1,'vg::VG']]],
+ ['edit_8688',['edit',['../classvg_1_1path__mapping__t.html#ab8f590be7d2d5dc9f847b315d48b4d9a',1,'vg::path_mapping_t::edit() const'],['../classvg_1_1path__mapping__t.html#a98a2810ae03cc5bc9ca241a3a1cbd7e2',1,'vg::path_mapping_t::edit(size_t i) const'],['../classvg_1_1VG.html#a5962aa939727f27cb7c62b2ce2706fe9',1,'vg::VG::edit(vector< Path > &paths_to_add, vector< Translation > *out_translations=nullptr, bool save_paths=false, bool update_paths=false, bool break_at_ends=false)'],['../classvg_1_1VG.html#aa800d382b361f1bdad0e5855dd4c05ca',1,'vg::VG::edit(const string &paths_to_add_path, vector< Translation > *out_translations=nullptr, bool save_paths=false, const string &out_gam_path="", bool break_at_ends=false, bool remove_softclips=false)']]],
+ ['edit_5fcount_8689',['edit_count',['../namespacevg.html#a2610da8a8fbe723e13519d79ac2d0afe',1,'vg']]],
+ ['edit_5ffast_8690',['edit_fast',['../classvg_1_1VG.html#a78f70eb7eddb0245be7cdfc048616638',1,'vg::VG']]],
+ ['edit_5fis_5fdeletion_8691',['edit_is_deletion',['../namespacevg_1_1io.html#af23faba545c4d2714c1c86c15db79433',1,'vg::io']]],
+ ['edit_5fis_5fempty_8692',['edit_is_empty',['../namespacevg_1_1io.html#a738f411081a82bfb4a1cb0d12bafc9bc',1,'vg::io']]],
+ ['edit_5fis_5finsertion_8693',['edit_is_insertion',['../namespacevg_1_1io.html#a26c4d6dee35ff3ed8365a87e0125813e',1,'vg::io']]],
+ ['edit_5fis_5fmatch_8694',['edit_is_match',['../namespacevg_1_1io.html#a5af2def0a0ebdab4130882eab0f0851d',1,'vg::io']]],
+ ['edit_5fis_5fsub_8695',['edit_is_sub',['../namespacevg_1_1io.html#a77d59f64a316fdbc91577079af83fbc4',1,'vg::io']]],
+ ['edit_5fsize_8696',['edit_size',['../classvg_1_1path__mapping__t.html#a03c9f7be25a6af86cb073f9bbc8fd310',1,'vg::path_mapping_t']]],
+ ['edit_5ft_8697',['edit_t',['../classvg_1_1edit__t.html#a4987eba1f565f0b9ad0ac035d324290c',1,'vg::edit_t::edit_t() noexcept'],['../classvg_1_1edit__t.html#a0b3a99d70c0f3ec050ad81a81e6afd06',1,'vg::edit_t::edit_t(const edit_t &other)=default'],['../classvg_1_1edit__t.html#a9369c96a6763e648e8aaec848623da25',1,'vg::edit_t::edit_t(edit_t &&other)=default']]],
+ ['edit_5fvalue_8698',['edit_value',['../classvg_1_1Packer.html#aff566a3e094a0e28bbc51a468d60b800',1,'vg::Packer']]],
+ ['editedtranscriptpath_8699',['EditedTranscriptPath',['../structvg_1_1EditedTranscriptPath.html#a8235f7b3dc4e3fac60234c849fecb2fb',1,'vg::EditedTranscriptPath::EditedTranscriptPath(const string &transcript_name, const string &embedded_path_name, const bool is_reference_in, const bool is_haplotype_in)'],['../structvg_1_1EditedTranscriptPath.html#af70d348a2aaf1ab702b4abe2106d95b8',1,'vg::EditedTranscriptPath::EditedTranscriptPath(const string &transcript_name, const gbwt::size_type &haplotype_gbwt_id, const bool is_reference_in, const bool is_haplotype_in)']]],
+ ['edits_5fare_5fcompatible_8700',['edits_are_compatible',['../namespacevg.html#abfba7a19cbb794cd210116be91c62d96',1,'vg']]],
+ ['edits_5fat_5fposition_8701',['edits_at_position',['../classvg_1_1Packer.html#a8b632f64e269417895cbc84d0e377a8a',1,'vg::Packer']]],
+ ['effective_5fposition_5funion_8702',['effective_position_union',['../classvg_1_1Funnel.html#a5195231cc0b426406133439d5a7d6026',1,'vg::Funnel']]],
+ ['embed_5fref_5fpath_5fsnarls_8703',['embed_ref_path_snarls',['../classvg_1_1SnarlGraph.html#a80d4241e20274286f95bbe35fa916481',1,'vg::SnarlGraph']]],
+ ['embed_5fsnarl_8704',['embed_snarl',['../classvg_1_1SnarlGraph.html#af1dc28423f51b60f019e08f716e9b082',1,'vg::SnarlGraph']]],
+ ['embed_5fsnarls_8705',['embed_snarls',['../classvg_1_1SnarlGraph.html#a30a11c3b13a39e23394731d982ce7f75',1,'vg::SnarlGraph']]],
+ ['embed_5ftranscript_5fpaths_8706',['embed_transcript_paths',['../classvg_1_1Transcriptome.html#a0f729698bd8dca0fdcd3f78a56f708cc',1,'vg::Transcriptome']]],
+ ['emit_8707',['emit',['../classvg_1_1ReadFilter.html#a50fce1e4c1159834e6371156040c6cbe',1,'vg::ReadFilter::emit(Read &read)'],['../classvg_1_1ReadFilter.html#a5beda5e781b3a4b1b6ec139b280785d9',1,'vg::ReadFilter::emit(Read &read1, Read &read2)'],['../classVectorizer.html#a086dc2c83d1627780103d9367b7d3191',1,'Vectorizer::emit()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a020229bc89c799a2d16ebcbb7a349b94',1,'vg::io::TSVAlignmentEmitter::emit()'],['../classvg_1_1ReadFilter.html#a4436cd59a7d2ed18c4a315ef157239ed',1,'vg::ReadFilter::emit(Alignment &aln)'],['../classvg_1_1ReadFilter.html#ae811413740325799e12d313149f2b15a',1,'vg::ReadFilter::emit(Alignment &aln1, Alignment &aln2)'],['../classvg_1_1ReadFilter.html#a95b5ca4213c6da0a174e53c2f91fb36b',1,'vg::ReadFilter::emit(MultipathAlignment &mp_aln)'],['../classvg_1_1ReadFilter.html#a3864d427682af9b6e0a67a157fddcfa2',1,'vg::ReadFilter::emit(MultipathAlignment &mp_aln1, MultipathAlignment &mp_aln2)']]],
+ ['emit_5fextra_5fmessage_8708',['emit_extra_message',['../classvg_1_1BackTranslatingAlignmentEmitter.html#aed2fce246283ef5280a9219229f1e6e1',1,'vg::BackTranslatingAlignmentEmitter::emit_extra_message()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a72579ae4d3ac98e946b9bef7c147ed81',1,'vg::SurjectingAlignmentEmitter::emit_extra_message()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a4eb6186a8322603353d123295e0558f1',1,'vg::io::AlignmentEmitter::emit_extra_message()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a5c128b83d74f99f7c7951a4d2f5fb27d',1,'vg::io::VGAlignmentEmitter::emit_extra_message()']]],
+ ['emit_5fgaf_5ftraversals_8709',['emit_gaf_traversals',['../classvg_1_1GAFOutputCaller.html#ac3ece689949d9d3d7c0078ab753532e7',1,'vg::GAFOutputCaller']]],
+ ['emit_5fgaf_5fvariant_8710',['emit_gaf_variant',['../classvg_1_1GAFOutputCaller.html#ac5a6e77d30c33cd4087bac27b9dc780f',1,'vg::GAFOutputCaller']]],
+ ['emit_5fgroup_8711',['emit_group',['../classvg_1_1io_1_1MessageEmitter.html#a1f37b89141a12819675b1d2a9dccdb10',1,'vg::io::MessageEmitter::emit_group()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a55b19615de43ba7ef0fc38487fe7e811',1,'vg::io::ProtobufEmitter::emit_group()']]],
+ ['emit_5fmapped_5fpair_8712',['emit_mapped_pair',['../classvg_1_1io_1_1AlignmentEmitter.html#a9fd17a6201b33a32f2bbb133952c0d26',1,'vg::io::AlignmentEmitter']]],
+ ['emit_5fmapped_5fpairs_8713',['emit_mapped_pairs',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a2e0b48b26e6563de0728055ee80947f4',1,'vg::BackTranslatingAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1HTSAlignmentEmitter.html#a144167b8b9b973a113beb3950d8f64e7',1,'vg::HTSAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a5f3a358a96878a701407a648dd925b28',1,'vg::SurjectingAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a430ea0461fdb40d7df836b92fc529a55',1,'vg::io::AlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#a9cf86d953fb199dc1be11a4a18020299',1,'vg::io::NullAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#ab2ead89927010b48bcc8788f6dc71445',1,'vg::io::TSVAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a16ef4e377610cdf7678faa0564aa83fa',1,'vg::io::VGAlignmentEmitter::emit_mapped_pairs()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a7f9275cb4115e8ea629a8c58f468ac66',1,'vg::io::GafAlignmentEmitter::emit_mapped_pairs()']]],
+ ['emit_5fmapped_5fsingle_8714',['emit_mapped_single',['../classvg_1_1io_1_1AlignmentEmitter.html#a424cb81bfd87685b3be4823e95a023eb',1,'vg::io::AlignmentEmitter']]],
+ ['emit_5fmapped_5fsingles_8715',['emit_mapped_singles',['../classvg_1_1BackTranslatingAlignmentEmitter.html#abe1c7762c88dd018e0e949afdfce33b1',1,'vg::BackTranslatingAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1HTSAlignmentEmitter.html#a3137223a14396af5a6284830c716b943',1,'vg::HTSAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a96d4bea40f617e8083c732ce3ce6d9f8',1,'vg::SurjectingAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a3314c504ff0d278f5f44a316ec573b30',1,'vg::io::AlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#ab4da7694c104089d8f25b715aedb76bc',1,'vg::io::NullAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#adcda781ada60a6d3116f5a7bc57ae513',1,'vg::io::TSVAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a6e54f94f8e7e772b3d98aa51deb8723e',1,'vg::io::VGAlignmentEmitter::emit_mapped_singles()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a4762f418851fc7aac06333590e51ade2',1,'vg::io::GafAlignmentEmitter::emit_mapped_singles()']]],
+ ['emit_5fpair_8716',['emit_pair',['../classvg_1_1io_1_1AlignmentEmitter.html#a719d2cbafa6160bf55e724be1ef9d6f9',1,'vg::io::AlignmentEmitter']]],
+ ['emit_5fpairs_8717',['emit_pairs',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a37bb7f41cd3d94ee37b837e5254d2122',1,'vg::BackTranslatingAlignmentEmitter::emit_pairs()'],['../classvg_1_1HTSAlignmentEmitter.html#a6c2dbcf61c25fe6646b6753d51b73771',1,'vg::HTSAlignmentEmitter::emit_pairs()'],['../classvg_1_1MultipathAlignmentEmitter.html#a7467c3e0ce1525f32e27f4f99d00c8b5',1,'vg::MultipathAlignmentEmitter::emit_pairs()'],['../classvg_1_1SurjectingAlignmentEmitter.html#ac053805811c71dfffc31eb3decab4279',1,'vg::SurjectingAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1AlignmentEmitter.html#aae5f5e6108e47d0a481d656abd4a8075',1,'vg::io::AlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#a2313d024a104c2771531a6e2a725b0e1',1,'vg::io::NullAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a57c0cd7c8a5bd41a358de2430ca40e5f',1,'vg::io::TSVAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a72a72eef5e85e422acdfacb788bee8d0',1,'vg::io::VGAlignmentEmitter::emit_pairs()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#affa85e71afb3d28d219a0cce2703e45e',1,'vg::io::GafAlignmentEmitter::emit_pairs()']]],
+ ['emit_5fsingle_8718',['emit_single',['../classvg_1_1io_1_1AlignmentEmitter.html#a9c09a54a452278ec02084ca498105b8d',1,'vg::io::AlignmentEmitter']]],
+ ['emit_5fsingles_8719',['emit_singles',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a7a9bacd81bff0b873c4449e2fe698305',1,'vg::BackTranslatingAlignmentEmitter::emit_singles()'],['../classvg_1_1HTSAlignmentEmitter.html#a90e671da1b62eebf423f95c01a865fdd',1,'vg::HTSAlignmentEmitter::emit_singles()'],['../classvg_1_1MultipathAlignmentEmitter.html#a923124cdc8bdc96e95db68281bb79fcd',1,'vg::MultipathAlignmentEmitter::emit_singles()'],['../classvg_1_1SurjectingAlignmentEmitter.html#a60e0c7fa81a98961a04bfaa42dc8e3af',1,'vg::SurjectingAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1AlignmentEmitter.html#a132fc9cf3a53a99f1ac61538d6433760',1,'vg::io::AlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1NullAlignmentEmitter.html#a83b9c08b6d394dccbd7321f0b75294fe',1,'vg::io::NullAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#aef4194a290204811292491db459d49d1',1,'vg::io::TSVAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#ac8b4fed94e74172899ba065cc3f8ce5d',1,'vg::io::VGAlignmentEmitter::emit_singles()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a2b4af0175e6a6b928d77bc2ab9085e17',1,'vg::io::GafAlignmentEmitter::emit_singles()']]],
+ ['emit_5fsnarl_5frecursive_8720',['emit_snarl_recursive',['../classvg_1_1NestedFlowCaller.html#afa870673ddc9fbcc7a1f321a5aaa0746',1,'vg::NestedFlowCaller']]],
+ ['emit_5fstacktrace_8721',['emit_stacktrace',['../namespacevg.html#a40556998a17c0f59c8ecc682af3a99a3',1,'vg']]],
+ ['emit_5fto_8722',['emit_to',['../namespacevg_1_1io.html#ae5ab0e97965e5b5e461a997ed374423e',1,'vg::io']]],
+ ['emit_5ftsv_8723',['emit_tsv',['../classvg_1_1ReadFilter.html#a02ed848e6d5395a8b966f883bd318a8e',1,'vg::ReadFilter::emit_tsv(Read &read, std::ostream &out)'],['../classvg_1_1ReadFilter.html#a8ee0191017a8bf8b6c09ea5ef01e9517',1,'vg::ReadFilter::emit_tsv(MultipathAlignment &read, std::ostream &out)'],['../classvg_1_1ReadFilter.html#a7ce4a34cb9883643cfc277ac0c213f64',1,'vg::ReadFilter::emit_tsv(Alignment &read, std::ostream &out)']]],
+ ['emit_5fvariant_8724',['emit_variant',['../classvg_1_1VCFOutputCaller.html#a3ed9068c446bfd72f912184421c3d7ce',1,'vg::VCFOutputCaller::emit_variant()'],['../classvg_1_1MCMCCaller.html#ac5c178b336cdc31a491a2166137805ea',1,'vg::MCMCCaller::emit_variant()']]],
+ ['emplace_5fback_8725',['emplace_back',['../classvg_1_1ZipCodeCollection.html#ad7cf238df94a2d6016a499f4a66a40bc',1,'vg::ZipCodeCollection']]],
+ ['empty_8726',['empty',['../structvg_1_1MatchPos_1_1PathList.html#a2782600d1fa18f7f6ec09b52c6dae0d6',1,'vg::MatchPos::PathList::empty()'],['../structvg_1_1MatchPos.html#a3cfc20cb1d5f87a78aa4cf0187ea109b',1,'vg::MatchPos::empty()'],['../structvg_1_1GaplessExtension.html#a72542968a383c49ac29cc4f939cb3d9d',1,'vg::GaplessExtension::empty()'],['../structvg_1_1WFAAlignment.html#a3dd26de023774ab65b2c7e115e0aa88a',1,'vg::WFAAlignment::empty()'],['../structhaplo_1_1int__itvl__t.html#ad491ab3b9181c1601580d0458d4017eb',1,'haplo::int_itvl_t::empty()'],['../classvg_1_1MultipathAlignmentGraph.html#a91dd7a4bc802e510067ae6bcb0fc5b74',1,'vg::MultipathAlignmentGraph::empty()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a2916bfc8fc45ebb3160f4cdab7c67eab',1,'vg::Option< vector< Item >, Parser >::empty()'],['../classvg_1_1Paths.html#a6488500dc1c44646ad3003ce29816b08',1,'vg::Paths::empty()'],['../classvg_1_1BitString.html#a82ccba78adaa516a8223a74d53886b0b',1,'vg::BitString::empty()'],['../structvg_1_1VectorView.html#a468cbc6d153bdc27f394a4bd81d8bffe',1,'vg::VectorView::empty()'],['../classvg_1_1VG.html#a42d7f84de5d99fe0ce51186fcbea420c',1,'vg::VG::empty()'],['../classvg_1_1ZipCodeCollection.html#a89ed6fc02819ba84907ee24ff1daa98c',1,'vg::ZipCodeCollection::empty()'],['../classvg_1_1algorithms_1_1GFAParser.html#a3b8240590446e1ee287c9c05a74e2a9e',1,'vg::algorithms::GFAParser::empty()']]],
+ ['empty_5fdiagonal_5frange_8727',['empty_diagonal_range',['../classvg_1_1WFATree.html#a599b32ec4cbb624705c893caa34c6561',1,'vg::WFATree']]],
+ ['empty_5fgbwtgraph_5fhandle_8728',['empty_gbwtgraph_handle',['../namespacevg.html#a8811548042613f9e65545d1ed377643e',1,'vg']]],
+ ['empty_5fpos_5ft_8729',['empty_pos_t',['../namespacevg.html#ad0576520eed494787a895b6ce862e1f0',1,'vg']]],
+ ['enable_5fcrash_5fhandling_8730',['enable_crash_handling',['../namespacevg.html#a1f4461f901aba4b67353768ee25e23d7',1,'vg']]],
+ ['encode_8731',['encode',['../classvg_1_1MEMAccelerator.html#a5e9b9dd9f3b1f278675404da99c37166',1,'vg::MEMAccelerator']]],
+ ['encode_5fchars_8732',['encode_chars',['../namespacevg.html#aa25419c15b3dcae6b217f893c243c487',1,'vg']]],
+ ['encode_5fedge_8733',['encode_edge',['../classxg_1_1XG.html#a9aaeb0232bdc092f1097704b8595b50a',1,'xg::XG']]],
+ ['end_8734',['end',['../classvg_1_1ShuffledPairs.html#ad670dd24e999776922243cf7d212764e',1,'vg::ShuffledPairs::end()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a8392b88a5dc4781f64868bfaafbffb3d',1,'vg::Option< vector< Item >, Parser >::end()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a4bae8cab0824d37275f78170e9e3a319',1,'vg::Option< vector< Item >, Parser >::end() const'],['../structvg_1_1PathIndex.html#ada3ccf7b77f16b46373ff5bb19fdbc11',1,'vg::PathIndex::end()'],['../classvg_1_1PhasedGenome.html#a621ecd8fc372256aa037a8beb9ea4c39',1,'vg::PhasedGenome::end()'],['../structvg_1_1VectorView.html#ac7d28343b9bc2318a35ed2b029a7c052',1,'vg::VectorView::end()'],['../classvg_1_1ZipCodeTree.html#a952f6619fc095e7ab40e839ac0189692',1,'vg::ZipCodeTree::end()'],['../classhandlegraph_1_1PathForEachSocket.html#ae4a2081511b675e49566d335bdbe4945',1,'handlegraph::PathForEachSocket::end()']]],
+ ['end_5fbackward_8735',['end_backward',['../namespacevg.html#acab8d2ef076a0e866c7849aace290124',1,'vg']]],
+ ['end_5fdegree_8736',['end_degree',['../classvg_1_1VG.html#af3cf82dca43799a03d93b199133f1d4b',1,'vg::VG']]],
+ ['end_5fhandle_8737',['end_handle',['../structvg_1_1Haplotypes_1_1Subchain.html#a7cee546f2ab356b0ed2920209011c2e5',1,'vg::Haplotypes::Subchain']]],
+ ['end_5fhint_8738',['end_hint',['../classvg_1_1algorithms_1_1Anchor.html#a4911502b781ce9d07369a4e2ccb5d27a',1,'vg::algorithms::Anchor']]],
+ ['end_5fhint_5foffset_8739',['end_hint_offset',['../classvg_1_1algorithms_1_1Anchor.html#afea64615714994d6e170242e1c4b17fc',1,'vg::algorithms::Anchor']]],
+ ['endfile_8740',['EndFile',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aa6cf204591880e126bacc2d01799f3e6',1,'vg::io::BlockedGzipOutputStream']]],
+ ['ends_5fat_8741',['ends_at',['../classhandlegraph_1_1SnarlDecomposition.html#a4f345867fbee2cbcd283e5c0ed4f5920',1,'handlegraph::SnarlDecomposition']]],
+ ['ends_5fat_5fend_8742',['ends_at_end',['../classhandlegraph_1_1SnarlDecomposition.html#a5f13d153fedcd2e24575fb69672650cd',1,'handlegraph::SnarlDecomposition']]],
+ ['ends_5fat_5fstart_8743',['ends_at_start',['../classhandlegraph_1_1SnarlDecomposition.html#a63e795bd9764b2b793472d46069cecab',1,'handlegraph::SnarlDecomposition']]],
+ ['ends_5fat_5ftip_8744',['ends_at_tip',['../classhandlegraph_1_1SnarlDecomposition.html#ae397ce26e9c979cf64c18f56546e490c',1,'handlegraph::SnarlDecomposition']]],
+ ['ends_5fwith_8745',['ends_with',['../haplotypes__main_8cpp.html#a1ffaf31343dd95074c3237bf89b38a33',1,'haplotypes_main.cpp']]],
+ ['ensure_5fbreakpoints_8746',['ensure_breakpoints',['../namespacevg.html#a35bec7a1758e5eb88a359da78174d8d9',1,'vg']]],
+ ['ensure_5fedge_8747',['ensure_edge',['../classvg_1_1DiagramExplainer.html#a4e632e8785e76ea1b2e3e27ef9315465',1,'vg::DiagramExplainer']]],
+ ['ensure_5fedit_5ftmpfiles_5fopen_8748',['ensure_edit_tmpfiles_open',['../classvg_1_1Packer.html#a3120b075177c3ca1916d20557b175733',1,'vg::Packer']]],
+ ['ensure_5fheader_8749',['ensure_header',['../classvg_1_1HTSWriter.html#a5eff59af09a0169f3da8510b8359b098',1,'vg::HTSWriter']]],
+ ['ensure_5fnode_8750',['ensure_node',['../classvg_1_1DiagramExplainer.html#a72d8b7ba51d152e410146ccad7afcaed',1,'vg::DiagramExplainer']]],
+ ['ensure_5fparent_5fdirectory_8751',['ensure_parent_directory',['../structvg_1_1temp__file_1_1Handler.html#a150465560cdc7dc8ffdab2a4b0cbbcc1',1,'vg::temp_file::Handler']]],
+ ['entropy_8752',['entropy',['../namespacevg.html#ac3165438256db24864e88601839197df',1,'vg::entropy(const string &st)'],['../namespacevg.html#a77c1cb6069f865239d0365b55649bc8a',1,'vg::entropy(const char *st, size_t len)']]],
+ ['erase_8753',['erase',['../classvg_1_1SnarlState.html#a92e53694dd3b0169ad55103076997660',1,'vg::SnarlState']]],
+ ['erase_5fin_5fout_5fedges_8754',['erase_in_out_edges',['../classvg_1_1FlowSort.html#a8c021f7aad3257d61f531d1084484f23',1,'vg::FlowSort']]],
+ ['escape_5fdelim_8755',['escape_delim',['../classvg_1_1Packer.html#aed800a1a6084d971951240a7791282bb',1,'vg::Packer']]],
+ ['escape_5fdelims_8756',['escape_delims',['../classvg_1_1Packer.html#a6b86be5851966fc9da0c793b70496564',1,'vg::Packer']]],
+ ['establish_5fstrand_5fconsistency_8757',['establish_strand_consistency',['../classvg_1_1MultipathMapper.html#a362ad957c6634b60317158966c3e02f7',1,'vg::MultipathMapper']]],
+ ['estimate_5fbatch_5fsize_8758',['estimate_batch_size',['../classvg_1_1Packer.html#ad155cc551af3e3f306c35c36ec3d048f',1,'vg::Packer']]],
+ ['estimate_5fbin_5fcount_8759',['estimate_bin_count',['../classvg_1_1Packer.html#ad88597461d2fdf1eb998a609c91bda0d',1,'vg::Packer']]],
+ ['estimate_5fdata_5fwidth_8760',['estimate_data_width',['../classvg_1_1Packer.html#adda3242dea599a49f281fc56c66e5965',1,'vg::Packer']]],
+ ['estimate_5fdistribution_8761',['estimate_distribution',['../classvg_1_1FragmentLengthDistribution.html#a87a5794f706a81748136f0890f2168cd',1,'vg::FragmentLengthDistribution']]],
+ ['estimate_5fedge_5fscore_8762',['estimate_edge_score',['../classvg_1_1MEMClusterer.html#a941476ae17420e703a8ef743232643ab',1,'vg::MEMClusterer']]],
+ ['estimate_5fgc_5fcontent_8763',['estimate_gc_content',['../classvg_1_1BaseMapper.html#aa08b00e5a349252d013d76651f754f8d',1,'vg::BaseMapper']]],
+ ['estimate_5fhash_5ftable_5fsize_8764',['estimate_hash_table_size',['../minimizer__main_8cpp.html#a2f3588cd2c21ddbe85727345718e9ca3',1,'minimizer_main.cpp']]],
+ ['estimate_5fmax_5fpossible_5fmapping_5fquality_8765',['estimate_max_possible_mapping_quality',['../classvg_1_1GSSWAligner.html#a0dc19c58a3f70a67a4b2a1ad475af79d',1,'vg::GSSWAligner::estimate_max_possible_mapping_quality()'],['../classvg_1_1Mapper.html#ac8613c49c8390b280aef7323151a4fd8',1,'vg::Mapper::estimate_max_possible_mapping_quality()']]],
+ ['estimate_5fmissed_5frescue_5fmultiplicity_8766',['estimate_missed_rescue_multiplicity',['../classvg_1_1MultipathMapper.html#a46edc0708ffa290b067a937c1876904c',1,'vg::MultipathMapper']]],
+ ['estimate_5fnext_5fbest_5fscore_8767',['estimate_next_best_score',['../classvg_1_1GSSWAligner.html#a439ed0a50959b73b99d08d5ec0af4bc6',1,'vg::GSSWAligner']]],
+ ['evaluate_8768',['evaluate',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a10e095ce1c007e526ac2506808aec71c',1,'vg::WFAExtender::ErrorModel::Event']]],
+ ['ewens_5faf_5fprob_5fln_8769',['ewens_af_prob_ln',['../namespacevg.html#a59d4b5d91539506f52c32664fc1c0ddd',1,'vg']]],
+ ['exact_8770',['exact',['../structvg_1_1GaplessExtension.html#aad05249efda81ed89bc782040bc3ba33',1,'vg::GaplessExtension']]],
+ ['exclude_5fdist_5ftree_5fmerges_8771',['exclude_dist_tree_merges',['../classvg_1_1OrientedDistanceClusterer.html#af55b22c582dd1fdeb6a62061830c52ad',1,'vg::OrientedDistanceClusterer']]],
+ ['exclude_5fmerges_8772',['exclude_merges',['../classvg_1_1OrientedDistanceMeasurer.html#a738f242df59c42bc9da14b07071b7ea3',1,'vg::OrientedDistanceMeasurer::exclude_merges()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a1791e7bf9d420b6303c16de3a1d7305e',1,'vg::PathOrientedDistanceMeasurer::exclude_merges()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a77a7d291ff3ea117e59861914ee84998',1,'vg::SnarlOrientedDistanceMeasurer::exclude_merges()']]],
+ ['execute_8773',['execute',['../structvg_1_1GenomeStateCommand.html#a6ab4d8d0b53557324a094eba903ac74e',1,'vg::GenomeStateCommand::execute()'],['../structvg_1_1InsertHaplotypeCommand.html#a37b0c787712d1d3f9b0c0c64f0ab39c6',1,'vg::InsertHaplotypeCommand::execute()'],['../structvg_1_1DeleteHaplotypeCommand.html#af187726ffac73739f1a88552f12ae508',1,'vg::DeleteHaplotypeCommand::execute()'],['../structvg_1_1SwapHaplotypesCommand.html#afaccc42cb694c2b393955a39d7f0bd8f',1,'vg::SwapHaplotypesCommand::execute()'],['../structvg_1_1AppendHaplotypeCommand.html#a32ff3ddd9ff5bfbd6aef198d56ad07b6',1,'vg::AppendHaplotypeCommand::execute()'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#adc46192413e975507c86df1cda095e62',1,'vg::ReplaceSnarlHaplotypeCommand::execute()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a50908d3a7dc5da9f81a8c1c77be6ead0',1,'vg::ReplaceLocalHaplotypeCommand::execute()'],['../classvg_1_1GenomeState.html#a4150ec08000ac81447d631bcc5801543',1,'vg::GenomeState::execute()'],['../structvg_1_1IndexRecipe.html#a086051f9a92e58402095aa174274345c',1,'vg::IndexRecipe::execute()'],['../classvg_1_1JobSchedule.html#a048bac48af4bb855daf57e8738f981e4',1,'vg::JobSchedule::execute()']]],
+ ['execute_5fin_5ffork_8774',['execute_in_fork',['../namespacevg.html#ae09739a5bb4d6d49b5c3a44264103606',1,'vg']]],
+ ['execute_5frecipe_8775',['execute_recipe',['../classvg_1_1IndexRegistry.html#ab22b81a5248cf4b12a8be5fb424c9bd4',1,'vg::IndexRegistry']]],
+ ['exhaustivetraversalfinder_8776',['ExhaustiveTraversalFinder',['../classvg_1_1ExhaustiveTraversalFinder.html#a4c35877fcb69aefe449943a4646bd469',1,'vg::ExhaustiveTraversalFinder']]],
+ ['expand_8777',['expand',['../classvg_1_1Funnel.html#a9440c3268e8c60b664a37283d9fc5cff',1,'vg::Funnel']]],
+ ['expand_5fcontext_8778',['expand_context',['../classvg_1_1VG.html#a6a525e3290d6968c79314c2500f13cc3',1,'vg::VG::expand_context()'],['../namespacevg_1_1algorithms.html#aec7fcd701af4fdcbb87e83f0ea5b420a',1,'vg::algorithms::expand_context()']]],
+ ['expand_5fcontext_5fby_5flength_8779',['expand_context_by_length',['../classvg_1_1VG.html#a5ba5a5416ee9eaf67c7ae5607fc7ae1f',1,'vg::VG::expand_context_by_length()'],['../namespacevg_1_1algorithms.html#a238775e0e0ecf0b7576f7c2265dfd5e0',1,'vg::algorithms::expand_context_by_length()']]],
+ ['expand_5fcontext_5fby_5fsteps_8780',['expand_context_by_steps',['../classvg_1_1VG.html#aca4ead561b46cd1cde77ada1f611befa',1,'vg::VG::expand_context_by_steps()'],['../namespacevg_1_1algorithms.html#a354ea4a2a6aed208945fc0994ec50d9d',1,'vg::algorithms::expand_context_by_steps()']]],
+ ['expand_5fcontext_5fwith_5fpaths_8781',['expand_context_with_paths',['../namespacevg_1_1algorithms.html#a8a0c0c6d333cb438f96e5df6faec3621',1,'vg::algorithms']]],
+ ['expand_5ffor_5fsoftclips_8782',['expand_for_softclips',['../classvg_1_1MultipathMapper.html#af2e4bfb6634ee5d318cc5a84d35cb1ef',1,'vg::MultipathMapper']]],
+ ['expand_5fif_5fnecessary_8783',['expand_if_necessary',['../classvg_1_1WFATree.html#a2e014cad6e29600bc11b82855a74dd6b',1,'vg::WFATree']]],
+ ['expand_5fpath_8784',['expand_path',['../classvg_1_1VG.html#aa9273361525befc57536dc96a762c29d',1,'vg::VG::expand_path(const list< NodeTraversal > &path, vector< NodeTraversal > &expanded)'],['../classvg_1_1VG.html#ae151983cac753c02ce3852274798f8d5',1,'vg::VG::expand_path(list< NodeTraversal > &path, vector< list< NodeTraversal >::iterator > &expanded)']]],
+ ['expand_5fsubgraph_5fby_5flength_8785',['expand_subgraph_by_length',['../namespacevg_1_1algorithms.html#a5b57bed3b0fc8427419ccddc077fe20c',1,'vg::algorithms']]],
+ ['expand_5fsubgraph_5fby_5fsteps_8786',['expand_subgraph_by_steps',['../namespacevg_1_1algorithms.html#ac8ff68675a6735fbd34ce736e67a9d52',1,'vg::algorithms']]],
+ ['expand_5fsubgraph_5fto_5flength_8787',['expand_subgraph_to_length',['../namespacevg_1_1algorithms.html#aa93f6a90a43d95f7340318a0d9ac4fe6',1,'vg::algorithms']]],
+ ['expand_5fsubgraph_5fto_5fnode_5fcount_8788',['expand_subgraph_to_node_count',['../namespacevg_1_1algorithms.html#ae1998da7905d222d25839ca3b9b6c52c',1,'vg::algorithms']]],
+ ['expanded_8789',['expanded',['../structvg_1_1WFANode.html#a80571c88f088ee4b4267f2548d57cda2',1,'vg::WFANode']]],
+ ['expanded_5fsubgraph_8790',['expanded_subgraph',['../classvg_1_1RegionExpander.html#ab814b5c541d4d651791fda99d380133b',1,'vg::RegionExpander']]],
+ ['expected_5fgot_8791',['expected_got',['../haplotypes__main_8cpp.html#aa2d607487bc2383196fd7f59936075b1',1,'haplotypes_main.cpp']]],
+ ['explainer_8792',['Explainer',['../classvg_1_1Explainer.html#a6731729e992afae0857c09c646df3418',1,'vg::Explainer']]],
+ ['explaining_8793',['explaining',['../classvg_1_1Explainer.html#a9cc8dab32c3fb040cf2b6da4d0bdef49',1,'vg::Explainer']]],
+ ['extend_8794',['extend',['../classvg_1_1DozeuInterface.html#ab8102472215beaaa523c33e34be6c849',1,'vg::DozeuInterface::extend()'],['../classvg_1_1XdropAligner.html#a9c65c36083d9f587665bf1fbcf4ba208',1,'vg::XdropAligner::extend()'],['../classvg_1_1QualAdjXdropAligner.html#a3f2fec934929a0dacc2f2870755e117f',1,'vg::QualAdjXdropAligner::extend()'],['../classvg_1_1WFATree.html#aea8b15c95221c9d56bc545b2a4b66719',1,'vg::WFATree::extend()'],['../classvg_1_1GaplessExtender.html#a0bc61b755c3d208a07bac12fea248ff4',1,'vg::GaplessExtender::extend()'],['../structhaplo_1_1haplo__DP__rectangle.html#a46ffe0af953ecd6abf889315d50153a4',1,'haplo::haplo_DP_rectangle::extend()'],['../structhaplo_1_1haplo__DP__column.html#af2d28d03a6d456b0f17453e4ae0a8c16',1,'haplo::haplo_DP_column::extend()'],['../classvg_1_1IncrementalSubgraph.html#a35e5051258b792c91da00cc0810ed178',1,'vg::IncrementalSubgraph::extend()'],['../classvg_1_1Paths.html#a1b630067f63b3e4e1ef143902bbdcca1',1,'vg::Paths::extend(const Paths &paths, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1Paths.html#a36f713f6d40d4c42a0426b7cb932da1d',1,'vg::Paths::extend(const Path &p, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../classvg_1_1Paths.html#a83e61d4adfdb931c93a06dbc119a6963',1,'vg::Paths::extend(const vector< Path > &paths, bool warn_on_duplicates=false, bool rebuild_indexes=true)'],['../structvg_1_1RecombinatorHaplotype.html#a5b69c19b38c982602eb05c759bfa82eb',1,'vg::RecombinatorHaplotype::extend()'],['../classvg_1_1VG.html#a2519c3b939f48bca226e6fdea4c91f9d',1,'vg::VG::extend(const VG &g, bool warn_on_duplicates=false)'],['../classvg_1_1VG.html#a5e517214b33812b16f195a1f87841c0d',1,'vg::VG::extend(const Graph &graph, bool warn_on_duplicates=false)'],['../namespacehandlegraph_1_1algorithms.html#ab9dd25807e2edab1a0b14462dacfadcf',1,'handlegraph::algorithms::extend()']]],
+ ['extend_5falignment_8795',['extend_alignment',['../namespacevg.html#a491e9c11712ae965b8c6745ab33aba21',1,'vg']]],
+ ['extend_5fdist_5ftree_5fby_5fbuckets_8796',['extend_dist_tree_by_buckets',['../classvg_1_1OrientedDistanceClusterer.html#ac18b00f6a4f810b76f05aa6c3dfb35cf',1,'vg::OrientedDistanceClusterer']]],
+ ['extend_5fdist_5ftree_5fby_5fpermutations_8797',['extend_dist_tree_by_permutations',['../classvg_1_1OrientedDistanceClusterer.html#acb079f0634a19d2d8185a3e338443819',1,'vg::OrientedDistanceClusterer']]],
+ ['extend_5fover_8798',['extend_over',['../classvg_1_1WFATree.html#af4370990b94837e5d873ba2c5a65ca59',1,'vg::WFATree']]],
+ ['extend_5fpath_8799',['extend_path',['../classvg_1_1PhaseUnfolder.html#a40a20697627b7742f98776111b8dbc66',1,'vg::PhaseUnfolder::extend_path()'],['../namespacevg.html#afcc55b3037b4e078c4268f08dda7cf4b',1,'vg::extend_path()']]],
+ ['extend_5fseed_5fgroup_8800',['extend_seed_group',['../classvg_1_1MinimizerMapper.html#adf57055010f3109518838b251663cc20',1,'vg::MinimizerMapper']]],
+ ['extend_5fstate_8801',['extend_state',['../classvg_1_1PhaseUnfolder.html#a610d8256b9dc58fe6d04b1ff7aaafebb',1,'vg::PhaseUnfolder']]],
+ ['extension_5fto_5falignment_8802',['extension_to_alignment',['../classvg_1_1MinimizerMapper.html#a33fac2713ca1929fc6f870f4bb9e82b8',1,'vg::MinimizerMapper']]],
+ ['external_5fhandle_8803',['external_handle',['../classxg_1_1XGPath.html#a002267f235e618bb59e28cad12bb02a3',1,'xg::XGPath']]],
+ ['extract_8804',['extract',['../classvg_1_1algorithms_1_1GFAParser.html#af845e3a9176f98ccbb7c04b31f4f6dc0',1,'vg::algorithms::GFAParser']]],
+ ['extract_5fas_5fgbwt_5fpath_8805',['extract_as_gbwt_path',['../namespacevg.html#a0d1c00a44e9aeb5c4294edd60fcbaa61',1,'vg']]],
+ ['extract_5fcluster_5fgraph_8806',['extract_cluster_graph',['../classvg_1_1MultipathMapper.html#a411882d1f1f4908582333944ac346443',1,'vg::MultipathMapper']]],
+ ['extract_5fcomponent_8807',['extract_component',['../classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54',1,'vg::PathChunker']]],
+ ['extract_5fconnecting_5fgraph_8808',['extract_connecting_graph',['../namespacevg_1_1algorithms.html#ac0d0446bde00e10bd77816c968ae97b0',1,'vg::algorithms']]],
+ ['extract_5fcontaining_5fgraph_8809',['extract_containing_graph',['../namespacevg_1_1algorithms.html#a4270da794ad0185dacef1874a1e4d3c2',1,'vg::algorithms::extract_containing_graph(const HandleGraph *source, MutableHandleGraph *into, const vector< pos_t > &positions, const vector< size_t > &forward_search_lengths, const vector< size_t > &backward_search_lengths, size_t reversing_walk_length)'],['../namespacevg_1_1algorithms.html#a0ecd79b7d4b622b583a8e08df594e45c',1,'vg::algorithms::extract_containing_graph(const HandleGraph *source, MutableHandleGraph *into, const vector< pos_t > &positions, size_t max_dist, size_t reversing_walk_length)'],['../namespacevg_1_1algorithms.html#ab31b1b707c93f96d6f013e579c4d8783',1,'vg::algorithms::extract_containing_graph(const HandleGraph *source, MutableHandleGraph *into, const vector< pos_t > &positions, const vector< size_t > &position_max_dist, size_t reversing_walk_length)']]],
+ ['extract_5fcontext_8810',['extract_context',['../namespacevg_1_1algorithms.html#a38ea20ebc7800702ec0cdb96920c6184',1,'vg::algorithms']]],
+ ['extract_5fextending_5fgraph_8811',['extract_extending_graph',['../namespacevg_1_1algorithms.html#a1f600eb589d48607c2616bed69ff2e27',1,'vg::algorithms']]],
+ ['extract_5fgbwt_5fpath_8812',['extract_gbwt_path',['../namespacevg.html#a768828fcd9f2ecf7661e7d873f23bc58',1,'vg']]],
+ ['extract_5fhaplotypes_8813',['extract_haplotypes',['../haplotypes__main_8cpp.html#a56be3686d2a011df59c271f092f6f40c',1,'haplotypes_main.cpp']]],
+ ['extract_5fid_5frange_8814',['extract_id_range',['../classvg_1_1PathChunker.html#a140b4a86b4f8ea18d29a39c7b1aab66f',1,'vg::PathChunker::extract_id_range()'],['../namespacevg_1_1algorithms.html#ac53dd7f2ff1b53bec309f368a79db951',1,'vg::algorithms::extract_id_range()']]],
+ ['extract_5fmaximal_5fgraph_8815',['extract_maximal_graph',['../classvg_1_1MultipathMapper.html#a2688faa30ec227f9c9266ce37ce5ca6b',1,'vg::MultipathMapper']]],
+ ['extract_5foverlapping_5fpaths_8816',['extract_overlapping_paths',['../classvg_1_1Surjector.html#af4b7099431a6a5334141760cc8922281',1,'vg::Surjector::extract_overlapping_paths(const PathPositionHandleGraph *graph, const Alignment &source, const unordered_set< path_handle_t > &surjection_paths) const'],['../classvg_1_1Surjector.html#adc4dbb4ce6f48d755c91e4931028c6d8',1,'vg::Surjector::extract_overlapping_paths(const PathPositionHandleGraph *graph, const multipath_alignment_t &source, const unordered_set< path_handle_t > &surjection_paths, unordered_map< pair< path_handle_t, bool >, vector< tuple< size_t, size_t, int32_t >>> &connections_out) const']]],
+ ['extract_5fpath_5fcomponent_8817',['extract_path_component',['../classvg_1_1PathChunker.html#aca0d2bec2834fdc534d42238a0a53b46',1,'vg::PathChunker']]],
+ ['extract_5fpath_5fmetadata_8818',['extract_path_metadata',['../namespacevg.html#aa381cdc7f966379fc7cc9ea11257f632',1,'vg']]],
+ ['extract_5fpath_5frange_8819',['extract_path_range',['../namespacevg_1_1algorithms.html#a6da60961fae57a5568354ef5b541bcf7',1,'vg::algorithms']]],
+ ['extract_5frescue_5fgraph_8820',['extract_rescue_graph',['../classvg_1_1MultipathMapper.html#a6cecbd08d03efe5b248cf2e93e5f619c',1,'vg::MultipathMapper']]],
+ ['extract_5frestrained_5fgraph_8821',['extract_restrained_graph',['../classvg_1_1MultipathMapper.html#a282d59b6aa693b4f454ab25c5f7f328c',1,'vg::MultipathMapper']]],
+ ['extract_5fsequences_8822',['extract_sequences',['../classvg_1_1Recombinator.html#a5267a1c51ed0caf5e78834e1b6221e0a',1,'vg::Recombinator']]],
+ ['extract_5fsnarls_8823',['extract_snarls',['../classvg_1_1PathChunker.html#a20d6a2e56df993a7420e5b1c62df5154',1,'vg::PathChunker']]],
+ ['extract_5fsub_5fmultipath_5falignment_8824',['extract_sub_multipath_alignment',['../namespacevg.html#a2b9703408d4c7160e8d9e83303c4d1c7',1,'vg']]],
+ ['extract_5fsubgraph_8825',['extract_subgraph',['../classvg_1_1PathChunker.html#a90aac076d1669b467ca5ca5868c7ed2e',1,'vg::PathChunker']]],
+ ['extracting_5fleft_8826',['extracting_left',['../classvg_1_1IncrementalSubgraph.html#a91bb045370337f4f91aea10c14fdca95',1,'vg::IncrementalSubgraph']]],
+ ['extranodegraph_8827',['ExtraNodeGraph',['../classvg_1_1ExtraNodeGraph.html#aafddbd22f8123df59e0bbdb634f5ba0a',1,'vg::ExtraNodeGraph']]]
];
diff --git a/search/functions_6.js b/search/functions_6.js
index 2b1924bc9c..03f294ebf2 100644
--- a/search/functions_6.js
+++ b/search/functions_6.js
@@ -1,252 +1,253 @@
var searchData=
[
- ['factorial_5fln_8826',['factorial_ln',['../namespacevg.html#a54a32f7feb38c9f86d7796f0b4f1dac7',1,'vg']]],
- ['fail_8827',['fail',['../classvg_1_1Funnel.html#a38e1d7d328fe8ea456c2631abffaebb4',1,'vg::Funnel']]],
- ['false_5fextend_8828',['false_extend',['../structhaplo_1_1haplo__DP__rectangle.html#af4b704f2932b2ce43bddbace287674b8',1,'haplo::haplo_DP_rectangle']]],
- ['fast_5flinear_5fsort_8829',['fast_linear_sort',['../classvg_1_1FlowSort.html#ab7f9051ee8d6e2118e4da7465c9c2a98',1,'vg::FlowSort']]],
- ['fasta_5fto_5fvcf_8830',['fasta_to_vcf',['../classvg_1_1NameMapper.html#a73bd759074f9643a838c020f17120432',1,'vg::NameMapper']]],
- ['faster_5fcap_8831',['faster_cap',['../classvg_1_1MinimizerMapper.html#a720abb2308e147350b147da0781f8f21',1,'vg::MinimizerMapper']]],
- ['fastq_5fpaired_5finterleaved_5ffor_5feach_8832',['fastq_paired_interleaved_for_each',['../namespacevg.html#a0213498a2e9a6cc5c9cb64d30754b4c5',1,'vg']]],
- ['fastq_5fpaired_5finterleaved_5ffor_5feach_5fparallel_8833',['fastq_paired_interleaved_for_each_parallel',['../namespacevg.html#a49b9a6f2e5573cf854f631ee6f314cbf',1,'vg']]],
- ['fastq_5fpaired_5finterleaved_5ffor_5feach_5fparallel_5fafter_5fwait_8834',['fastq_paired_interleaved_for_each_parallel_after_wait',['../namespacevg.html#afcbfef4da296d2545850a22e542ea546',1,'vg']]],
- ['fastq_5fpaired_5ftwo_5ffiles_5ffor_5feach_8835',['fastq_paired_two_files_for_each',['../namespacevg.html#a7112300f258fd0f25fea0ecf56579373',1,'vg']]],
- ['fastq_5fpaired_5ftwo_5ffiles_5ffor_5feach_5fparallel_8836',['fastq_paired_two_files_for_each_parallel',['../namespacevg.html#a32aee624484aa44bb893f82b03169a3e',1,'vg']]],
- ['fastq_5fpaired_5ftwo_5ffiles_5ffor_5feach_5fparallel_5fafter_5fwait_8837',['fastq_paired_two_files_for_each_parallel_after_wait',['../namespacevg.html#a47574d693a9ae86d771ea34a0c91afaa',1,'vg']]],
- ['fastq_5funpaired_5ffor_5feach_8838',['fastq_unpaired_for_each',['../namespacevg.html#a68d737fbcb121fa0192309596a9eddf9',1,'vg']]],
- ['fastq_5funpaired_5ffor_5feach_5fparallel_8839',['fastq_unpaired_for_each_parallel',['../namespacevg.html#a45ce2f6fbc86f1fab63f3eb22eb9a124',1,'vg']]],
- ['fdinbuf_8840',['fdinbuf',['../classvg_1_1io_1_1fdinbuf.html#a8ae41cbaad91f66b63085182afa3f657',1,'vg::io::fdinbuf']]],
- ['fdistream_8841',['fdistream',['../classvg_1_1io_1_1fdistream.html#acdb9ac3f7b60bb31c8a4d1ff307688f4',1,'vg::io::fdistream']]],
- ['fdostream_8842',['fdostream',['../classvg_1_1io_1_1fdostream.html#a8549f4b673b255a447cad6a06c587ec7',1,'vg::io::fdostream']]],
- ['fdoutbuf_8843',['fdoutbuf',['../classvg_1_1io_1_1fdoutbuf.html#a4761de2464fb50257c74d5e6e5a13fad',1,'vg::io::fdoutbuf']]],
- ['field_8844',['field',['../classvg_1_1TSVExplainer.html#a855b258874af7d9be7db4ffb3ecebcc1',1,'vg::TSVExplainer::field(const std::string &value)'],['../classvg_1_1TSVExplainer.html#a0ff0223ddab66b4a904c291e208eb5f5',1,'vg::TSVExplainer::field(size_t value)']]],
- ['file_5fbase_5fname_8845',['file_base_name',['../namespacevg.html#aeaf52003fcf4fa34ded0aeabafacb3fc',1,'vg']]],
- ['file_5fexists_8846',['file_exists',['../namespacevg.html#abebdd1477a436020f3d3f8368d825054',1,'vg']]],
- ['fill_5fbuffer_8847',['fill_buffer',['../classvg_1_1VcfBuffer.html#afff803310f8c3bca9788b30ebba8450f',1,'vg::VcfBuffer']]],
- ['fill_5fin_5fdistance_5findex_8848',['fill_in_distance_index',['../namespacevg.html#ac7b8c3e17638ecacbdf519c4095bc20e',1,'vg']]],
- ['fill_5fin_5fforest_8849',['fill_in_forest',['../classvg_1_1ZipCodeForest.html#abeea5f048e6e7711971b764591ee63ec',1,'vg::ZipCodeForest']]],
- ['fill_5fin_5ffull_5fdecoder_8850',['fill_in_full_decoder',['../classvg_1_1ZipCode.html#aea9e1d42e1a0b31941401212fd87d76a',1,'vg::ZipCode']]],
- ['fill_5fin_5fnext_5fdecoder_8851',['fill_in_next_decoder',['../classvg_1_1ZipCode.html#a020fef499f038a3dac191667b2fb8e16',1,'vg::ZipCode']]],
- ['fill_5fin_5fzipcode_8852',['fill_in_zipcode',['../classvg_1_1ZipCode.html#ac232fe003bd30dfbba804cf0bc81b580',1,'vg::ZipCode']]],
- ['fill_5fin_5fzipcode_5ffrom_5fpayload_8853',['fill_in_zipcode_from_payload',['../classvg_1_1ZipCode.html#ad53005c4c44463b1226835f7f7da83e0',1,'vg::ZipCode']]],
- ['fill_5fmatrix_8854',['fill_matrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a54be0f91b1460bbd03e87e6da6be6e32',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['fill_5fnode_5fto_5fposition_8855',['fill_node_to_position',['../classvg_1_1Filter.html#ac7216130c6fbd20580901090f8185048',1,'vg::Filter']]],
- ['fill_5fvalue_8856',['fill_value',['../classvg_1_1io_1_1ProtobufIterator.html#aec100b14b027d294e2a0aaaaad3b4abd',1,'vg::io::ProtobufIterator']]],
- ['filter_8857',['Filter',['../classvg_1_1Filter.html#a1a9dadc8fe8b9abe295373627e033b89',1,'vg::Filter::Filter()'],['../classvg_1_1ReadFilter.html#a36c3ff48009706f3853bddd02a98de9c',1,'vg::ReadFilter::filter(istream *alignment_stream)'],['../classvg_1_1ReadFilter.html#a1fb619abfe77d0b02cc7f8aa4ad47af5',1,'vg::ReadFilter::filter(istream *alignment_stream)'],['../classvg_1_1ReadFilter.html#ab56d51dbf343ea44e78c31d54f1f317f',1,'vg::ReadFilter::filter(istream *alignment_stream)']]],
- ['filter_5falignment_8858',['filter_alignment',['../classvg_1_1ReadFilter.html#a1398f727931b41bfff0d9e058f442ebc',1,'vg::ReadFilter']]],
- ['filter_5fand_5fprocess_5fmultimaps_8859',['filter_and_process_multimaps',['../classvg_1_1Mapper.html#a7b5db2f8b56cb6210431cc7d0d25a18f',1,'vg::Mapper']]],
- ['filter_5fbreakpoints_5fby_5fcoverage_8860',['filter_breakpoints_by_coverage',['../namespacevg.html#a5ddba9dd6dcb384cbbea06c535e00d6d',1,'vg']]],
- ['filter_5fhits_5fto_8861',['filter_hits_to',['../classvg_1_1MaximalExactMatch.html#a106b116185bf9cc3e3e675ce0ed81da0',1,'vg::MaximalExactMatch']]],
- ['filter_5finternal_8862',['filter_internal',['../classvg_1_1ReadFilter.html#a3220ffe3aa6042a1423c6251c95a2b05',1,'vg::ReadFilter']]],
- ['filter_5flocal_5fvariants_8863',['filter_local_variants',['../classvg_1_1VariantAdder.html#ae72dcbf9e0cb036aa675ad9db3bcf286',1,'vg::VariantAdder']]],
- ['filter_5fredundant_5fpath_5fchunks_8864',['filter_redundant_path_chunks',['../classvg_1_1Surjector.html#ac1ef0f552e2bd46b48a773837cee6c7c',1,'vg::Surjector']]],
- ['final_5foffset_8865',['final_offset',['../structvg_1_1WFAAlignment.html#a572300197e78708a3aa53c598f76a932',1,'vg::WFAAlignment']]],
- ['final_5fposition_8866',['final_position',['../namespacevg.html#ad435098725ff21d822052abee009d2bd',1,'vg::final_position(const Path &path)'],['../namespacevg.html#a28e15d36e2ee202f8a194cca31d91d65',1,'vg::final_position(const path_t &path)']]],
- ['finalize_8867',['finalize',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a43e6001b25d634ccd6e3fd026c970b45',1,'vg::NGSSimulator::MarkovDistribution::finalize()'],['../classvg_1_1NGSSimulator.html#ab5cda05ad8931a60efd9f19c3889b0d2',1,'vg::NGSSimulator::finalize()']]],
- ['finalize_5falignment_8868',['finalize_alignment',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#aa88bda9825a69406a7913f4a911cc242',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['finalize_5ffragment_5flength_5fdistr_8869',['finalize_fragment_length_distr',['../classvg_1_1MinimizerMapper.html#a4ae627a418357792cd5b9f6d6b9cc19c',1,'vg::MinimizerMapper']]],
- ['find_8870',['find',['../classvg_1_1IndexedVG.html#a7a77bdb39f0fd7e1ad73df9539ce1471',1,'vg::IndexedVG::find()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#aa4010a6423dd9c113ad7949be709eefb',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::find()'],['../classvg_1_1StreamIndexBase.html#a7c332ce59d0a99ac7c2ef69d77b0f749',1,'vg::StreamIndexBase::find(id_t node_id) const'],['../classvg_1_1StreamIndexBase.html#ad520b5b3241ee162ffd02c2cac5bd702',1,'vg::StreamIndexBase::find(id_t node_id, const function< bool(int64_t, int64_t)> scan_callback) const'],['../classvg_1_1StreamIndexBase.html#a6448cab1126089223a17c2ed6d943a97',1,'vg::StreamIndexBase::find(id_t min_node, id_t max_node, const function< bool(int64_t, int64_t)> scan_callback) const'],['../classvg_1_1StreamIndex.html#ab459a3f4f93a448b0d7a49238927cc0f',1,'vg::StreamIndex::find(cursor_t &cursor, id_t node_id, const function< void(const Message &)> handle_result) const'],['../classvg_1_1StreamIndex.html#a62f171f0ffa154ab0fed67e277a6d73e',1,'vg::StreamIndex::find(cursor_t &cursor, id_t min_node, id_t max_node, const function< void(const Message &)> handle_result) const'],['../classvg_1_1StreamIndex.html#afcbd0c740c5257066ac0cffa1215eafe',1,'vg::StreamIndex::find(cursor_t &cursor, const vector< pair< id_t, id_t >> &ranges, const function< void(const Message &)> handle_result, bool only_fully_contained=false) const']]],
- ['find_5fallele_5ftraversals_8871',['find_allele_traversals',['../classvg_1_1VCFTraversalFinder.html#ad660814265b5989408dace8da768edfe',1,'vg::VCFTraversalFinder']]],
- ['find_5fanchor_5fintervals_8872',['find_anchor_intervals',['../namespacevg.html#a6058ba7e46dc3e0b34b06ff01ed5f22d',1,'vg']]],
- ['find_5fbackbone_8873',['find_backbone',['../classvg_1_1RepresentativeTraversalFinder.html#aacdab17c6c32685e0ed3f8f0c221453e',1,'vg::RepresentativeTraversalFinder']]],
- ['find_5fbanded_5fpaths_8874',['find_banded_paths',['../classvg_1_1BandedGlobalAligner.html#adfad0975f34dcf90211d239ee6c126a8',1,'vg::BandedGlobalAligner']]],
- ['find_5fbare_5floaders_8875',['find_bare_loaders',['../classvg_1_1io_1_1Registry.html#a45bd0585d64d2ff1751463333a21b47d',1,'vg::io::Registry']]],
- ['find_5fbest_5fchain_8876',['find_best_chain',['../namespacevg_1_1algorithms.html#ac3f3eeb71fb9bd08889b08aa20fe9605',1,'vg::algorithms']]],
- ['find_5fbest_5fchains_8877',['find_best_chains',['../namespacevg_1_1algorithms.html#a67dc5da4c5935ba307303798c521c1c8',1,'vg::algorithms']]],
- ['find_5fbreakpoints_8878',['find_breakpoints',['../namespacevg.html#ac80bc94af296d0a543d983eae79afac0',1,'vg']]],
- ['find_5fbubble_8879',['find_bubble',['../classvg_1_1NestedTraversalFinder.html#ad9fd7aef8b98fdc56b429e4613113c6f',1,'vg::NestedTraversalFinder::find_bubble()'],['../classvg_1_1RepresentativeTraversalFinder.html#ad8cc120dc63491eadfdc7b00cd1dc519',1,'vg::RepresentativeTraversalFinder::find_bubble()']]],
- ['find_5fchain_5falignment_8880',['find_chain_alignment',['../classvg_1_1MinimizerMapper.html#a3b83e5072a6a0654ba90ed097e8e7a52',1,'vg::MinimizerMapper']]],
- ['find_5fconstriction_5fbicliques_8881',['find_constriction_bicliques',['../classvg_1_1Surjector.html#a54b0b7fe9db83a6cfdbebf9dbeb81f04',1,'vg::Surjector']]],
- ['find_5fcycle_5fpath_5fin_5fcactus_8882',['find_cycle_path_in_cactus',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#af554cefbab4c2bd70529342b2916d30e',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['find_5fedges_5fto_5fprune_8883',['find_edges_to_prune',['../namespacevg_1_1algorithms.html#a8529f1718d5f0330dbb301d1148f12e1',1,'vg::algorithms']]],
- ['find_5fexisting_5fsequence_5fid_8884',['find_existing_sequence_id',['../classvg_1_1algorithms_1_1GFAParser.html#a8cc4a34d40334bb97f7af561db414e33',1,'vg::algorithms::GFAParser']]],
- ['find_5ffanout_5fmems_8885',['find_fanout_mems',['../classvg_1_1BaseMapper.html#aeb048d786d78b3a545f724bf45cf11d6',1,'vg::BaseMapper']]],
- ['find_5fgbwt_8886',['find_gbwt',['../namespacevg_1_1algorithms.html#a92780d34d13ab2a6be9fe477543179ce',1,'vg::algorithms::find_gbwt(const HandleGraph *graph)'],['../namespacevg_1_1algorithms.html#a5783b30c1ad6ea3ff4bc4576f447b615',1,'vg::algorithms::find_gbwt(const HandleGraph *graph, std::unique_ptr< gbwt::GBWT > &holder, const std::string &filename)']]],
- ['find_5fgbwt_5ftraversals_8887',['find_gbwt_traversals',['../classvg_1_1GBWTTraversalFinder.html#ac924b0bf3140cb64411f1e1123effff6',1,'vg::GBWTTraversalFinder::find_gbwt_traversals(const Snarl &site, bool return_paths=true)'],['../classvg_1_1GBWTTraversalFinder.html#aec2c482e376c389df848610dc5fec3db',1,'vg::GBWTTraversalFinder::find_gbwt_traversals(const handle_t &snarl_start, const handle_t &snarl_end, bool return_paths=true)']]],
- ['find_5fgbwtgraph_8888',['find_gbwtgraph',['../namespacevg_1_1algorithms.html#a1e8867ea22636dc22aa53bd8fe1d0aaa',1,'vg::algorithms']]],
- ['find_5fgroup_8889',['find_group',['../classvg_1_1SparseUnionFind.html#ae5dcefb7ec434f8405094360b49ebae1',1,'vg::SparseUnionFind']]],
- ['find_5fin_5forientation_8890',['find_in_orientation',['../structvg_1_1PathIndex.html#ae448ae2af8e4073b9db8b678e3b97e00',1,'vg::PathIndex']]],
- ['find_5fin_5fout_5fweb_8891',['find_in_out_web',['../classvg_1_1FlowSort.html#aa5e485f218cdc874e5519ef61843358c',1,'vg::FlowSort']]],
- ['find_5findex_8892',['find_index',['../classvg_1_1LegacyCaller.html#a280eb6052ea0781644047711b7fb17d4',1,'vg::LegacyCaller']]],
- ['find_5fkmer_8893',['find_kmer',['../namespacevg.html#afdd5134ae715117de1b7ba9283fa8651',1,'vg']]],
- ['find_5floader_8894',['find_loader',['../classvg_1_1io_1_1Registry.html#a7414063ac702dd6cbe8a7149a49be922',1,'vg::io::Registry']]],
- ['find_5fmapping_8895',['find_mapping',['../classvg_1_1Paths.html#a9403cc6f97e199f03b365f9a7eb1de63',1,'vg::Paths']]],
- ['find_5fmax_5fnode_8896',['find_max_node',['../classvg_1_1FlowSort.html#ab05b9f1737b5cef5e719a33d150b7529',1,'vg::FlowSort']]],
- ['find_5fmems_8897',['find_mems',['../classvg_1_1MultipathMapper.html#af1bca7d5555a38a74cb04a362268b972',1,'vg::MultipathMapper']]],
- ['find_5fmems_5fdeep_8898',['find_mems_deep',['../classvg_1_1BaseMapper.html#af64a7b36c1880606372d0849842708b0',1,'vg::BaseMapper']]],
- ['find_5fmems_5fsimple_8899',['find_mems_simple',['../classvg_1_1BaseMapper.html#a4dd3272837211543ba461472833734a9',1,'vg::BaseMapper']]],
- ['find_5fminimizers_8900',['find_minimizers',['../classvg_1_1MinimizerMapper.html#af3e5c53b0250173b6d0eb097cf884986',1,'vg::MinimizerMapper']]],
- ['find_5fmismatches_8901',['find_mismatches',['../namespacevg.html#a050aedf4b2e047e04f31a6e8b7ad55ce',1,'vg']]],
- ['find_5fnamed_5ftraversals_8902',['find_named_traversals',['../classvg_1_1PathRestrictedTraversalFinder.html#ab046472d6a0a26a52c91574e7a09373d',1,'vg::PathRestrictedTraversalFinder']]],
- ['find_5fnode_5fby_5fname_5for_5fadd_5fnew_8903',['find_node_by_name_or_add_new',['../classvg_1_1VG.html#a04774a86b07508e9e5955abfba2171ff',1,'vg::VG']]],
- ['find_5foptimal_5ftail_5falignments_8904',['find_optimal_tail_alignments',['../classvg_1_1MinimizerMapper.html#a4247391b8d74dc68b48a792a31ed6d60',1,'vg::MinimizerMapper']]],
- ['find_5fpacked_5fbreakpoints_8905',['find_packed_breakpoints',['../namespacevg.html#a808481f23dac7bc58c339cf36a9a0aaf',1,'vg']]],
- ['find_5fpath_5ftraversals_8906',['find_path_traversals',['../classvg_1_1PathTraversalFinder.html#a4adb802f78ec1893954d052156953541',1,'vg::PathTraversalFinder::find_path_traversals(const Snarl &site)'],['../classvg_1_1PathTraversalFinder.html#a4e1ad0b033b6fb33991f70271a252749',1,'vg::PathTraversalFinder::find_path_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../classvg_1_1GBWTTraversalFinder.html#aaabea1b758eb8fecbefe2e5966971b47',1,'vg::GBWTTraversalFinder::find_path_traversals(const Snarl &site)'],['../classvg_1_1GBWTTraversalFinder.html#ae5c1c58803837ee498776e964039440d',1,'vg::GBWTTraversalFinder::find_path_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../namespacevg.html#a3b97a34752ff7bf3c8c2c524c84796df',1,'vg::find_path_traversals()']]],
- ['find_5fpos_8907',['find_pos',['../structvg_1_1WFANode.html#a4460062120b4153f4ea19b4bfc916ef5',1,'vg::WFANode::find_pos()'],['../classvg_1_1WFATree.html#af216283dfd08d2cee4b17d418d0aa98d',1,'vg::WFATree::find_pos()']]],
- ['find_5fposition_8908',['find_position',['../structvg_1_1PathIndex.html#a377bc15c246c708fe4a0264cb05588af',1,'vg::PathIndex']]],
- ['find_5frescuable_5fspliced_5falignments_8909',['find_rescuable_spliced_alignments',['../classvg_1_1MultipathMapper.html#a10cf9d266ae6da1651c9d07a7fc5f14d',1,'vg::MultipathMapper']]],
- ['find_5fsaver_8910',['find_saver',['../classvg_1_1io_1_1Registry.html#acfad8c6a18a1443150d0818fe1a14857',1,'vg::io::Registry']]],
- ['find_5fseeds_8911',['find_seeds',['../classvg_1_1MinimizerMapper.html#a8e760f140ec23f170d4a6643fa44ce58',1,'vg::MinimizerMapper']]],
- ['find_5fshortest_5fpaths_8912',['find_shortest_paths',['../namespacehandlegraph_1_1algorithms.html#af7d99cdf4ea48244031b209b483c8e6a',1,'handlegraph::algorithms']]],
- ['find_5fsnarls_8913',['find_snarls',['../classvg_1_1CactusSnarlFinder.html#a3060bcff3b01e21176f17ebb74d31452',1,'vg::CactusSnarlFinder::find_snarls()'],['../classvg_1_1SnarlFinder.html#a28d2aa85a748836df818c8c4ac8a8fd9',1,'vg::SnarlFinder::find_snarls()'],['../classvg_1_1HandleGraphSnarlFinder.html#a3b6820315dc0a0a15fcd61076f87fcf7',1,'vg::HandleGraphSnarlFinder::find_snarls()']]],
- ['find_5fsnarls_5fimpl_8914',['find_snarls_impl',['../classvg_1_1CactusSnarlFinder.html#a9ff89d5f26398349404796d325b32f69',1,'vg::CactusSnarlFinder']]],
- ['find_5fsnarls_5fparallel_8915',['find_snarls_parallel',['../classvg_1_1CactusSnarlFinder.html#a712cd81719c13a172c3da46349419524',1,'vg::CactusSnarlFinder::find_snarls_parallel()'],['../classvg_1_1IntegratedSnarlFinder.html#a42a292777287dc89cdb9e58bbe5c50b8',1,'vg::IntegratedSnarlFinder::find_snarls_parallel()'],['../classvg_1_1SnarlFinder.html#a7b8b315c1129de42cfb3120de7281291',1,'vg::SnarlFinder::find_snarls_parallel()']]],
- ['find_5fsnarls_5funindexed_8916',['find_snarls_unindexed',['../classvg_1_1HandleGraphSnarlFinder.html#af4fb35065d83a2ed2f4daa687c114dbc',1,'vg::HandleGraphSnarlFinder']]],
- ['find_5fspliced_5falignments_8917',['find_spliced_alignments',['../classvg_1_1MultipathMapper.html#ad907bb6d98eaa48a8a013ddfb0fd7449',1,'vg::MultipathMapper::find_spliced_alignments(const Alignment &alignment, vector< multipath_alignment_t > &multipath_alns_out, vector< double > &multiplicities, vector< size_t > &cluster_idxs, const vector< MaximalExactMatch > &mems, vector< clustergraph_t > &cluster_graphs, const match_fanouts_t *fanouts=nullptr, const multipath_alignment_t *rescue_anchor=nullptr, bool rescue_left=false, double rescue_multiplicity=1.0)'],['../classvg_1_1MultipathMapper.html#ad33f09dde45f1498ffa1ac6996cc0c6d',1,'vg::MultipathMapper::find_spliced_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &pair_multiplicities, const vector< MaximalExactMatch > &mems1, const vector< MaximalExactMatch > &mems2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, const match_fanouts_t *fanouts=nullptr)']]],
- ['find_5fstripped_5fmatches_8918',['find_stripped_matches',['../classvg_1_1BaseMapper.html#ad0ca6fe6e3a407bd1bff38bb05cbe794',1,'vg::BaseMapper']]],
- ['find_5fsub_5fmems_8919',['find_sub_mems',['../classvg_1_1BaseMapper.html#a77079f609cab775e59ff0750ef9e84d9',1,'vg::BaseMapper']]],
- ['find_5fsub_5fmems_5ffast_8920',['find_sub_mems_fast',['../classvg_1_1BaseMapper.html#a81fa3eae0321720511b1f54fa28968bb',1,'vg::BaseMapper']]],
- ['find_5ftips_8921',['find_tips',['../namespacehandlegraph_1_1algorithms.html#a4339886e547b09009bf391d77596c280',1,'handlegraph::algorithms']]],
- ['find_5ftranslation_8922',['find_translation',['../namespacevg_1_1algorithms.html#af38c05b9c1e56c79faccfbbf6b3ade95',1,'vg::algorithms']]],
- ['find_5ftraversals_8923',['find_traversals',['../classvg_1_1NestedTraversalFinder.html#a491e535921c67bb8891a99aa314b6e94',1,'vg::NestedTraversalFinder::find_traversals()'],['../classvg_1_1TraversalFinder.html#a53611f0deaac0fcfb0a440f272c69637',1,'vg::TraversalFinder::find_traversals(const Snarl &site)=0'],['../classvg_1_1TraversalFinder.html#a41ed015cfd3f95104f530943e643e883',1,'vg::TraversalFinder::find_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../classvg_1_1ExhaustiveTraversalFinder.html#a47d24a43aef54ca51318b8ae89e51328',1,'vg::ExhaustiveTraversalFinder::find_traversals()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#ad97b9e1c48374c3212621422f0ce0d9c',1,'vg::ReadRestrictedTraversalFinder::find_traversals()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a78b03570bd5d59d3c870bbd192eae685',1,'vg::PathRestrictedTraversalFinder::find_traversals()'],['../classvg_1_1PathBasedTraversalFinder.html#af58be82fdbce530b2662a6329e08bd77',1,'vg::PathBasedTraversalFinder::find_traversals()'],['../classvg_1_1PathTraversalFinder.html#a3da29145d1ed82d950bdeb895d3b3bf4',1,'vg::PathTraversalFinder::find_traversals(const Snarl &site)'],['../classvg_1_1PathTraversalFinder.html#ab67194f7b0302ae860bb9e802d2ebfc8',1,'vg::PathTraversalFinder::find_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../classvg_1_1TrivialTraversalFinder.html#ae1b3ebce09b8641fe713cc9628909bfe',1,'vg::TrivialTraversalFinder::find_traversals()'],['../classvg_1_1RepresentativeTraversalFinder.html#ae2280a86a06849b3c4ae0dfef3fe85c0',1,'vg::RepresentativeTraversalFinder::find_traversals()'],['../classvg_1_1VCFTraversalFinder.html#acd33847fcb02a4ea1eb6bd2768549daf',1,'vg::VCFTraversalFinder::find_traversals()'],['../classvg_1_1FlowTraversalFinder.html#a3bf6dff88b07d23e8877ed263d951d40',1,'vg::FlowTraversalFinder::find_traversals()'],['../classvg_1_1GBWTTraversalFinder.html#a3f4f3f644df9755b387bab551451827d',1,'vg::GBWTTraversalFinder::find_traversals(const Snarl &site)'],['../classvg_1_1GBWTTraversalFinder.html#af15fc7ee19296e40cf7b101293a61b26',1,'vg::GBWTTraversalFinder::find_traversals(const handle_t &snarl_start, const handle_t &snarl_end)']]],
- ['find_5fweighted_5ftraversals_8924',['find_weighted_traversals',['../classvg_1_1FlowTraversalFinder.html#aea197651f2464c68fe06eab925ec8744',1,'vg::FlowTraversalFinder']]],
- ['finish_8925',['finish',['../structvg_1_1RecombinatorHaplotype.html#acc9e723823910751f19553857c10acf4',1,'vg::RecombinatorHaplotype::finish()'],['../classvg_1_1SnarlManager.html#aacf5fd439b35298107ddf2900559259c',1,'vg::SnarlManager::finish()'],['../namespacevg_1_1io.html#a9b562b3e8bd001bb10bcd0353bf5a929',1,'vg::io::finish()']]],
- ['finish_5fcurrent_5fedit_8926',['finish_current_edit',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a7bafadc0a8c3160bcc2b3949edc3de17',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['finish_5fcurrent_5fnode_8927',['finish_current_node',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#ad460ee763b7b15cf8206038283423e89',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['first_5fmapping_5fquality_5fapprox_8928',['first_mapping_quality_approx',['../classvg_1_1GSSWAligner.html#a20cfadad5c8d3807320cd206427ef243',1,'vg::GSSWAligner']]],
- ['first_5fmapping_5fquality_5fexact_8929',['first_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#a25cb693e3eb45f8c7d1e0ae7c6dcf0af',1,'vg::GSSWAligner']]],
- ['first_5fpath_5fposition_8930',['first_path_position',['../namespacevg.html#ada7557d06abd0fca3d66f9ca73fe81db',1,'vg']]],
- ['fit_5ffixed_5frate_5fmax_5fexponential_8931',['fit_fixed_rate_max_exponential',['../namespacevg.html#a4b47bdda079acc49d455953a91db12bd',1,'vg']]],
- ['fit_5ffixed_5fshape_5fmax_5fexponential_8932',['fit_fixed_shape_max_exponential',['../namespacevg.html#a79672e0d9b7e8abdb60ec0f181eec6f0',1,'vg']]],
- ['fit_5fmax_5fexponential_8933',['fit_max_exponential',['../namespacevg.html#aafca6820103f98f205de4774a9d35f09',1,'vg']]],
- ['fit_5foffset_5fweibull_8934',['fit_offset_weibull',['../namespacevg.html#ad9f14b8e66ba0c5c28961e8da4aba4b6',1,'vg']]],
- ['fit_5fweibull_8935',['fit_weibull',['../namespacevg.html#aa64cff8c9c4b3c3baefb49c57614643d',1,'vg']]],
- ['fit_5fzipf_8936',['fit_zipf',['../namespacevg.html#a9fa3b08acc22f29ea5d940317f6948ab',1,'vg']]],
- ['fix_5fdozeu_5fend_5fdeletions_8937',['fix_dozeu_end_deletions',['../classvg_1_1MinimizerMapper.html#a4ec441e3df74303c16a60529f08cb70a',1,'vg::MinimizerMapper']]],
- ['fix_5fdozeu_5fscore_8938',['fix_dozeu_score',['../classvg_1_1MinimizerMapper.html#ab6a0d266ef94fbda125ebdde64617c84',1,'vg::MinimizerMapper']]],
- ['flag_5frepetitive_5fminimizers_8939',['flag_repetitive_minimizers',['../classvg_1_1MinimizerMapper.html#a26fbad6474a8510b5154bbe0e11f6794',1,'vg::MinimizerMapper']]],
- ['flatfilebacktranslation_8940',['FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html#aceb24b5209b6448ae6f36080e9f676d3',1,'vg::FlatFileBackTranslation']]],
- ['flatten_5falt_5fallele_8941',['flatten_alt_allele',['../classvg_1_1NestedFlowCaller.html#ace4500b677170eff3c9c9f556425ac23',1,'vg::NestedFlowCaller']]],
- ['flatten_5fcommon_5fallele_5fends_8942',['flatten_common_allele_ends',['../classvg_1_1VCFOutputCaller.html#aa2d19e56299e843d868e8e5fa5b45d49',1,'vg::VCFOutputCaller::flatten_common_allele_ends()'],['../classvg_1_1MCMCCaller.html#ab238d542ffad3a3919dfc873ed39e54a',1,'vg::MCMCCaller::flatten_common_allele_ends()']]],
- ['flatten_5fdistance_5ftree_8943',['flatten_distance_tree',['../classvg_1_1OrientedDistanceClusterer.html#aa31d8ef9e3eb3de2724b4a4a04452da1',1,'vg::OrientedDistanceClusterer']]],
- ['flatten_5freference_5fallele_8944',['flatten_reference_allele',['../classvg_1_1NestedFlowCaller.html#aeb2b3e99d2ab50bcfb12874148cb644d',1,'vg::NestedFlowCaller']]],
- ['flip_8945',['flip',['../classvg_1_1DagifiedGraph.html#a570cd39e720ecbaadb6ff49ae3f0e23e',1,'vg::DagifiedGraph::flip()'],['../classvg_1_1DozeuPinningOverlay.html#aa28af0d1bfc6cc3952bec3904b688e7a',1,'vg::DozeuPinningOverlay::flip()'],['../classvg_1_1ExtraNodeGraph.html#a755ee2394bad62e0f4e6d17aa0212a72',1,'vg::ExtraNodeGraph::flip()'],['../structvg_1_1WFAAlignment.html#a40b15ca8baa18801c97277da6e830810',1,'vg::WFAAlignment::flip()'],['../classvg_1_1SnarlGraph.html#afacfbb0fb244f3004ff0d8c9fbf76f37',1,'vg::SnarlGraph::flip()'],['../classvg_1_1IdentityOverlay.html#a34ea51454cdd3a12d73992563f514f02',1,'vg::IdentityOverlay::flip()'],['../classvg_1_1IncrementalSubgraph.html#a1dad5cc9948fd536f67bdd2f40ef6765',1,'vg::IncrementalSubgraph::flip()'],['../classvg_1_1IndexedVG.html#a984084b7b8770329963b23845c53e820',1,'vg::IndexedVG::flip()'],['../classvg_1_1MemoizingGraph.html#afc634cf011767c68b0de3c205d24c251',1,'vg::MemoizingGraph::flip()'],['../classvg_1_1NodeSide.html#ae67ce8a411767a0b6883b6c9395b09a1',1,'vg::NodeSide::flip()'],['../classvg_1_1NullMaskingGraph.html#ade5b77f51f0749cba197c55d741ceb89',1,'vg::NullMaskingGraph::flip()'],['../classvg_1_1PathSubgraph.html#ae898f2e9d1b456f2e35f5307e2045283',1,'vg::PathSubgraph::flip()'],['../classvg_1_1ReverseGraph.html#a9a074446252aeab52d5922480c861e4f',1,'vg::ReverseGraph::flip()'],['../classvg_1_1NetGraph.html#a4f1db15a73fdce232fcd55a547986f82',1,'vg::NetGraph::flip()'],['../classvg_1_1SnarlManager.html#a634d4253e7fa5c09aa00f909f171bc61',1,'vg::SnarlManager::flip(const Snarl *snarl)'],['../classvg_1_1SnarlManager.html#ab05aac472334ea39d3b7e5ce95e0ffb2',1,'vg::SnarlManager::flip(const Chain *snarl)'],['../classvg_1_1SourceSinkOverlay.html#a1679195a16f99684463e3560352339a4',1,'vg::SourceSinkOverlay::flip()'],['../classvg_1_1JoinedSpliceGraph.html#a603e8b014c4f3c9041ac8edfcdc355e0',1,'vg::JoinedSpliceGraph::flip()'],['../classvg_1_1StrandSplitGraph.html#a6e4ce04f8b55b54e737e5f9d102b6149',1,'vg::StrandSplitGraph::flip()'],['../classvg_1_1SubHandleGraph.html#a00c5d8d2c19e965ee99a76bb4cd353bf',1,'vg::SubHandleGraph::flip()'],['../classvg_1_1SubgraphOverlay.html#a7520f901a2194ed3241b4097ce720481',1,'vg::SubgraphOverlay::flip()'],['../classvg_1_1SubpathOverlay.html#aaaadc6f282728d352baa0a8f78d5e852',1,'vg::SubpathOverlay::flip()'],['../classvg_1_1TreeSubgraph.html#af2ff96076aa4e658f15c4a6d4c1460e3',1,'vg::TreeSubgraph::flip()'],['../classvg_1_1VG.html#a48a5e160f098327f149b7a8a7a5b3558',1,'vg::VG::flip()'],['../classxg_1_1XG.html#acc7c6296fefeacf908acca84e5d6d14c',1,'xg::XG::flip()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af37976fbc4774d7cc444a7839b65c849',1,'handlegraph::algorithms::SubHandleGraph::flip()'],['../classhandlegraph_1_1HandleGraph.html#aaa3f94ae7e884408ef6e8ca8fd45c7d7',1,'handlegraph::HandleGraph::flip()'],['../classhandlegraph_1_1SnarlDecomposition.html#afd6553c0f17bb766c59ed2234fa2d13e',1,'handlegraph::SnarlDecomposition::flip()'],['../namespacevg.html#ad8a651561299e3236ec62af61d509112',1,'vg::flip()']]],
- ['flip_5fdoubly_5freversed_5fedges_8946',['flip_doubly_reversed_edges',['../classvg_1_1VG.html#a8e5079416ab826cbc8a5eea3869eb892',1,'vg::VG::flip_doubly_reversed_edges()'],['../namespacevg.html#a89c2bb28b708cb4acf67eabfaa4b0168',1,'vg::flip_doubly_reversed_edges()']]],
- ['flip_5fnodes_8947',['flip_nodes',['../namespacevg.html#a1f4eaa1a100e433af698e794afa8857b',1,'vg']]],
- ['flow_5fsort_5fnodes_8948',['flow_sort_nodes',['../classvg_1_1FlowSort.html#a8d35f6283c659052a8710b18e26eb98e',1,'vg::FlowSort']]],
- ['flowcaller_8949',['FlowCaller',['../classvg_1_1FlowCaller.html#a4afea3877bac0d289ffc6c3702d19984',1,'vg::FlowCaller']]],
- ['flowsort_8950',['FlowSort',['../classvg_1_1FlowSort.html#a30687a5f5f16d28996b810d49ae384a6',1,'vg::FlowSort']]],
- ['flowtraversalfinder_8951',['FlowTraversalFinder',['../classvg_1_1FlowTraversalFinder.html#afdefce6c5a69e6ab8ca529c3b4754e8b',1,'vg::FlowTraversalFinder']]],
- ['flush_8952',['flush',['../classvg_1_1DozeuInterface.html#ac51a02b103eb50f4f458c0f756152302',1,'vg::DozeuInterface::flush()'],['../classvg_1_1XdropAligner.html#a06cf48f7dd057db6268218733cc9c991',1,'vg::XdropAligner::flush()'],['../classvg_1_1QualAdjXdropAligner.html#a9e0a9d6587bcc78fc8453a2d5a6c00ae',1,'vg::QualAdjXdropAligner::flush()'],['../classvg_1_1io_1_1MessageEmitter.html#aa1a5812e1ef02893eca24e2c74870e41',1,'vg::io::MessageEmitter::flush()'],['../classvg_1_1io_1_1ProtobufEmitter.html#aefba5ddea6beff54f293b95f7549d944',1,'vg::io::ProtobufEmitter::flush()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a9e2d51e5f860d576390722d3f80e6417',1,'vg::io::BlockedGzipOutputStream::Flush()']]],
- ['flush_5fself_8953',['flush_self',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ad9f92e40584b24a5f1ff20750826bfe7',1,'vg::io::BlockedGzipOutputStream']]],
- ['follow_5fedges_8954',['follow_edges',['../classhandlegraph_1_1HandleGraph.html#a4d21f30e62ad0b0c5919b2fe95e6f8aa',1,'handlegraph::HandleGraph']]],
- ['follow_5fedges_5fimpl_8955',['follow_edges_impl',['../classvg_1_1DagifiedGraph.html#a1ef9323238f5c634e37a1901fe70cac7',1,'vg::DagifiedGraph::follow_edges_impl()'],['../classvg_1_1DozeuPinningOverlay.html#a8e496a98643c334cd90fb6c637b44a7f',1,'vg::DozeuPinningOverlay::follow_edges_impl()'],['../classvg_1_1ExtraNodeGraph.html#a5a4a8e88008abe18acb3e5365277d571',1,'vg::ExtraNodeGraph::follow_edges_impl()'],['../classvg_1_1SnarlGraph.html#a058d9545317220176574196c0856771c',1,'vg::SnarlGraph::follow_edges_impl()'],['../classvg_1_1IdentityOverlay.html#aeee6d38137e8e42da91d3217c04eb19e',1,'vg::IdentityOverlay::follow_edges_impl()'],['../classvg_1_1IncrementalSubgraph.html#ae130a9900ded50f9e69b24d5201bfcfc',1,'vg::IncrementalSubgraph::follow_edges_impl()'],['../classvg_1_1IndexedVG.html#a8f662f88594725f38108936b3cdd4557',1,'vg::IndexedVG::follow_edges_impl()'],['../classvg_1_1MemoizingGraph.html#aa66371807bdc15cb984bcc4d1c2e9728',1,'vg::MemoizingGraph::follow_edges_impl()'],['../classvg_1_1NullMaskingGraph.html#ab940c4f1423710ee763cc9d354bdf62a',1,'vg::NullMaskingGraph::follow_edges_impl()'],['../classvg_1_1PathSubgraph.html#aba4939b647863200fe9c00a1dd7b29cb',1,'vg::PathSubgraph::follow_edges_impl()'],['../classvg_1_1ReverseGraph.html#aa9254d4034163f9d7eb7c3e54be18cad',1,'vg::ReverseGraph::follow_edges_impl()'],['../classvg_1_1NetGraph.html#af71e4e3a211399f47cb2a5952b6f08af',1,'vg::NetGraph::follow_edges_impl()'],['../classvg_1_1SourceSinkOverlay.html#a3509d1a95f4bce832ebdefd6755f396d',1,'vg::SourceSinkOverlay::follow_edges_impl()'],['../classvg_1_1JoinedSpliceGraph.html#af1e1213617cd63487dc6194a9934a11f',1,'vg::JoinedSpliceGraph::follow_edges_impl()'],['../classvg_1_1StrandSplitGraph.html#aab7d8a7945878c5ff24f186c0cc290aa',1,'vg::StrandSplitGraph::follow_edges_impl()'],['../classvg_1_1SubHandleGraph.html#a4e1ce2518f49205daf2be98a765c79fd',1,'vg::SubHandleGraph::follow_edges_impl()'],['../classvg_1_1SubgraphOverlay.html#a421ab670d9cfbdf1faff768e77b854a0',1,'vg::SubgraphOverlay::follow_edges_impl()'],['../classvg_1_1SubpathOverlay.html#ab4f4b9d7ab05f53920a9d422ecac8a36',1,'vg::SubpathOverlay::follow_edges_impl()'],['../classvg_1_1TreeSubgraph.html#a1da92feba77602818f76b284739b071d',1,'vg::TreeSubgraph::follow_edges_impl()'],['../classvg_1_1VG.html#a4c1118bd664e83254db09ba3e8a3ec3f',1,'vg::VG::follow_edges_impl()'],['../classxg_1_1XG.html#a6c68a283c56d458bbb66d77684be0583',1,'xg::XG::follow_edges_impl()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a5b89d8a4c29cf73a906761257c3f18d0',1,'handlegraph::algorithms::SubHandleGraph::follow_edges_impl()'],['../classhandlegraph_1_1HandleGraph.html#a89bbc118fe1e8e1acb162c14be33e8b5',1,'handlegraph::HandleGraph::follow_edges_impl()']]],
- ['follow_5fnet_5fedges_8956',['follow_net_edges',['../classhandlegraph_1_1SnarlDecomposition.html#a038431d41747c9216de0ed827ce7e919',1,'handlegraph::SnarlDecomposition']]],
- ['follow_5fnet_5fedges_5fimpl_8957',['follow_net_edges_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a5be2bda480dac57d09e1c305ce6c8e20',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_8958',['for_each',['../classvg_1_1Paths.html#ac86fa87134c58faea8d70822fe00990c',1,'vg::Paths::for_each()'],['../classvg_1_1VGset.html#a998c782d65a9abe5610ce86925f91762',1,'vg::VGset::for_each()'],['../classvg_1_1subcommand_1_1Subcommand.html#a00984ebffd918ad9e78bda1686ca035c',1,'vg::subcommand::Subcommand::for_each(const std::function< void(const Subcommand &)> &lambda)'],['../classvg_1_1subcommand_1_1Subcommand.html#ab8948845550b743c7dc1be41d8458e8d',1,'vg::subcommand::Subcommand::for_each(CommandCategory category, const std::function< void(const Subcommand &)> &lambda)'],['../namespacevg_1_1io.html#a08997ecc2a7d17c35a27418b5f21ab3d',1,'vg::io::for_each(std::istream &in, const std::function< void(int64_t, T &)> &lambda, const std::function< void(size_t, size_t)> &progress=NO_PROGRESS)'],['../namespacevg_1_1io.html#a6e19f6d7cb7f7c3d6a396268dcbd8007',1,'vg::io::for_each(std::istream &in, const std::function< void(T &)> &lambda, const std::function< void(size_t, size_t)> &progress=NO_PROGRESS)']]],
- ['for_5feach_5fagglomeration_5finterval_8959',['for_each_agglomeration_interval',['../classvg_1_1MinimizerMapper.html#a59a7bf123788c471bdf900c4b47b5c4a',1,'vg::MinimizerMapper']]],
- ['for_5feach_5fannotation_8960',['for_each_annotation',['../classvg_1_1multipath__alignment__t.html#ac1aec26be5837a73a84df48a70b82a06',1,'vg::multipath_alignment_t']]],
- ['for_5feach_5fbasic_5fannotation_8961',['for_each_basic_annotation',['../namespacevg.html#a8f0eee097c87cbab2bc44f096b463d8b',1,'vg']]],
- ['for_5feach_5fcg_8962',['for_each_cg',['../namespacegafkluge.html#ad32038d9fe60950ec4ba0ee6c05040b3',1,'gafkluge']]],
- ['for_5feach_5fchain_8963',['for_each_chain',['../classvg_1_1SnarlManager.html#a83a481b702deda84aadf24171a860769',1,'vg::SnarlManager']]],
- ['for_5feach_5fchain_5fparallel_8964',['for_each_chain_parallel',['../classvg_1_1SnarlManager.html#a2d3b980bed56de4cc909590a51264a6c',1,'vg::SnarlManager']]],
- ['for_5feach_5fchild_8965',['for_each_child',['../classhandlegraph_1_1SnarlDecomposition.html#a4790373e0405cc715b0116142aefc42e',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5fchild_5fimpl_8966',['for_each_child_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a8dcbdccb1422d034b16da6ff31412d5a',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5fcigar_8967',['for_each_cigar',['../namespacegafkluge.html#ad34ac0b7ed3c066acbc4fb6c82f42475',1,'gafkluge']]],
- ['for_5feach_5fconnected_5fnode_8968',['for_each_connected_node',['../classvg_1_1VG.html#a892abc4056e30044ae9ce0db9e4871f0',1,'vg::VG']]],
- ['for_5feach_5fcs_8969',['for_each_cs',['../namespacegafkluge.html#a97dfb71592c41879c5d3a5abdd4f3276',1,'gafkluge']]],
- ['for_5feach_5fedge_8970',['for_each_edge',['../classvg_1_1DiagramExplainer.html#a9509e0d2a9b1cd5dce5bf058ba9f0511',1,'vg::DiagramExplainer::for_each_edge()'],['../classvg_1_1VG.html#a3d7fdd8c951cbf8b25e116435b5e1e0e',1,'vg::VG::for_each_edge(function< void(Edge *)> lambda)'],['../classvg_1_1VG.html#aed86f57c2e9766da9757e18ef543d35d',1,'vg::VG::for_each_edge(function< void(const Edge *)> lambda) const'],['../classhandlegraph_1_1HandleGraph.html#a61570ded026f825d62ea7608a1e92349',1,'handlegraph::HandleGraph::for_each_edge()']]],
- ['for_5feach_5fedge_5fparallel_8971',['for_each_edge_parallel',['../classvg_1_1VG.html#a46a20aa427767a27fd15d181ccca8c42',1,'vg::VG']]],
- ['for_5feach_5ffilter_8972',['for_each_filter',['../classvg_1_1Funnel.html#afc114c16e43a80739d292e03b65fa8ab',1,'vg::Funnel']]],
- ['for_5feach_5fgff_5frecord_8973',['for_each_gff_record',['../classvg_1_1GFFReader.html#a73afc9447d2bcf2f1ca11de90c822ecb',1,'vg::GFFReader']]],
- ['for_5feach_5fhandle_8974',['for_each_handle',['../classhandlegraph_1_1HandleGraph.html#a928bdeabd328d357b538e30590164ab4',1,'handlegraph::HandleGraph']]],
- ['for_5feach_5fhandle_5fimpl_8975',['for_each_handle_impl',['../classvg_1_1DagifiedGraph.html#af93a535f9e600f583795c7192b16a5af',1,'vg::DagifiedGraph::for_each_handle_impl()'],['../classvg_1_1DozeuPinningOverlay.html#a8433f3777f985ff1307c8f907b7a51d0',1,'vg::DozeuPinningOverlay::for_each_handle_impl()'],['../classvg_1_1ExtraNodeGraph.html#a80dada6b10cc3775bb77962bdae6a3c0',1,'vg::ExtraNodeGraph::for_each_handle_impl()'],['../classvg_1_1SnarlGraph.html#a2312825b11c4c4046e79a35cacadfe27',1,'vg::SnarlGraph::for_each_handle_impl()'],['../classvg_1_1IdentityOverlay.html#ac1eddf95e1828bc39e4422d6fa10f64e',1,'vg::IdentityOverlay::for_each_handle_impl()'],['../classvg_1_1IncrementalSubgraph.html#aabc1cb22610d6c41a79dc91617f785c1',1,'vg::IncrementalSubgraph::for_each_handle_impl()'],['../classvg_1_1IndexedVG.html#a1fd2d5d78e3f3c6e5ae6b8c20ad127ea',1,'vg::IndexedVG::for_each_handle_impl()'],['../classvg_1_1MemoizingGraph.html#a5e0a5d23cda378e3b035b76877a96c2c',1,'vg::MemoizingGraph::for_each_handle_impl()'],['../classvg_1_1NullMaskingGraph.html#a0308e0413cd69b3b4672702a98aef320',1,'vg::NullMaskingGraph::for_each_handle_impl()'],['../classvg_1_1PathSubgraph.html#a4166c30daddecab93040a34fb9d92bd6',1,'vg::PathSubgraph::for_each_handle_impl()'],['../classvg_1_1ReverseGraph.html#af7bef018b5871832fad7c0fe285077a0',1,'vg::ReverseGraph::for_each_handle_impl()'],['../classvg_1_1NetGraph.html#a8a71e3e2d8d35cc230ec809d54a320c7',1,'vg::NetGraph::for_each_handle_impl()'],['../classvg_1_1SourceSinkOverlay.html#a6f4d5b7d57f650585061f5e717163dea',1,'vg::SourceSinkOverlay::for_each_handle_impl()'],['../classvg_1_1JoinedSpliceGraph.html#ada8a6087f4b7bfa2aa6a2d9f88a93d60',1,'vg::JoinedSpliceGraph::for_each_handle_impl()'],['../classvg_1_1StrandSplitGraph.html#aaaac2dfd01ba39cf84f02296e6d5c97c',1,'vg::StrandSplitGraph::for_each_handle_impl()'],['../classvg_1_1SubHandleGraph.html#a39e05cb649e7a0e979751b1287e4d30f',1,'vg::SubHandleGraph::for_each_handle_impl()'],['../classvg_1_1SubgraphOverlay.html#a054f387a6c02302e47815f501034a068',1,'vg::SubgraphOverlay::for_each_handle_impl()'],['../classvg_1_1SubpathOverlay.html#a545dda4c5916239d0f473026324ab5a1',1,'vg::SubpathOverlay::for_each_handle_impl()'],['../classvg_1_1TreeSubgraph.html#a3304940da26d12fd579a72c90f1d0480',1,'vg::TreeSubgraph::for_each_handle_impl()'],['../classvg_1_1VG.html#afa7a11323fdb8a632f4dc5e405e74848',1,'vg::VG::for_each_handle_impl()'],['../classxg_1_1XG.html#af0b6c8a9c8e12575b345ab8a5209874b',1,'xg::XG::for_each_handle_impl()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a62f7884d8f69c4c32304722bf5a7ee8c',1,'handlegraph::algorithms::SubHandleGraph::for_each_handle_impl()'],['../classhandlegraph_1_1HandleGraph.html#af48ba081fcb810267dc50e3a3e7ad391',1,'handlegraph::HandleGraph::for_each_handle_impl()']]],
- ['for_5feach_5fhandle_5fin_5fshortest_5fpath_8976',['for_each_handle_in_shortest_path',['../namespacehandlegraph_1_1algorithms.html#a62990356f8196e5cb3b2e6601cc41eee',1,'handlegraph::algorithms']]],
- ['for_5feach_5fhead_8977',['for_each_head',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ae26744448bb18253ff054565bbed4b14',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['for_5feach_5fid_8978',['for_each_id',['../classvg_1_1StreamIndex.html#a88788f5837112b38e2c182b37efd608e',1,'vg::StreamIndex']]],
- ['for_5feach_5finterleaved_5fpair_5fparallel_8979',['for_each_interleaved_pair_parallel',['../namespacevg_1_1io.html#aeb40cd1227130aa2b23a1a7c91aa7f2d',1,'vg::io']]],
- ['for_5feach_5finterleaved_5fpair_5fparallel_5fafter_5fwait_8980',['for_each_interleaved_pair_parallel_after_wait',['../namespacevg_1_1io.html#aa420d6f551083405c508bee6242ef123',1,'vg::io']]],
- ['for_5feach_5fkmer_8981',['for_each_kmer',['../namespacevg.html#ab3d4de4fa2fda6bfcd6eaa77080c67ad',1,'vg::for_each_kmer()'],['../namespacevg_1_1algorithms.html#a30b8fd7a0d56e1827faa3aa56c8828f0',1,'vg::algorithms::for_each_kmer()']]],
- ['for_5feach_5fkmer_5fparallel_8982',['for_each_kmer_parallel',['../classvg_1_1VGset.html#a8018547ffd3175ab28ebd8fb92b8f842',1,'vg::VGset']]],
- ['for_5feach_5fmapping_8983',['for_each_mapping',['../classvg_1_1Paths.html#a059807c77ba1efd246c25d2070947792',1,'vg::Paths']]],
- ['for_5feach_5fmember_8984',['for_each_member',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a63dbabae3b8851ee15900e79735038b0',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['for_5feach_5fmembership_8985',['for_each_membership',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ae0a46944ed58b73109148a1cf1bd8b79',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['for_5feach_5fname_8986',['for_each_name',['../classvg_1_1Paths.html#a26c3854ce2cfcfd56064077e5062a440',1,'vg::Paths']]],
- ['for_5feach_5fname_5fstoppable_8987',['for_each_name_stoppable',['../classvg_1_1Paths.html#af5231f3d55b57ca9ec341be62d18155d',1,'vg::Paths']]],
- ['for_5feach_5fneighbor_8988',['for_each_neighbor',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a1e63b71aba9a614f17b497908c638797',1,'vg::DozeuInterface::OrderedGraph']]],
- ['for_5feach_5fnode_8989',['for_each_node',['../classvg_1_1VG.html#af585f2161de09403d197e05fbcfb9a07',1,'vg::VG::for_each_node(function< void(Node *)> lambda)'],['../classvg_1_1VG.html#a23b34b164590c0537bf704dd1b816760',1,'vg::VG::for_each_node(function< void(const Node *)> lambda) const']]],
- ['for_5feach_5fnode_5fparallel_8990',['for_each_node_parallel',['../classvg_1_1VG.html#a39790d52fe4c09804086d58164258fcf',1,'vg::VG']]],
- ['for_5feach_5fother_5fmember_8991',['for_each_other_member',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ad0cfb071a138beff3fea1728104beb98',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['for_5feach_5fparallel_8992',['for_each_parallel',['../namespacevg_1_1io.html#a2c3c1dbfdd613d8d70e6354d680b342e',1,'vg::io']]],
- ['for_5feach_5fparallel_5fimpl_8993',['for_each_parallel_impl',['../namespacevg_1_1io.html#a1347d6f25fb95f2e4fd6cf5d2ff7f92d',1,'vg::io']]],
- ['for_5feach_5fpath_5fhandle_8994',['for_each_path_handle',['../classhandlegraph_1_1PathHandleGraph.html#aa3f1d0595543d760322042770201297c',1,'handlegraph::PathHandleGraph']]],
- ['for_5feach_5fpath_5fhandle_5fimpl_8995',['for_each_path_handle_impl',['../classvg_1_1MemoizingGraph.html#a37322d14220aeea194062380da0cc943',1,'vg::MemoizingGraph::for_each_path_handle_impl()'],['../classvg_1_1PathSubgraphOverlay.html#aad99a886a4ea032b781d57c5af6b9e2a',1,'vg::PathSubgraphOverlay::for_each_path_handle_impl()'],['../classvg_1_1VG.html#a527e1ab441e93f73902b7a02b29c1bd6',1,'vg::VG::for_each_path_handle_impl()'],['../classxg_1_1XG.html#aff636eab67405c3c27ba4f2be4f0a6f5',1,'xg::XG::for_each_path_handle_impl()'],['../classhandlegraph_1_1PathHandleGraph.html#a79f48793555f6be311f6df6603324e7b',1,'handlegraph::PathHandleGraph::for_each_path_handle_impl()'],['../classhandlegraph_1_1PathMetadata.html#a8cd1fd8be6b3cd868fc7124181407bd0',1,'handlegraph::PathMetadata::for_each_path_handle_impl()']]],
- ['for_5feach_5fpath_5fmatching_8996',['for_each_path_matching',['../classhandlegraph_1_1PathMetadata.html#a01967c3713408b24ed6c3c20ff2ddd23',1,'handlegraph::PathMetadata::for_each_path_matching(const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) const'],['../classhandlegraph_1_1PathMetadata.html#aef274133ea4ac6c96fd5e5330e2c620c',1,'handlegraph::PathMetadata::for_each_path_matching(const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) const']]],
- ['for_5feach_5fpath_5fmatching_5fimpl_8997',['for_each_path_matching_impl',['../classhandlegraph_1_1PathMetadata.html#af040579085f8d49fcb6733e1f9cc8c27',1,'handlegraph::PathMetadata']]],
- ['for_5feach_5fpath_5fof_5fsample_8998',['for_each_path_of_sample',['../classhandlegraph_1_1PathMetadata.html#a01becc6f1373c256aebdb41cab2e1e2a',1,'handlegraph::PathMetadata']]],
- ['for_5feach_5fpath_5fof_5fsense_8999',['for_each_path_of_sense',['../classhandlegraph_1_1PathMetadata.html#a7afd82569e409e86b4bcdafe8d39cc86',1,'handlegraph::PathMetadata']]],
- ['for_5feach_5fpostorder_9000',['for_each_postorder',['../structvg_1_1TreeNode.html#a28eeb006a851d066d62cb26b93cd4b24',1,'vg::TreeNode::for_each_postorder()'],['../structvg_1_1Tree.html#af5981fac59c0b2549cc0f70b98b675d2',1,'vg::Tree::for_each_postorder()']]],
- ['for_5feach_5fpreorder_9001',['for_each_preorder',['../structvg_1_1TreeNode.html#a52c407f5434c0fa0c7b25b66758b7a75',1,'vg::TreeNode::for_each_preorder()'],['../structvg_1_1Tree.html#a5b5e4073edee56fd62feac705f4ce4e8',1,'vg::Tree::for_each_preorder()']]],
- ['for_5feach_5fread_5finterval_9002',['for_each_read_interval',['../structvg_1_1GaplessExtension.html#a5bc9436d24978ebb2d0df881d0838ff2',1,'vg::GaplessExtension']]],
- ['for_5feach_5fsnarl_5fparallel_9003',['for_each_snarl_parallel',['../classvg_1_1SnarlManager.html#a4b1681aedec889820afa7ba06ca99523',1,'vg::SnarlManager']]],
- ['for_5feach_5fsnarl_5fpreorder_9004',['for_each_snarl_preorder',['../classvg_1_1SnarlManager.html#af8f351725cc98913a211aa9d1535a841',1,'vg::SnarlManager']]],
- ['for_5feach_5fsnarl_5funindexed_9005',['for_each_snarl_unindexed',['../classvg_1_1SnarlManager.html#a053c63fb829fbb9204b1b1a5502e94dd',1,'vg::SnarlManager']]],
- ['for_5feach_5fstage_9006',['for_each_stage',['../classvg_1_1Funnel.html#a6b8e05750253de736a8a44de5932e352',1,'vg::Funnel']]],
- ['for_5feach_5fstep_5fin_5fpath_9007',['for_each_step_in_path',['../classhandlegraph_1_1PathHandleGraph.html#a184353db571dd2086d79e4e31f2f97f1',1,'handlegraph::PathHandleGraph']]],
- ['for_5feach_5fstep_5fof_5fsense_9008',['for_each_step_of_sense',['../classhandlegraph_1_1PathMetadata.html#a85b539a3b2ee842030068d7556be10a1',1,'handlegraph::PathMetadata']]],
- ['for_5feach_5fstep_5fof_5fsense_5fimpl_9009',['for_each_step_of_sense_impl',['../classhandlegraph_1_1PathMetadata.html#a87e4c1bede87504ea011544c3e35651a',1,'handlegraph::PathMetadata']]],
- ['for_5feach_5fstep_5fon_5fhandle_9010',['for_each_step_on_handle',['../classhandlegraph_1_1PathHandleGraph.html#a006a8e3ab9e2783ef7bf80b98b35959c',1,'handlegraph::PathHandleGraph']]],
- ['for_5feach_5fstep_5fon_5fhandle_5fimpl_9011',['for_each_step_on_handle_impl',['../classvg_1_1MemoizingGraph.html#aeff170a12e414f058e658317060798b4',1,'vg::MemoizingGraph::for_each_step_on_handle_impl()'],['../classvg_1_1PathSubgraphOverlay.html#a9e042a3f29d7182fa8510dd46c259b41',1,'vg::PathSubgraphOverlay::for_each_step_on_handle_impl()'],['../classvg_1_1VG.html#a68b4c3665812b5be48d01677367382fd',1,'vg::VG::for_each_step_on_handle_impl()'],['../classxg_1_1XG.html#a0c05acc85982c493ac91b6199ca1cfd4',1,'xg::XG::for_each_step_on_handle_impl()'],['../classhandlegraph_1_1PathHandleGraph.html#a2bbdf56b268001c629cf000f5bd8bb9a',1,'handlegraph::PathHandleGraph::for_each_step_on_handle_impl()'],['../classhandlegraph_1_1PathMetadata.html#a25e78685ad8a987422d9bf6c131c854f',1,'handlegraph::PathMetadata::for_each_step_on_handle_impl()']]],
- ['for_5feach_5fstep_5fposition_5fon_5fhandle_9012',['for_each_step_position_on_handle',['../classvg_1_1MemoizingGraph.html#aca0068b6da055640d5dbc6034aa6aaa4',1,'vg::MemoizingGraph::for_each_step_position_on_handle()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#a5c30215753a62ebaffcbeffe40009829',1,'handlegraph::PathPositionHandleGraph::for_each_step_position_on_handle()']]],
- ['for_5feach_5fstream_9013',['for_each_stream',['../classvg_1_1Paths.html#a8ceb67abc89bd22659c751c946906e23',1,'vg::Paths']]],
- ['for_5feach_5ftippy_5fchild_9014',['for_each_tippy_child',['../classhandlegraph_1_1SnarlDecomposition.html#ac28fd7719d52d2148443d31617ae8a3c',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftippy_5fchild_5fimpl_9015',['for_each_tippy_child_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a0f14086d5470e4a95955e9bc3787574a',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftop_5flevel_5fchain_9016',['for_each_top_level_chain',['../classvg_1_1SnarlManager.html#a4bce7b961c24e5a18c834c6a78df8d2e',1,'vg::SnarlManager']]],
- ['for_5feach_5ftop_5flevel_5fchain_5fparallel_9017',['for_each_top_level_chain_parallel',['../classvg_1_1SnarlManager.html#aba6a74d03b6064e29b7ede95ddb2195d',1,'vg::SnarlManager']]],
- ['for_5feach_5ftop_5flevel_5fsnarl_9018',['for_each_top_level_snarl',['../classvg_1_1SnarlManager.html#ac4cf6c9ca0c953ec32bc3677d3171cf0',1,'vg::SnarlManager']]],
- ['for_5feach_5ftop_5flevel_5fsnarl_5fparallel_9019',['for_each_top_level_snarl_parallel',['../classvg_1_1SnarlManager.html#a458f5a996e7352ae749178d08f575a3e',1,'vg::SnarlManager']]],
- ['for_5feach_5ftraversal_9020',['for_each_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a64144f35a85a36bb472044663bd3a618',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fend_9021',['for_each_traversal_end',['../classhandlegraph_1_1SnarlDecomposition.html#ac7ccef73cd4793c0f303b951352b954b',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fend_5fimpl_9022',['for_each_traversal_end_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a5d7c6809f7636d1afae03c34e4747179',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fimpl_9023',['for_each_traversal_impl',['../classhandlegraph_1_1SnarlDecomposition.html#ac5ea5843f70f1550afe868a8fa1bf2ae',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fstart_9024',['for_each_traversal_start',['../classhandlegraph_1_1SnarlDecomposition.html#a0ccdbfddf02159200884e27ae34af0a8',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5ftraversal_5fstart_5fimpl_9025',['for_each_traversal_start_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a688f4614f5dd84aa01734c5eaf5d0400',1,'handlegraph::SnarlDecomposition']]],
- ['for_5feach_5fwalk_9026',['for_each_walk',['../namespacevg_1_1algorithms.html#ace1ad4f4eccc7041eb1e700463492540',1,'vg::algorithms']]],
- ['for_5fpath_5frange_9027',['for_path_range',['../classxg_1_1XG.html#a2ba1a725e15e5693156a5870701ceac0',1,'xg::XG']]],
- ['force_5fclose_9028',['force_close',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ac677874552857f22f89ee9571eb183db',1,'vg::io::BlockedGzipOutputStream']]],
- ['force_5ffragment_5flength_5fdistr_9029',['force_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ac2731944023ede8d7fb00379ffd8ecbf',1,'vg::PairedEndMapper::force_fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#a7f1925a1c2071ed65c543cc25b4d4f02',1,'vg::MinimizerMapper::force_fragment_length_distr()']]],
- ['force_5fparameters_9030',['force_parameters',['../classvg_1_1FragmentLengthDistribution.html#a5751543486d54066f30e943ec188b279',1,'vg::FragmentLengthDistribution']]],
- ['forest_5fgrowing_5fstate_5ft_9031',['forest_growing_state_t',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a8617325ab6eae778a65b13a4f21bdd16',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['forget_9032',['forget',['../namespacevg_1_1temp__file.html#a478c3b30251f8866550b1497bb22ede4',1,'vg::temp_file::forget()'],['../namespacexg_1_1temp__file.html#ab7efd4c620ca53aecb448de975525885',1,'xg::temp_file::forget()']]],
- ['format_9033',['format',['../classVectorizer.html#a30aa5bafd8a44b2e1259245b6e046062',1,'Vectorizer']]],
- ['format_5fmultiplier_9034',['format_multiplier',['../namespacevg.html#a3ae70effc22331b3e4667ed48808602c',1,'vg']]],
- ['forward_9035',['forward',['../classhandlegraph_1_1HandleGraph.html#a9e946bb4ed53f9423072955cdaab6386',1,'handlegraph::HandleGraph']]],
- ['forward_5foffset_9036',['forward_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a3ffe7fc7ef04c67add8a6fae372dcee9',1,'vg::MinimizerMapper::Minimizer']]],
- ['forward_5fsequence_9037',['forward_sequence',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ae02ecd440346f71b3d36ab8f291abb82',1,'vg::MinimizerMapper::Minimizer']]],
- ['forwardize_5fbreakpoints_9038',['forwardize_breakpoints',['../namespacevg.html#a9e9c975d7bec4a22a46b72736915ceb1',1,'vg']]],
- ['fragment_5fdirection_9039',['fragment_direction',['../classvg_1_1FragmentLengthStatistics.html#af43d1fa0b2d07be1cd3f7d658fa932c5',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fdistr_5fis_5ffinalized_9040',['fragment_distr_is_finalized',['../classvg_1_1MinimizerMapper.html#a692470c7551c4966126aa7bf357e60a4',1,'vg::MinimizerMapper']]],
- ['fragment_5flength_5flog_5flikelihood_9041',['fragment_length_log_likelihood',['../classvg_1_1MultipathMapper.html#ac9fbf8240e86c6753e0a55d89752f70d',1,'vg::MultipathMapper']]],
- ['fragment_5flength_5fmean_9042',['fragment_length_mean',['../classvg_1_1FragmentLengthStatistics.html#a0379d61cc368d8f7cea2babfacb24f06',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fpdf_9043',['fragment_length_pdf',['../classvg_1_1FragmentLengthStatistics.html#a929c0b89511551c913882cc65d4de180',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fpval_9044',['fragment_length_pval',['../classvg_1_1FragmentLengthStatistics.html#a5881926df69d005966f59b6dbead8253',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fstdev_9045',['fragment_length_stdev',['../classvg_1_1FragmentLengthStatistics.html#a83626df3ef00fa066df4fcf22a5c9862',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fmodel_5fstr_9046',['fragment_model_str',['../classvg_1_1FragmentLengthStatistics.html#acdcb4761860132d14be1bbe2da236a69',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5forientation_9047',['fragment_orientation',['../classvg_1_1FragmentLengthStatistics.html#aa486f0551d5848bfaaa304cc1c93d636',1,'vg::FragmentLengthStatistics']]],
- ['fragmentlengthdistribution_9048',['FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html#a8788ddb09653e64eb868cbc942df95c6',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(size_t maximum_sample_size, size_t reestimation_frequency, double robust_estimation_fraction)'],['../classvg_1_1FragmentLengthDistribution.html#a8551fd1f0ad1270145483715f35c7b6b',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(void)']]],
- ['from_5fbacking_9049',['from_backing',['../classvg_1_1ExtraNodeGraph.html#a4d788b60f65afb7c33ae42481d7244ab',1,'vg::ExtraNodeGraph::from_backing()'],['../classvg_1_1ReverseGraph.html#a4f86e4320b018dd684e48250d8c2e455',1,'vg::ReverseGraph::from_backing()'],['../classvg_1_1SourceSinkOverlay.html#ad6d335a0dc7d4d42c7d21a814d79d8eb',1,'vg::SourceSinkOverlay::from_backing()']]],
- ['from_5fbig_5fendian_9050',['from_big_endian',['../structvg_1_1endianness.html#a473244129a68f42dcc05119ffe1132c5',1,'vg::endianness']]],
- ['from_5fenumerators_9051',['from_enumerators',['../classxg_1_1XG.html#a52b214cf4125206aa7d2d43dd3baf4d5',1,'xg::XG']]],
- ['from_5fextension_9052',['from_extension',['../structvg_1_1WFAAlignment.html#ac10be60010c306c84bc522f87e5fd5e5',1,'vg::WFAAlignment']]],
- ['from_5fgfa_9053',['from_gfa',['../classxg_1_1XG.html#a1c89b39930820e72b8365d8984eaf531',1,'xg::XG']]],
- ['from_5fhandle_5fgraph_9054',['from_handle_graph',['../classxg_1_1XG.html#aae49bbd7a7886919ab4adf1629517bb1',1,'xg::XG::from_handle_graph()'],['../namespacevg.html#ae968813905d72a9d49a1822b390cbe5d',1,'vg::from_handle_graph()']]],
- ['from_5fhit_9055',['from_hit',['../namespacevg.html#a61a0d273871a7d0feea0e9f0b1901931',1,'vg']]],
- ['from_5fistream_9056',['from_istream',['../classvg_1_1VG.html#a3c22829197fc65ced4dd2e0f53cb20ff',1,'vg::VG']]],
- ['from_5fkey_5fvalue_9057',['from_key_value',['../structvg_1_1WFAPoint.html#ad32f3fd03ce3f9bb91f2dd7fe1bf52c4',1,'vg::WFAPoint']]],
- ['from_5flength_9058',['from_length',['../classvg_1_1edit__t.html#a5ff1f97ea22b67b22fbc1c1b54c1d2af',1,'vg::edit_t::from_length()'],['../namespacevg.html#a83d1f079508a3ee8a2705773109a5a8e',1,'vg::from_length()']]],
- ['from_5flength_5fafter_5fpos_9059',['from_length_after_pos',['../namespacevg.html#a59b4e98d0d99a9b58b56f0946f49b1ab',1,'vg']]],
- ['from_5flength_5fbefore_5fpos_9060',['from_length_before_pos',['../namespacevg.html#a21d316f0ae049289cacab5117678d6ab',1,'vg']]],
- ['from_5fmap_5fentry_9061',['from_map_entry',['../structvg_1_1WFAPoint.html#aa547dad190435d35174a40b7ed0094f8',1,'vg::WFAPoint']]],
- ['from_5fpath_5fhandle_5fgraph_9062',['from_path_handle_graph',['../classxg_1_1XG.html#a249328f04690e8022442c0ed845dd042',1,'xg::XG::from_path_handle_graph()'],['../namespacevg.html#a0eaa4d69a029a84c1d3028745c84bc4c',1,'vg::from_path_handle_graph()']]],
- ['from_5fproto_5fedit_9063',['from_proto_edit',['../namespacevg.html#a4b8b4c6f298818989d39189d631980a8',1,'vg']]],
- ['from_5fproto_5fmapping_9064',['from_proto_mapping',['../namespacevg.html#a1e6878ce34057ea3c8e8c0deacc1726b',1,'vg']]],
- ['from_5fproto_5fmultipath_5falignment_9065',['from_proto_multipath_alignment',['../namespacevg.html#a8630566250dfefc57ec84cbf6c22c3e2',1,'vg']]],
- ['from_5fproto_5fpath_9066',['from_proto_path',['../namespacevg.html#a01ce1f20da22c85b09e4bae9bf9a3d1f',1,'vg']]],
- ['from_5fproto_5fposition_9067',['from_proto_position',['../namespacevg.html#ae7d3ba6e34f59b610d86a84d0d6c32d1',1,'vg']]],
- ['from_5fsimple_5freverse_9068',['from_simple_reverse',['../classvg_1_1FlowSort.html#a920aae02af49b5fdd03397b70cda0640',1,'vg::FlowSort']]],
- ['from_5fsimple_5freverse_5forientation_9069',['from_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a7d43a991e41fd1af563ee17bfa82dc06',1,'vg::FlowSort']]],
- ['from_5fturtle_9070',['from_turtle',['../classvg_1_1VG.html#a8aef48163c0dd4267d24b629de8a04c8',1,'vg::VG']]],
- ['from_5fvector_9071',['from_vector',['../structvg_1_1varint__vector__t.html#a6a568813ee83039d59a8af1dad7b2138',1,'vg::varint_vector_t::from_vector()'],['../classvg_1_1ZipCode.html#acbad7130678653add25cc79639b0f886',1,'vg::ZipCode::from_vector()']]],
- ['full_9072',['full',['../structvg_1_1GaplessExtension.html#a1d1eb14643690ee92b30b2f0bdb5d82c',1,'vg::GaplessExtension']]],
- ['full_5flength_5fextensions_9073',['full_length_extensions',['../classvg_1_1GaplessExtender.html#a0381d55bcbba7e1ea297dc9a915dac1d',1,'vg::GaplessExtender']]],
- ['fuse_5fspliced_5falignments_9074',['fuse_spliced_alignments',['../namespacevg.html#a5b37106006a0286045cd12f9159ac245',1,'vg']]]
+ ['factorial_5fln_8828',['factorial_ln',['../namespacevg.html#a54a32f7feb38c9f86d7796f0b4f1dac7',1,'vg']]],
+ ['fail_8829',['fail',['../classvg_1_1Funnel.html#a38e1d7d328fe8ea456c2631abffaebb4',1,'vg::Funnel']]],
+ ['false_5fextend_8830',['false_extend',['../structhaplo_1_1haplo__DP__rectangle.html#af4b704f2932b2ce43bddbace287674b8',1,'haplo::haplo_DP_rectangle']]],
+ ['fast_5flinear_5fsort_8831',['fast_linear_sort',['../classvg_1_1FlowSort.html#ab7f9051ee8d6e2118e4da7465c9c2a98',1,'vg::FlowSort']]],
+ ['fasta_5fto_5fvcf_8832',['fasta_to_vcf',['../classvg_1_1NameMapper.html#a73bd759074f9643a838c020f17120432',1,'vg::NameMapper']]],
+ ['faster_5fcap_8833',['faster_cap',['../classvg_1_1MinimizerMapper.html#a720abb2308e147350b147da0781f8f21',1,'vg::MinimizerMapper']]],
+ ['fastq_5fpaired_5finterleaved_5ffor_5feach_8834',['fastq_paired_interleaved_for_each',['../namespacevg.html#a0213498a2e9a6cc5c9cb64d30754b4c5',1,'vg']]],
+ ['fastq_5fpaired_5finterleaved_5ffor_5feach_5fparallel_8835',['fastq_paired_interleaved_for_each_parallel',['../namespacevg.html#a49b9a6f2e5573cf854f631ee6f314cbf',1,'vg']]],
+ ['fastq_5fpaired_5finterleaved_5ffor_5feach_5fparallel_5fafter_5fwait_8836',['fastq_paired_interleaved_for_each_parallel_after_wait',['../namespacevg.html#afcbfef4da296d2545850a22e542ea546',1,'vg']]],
+ ['fastq_5fpaired_5ftwo_5ffiles_5ffor_5feach_8837',['fastq_paired_two_files_for_each',['../namespacevg.html#a7112300f258fd0f25fea0ecf56579373',1,'vg']]],
+ ['fastq_5fpaired_5ftwo_5ffiles_5ffor_5feach_5fparallel_8838',['fastq_paired_two_files_for_each_parallel',['../namespacevg.html#a32aee624484aa44bb893f82b03169a3e',1,'vg']]],
+ ['fastq_5fpaired_5ftwo_5ffiles_5ffor_5feach_5fparallel_5fafter_5fwait_8839',['fastq_paired_two_files_for_each_parallel_after_wait',['../namespacevg.html#a47574d693a9ae86d771ea34a0c91afaa',1,'vg']]],
+ ['fastq_5funpaired_5ffor_5feach_8840',['fastq_unpaired_for_each',['../namespacevg.html#a68d737fbcb121fa0192309596a9eddf9',1,'vg']]],
+ ['fastq_5funpaired_5ffor_5feach_5fparallel_8841',['fastq_unpaired_for_each_parallel',['../namespacevg.html#a45ce2f6fbc86f1fab63f3eb22eb9a124',1,'vg']]],
+ ['fdinbuf_8842',['fdinbuf',['../classvg_1_1io_1_1fdinbuf.html#a8ae41cbaad91f66b63085182afa3f657',1,'vg::io::fdinbuf']]],
+ ['fdistream_8843',['fdistream',['../classvg_1_1io_1_1fdistream.html#acdb9ac3f7b60bb31c8a4d1ff307688f4',1,'vg::io::fdistream']]],
+ ['fdostream_8844',['fdostream',['../classvg_1_1io_1_1fdostream.html#a8549f4b673b255a447cad6a06c587ec7',1,'vg::io::fdostream']]],
+ ['fdoutbuf_8845',['fdoutbuf',['../classvg_1_1io_1_1fdoutbuf.html#a4761de2464fb50257c74d5e6e5a13fad',1,'vg::io::fdoutbuf']]],
+ ['field_8846',['field',['../classvg_1_1TSVExplainer.html#a855b258874af7d9be7db4ffb3ecebcc1',1,'vg::TSVExplainer::field(const std::string &value)'],['../classvg_1_1TSVExplainer.html#a0ff0223ddab66b4a904c291e208eb5f5',1,'vg::TSVExplainer::field(size_t value)']]],
+ ['file_5fbase_5fname_8847',['file_base_name',['../namespacevg.html#aeaf52003fcf4fa34ded0aeabafacb3fc',1,'vg']]],
+ ['file_5fexists_8848',['file_exists',['../namespacevg.html#abebdd1477a436020f3d3f8368d825054',1,'vg']]],
+ ['fill_5fbuffer_8849',['fill_buffer',['../classvg_1_1VcfBuffer.html#afff803310f8c3bca9788b30ebba8450f',1,'vg::VcfBuffer']]],
+ ['fill_5fin_5fdistance_5findex_8850',['fill_in_distance_index',['../namespacevg.html#ac7b8c3e17638ecacbdf519c4095bc20e',1,'vg']]],
+ ['fill_5fin_5fforest_8851',['fill_in_forest',['../classvg_1_1ZipCodeForest.html#abeea5f048e6e7711971b764591ee63ec',1,'vg::ZipCodeForest']]],
+ ['fill_5fin_5ffull_5fdecoder_8852',['fill_in_full_decoder',['../classvg_1_1ZipCode.html#aea9e1d42e1a0b31941401212fd87d76a',1,'vg::ZipCode']]],
+ ['fill_5fin_5fnext_5fdecoder_8853',['fill_in_next_decoder',['../classvg_1_1ZipCode.html#a020fef499f038a3dac191667b2fb8e16',1,'vg::ZipCode']]],
+ ['fill_5fin_5fzipcode_8854',['fill_in_zipcode',['../classvg_1_1ZipCode.html#ac232fe003bd30dfbba804cf0bc81b580',1,'vg::ZipCode']]],
+ ['fill_5fin_5fzipcode_5ffrom_5fpayload_8855',['fill_in_zipcode_from_payload',['../classvg_1_1ZipCode.html#ad53005c4c44463b1226835f7f7da83e0',1,'vg::ZipCode']]],
+ ['fill_5fmatrix_8856',['fill_matrix',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a54be0f91b1460bbd03e87e6da6be6e32',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['fill_5fnode_5fto_5fposition_8857',['fill_node_to_position',['../classvg_1_1Filter.html#ac7216130c6fbd20580901090f8185048',1,'vg::Filter']]],
+ ['fill_5fvalue_8858',['fill_value',['../classvg_1_1io_1_1ProtobufIterator.html#aec100b14b027d294e2a0aaaaad3b4abd',1,'vg::io::ProtobufIterator']]],
+ ['filter_8859',['Filter',['../classvg_1_1Filter.html#a1a9dadc8fe8b9abe295373627e033b89',1,'vg::Filter::Filter()'],['../classvg_1_1ReadFilter.html#a36c3ff48009706f3853bddd02a98de9c',1,'vg::ReadFilter::filter(istream *alignment_stream)'],['../classvg_1_1ReadFilter.html#a1fb619abfe77d0b02cc7f8aa4ad47af5',1,'vg::ReadFilter::filter(istream *alignment_stream)'],['../classvg_1_1ReadFilter.html#ab56d51dbf343ea44e78c31d54f1f317f',1,'vg::ReadFilter::filter(istream *alignment_stream)']]],
+ ['filter_5falignment_8860',['filter_alignment',['../classvg_1_1ReadFilter.html#a1398f727931b41bfff0d9e058f442ebc',1,'vg::ReadFilter']]],
+ ['filter_5fand_5fprocess_5fmultimaps_8861',['filter_and_process_multimaps',['../classvg_1_1Mapper.html#a7b5db2f8b56cb6210431cc7d0d25a18f',1,'vg::Mapper']]],
+ ['filter_5fbreakpoints_5fby_5fcoverage_8862',['filter_breakpoints_by_coverage',['../namespacevg.html#a5ddba9dd6dcb384cbbea06c535e00d6d',1,'vg']]],
+ ['filter_5fhits_5fto_8863',['filter_hits_to',['../classvg_1_1MaximalExactMatch.html#a106b116185bf9cc3e3e675ce0ed81da0',1,'vg::MaximalExactMatch']]],
+ ['filter_5finternal_8864',['filter_internal',['../classvg_1_1ReadFilter.html#a3220ffe3aa6042a1423c6251c95a2b05',1,'vg::ReadFilter']]],
+ ['filter_5flocal_5fvariants_8865',['filter_local_variants',['../classvg_1_1VariantAdder.html#ae72dcbf9e0cb036aa675ad9db3bcf286',1,'vg::VariantAdder']]],
+ ['filter_5fredundant_5fpath_5fchunks_8866',['filter_redundant_path_chunks',['../classvg_1_1Surjector.html#ac1ef0f552e2bd46b48a773837cee6c7c',1,'vg::Surjector']]],
+ ['final_5foffset_8867',['final_offset',['../structvg_1_1WFAAlignment.html#a572300197e78708a3aa53c598f76a932',1,'vg::WFAAlignment']]],
+ ['final_5fposition_8868',['final_position',['../namespacevg.html#ad435098725ff21d822052abee009d2bd',1,'vg::final_position(const Path &path)'],['../namespacevg.html#a28e15d36e2ee202f8a194cca31d91d65',1,'vg::final_position(const path_t &path)']]],
+ ['finalize_8869',['finalize',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a43e6001b25d634ccd6e3fd026c970b45',1,'vg::NGSSimulator::MarkovDistribution::finalize()'],['../classvg_1_1NGSSimulator.html#ab5cda05ad8931a60efd9f19c3889b0d2',1,'vg::NGSSimulator::finalize()']]],
+ ['finalize_5falignment_8870',['finalize_alignment',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#aa88bda9825a69406a7913f4a911cc242',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['finalize_5ffragment_5flength_5fdistr_8871',['finalize_fragment_length_distr',['../classvg_1_1MinimizerMapper.html#a4ae627a418357792cd5b9f6d6b9cc19c',1,'vg::MinimizerMapper']]],
+ ['find_8872',['find',['../classvg_1_1IndexedVG.html#a7a77bdb39f0fd7e1ad73df9539ce1471',1,'vg::IndexedVG::find()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#aa4010a6423dd9c113ad7949be709eefb',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::find()'],['../classvg_1_1StreamIndexBase.html#a7c332ce59d0a99ac7c2ef69d77b0f749',1,'vg::StreamIndexBase::find(id_t node_id) const'],['../classvg_1_1StreamIndexBase.html#ad520b5b3241ee162ffd02c2cac5bd702',1,'vg::StreamIndexBase::find(id_t node_id, const function< bool(int64_t, int64_t)> scan_callback) const'],['../classvg_1_1StreamIndexBase.html#a6448cab1126089223a17c2ed6d943a97',1,'vg::StreamIndexBase::find(id_t min_node, id_t max_node, const function< bool(int64_t, int64_t)> scan_callback) const'],['../classvg_1_1StreamIndex.html#ab459a3f4f93a448b0d7a49238927cc0f',1,'vg::StreamIndex::find(cursor_t &cursor, id_t node_id, const function< void(const Message &)> handle_result) const'],['../classvg_1_1StreamIndex.html#a62f171f0ffa154ab0fed67e277a6d73e',1,'vg::StreamIndex::find(cursor_t &cursor, id_t min_node, id_t max_node, const function< void(const Message &)> handle_result) const'],['../classvg_1_1StreamIndex.html#afcbd0c740c5257066ac0cffa1215eafe',1,'vg::StreamIndex::find(cursor_t &cursor, const vector< pair< id_t, id_t >> &ranges, const function< void(const Message &)> handle_result, bool only_fully_contained=false) const']]],
+ ['find_5fallele_5ftraversals_8873',['find_allele_traversals',['../classvg_1_1VCFTraversalFinder.html#ad660814265b5989408dace8da768edfe',1,'vg::VCFTraversalFinder']]],
+ ['find_5fanchor_5fintervals_8874',['find_anchor_intervals',['../namespacevg.html#a6058ba7e46dc3e0b34b06ff01ed5f22d',1,'vg']]],
+ ['find_5fbackbone_8875',['find_backbone',['../classvg_1_1RepresentativeTraversalFinder.html#aacdab17c6c32685e0ed3f8f0c221453e',1,'vg::RepresentativeTraversalFinder']]],
+ ['find_5fbanded_5fpaths_8876',['find_banded_paths',['../classvg_1_1BandedGlobalAligner.html#adfad0975f34dcf90211d239ee6c126a8',1,'vg::BandedGlobalAligner']]],
+ ['find_5fbare_5floaders_8877',['find_bare_loaders',['../classvg_1_1io_1_1Registry.html#a45bd0585d64d2ff1751463333a21b47d',1,'vg::io::Registry']]],
+ ['find_5fbest_5fchain_8878',['find_best_chain',['../namespacevg_1_1algorithms.html#ac3f3eeb71fb9bd08889b08aa20fe9605',1,'vg::algorithms']]],
+ ['find_5fbest_5fchains_8879',['find_best_chains',['../namespacevg_1_1algorithms.html#a67dc5da4c5935ba307303798c521c1c8',1,'vg::algorithms']]],
+ ['find_5fbreakpoints_8880',['find_breakpoints',['../namespacevg.html#ac80bc94af296d0a543d983eae79afac0',1,'vg']]],
+ ['find_5fbubble_8881',['find_bubble',['../classvg_1_1NestedTraversalFinder.html#ad9fd7aef8b98fdc56b429e4613113c6f',1,'vg::NestedTraversalFinder::find_bubble()'],['../classvg_1_1RepresentativeTraversalFinder.html#ad8cc120dc63491eadfdc7b00cd1dc519',1,'vg::RepresentativeTraversalFinder::find_bubble()']]],
+ ['find_5fchain_5falignment_8882',['find_chain_alignment',['../classvg_1_1MinimizerMapper.html#a3b83e5072a6a0654ba90ed097e8e7a52',1,'vg::MinimizerMapper']]],
+ ['find_5fconstriction_5fbicliques_8883',['find_constriction_bicliques',['../classvg_1_1Surjector.html#a54b0b7fe9db83a6cfdbebf9dbeb81f04',1,'vg::Surjector']]],
+ ['find_5fcycle_5fpath_5fin_5fcactus_8884',['find_cycle_path_in_cactus',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#af554cefbab4c2bd70529342b2916d30e',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['find_5fedges_5fto_5fprune_8885',['find_edges_to_prune',['../namespacevg_1_1algorithms.html#a8529f1718d5f0330dbb301d1148f12e1',1,'vg::algorithms']]],
+ ['find_5fexisting_5fsequence_5fid_8886',['find_existing_sequence_id',['../classvg_1_1algorithms_1_1GFAParser.html#a8cc4a34d40334bb97f7af561db414e33',1,'vg::algorithms::GFAParser']]],
+ ['find_5ffanout_5fmems_8887',['find_fanout_mems',['../classvg_1_1BaseMapper.html#aeb048d786d78b3a545f724bf45cf11d6',1,'vg::BaseMapper']]],
+ ['find_5fgbwt_8888',['find_gbwt',['../namespacevg_1_1algorithms.html#a92780d34d13ab2a6be9fe477543179ce',1,'vg::algorithms::find_gbwt(const HandleGraph *graph)'],['../namespacevg_1_1algorithms.html#a5783b30c1ad6ea3ff4bc4576f447b615',1,'vg::algorithms::find_gbwt(const HandleGraph *graph, std::unique_ptr< gbwt::GBWT > &holder, const std::string &filename)']]],
+ ['find_5fgbwt_5ftraversals_8889',['find_gbwt_traversals',['../classvg_1_1GBWTTraversalFinder.html#ac924b0bf3140cb64411f1e1123effff6',1,'vg::GBWTTraversalFinder::find_gbwt_traversals(const Snarl &site, bool return_paths=true)'],['../classvg_1_1GBWTTraversalFinder.html#aec2c482e376c389df848610dc5fec3db',1,'vg::GBWTTraversalFinder::find_gbwt_traversals(const handle_t &snarl_start, const handle_t &snarl_end, bool return_paths=true)']]],
+ ['find_5fgbwtgraph_8890',['find_gbwtgraph',['../namespacevg_1_1algorithms.html#a1e8867ea22636dc22aa53bd8fe1d0aaa',1,'vg::algorithms']]],
+ ['find_5fgroup_8891',['find_group',['../classvg_1_1SparseUnionFind.html#ae5dcefb7ec434f8405094360b49ebae1',1,'vg::SparseUnionFind']]],
+ ['find_5fin_5forientation_8892',['find_in_orientation',['../structvg_1_1PathIndex.html#ae448ae2af8e4073b9db8b678e3b97e00',1,'vg::PathIndex']]],
+ ['find_5fin_5fout_5fweb_8893',['find_in_out_web',['../classvg_1_1FlowSort.html#aa5e485f218cdc874e5519ef61843358c',1,'vg::FlowSort']]],
+ ['find_5findex_8894',['find_index',['../classvg_1_1LegacyCaller.html#a280eb6052ea0781644047711b7fb17d4',1,'vg::LegacyCaller']]],
+ ['find_5fkmer_8895',['find_kmer',['../namespacevg.html#afdd5134ae715117de1b7ba9283fa8651',1,'vg']]],
+ ['find_5floader_8896',['find_loader',['../classvg_1_1io_1_1Registry.html#a7414063ac702dd6cbe8a7149a49be922',1,'vg::io::Registry']]],
+ ['find_5fmapping_8897',['find_mapping',['../classvg_1_1Paths.html#a9403cc6f97e199f03b365f9a7eb1de63',1,'vg::Paths']]],
+ ['find_5fmax_5fnode_8898',['find_max_node',['../classvg_1_1FlowSort.html#ab05b9f1737b5cef5e719a33d150b7529',1,'vg::FlowSort']]],
+ ['find_5fmems_8899',['find_mems',['../classvg_1_1MultipathMapper.html#af1bca7d5555a38a74cb04a362268b972',1,'vg::MultipathMapper']]],
+ ['find_5fmems_5fdeep_8900',['find_mems_deep',['../classvg_1_1BaseMapper.html#af64a7b36c1880606372d0849842708b0',1,'vg::BaseMapper']]],
+ ['find_5fmems_5fsimple_8901',['find_mems_simple',['../classvg_1_1BaseMapper.html#a4dd3272837211543ba461472833734a9',1,'vg::BaseMapper']]],
+ ['find_5fminimizers_8902',['find_minimizers',['../classvg_1_1MinimizerMapper.html#af3e5c53b0250173b6d0eb097cf884986',1,'vg::MinimizerMapper']]],
+ ['find_5fmismatches_8903',['find_mismatches',['../namespacevg.html#a050aedf4b2e047e04f31a6e8b7ad55ce',1,'vg']]],
+ ['find_5fnamed_5ftraversals_8904',['find_named_traversals',['../classvg_1_1PathRestrictedTraversalFinder.html#ab046472d6a0a26a52c91574e7a09373d',1,'vg::PathRestrictedTraversalFinder']]],
+ ['find_5fnode_5fby_5fname_5for_5fadd_5fnew_8905',['find_node_by_name_or_add_new',['../classvg_1_1VG.html#a04774a86b07508e9e5955abfba2171ff',1,'vg::VG']]],
+ ['find_5foptimal_5ftail_5falignments_8906',['find_optimal_tail_alignments',['../classvg_1_1MinimizerMapper.html#a4247391b8d74dc68b48a792a31ed6d60',1,'vg::MinimizerMapper']]],
+ ['find_5fpacked_5fbreakpoints_8907',['find_packed_breakpoints',['../namespacevg.html#a808481f23dac7bc58c339cf36a9a0aaf',1,'vg']]],
+ ['find_5fpath_5ftraversals_8908',['find_path_traversals',['../classvg_1_1PathTraversalFinder.html#a4adb802f78ec1893954d052156953541',1,'vg::PathTraversalFinder::find_path_traversals(const Snarl &site)'],['../classvg_1_1PathTraversalFinder.html#a4e1ad0b033b6fb33991f70271a252749',1,'vg::PathTraversalFinder::find_path_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../classvg_1_1GBWTTraversalFinder.html#aaabea1b758eb8fecbefe2e5966971b47',1,'vg::GBWTTraversalFinder::find_path_traversals(const Snarl &site)'],['../classvg_1_1GBWTTraversalFinder.html#ae5c1c58803837ee498776e964039440d',1,'vg::GBWTTraversalFinder::find_path_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../namespacevg.html#a3b97a34752ff7bf3c8c2c524c84796df',1,'vg::find_path_traversals()']]],
+ ['find_5fpos_8909',['find_pos',['../structvg_1_1WFANode.html#a4460062120b4153f4ea19b4bfc916ef5',1,'vg::WFANode::find_pos()'],['../classvg_1_1WFATree.html#af216283dfd08d2cee4b17d418d0aa98d',1,'vg::WFATree::find_pos()']]],
+ ['find_5fposition_8910',['find_position',['../structvg_1_1PathIndex.html#a377bc15c246c708fe4a0264cb05588af',1,'vg::PathIndex']]],
+ ['find_5frescuable_5fspliced_5falignments_8911',['find_rescuable_spliced_alignments',['../classvg_1_1MultipathMapper.html#a10cf9d266ae6da1651c9d07a7fc5f14d',1,'vg::MultipathMapper']]],
+ ['find_5fsaver_8912',['find_saver',['../classvg_1_1io_1_1Registry.html#acfad8c6a18a1443150d0818fe1a14857',1,'vg::io::Registry']]],
+ ['find_5fseeds_8913',['find_seeds',['../classvg_1_1MinimizerMapper.html#a8e760f140ec23f170d4a6643fa44ce58',1,'vg::MinimizerMapper']]],
+ ['find_5fshortest_5fpaths_8914',['find_shortest_paths',['../namespacehandlegraph_1_1algorithms.html#af7d99cdf4ea48244031b209b483c8e6a',1,'handlegraph::algorithms']]],
+ ['find_5fsnarls_8915',['find_snarls',['../classvg_1_1CactusSnarlFinder.html#a3060bcff3b01e21176f17ebb74d31452',1,'vg::CactusSnarlFinder::find_snarls()'],['../classvg_1_1SnarlFinder.html#a28d2aa85a748836df818c8c4ac8a8fd9',1,'vg::SnarlFinder::find_snarls()'],['../classvg_1_1HandleGraphSnarlFinder.html#a3b6820315dc0a0a15fcd61076f87fcf7',1,'vg::HandleGraphSnarlFinder::find_snarls()']]],
+ ['find_5fsnarls_5fimpl_8916',['find_snarls_impl',['../classvg_1_1CactusSnarlFinder.html#a9ff89d5f26398349404796d325b32f69',1,'vg::CactusSnarlFinder']]],
+ ['find_5fsnarls_5fparallel_8917',['find_snarls_parallel',['../classvg_1_1CactusSnarlFinder.html#a712cd81719c13a172c3da46349419524',1,'vg::CactusSnarlFinder::find_snarls_parallel()'],['../classvg_1_1IntegratedSnarlFinder.html#a42a292777287dc89cdb9e58bbe5c50b8',1,'vg::IntegratedSnarlFinder::find_snarls_parallel()'],['../classvg_1_1SnarlFinder.html#a7b8b315c1129de42cfb3120de7281291',1,'vg::SnarlFinder::find_snarls_parallel()']]],
+ ['find_5fsnarls_5funindexed_8918',['find_snarls_unindexed',['../classvg_1_1HandleGraphSnarlFinder.html#af4fb35065d83a2ed2f4daa687c114dbc',1,'vg::HandleGraphSnarlFinder']]],
+ ['find_5fspliced_5falignments_8919',['find_spliced_alignments',['../classvg_1_1MultipathMapper.html#ad907bb6d98eaa48a8a013ddfb0fd7449',1,'vg::MultipathMapper::find_spliced_alignments(const Alignment &alignment, vector< multipath_alignment_t > &multipath_alns_out, vector< double > &multiplicities, vector< size_t > &cluster_idxs, const vector< MaximalExactMatch > &mems, vector< clustergraph_t > &cluster_graphs, const match_fanouts_t *fanouts=nullptr, const multipath_alignment_t *rescue_anchor=nullptr, bool rescue_left=false, double rescue_multiplicity=1.0)'],['../classvg_1_1MultipathMapper.html#ad33f09dde45f1498ffa1ac6996cc0c6d',1,'vg::MultipathMapper::find_spliced_alignments(const Alignment &alignment1, const Alignment &alignment2, vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs_out, vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, vector< double > &pair_multiplicities, const vector< MaximalExactMatch > &mems1, const vector< MaximalExactMatch > &mems2, vector< clustergraph_t > &cluster_graphs1, vector< clustergraph_t > &cluster_graphs2, const match_fanouts_t *fanouts=nullptr)']]],
+ ['find_5fstripped_5fmatches_8920',['find_stripped_matches',['../classvg_1_1BaseMapper.html#ad0ca6fe6e3a407bd1bff38bb05cbe794',1,'vg::BaseMapper']]],
+ ['find_5fsub_5fmems_8921',['find_sub_mems',['../classvg_1_1BaseMapper.html#a77079f609cab775e59ff0750ef9e84d9',1,'vg::BaseMapper']]],
+ ['find_5fsub_5fmems_5ffast_8922',['find_sub_mems_fast',['../classvg_1_1BaseMapper.html#a81fa3eae0321720511b1f54fa28968bb',1,'vg::BaseMapper']]],
+ ['find_5ftips_8923',['find_tips',['../namespacehandlegraph_1_1algorithms.html#a4339886e547b09009bf391d77596c280',1,'handlegraph::algorithms']]],
+ ['find_5ftranslation_8924',['find_translation',['../namespacevg_1_1algorithms.html#af38c05b9c1e56c79faccfbbf6b3ade95',1,'vg::algorithms']]],
+ ['find_5ftraversals_8925',['find_traversals',['../classvg_1_1NestedTraversalFinder.html#a491e535921c67bb8891a99aa314b6e94',1,'vg::NestedTraversalFinder::find_traversals()'],['../classvg_1_1TraversalFinder.html#a53611f0deaac0fcfb0a440f272c69637',1,'vg::TraversalFinder::find_traversals(const Snarl &site)=0'],['../classvg_1_1TraversalFinder.html#a41ed015cfd3f95104f530943e643e883',1,'vg::TraversalFinder::find_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../classvg_1_1ExhaustiveTraversalFinder.html#a47d24a43aef54ca51318b8ae89e51328',1,'vg::ExhaustiveTraversalFinder::find_traversals()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#ad97b9e1c48374c3212621422f0ce0d9c',1,'vg::ReadRestrictedTraversalFinder::find_traversals()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a78b03570bd5d59d3c870bbd192eae685',1,'vg::PathRestrictedTraversalFinder::find_traversals()'],['../classvg_1_1PathBasedTraversalFinder.html#af58be82fdbce530b2662a6329e08bd77',1,'vg::PathBasedTraversalFinder::find_traversals()'],['../classvg_1_1PathTraversalFinder.html#a3da29145d1ed82d950bdeb895d3b3bf4',1,'vg::PathTraversalFinder::find_traversals(const Snarl &site)'],['../classvg_1_1PathTraversalFinder.html#ab67194f7b0302ae860bb9e802d2ebfc8',1,'vg::PathTraversalFinder::find_traversals(const handle_t &snarl_start, const handle_t &snarl_end)'],['../classvg_1_1TrivialTraversalFinder.html#ae1b3ebce09b8641fe713cc9628909bfe',1,'vg::TrivialTraversalFinder::find_traversals()'],['../classvg_1_1RepresentativeTraversalFinder.html#ae2280a86a06849b3c4ae0dfef3fe85c0',1,'vg::RepresentativeTraversalFinder::find_traversals()'],['../classvg_1_1VCFTraversalFinder.html#acd33847fcb02a4ea1eb6bd2768549daf',1,'vg::VCFTraversalFinder::find_traversals()'],['../classvg_1_1FlowTraversalFinder.html#a3bf6dff88b07d23e8877ed263d951d40',1,'vg::FlowTraversalFinder::find_traversals()'],['../classvg_1_1GBWTTraversalFinder.html#a3f4f3f644df9755b387bab551451827d',1,'vg::GBWTTraversalFinder::find_traversals(const Snarl &site)'],['../classvg_1_1GBWTTraversalFinder.html#af15fc7ee19296e40cf7b101293a61b26',1,'vg::GBWTTraversalFinder::find_traversals(const handle_t &snarl_start, const handle_t &snarl_end)']]],
+ ['find_5fweighted_5ftraversals_8926',['find_weighted_traversals',['../classvg_1_1FlowTraversalFinder.html#aea197651f2464c68fe06eab925ec8744',1,'vg::FlowTraversalFinder']]],
+ ['finish_8927',['finish',['../structvg_1_1RecombinatorHaplotype.html#acc9e723823910751f19553857c10acf4',1,'vg::RecombinatorHaplotype::finish()'],['../classvg_1_1SnarlManager.html#aacf5fd439b35298107ddf2900559259c',1,'vg::SnarlManager::finish()'],['../namespacevg_1_1io.html#a9b562b3e8bd001bb10bcd0353bf5a929',1,'vg::io::finish()']]],
+ ['finish_5fcurrent_5fedit_8928',['finish_current_edit',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a7bafadc0a8c3160bcc2b3949edc3de17',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['finish_5fcurrent_5fnode_8929',['finish_current_node',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#ad460ee763b7b15cf8206038283423e89',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['first_5fmapping_5fquality_5fapprox_8930',['first_mapping_quality_approx',['../classvg_1_1GSSWAligner.html#a20cfadad5c8d3807320cd206427ef243',1,'vg::GSSWAligner']]],
+ ['first_5fmapping_5fquality_5fexact_8931',['first_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#a25cb693e3eb45f8c7d1e0ae7c6dcf0af',1,'vg::GSSWAligner']]],
+ ['first_5fpath_5fposition_8932',['first_path_position',['../namespacevg.html#ada7557d06abd0fca3d66f9ca73fe81db',1,'vg']]],
+ ['fit_5ffixed_5frate_5fmax_5fexponential_8933',['fit_fixed_rate_max_exponential',['../namespacevg.html#a4b47bdda079acc49d455953a91db12bd',1,'vg']]],
+ ['fit_5ffixed_5fshape_5fmax_5fexponential_8934',['fit_fixed_shape_max_exponential',['../namespacevg.html#a79672e0d9b7e8abdb60ec0f181eec6f0',1,'vg']]],
+ ['fit_5fmax_5fexponential_8935',['fit_max_exponential',['../namespacevg.html#aafca6820103f98f205de4774a9d35f09',1,'vg']]],
+ ['fit_5foffset_5fweibull_8936',['fit_offset_weibull',['../namespacevg.html#ad9f14b8e66ba0c5c28961e8da4aba4b6',1,'vg']]],
+ ['fit_5fweibull_8937',['fit_weibull',['../namespacevg.html#aa64cff8c9c4b3c3baefb49c57614643d',1,'vg']]],
+ ['fit_5fzipf_8938',['fit_zipf',['../namespacevg.html#a9fa3b08acc22f29ea5d940317f6948ab',1,'vg']]],
+ ['fix_5fdozeu_5fend_5fdeletions_8939',['fix_dozeu_end_deletions',['../classvg_1_1MinimizerMapper.html#a4ec441e3df74303c16a60529f08cb70a',1,'vg::MinimizerMapper']]],
+ ['fix_5fdozeu_5fscore_8940',['fix_dozeu_score',['../classvg_1_1MinimizerMapper.html#ab6a0d266ef94fbda125ebdde64617c84',1,'vg::MinimizerMapper']]],
+ ['flag_5frepetitive_5fminimizers_8941',['flag_repetitive_minimizers',['../classvg_1_1MinimizerMapper.html#a26fbad6474a8510b5154bbe0e11f6794',1,'vg::MinimizerMapper']]],
+ ['flatfilebacktranslation_8942',['FlatFileBackTranslation',['../classvg_1_1FlatFileBackTranslation.html#aceb24b5209b6448ae6f36080e9f676d3',1,'vg::FlatFileBackTranslation']]],
+ ['flatten_5falt_5fallele_8943',['flatten_alt_allele',['../classvg_1_1NestedFlowCaller.html#ace4500b677170eff3c9c9f556425ac23',1,'vg::NestedFlowCaller']]],
+ ['flatten_5fcommon_5fallele_5fends_8944',['flatten_common_allele_ends',['../classvg_1_1VCFOutputCaller.html#aa2d19e56299e843d868e8e5fa5b45d49',1,'vg::VCFOutputCaller::flatten_common_allele_ends()'],['../classvg_1_1MCMCCaller.html#ab238d542ffad3a3919dfc873ed39e54a',1,'vg::MCMCCaller::flatten_common_allele_ends()']]],
+ ['flatten_5fdistance_5ftree_8945',['flatten_distance_tree',['../classvg_1_1OrientedDistanceClusterer.html#aa31d8ef9e3eb3de2724b4a4a04452da1',1,'vg::OrientedDistanceClusterer']]],
+ ['flatten_5freference_5fallele_8946',['flatten_reference_allele',['../classvg_1_1NestedFlowCaller.html#aeb2b3e99d2ab50bcfb12874148cb644d',1,'vg::NestedFlowCaller']]],
+ ['flip_8947',['flip',['../classvg_1_1DagifiedGraph.html#a570cd39e720ecbaadb6ff49ae3f0e23e',1,'vg::DagifiedGraph::flip()'],['../classvg_1_1DozeuPinningOverlay.html#aa28af0d1bfc6cc3952bec3904b688e7a',1,'vg::DozeuPinningOverlay::flip()'],['../classvg_1_1ExtraNodeGraph.html#a755ee2394bad62e0f4e6d17aa0212a72',1,'vg::ExtraNodeGraph::flip()'],['../structvg_1_1WFAAlignment.html#a40b15ca8baa18801c97277da6e830810',1,'vg::WFAAlignment::flip()'],['../classvg_1_1SnarlGraph.html#afacfbb0fb244f3004ff0d8c9fbf76f37',1,'vg::SnarlGraph::flip()'],['../classvg_1_1IdentityOverlay.html#a34ea51454cdd3a12d73992563f514f02',1,'vg::IdentityOverlay::flip()'],['../classvg_1_1IncrementalSubgraph.html#a1dad5cc9948fd536f67bdd2f40ef6765',1,'vg::IncrementalSubgraph::flip()'],['../classvg_1_1IndexedVG.html#a984084b7b8770329963b23845c53e820',1,'vg::IndexedVG::flip()'],['../classvg_1_1MemoizingGraph.html#afc634cf011767c68b0de3c205d24c251',1,'vg::MemoizingGraph::flip()'],['../classvg_1_1NodeSide.html#ae67ce8a411767a0b6883b6c9395b09a1',1,'vg::NodeSide::flip()'],['../classvg_1_1NullMaskingGraph.html#ade5b77f51f0749cba197c55d741ceb89',1,'vg::NullMaskingGraph::flip()'],['../classvg_1_1PathSubgraph.html#ae898f2e9d1b456f2e35f5307e2045283',1,'vg::PathSubgraph::flip()'],['../classvg_1_1ReverseGraph.html#a9a074446252aeab52d5922480c861e4f',1,'vg::ReverseGraph::flip()'],['../classvg_1_1NetGraph.html#a4f1db15a73fdce232fcd55a547986f82',1,'vg::NetGraph::flip()'],['../classvg_1_1SnarlManager.html#a634d4253e7fa5c09aa00f909f171bc61',1,'vg::SnarlManager::flip(const Snarl *snarl)'],['../classvg_1_1SnarlManager.html#ab05aac472334ea39d3b7e5ce95e0ffb2',1,'vg::SnarlManager::flip(const Chain *snarl)'],['../classvg_1_1SourceSinkOverlay.html#a1679195a16f99684463e3560352339a4',1,'vg::SourceSinkOverlay::flip()'],['../classvg_1_1JoinedSpliceGraph.html#a603e8b014c4f3c9041ac8edfcdc355e0',1,'vg::JoinedSpliceGraph::flip()'],['../classvg_1_1StrandSplitGraph.html#a6e4ce04f8b55b54e737e5f9d102b6149',1,'vg::StrandSplitGraph::flip()'],['../classvg_1_1SubHandleGraph.html#a00c5d8d2c19e965ee99a76bb4cd353bf',1,'vg::SubHandleGraph::flip()'],['../classvg_1_1SubgraphOverlay.html#a7520f901a2194ed3241b4097ce720481',1,'vg::SubgraphOverlay::flip()'],['../classvg_1_1SubpathOverlay.html#aaaadc6f282728d352baa0a8f78d5e852',1,'vg::SubpathOverlay::flip()'],['../classvg_1_1TreeSubgraph.html#af2ff96076aa4e658f15c4a6d4c1460e3',1,'vg::TreeSubgraph::flip()'],['../classvg_1_1VG.html#a48a5e160f098327f149b7a8a7a5b3558',1,'vg::VG::flip()'],['../classxg_1_1XG.html#acc7c6296fefeacf908acca84e5d6d14c',1,'xg::XG::flip()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af37976fbc4774d7cc444a7839b65c849',1,'handlegraph::algorithms::SubHandleGraph::flip()'],['../classhandlegraph_1_1HandleGraph.html#aaa3f94ae7e884408ef6e8ca8fd45c7d7',1,'handlegraph::HandleGraph::flip()'],['../classhandlegraph_1_1SnarlDecomposition.html#afd6553c0f17bb766c59ed2234fa2d13e',1,'handlegraph::SnarlDecomposition::flip()'],['../namespacevg.html#ad8a651561299e3236ec62af61d509112',1,'vg::flip()']]],
+ ['flip_5fdoubly_5freversed_5fedges_8948',['flip_doubly_reversed_edges',['../classvg_1_1VG.html#a8e5079416ab826cbc8a5eea3869eb892',1,'vg::VG::flip_doubly_reversed_edges()'],['../namespacevg.html#a89c2bb28b708cb4acf67eabfaa4b0168',1,'vg::flip_doubly_reversed_edges()']]],
+ ['flip_5fnodes_8949',['flip_nodes',['../namespacevg.html#a1f4eaa1a100e433af698e794afa8857b',1,'vg']]],
+ ['flow_5fsort_5fnodes_8950',['flow_sort_nodes',['../classvg_1_1FlowSort.html#a8d35f6283c659052a8710b18e26eb98e',1,'vg::FlowSort']]],
+ ['flowcaller_8951',['FlowCaller',['../classvg_1_1FlowCaller.html#a4afea3877bac0d289ffc6c3702d19984',1,'vg::FlowCaller']]],
+ ['flowsort_8952',['FlowSort',['../classvg_1_1FlowSort.html#a30687a5f5f16d28996b810d49ae384a6',1,'vg::FlowSort']]],
+ ['flowtraversalfinder_8953',['FlowTraversalFinder',['../classvg_1_1FlowTraversalFinder.html#afdefce6c5a69e6ab8ca529c3b4754e8b',1,'vg::FlowTraversalFinder']]],
+ ['flush_8954',['flush',['../classvg_1_1DozeuInterface.html#ac51a02b103eb50f4f458c0f756152302',1,'vg::DozeuInterface::flush()'],['../classvg_1_1XdropAligner.html#a06cf48f7dd057db6268218733cc9c991',1,'vg::XdropAligner::flush()'],['../classvg_1_1QualAdjXdropAligner.html#a9e0a9d6587bcc78fc8453a2d5a6c00ae',1,'vg::QualAdjXdropAligner::flush()'],['../classvg_1_1io_1_1MessageEmitter.html#aa1a5812e1ef02893eca24e2c74870e41',1,'vg::io::MessageEmitter::flush()'],['../classvg_1_1io_1_1ProtobufEmitter.html#aefba5ddea6beff54f293b95f7549d944',1,'vg::io::ProtobufEmitter::flush()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a9e2d51e5f860d576390722d3f80e6417',1,'vg::io::BlockedGzipOutputStream::Flush()']]],
+ ['flush_5fself_8955',['flush_self',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ad9f92e40584b24a5f1ff20750826bfe7',1,'vg::io::BlockedGzipOutputStream']]],
+ ['follow_5fedges_8956',['follow_edges',['../classhandlegraph_1_1HandleGraph.html#a4d21f30e62ad0b0c5919b2fe95e6f8aa',1,'handlegraph::HandleGraph']]],
+ ['follow_5fedges_5fimpl_8957',['follow_edges_impl',['../classvg_1_1DagifiedGraph.html#a1ef9323238f5c634e37a1901fe70cac7',1,'vg::DagifiedGraph::follow_edges_impl()'],['../classvg_1_1DozeuPinningOverlay.html#a8e496a98643c334cd90fb6c637b44a7f',1,'vg::DozeuPinningOverlay::follow_edges_impl()'],['../classvg_1_1ExtraNodeGraph.html#a5a4a8e88008abe18acb3e5365277d571',1,'vg::ExtraNodeGraph::follow_edges_impl()'],['../classvg_1_1SnarlGraph.html#a058d9545317220176574196c0856771c',1,'vg::SnarlGraph::follow_edges_impl()'],['../classvg_1_1IdentityOverlay.html#aeee6d38137e8e42da91d3217c04eb19e',1,'vg::IdentityOverlay::follow_edges_impl()'],['../classvg_1_1IncrementalSubgraph.html#ae130a9900ded50f9e69b24d5201bfcfc',1,'vg::IncrementalSubgraph::follow_edges_impl()'],['../classvg_1_1IndexedVG.html#a8f662f88594725f38108936b3cdd4557',1,'vg::IndexedVG::follow_edges_impl()'],['../classvg_1_1MemoizingGraph.html#aa66371807bdc15cb984bcc4d1c2e9728',1,'vg::MemoizingGraph::follow_edges_impl()'],['../classvg_1_1NullMaskingGraph.html#ab940c4f1423710ee763cc9d354bdf62a',1,'vg::NullMaskingGraph::follow_edges_impl()'],['../classvg_1_1PathSubgraph.html#aba4939b647863200fe9c00a1dd7b29cb',1,'vg::PathSubgraph::follow_edges_impl()'],['../classvg_1_1ReverseGraph.html#aa9254d4034163f9d7eb7c3e54be18cad',1,'vg::ReverseGraph::follow_edges_impl()'],['../classvg_1_1NetGraph.html#af71e4e3a211399f47cb2a5952b6f08af',1,'vg::NetGraph::follow_edges_impl()'],['../classvg_1_1SourceSinkOverlay.html#a3509d1a95f4bce832ebdefd6755f396d',1,'vg::SourceSinkOverlay::follow_edges_impl()'],['../classvg_1_1JoinedSpliceGraph.html#af1e1213617cd63487dc6194a9934a11f',1,'vg::JoinedSpliceGraph::follow_edges_impl()'],['../classvg_1_1StrandSplitGraph.html#aab7d8a7945878c5ff24f186c0cc290aa',1,'vg::StrandSplitGraph::follow_edges_impl()'],['../classvg_1_1SubHandleGraph.html#a4e1ce2518f49205daf2be98a765c79fd',1,'vg::SubHandleGraph::follow_edges_impl()'],['../classvg_1_1SubgraphOverlay.html#a421ab670d9cfbdf1faff768e77b854a0',1,'vg::SubgraphOverlay::follow_edges_impl()'],['../classvg_1_1SubpathOverlay.html#ab4f4b9d7ab05f53920a9d422ecac8a36',1,'vg::SubpathOverlay::follow_edges_impl()'],['../classvg_1_1TreeSubgraph.html#a1da92feba77602818f76b284739b071d',1,'vg::TreeSubgraph::follow_edges_impl()'],['../classvg_1_1VG.html#a4c1118bd664e83254db09ba3e8a3ec3f',1,'vg::VG::follow_edges_impl()'],['../classxg_1_1XG.html#a6c68a283c56d458bbb66d77684be0583',1,'xg::XG::follow_edges_impl()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a5b89d8a4c29cf73a906761257c3f18d0',1,'handlegraph::algorithms::SubHandleGraph::follow_edges_impl()'],['../classhandlegraph_1_1HandleGraph.html#a89bbc118fe1e8e1acb162c14be33e8b5',1,'handlegraph::HandleGraph::follow_edges_impl()']]],
+ ['follow_5fnet_5fedges_8958',['follow_net_edges',['../classhandlegraph_1_1SnarlDecomposition.html#a038431d41747c9216de0ed827ce7e919',1,'handlegraph::SnarlDecomposition']]],
+ ['follow_5fnet_5fedges_5fimpl_8959',['follow_net_edges_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a5be2bda480dac57d09e1c305ce6c8e20',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_8960',['for_each',['../classvg_1_1Paths.html#ac86fa87134c58faea8d70822fe00990c',1,'vg::Paths::for_each()'],['../classvg_1_1VGset.html#a998c782d65a9abe5610ce86925f91762',1,'vg::VGset::for_each()'],['../classvg_1_1subcommand_1_1Subcommand.html#a00984ebffd918ad9e78bda1686ca035c',1,'vg::subcommand::Subcommand::for_each(const std::function< void(const Subcommand &)> &lambda)'],['../classvg_1_1subcommand_1_1Subcommand.html#ab8948845550b743c7dc1be41d8458e8d',1,'vg::subcommand::Subcommand::for_each(CommandCategory category, const std::function< void(const Subcommand &)> &lambda)'],['../namespacevg_1_1io.html#a08997ecc2a7d17c35a27418b5f21ab3d',1,'vg::io::for_each(std::istream &in, const std::function< void(int64_t, T &)> &lambda, const std::function< void(size_t, size_t)> &progress=NO_PROGRESS)'],['../namespacevg_1_1io.html#a6e19f6d7cb7f7c3d6a396268dcbd8007',1,'vg::io::for_each(std::istream &in, const std::function< void(T &)> &lambda, const std::function< void(size_t, size_t)> &progress=NO_PROGRESS)']]],
+ ['for_5feach_5fagglomeration_5finterval_8961',['for_each_agglomeration_interval',['../classvg_1_1MinimizerMapper.html#a59a7bf123788c471bdf900c4b47b5c4a',1,'vg::MinimizerMapper']]],
+ ['for_5feach_5fannotation_8962',['for_each_annotation',['../classvg_1_1multipath__alignment__t.html#ac1aec26be5837a73a84df48a70b82a06',1,'vg::multipath_alignment_t']]],
+ ['for_5feach_5fbasic_5fannotation_8963',['for_each_basic_annotation',['../namespacevg.html#a8f0eee097c87cbab2bc44f096b463d8b',1,'vg']]],
+ ['for_5feach_5fcg_8964',['for_each_cg',['../namespacegafkluge.html#ad32038d9fe60950ec4ba0ee6c05040b3',1,'gafkluge']]],
+ ['for_5feach_5fchain_8965',['for_each_chain',['../classvg_1_1SnarlManager.html#a83a481b702deda84aadf24171a860769',1,'vg::SnarlManager']]],
+ ['for_5feach_5fchain_5fparallel_8966',['for_each_chain_parallel',['../classvg_1_1SnarlManager.html#a2d3b980bed56de4cc909590a51264a6c',1,'vg::SnarlManager']]],
+ ['for_5feach_5fchild_8967',['for_each_child',['../classhandlegraph_1_1SnarlDecomposition.html#a4790373e0405cc715b0116142aefc42e',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5fchild_5fimpl_8968',['for_each_child_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a8dcbdccb1422d034b16da6ff31412d5a',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5fcigar_8969',['for_each_cigar',['../namespacegafkluge.html#ad34ac0b7ed3c066acbc4fb6c82f42475',1,'gafkluge']]],
+ ['for_5feach_5fconnected_5fnode_8970',['for_each_connected_node',['../classvg_1_1VG.html#a892abc4056e30044ae9ce0db9e4871f0',1,'vg::VG']]],
+ ['for_5feach_5fcs_8971',['for_each_cs',['../namespacegafkluge.html#a97dfb71592c41879c5d3a5abdd4f3276',1,'gafkluge']]],
+ ['for_5feach_5fedge_8972',['for_each_edge',['../classvg_1_1DiagramExplainer.html#a9509e0d2a9b1cd5dce5bf058ba9f0511',1,'vg::DiagramExplainer::for_each_edge()'],['../classvg_1_1VG.html#a3d7fdd8c951cbf8b25e116435b5e1e0e',1,'vg::VG::for_each_edge(function< void(Edge *)> lambda)'],['../classvg_1_1VG.html#aed86f57c2e9766da9757e18ef543d35d',1,'vg::VG::for_each_edge(function< void(const Edge *)> lambda) const'],['../classhandlegraph_1_1HandleGraph.html#a61570ded026f825d62ea7608a1e92349',1,'handlegraph::HandleGraph::for_each_edge()']]],
+ ['for_5feach_5fedge_5fparallel_8973',['for_each_edge_parallel',['../classvg_1_1VG.html#a46a20aa427767a27fd15d181ccca8c42',1,'vg::VG']]],
+ ['for_5feach_5ffilter_8974',['for_each_filter',['../classvg_1_1Funnel.html#afc114c16e43a80739d292e03b65fa8ab',1,'vg::Funnel']]],
+ ['for_5feach_5fgff_5frecord_8975',['for_each_gff_record',['../classvg_1_1GFFReader.html#a73afc9447d2bcf2f1ca11de90c822ecb',1,'vg::GFFReader']]],
+ ['for_5feach_5fhandle_8976',['for_each_handle',['../classhandlegraph_1_1HandleGraph.html#a928bdeabd328d357b538e30590164ab4',1,'handlegraph::HandleGraph']]],
+ ['for_5feach_5fhandle_5fimpl_8977',['for_each_handle_impl',['../classvg_1_1DagifiedGraph.html#af93a535f9e600f583795c7192b16a5af',1,'vg::DagifiedGraph::for_each_handle_impl()'],['../classvg_1_1DozeuPinningOverlay.html#a8433f3777f985ff1307c8f907b7a51d0',1,'vg::DozeuPinningOverlay::for_each_handle_impl()'],['../classvg_1_1ExtraNodeGraph.html#a80dada6b10cc3775bb77962bdae6a3c0',1,'vg::ExtraNodeGraph::for_each_handle_impl()'],['../classvg_1_1SnarlGraph.html#a2312825b11c4c4046e79a35cacadfe27',1,'vg::SnarlGraph::for_each_handle_impl()'],['../classvg_1_1IdentityOverlay.html#ac1eddf95e1828bc39e4422d6fa10f64e',1,'vg::IdentityOverlay::for_each_handle_impl()'],['../classvg_1_1IncrementalSubgraph.html#aabc1cb22610d6c41a79dc91617f785c1',1,'vg::IncrementalSubgraph::for_each_handle_impl()'],['../classvg_1_1IndexedVG.html#a1fd2d5d78e3f3c6e5ae6b8c20ad127ea',1,'vg::IndexedVG::for_each_handle_impl()'],['../classvg_1_1MemoizingGraph.html#a5e0a5d23cda378e3b035b76877a96c2c',1,'vg::MemoizingGraph::for_each_handle_impl()'],['../classvg_1_1NullMaskingGraph.html#a0308e0413cd69b3b4672702a98aef320',1,'vg::NullMaskingGraph::for_each_handle_impl()'],['../classvg_1_1PathSubgraph.html#a4166c30daddecab93040a34fb9d92bd6',1,'vg::PathSubgraph::for_each_handle_impl()'],['../classvg_1_1ReverseGraph.html#af7bef018b5871832fad7c0fe285077a0',1,'vg::ReverseGraph::for_each_handle_impl()'],['../classvg_1_1NetGraph.html#a8a71e3e2d8d35cc230ec809d54a320c7',1,'vg::NetGraph::for_each_handle_impl()'],['../classvg_1_1SourceSinkOverlay.html#a6f4d5b7d57f650585061f5e717163dea',1,'vg::SourceSinkOverlay::for_each_handle_impl()'],['../classvg_1_1JoinedSpliceGraph.html#ada8a6087f4b7bfa2aa6a2d9f88a93d60',1,'vg::JoinedSpliceGraph::for_each_handle_impl()'],['../classvg_1_1StrandSplitGraph.html#aaaac2dfd01ba39cf84f02296e6d5c97c',1,'vg::StrandSplitGraph::for_each_handle_impl()'],['../classvg_1_1SubHandleGraph.html#a39e05cb649e7a0e979751b1287e4d30f',1,'vg::SubHandleGraph::for_each_handle_impl()'],['../classvg_1_1SubgraphOverlay.html#a054f387a6c02302e47815f501034a068',1,'vg::SubgraphOverlay::for_each_handle_impl()'],['../classvg_1_1SubpathOverlay.html#a545dda4c5916239d0f473026324ab5a1',1,'vg::SubpathOverlay::for_each_handle_impl()'],['../classvg_1_1TreeSubgraph.html#a3304940da26d12fd579a72c90f1d0480',1,'vg::TreeSubgraph::for_each_handle_impl()'],['../classvg_1_1VG.html#afa7a11323fdb8a632f4dc5e405e74848',1,'vg::VG::for_each_handle_impl()'],['../classxg_1_1XG.html#af0b6c8a9c8e12575b345ab8a5209874b',1,'xg::XG::for_each_handle_impl()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a62f7884d8f69c4c32304722bf5a7ee8c',1,'handlegraph::algorithms::SubHandleGraph::for_each_handle_impl()'],['../classhandlegraph_1_1HandleGraph.html#af48ba081fcb810267dc50e3a3e7ad391',1,'handlegraph::HandleGraph::for_each_handle_impl()']]],
+ ['for_5feach_5fhandle_5fin_5fshortest_5fpath_8978',['for_each_handle_in_shortest_path',['../namespacehandlegraph_1_1algorithms.html#a62990356f8196e5cb3b2e6601cc41eee',1,'handlegraph::algorithms']]],
+ ['for_5feach_5fhead_8979',['for_each_head',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ae26744448bb18253ff054565bbed4b14',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['for_5feach_5fid_8980',['for_each_id',['../classvg_1_1StreamIndex.html#a88788f5837112b38e2c182b37efd608e',1,'vg::StreamIndex']]],
+ ['for_5feach_5finterleaved_5fpair_5fparallel_8981',['for_each_interleaved_pair_parallel',['../namespacevg_1_1io.html#aeb40cd1227130aa2b23a1a7c91aa7f2d',1,'vg::io']]],
+ ['for_5feach_5finterleaved_5fpair_5fparallel_5fafter_5fwait_8982',['for_each_interleaved_pair_parallel_after_wait',['../namespacevg_1_1io.html#aa420d6f551083405c508bee6242ef123',1,'vg::io']]],
+ ['for_5feach_5fkmer_8983',['for_each_kmer',['../namespacevg.html#ab3d4de4fa2fda6bfcd6eaa77080c67ad',1,'vg::for_each_kmer()'],['../namespacevg_1_1algorithms.html#a30b8fd7a0d56e1827faa3aa56c8828f0',1,'vg::algorithms::for_each_kmer()']]],
+ ['for_5feach_5fkmer_5fparallel_8984',['for_each_kmer_parallel',['../classvg_1_1VGset.html#a8018547ffd3175ab28ebd8fb92b8f842',1,'vg::VGset']]],
+ ['for_5feach_5fmapping_8985',['for_each_mapping',['../classvg_1_1Paths.html#a059807c77ba1efd246c25d2070947792',1,'vg::Paths']]],
+ ['for_5feach_5fmember_8986',['for_each_member',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a63dbabae3b8851ee15900e79735038b0',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['for_5feach_5fmembership_8987',['for_each_membership',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ae0a46944ed58b73109148a1cf1bd8b79',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['for_5feach_5fname_8988',['for_each_name',['../classvg_1_1Paths.html#a26c3854ce2cfcfd56064077e5062a440',1,'vg::Paths']]],
+ ['for_5feach_5fname_5fstoppable_8989',['for_each_name_stoppable',['../classvg_1_1Paths.html#af5231f3d55b57ca9ec341be62d18155d',1,'vg::Paths']]],
+ ['for_5feach_5fneighbor_8990',['for_each_neighbor',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a1e63b71aba9a614f17b497908c638797',1,'vg::DozeuInterface::OrderedGraph']]],
+ ['for_5feach_5fnode_8991',['for_each_node',['../classvg_1_1VG.html#af585f2161de09403d197e05fbcfb9a07',1,'vg::VG::for_each_node(function< void(Node *)> lambda)'],['../classvg_1_1VG.html#a23b34b164590c0537bf704dd1b816760',1,'vg::VG::for_each_node(function< void(const Node *)> lambda) const']]],
+ ['for_5feach_5fnode_5fparallel_8992',['for_each_node_parallel',['../classvg_1_1VG.html#a39790d52fe4c09804086d58164258fcf',1,'vg::VG']]],
+ ['for_5feach_5fother_5fmember_8993',['for_each_other_member',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ad0cfb071a138beff3fea1728104beb98',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['for_5feach_5fparallel_8994',['for_each_parallel',['../namespacevg_1_1io.html#a2c3c1dbfdd613d8d70e6354d680b342e',1,'vg::io']]],
+ ['for_5feach_5fparallel_5fimpl_8995',['for_each_parallel_impl',['../namespacevg_1_1io.html#a1347d6f25fb95f2e4fd6cf5d2ff7f92d',1,'vg::io']]],
+ ['for_5feach_5fpath_5fhandle_8996',['for_each_path_handle',['../classhandlegraph_1_1PathHandleGraph.html#aa3f1d0595543d760322042770201297c',1,'handlegraph::PathHandleGraph']]],
+ ['for_5feach_5fpath_5fhandle_5fimpl_8997',['for_each_path_handle_impl',['../classvg_1_1MemoizingGraph.html#a37322d14220aeea194062380da0cc943',1,'vg::MemoizingGraph::for_each_path_handle_impl()'],['../classvg_1_1PathSubgraphOverlay.html#aad99a886a4ea032b781d57c5af6b9e2a',1,'vg::PathSubgraphOverlay::for_each_path_handle_impl()'],['../classvg_1_1VG.html#a527e1ab441e93f73902b7a02b29c1bd6',1,'vg::VG::for_each_path_handle_impl()'],['../classxg_1_1XG.html#aff636eab67405c3c27ba4f2be4f0a6f5',1,'xg::XG::for_each_path_handle_impl()'],['../classhandlegraph_1_1PathHandleGraph.html#a79f48793555f6be311f6df6603324e7b',1,'handlegraph::PathHandleGraph::for_each_path_handle_impl()'],['../classhandlegraph_1_1PathMetadata.html#a8cd1fd8be6b3cd868fc7124181407bd0',1,'handlegraph::PathMetadata::for_each_path_handle_impl()']]],
+ ['for_5feach_5fpath_5fmatching_8998',['for_each_path_matching',['../classhandlegraph_1_1PathMetadata.html#a01967c3713408b24ed6c3c20ff2ddd23',1,'handlegraph::PathMetadata::for_each_path_matching(const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) const'],['../classhandlegraph_1_1PathMetadata.html#aef274133ea4ac6c96fd5e5330e2c620c',1,'handlegraph::PathMetadata::for_each_path_matching(const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) const']]],
+ ['for_5feach_5fpath_5fmatching_5fimpl_8999',['for_each_path_matching_impl',['../classhandlegraph_1_1PathMetadata.html#af040579085f8d49fcb6733e1f9cc8c27',1,'handlegraph::PathMetadata']]],
+ ['for_5feach_5fpath_5fof_5fsample_9000',['for_each_path_of_sample',['../classhandlegraph_1_1PathMetadata.html#a01becc6f1373c256aebdb41cab2e1e2a',1,'handlegraph::PathMetadata']]],
+ ['for_5feach_5fpath_5fof_5fsense_9001',['for_each_path_of_sense',['../classhandlegraph_1_1PathMetadata.html#a7afd82569e409e86b4bcdafe8d39cc86',1,'handlegraph::PathMetadata']]],
+ ['for_5feach_5fpostorder_9002',['for_each_postorder',['../structvg_1_1TreeNode.html#a28eeb006a851d066d62cb26b93cd4b24',1,'vg::TreeNode::for_each_postorder()'],['../structvg_1_1Tree.html#af5981fac59c0b2549cc0f70b98b675d2',1,'vg::Tree::for_each_postorder()']]],
+ ['for_5feach_5fpreorder_9003',['for_each_preorder',['../structvg_1_1TreeNode.html#a52c407f5434c0fa0c7b25b66758b7a75',1,'vg::TreeNode::for_each_preorder()'],['../structvg_1_1Tree.html#a5b5e4073edee56fd62feac705f4ce4e8',1,'vg::Tree::for_each_preorder()']]],
+ ['for_5feach_5fread_5finterval_9004',['for_each_read_interval',['../structvg_1_1GaplessExtension.html#a5bc9436d24978ebb2d0df881d0838ff2',1,'vg::GaplessExtension']]],
+ ['for_5feach_5fsnarl_5fparallel_9005',['for_each_snarl_parallel',['../classvg_1_1SnarlManager.html#a4b1681aedec889820afa7ba06ca99523',1,'vg::SnarlManager']]],
+ ['for_5feach_5fsnarl_5fpreorder_9006',['for_each_snarl_preorder',['../classvg_1_1SnarlManager.html#af8f351725cc98913a211aa9d1535a841',1,'vg::SnarlManager']]],
+ ['for_5feach_5fsnarl_5funindexed_9007',['for_each_snarl_unindexed',['../classvg_1_1SnarlManager.html#a053c63fb829fbb9204b1b1a5502e94dd',1,'vg::SnarlManager']]],
+ ['for_5feach_5fstage_9008',['for_each_stage',['../classvg_1_1Funnel.html#a6b8e05750253de736a8a44de5932e352',1,'vg::Funnel']]],
+ ['for_5feach_5fstep_5fin_5fpath_9009',['for_each_step_in_path',['../classhandlegraph_1_1PathHandleGraph.html#a184353db571dd2086d79e4e31f2f97f1',1,'handlegraph::PathHandleGraph']]],
+ ['for_5feach_5fstep_5fof_5fsense_9010',['for_each_step_of_sense',['../classhandlegraph_1_1PathMetadata.html#a85b539a3b2ee842030068d7556be10a1',1,'handlegraph::PathMetadata']]],
+ ['for_5feach_5fstep_5fof_5fsense_5fimpl_9011',['for_each_step_of_sense_impl',['../classhandlegraph_1_1PathMetadata.html#a87e4c1bede87504ea011544c3e35651a',1,'handlegraph::PathMetadata']]],
+ ['for_5feach_5fstep_5fon_5fhandle_9012',['for_each_step_on_handle',['../classhandlegraph_1_1PathHandleGraph.html#a006a8e3ab9e2783ef7bf80b98b35959c',1,'handlegraph::PathHandleGraph']]],
+ ['for_5feach_5fstep_5fon_5fhandle_5fimpl_9013',['for_each_step_on_handle_impl',['../classvg_1_1MemoizingGraph.html#aeff170a12e414f058e658317060798b4',1,'vg::MemoizingGraph::for_each_step_on_handle_impl()'],['../classvg_1_1PathSubgraphOverlay.html#a9e042a3f29d7182fa8510dd46c259b41',1,'vg::PathSubgraphOverlay::for_each_step_on_handle_impl()'],['../classvg_1_1VG.html#a68b4c3665812b5be48d01677367382fd',1,'vg::VG::for_each_step_on_handle_impl()'],['../classxg_1_1XG.html#a0c05acc85982c493ac91b6199ca1cfd4',1,'xg::XG::for_each_step_on_handle_impl()'],['../classhandlegraph_1_1PathHandleGraph.html#a2bbdf56b268001c629cf000f5bd8bb9a',1,'handlegraph::PathHandleGraph::for_each_step_on_handle_impl()'],['../classhandlegraph_1_1PathMetadata.html#a25e78685ad8a987422d9bf6c131c854f',1,'handlegraph::PathMetadata::for_each_step_on_handle_impl()']]],
+ ['for_5feach_5fstep_5fposition_5fon_5fhandle_9014',['for_each_step_position_on_handle',['../classvg_1_1MemoizingGraph.html#aca0068b6da055640d5dbc6034aa6aaa4',1,'vg::MemoizingGraph::for_each_step_position_on_handle()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#a5c30215753a62ebaffcbeffe40009829',1,'handlegraph::PathPositionHandleGraph::for_each_step_position_on_handle()']]],
+ ['for_5feach_5fstream_9015',['for_each_stream',['../classvg_1_1Paths.html#a8ceb67abc89bd22659c751c946906e23',1,'vg::Paths']]],
+ ['for_5feach_5fsubpath_5fof_9016',['for_each_subpath_of',['../namespacevg.html#a9534c53c98412f2d43982fc0b809e7bd',1,'vg']]],
+ ['for_5feach_5ftippy_5fchild_9017',['for_each_tippy_child',['../classhandlegraph_1_1SnarlDecomposition.html#ac28fd7719d52d2148443d31617ae8a3c',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftippy_5fchild_5fimpl_9018',['for_each_tippy_child_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a0f14086d5470e4a95955e9bc3787574a',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftop_5flevel_5fchain_9019',['for_each_top_level_chain',['../classvg_1_1SnarlManager.html#a4bce7b961c24e5a18c834c6a78df8d2e',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftop_5flevel_5fchain_5fparallel_9020',['for_each_top_level_chain_parallel',['../classvg_1_1SnarlManager.html#aba6a74d03b6064e29b7ede95ddb2195d',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftop_5flevel_5fsnarl_9021',['for_each_top_level_snarl',['../classvg_1_1SnarlManager.html#ac4cf6c9ca0c953ec32bc3677d3171cf0',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftop_5flevel_5fsnarl_5fparallel_9022',['for_each_top_level_snarl_parallel',['../classvg_1_1SnarlManager.html#a458f5a996e7352ae749178d08f575a3e',1,'vg::SnarlManager']]],
+ ['for_5feach_5ftraversal_9023',['for_each_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a64144f35a85a36bb472044663bd3a618',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fend_9024',['for_each_traversal_end',['../classhandlegraph_1_1SnarlDecomposition.html#ac7ccef73cd4793c0f303b951352b954b',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fend_5fimpl_9025',['for_each_traversal_end_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a5d7c6809f7636d1afae03c34e4747179',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fimpl_9026',['for_each_traversal_impl',['../classhandlegraph_1_1SnarlDecomposition.html#ac5ea5843f70f1550afe868a8fa1bf2ae',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fstart_9027',['for_each_traversal_start',['../classhandlegraph_1_1SnarlDecomposition.html#a0ccdbfddf02159200884e27ae34af0a8',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5ftraversal_5fstart_5fimpl_9028',['for_each_traversal_start_impl',['../classhandlegraph_1_1SnarlDecomposition.html#a688f4614f5dd84aa01734c5eaf5d0400',1,'handlegraph::SnarlDecomposition']]],
+ ['for_5feach_5fwalk_9029',['for_each_walk',['../namespacevg_1_1algorithms.html#ace1ad4f4eccc7041eb1e700463492540',1,'vg::algorithms']]],
+ ['for_5fpath_5frange_9030',['for_path_range',['../classxg_1_1XG.html#a2ba1a725e15e5693156a5870701ceac0',1,'xg::XG']]],
+ ['force_5fclose_9031',['force_close',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ac677874552857f22f89ee9571eb183db',1,'vg::io::BlockedGzipOutputStream']]],
+ ['force_5ffragment_5flength_5fdistr_9032',['force_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ac2731944023ede8d7fb00379ffd8ecbf',1,'vg::PairedEndMapper::force_fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#a7f1925a1c2071ed65c543cc25b4d4f02',1,'vg::MinimizerMapper::force_fragment_length_distr()']]],
+ ['force_5fparameters_9033',['force_parameters',['../classvg_1_1FragmentLengthDistribution.html#a5751543486d54066f30e943ec188b279',1,'vg::FragmentLengthDistribution']]],
+ ['forest_5fgrowing_5fstate_5ft_9034',['forest_growing_state_t',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a8617325ab6eae778a65b13a4f21bdd16',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['forget_9035',['forget',['../namespacevg_1_1temp__file.html#a478c3b30251f8866550b1497bb22ede4',1,'vg::temp_file::forget()'],['../namespacexg_1_1temp__file.html#ab7efd4c620ca53aecb448de975525885',1,'xg::temp_file::forget()']]],
+ ['format_9036',['format',['../classVectorizer.html#a30aa5bafd8a44b2e1259245b6e046062',1,'Vectorizer']]],
+ ['format_5fmultiplier_9037',['format_multiplier',['../namespacevg.html#a3ae70effc22331b3e4667ed48808602c',1,'vg']]],
+ ['forward_9038',['forward',['../classhandlegraph_1_1HandleGraph.html#a9e946bb4ed53f9423072955cdaab6386',1,'handlegraph::HandleGraph']]],
+ ['forward_5foffset_9039',['forward_offset',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a3ffe7fc7ef04c67add8a6fae372dcee9',1,'vg::MinimizerMapper::Minimizer']]],
+ ['forward_5fsequence_9040',['forward_sequence',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ae02ecd440346f71b3d36ab8f291abb82',1,'vg::MinimizerMapper::Minimizer']]],
+ ['forwardize_5fbreakpoints_9041',['forwardize_breakpoints',['../namespacevg.html#a9e9c975d7bec4a22a46b72736915ceb1',1,'vg']]],
+ ['fragment_5fdirection_9042',['fragment_direction',['../classvg_1_1FragmentLengthStatistics.html#af43d1fa0b2d07be1cd3f7d658fa932c5',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fdistr_5fis_5ffinalized_9043',['fragment_distr_is_finalized',['../classvg_1_1MinimizerMapper.html#a692470c7551c4966126aa7bf357e60a4',1,'vg::MinimizerMapper']]],
+ ['fragment_5flength_5flog_5flikelihood_9044',['fragment_length_log_likelihood',['../classvg_1_1MultipathMapper.html#ac9fbf8240e86c6753e0a55d89752f70d',1,'vg::MultipathMapper']]],
+ ['fragment_5flength_5fmean_9045',['fragment_length_mean',['../classvg_1_1FragmentLengthStatistics.html#a0379d61cc368d8f7cea2babfacb24f06',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fpdf_9046',['fragment_length_pdf',['../classvg_1_1FragmentLengthStatistics.html#a929c0b89511551c913882cc65d4de180',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fpval_9047',['fragment_length_pval',['../classvg_1_1FragmentLengthStatistics.html#a5881926df69d005966f59b6dbead8253',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fstdev_9048',['fragment_length_stdev',['../classvg_1_1FragmentLengthStatistics.html#a83626df3ef00fa066df4fcf22a5c9862',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fmodel_5fstr_9049',['fragment_model_str',['../classvg_1_1FragmentLengthStatistics.html#acdcb4761860132d14be1bbe2da236a69',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5forientation_9050',['fragment_orientation',['../classvg_1_1FragmentLengthStatistics.html#aa486f0551d5848bfaaa304cc1c93d636',1,'vg::FragmentLengthStatistics']]],
+ ['fragmentlengthdistribution_9051',['FragmentLengthDistribution',['../classvg_1_1FragmentLengthDistribution.html#a8788ddb09653e64eb868cbc942df95c6',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(size_t maximum_sample_size, size_t reestimation_frequency, double robust_estimation_fraction)'],['../classvg_1_1FragmentLengthDistribution.html#a8551fd1f0ad1270145483715f35c7b6b',1,'vg::FragmentLengthDistribution::FragmentLengthDistribution(void)']]],
+ ['from_5fbacking_9052',['from_backing',['../classvg_1_1ExtraNodeGraph.html#a4d788b60f65afb7c33ae42481d7244ab',1,'vg::ExtraNodeGraph::from_backing()'],['../classvg_1_1ReverseGraph.html#a4f86e4320b018dd684e48250d8c2e455',1,'vg::ReverseGraph::from_backing()'],['../classvg_1_1SourceSinkOverlay.html#ad6d335a0dc7d4d42c7d21a814d79d8eb',1,'vg::SourceSinkOverlay::from_backing()']]],
+ ['from_5fbig_5fendian_9053',['from_big_endian',['../structvg_1_1endianness.html#a473244129a68f42dcc05119ffe1132c5',1,'vg::endianness']]],
+ ['from_5fenumerators_9054',['from_enumerators',['../classxg_1_1XG.html#a52b214cf4125206aa7d2d43dd3baf4d5',1,'xg::XG']]],
+ ['from_5fextension_9055',['from_extension',['../structvg_1_1WFAAlignment.html#ac10be60010c306c84bc522f87e5fd5e5',1,'vg::WFAAlignment']]],
+ ['from_5fgfa_9056',['from_gfa',['../classxg_1_1XG.html#a1c89b39930820e72b8365d8984eaf531',1,'xg::XG']]],
+ ['from_5fhandle_5fgraph_9057',['from_handle_graph',['../classxg_1_1XG.html#aae49bbd7a7886919ab4adf1629517bb1',1,'xg::XG::from_handle_graph()'],['../namespacevg.html#ae968813905d72a9d49a1822b390cbe5d',1,'vg::from_handle_graph()']]],
+ ['from_5fhit_9058',['from_hit',['../namespacevg.html#a61a0d273871a7d0feea0e9f0b1901931',1,'vg']]],
+ ['from_5fistream_9059',['from_istream',['../classvg_1_1VG.html#a3c22829197fc65ced4dd2e0f53cb20ff',1,'vg::VG']]],
+ ['from_5fkey_5fvalue_9060',['from_key_value',['../structvg_1_1WFAPoint.html#ad32f3fd03ce3f9bb91f2dd7fe1bf52c4',1,'vg::WFAPoint']]],
+ ['from_5flength_9061',['from_length',['../classvg_1_1edit__t.html#a5ff1f97ea22b67b22fbc1c1b54c1d2af',1,'vg::edit_t::from_length()'],['../namespacevg.html#a83d1f079508a3ee8a2705773109a5a8e',1,'vg::from_length()']]],
+ ['from_5flength_5fafter_5fpos_9062',['from_length_after_pos',['../namespacevg.html#a59b4e98d0d99a9b58b56f0946f49b1ab',1,'vg']]],
+ ['from_5flength_5fbefore_5fpos_9063',['from_length_before_pos',['../namespacevg.html#a21d316f0ae049289cacab5117678d6ab',1,'vg']]],
+ ['from_5fmap_5fentry_9064',['from_map_entry',['../structvg_1_1WFAPoint.html#aa547dad190435d35174a40b7ed0094f8',1,'vg::WFAPoint']]],
+ ['from_5fpath_5fhandle_5fgraph_9065',['from_path_handle_graph',['../classxg_1_1XG.html#a249328f04690e8022442c0ed845dd042',1,'xg::XG::from_path_handle_graph()'],['../namespacevg.html#a0eaa4d69a029a84c1d3028745c84bc4c',1,'vg::from_path_handle_graph()']]],
+ ['from_5fproto_5fedit_9066',['from_proto_edit',['../namespacevg.html#a4b8b4c6f298818989d39189d631980a8',1,'vg']]],
+ ['from_5fproto_5fmapping_9067',['from_proto_mapping',['../namespacevg.html#a1e6878ce34057ea3c8e8c0deacc1726b',1,'vg']]],
+ ['from_5fproto_5fmultipath_5falignment_9068',['from_proto_multipath_alignment',['../namespacevg.html#a8630566250dfefc57ec84cbf6c22c3e2',1,'vg']]],
+ ['from_5fproto_5fpath_9069',['from_proto_path',['../namespacevg.html#a01ce1f20da22c85b09e4bae9bf9a3d1f',1,'vg']]],
+ ['from_5fproto_5fposition_9070',['from_proto_position',['../namespacevg.html#ae7d3ba6e34f59b610d86a84d0d6c32d1',1,'vg']]],
+ ['from_5fsimple_5freverse_9071',['from_simple_reverse',['../classvg_1_1FlowSort.html#a920aae02af49b5fdd03397b70cda0640',1,'vg::FlowSort']]],
+ ['from_5fsimple_5freverse_5forientation_9072',['from_simple_reverse_orientation',['../classvg_1_1FlowSort.html#a7d43a991e41fd1af563ee17bfa82dc06',1,'vg::FlowSort']]],
+ ['from_5fturtle_9073',['from_turtle',['../classvg_1_1VG.html#a8aef48163c0dd4267d24b629de8a04c8',1,'vg::VG']]],
+ ['from_5fvector_9074',['from_vector',['../structvg_1_1varint__vector__t.html#a6a568813ee83039d59a8af1dad7b2138',1,'vg::varint_vector_t::from_vector()'],['../classvg_1_1ZipCode.html#acbad7130678653add25cc79639b0f886',1,'vg::ZipCode::from_vector()']]],
+ ['full_9075',['full',['../structvg_1_1GaplessExtension.html#a1d1eb14643690ee92b30b2f0bdb5d82c',1,'vg::GaplessExtension']]],
+ ['full_5flength_5fextensions_9076',['full_length_extensions',['../classvg_1_1GaplessExtender.html#a0381d55bcbba7e1ea297dc9a915dac1d',1,'vg::GaplessExtender']]],
+ ['fuse_5fspliced_5falignments_9077',['fuse_spliced_alignments',['../namespacevg.html#a5b37106006a0286045cd12f9159ac245',1,'vg']]]
];
diff --git a/search/functions_7.js b/search/functions_7.js
index 7417a64cba..76360eb102 100644
--- a/search/functions_7.js
+++ b/search/functions_7.js
@@ -1,417 +1,418 @@
var searchData=
[
- ['gaf_5fpaired_5finterleaved_5ffor_5feach_9075',['gaf_paired_interleaved_for_each',['../namespacevg_1_1io.html#a1509c614371533861fa7552febf7af92',1,'vg::io::gaf_paired_interleaved_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda)'],['../namespacevg_1_1io.html#ad242e1399847a5c894201b9e32c13a6d',1,'vg::io::gaf_paired_interleaved_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda)']]],
- ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_9076',['gaf_paired_interleaved_for_each_parallel',['../namespacevg_1_1io.html#a7b473c9f170444107256aa76f522d27a',1,'vg::io::gaf_paired_interleaved_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#a8662ca54b9e1f26e421884a43a4e0e21',1,'vg::io::gaf_paired_interleaved_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)']]],
- ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_5fafter_5fwait_9077',['gaf_paired_interleaved_for_each_parallel_after_wait',['../namespacevg_1_1io.html#a44d7cb48aae7d9c3621fabc6b31faa6e',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)'],['../namespacevg_1_1io.html#a63b12354bf13d6a19b5addc71fc512c7',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)']]],
- ['gaf_5fto_5falignment_9078',['gaf_to_alignment',['../namespacevg_1_1io.html#a44a872a40072dc128fa898a795eeff79',1,'vg::io::gaf_to_alignment(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const gafkluge::GafRecord &gaf, Alignment &aln)'],['../namespacevg_1_1io.html#a363656cc5c1a09f178e3c83785488bad',1,'vg::io::gaf_to_alignment(const HandleGraph &graph, const gafkluge::GafRecord &gaf, Alignment &aln)']]],
- ['gaf_5funpaired_5ffor_5feach_9079',['gaf_unpaired_for_each',['../namespacevg_1_1io.html#a83d5011d88f6ef27ed8837957505284b',1,'vg::io::gaf_unpaired_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda)'],['../namespacevg_1_1io.html#ada4771a7ea674ee9d986af264ab3c00d',1,'vg::io::gaf_unpaired_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda)']]],
- ['gaf_5funpaired_5ffor_5feach_5fparallel_9080',['gaf_unpaired_for_each_parallel',['../namespacevg_1_1io.html#a88d2dffc472bbcfded0b1190fc5bc933',1,'vg::io::gaf_unpaired_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#add46b11d285f6b94896c1f5e91a405a7',1,'vg::io::gaf_unpaired_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)']]],
- ['gafalignmentemitter_9081',['GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html#ad7b537251b10534375e90a22b795b9cc',1,'vg::io::GafAlignmentEmitter']]],
- ['gafoutputcaller_9082',['GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html#a2def7ee0c3eb2f0cbfd139ad0eeeec8b',1,'vg::GAFOutputCaller']]],
- ['gafrecord_9083',['GafRecord',['../structgafkluge_1_1GafRecord.html#a81394a04ad249c56b3f757484a7663bc',1,'gafkluge::GafRecord']]],
- ['gamma_5fln_9084',['gamma_ln',['../namespacevg.html#a05748ab256c93e2393252aa8ebbdde3d',1,'vg']]],
- ['gap_5fextend_5fpenalty_9085',['gap_extend_penalty',['../classvg_1_1WFATree.html#a705cd842a3204b5dbc0c669f3e1c60c7',1,'vg::WFATree']]],
- ['gap_5fpenalty_9086',['gap_penalty',['../classvg_1_1WFATree.html#a46f357dbdd6957c1c08bb82a275a3bcf',1,'vg::WFATree']]],
- ['gaplessextender_9087',['GaplessExtender',['../classvg_1_1GaplessExtender.html#a497cc4e85c6433a3e41f04895703f271',1,'vg::GaplessExtender::GaplessExtender()'],['../classvg_1_1GaplessExtender.html#aaebc8d221df2787a68023fce2d99290a',1,'vg::GaplessExtender::GaplessExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner)']]],
- ['gbwt_5fnode_5fwidth_9088',['gbwt_node_width',['../namespacevg.html#ada6300e45d21f1171c5ff2b71f4d173b',1,'vg']]],
- ['gbwt_5fthread_5ft_9089',['gbwt_thread_t',['../structhaplo_1_1gbwt__thread__t.html#a5b148ae0a27b81b4b4af07f200a1255b',1,'haplo::gbwt_thread_t::gbwt_thread_t()'],['../structhaplo_1_1gbwt__thread__t.html#aa52a0e84c11044abd6ce20969629e3a9',1,'haplo::gbwt_thread_t::gbwt_thread_t(const gbwt::vector_type &nodes, const vector< size_t > &node_lengths)']]],
- ['gbwt_5fto_5fhandle_9090',['gbwt_to_handle',['../namespacevg.html#a28c93b1c4a71fadf62fc2582cc8f0ed2',1,'vg']]],
- ['gbwt_5fto_5fpos_9091',['gbwt_to_pos',['../namespacevg.html#ae7b5f995eb3e1e824cc4e7db99c81042',1,'vg']]],
- ['gbwtconfig_9092',['GBWTConfig',['../structGBWTConfig.html#a20a8123e9a054bab77de5e8d9f9c1bd5',1,'GBWTConfig']]],
- ['gbwtscoreprovider_9093',['GBWTScoreProvider',['../classhaplo_1_1GBWTScoreProvider.html#abf8bd05e480afa9a2ac2832a13f5b181',1,'haplo::GBWTScoreProvider']]],
- ['gbwttraversalfinder_9094',['GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html#af415423d43372c2770c201a10ace0385',1,'vg::GBWTTraversalFinder']]],
- ['gcsa_5fnodes_5fto_5fpositions_9095',['gcsa_nodes_to_positions',['../namespacevg.html#a3240e7b9bf787fb218d6324389ea234e',1,'vg']]],
- ['generate_9096',['generate',['../structvg_1_1RecombinatorFragment.html#a411831e7ba9db75f1d14708bb79f7eef',1,'vg::RecombinatorFragment']]],
- ['generate_5fcontinuous_5funiform_9097',['generate_continuous_uniform',['../classvg_1_1MCMCGenotyper.html#a5ebeff817c6548c32c5377ed00c041c6',1,'vg::MCMCGenotyper']]],
- ['generate_5fdiscrete_5funiform_9098',['generate_discrete_uniform',['../classvg_1_1MCMCGenotyper.html#a8b76754fc9611d38463cccd3051c0589',1,'vg::MCMCGenotyper']]],
- ['generate_5ffrom_5fwide_5fgenerator_9099',['generate_from_wide_generator',['../classvg_1_1uniform__int__distribution.html#a6efdc1be7572287df4cfad1acd044d90',1,'vg::uniform_int_distribution']]],
- ['generate_5fhaplotype_9100',['generate_haplotype',['../namespacevg.html#a117021c748aad14cfa190bbd2452405d',1,'vg']]],
- ['generate_5fhaplotypes_9101',['generate_haplotypes',['../classvg_1_1Recombinator.html#a7f803cd4d08d8c699877e274bc3f5ceb',1,'vg::Recombinator::generate_haplotypes(const std::string &kff_file, const Parameters ¶meters) const'],['../classvg_1_1Recombinator.html#a8ac8a32e83455572b44af1da347cd09d',1,'vg::Recombinator::generate_haplotypes(const Haplotypes::TopLevelChain &chain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata, const Parameters ¶meters, double coverage) const']]],
- ['generate_5finitial_5fguess_9102',['generate_initial_guess',['../classvg_1_1MCMCGenotyper.html#aac263c28f16acd3eb17d1f6013b5709e',1,'vg::MCMCGenotyper']]],
- ['generate_5fpaths_9103',['generate_paths',['../classvg_1_1PhaseUnfolder.html#a7a2015207e502ecd4d294af79936bda2',1,'vg::PhaseUnfolder']]],
- ['generate_5fthreads_9104',['generate_threads',['../classvg_1_1PhaseUnfolder.html#abc5cead86bec1446aedd4cb2ec291d3f',1,'vg::PhaseUnfolder']]],
- ['genomestate_9105',['GenomeState',['../classvg_1_1GenomeState.html#ab132518a611296d53c4f59a6b5737374',1,'vg::GenomeState']]],
- ['genotype_9106',['genotype',['../classvg_1_1SnarlCaller.html#a3e4d1ad4ece1a1bc1daa4ea6ecfbfa54',1,'vg::SnarlCaller::genotype()'],['../classvg_1_1RatioSupportSnarlCaller.html#afa1d42f1ba7e32ca274e23d0e9795278',1,'vg::RatioSupportSnarlCaller::genotype()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a1be3298970827475c5b96486d58fd833',1,'vg::PoissonSupportSnarlCaller::genotype()']]],
- ['genotype_5flikelihood_9107',['genotype_likelihood',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a555a22f275a83ade8fcd35a1572908',1,'vg::PoissonSupportSnarlCaller']]],
- ['genotype_5fsnarl_9108',['genotype_snarl',['../classvg_1_1Genotyper.html#ae6a3a060adcffc32724498bbfda2c771',1,'vg::Genotyper']]],
- ['genotype_5fsvs_9109',['genotype_svs',['../namespacevg.html#a7d3374c888c7c37f1de8370e151af7f9',1,'vg']]],
- ['geometric_5fsampling_5fprob_5fln_9110',['geometric_sampling_prob_ln',['../namespacevg.html#ae923ee7bdb53f33511c95f66a9c2773a',1,'vg']]],
- ['get_9111',['get',['../structvg_1_1Annotation.html#a00494075a8d051c16b2485b44c541dce',1,'vg::Annotation::get()'],['../classvg_1_1GBZGraph.html#a69ee920e1aa95a146e8e77f32a717a88',1,'vg::GBZGraph::get()'],['../classvg_1_1GBZGraph.html#a3eb7ff9317143e89c14bd15a682426ac',1,'vg::GBZGraph::get() const'],['../classvg_1_1VcfBuffer.html#ac855a338ea08f2ea75dc73206f9d7520',1,'vg::VcfBuffer::get()'],['../classvg_1_1WindowedVcfBuffer.html#a3c09bb140ab8f8d91f2f67f3dc0e7f0b',1,'vg::WindowedVcfBuffer::get()'],['../classvg_1_1subcommand_1_1Subcommand.html#aa44da5b424f5fcf7133f6a061680693f',1,'vg::subcommand::Subcommand::get()']]],
- ['get_5fadaptive_5fmin_5freseed_5flength_9112',['get_adaptive_min_reseed_length',['../classvg_1_1BaseMapper.html#a7f693887391ddeaebf4a4a609e2ab9b3',1,'vg::BaseMapper']]],
- ['get_5faffinities_9113',['get_affinities',['../classvg_1_1Genotyper.html#abea795c1969c4866c349a07c7f9c7102',1,'vg::Genotyper']]],
- ['get_5faffinities_5ffast_9114',['get_affinities_fast',['../classvg_1_1Genotyper.html#a966eee3f764281271904996546ef205b',1,'vg::Genotyper']]],
- ['get_5faligner_9115',['get_aligner',['../classvg_1_1AlignerClient.html#a683c04ab96b613ea3459738beffe5982',1,'vg::AlignerClient']]],
- ['get_5falignment_5femitter_9116',['get_alignment_emitter',['../namespacevg.html#aa95de659d860fc90fda95df414c89baf',1,'vg']]],
- ['get_5falignment_5fstart_9117',['get_alignment_start',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a5790a8cfd26dd12a19d33fc11cb84933',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['get_5falignments_9118',['get_alignments',['../structvg_1_1AugmentedGraph.html#ad92c283634470f6372777c38a9a70a79',1,'vg::AugmentedGraph::get_alignments(id_t node_id) const'],['../structvg_1_1AugmentedGraph.html#a61465a645ac54c62d4707d570ed56f76',1,'vg::AugmentedGraph::get_alignments(pair< NodeSide, NodeSide >) const'],['../structvg_1_1AugmentedGraph.html#ab3bf8e1a51696ba12329045956b7646a',1,'vg::AugmentedGraph::get_alignments() const']]],
- ['get_5fallele_9119',['get_allele',['../classvg_1_1PhasedGenome.html#a6f89ab856a31dfb7258fd7487c051a5a',1,'vg::PhasedGenome']]],
- ['get_5falleles_9120',['get_alleles',['../classvg_1_1Deconstructor.html#a7977882fef8c75836fede5338925f411',1,'vg::Deconstructor']]],
- ['get_5falt_5fpath_9121',['get_alt_path',['../classvg_1_1VCFTraversalFinder.html#acbbbaa19966bd2a939f9fdc05b414343',1,'vg::VCFTraversalFinder']]],
- ['get_5falt_5ftraversal_9122',['get_alt_traversal',['../classvg_1_1VCFTraversalFinder.html#afd039c87e92906ac02479d8d2df43f13',1,'vg::VCFTraversalFinder']]],
- ['get_5fannotation_9123',['get_annotation',['../classvg_1_1multipath__alignment__t.html#a401b9ef14924b463d54be7a4ced828d6',1,'vg::multipath_alignment_t::get_annotation()'],['../namespacevg.html#a1fda752e24eaed100f6c30904d2ca3e1',1,'vg::get_annotation(const Annotated &annotated, const string &name)'],['../namespacevg.html#a1c9f371af54160a44a44afd80c6cf71a',1,'vg::get_annotation(Annotated *annotated, const string &name)']]],
- ['get_5fany_5fgraph_9124',['get_any_graph',['../structGraphHandler.html#a7155dd41d244081487e79759707f29af',1,'GraphHandler']]],
- ['get_5faverage_5ftraversal_5fsupport_5fswitch_5fthreshold_9125',['get_average_traversal_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a62c1864ae422d93cba4eb248890fd3e4',1,'vg::TraversalSupportFinder']]],
- ['get_5favg_5fbaseq_9126',['get_avg_baseq',['../namespacevg.html#a680a465e72fbddeed584f27a6c3f7b27',1,'vg']]],
- ['get_5favg_5fnode_5fmapq_9127',['get_avg_node_mapq',['../classvg_1_1TraversalSupportFinder.html#a55880f595d8f607a73e8617e7b2aa216',1,'vg::TraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1PackedTraversalSupportFinder.html#a1fd604b1e8eac99954981aca81cafffd',1,'vg::PackedTraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aa3fab4fec47f870d3cc6e2c1fdb46ccb',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_mapq()']]],
- ['get_5favg_5fnode_5fsupport_9128',['get_avg_node_support',['../classvg_1_1TraversalSupportFinder.html#a42cf4393f0ff594d0eaf489b2127cdef',1,'vg::TraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a66cbea99df3ef78364f653a044bec308',1,'vg::PackedTraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#abb0f5d8c3967c099daaf2fb174620f3a',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_support()']]],
- ['get_5fback_5fgraph_5fnode_5fname_9129',['get_back_graph_node_name',['../classvg_1_1FlatFileBackTranslation.html#a816506e29e304f623d790d79271fd344',1,'vg::FlatFileBackTranslation::get_back_graph_node_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a5829e7992e105e0895a81a8aca82e70b',1,'vg::algorithms::GFAIDMapInfo::get_back_graph_node_name()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#acd81ad54c6a6ec680faaae76aaae4397',1,'handlegraph::NamedNodeBackTranslation::get_back_graph_node_name()']]],
- ['get_5fbase_9130',['get_base',['../classvg_1_1IncrementalSubgraph.html#a6ff73a10a56b8116b7d07c32d3f3160a',1,'vg::IncrementalSubgraph::get_base()'],['../classvg_1_1JoinedSpliceGraph.html#a7dcc1d1e3e9c2e1058a5995785b0a224',1,'vg::JoinedSpliceGraph::get_base()'],['../classvg_1_1VG.html#a7cb582e352f75cc9d66e6eff0f4ba659',1,'vg::VG::get_base()'],['../classxg_1_1XG.html#a355dd79f8449b462e7d98916f1a22d9f',1,'xg::XG::get_base()'],['../classhandlegraph_1_1HandleGraph.html#a64d58c3e26e9e7954dd25c3eff7af521',1,'handlegraph::HandleGraph::get_base()']]],
- ['get_5fbase_5fgbwt_5fpath_5fname_9131',['get_base_gbwt_path_name',['../classvg_1_1Transcriptome.html#a1c9af6904f1f282a0782c1e34bc4b9ab',1,'vg::Transcriptome']]],
- ['get_5fbest_5falignment_5fagainst_5fany_5ftree_9132',['get_best_alignment_against_any_tree',['../classvg_1_1MinimizerMapper.html#a12558b08552a22a9a28db3fb0fd3779d',1,'vg::MinimizerMapper']]],
- ['get_5fbest_5fchain_5fstats_9133',['get_best_chain_stats',['../classvg_1_1MinimizerMapper.html#a2f9b9b580ed851b00268f455c2d543cb',1,'vg::MinimizerMapper']]],
- ['get_5fbest_5fgbwtgraph_5fgfa_5fparsing_5fparameters_9134',['get_best_gbwtgraph_gfa_parsing_parameters',['../namespacevg.html#ab35317ee2bc53165662dd776516f341d',1,'vg']]],
- ['get_5fbest_5fsupport_9135',['get_best_support',['../classvg_1_1SupportBasedSnarlCaller.html#a1b5a50373729771229ada685b12627df',1,'vg::SupportBasedSnarlCaller']]],
- ['get_5fbias_9136',['get_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a3f5f06692eeabe27d7c00afc8658cb20',1,'vg::RatioSupportSnarlCaller']]],
- ['get_5fbin_5fsize_9137',['get_bin_size',['../classvg_1_1Packer.html#afef014ad5278ee08959c3ffe2cf15c17',1,'vg::Packer']]],
- ['get_5fbound_9138',['get_bound',['../classhandlegraph_1_1SnarlDecomposition.html#aabee8d2ebb1971ecfd5c4647b84081f2',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fbounds_9139',['get_bounds',['../classvg_1_1Constructor.html#a06078b6af1dc190c74806b30b669daae',1,'vg::Constructor']]],
- ['get_5fbuckets_9140',['get_buckets',['../classvg_1_1OrientedDistanceMeasurer.html#aa21aedba58999e7041483f077720d13b',1,'vg::OrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#aac5383ef03533609d85172e7821a8200',1,'vg::PathOrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#ac885044126300cab4750fd21fd4634fc',1,'vg::SnarlOrientedDistanceMeasurer::get_buckets()']]],
- ['get_5fcategory_9141',['get_category',['../classvg_1_1subcommand_1_1Subcommand.html#a252c8946e450ba4a194b7da6ece5ba2c',1,'vg::subcommand::Subcommand']]],
- ['get_5fcc_5fin_5fwg_9142',['get_cc_in_wg',['../classvg_1_1FlowSort.html#a27df1607587f1f1e1f03ab8369c34ebe',1,'vg::FlowSort']]],
- ['get_5fcenter_9143',['get_center',['../classvg_1_1VariantAdder.html#a2949d0ea5c46f477813df8f5162fe013',1,'vg::VariantAdder']]],
- ['get_5fcenter_5fand_5fradius_9144',['get_center_and_radius',['../classvg_1_1VariantAdder.html#a29a14a6579197519b35653f542d5c1ec',1,'vg::VariantAdder']]],
- ['get_5fchain_5fcode_9145',['get_chain_code',['../classvg_1_1ZipCode.html#aa0f40a265733bd4adfb920006fd9f57a',1,'vg::ZipCode']]],
- ['get_5fchain_5fcomponent_9146',['get_chain_component',['../classvg_1_1ZipCode.html#af85179af0d75add0b10023343c2a407a',1,'vg::ZipCode::get_chain_component()'],['../structvg_1_1ZipCode_1_1node__code__t.html#a52e72d7ff49bcb809cac2f7ab85ad004',1,'vg::ZipCode::node_code_t::get_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5dcd90a391b2382723f3b303687ca1c8',1,'vg::ZipCode::snarl_code_t::get_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#adc51b5f6e09b00eb41964c902d7eb033',1,'vg::ZipCodeForest::sort_value_t::get_chain_component()']]],
- ['get_5fchild_5fcount_9147',['get_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a315c9998b34918303feb08d5143fba7c',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fchild_5fsupport_9148',['get_child_support',['../classvg_1_1TraversalSupportFinder.html#ac46ef820b2a05e8b331677deb80871a9',1,'vg::TraversalSupportFinder::get_child_support()'],['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af112bf57cc9a16c9dc35f6578a3b1c14',1,'vg::NestedCachedPackedTraversalSupportFinder::get_child_support()']]],
- ['get_5fclipped_5fposition_9149',['get_clipped_position',['../classvg_1_1Filter.html#a5cc119894a6baeb450c31dc7c6b75bed',1,'vg::Filter']]],
- ['get_5fclipped_5fref_5fposition_9150',['get_clipped_ref_position',['../classvg_1_1Filter.html#ab1a309b366e677b179772e9bebd9f78f',1,'vg::Filter']]],
- ['get_5fclipped_5fseq_9151',['get_clipped_seq',['../classvg_1_1Filter.html#a4c29ccf736113bb95328467d22f98ad8',1,'vg::Filter']]],
- ['get_5fcluster_5fpairs_9152',['get_cluster_pairs',['../classvg_1_1MultipathMapper.html#a49fdf1a2efedda808c2d3a7bda5a7f98',1,'vg::MultipathMapper']]],
- ['get_5fclusters_9153',['get_clusters',['../classvg_1_1MultipathMapper.html#a0a588e4f282d38add8626debe86c455d',1,'vg::MultipathMapper']]],
- ['get_5fcode_5ftype_9154',['get_code_type',['../classvg_1_1ZipCode.html#ac91d59c7100fefc2011cda07996ed71a',1,'vg::ZipCode::get_code_type()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a0d7f3c9052df0ced4949b909d1ed20b5',1,'vg::ZipCode::snarl_code_t::get_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a9959da3b3a6e98968794073dc049eb0b',1,'vg::ZipCodeForest::sort_value_t::get_code_type()']]],
- ['get_5fcodename_9155',['get_codename',['../classvg_1_1Version.html#a0bab20984ed75b2df12c3ef4a409f922',1,'vg::Version']]],
- ['get_5fconnected_5fcomponents_9156',['get_connected_components',['../classvg_1_1MultipathAlignmentGraph.html#af4fc215d24f20c5ddc3916024c7ab62b',1,'vg::MultipathAlignmentGraph']]],
- ['get_5fconnectivity_9157',['get_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a0b28eb090f0d0f7b1b408a5e772b3105',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fcontained_5forientations_9158',['get_contained_orientations',['../structvg_1_1PathIndex.html#a6a7f7bbcd256a2ed34a58b8abefff712',1,'vg::PathIndex']]],
- ['get_5fcontext_9159',['get_context',['../classvg_1_1Deconstructor.html#a049890802f6b6036a779eb3645bb1307',1,'vg::Deconstructor']]],
- ['get_5fcorrelation_9160',['get_correlation',['../classvg_1_1ZipCodeForest.html#ab939e5ee856a9ac2531d0d8ac14e7cbe',1,'vg::ZipCodeForest']]],
- ['get_5fcount_9161',['get_count',['../classvg_1_1NoAlignmentInBandException.html#a4b5f7f90a2be571131fb12484a9b4c18',1,'vg::NoAlignmentInBandException']]],
- ['get_5fcreate_5fpath_9162',['get_create_path',['../classvg_1_1Paths.html#a4e79d7915cd2f68e55573bcc50c1d417',1,'vg::Paths']]],
- ['get_5fcreated_5fhandle_9163',['get_created_handle',['../classvg_1_1ExtraNodeGraph.html#aac84ee8139e0aa885b87f02ad9ccf8ef',1,'vg::ExtraNodeGraph']]],
- ['get_5fcurrent_5fcolumn_9164',['get_current_column',['../structhaplo_1_1haplo__DP.html#a0061c97ecd2330efdcf0fbabb69d808d',1,'haplo::haplo_DP']]],
- ['get_5fcurrent_5fvmem_5fkb_9165',['get_current_vmem_kb',['../namespacevg.html#a8cd30aaebcab130194ac375f23e6f098',1,'vg']]],
- ['get_5fcut_5fsegments_9166',['get_cut_segments',['../classvg_1_1MultipathAlignmentGraph.html#aaa64dbf4207ebe2fe75044d60be1d07e',1,'vg::MultipathAlignmentGraph']]],
- ['get_5fcyclic_5fsnarl_5fintervals_9167',['get_cyclic_snarl_intervals',['../classvg_1_1ZipCodeForest.html#ad32664318549a51d8727204d665a2bc6',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const interval_state_t &snarl_interval, const interval_state_t &parent_interval, const forward_list< interval_state_t > &child_intervals, forward_list< interval_state_t > &next_intervals) const'],['../classvg_1_1ZipCodeForest.html#a72304772e60e79909b71f8a51e65d6a5',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const ZipCodeForest::interval_state_t &snarl_interval, const ZipCodeForest::interval_state_t &parent_interval, const forward_list< ZipCodeForest::interval_state_t > &child_intervals, forward_list< ZipCodeForest::interval_state_t > &next_intervals) const']]],
- ['get_5fdefault_5flong_5fgiraffe_5findexes_9168',['get_default_long_giraffe_indexes',['../structvg_1_1VGIndexes.html#a8caf19bd7436cd7f9df4f9792aa86483',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fmap_5findexes_9169',['get_default_map_indexes',['../structvg_1_1VGIndexes.html#afcc2119cd690b16f57d4b9d137af58fe',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fmpmap_5findexes_9170',['get_default_mpmap_indexes',['../structvg_1_1VGIndexes.html#a9377b325c6e0f8bbca1368379ad60a0c',1,'vg::VGIndexes']]],
- ['get_5fdefault_5frpvg_5findexes_9171',['get_default_rpvg_indexes',['../structvg_1_1VGIndexes.html#ae56d5009377fed32d392fcff5ac02f7f',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fshort_5fgiraffe_5findexes_9172',['get_default_short_giraffe_indexes',['../structvg_1_1VGIndexes.html#ab0f962c74f9633fe27b0d59f9774358c',1,'vg::VGIndexes']]],
- ['get_5fdefault_5fthreads_9173',['get_default_threads',['../minimizer__main_8cpp.html#a849308cddbd36f5fc06c5e1289112bae',1,'minimizer_main.cpp']]],
- ['get_5fdefault_5fvalue_9174',['get_default_value',['../classvg_1_1OptionInterface.html#ade1ab38610fecb31821e13e5e296454c',1,'vg::OptionInterface::get_default_value()'],['../classvg_1_1BaseOption.html#af13c01c387907bb386b591bff8bbb5e9',1,'vg::BaseOption::get_default_value()']]],
- ['get_5fdegree_9175',['get_degree',['../classvg_1_1ExtraNodeGraph.html#a0cc5cb40e81623b3a3e11bea359e41c5',1,'vg::ExtraNodeGraph::get_degree()'],['../classvg_1_1IncrementalSubgraph.html#ae3365d87d1cd6bfe12d3433197d06a85',1,'vg::IncrementalSubgraph::get_degree()'],['../classvg_1_1SourceSinkOverlay.html#a8bfc476463b487d42c77bda6bdfe2a7d',1,'vg::SourceSinkOverlay::get_degree()'],['../classvg_1_1VG.html#afc0ac00267e00156e04c849a10b1cb74',1,'vg::VG::get_degree()'],['../classhandlegraph_1_1HandleGraph.html#ab259e3aba0da47b0ef1c9b5e43c7d209',1,'handlegraph::HandleGraph::get_degree()']]],
- ['get_5fdepth_5ffrom_5findex_9176',['get_depth_from_index',['../namespacevg_1_1algorithms.html#a4152fa019243d9fd4c41c73fafce2241',1,'vg::algorithms']]],
- ['get_5fdescription_9177',['get_description',['../classvg_1_1OptionInterface.html#aa53deb39285f0045257083eb38d703cd',1,'vg::OptionInterface::get_description()'],['../classvg_1_1BaseOption.html#a4343a02a0967d6f79c0b8ae83c6a0795',1,'vg::BaseOption::get_description()'],['../classvg_1_1subcommand_1_1Subcommand.html#aca3e8621a4002b48b733211c3adc52b5',1,'vg::subcommand::Subcommand::get_description()']]],
- ['get_5fdiagonals_9178',['get_diagonals',['../classvg_1_1WFATree.html#a2bd4732a5815c365d3790b76b9230973',1,'vg::WFATree']]],
- ['get_5fdir_9179',['get_dir',['../namespacevg_1_1temp__file.html#ab1b0884547b4f3403e8cde0ca8b75b7c',1,'vg::temp_file::get_dir()'],['../namespacexg_1_1temp__file.html#a1cef40a1b0f27d1693d827db9773c020',1,'xg::temp_file::get_dir()']]],
- ['get_5fdisjoint_5fsets_9180',['get_disjoint_sets',['../classvg_1_1ContractingGraph.html#acd929119b9b11170f1eb4893a7032fe6',1,'vg::ContractingGraph']]],
- ['get_5fdistance_9181',['get_distance',['../classvg_1_1HaplotypePartitioner.html#a8d98335b0032014b1e033a6610fb644d',1,'vg::HaplotypePartitioner']]],
- ['get_5fdistance_5fend_5fleft_9182',['get_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ad3e98278c0ca79470bc1a58e3fdcf370',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5fend_5fright_9183',['get_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa5d11da32ad7be1dfa88674efd4fa422',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5findex_5faddress_9184',['get_distance_index_address',['../classvg_1_1ZipCode.html#a6cc3964efc186615dab6bdd8bc52fbfb',1,'vg::ZipCode']]],
- ['get_5fdistance_5flimit_9185',['get_distance_limit',['../classvg_1_1MinimizerMapper.html#a27798cd4a1bee171ec38713d402e8793',1,'vg::MinimizerMapper']]],
- ['get_5fdistance_5fmeasurer_9186',['get_distance_measurer',['../classvg_1_1MultipathMapper.html#a56e1c69cfba7c1eebb4cae0af59a018d',1,'vg::MultipathMapper']]],
- ['get_5fdistance_5fstart_5fleft_9187',['get_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a678e476d61bcf781b1461cedb8801c68',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5fstart_5fright_9188',['get_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aedb473ac00ffbd480c09fd04e44fcbb8',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fdistance_5fto_5fsnarl_5fbound_9189',['get_distance_to_snarl_bound',['../classvg_1_1ZipCode.html#ad39662d894fe714c1d8596b0343557f6',1,'vg::ZipCode']]],
- ['get_5fdistance_5fvalue_9190',['get_distance_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a2a427abecffc91c8f56b715de43a43b3',1,'vg::ZipCodeForest::sort_value_t']]],
- ['get_5fduplicate_5fhandle_9191',['get_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#af51998490e3eac92e0d106b791eebbce',1,'vg::DozeuPinningOverlay']]],
- ['get_5fedge_9192',['get_edge',['../classvg_1_1VG.html#a8668ddc84b9abe4fe9cb5acb3efd877b',1,'vg::VG::get_edge(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a227023072262f46f7c423d30cf8bc443',1,'vg::VG::get_edge(const pair< NodeSide, NodeSide > &sides)'],['../classvg_1_1VG.html#af63d7ba7b69594ee99f3ad99dd394171',1,'vg::VG::get_edge(const NodeTraversal &left, const NodeTraversal &right)']]],
- ['get_5fedge_5fcount_9193',['get_edge_count',['../classvg_1_1IncrementalSubgraph.html#aeab323f77d0363867dc60be6dafe73ce',1,'vg::IncrementalSubgraph::get_edge_count()'],['../classvg_1_1VG.html#ad4577be9213932c313efd3d016b88a31',1,'vg::VG::get_edge_count()'],['../classxg_1_1XG.html#aa624840475fc83351c00ef2728480355',1,'xg::XG::get_edge_count()'],['../classhandlegraph_1_1HandleGraph.html#a20ff62014d7f0f0c01ada8a3d40a278d',1,'handlegraph::HandleGraph::get_edge_count()']]],
- ['get_5fedge_5flength_9194',['get_edge_length',['../classvg_1_1TraversalSupportFinder.html#a4902b9dcdaa53f74f45a394265163311',1,'vg::TraversalSupportFinder']]],
- ['get_5fedge_5fsupport_9195',['get_edge_support',['../classvg_1_1TraversalSupportFinder.html#a8b497d8e282da9696d2ae5df86664069',1,'vg::TraversalSupportFinder::get_edge_support(const edge_t &edge) const =0'],['../classvg_1_1TraversalSupportFinder.html#a958a20d44167e8c29f677e12b950b5fa',1,'vg::TraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const =0'],['../classvg_1_1PackedTraversalSupportFinder.html#a394485c49fb5d8043d9f98385dab1b4a',1,'vg::PackedTraversalSupportFinder::get_edge_support(const edge_t &edge) const'],['../classvg_1_1PackedTraversalSupportFinder.html#a5cfa1254fae043f9920761a533d63480',1,'vg::PackedTraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#a72ae391a14cf1625286d8c3aff3cd7a5',1,'vg::CachedPackedTraversalSupportFinder::get_edge_support()']]],
- ['get_5fedges_9196',['get_edges',['../classvg_1_1ContractingGraph.html#a9faff1ddfb92cfa26ba59803899148e7',1,'vg::ContractingGraph']]],
- ['get_5fend_9197',['get_end',['../classvg_1_1NetGraph.html#acccdda49a6444e96292b90218e273942',1,'vg::NetGraph']]],
- ['get_5fend_5fbound_9198',['get_end_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a4c500f039a8740ff6e771ddf4bf693ad',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fend_5fmatches_9199',['get_end_matches',['../classvg_1_1ReadFilter.html#a3cd3ee44928526e27e42e059b693ba76',1,'vg::ReadFilter::get_end_matches(const Read &read) const'],['../classvg_1_1ReadFilter.html#a1e40faa7aa74f7b17390b06da6ad32e4',1,'vg::ReadFilter::get_end_matches(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#a45116be7bd52bfd9fb40e30f08aee97f',1,'vg::ReadFilter::get_end_matches(const Alignment &read) const']]],
- ['get_5fend_5fof_9200',['get_end_of',['../namespacevg.html#af76e8a5e74f67093a40ed5f2cd15ff28',1,'vg']]],
- ['get_5fendpoints_9201',['get_endpoints',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a9e3d20d5ab60eb99688d6346a788d308',1,'vg::GraphSynchronizer::Lock']]],
- ['get_5fexon_5fhaplotypes_9202',['get_exon_haplotypes',['../classvg_1_1Transcriptome.html#a2753baecefb5f065854fd9fbc1a24dc9',1,'vg::Transcriptome']]],
- ['get_5ffeatures_9203',['get_features',['../classvg_1_1FeatureSet.html#a55b389aa1c68efddb28a188a757568fc',1,'vg::FeatureSet']]],
- ['get_5ffile_5fsize_9204',['get_file_size',['../namespacevg.html#a53098c7c826c3d8d2aab804ba5500fd5',1,'vg']]],
- ['get_5ffilenames_9205',['get_filenames',['../classvg_1_1IndexFile.html#a5833162264de6ce5f2a0d882b4b12839',1,'vg::IndexFile']]],
- ['get_5ffirst_5fnode_5fhandle_9206',['get_first_node_handle',['../structvg_1_1EditedTranscriptPath.html#aec08731a5fd5989db7721a3ecf0859e7',1,'vg::EditedTranscriptPath::get_first_node_handle()'],['../structvg_1_1CompletedTranscriptPath.html#af48eb44f24298e5f3efa4641eb91d813',1,'vg::CompletedTranscriptPath::get_first_node_handle()']]],
- ['get_5ffraction_5fof_5fns_9207',['get_fraction_of_ns',['../namespacevg.html#af8f8da6eb179ba0199fc2fdfe676fde7',1,'vg']]],
- ['get_5ffragment_5flength_5fmean_9208',['get_fragment_length_mean',['../classvg_1_1MinimizerMapper.html#a1e08dfa10f620ef44d102123b38b8fe8',1,'vg::MinimizerMapper']]],
- ['get_5ffragment_5flength_5fsample_5fsize_9209',['get_fragment_length_sample_size',['../classvg_1_1MinimizerMapper.html#ab4c62a806ad7b64072a770c9b4db3417',1,'vg::MinimizerMapper']]],
- ['get_5ffragment_5flength_5fstdev_9210',['get_fragment_length_stdev',['../classvg_1_1MinimizerMapper.html#ae048c4929acb22eabd55f54ac3cc6f18',1,'vg::MinimizerMapper']]],
- ['get_5fg_5fiv_5fsize_9211',['get_g_iv_size',['../classxg_1_1XG.html#a1162be39bbe491975cd47c56fc044489',1,'xg::XG']]],
- ['get_5fgbwt_9212',['get_gbwt',['../classvg_1_1GBWTTraversalFinder.html#a07c5e06ec89e54f2efc2d84974b71ca3',1,'vg::GBWTTraversalFinder::get_gbwt()'],['../namespacevg.html#a571047c58b73b78d02a767c3ab6ec222',1,'vg::get_gbwt()']]],
- ['get_5fgenotype_5flog_5flikelihood_9213',['get_genotype_log_likelihood',['../classvg_1_1Genotyper.html#a9071cdf5ae591b478feaac025b069772',1,'vg::Genotyper']]],
- ['get_5fgenotype_5flog_5fprior_9214',['get_genotype_log_prior',['../classvg_1_1Genotyper.html#a5fc66cb05c4ba80e39d078af9ddce715',1,'vg::Genotyper']]],
- ['get_5fgenotypes_9215',['get_genotypes',['../classvg_1_1Deconstructor.html#abed056375d448eeffebcf1b15633fe79',1,'vg::Deconstructor']]],
- ['get_5fgraph_9216',['get_graph',['../classvg_1_1Packer.html#a19b5aa3c38b65c9e35e2ab7604bdbec4',1,'vg::Packer::get_graph()'],['../classvg_1_1VariantAdder.html#a1271c6d39e6387bac452d9bf80689ed5',1,'vg::VariantAdder::get_graph()'],['../structGraphHandler.html#ab0c19a482787b623d946746f33b2fb80',1,'GraphHandler::get_graph()']]],
- ['get_5fgraph_5fdistance_9217',['get_graph_distance',['../namespacevg_1_1algorithms.html#a0b788763f4e6747ba55e5340de9da855',1,'vg::algorithms']]],
- ['get_5fhandle_9218',['get_handle',['../classvg_1_1DagifiedGraph.html#a57e727b78f3eac1ee34b5dabf08a278f',1,'vg::DagifiedGraph::get_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a78c76b68997b94da8bb714ad87b6ce55',1,'vg::DozeuPinningOverlay::get_handle()'],['../classvg_1_1ExtraNodeGraph.html#a76226cecc78c23a95db06f2765138e6f',1,'vg::ExtraNodeGraph::get_handle()'],['../classvg_1_1GaplessExtender.html#ace7698779da48ed9216169b935b0287c',1,'vg::GaplessExtender::get_handle()'],['../classvg_1_1SnarlGraph.html#a8c06fedda57c3e031d8d3b7fbcb696a8',1,'vg::SnarlGraph::get_handle()'],['../classvg_1_1IdentityOverlay.html#a3fc814950bd9b0b003b82637be9c1d06',1,'vg::IdentityOverlay::get_handle()'],['../classvg_1_1IncrementalSubgraph.html#ac2d018cb5a59b4f43e24a4f30643e0f1',1,'vg::IncrementalSubgraph::get_handle()'],['../classvg_1_1IndexedVG.html#ad9779976b07decd5b593b7a097cac44e',1,'vg::IndexedVG::get_handle()'],['../classvg_1_1MemoizingGraph.html#aa0b891348a82fe4fad7f60ab87fbd4b4',1,'vg::MemoizingGraph::get_handle()'],['../classvg_1_1NullMaskingGraph.html#aea8062f2a253f0397a91005b3924475e',1,'vg::NullMaskingGraph::get_handle()'],['../classvg_1_1PathSubgraph.html#a9d2fc4747e6c86125ba149c90041abcd',1,'vg::PathSubgraph::get_handle()'],['../classvg_1_1ReverseGraph.html#a34a79e8c3f5d5f029d5a1427ca10cfbd',1,'vg::ReverseGraph::get_handle()'],['../classvg_1_1NetGraph.html#a639a1a278626238fe98568320590c64f',1,'vg::NetGraph::get_handle()'],['../classvg_1_1SourceSinkOverlay.html#a7cc144d829750cfb85341d42bd4f7e4a',1,'vg::SourceSinkOverlay::get_handle()'],['../classvg_1_1JoinedSpliceGraph.html#a17636cfa63438f4b5941d54b7632d64b',1,'vg::JoinedSpliceGraph::get_handle()'],['../classvg_1_1StrandSplitGraph.html#a97db8ec5efb4280bfe358b0859e96659',1,'vg::StrandSplitGraph::get_handle()'],['../classvg_1_1SubHandleGraph.html#a4cf66400a93dee8a1e49fcc88ab24eb5',1,'vg::SubHandleGraph::get_handle()'],['../classvg_1_1SubgraphOverlay.html#ab36d552e3882740962729d19069f9ddc',1,'vg::SubgraphOverlay::get_handle()'],['../classvg_1_1SubpathOverlay.html#a3871270e3d47a023f27f9bac6959983b',1,'vg::SubpathOverlay::get_handle()'],['../classvg_1_1TreeSubgraph.html#ab7b56b78b8750cc6453180e7e531d925',1,'vg::TreeSubgraph::get_handle()'],['../classvg_1_1VG.html#a70f50e6766af9262c732de26243658f5',1,'vg::VG::get_handle()'],['../classxg_1_1XG.html#adc5660ffe20948888aeca0c6e6bba90a',1,'xg::XG::get_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0a950e73c94a514de69f95be80f96b7e',1,'handlegraph::algorithms::SubHandleGraph::get_handle()'],['../classhandlegraph_1_1HandleGraph.html#a6dd9d70931835f5c75518b23a780b744',1,'handlegraph::HandleGraph::get_handle()'],['../classhandlegraph_1_1SnarlDecomposition.html#a94e6360cbad97a084d6ec3a6a461e20c',1,'handlegraph::SnarlDecomposition::get_handle()']]],
- ['get_5fhandle_5ffrom_5finward_5fbacking_5fhandle_9219',['get_handle_from_inward_backing_handle',['../classvg_1_1NetGraph.html#a62b87ba5400e8c6d3f6335fc2198cc38',1,'vg::NetGraph']]],
- ['get_5fhandle_5fof_5fstep_9220',['get_handle_of_step',['../classvg_1_1MemoizingGraph.html#a2b4cd0c4ebef4dcefd5bbafcd1ab3e54',1,'vg::MemoizingGraph::get_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a05ce3d84e3e774a89d4d61a70381cee2',1,'vg::PathSubgraphOverlay::get_handle_of_step()'],['../classvg_1_1VG.html#acb73599cc743a392650a7002c8dc2906',1,'vg::VG::get_handle_of_step()'],['../classxg_1_1XG.html#abbfaa6afca08ec2aca7f2fd550221793',1,'xg::XG::get_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a339e690ce3e2bb8280dd1f3ea45abe42',1,'handlegraph::PathHandleGraph::get_handle_of_step()']]],
- ['get_5fhaplotype_9221',['get_haplotype',['../classhandlegraph_1_1PathMetadata.html#a8ea83e700d11830e7eb695b8a11cb17f',1,'handlegraph::PathMetadata::get_haplotype()'],['../haplotypes__main_8cpp.html#ada326bf02798916f16c46f5d308ebc5b',1,'get_haplotype(): haplotypes_main.cpp']]],
- ['get_5fhaplotype_5falt_5fcontents_9222',['get_haplotype_alt_contents',['../classvg_1_1VCFTraversalFinder.html#a3ce22629a99aae20002c43c7e581c2fb',1,'vg::VCFTraversalFinder']]],
- ['get_5fhaplotype_5fcount_9223',['get_haplotype_count',['../classhaplo_1_1ScoreProvider.html#aac21ae0e24c45170e81b4880f8c21f8d',1,'haplo::ScoreProvider::get_haplotype_count()'],['../classhaplo_1_1GBWTScoreProvider.html#a8aedfce11f295af0fba3ae7f17f20c9b',1,'haplo::GBWTScoreProvider::get_haplotype_count()']]],
- ['get_5fhaplotypes_5fwith_5fsnarl_9224',['get_haplotypes_with_snarl',['../classvg_1_1PhasedGenome.html#a81cff23c8687f759dd464fca51cf306e',1,'vg::PhasedGenome']]],
- ['get_5fhelp_9225',['get_help',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a9880c67cbeb3f5b7ba3bad714844702c',1,'vg::subcommand::BaseOptionGroup::get_help()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a958199095b53020a85a5abc2ae1f0a91',1,'vg::subcommand::OptionGroup::get_help()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a01f89740d89e82cf12c204c28ec01fd2',1,'vg::subcommand::GroupedOptionGroup::get_help()']]],
- ['get_5fid_9226',['get_id',['../classvg_1_1DagifiedGraph.html#ae510cacf154e272f63b37a3207046c96',1,'vg::DagifiedGraph::get_id()'],['../classvg_1_1DozeuPinningOverlay.html#ad84aae5d9cce852e254d5da05da40fa8',1,'vg::DozeuPinningOverlay::get_id()'],['../classvg_1_1ExtraNodeGraph.html#aef3ca5fb2071fdb33a7a8f663473de32',1,'vg::ExtraNodeGraph::get_id()'],['../classvg_1_1SnarlGraph.html#aba421b2e2cd40a7d489c13e0ab81f179',1,'vg::SnarlGraph::get_id()'],['../classvg_1_1IdentityOverlay.html#ab144f5ecbf4a5f49a5ffbea80ebd56ec',1,'vg::IdentityOverlay::get_id()'],['../classvg_1_1IncrementalSubgraph.html#a825edf9eddd3fa6093f2045656ae98f1',1,'vg::IncrementalSubgraph::get_id()'],['../classvg_1_1IndexedVG.html#ad23ba69aad4d8c94f58319bb657e3235',1,'vg::IndexedVG::get_id()'],['../classvg_1_1MemoizingGraph.html#a23b6df961f0e8253fba88423f2bcf128',1,'vg::MemoizingGraph::get_id()'],['../classvg_1_1NullMaskingGraph.html#a541f81de46db62d5e8f37e3cfc51f08e',1,'vg::NullMaskingGraph::get_id()'],['../classvg_1_1PathSubgraph.html#a47ff1fe374dccd07542ed1523327553e',1,'vg::PathSubgraph::get_id()'],['../classvg_1_1ReverseGraph.html#aef09dbb8dd08735bdd123b2a9d0066e0',1,'vg::ReverseGraph::get_id()'],['../classvg_1_1NetGraph.html#a9964476cfff61404eeb9d65cc182aa4a',1,'vg::NetGraph::get_id()'],['../classvg_1_1SourceSinkOverlay.html#a9c10b6562749e62bc1038ef23e8b9b28',1,'vg::SourceSinkOverlay::get_id()'],['../classvg_1_1JoinedSpliceGraph.html#a716f0b44bb48b6148617dc772d66959c',1,'vg::JoinedSpliceGraph::get_id()'],['../classvg_1_1StrandSplitGraph.html#a07bd24e1ed6a14843ddb87108a11c7f8',1,'vg::StrandSplitGraph::get_id()'],['../classvg_1_1SubHandleGraph.html#af40f7f453c71d4e52273479d0b600612',1,'vg::SubHandleGraph::get_id()'],['../classvg_1_1SubgraphOverlay.html#a301c8016ac2769d041c611cebd738c1e',1,'vg::SubgraphOverlay::get_id()'],['../classvg_1_1SubpathOverlay.html#ab58cd06e1330b752ad55e32878e8e64e',1,'vg::SubpathOverlay::get_id()'],['../classvg_1_1TreeSubgraph.html#ae48a59a93737e729ada7660a39fafa50',1,'vg::TreeSubgraph::get_id()'],['../classvg_1_1VG.html#a6f4b9ac16f23eb0420544ce8357736a3',1,'vg::VG::get_id()'],['../classxg_1_1XG.html#a0a9d6bce054a3ebf14807869883e9b98',1,'xg::XG::get_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a8150ada3f96723110a2ec7c1ed16323b',1,'handlegraph::algorithms::SubHandleGraph::get_id()'],['../classhandlegraph_1_1HandleGraph.html#adb7f6e144bf2a59679f7b2eddad934eb',1,'handlegraph::HandleGraph::get_id()'],['../namespacevg.html#ae4370b5cb4b42e8556b0fbc793fbdfc0',1,'vg::get_id()'],['../namespacexg.html#a5aab54915cd81fa71fd2ebc3b9e52fb8',1,'xg::get_id()']]],
- ['get_5fidentifier_9227',['get_identifier',['../classvg_1_1IndexFile.html#a0dde670fabfa3890d26c9e89c8564429',1,'vg::IndexFile::get_identifier()'],['../classvg_1_1ZipCode.html#a9cb3141131af81b42741bc9e7349e58b',1,'vg::ZipCode::get_identifier()']]],
- ['get_5findex_9228',['get_index',['../classvg_1_1IndexRegistry.html#a3738a3916a17ca5a2716e7530b10c434',1,'vg::IndexRegistry::get_index(const IndexName &identifier)'],['../classvg_1_1IndexRegistry.html#a2cde822432825ea731fed5318bd94152',1,'vg::IndexRegistry::get_index(const IndexName &identifier) const']]],
- ['get_5findexes_9229',['get_indexes',['../classvg_1_1RewindPlanException.html#a80a898014c62738052c18e85a0403a24',1,'vg::RewindPlanException']]],
- ['get_5finput_5ffile_9230',['get_input_file',['../namespacevg.html#ab1b8b686ef6eca09515be1abe566c013',1,'vg::get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)'],['../namespacevg.html#a09969fef23098c7729a2f190cecb4694',1,'vg::get_input_file(const string &file_name, function< void(istream &)> callback)']]],
- ['get_5finput_5ffile_5fname_9231',['get_input_file_name',['../namespacevg.html#a5026b599b1094a6c8e157f23b204b09b',1,'vg']]],
- ['get_5finward_5fbacking_5fhandle_9232',['get_inward_backing_handle',['../classvg_1_1NetGraph.html#adc4841db50e7f3073cad16d59426ba5a',1,'vg::NetGraph']]],
- ['get_5firregular_5fsnarl_5fcode_9233',['get_irregular_snarl_code',['../classvg_1_1ZipCode.html#a2057ff4f25f04aa76066c3c5a83239fc',1,'vg::ZipCode']]],
- ['get_5fis_5fcircular_9234',['get_is_circular',['../classvg_1_1MemoizingGraph.html#a2fb48c82bc92aa1fa263a4be92e21891',1,'vg::MemoizingGraph::get_is_circular()'],['../classvg_1_1PathSubgraphOverlay.html#ac33d15bc06e31045d07ecf22e018f0a8',1,'vg::PathSubgraphOverlay::get_is_circular()'],['../classvg_1_1VG.html#a1463f13c63b965a3663932e6fa87537e',1,'vg::VG::get_is_circular()'],['../classxg_1_1XG.html#a841e1c50686d3ea941fb9a01d9639784',1,'xg::XG::get_is_circular()'],['../classhandlegraph_1_1PathHandleGraph.html#a9391c34d9f0c16b21d5bb3bb7ec772e4',1,'handlegraph::PathHandleGraph::get_is_circular()']]],
- ['get_5fis_5flooping_5fchain_9235',['get_is_looping_chain',['../classvg_1_1ZipCode.html#a2c0fa7d7130b57bee9b557750eb97eab',1,'vg::ZipCode::get_is_looping_chain()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#ac917c5b03c10bd9e57b344a708c6b033',1,'vg::ZipCode::chain_code_t::get_is_looping_chain()']]],
- ['get_5fis_5fpaired_9236',['get_is_paired',['../classvg_1_1ReadFilter.html#a8b78c03c1379b1ed5576db5c6772adb3',1,'vg::ReadFilter::get_is_paired(const Read &read) const'],['../classvg_1_1ReadFilter.html#aaf6db93c73e3030a098aa54a21416cd7',1,'vg::ReadFilter::get_is_paired(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#a1aa38e8c41e26d7932caa918cfcfe76e',1,'vg::ReadFilter::get_is_paired(const MultipathAlignment &mp_aln) const']]],
- ['get_5fis_5frev_9237',['get_is_rev',['../namespacevg.html#a1919abd090eae3a01120e0859d434ed9',1,'vg::get_is_rev()'],['../namespacexg.html#aca811d060bb9ddd2ff278e107c882e49',1,'xg::get_is_rev()']]],
- ['get_5fis_5freverse_9238',['get_is_reverse',['../classvg_1_1DagifiedGraph.html#a0a5fa33f94733bb8470ccbc49e608a0d',1,'vg::DagifiedGraph::get_is_reverse()'],['../classvg_1_1DozeuPinningOverlay.html#a02b35f6198096c08f660df1170d556b4',1,'vg::DozeuPinningOverlay::get_is_reverse()'],['../classvg_1_1ExtraNodeGraph.html#ab3b496b4e1d8067cd7ed0e0ae9fb0aa9',1,'vg::ExtraNodeGraph::get_is_reverse()'],['../classvg_1_1SnarlGraph.html#a9deed0e8a0312d6ff12868e86c83cc0f',1,'vg::SnarlGraph::get_is_reverse()'],['../classvg_1_1IdentityOverlay.html#aa7bba299ded8eb2fff2af0adeb52000b',1,'vg::IdentityOverlay::get_is_reverse()'],['../classvg_1_1IncrementalSubgraph.html#ad4282dc0e503dc17e3724a41dbb0462c',1,'vg::IncrementalSubgraph::get_is_reverse()'],['../classvg_1_1IndexedVG.html#acf50f1ad8e40ac18d8a5469d63155a50',1,'vg::IndexedVG::get_is_reverse()'],['../classvg_1_1MemoizingGraph.html#aac8372783c6657f5473b1d33b4495e7c',1,'vg::MemoizingGraph::get_is_reverse()'],['../classvg_1_1NullMaskingGraph.html#ab99a483165208a4aabc1e2275f126a18',1,'vg::NullMaskingGraph::get_is_reverse()'],['../classvg_1_1PathSubgraph.html#a5305f2276ec4eecae4a59a4892cb63ab',1,'vg::PathSubgraph::get_is_reverse()'],['../classvg_1_1ReverseGraph.html#aaa65f6a0677677af70608a0294ec36f5',1,'vg::ReverseGraph::get_is_reverse()'],['../classvg_1_1NetGraph.html#a4581f8ffa5738a409e9e856f15c48a99',1,'vg::NetGraph::get_is_reverse()'],['../classvg_1_1SourceSinkOverlay.html#a274359d605130e8efec7c14791d5044b',1,'vg::SourceSinkOverlay::get_is_reverse()'],['../classvg_1_1JoinedSpliceGraph.html#a7179e1f5120aebb9670120b6cddf51ca',1,'vg::JoinedSpliceGraph::get_is_reverse()'],['../classvg_1_1StrandSplitGraph.html#a2882b925a09ba0ee35cdf8bdac0c4605',1,'vg::StrandSplitGraph::get_is_reverse()'],['../classvg_1_1SubHandleGraph.html#a050d46f68a21d9169d17a6e9580a542f',1,'vg::SubHandleGraph::get_is_reverse()'],['../classvg_1_1SubgraphOverlay.html#a797e1524539c9c96ef96dc5454d35c3a',1,'vg::SubgraphOverlay::get_is_reverse()'],['../classvg_1_1SubpathOverlay.html#ae1560abd95e0a6e64306622a68f7e6ac',1,'vg::SubpathOverlay::get_is_reverse()'],['../classvg_1_1TreeSubgraph.html#aa581eda84f6ae51edb0363b76075fe47',1,'vg::TreeSubgraph::get_is_reverse()'],['../classvg_1_1VG.html#a53e796617804bffe0203e422f2a23148',1,'vg::VG::get_is_reverse()'],['../classxg_1_1XG.html#a7a52d5c8396e40930cfed5f79ea9c201',1,'xg::XG::get_is_reverse()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade72d1d3264d1022227c44edc9329a26',1,'handlegraph::algorithms::SubHandleGraph::get_is_reverse()'],['../classhandlegraph_1_1HandleGraph.html#a92773f90eb58f18adb9418a4440223c1',1,'handlegraph::HandleGraph::get_is_reverse()']]],
- ['get_5fis_5freversed_9239',['get_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#ae65abc62608f0643537bacfa78e0e7aa',1,'vg::ZipCode::node_code_t::get_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae6b247dcfb508636f982df6b3353001e',1,'vg::ZipCode::snarl_code_t::get_is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a79691714f5f3bb06aed0d1a7a4b646ee',1,'vg::ZipCodeTree::tree_item_t::get_is_reversed()']]],
- ['get_5fis_5freversed_5fin_5fparent_9240',['get_is_reversed_in_parent',['../classvg_1_1ZipCode.html#af27a1ca0026e32e588d0bb3b62a5bade',1,'vg::ZipCode']]],
- ['get_5fitem_9241',['get_item',['../classvg_1_1Funnel.html#a5f8f988df65fc91adc7da9dd8d4446ef',1,'vg::Funnel']]],
- ['get_5fitem_5fat_5findex_9242',['get_item_at_index',['../classvg_1_1ZipCodeTree.html#a66ff501bf5fa0044978550b188691068',1,'vg::ZipCodeTree']]],
- ['get_5fiterator_9243',['get_iterator',['../structvg_1_1subcommand_1_1TickChainLink.html#aa21e2c735dba10a3b97c739d66008937',1,'vg::subcommand::TickChainLink']]],
- ['get_5flast_5fchain_5fcomponent_9244',['get_last_chain_component',['../classvg_1_1ZipCode.html#aaf980083db4440866ee59d2a1b89e957',1,'vg::ZipCode']]],
- ['get_5flast_5fcomponent_9245',['get_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa98d04c4d61201facf9e01c189b44f43',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fleaves_9246',['get_leaves',['../classvg_1_1WFATree.html#adea6d9333092f49afcc26f34e4bfc016',1,'vg::WFATree']]],
- ['get_5flength_9247',['get_length',['../classvg_1_1DagifiedGraph.html#a5feaa48467ad288848fb2d1ffcd29fc1',1,'vg::DagifiedGraph::get_length()'],['../classvg_1_1DozeuPinningOverlay.html#a0d9fc0dbb4e18cfe9d7496b72d0f63fb',1,'vg::DozeuPinningOverlay::get_length()'],['../classvg_1_1ExtraNodeGraph.html#ab4385934c980deef266d30118b83a4df',1,'vg::ExtraNodeGraph::get_length()'],['../classvg_1_1SnarlGraph.html#ac521452a597e9159b8c281cc49239ccb',1,'vg::SnarlGraph::get_length()'],['../classvg_1_1IdentityOverlay.html#a659b0f5b71286479ef910bd984c525e6',1,'vg::IdentityOverlay::get_length()'],['../classvg_1_1IncrementalSubgraph.html#a84ee16f64d60195d6ead2a57933af720',1,'vg::IncrementalSubgraph::get_length()'],['../classvg_1_1IndexedVG.html#a235824616974770831a2ce006a954bbe',1,'vg::IndexedVG::get_length()'],['../classvg_1_1MemoizingGraph.html#ab5f66c5dae9ddc74750cb86595fef07e',1,'vg::MemoizingGraph::get_length()'],['../classvg_1_1NullMaskingGraph.html#a2144c791b97d05bf625a50442649def2',1,'vg::NullMaskingGraph::get_length()'],['../classvg_1_1PathSubgraph.html#a777f23f7156addc72dd508d08f069cc7',1,'vg::PathSubgraph::get_length()'],['../classvg_1_1ReadFilter.html#ae2ef22beb751d9415759fc1985da1946',1,'vg::ReadFilter::get_length()'],['../classvg_1_1ReverseGraph.html#a54f7adad266466143efaa59270432d8f',1,'vg::ReverseGraph::get_length()'],['../classvg_1_1NetGraph.html#a8170045aa0032b33628858c0717cc74a',1,'vg::NetGraph::get_length()'],['../classvg_1_1SourceSinkOverlay.html#a03f1de876e4731012b5e7168556d5236',1,'vg::SourceSinkOverlay::get_length()'],['../classvg_1_1JoinedSpliceGraph.html#aafba33cc8aa854fb9dc8d654bb2a3325',1,'vg::JoinedSpliceGraph::get_length()'],['../classvg_1_1StrandSplitGraph.html#a46c7611ab9f71f86e3192a34406860b4',1,'vg::StrandSplitGraph::get_length()'],['../classvg_1_1SubHandleGraph.html#a829ddac36b7fcb67ca87c058fe691a88',1,'vg::SubHandleGraph::get_length()'],['../classvg_1_1SubgraphOverlay.html#a5bc6640c35b21807f14332a51f84a2d9',1,'vg::SubgraphOverlay::get_length()'],['../classvg_1_1SubpathOverlay.html#ae15f1a187d3bf9a590f173fdf4bd8f9b',1,'vg::SubpathOverlay::get_length()'],['../classvg_1_1TreeSubgraph.html#ac6d8e68e5bff645f58f741291a810abe',1,'vg::TreeSubgraph::get_length()'],['../classvg_1_1VG.html#aff75e522e40559f5a5257a5cef776cdc',1,'vg::VG::get_length()'],['../classvg_1_1ZipCode.html#a8a5fd40be34ed83736e027a3ca6d9889',1,'vg::ZipCode::get_length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#ad67b89184b6f5d83cb888b5f14647ae3',1,'vg::ZipCode::node_code_t::get_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a214243244b7e99dfe24df8665860dbb2',1,'vg::ZipCode::chain_code_t::get_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa80045f926e1bfde2fb07e2c2e442732',1,'vg::ZipCode::snarl_code_t::get_length()'],['../classxg_1_1XG.html#aa52bb123eca4dbff84b316a7f56a98cc',1,'xg::XG::get_length()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af858e2c9467b674d836879d39f049a05',1,'handlegraph::algorithms::SubHandleGraph::get_length()'],['../classhandlegraph_1_1HandleGraph.html#a569ff35fb85c725b0b6b6933ed303e49',1,'handlegraph::HandleGraph::get_length()']]],
- ['get_5flocus_5fname_9248',['get_locus_name',['../classhandlegraph_1_1PathMetadata.html#aeea07376b756bc5410dacf86f2c3983d',1,'handlegraph::PathMetadata']]],
- ['get_5flog10_5fprob_5fof_5fdisruption_5fin_5finterval_9249',['get_log10_prob_of_disruption_in_interval',['../classvg_1_1MinimizerMapper.html#a4a680ca76191f68a70d17af1e0548f60',1,'vg::MinimizerMapper']]],
- ['get_5flong_9250',['get_long',['../classvg_1_1Version.html#a5132823f48bf6019f1b94ace3a479de4',1,'vg::Version']]],
- ['get_5flong_5foption_9251',['get_long_option',['../classvg_1_1OptionInterface.html#afba994fe31561a26b7495e78d9423679',1,'vg::OptionInterface::get_long_option()'],['../classvg_1_1BaseOption.html#ad990f7324262866fbc67f6e8adeeecfd',1,'vg::BaseOption::get_long_option()']]],
- ['get_5fmagic_5fnumber_9252',['get_magic_number',['../classvg_1_1ZipCodeCollection.html#a59d0bd8bac747766d3471225e5a6ae05',1,'vg::ZipCodeCollection::get_magic_number()'],['../classxg_1_1XG.html#ac8ed9c987e2693c548ad834b39df7a80',1,'xg::XG::get_magic_number()'],['../classhandlegraph_1_1Serializable.html#a8879f13f2204a80a6c428883187961db',1,'handlegraph::Serializable::get_magic_number()']]],
- ['get_5fmagic_5fnumber_5fas_5fstring_9253',['get_magic_number_as_string',['../classvg_1_1ZipCodeCollection.html#a6ee9653e5766e260ca6c903ca0920265',1,'vg::ZipCodeCollection']]],
- ['get_5fmain_9254',['get_main',['../classvg_1_1subcommand_1_1Subcommand.html#a5a7af092ca69792ed2543bbcc3847ad4',1,'vg::subcommand::Subcommand']]],
- ['get_5fmapping_9255',['get_mapping',['../classvg_1_1PhaseUnfolder.html#aae984d6ac43200dc82e6ef3066e01f15',1,'vg::PhaseUnfolder']]],
- ['get_5fmapq_9256',['get_mapq',['../classvg_1_1ReadFilter.html#a0550e932f7becd1fbccd46787b580216',1,'vg::ReadFilter']]],
- ['get_5fmax_5frss_5fkb_9257',['get_max_rss_kb',['../namespacevg.html#a546b60e87f7fc326074f6dcf2cdd0659',1,'vg']]],
- ['get_5fmax_5fvmem_5fkb_9258',['get_max_vmem_kb',['../namespacevg.html#a917d8892f93a31e2d8c3161de264fea1',1,'vg']]],
- ['get_5fmetavar_9259',['get_metavar',['../namespacevg_1_1subcommand.html#accfa400696eb815cf8c43d0909c0350f',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20bool_20_3e_9260',['get_metavar< bool >',['../namespacevg_1_1subcommand.html#a901fbf8366695921cb7844ee2da2d2a2',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20double_20_3e_9261',['get_metavar< double >',['../namespacevg_1_1subcommand.html#a6ab814763fe6f21091083e68bcf47a92',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20int_20_3e_9262',['get_metavar< int >',['../namespacevg_1_1subcommand.html#ac4cbf20c4fbaa1109469f8a358e1a213',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20int8_5ft_20_3e_9263',['get_metavar< int8_t >',['../namespacevg_1_1subcommand.html#a4945a3300d2d189e4c7fa6ad5d27ddf6',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20size_5ft_20_3e_9264',['get_metavar< size_t >',['../namespacevg_1_1subcommand.html#aebb27d4a98b972c03f63c8715bbd706c',1,'vg::subcommand']]],
- ['get_5fmetavar_3c_20std_3a_3astring_20_3e_9265',['get_metavar< std::string >',['../namespacevg_1_1subcommand.html#a1615e3bd0398f56dfcdd1c9dfb864ec9',1,'vg::subcommand']]],
- ['get_5fmin_5fbase_5fqual_5ffraction_9266',['get_min_base_qual_fraction',['../classvg_1_1ReadFilter.html#ad2ca26c062585494f69520f9997d34eb',1,'vg::ReadFilter']]],
- ['get_5fmin_5fnode_5fsupport_9267',['get_min_node_support',['../classvg_1_1TraversalSupportFinder.html#ad166403d1a92690fe10e976d9789c065',1,'vg::TraversalSupportFinder::get_min_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a5a19f9777ecf01f0e8ea86870a993aea',1,'vg::PackedTraversalSupportFinder::get_min_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aeeb7ecc5e9a3fa6f5030d3d41a436c59',1,'vg::CachedPackedTraversalSupportFinder::get_min_node_support()']]],
- ['get_5fmin_5fposition_9268',['get_min_position',['../classvg_1_1StreamSorter.html#a4240a47a167f22d3815de6fe976420b5',1,'vg::StreamSorter']]],
- ['get_5fmin_5ftotal_5fsupport_5ffor_5fcall_9269',['get_min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#ac7e36771ace6cf84d9f4f732cdbc692f',1,'vg::SupportBasedSnarlCaller']]],
- ['get_5fmutable_9270',['get_mutable',['../structvg_1_1Annotation.html#a065db30c6b14ca2938254d603777e5c8',1,'vg::Annotation']]],
- ['get_5fn_5fbins_9271',['get_n_bins',['../classvg_1_1Packer.html#a01716de1dc4501804d81fc38256dd2b5',1,'vg::Packer']]],
- ['get_5fname_9272',['get_name',['../classvg_1_1Configurable.html#aee830d6a5cdcf8e7a2896a443bcc80cc',1,'vg::Configurable::get_name()'],['../structvg_1_1TranscriptPath.html#a0adaddaa3b952ed1f06bd7029673d2aa',1,'vg::TranscriptPath::get_name()'],['../classvg_1_1subcommand_1_1Subcommand.html#ab6c41ce3fe77e286f2caa1672b553293',1,'vg::subcommand::Subcommand::get_name()'],['../haplotypes__main_8cpp.html#a3781abae7c3253f254c4e795863d0c09',1,'get_name(): haplotypes_main.cpp']]],
- ['get_5fnet_9273',['get_net',['../classhandlegraph_1_1SnarlDecomposition.html#a84b4951e1bf931d03539ac6e048fdb98',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fnet_5fgraph_9274',['get_net_graph',['../classvg_1_1GenomeState.html#ad07741efc2a949dd69aee266dbb4500b',1,'vg::GenomeState']]],
- ['get_5fnet_5fhandle_9275',['get_net_handle',['../classvg_1_1ZipCode.html#a051a9144646b660f213fe44d5b123d77',1,'vg::ZipCode']]],
- ['get_5fnet_5fhandle_5fslow_9276',['get_net_handle_slow',['../classvg_1_1ZipCode.html#ad1d40ef72bc5fa0f9e0e933add4265a2',1,'vg::ZipCode']]],
- ['get_5fnext_5falignment_5ffrom_5ffastq_9277',['get_next_alignment_from_fastq',['../namespacevg.html#aca76d8e219f90833fdabe3528c3c6441',1,'vg']]],
- ['get_5fnext_5falignment_5fpair_5ffrom_5ffastqs_9278',['get_next_alignment_pair_from_fastqs',['../namespacevg.html#a3255bd8bf9846a34da799947f7642dc7',1,'vg']]],
- ['get_5fnext_5finterleaved_5falignment_5fpair_5ffrom_5ffastq_9279',['get_next_interleaved_alignment_pair_from_fastq',['../namespacevg.html#ab58cf3da638d7e8833a14ef801c7e2db',1,'vg']]],
- ['get_5fnext_5finterleaved_5frecord_5fpair_5ffrom_5fgaf_9280',['get_next_interleaved_record_pair_from_gaf',['../namespacevg_1_1io.html#a0f27b2a472320e0e45a130b73827d1fd',1,'vg::io']]],
- ['get_5fnext_5fintervals_9281',['get_next_intervals',['../classvg_1_1ZipCodeForest.html#a2c9a60acfcb3f8521eeb7bbf5e36007b',1,'vg::ZipCodeForest']]],
- ['get_5fnext_5fnode_5frecalc_5fdegrees_9282',['get_next_node_recalc_degrees',['../classvg_1_1FlowSort.html#a1fac8545c184446eee5cae0f55567b1f',1,'vg::FlowSort']]],
- ['get_5fnext_5frank_9283',['get_next_rank',['../classvg_1_1Paths.html#aad2977756f0166a341fb488cd5c6a9b0',1,'vg::Paths']]],
- ['get_5fnext_5frecord_5ffrom_5fgaf_9284',['get_next_record_from_gaf',['../namespacevg_1_1io.html#aa357ed5eaa447e495149c7bd7df356b9',1,'vg::io']]],
- ['get_5fnext_5frecord_5fpair_5ffrom_5fgaf_9285',['get_next_record_pair_from_gaf',['../namespacevg_1_1io.html#ab11e877e850b127b8004e7223cc77247',1,'vg::io']]],
- ['get_5fnext_5fstep_9286',['get_next_step',['../classvg_1_1MemoizingGraph.html#a91e5d4f1ce3028d58c162adf8d19e70f',1,'vg::MemoizingGraph::get_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a2e18088c831f6757a4eafa7d862d0329',1,'vg::PathSubgraphOverlay::get_next_step()'],['../classvg_1_1VG.html#a144fb8b69eb2274b8dcea914898919f0',1,'vg::VG::get_next_step()'],['../classxg_1_1XG.html#a6595e2654ee4955763a08ab51780941a',1,'xg::XG::get_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a209786f5c9e2c0210b383f2022ee221f',1,'handlegraph::PathHandleGraph::get_next_step()']]],
- ['get_5fnode_9287',['get_node',['../classvg_1_1VG.html#a95223ec6984efc003e5cac69acd43445',1,'vg::VG::get_node(nid_t id)'],['../classvg_1_1VG.html#aa264e9386b98b57c3549a56870d8e29e',1,'vg::VG::get_node(nid_t id) const']]],
- ['get_5fnode_5fat_5fnucleotide_9288',['get_node_at_nucleotide',['../classvg_1_1VG.html#a07462d3f895e77cb407695e6c8e85727',1,'vg::VG']]],
- ['get_5fnode_5fby_5fid_9289',['get_node_by_id',['../structvg_1_1algorithms_1_1Graph.html#a6113178f0138c18d19ed32a08a4a474e',1,'vg::algorithms::Graph']]],
- ['get_5fnode_5fcode_9290',['get_node_code',['../classvg_1_1ZipCode.html#a1a37e35bfbd8910f64b95906f2930e28',1,'vg::ZipCode']]],
- ['get_5fnode_5fcount_9291',['get_node_count',['../classvg_1_1DagifiedGraph.html#a46afdba1fbffa6ffebce5966a1829918',1,'vg::DagifiedGraph::get_node_count()'],['../classvg_1_1DozeuPinningOverlay.html#ab324121c34fdc2ab5edfaf742f26280d',1,'vg::DozeuPinningOverlay::get_node_count()'],['../classvg_1_1ExtraNodeGraph.html#a0c55bc093996c9148a3b6c4e46634759',1,'vg::ExtraNodeGraph::get_node_count()'],['../classvg_1_1SnarlGraph.html#aa797abb0b6518ca38b557759d074cd33',1,'vg::SnarlGraph::get_node_count()'],['../classvg_1_1IdentityOverlay.html#a9a58eb7938308dad847ded70b1abec56',1,'vg::IdentityOverlay::get_node_count()'],['../classvg_1_1IncrementalSubgraph.html#a076dbda3b4b724157cad61f5f7b76b2b',1,'vg::IncrementalSubgraph::get_node_count()'],['../classvg_1_1IndexedVG.html#aa275aa5b547bf464b95ce162e9a2fcd5',1,'vg::IndexedVG::get_node_count()'],['../classvg_1_1MemoizingGraph.html#a4276a59439fc7edc984fe6e666e3b69e',1,'vg::MemoizingGraph::get_node_count()'],['../classvg_1_1NullMaskingGraph.html#a7a7eeb58c5787789e6b8ae8a9e58101b',1,'vg::NullMaskingGraph::get_node_count()'],['../classvg_1_1PathSubgraph.html#a52f431143ff624475a16629fa46898f0',1,'vg::PathSubgraph::get_node_count()'],['../classvg_1_1ReverseGraph.html#a075661952d5a567b1e09ad9a5624c5a7',1,'vg::ReverseGraph::get_node_count()'],['../classvg_1_1NetGraph.html#a49f4b9958557920e8b81c3f6b6c62de2',1,'vg::NetGraph::get_node_count()'],['../classvg_1_1SourceSinkOverlay.html#ac49954276cde4384262f3501f4ed70ce',1,'vg::SourceSinkOverlay::get_node_count()'],['../classvg_1_1JoinedSpliceGraph.html#a15ac4bff9b6862ec0d7c6cefabb916c9',1,'vg::JoinedSpliceGraph::get_node_count()'],['../classvg_1_1StrandSplitGraph.html#a2a4f01cb39da9b46431a7ea3b46f540f',1,'vg::StrandSplitGraph::get_node_count()'],['../classvg_1_1SubHandleGraph.html#a0ea741c8d98e8c12b9f83b3427bee115',1,'vg::SubHandleGraph::get_node_count()'],['../classvg_1_1SubgraphOverlay.html#a40d036bc03e5bb02b1b0fe657b283b2b',1,'vg::SubgraphOverlay::get_node_count()'],['../classvg_1_1SubpathOverlay.html#a1d0208a9cfe646b6d25741c2bbfbd4b3',1,'vg::SubpathOverlay::get_node_count()'],['../classvg_1_1TreeSubgraph.html#a63dd0c1a1fce7a59a563be0448085246',1,'vg::TreeSubgraph::get_node_count()'],['../classvg_1_1VG.html#a495649c1646b865d6c88b8dc126589b0',1,'vg::VG::get_node_count()'],['../classxg_1_1XG.html#ae7b3b8008c6779aafb72b8e2fc47d4a1',1,'xg::XG::get_node_count()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0c17ba8c59000d2562fb0318a1faaa7c',1,'handlegraph::algorithms::SubHandleGraph::get_node_count()'],['../classhandlegraph_1_1HandleGraph.html#a9f95108e6c3f68f404fa93bd3306e4c6',1,'handlegraph::HandleGraph::get_node_count()']]],
- ['get_5fnode_5fdegree_9292',['get_node_degree',['../classvg_1_1FlowSort.html#a033cbc4da28f5ad6c3be63374eb55ac3',1,'vg::FlowSort']]],
- ['get_5fnode_5fids_9293',['get_node_ids',['../structvg_1_1algorithms_1_1Graph.html#afe478cbb3ccb5f5125b59467db143b59',1,'vg::algorithms::Graph']]],
- ['get_5fnode_5flength_9294',['get_node_length',['../classvg_1_1Mapper.html#a99717b5d61b6db599c177b8bafcb6dd8',1,'vg::Mapper']]],
- ['get_5fnode_5fmapping_9295',['get_node_mapping',['../classvg_1_1Paths.html#a6314d7f8036a65b31d4dfac643bc3598',1,'vg::Paths::get_node_mapping(Node *n)'],['../classvg_1_1Paths.html#a7fa795ccee1427d6cac6e44fafe41e1e',1,'vg::Paths::get_node_mapping(id_t id)'],['../classvg_1_1Paths.html#a99f8491f18c0ccaf1bb7b7bf45500517',1,'vg::Paths::get_node_mapping(id_t id) const']]],
- ['get_5fnode_5fmapping_5fby_5fpath_5fname_9296',['get_node_mapping_by_path_name',['../classvg_1_1Paths.html#a9c9cf2b7f26c788195812e2b8170a6ce',1,'vg::Paths::get_node_mapping_by_path_name(Node *n)'],['../classvg_1_1Paths.html#a72c6a29a41521996fd3454170b1a76f6',1,'vg::Paths::get_node_mapping_by_path_name(id_t id)']]],
- ['get_5fnode_5fmapping_5fcopies_5fby_5frank_9297',['get_node_mapping_copies_by_rank',['../classvg_1_1Paths.html#a36a26abe18d10e17e273fa658be9d5c6',1,'vg::Paths']]],
- ['get_5fnode_5fmappings_5fby_5frank_9298',['get_node_mappings_by_rank',['../classvg_1_1Paths.html#a5a40b701389bcc2c513083b02f17b4f4',1,'vg::Paths']]],
- ['get_5fnode_5fnid_5fto_5fvariant_9299',['get_node_nid_to_variant',['../classvg_1_1VG.html#a52fa15aebd7d190eb743311f31037e55',1,'vg::VG']]],
- ['get_5fnode_5foffset_9300',['get_node_offset',['../classvg_1_1GaplessExtender.html#a12663a32f4bc41137eb372c845f0eafe',1,'vg::GaplessExtender']]],
- ['get_5fnodes_9301',['get_nodes',['../classvg_1_1ContractingGraph.html#a9c960fb16e62bc152fcf2f4230eead9c',1,'vg::ContractingGraph::get_nodes()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a932649a134317ad387ee70adc03d4474',1,'vg::SnarlDistanceIndexClusterer::get_nodes()']]],
- ['get_5fnon_5fhts_5falignment_5femitter_9302',['get_non_hts_alignment_emitter',['../namespacevg_1_1io.html#a2f9f4db8b0374c57d2963881784c40d3',1,'vg::io']]],
- ['get_5fnonoverlapping_9303',['get_nonoverlapping',['../classvg_1_1WindowedVcfBuffer.html#a63b89391977d77c5320003d0e0f70469',1,'vg::WindowedVcfBuffer']]],
- ['get_5fnum_5fsamples_9304',['get_num_samples',['../namespacevg.html#afe9d79548464e7842327275008447299',1,'vg']]],
- ['get_5foffset_9305',['get_offset',['../namespacevg.html#af826519a2b2e0cf58394e35d7ab7b84c',1,'vg::get_offset()'],['../namespacexg.html#a6e76d42101c987bf595a807522766cfa',1,'xg::get_offset()']]],
- ['get_5foffset_5fin_5fchain_9306',['get_offset_in_chain',['../classvg_1_1ZipCode.html#a5d8b333ee954fa9a513b6190e1910843',1,'vg::ZipCode']]],
- ['get_5fon_5fstrand_5fdistance_5ftree_9307',['get_on_strand_distance_tree',['../classvg_1_1OrientedDistanceClusterer.html#a736cd908b11ed3a000698291c541bbc0',1,'vg::OrientedDistanceClusterer']]],
- ['get_5foption_5fid_9308',['get_option_id',['../namespacevg_1_1subcommand.html#a7e03678789f1a34608294f43e1047457',1,'vg::subcommand']]],
- ['get_5foption_5fstruct_9309',['get_option_struct',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a58bddced5eb3503314ae1f7ef2bd60d1',1,'vg::subcommand::BaseArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aeeb773f962b7de9459a67f2b74cce151',1,'vg::subcommand::ValueArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a4287432c965cf788c3619aa13634c613',1,'vg::subcommand::FlagArgSpec::get_option_struct()']]],
- ['get_5foption_5fvalue_9310',['get_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#af234d02566c656202396f78df73d35d7',1,'vg::subcommand::BaseOptionGroup']]],
- ['get_5foptions_9311',['get_options',['../classvg_1_1Configurable.html#a553f14c4f4a19bb51d40ffb211945b3a',1,'vg::Configurable']]],
- ['get_5for_5festimate_5fcoverage_9312',['get_or_estimate_coverage',['../namespacevg.html#aba3f6bc9cc27f9c6bb91dc27c7fb28b8',1,'vg']]],
- ['get_5for_5fmake_5fvariant_5fid_9313',['get_or_make_variant_id',['../namespacevg.html#ae9fc5855bb49062ce72e56c805e1545a',1,'vg']]],
- ['get_5foutput_5ffile_5fname_9314',['get_output_file_name',['../namespacevg.html#ae2a0425675c4a85289b230eef2c985b8',1,'vg']]],
- ['get_5foverhang_9315',['get_overhang',['../classvg_1_1ReadFilter.html#a71bb794016b2f59d6495a98b9716e0b5',1,'vg::ReadFilter::get_overhang(const Read &read) const'],['../classvg_1_1ReadFilter.html#a50797c8911ec77ac3a392370a1c91cbe',1,'vg::ReadFilter::get_overhang(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#ab3bff405c9a8994993ea71e0c03b8772',1,'vg::ReadFilter::get_overhang(const MultipathAlignment &mp_aln) const']]],
- ['get_5foverlay_5fhandle_9316',['get_overlay_handle',['../classvg_1_1StrandSplitGraph.html#ab60c1d256ba23abea598861ca7cf7f42',1,'vg::StrandSplitGraph']]],
- ['get_5fparent_9317',['get_parent',['../classhandlegraph_1_1SnarlDecomposition.html#afb665da6af9e2ccfc10e6e667254b91d',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fparent_5fidentifier_9318',['get_parent_identifier',['../classvg_1_1ZipCode.html#a487d7a307e6b728df95581d6d261d526',1,'vg::ZipCode']]],
- ['get_5fparent_5ftraversal_9319',['get_parent_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a2738b92f35c61666df57cd6088f3def1',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fparsed_5fgenotypes_9320',['get_parsed_genotypes',['../classvg_1_1WindowedVcfBuffer.html#a8970a1ba82342645b319a1f7091c6cea',1,'vg::WindowedVcfBuffer']]],
- ['get_5fpath_9321',['get_path',['../classvg_1_1Paths.html#a386fefa3ef22c69bdfa06711ec43ca93',1,'vg::Paths::get_path()'],['../classxg_1_1XG.html#a79017177d025a7608c76a7901da5a463',1,'xg::XG::get_path()'],['../namespacevg.html#a3d972910bf64084a1ee50ca4350c5b59',1,'vg::get_path(const std::vector< handle_t > &first, handle_t second)'],['../namespacevg.html#aa5fc35eee866d216357a5818cd1fb927',1,'vg::get_path(handle_t first, const std::vector< handle_t > &second)'],['../namespacevg.html#a162ed4c8f358ca4c33ab05a27f8349cb',1,'vg::get_path(const std::vector< handle_t > &first, gbwt::node_type second)'],['../namespacevg.html#a66796444cb3b92c35ebeddbb7a9bc6bf',1,'vg::get_path(gbwt::node_type reverse_first, const std::vector< handle_t > &second)']]],
- ['get_5fpath_5fcount_9322',['get_path_count',['../classvg_1_1MemoizingGraph.html#ae0625c7cd87213ce030e03d7373c7216',1,'vg::MemoizingGraph::get_path_count()'],['../classvg_1_1PathSubgraphOverlay.html#a589dea47ddf887c61f88d4ef2f9110a2',1,'vg::PathSubgraphOverlay::get_path_count()'],['../classvg_1_1VG.html#a7b20ecaa6a8a3155b5abb90a3139f6de',1,'vg::VG::get_path_count()'],['../classxg_1_1XG.html#af7b58d4d10af78ac88675a40661967c2',1,'xg::XG::get_path_count()'],['../classhandlegraph_1_1PathHandleGraph.html#acd5df753593ecdfb7aa8c411b98ebad9',1,'handlegraph::PathHandleGraph::get_path_count()']]],
- ['get_5fpath_5fedge_5findex_9323',['get_path_edge_index',['../classvg_1_1PathChunker.html#aef30dd2569597b64d36b19824ebee37f',1,'vg::PathChunker']]],
- ['get_5fpath_5fedges_9324',['get_path_edges',['../classvg_1_1VG.html#a26f160750dfed33c16a257bd5cbecddf',1,'vg::VG']]],
- ['get_5fpath_5fhandle_9325',['get_path_handle',['../classvg_1_1MemoizingGraph.html#ad26dd5209b1364601acf977df6cc52dc',1,'vg::MemoizingGraph::get_path_handle()'],['../classvg_1_1PathSubgraphOverlay.html#a45c63b93ee36ea86ce966aa2f6fc1530',1,'vg::PathSubgraphOverlay::get_path_handle()'],['../classvg_1_1VG.html#a6261550a7c6bbe7eb6ee0976639bc1d7',1,'vg::VG::get_path_handle()'],['../classxg_1_1XG.html#a0cca09a102d01c9f952b857f23f165e1',1,'xg::XG::get_path_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a5d6059d716882a80e3982de17011866e',1,'handlegraph::PathHandleGraph::get_path_handle()']]],
- ['get_5fpath_5fhandle_5fof_5fstep_9326',['get_path_handle_of_step',['../classvg_1_1MemoizingGraph.html#a7a7ec48fc32e5798b58216b3f8fc2624',1,'vg::MemoizingGraph::get_path_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a8a369e743f3f797db333ef04505bb292',1,'vg::PathSubgraphOverlay::get_path_handle_of_step()'],['../classvg_1_1VG.html#aae55721d38d4db3068ca93b4aac8e962',1,'vg::VG::get_path_handle_of_step()'],['../classxg_1_1XG.html#ab12dcc61dc8227d5dfde03b0f6b5ef16',1,'xg::XG::get_path_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a1d1ca9865da585257709f54769f5d6a9',1,'handlegraph::PathHandleGraph::get_path_handle_of_step()'],['../classhandlegraph_1_1PathMetadata.html#a38041ec30b5c66bd94f951f4e61b8bab',1,'handlegraph::PathMetadata::get_path_handle_of_step()']]],
- ['get_5fpath_5fid_9327',['get_path_id',['../classvg_1_1Paths.html#a8fba2fa812589af544a4a0406f78cca7',1,'vg::Paths']]],
- ['get_5fpath_5findex_9328',['get_path_index',['../classvg_1_1GraphSynchronizer.html#aa13b46c21814ff09172452e28a4da71d',1,'vg::GraphSynchronizer']]],
- ['get_5fpath_5flength_9329',['get_path_length',['../classvg_1_1MemoizingGraph.html#a34c10df2b34669fffd3c036636f4f608',1,'vg::MemoizingGraph::get_path_length()'],['../classxg_1_1XG.html#a458bf40b2282e7bd4743781d20f7072b',1,'xg::XG::get_path_length()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#ab71f007638c65db10efbe198f923413b',1,'handlegraph::PathPositionHandleGraph::get_path_length()']]],
- ['get_5fpath_5fname_9330',['get_path_name',['../classvg_1_1MemoizingGraph.html#ad6e5c2da620079ff9fc488a282cb88f9',1,'vg::MemoizingGraph::get_path_name()'],['../classvg_1_1Paths.html#a56b39299430400066796a0332492f7a5',1,'vg::Paths::get_path_name()'],['../classvg_1_1PathSubgraphOverlay.html#a4331971206c3b9cb069b01abad5d965c',1,'vg::PathSubgraphOverlay::get_path_name()'],['../classvg_1_1VG.html#a8ad62c3977b6f38f0b570ea78251dc6d',1,'vg::VG::get_path_name()'],['../classxg_1_1XG.html#acc895561f10e41d82329a45e78bcdbac',1,'xg::XG::get_path_name()'],['../classhandlegraph_1_1PathHandleGraph.html#a565f4312a42dfe77ae14c1ee9ed9f2ba',1,'handlegraph::PathHandleGraph::get_path_name()'],['../classhandlegraph_1_1PathMetadata.html#acf37917fbe8c308de24264854b535018',1,'handlegraph::PathMetadata::get_path_name()']]],
- ['get_5fpath_5fsequence_9331',['get_path_sequence',['../classvg_1_1GraphSynchronizer.html#ac33a770c7ce8206e4649133062333898',1,'vg::GraphSynchronizer']]],
- ['get_5fpayload_5ffrom_5fzip_9332',['get_payload_from_zip',['../classvg_1_1ZipCode.html#a05895f989a23d97b08bd0c1c56bbc3bc',1,'vg::ZipCode']]],
- ['get_5fpayload_5ffrom_5fzipcode_9333',['get_payload_from_zipcode',['../classvg_1_1ZipCode.html#ae9a95e07dd615b3692fe7742990c6c8b',1,'vg::ZipCode']]],
- ['get_5fperipheral_5fattachments_9334',['get_peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#afbd7c2ce70efdcc6c25c20cc7710faa0',1,'vg::GraphSynchronizer::Lock']]],
- ['get_5fphase_5fblock_9335',['get_phase_block',['../classhandlegraph_1_1PathMetadata.html#aadcc53d7a55b54eb2499b66a02500065',1,'handlegraph::PathMetadata']]],
- ['get_5fpos_9336',['get_pos',['../classvg_1_1GaplessExtender.html#a92241e0a9691fc7b06f5258a21d1c9c4',1,'vg::GaplessExtender']]],
- ['get_5fposition_5fof_5fstep_9337',['get_position_of_step',['../classvg_1_1MemoizingGraph.html#ade585496ff8b0d082500a1a76c2b187b',1,'vg::MemoizingGraph::get_position_of_step()'],['../classxg_1_1XG.html#ab6e8ce09a0ed201a56b9f8bd387b4e4d',1,'xg::XG::get_position_of_step()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#a473d58ac35a06551e06ae7f5ad5073be',1,'handlegraph::PathPositionHandleGraph::get_position_of_step()']]],
- ['get_5fpositions_9338',['get_positions',['../classvg_1_1Funnel.html#a617af9590f607720de6a87dfcddbe553',1,'vg::Funnel']]],
- ['get_5fpossible_5ffilenames_9339',['get_possible_filenames',['../classvg_1_1IndexRegistry.html#a6dc3fd500ab65621ad72ae968cedecf0',1,'vg::IndexRegistry']]],
- ['get_5fprefix_9340',['get_prefix',['../classvg_1_1IndexRegistry.html#aa3748affd87c03e3a883ccb9d913eb73',1,'vg::IndexRegistry::get_prefix()'],['../classvg_1_1PhaseUnfolder.html#abae52ee7605f03c82622c63c55463db7',1,'vg::PhaseUnfolder::get_prefix()']]],
- ['get_5fprefix_5fsum_5for_5fidentifier_9341',['get_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#ab2390c393bb641b64ca80183686df54a',1,'vg::ZipCode::node_code_t::get_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34832c0fc381d48cb1424a224f8d9dae',1,'vg::ZipCode::snarl_code_t::get_prefix_sum_or_identifier()']]],
- ['get_5fprevious_5fstep_9342',['get_previous_step',['../classvg_1_1MemoizingGraph.html#a2ceee67be1ab5744fe53de6e1fa5e718',1,'vg::MemoizingGraph::get_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#a5b3b4cb54c2f5fedc9fc4d765c6f8b3a',1,'vg::PathSubgraphOverlay::get_previous_step()'],['../classvg_1_1VG.html#a95d4b19a83f11ac6244855f86555fe76',1,'vg::VG::get_previous_step()'],['../classxg_1_1XG.html#aedec198c2181d7f729c10317e5ca8089',1,'xg::XG::get_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a71040226b29aa5046f4cc04c8c9aa9fb',1,'handlegraph::PathHandleGraph::get_previous_step()']]],
- ['get_5fpriority_9343',['get_priority',['../classvg_1_1subcommand_1_1Subcommand.html#a4dccbaf1dc530dc55b57e1dd9dbc09e1',1,'vg::subcommand::Subcommand']]],
- ['get_5fprob_5fof_5fdisruption_5fin_5fcolumn_9344',['get_prob_of_disruption_in_column',['../classvg_1_1MinimizerMapper.html#a6d4969130b9f7cb75efec316774b8e82',1,'vg::MinimizerMapper']]],
- ['get_5fproc_5fstatus_5fvalue_9345',['get_proc_status_value',['../namespacevg.html#a9fb67697fd1e49bcb389a735ba9fa8f2',1,'vg']]],
- ['get_5fprotobuf_5ftag_9346',['get_protobuf_tag',['../classvg_1_1io_1_1Registry.html#a9ccb7ac94bdb24687992af702d387620',1,'vg::io::Registry']]],
- ['get_5fpruned_5falt_5falleles_9347',['get_pruned_alt_alleles',['../classvg_1_1VCFTraversalFinder.html#a116466101f77d992e54bb3328a42c90b',1,'vg::VCFTraversalFinder']]],
- ['get_5fqual_5fadj_5faligner_9348',['get_qual_adj_aligner',['../classvg_1_1AlignerClient.html#aa84332f52915c20b2f2db1e060736fb5',1,'vg::AlignerClient']]],
- ['get_5fqualities_5fin_5fsnarl_9349',['get_qualities_in_snarl',['../classvg_1_1Genotyper.html#af6518141a6e6f122e5f534c041d16918',1,'vg::Genotyper']]],
- ['get_5fradius_9350',['get_radius',['../classvg_1_1VariantAdder.html#ae974fd5d06287893b0b1f8690624d18f',1,'vg::VariantAdder']]],
- ['get_5frank_5fin_5fsnarl_9351',['get_rank_in_snarl',['../classvg_1_1ZipCode.html#a32750209d049ac9e5fea67c97be1f151',1,'vg::ZipCode']]],
- ['get_5fraw_5fchain_5fcomponent_9352',['get_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a0ab97119fa36e9682bb28118190cb8e4',1,'vg::ZipCode::node_code_t::get_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af202024a5bb84df848c92b06535682c4',1,'vg::ZipCode::snarl_code_t::get_raw_chain_component()']]],
- ['get_5fraw_5fchild_5fcount_9353',['get_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#af740b35df2d7b5cd84b3ab439440e492',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fcode_5ftype_9354',['get_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#abca762bde40792cc01251c5372cd8b61',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fconnectivity_9355',['get_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4f3a37a0ed45286df4f4d3cf254ac376',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fraw_5fdistance_5fend_5fleft_9356',['get_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2619d7eccb0849542a6c8a86bb7937c1',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fdistance_5fend_5fright_9357',['get_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a1fe89643eb1a0f051e5ac71465984a71',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fdistance_5fstart_5fleft_9358',['get_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a39806103fa11d9969668f75045732bec',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fdistance_5fstart_5fright_9359',['get_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a168236545b3436928b1099c1fe572379',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fis_5freversed_9360',['get_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a5009106b8ce3273a9db11d5c177e5760',1,'vg::ZipCode::node_code_t::get_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa00b0cb7326f1fabc61bc7330936f0ee',1,'vg::ZipCode::snarl_code_t::get_raw_is_reversed()']]],
- ['get_5fraw_5flast_5fcomponent_9361',['get_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa3fc8437a85ebad068b816cb2c04d0e3',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fraw_5flength_9362',['get_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ac1eeeb4a44eec49317c89ec69ec5e0',1,'vg::ZipCode::node_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a31621cf955a3423ca4fa85b440597df2',1,'vg::ZipCode::chain_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aabb9e23dfe383bcf8d241675975a80d6',1,'vg::ZipCode::snarl_code_t::get_raw_length()']]],
- ['get_5fraw_5fprefix_5fsum_5for_5fidentifier_9363',['get_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a2382df4c7c2f34b2e538edd9c2c27c66',1,'vg::ZipCode::node_code_t::get_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#adfcdf800c56ed38d46c5d2db8f291e62',1,'vg::ZipCode::snarl_code_t::get_raw_prefix_sum_or_identifier()']]],
- ['get_5fraw_5frecord_5foffset_9364',['get_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04bf6c411365529b20b893c2b30b9f8e',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fraw_5fsnarl_5frank_5for_5fidentifier_9365',['get_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#af4bfbe05a99156b9cc18446647c88830',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fread_5fcoverage_9366',['get_read_coverage',['../classvg_1_1MinimizerMapper.html#a59563aa4a1d0f00d909edd4cf8b8aa7a',1,'vg::MinimizerMapper']]],
- ['get_5fread_5fdistance_9367',['get_read_distance',['../namespacevg_1_1algorithms.html#a5d8762b533e64039ce1a917b047097d8',1,'vg::algorithms']]],
- ['get_5fread_5ffn_9368',['get_read_fn',['../classvg_1_1io_1_1JSONStreamHelper.html#a549e248d11b13f164c871cbf3ccbf935',1,'vg::io::JSONStreamHelper']]],
- ['get_5fread_5fname_9369',['get_read_name',['../classvg_1_1NGSSimulator.html#a44c1fcd6a665cc7804e561a7c8700a04',1,'vg::NGSSimulator']]],
- ['get_5fread_5foffset_9370',['get_read_offset',['../classvg_1_1GaplessExtender.html#a5c568cad31cb0cc1007ef05183c197ab',1,'vg::GaplessExtender']]],
- ['get_5frecipe_9371',['get_recipe',['../classvg_1_1IndexRegistry.html#a1f378b76124b73c85111a81be74f92b3',1,'vg::IndexRegistry']]],
- ['get_5frecord_5foffset_9372',['get_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae3dde9ebd7b44658b083f4bd372e823f',1,'vg::ZipCode::snarl_code_t']]],
- ['get_5fref_5ffollowing_9373',['get_ref_following',['../structhaplo_1_1linear__haplo__structure.html#a2e9ec5540a31571c3daba83abf03d18d',1,'haplo::linear_haplo_structure']]],
- ['get_5fref_5finterval_9374',['get_ref_interval',['../classvg_1_1VCFOutputCaller.html#ab382edfcd67f4f3e73fe032cf8f96b04',1,'vg::VCFOutputCaller']]],
- ['get_5fref_5foffsets_9375',['get_ref_offsets',['../classvg_1_1RatioSupportSnarlCaller.html#a7f838a459153e23e7963a2bd779711de',1,'vg::RatioSupportSnarlCaller::get_ref_offsets()'],['../classvg_1_1TraversalSupportFinder.html#a437e9478fc7551f23246d954af4b0d90',1,'vg::TraversalSupportFinder::get_ref_offsets()']]],
- ['get_5fref_5fposition_9376',['get_ref_position',['../classvg_1_1VCFOutputCaller.html#a9398350530fc4df45918dc1a14eed549',1,'vg::VCFOutputCaller::get_ref_position()'],['../classvg_1_1MCMCCaller.html#a368d2f5dbd85941acceec2a1d7d44d41',1,'vg::MCMCCaller::get_ref_position()']]],
- ['get_5fref_5fpositions_9377',['get_ref_positions',['../classvg_1_1VCFGenotyper.html#a60af53e97463c30ff180d3c1b8356df7',1,'vg::VCFGenotyper']]],
- ['get_5freference_5ftraversal_9378',['get_reference_traversal',['../classvg_1_1LegacyCaller.html#a6d00fa81c7923b88b886f87f28984184',1,'vg::LegacyCaller']]],
- ['get_5fregistry_9379',['get_registry',['../classvg_1_1subcommand_1_1Subcommand.html#a0e3707f1f4e9ce445faea71fddd61a00',1,'vg::subcommand::Subcommand']]],
- ['get_5fregular_5faligner_9380',['get_regular_aligner',['../classvg_1_1AlignerClient.html#a60d4602ba9be4861136af507f8eacaec',1,'vg::AlignerClient']]],
- ['get_5fregular_5fsnarl_5fcode_9381',['get_regular_snarl_code',['../classvg_1_1ZipCode.html#a13c0515e594e7da8c54e29314b1af6a6',1,'vg::ZipCode']]],
- ['get_5frelease_9382',['get_release',['../classvg_1_1Version.html#a3e99ae82ab6bcc07d982012d731e7091',1,'vg::Version']]],
- ['get_5fresolver_9383',['get_resolver',['../classvg_1_1io_1_1Registry.html#a45f5ca692e2d85618f2081e7aa967730',1,'vg::io::Registry']]],
- ['get_5froot_9384',['get_root',['../classvg_1_1TreeSubgraph.html#a16b12e54e0c87d9a84f4d3a809a8171b',1,'vg::TreeSubgraph::get_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#af94fd9c82aaa2742123b25b0ec95311f',1,'handlegraph::SnarlDecomposition::get_root()']]],
- ['get_5frr_5fmemo_9385',['get_rr_memo',['../classvg_1_1MultipathMapper.html#a42169ca0715c4c784584ba3d2a5d34bb',1,'vg::MultipathMapper']]],
- ['get_5fsample_5fname_9386',['get_sample_name',['../classhandlegraph_1_1PathMetadata.html#ada7fda320c3b28c0fb642d7e4a789045',1,'handlegraph::PathMetadata']]],
- ['get_5fscore_9387',['get_score',['../classvg_1_1ReadFilter.html#a3e168659158cf4372fc11b8cda05883d',1,'vg::ReadFilter::get_score()'],['../classvg_1_1Surjector.html#a42d2fa6bd9590a02329f31666fbe0cd5',1,'vg::Surjector::get_score()'],['../classvg_1_1ReadFilter.html#a2144e5b768ebd71768d37265c07deda2',1,'vg::ReadFilter::get_score(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#af800d67aa469136b6318c02e282c5a30',1,'vg::ReadFilter::get_score(const MultipathAlignment &read) const'],['../classvg_1_1Surjector.html#aafe9672e0a82c6540c4d1360070725ec',1,'vg::Surjector::get_score(const Alignment &aln)'],['../classvg_1_1Surjector.html#a4df48f23da07159bb99bc6577d992938',1,'vg::Surjector::get_score(const multipath_alignment_t &mp_aln)']]],
- ['get_5fscores_9388',['get_scores',['../structhaplo_1_1haplo__DP__column.html#a784a7e41856ad01f9bdd88ca59dfb146',1,'haplo::haplo_DP_column']]],
- ['get_5fseed_5fpos_9389',['get_seed_pos',['../classvg_1_1SpliceRegion.html#ab79a29d07732a726cffffea140af98c4',1,'vg::SpliceRegion']]],
- ['get_5fsense_9390',['get_sense',['../classhandlegraph_1_1PathMetadata.html#a6cf06655af059252487f9581cad0dc4a',1,'handlegraph::PathMetadata']]],
- ['get_5fsequence_9391',['get_sequence',['../classvg_1_1DagifiedGraph.html#a5d47d90eeaac4f0a6f1e12f0ed2d197e',1,'vg::DagifiedGraph::get_sequence()'],['../classvg_1_1DozeuPinningOverlay.html#ab7eabd260a4585f04809d8da64b7f2f4',1,'vg::DozeuPinningOverlay::get_sequence()'],['../classvg_1_1ExtraNodeGraph.html#a4b9d7578f0f601b186295d365cf7e487',1,'vg::ExtraNodeGraph::get_sequence()'],['../classvg_1_1SnarlGraph.html#a4a97ed146e23b853fd66a0ad827823e5',1,'vg::SnarlGraph::get_sequence()'],['../classvg_1_1IdentityOverlay.html#ada02cf10738e4fc81c7bb21ecf5d4b56',1,'vg::IdentityOverlay::get_sequence()'],['../classvg_1_1IncrementalSubgraph.html#a61eef0cd10c65efae0cac12816084bb2',1,'vg::IncrementalSubgraph::get_sequence()'],['../classvg_1_1IndexedVG.html#a64c03afcfd0c1c210e8b84a9b78a06dc',1,'vg::IndexedVG::get_sequence()'],['../classvg_1_1MemoizingGraph.html#a841433ccb7c64a657e43130c81c47c39',1,'vg::MemoizingGraph::get_sequence()'],['../classvg_1_1NullMaskingGraph.html#a7a92b5f2747dca58d2fe63368e1294d4',1,'vg::NullMaskingGraph::get_sequence()'],['../classvg_1_1PathSubgraph.html#a1549c36d974dfc4e8bcc54e0e9950646',1,'vg::PathSubgraph::get_sequence()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af008e59ecc555d391149053284ca0cbb',1,'vg::Haplotypes::Subchain::get_sequence()'],['../classvg_1_1ReverseGraph.html#ad815813ebd0d2b33515473bc974c53ad',1,'vg::ReverseGraph::get_sequence()'],['../classvg_1_1NetGraph.html#a4278d3e414d6e5b8e8055d7bdf87c7ac',1,'vg::NetGraph::get_sequence()'],['../classvg_1_1SourceSinkOverlay.html#a4a3eb7401c1b90b33d97672f50a17d39',1,'vg::SourceSinkOverlay::get_sequence()'],['../classvg_1_1JoinedSpliceGraph.html#a6b4f089ed86cdb7ff6ba9177d1187066',1,'vg::JoinedSpliceGraph::get_sequence()'],['../classvg_1_1StrandSplitGraph.html#a878c4be6f6ad6652d3b33f2691bbb570',1,'vg::StrandSplitGraph::get_sequence()'],['../classvg_1_1SubHandleGraph.html#ae9915dd52c55a51616822713509afab0',1,'vg::SubHandleGraph::get_sequence()'],['../classvg_1_1SubgraphOverlay.html#af924de823a9ef5c1a846136eb34637f4',1,'vg::SubgraphOverlay::get_sequence()'],['../classvg_1_1SubpathOverlay.html#a425e89bc05405ef207305c302c18a259',1,'vg::SubpathOverlay::get_sequence()'],['../classvg_1_1TreeSubgraph.html#ae9859d1486d3023b44ab83b3f8c5438c',1,'vg::TreeSubgraph::get_sequence()'],['../classvg_1_1VG.html#a353df9b2449ac859804359632283078b',1,'vg::VG::get_sequence()'],['../classxg_1_1XG.html#ad748df5f6e521774c1d5871ab3519bd8',1,'xg::XG::get_sequence()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4c93978f2d225b926991b34b27528bfd',1,'handlegraph::algorithms::SubHandleGraph::get_sequence()'],['../classhandlegraph_1_1HandleGraph.html#a8cc2ab8a1292e30ba5e167a823f66d92',1,'handlegraph::HandleGraph::get_sequence()']]],
- ['get_5fsequence_5fdictionary_9392',['get_sequence_dictionary',['../namespacevg.html#a2e23f130325e05c894696771e50f2636',1,'vg']]],
- ['get_5fsequence_5fvisits_9393',['get_sequence_visits',['../classvg_1_1HaplotypePartitioner.html#acbe0f7f081cf6db06a894e451d8915b6',1,'vg::HaplotypePartitioner']]],
- ['get_5fsequences_9394',['get_sequences',['../classvg_1_1HaplotypePartitioner.html#a8bdd15927542e95eb536fc9e9bb69aa7',1,'vg::HaplotypePartitioner::get_sequences(handle_t handle) const'],['../classvg_1_1HaplotypePartitioner.html#af88d6e4839d697b5780c453441d3abb0',1,'vg::HaplotypePartitioner::get_sequences(Subchain subchain) const']]],
- ['get_5fshort_9395',['get_short',['../classvg_1_1Version.html#a8105cc0ae9049ca2daf91fbce5efa5e9',1,'vg::Version']]],
- ['get_5fshort_5foptions_9396',['get_short_options',['../classvg_1_1OptionInterface.html#a7c1a8f1f6a3071a502362d9765c94add',1,'vg::OptionInterface::get_short_options()'],['../classvg_1_1BaseOption.html#a5b77fd0a8211f8cabd07b14db491fb64',1,'vg::BaseOption::get_short_options()']]],
- ['get_5fsink_5fhandle_9397',['get_sink_handle',['../classvg_1_1SourceSinkOverlay.html#a71ce03b168ed695659a6ed61a946d089',1,'vg::SourceSinkOverlay']]],
- ['get_5fsize_9398',['get_size',['../structvg_1_1algorithms_1_1Graph.html#ae7a493be0a453a3e82c7c36f0ad70e07',1,'vg::algorithms::Graph']]],
- ['get_5fsizes_9399',['get_sizes',['../structhaplo_1_1haplo__DP__column.html#aa2c307962df62885eaca8caa4723d8a4',1,'haplo::haplo_DP_column']]],
- ['get_5fskip_5fallele_5ffn_9400',['get_skip_allele_fn',['../classvg_1_1SnarlCaller.html#acbc3b71e19fca0c018ff9dd713f2b052',1,'vg::SnarlCaller::get_skip_allele_fn()'],['../classvg_1_1SupportBasedSnarlCaller.html#aa702e223a90771c4090511c23b7c55a7',1,'vg::SupportBasedSnarlCaller::get_skip_allele_fn()']]],
- ['get_5fsnarl_5fchild_5fcount_9401',['get_snarl_child_count',['../classvg_1_1ZipCode.html#ad6d78deca4d723ac8d5ede306abd5578',1,'vg::ZipCode']]],
- ['get_5fsnarl_5frank_5for_5fidentifier_9402',['get_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a078386aa48caae9dda52e73c2975f8b7',1,'vg::ZipCode::chain_code_t']]],
- ['get_5fsnarl_5freference_5fbounds_9403',['get_snarl_reference_bounds',['../classvg_1_1Genotyper.html#a29a6f2fd20161c9313498760578c091a',1,'vg::Genotyper']]],
- ['get_5fsnarl_5ftraversals_9404',['get_snarl_traversals',['../classvg_1_1Genotyper.html#a7a14f1e259fe612b944aadf701ca1585',1,'vg::Genotyper']]],
- ['get_5fsnp_5fref_5fposition_9405',['get_SNP_ref_position',['../structhaplo_1_1linear__haplo__structure.html#a312a7a7a748cc4acd3c4b75717db1fe6',1,'haplo::linear_haplo_structure']]],
- ['get_5fsnv_5fallele_9406',['get_SNV_allele',['../structhaplo_1_1linear__haplo__structure.html#a353eefc81d042a96f98980b7cb2a72aa',1,'haplo::linear_haplo_structure']]],
- ['get_5fsort_5fvalue_9407',['get_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aae5b7a35573e7133c368eb6bf4678aab',1,'vg::ZipCodeForest::sort_value_t']]],
- ['get_5fsource_5fhandle_9408',['get_source_handle',['../classvg_1_1SourceSinkOverlay.html#a4126d6851b442614cb115668eaeeb89f',1,'vg::SourceSinkOverlay']]],
- ['get_5fspanning_5fhaplotypes_9409',['get_spanning_haplotypes',['../classvg_1_1GBWTTraversalFinder.html#a88b35f62878ceab005faf07f7386691c',1,'vg::GBWTTraversalFinder']]],
- ['get_5fstart_9410',['get_start',['../classvg_1_1NetGraph.html#a35e17fbdc2bade4b5b0195d03cb0dc22',1,'vg::NetGraph']]],
- ['get_5fstart_5fbound_9411',['get_start_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a63eea99ca9840f16ef358ee664ecda23',1,'handlegraph::SnarlDecomposition']]],
- ['get_5fstart_5fof_9412',['get_start_of',['../namespacevg.html#afa918cf29c1c8238d88f2bbc94b6abef',1,'vg']]],
- ['get_5fstep_5fat_5fposition_9413',['get_step_at_position',['../classvg_1_1MemoizingGraph.html#acbae8703ecc85597b33e36d5208a4f1e',1,'vg::MemoizingGraph::get_step_at_position()'],['../classxg_1_1XG.html#a087db8dbe184e5a22dda11d61f8fff6a',1,'xg::XG::get_step_at_position()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#aefbae4c3392c32ec13534a44bcc21136',1,'handlegraph::PathPositionHandleGraph::get_step_at_position()']]],
- ['get_5fstep_5fcount_9414',['get_step_count',['../classvg_1_1MemoizingGraph.html#ae0bc7232272e70adab6333dbe3718f46',1,'vg::MemoizingGraph::get_step_count()'],['../classvg_1_1PathSubgraphOverlay.html#ae2df84b76bcec7b4899838a99d3799f5',1,'vg::PathSubgraphOverlay::get_step_count()'],['../classvg_1_1VG.html#a3efe30807d096a6175373bc3f4863dd7',1,'vg::VG::get_step_count()'],['../classxg_1_1XG.html#a0609241ee4795d7c9dd2a2b5cc8ce3a4',1,'xg::XG::get_step_count()'],['../classhandlegraph_1_1PathHandleGraph.html#add91075c3490f8dc5acf667f2b26832c',1,'handlegraph::PathHandleGraph::get_step_count(const path_handle_t &path_handle) const =0'],['../classhandlegraph_1_1PathHandleGraph.html#a6d3a31f0c19054cd2908525119869b80',1,'handlegraph::PathHandleGraph::get_step_count(const handle_t &handle) const']]],
- ['get_5fsteps_9415',['get_steps',['../classvg_1_1IndexingPlan.html#a52c631c507d1cd0f0451ce7de71f2091',1,'vg::IndexingPlan']]],
- ['get_5fstream_5flength_9416',['get_stream_length',['../namespacevg_1_1io.html#aff18a599bd6affc6e2709cb2cff9154c',1,'vg::io']]],
- ['get_5fstream_5fposition_9417',['get_stream_position',['../namespacevg_1_1io.html#aca3b265c558db37b69a837668d2fdf12',1,'vg::io']]],
- ['get_5fsubchains_9418',['get_subchains',['../classvg_1_1HaplotypePartitioner.html#a27be1484d044a8f872083ea6e98d9786',1,'vg::HaplotypePartitioner']]],
- ['get_5fsubgraph_9419',['get_subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a8754c28fbea6df69e6204a9128912a20',1,'vg::GraphSynchronizer::Lock::get_subgraph()'],['../classvg_1_1SpliceRegion.html#ae10fef3784f1d382cb8f3973e1c9ff1b',1,'vg::SpliceRegion::get_subgraph()']]],
- ['get_5fsubrange_9420',['get_subrange',['../classhandlegraph_1_1PathMetadata.html#a80f47deffdb584fa74ea43dad580cce7',1,'handlegraph::PathMetadata']]],
- ['get_5fsubsequence_9421',['get_subsequence',['../classvg_1_1IncrementalSubgraph.html#a258698c76e4d96ecefd38505894f778b',1,'vg::IncrementalSubgraph::get_subsequence()'],['../classvg_1_1JoinedSpliceGraph.html#a2348c9a3357615ce0eea301366344376',1,'vg::JoinedSpliceGraph::get_subsequence()'],['../classvg_1_1VG.html#a45075c22efc7cfb1ed06a8996fec119c',1,'vg::VG::get_subsequence()'],['../classxg_1_1XG.html#a0368861cc6c99d2a1d40c059db62c2a9',1,'xg::XG::get_subsequence()'],['../classhandlegraph_1_1HandleGraph.html#a74c6fcda357516b1160996c63ed40d63',1,'handlegraph::HandleGraph::get_subsequence()']]],
- ['get_5fsuffix_9422',['get_suffix',['../classvg_1_1IndexFile.html#ac81438a82e18b86b443e7d853245d599',1,'vg::IndexFile::get_suffix()'],['../classvg_1_1PhaseUnfolder.html#a97128de268b43c9ccf9dd117829adedf',1,'vg::PhaseUnfolder::get_suffix()']]],
- ['get_5fsupport_9423',['get_support',['../structvg_1_1AugmentedGraph.html#ad239a8516427304ef304e944f7d20c00',1,'vg::AugmentedGraph::get_support(id_t node)'],['../structvg_1_1AugmentedGraph.html#a87c6ed55516068757be3b1ad54a6cfd0',1,'vg::AugmentedGraph::get_support(edge_t edge)'],['../structvg_1_1SupportAugmentedGraph.html#a0ffa85683b46b7f8d6b64da42ba19fbb',1,'vg::SupportAugmentedGraph::get_support(id_t node)'],['../structvg_1_1SupportAugmentedGraph.html#a4c86be41ce8680c5473080c704ddcc10',1,'vg::SupportAugmentedGraph::get_support(edge_t edge)']]],
- ['get_5fsupport_5ffinder_9424',['get_support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a04ebbd23ec0162a72c959351131e17ba',1,'vg::SupportBasedSnarlCaller']]],
- ['get_5fsymbolic_5fbounds_9425',['get_symbolic_bounds',['../classvg_1_1Constructor.html#a31a7837804bd45819ab249687a858fbb',1,'vg::Constructor']]],
- ['get_5fsystem_5fmemory_9426',['get_system_memory',['../classvg_1_1IndexRegistry.html#a1f03f21a783cad871997b03bcd0c8dff',1,'vg::IndexRegistry']]],
- ['get_5ftables_9427',['get_tables',['../classvg_1_1io_1_1Registry.html#aa9f3d682e2b43bfdc3fc30e252a716b9',1,'vg::io::Registry']]],
- ['get_5ftail_5fforest_9428',['get_tail_forest',['../classvg_1_1MinimizerMapper.html#afdbaa5b2938d0050476d078d336286cf',1,'vg::MinimizerMapper']]],
- ['get_5ftarget_5fmemory_5fusage_9429',['get_target_memory_usage',['../classvg_1_1IndexRegistry.html#aa8aae29f234def70dc6de5f1a291cbc0',1,'vg::IndexRegistry']]],
- ['get_5fthread_5fcount_9430',['get_thread_count',['../namespacevg.html#ade988dd38efaa705be15ba17500fe219',1,'vg::get_thread_count()'],['../namespacexg.html#a025cd6958c94d7ce14c1be1425792161',1,'xg::get_thread_count()']]],
- ['get_5fthread_5fstream_9431',['get_thread_stream',['../classvg_1_1io_1_1StreamMultiplexer.html#a749ab082e0364d470d84978c9757ef76',1,'vg::io::StreamMultiplexer']]],
- ['get_5ftop_5flevel_5fchain_5foffset_9432',['get_top_level_chain_offset',['../classvg_1_1ZipCode.html#a304ce8419239ce69dfb69e85e50d3c8c',1,'vg::ZipCode']]],
- ['get_5ftopological_5forder_9433',['get_topological_order',['../classvg_1_1PathSubgraph.html#a591e8f29ef3f356a38aca18e466ae954',1,'vg::PathSubgraph::get_topological_order()'],['../classvg_1_1TreeSubgraph.html#a850f30c11c28ab61148215970b5c6129',1,'vg::TreeSubgraph::get_topological_order()']]],
- ['get_5ftotal_5flength_9434',['get_total_length',['../classxg_1_1XG.html#a4437293fdec75f15a296fb545a6d539d',1,'xg::XG::get_total_length()'],['../classhandlegraph_1_1HandleGraph.html#a4c98da99e0d32ebcc9fd31be4b779e29',1,'handlegraph::HandleGraph::get_total_length()']]],
- ['get_5ftranslation_9435',['get_translation',['../classvg_1_1Translator.html#ac76452dc0c74164d2bcfa25f53ca9828',1,'vg::Translator']]],
- ['get_5ftraversal_5fgenotype_5fsupport_9436',['get_traversal_genotype_support',['../classvg_1_1TraversalSupportFinder.html#a1b818e6111dd2eec62067a562ecc2078',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fmapqs_9437',['get_traversal_mapqs',['../classvg_1_1TraversalSupportFinder.html#a1a7ce9dabeac1835ce0c9765301fcafd',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fof_5fsnarl_9438',['get_traversal_of_snarl',['../namespacevg.html#a871d5cdd29e1806636314021d0b6d451',1,'vg']]],
- ['get_5ftraversal_5forder_9439',['get_traversal_order',['../namespacevg.html#aaa05224d1b8daa421ebfb9320fc1d2d1',1,'vg']]],
- ['get_5ftraversal_5fset_5fsupport_9440',['get_traversal_set_support',['../classvg_1_1TraversalSupportFinder.html#aead4beb53b5148baa538c6481be8700d',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fsizes_9441',['get_traversal_sizes',['../classvg_1_1TraversalSupportFinder.html#a95944f27ca78da63466f5623ad646ee4',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversal_5fsupport_9442',['get_traversal_support',['../classvg_1_1TraversalSupportFinder.html#a28c6f9088f6c28d64855d6cac9a65322',1,'vg::TraversalSupportFinder']]],
- ['get_5ftraversals_9443',['get_traversals',['../classvg_1_1Deconstructor.html#ad58319907ec3f7bf3e6d130f6469a9a9',1,'vg::Deconstructor']]],
- ['get_5ftree_5fsize_9444',['get_tree_size',['../classvg_1_1ZipCodeTree.html#a1207ebf8f31cd6f17593f100be3c7f00',1,'vg::ZipCodeTree']]],
- ['get_5ftype_9445',['get_type',['../structhaplo_1_1linear__haplo__structure.html#ac0dcdb90717d1585bbc847206746e293',1,'haplo::linear_haplo_structure::get_type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#aef1abc2e62fd2ebcc722e26978bb56b7',1,'vg::ZipCodeTree::tree_item_t::get_type()']]],
- ['get_5funderlying_5fhandle_9446',['get_underlying_handle',['../classvg_1_1DagifiedGraph.html#aea86fce4d0f22943935bad1e5cc17f48',1,'vg::DagifiedGraph::get_underlying_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a5cfe7e76c343f768037c84df85037ace',1,'vg::DozeuPinningOverlay::get_underlying_handle()'],['../classvg_1_1IdentityOverlay.html#a5bfd0bebd074847b5504b9ad3f968836',1,'vg::IdentityOverlay::get_underlying_handle()'],['../classvg_1_1IncrementalSubgraph.html#a6b3e5f09eb2a9edb698eb08c55cc9486',1,'vg::IncrementalSubgraph::get_underlying_handle()'],['../classvg_1_1NullMaskingGraph.html#aa903d2c61cf2ba035aac11a3015c2cab',1,'vg::NullMaskingGraph::get_underlying_handle()'],['../classvg_1_1PathSubgraph.html#aa6c521d9a3770f20483f3f16b0686eeb',1,'vg::PathSubgraph::get_underlying_handle()'],['../classvg_1_1ReverseGraph.html#a246e5d5c82508b512fb4c041bfe38892',1,'vg::ReverseGraph::get_underlying_handle()'],['../classvg_1_1SourceSinkOverlay.html#abe2d0e58471d1ab7840618a02958fc96',1,'vg::SourceSinkOverlay::get_underlying_handle()'],['../classvg_1_1StrandSplitGraph.html#aa6379c95c71b6a6682311733de098d1f',1,'vg::StrandSplitGraph::get_underlying_handle()'],['../classvg_1_1SubHandleGraph.html#a434e6cd60bb278307df255a43681e08a',1,'vg::SubHandleGraph::get_underlying_handle()'],['../classvg_1_1SubpathOverlay.html#a595889f41331fbbc8a049ae56ba29624',1,'vg::SubpathOverlay::get_underlying_handle()'],['../classvg_1_1TreeSubgraph.html#a2d88a6edb6d6d586b6fe26a88e13248f',1,'vg::TreeSubgraph::get_underlying_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ada7dab5b4c9e55607563d1bcf546d401',1,'handlegraph::algorithms::SubHandleGraph::get_underlying_handle()'],['../classhandlegraph_1_1ExpandingOverlayGraph.html#aacfa30b0166f91f1aa80f0fd566d2b65',1,'handlegraph::ExpandingOverlayGraph::get_underlying_handle()']]],
- ['get_5funderlying_5fid_9447',['get_underlying_id',['../classvg_1_1DagifiedGraph.html#ae8707e0886baf125d0c0a25a3cc3a4cc',1,'vg::DagifiedGraph::get_underlying_id()'],['../classvg_1_1DozeuPinningOverlay.html#a45047bf7a55843a4099d9db6b83e2d17',1,'vg::DozeuPinningOverlay::get_underlying_id()']]],
- ['get_5funique_5fhaplotypes_9448',['get_unique_haplotypes',['../classvg_1_1VariantAdder.html#aa9ae7b7fa8ad3ac6bec72ada43a3d4b7',1,'vg::VariantAdder']]],
- ['get_5fvalue_9449',['get_value',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#adf719dd5d99dd4b31952df3af1911ed1',1,'vg::ZipCodeTree::tree_item_t::get_value()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a6d28a735e7c8a6a0cc8b11675fb8d261',1,'vg::subcommand::ArgSpec::get_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#acb802adcf83734cc84ee4745ed4ee505',1,'vg::subcommand::ValueArgSpec::get_value()']]],
- ['get_5fvalue_5fand_5fnext_5findex_9450',['get_value_and_next_index',['../structvg_1_1varint__vector__t.html#afee3663cabce117ecf7b114b0179ae31',1,'vg::varint_vector_t']]],
- ['get_5fvariants_5fin_5fsite_9451',['get_variants_in_site',['../classvg_1_1VCFTraversalFinder.html#ae45b4f713e847be11c4aa07482de3e12',1,'vg::VCFTraversalFinder']]],
- ['get_5fvcf_5fheader_9452',['get_vcf_header',['../classvg_1_1Deconstructor.html#a6c14aa01fabc63b945bc69550335408b',1,'vg::Deconstructor']]],
- ['get_5fversion_9453',['get_version',['../classvg_1_1Version.html#aa6e698d728ebd5e3318511dfde778eaf',1,'vg::Version']]],
- ['get_5fvg_5findex_5fregistry_9454',['get_vg_index_registry',['../structvg_1_1VGIndexes.html#a4291997834048ac385331f19390889c0',1,'vg::VGIndexes']]],
- ['get_5fweight_5fusing_5fother_9455',['get_weight_using_other',['../structvg_1_1algorithms_1_1Graph.html#ad0741db7b09040c706ffaffbb7337098',1,'vg::algorithms::Graph']]],
- ['get_5fwork_5fdir_9456',['get_work_dir',['../classvg_1_1IndexRegistry.html#ac587073860174b6c074d2be7ad53e103',1,'vg::IndexRegistry']]],
- ['getreachablebridges_9457',['getReachableBridges',['../namespacevg.html#af601021f7ec2c0b0d7404030ee7271c9',1,'vg']]],
- ['getreachablebridges2_9458',['getReachableBridges2',['../namespacevg.html#a2dc613a63afb3f23851c96494006630d',1,'vg']]],
- ['gfa_5fhas_5fhaplotypes_9459',['gfa_has_haplotypes',['../classvg_1_1IndexRegistry.html#a019e2efc800d3280acdce7814db8b096',1,'vg::IndexRegistry']]],
- ['gfa_5fto_5fhandle_5fgraph_9460',['gfa_to_handle_graph',['../namespacevg_1_1algorithms.html#aedfca626dc003dc3fee77c6bbfcde297',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, GFAIDMapInfo *translation)'],['../namespacevg_1_1algorithms.html#adca14b7dcba0bb21f3fdb0c98d867c72',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, const string &translation_filename)'],['../namespacevg_1_1algorithms.html#a031cb6d0db20a6aaee020c5a6909ba80',1,'vg::algorithms::gfa_to_handle_graph(istream &in, MutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr)']]],
- ['gfa_5fto_5fpath_5fhandle_5fgraph_9461',['gfa_to_path_handle_graph',['../namespacevg_1_1algorithms.html#a9f5c41c06269c778d2c97f39cbc79de8',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a61f2c7006c531ad5dd319ea30ec0087f',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, int64_t max_rgfa_rank, const string &translation_filename, unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a8baa82611439357dc02996ba17ce6aa9',1,'vg::algorithms::gfa_to_path_handle_graph(istream &in, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)']]],
- ['gfaduplicatepatherror_9462',['GFADuplicatePathError',['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#aa815b9f84fdf80d9bf29c38d3d68408c',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name)'],['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#a05dd140439b17113dec810a3cdc26bab',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
- ['gfaformaterror_9463',['GFAFormatError',['../structvg_1_1algorithms_1_1GFAFormatError.html#add2d72c679e2b69e1c9f9c481228e0fb',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message)'],['../structvg_1_1algorithms_1_1GFAFormatError.html#afdf6dea244cc33a30ae5d9446199bea2',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
- ['gfahandlegraph_9464',['GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html#aeffc2278ffcad22cd6950f3fa831f60d',1,'vg::GFAHandleGraph']]],
- ['gffreader_9465',['GFFReader',['../classvg_1_1GFFReader.html#a886d9cf2d287f8d0f6c87b206c26d893',1,'vg::GFFReader']]],
- ['gffrecord_9466',['GFFRecord',['../structvg_1_1GFFRecord.html#a8fc2a234093eccb6ed958325887e0f08',1,'vg::GFFRecord']]],
- ['golden_5fsection_5fsearch_9467',['golden_section_search',['../namespacevg.html#a314ff925fad534d112e4531617e408fa',1,'vg']]],
- ['graph_9468',['graph',['../classvg_1_1Transcriptome.html#aee456b8b8e3acaf836914c987d89a16a',1,'vg::Transcriptome']]],
- ['graph_5fcigar_9469',['graph_cigar',['../classvg_1_1GSSWAligner.html#a429c1cbb1e166acba4e29a8dc172da7d',1,'vg::GSSWAligner']]],
- ['graph_5fend_9470',['graph_end',['../classvg_1_1algorithms_1_1Anchor.html#a3ddb866c3cb925619705602580076942',1,'vg::algorithms::Anchor']]],
- ['graph_5finterval_5fto_5fstring_9471',['graph_interval_to_string',['../namespacevg.html#aeade23d997b1899023cfe7f560cc6bc1',1,'vg']]],
- ['graph_5fmixed_5fdistance_5festimate_9472',['graph_mixed_distance_estimate',['../classvg_1_1Mapper.html#a67fb2b4bc540b81be063075ce5593569',1,'vg::Mapper']]],
- ['graph_5fpos_5fat_5fpath_5fposition_9473',['graph_pos_at_path_position',['../classxg_1_1XG.html#a85c47feeb19e96486140c5e1b8184bc7',1,'xg::XG::graph_pos_at_path_position(const path_handle_t &path, size_t path_pos) const'],['../classxg_1_1XG.html#a31c733ed1c2045b1e2a7e9f343dc9296',1,'xg::XG::graph_pos_at_path_position(const std::string &name, size_t path_pos) const']]],
- ['graph_5fstart_9474',['graph_start',['../classvg_1_1algorithms_1_1Anchor.html#ac7bd5f21e10bae0f6dacb3fcc623752f',1,'vg::algorithms::Anchor']]],
- ['graph_5fto_5fgfa_9475',['graph_to_gfa',['../namespacevg.html#ad8c4a075bb9301c8050d89ed8e6a33b9',1,'vg']]],
- ['graph_5fto_5fxg_5fadjusting_5fpaths_9476',['graph_to_xg_adjusting_paths',['../convert__main_8cpp.html#afe37e7186bce3c6128d32b210f99a9a5',1,'convert_main.cpp']]],
- ['graphcaller_9477',['GraphCaller',['../classvg_1_1GraphCaller.html#a621386ff80a0fe3289719c75c282bc5a',1,'vg::GraphCaller']]],
- ['graphsynchronizer_9478',['GraphSynchronizer',['../classvg_1_1GraphSynchronizer.html#addf1e96558546d4f5e708827b9eb4d67',1,'vg::GraphSynchronizer']]],
- ['greedymindistanceclusterer_9479',['GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html#a603a74649e16204cace3e714ebe67a74',1,'vg::GreedyMinDistanceClusterer']]],
- ['groom_5fcomponents_9480',['groom_components',['../classvg_1_1FlowSort.html#a2a52b4d445acf50ebfd8f7dc3a07d044',1,'vg::FlowSort']]],
- ['group_9481',['group',['../classvg_1_1SparseUnionFind.html#af91351abb606a1bc16c1cbb5f1b668ab',1,'vg::SparseUnionFind']]],
- ['group_5fmapping_5fquality_5fexact_9482',['group_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#a7e03bd79bceb8a8034ae57ba640069bc',1,'vg::GSSWAligner']]],
- ['group_5fsize_9483',['group_size',['../classvg_1_1SparseUnionFind.html#aff34e4252e15a68b1e8e79c8cef27a66',1,'vg::SparseUnionFind']]],
- ['groupedoptiongroup_9484',['GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a6da6deb7ccf8697e84db1c266dd9180f',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup()=default'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af4f06c1eff0303d1c982b0c2d34c2b55',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(const GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ab1c7b6f34e8d53cf4536625ea6709e80',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(GroupedOptionGroup &&other)=delete']]],
- ['growth_9485',['Growth',['../structvg_1_1FlowSort_1_1Growth.html#aa156ae24695e73aee936d00a7ef70d22',1,'vg::FlowSort::Growth']]],
- ['gssw_5fmapping_5fto_5falignment_9486',['gssw_mapping_to_alignment',['../classvg_1_1GSSWAligner.html#ab45f7399b68bdc980499d4384515b9b7',1,'vg::GSSWAligner']]],
- ['gsswaligner_9487',['GSSWAligner',['../classvg_1_1GSSWAligner.html#a02c1c427118eb1a8244274d852684c79',1,'vg::GSSWAligner::GSSWAligner()=default'],['../classvg_1_1GSSWAligner.html#a6c3f1338e6a66850b779e8331a65a61c',1,'vg::GSSWAligner::GSSWAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int8_t _full_length_bonus, double _gc_content)']]],
- ['guess_5fparallel_5fgbwt_5fjobs_9488',['guess_parallel_gbwt_jobs',['../namespacevg.html#a70ebd70e5b26c5fefe30895fa313f3b9',1,'vg']]]
+ ['gaf_5fpaired_5finterleaved_5ffor_5feach_9078',['gaf_paired_interleaved_for_each',['../namespacevg_1_1io.html#a1509c614371533861fa7552febf7af92',1,'vg::io::gaf_paired_interleaved_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda)'],['../namespacevg_1_1io.html#ad242e1399847a5c894201b9e32c13a6d',1,'vg::io::gaf_paired_interleaved_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda)']]],
+ ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_9079',['gaf_paired_interleaved_for_each_parallel',['../namespacevg_1_1io.html#a7b473c9f170444107256aa76f522d27a',1,'vg::io::gaf_paired_interleaved_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#a8662ca54b9e1f26e421884a43a4e0e21',1,'vg::io::gaf_paired_interleaved_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, uint64_t batch_size)']]],
+ ['gaf_5fpaired_5finterleaved_5ffor_5feach_5fparallel_5fafter_5fwait_9080',['gaf_paired_interleaved_for_each_parallel_after_wait',['../namespacevg_1_1io.html#a44d7cb48aae7d9c3621fabc6b31faa6e',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)'],['../namespacevg_1_1io.html#a63b12354bf13d6a19b5addc71fc512c7',1,'vg::io::gaf_paired_interleaved_for_each_parallel_after_wait(const HandleGraph &graph, const string &filename, function< void(Alignment &, Alignment &)> lambda, function< bool(void)> single_threaded_until_true, uint64_t batch_size)']]],
+ ['gaf_5fto_5falignment_9081',['gaf_to_alignment',['../namespacevg_1_1io.html#a44a872a40072dc128fa898a795eeff79',1,'vg::io::gaf_to_alignment(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const gafkluge::GafRecord &gaf, Alignment &aln)'],['../namespacevg_1_1io.html#a363656cc5c1a09f178e3c83785488bad',1,'vg::io::gaf_to_alignment(const HandleGraph &graph, const gafkluge::GafRecord &gaf, Alignment &aln)']]],
+ ['gaf_5funpaired_5ffor_5feach_9082',['gaf_unpaired_for_each',['../namespacevg_1_1io.html#a83d5011d88f6ef27ed8837957505284b',1,'vg::io::gaf_unpaired_for_each(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda)'],['../namespacevg_1_1io.html#ada4771a7ea674ee9d986af264ab3c00d',1,'vg::io::gaf_unpaired_for_each(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda)']]],
+ ['gaf_5funpaired_5ffor_5feach_5fparallel_9083',['gaf_unpaired_for_each_parallel',['../namespacevg_1_1io.html#a88d2dffc472bbcfded0b1190fc5bc933',1,'vg::io::gaf_unpaired_for_each_parallel(function< size_t(nid_t)> node_to_length, function< string(nid_t, bool)> node_to_sequence, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)'],['../namespacevg_1_1io.html#add46b11d285f6b94896c1f5e91a405a7',1,'vg::io::gaf_unpaired_for_each_parallel(const HandleGraph &graph, const string &filename, function< void(Alignment &)> lambda, uint64_t batch_size)']]],
+ ['gafalignmentemitter_9084',['GafAlignmentEmitter',['../classvg_1_1io_1_1GafAlignmentEmitter.html#ad7b537251b10534375e90a22b795b9cc',1,'vg::io::GafAlignmentEmitter']]],
+ ['gafoutputcaller_9085',['GAFOutputCaller',['../classvg_1_1GAFOutputCaller.html#a2def7ee0c3eb2f0cbfd139ad0eeeec8b',1,'vg::GAFOutputCaller']]],
+ ['gafrecord_9086',['GafRecord',['../structgafkluge_1_1GafRecord.html#a81394a04ad249c56b3f757484a7663bc',1,'gafkluge::GafRecord']]],
+ ['gamma_5fln_9087',['gamma_ln',['../namespacevg.html#a05748ab256c93e2393252aa8ebbdde3d',1,'vg']]],
+ ['gap_5fextend_5fpenalty_9088',['gap_extend_penalty',['../classvg_1_1WFATree.html#a705cd842a3204b5dbc0c669f3e1c60c7',1,'vg::WFATree']]],
+ ['gap_5fpenalty_9089',['gap_penalty',['../classvg_1_1WFATree.html#a46f357dbdd6957c1c08bb82a275a3bcf',1,'vg::WFATree']]],
+ ['gaplessextender_9090',['GaplessExtender',['../classvg_1_1GaplessExtender.html#a497cc4e85c6433a3e41f04895703f271',1,'vg::GaplessExtender::GaplessExtender()'],['../classvg_1_1GaplessExtender.html#aaebc8d221df2787a68023fce2d99290a',1,'vg::GaplessExtender::GaplessExtender(const gbwtgraph::GBWTGraph &graph, const Aligner &aligner)']]],
+ ['gbwt_5fnode_5fwidth_9091',['gbwt_node_width',['../namespacevg.html#ada6300e45d21f1171c5ff2b71f4d173b',1,'vg']]],
+ ['gbwt_5fthread_5ft_9092',['gbwt_thread_t',['../structhaplo_1_1gbwt__thread__t.html#a5b148ae0a27b81b4b4af07f200a1255b',1,'haplo::gbwt_thread_t::gbwt_thread_t()'],['../structhaplo_1_1gbwt__thread__t.html#aa52a0e84c11044abd6ce20969629e3a9',1,'haplo::gbwt_thread_t::gbwt_thread_t(const gbwt::vector_type &nodes, const vector< size_t > &node_lengths)']]],
+ ['gbwt_5fto_5fhandle_9093',['gbwt_to_handle',['../namespacevg.html#a28c93b1c4a71fadf62fc2582cc8f0ed2',1,'vg']]],
+ ['gbwt_5fto_5fpos_9094',['gbwt_to_pos',['../namespacevg.html#ae7b5f995eb3e1e824cc4e7db99c81042',1,'vg']]],
+ ['gbwtconfig_9095',['GBWTConfig',['../structGBWTConfig.html#a20a8123e9a054bab77de5e8d9f9c1bd5',1,'GBWTConfig']]],
+ ['gbwtscoreprovider_9096',['GBWTScoreProvider',['../classhaplo_1_1GBWTScoreProvider.html#abf8bd05e480afa9a2ac2832a13f5b181',1,'haplo::GBWTScoreProvider']]],
+ ['gbwttraversalfinder_9097',['GBWTTraversalFinder',['../classvg_1_1GBWTTraversalFinder.html#af415423d43372c2770c201a10ace0385',1,'vg::GBWTTraversalFinder']]],
+ ['gcsa_5fnodes_5fto_5fpositions_9098',['gcsa_nodes_to_positions',['../namespacevg.html#a3240e7b9bf787fb218d6324389ea234e',1,'vg']]],
+ ['generate_9099',['generate',['../structvg_1_1RecombinatorFragment.html#a411831e7ba9db75f1d14708bb79f7eef',1,'vg::RecombinatorFragment']]],
+ ['generate_5fcontinuous_5funiform_9100',['generate_continuous_uniform',['../classvg_1_1MCMCGenotyper.html#a5ebeff817c6548c32c5377ed00c041c6',1,'vg::MCMCGenotyper']]],
+ ['generate_5fdiscrete_5funiform_9101',['generate_discrete_uniform',['../classvg_1_1MCMCGenotyper.html#a8b76754fc9611d38463cccd3051c0589',1,'vg::MCMCGenotyper']]],
+ ['generate_5ffrom_5fwide_5fgenerator_9102',['generate_from_wide_generator',['../classvg_1_1uniform__int__distribution.html#a6efdc1be7572287df4cfad1acd044d90',1,'vg::uniform_int_distribution']]],
+ ['generate_5fhaplotype_9103',['generate_haplotype',['../namespacevg.html#a117021c748aad14cfa190bbd2452405d',1,'vg']]],
+ ['generate_5fhaplotypes_9104',['generate_haplotypes',['../classvg_1_1Recombinator.html#a7f803cd4d08d8c699877e274bc3f5ceb',1,'vg::Recombinator::generate_haplotypes(const std::string &kff_file, const Parameters ¶meters) const'],['../classvg_1_1Recombinator.html#a8ac8a32e83455572b44af1da347cd09d',1,'vg::Recombinator::generate_haplotypes(const Haplotypes::TopLevelChain &chain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata, const Parameters ¶meters, double coverage) const']]],
+ ['generate_5finitial_5fguess_9105',['generate_initial_guess',['../classvg_1_1MCMCGenotyper.html#aac263c28f16acd3eb17d1f6013b5709e',1,'vg::MCMCGenotyper']]],
+ ['generate_5fpaths_9106',['generate_paths',['../classvg_1_1PhaseUnfolder.html#a7a2015207e502ecd4d294af79936bda2',1,'vg::PhaseUnfolder']]],
+ ['generate_5fthreads_9107',['generate_threads',['../classvg_1_1PhaseUnfolder.html#abc5cead86bec1446aedd4cb2ec291d3f',1,'vg::PhaseUnfolder']]],
+ ['genomestate_9108',['GenomeState',['../classvg_1_1GenomeState.html#ab132518a611296d53c4f59a6b5737374',1,'vg::GenomeState']]],
+ ['genotype_9109',['genotype',['../classvg_1_1SnarlCaller.html#a3e4d1ad4ece1a1bc1daa4ea6ecfbfa54',1,'vg::SnarlCaller::genotype()'],['../classvg_1_1RatioSupportSnarlCaller.html#afa1d42f1ba7e32ca274e23d0e9795278',1,'vg::RatioSupportSnarlCaller::genotype()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a1be3298970827475c5b96486d58fd833',1,'vg::PoissonSupportSnarlCaller::genotype()']]],
+ ['genotype_5flikelihood_9110',['genotype_likelihood',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a555a22f275a83ade8fcd35a1572908',1,'vg::PoissonSupportSnarlCaller']]],
+ ['genotype_5fsnarl_9111',['genotype_snarl',['../classvg_1_1Genotyper.html#ae6a3a060adcffc32724498bbfda2c771',1,'vg::Genotyper']]],
+ ['genotype_5fsvs_9112',['genotype_svs',['../namespacevg.html#a7d3374c888c7c37f1de8370e151af7f9',1,'vg']]],
+ ['geometric_5fsampling_5fprob_5fln_9113',['geometric_sampling_prob_ln',['../namespacevg.html#ae923ee7bdb53f33511c95f66a9c2773a',1,'vg']]],
+ ['get_9114',['get',['../structvg_1_1Annotation.html#a00494075a8d051c16b2485b44c541dce',1,'vg::Annotation::get()'],['../classvg_1_1GBZGraph.html#a69ee920e1aa95a146e8e77f32a717a88',1,'vg::GBZGraph::get()'],['../classvg_1_1GBZGraph.html#a3eb7ff9317143e89c14bd15a682426ac',1,'vg::GBZGraph::get() const'],['../classvg_1_1VcfBuffer.html#ac855a338ea08f2ea75dc73206f9d7520',1,'vg::VcfBuffer::get()'],['../classvg_1_1WindowedVcfBuffer.html#a3c09bb140ab8f8d91f2f67f3dc0e7f0b',1,'vg::WindowedVcfBuffer::get()'],['../classvg_1_1subcommand_1_1Subcommand.html#aa44da5b424f5fcf7133f6a061680693f',1,'vg::subcommand::Subcommand::get()']]],
+ ['get_5fadaptive_5fmin_5freseed_5flength_9115',['get_adaptive_min_reseed_length',['../classvg_1_1BaseMapper.html#a7f693887391ddeaebf4a4a609e2ab9b3',1,'vg::BaseMapper']]],
+ ['get_5faffinities_9116',['get_affinities',['../classvg_1_1Genotyper.html#abea795c1969c4866c349a07c7f9c7102',1,'vg::Genotyper']]],
+ ['get_5faffinities_5ffast_9117',['get_affinities_fast',['../classvg_1_1Genotyper.html#a966eee3f764281271904996546ef205b',1,'vg::Genotyper']]],
+ ['get_5faligner_9118',['get_aligner',['../classvg_1_1AlignerClient.html#a683c04ab96b613ea3459738beffe5982',1,'vg::AlignerClient']]],
+ ['get_5falignment_5femitter_9119',['get_alignment_emitter',['../namespacevg.html#aa95de659d860fc90fda95df414c89baf',1,'vg']]],
+ ['get_5falignment_5fstart_9120',['get_alignment_start',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a5790a8cfd26dd12a19d33fc11cb84933',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['get_5falignments_9121',['get_alignments',['../structvg_1_1AugmentedGraph.html#ad92c283634470f6372777c38a9a70a79',1,'vg::AugmentedGraph::get_alignments(id_t node_id) const'],['../structvg_1_1AugmentedGraph.html#a61465a645ac54c62d4707d570ed56f76',1,'vg::AugmentedGraph::get_alignments(pair< NodeSide, NodeSide >) const'],['../structvg_1_1AugmentedGraph.html#ab3bf8e1a51696ba12329045956b7646a',1,'vg::AugmentedGraph::get_alignments() const']]],
+ ['get_5fallele_9122',['get_allele',['../classvg_1_1PhasedGenome.html#a6f89ab856a31dfb7258fd7487c051a5a',1,'vg::PhasedGenome']]],
+ ['get_5falleles_9123',['get_alleles',['../classvg_1_1Deconstructor.html#a7977882fef8c75836fede5338925f411',1,'vg::Deconstructor']]],
+ ['get_5falt_5fpath_9124',['get_alt_path',['../classvg_1_1VCFTraversalFinder.html#acbbbaa19966bd2a939f9fdc05b414343',1,'vg::VCFTraversalFinder']]],
+ ['get_5falt_5ftraversal_9125',['get_alt_traversal',['../classvg_1_1VCFTraversalFinder.html#afd039c87e92906ac02479d8d2df43f13',1,'vg::VCFTraversalFinder']]],
+ ['get_5fannotation_9126',['get_annotation',['../classvg_1_1multipath__alignment__t.html#a401b9ef14924b463d54be7a4ced828d6',1,'vg::multipath_alignment_t::get_annotation()'],['../namespacevg.html#a1fda752e24eaed100f6c30904d2ca3e1',1,'vg::get_annotation(const Annotated &annotated, const string &name)'],['../namespacevg.html#a1c9f371af54160a44a44afd80c6cf71a',1,'vg::get_annotation(Annotated *annotated, const string &name)']]],
+ ['get_5fany_5fgraph_9127',['get_any_graph',['../structGraphHandler.html#a7155dd41d244081487e79759707f29af',1,'GraphHandler']]],
+ ['get_5faverage_5ftraversal_5fsupport_5fswitch_5fthreshold_9128',['get_average_traversal_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a62c1864ae422d93cba4eb248890fd3e4',1,'vg::TraversalSupportFinder']]],
+ ['get_5favg_5fbaseq_9129',['get_avg_baseq',['../namespacevg.html#a680a465e72fbddeed584f27a6c3f7b27',1,'vg']]],
+ ['get_5favg_5fnode_5fmapq_9130',['get_avg_node_mapq',['../classvg_1_1TraversalSupportFinder.html#a55880f595d8f607a73e8617e7b2aa216',1,'vg::TraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1PackedTraversalSupportFinder.html#a1fd604b1e8eac99954981aca81cafffd',1,'vg::PackedTraversalSupportFinder::get_avg_node_mapq()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aa3fab4fec47f870d3cc6e2c1fdb46ccb',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_mapq()']]],
+ ['get_5favg_5fnode_5fsupport_9131',['get_avg_node_support',['../classvg_1_1TraversalSupportFinder.html#a42cf4393f0ff594d0eaf489b2127cdef',1,'vg::TraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a66cbea99df3ef78364f653a044bec308',1,'vg::PackedTraversalSupportFinder::get_avg_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#abb0f5d8c3967c099daaf2fb174620f3a',1,'vg::CachedPackedTraversalSupportFinder::get_avg_node_support()']]],
+ ['get_5fback_5fgraph_5fnode_5fname_9132',['get_back_graph_node_name',['../classvg_1_1FlatFileBackTranslation.html#a816506e29e304f623d790d79271fd344',1,'vg::FlatFileBackTranslation::get_back_graph_node_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a5829e7992e105e0895a81a8aca82e70b',1,'vg::algorithms::GFAIDMapInfo::get_back_graph_node_name()'],['../classhandlegraph_1_1NamedNodeBackTranslation.html#acd81ad54c6a6ec680faaae76aaae4397',1,'handlegraph::NamedNodeBackTranslation::get_back_graph_node_name()']]],
+ ['get_5fbase_9133',['get_base',['../classvg_1_1IncrementalSubgraph.html#a6ff73a10a56b8116b7d07c32d3f3160a',1,'vg::IncrementalSubgraph::get_base()'],['../classvg_1_1JoinedSpliceGraph.html#a7dcc1d1e3e9c2e1058a5995785b0a224',1,'vg::JoinedSpliceGraph::get_base()'],['../classvg_1_1VG.html#a7cb582e352f75cc9d66e6eff0f4ba659',1,'vg::VG::get_base()'],['../classxg_1_1XG.html#a355dd79f8449b462e7d98916f1a22d9f',1,'xg::XG::get_base()'],['../classhandlegraph_1_1HandleGraph.html#a64d58c3e26e9e7954dd25c3eff7af521',1,'handlegraph::HandleGraph::get_base()']]],
+ ['get_5fbase_5fgbwt_5fpath_5fname_9134',['get_base_gbwt_path_name',['../classvg_1_1Transcriptome.html#a1c9af6904f1f282a0782c1e34bc4b9ab',1,'vg::Transcriptome']]],
+ ['get_5fbest_5falignment_5fagainst_5fany_5ftree_9135',['get_best_alignment_against_any_tree',['../classvg_1_1MinimizerMapper.html#a12558b08552a22a9a28db3fb0fd3779d',1,'vg::MinimizerMapper']]],
+ ['get_5fbest_5fchain_5fstats_9136',['get_best_chain_stats',['../classvg_1_1MinimizerMapper.html#a2f9b9b580ed851b00268f455c2d543cb',1,'vg::MinimizerMapper']]],
+ ['get_5fbest_5fgbwtgraph_5fgfa_5fparsing_5fparameters_9137',['get_best_gbwtgraph_gfa_parsing_parameters',['../namespacevg.html#ab35317ee2bc53165662dd776516f341d',1,'vg']]],
+ ['get_5fbest_5fsupport_9138',['get_best_support',['../classvg_1_1SupportBasedSnarlCaller.html#a1b5a50373729771229ada685b12627df',1,'vg::SupportBasedSnarlCaller']]],
+ ['get_5fbias_9139',['get_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a3f5f06692eeabe27d7c00afc8658cb20',1,'vg::RatioSupportSnarlCaller']]],
+ ['get_5fbin_5fsize_9140',['get_bin_size',['../classvg_1_1Packer.html#afef014ad5278ee08959c3ffe2cf15c17',1,'vg::Packer']]],
+ ['get_5fbound_9141',['get_bound',['../classhandlegraph_1_1SnarlDecomposition.html#aabee8d2ebb1971ecfd5c4647b84081f2',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fbounds_9142',['get_bounds',['../classvg_1_1Constructor.html#a06078b6af1dc190c74806b30b669daae',1,'vg::Constructor']]],
+ ['get_5fbuckets_9143',['get_buckets',['../classvg_1_1OrientedDistanceMeasurer.html#aa21aedba58999e7041483f077720d13b',1,'vg::OrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#aac5383ef03533609d85172e7821a8200',1,'vg::PathOrientedDistanceMeasurer::get_buckets()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#ac885044126300cab4750fd21fd4634fc',1,'vg::SnarlOrientedDistanceMeasurer::get_buckets()']]],
+ ['get_5fcategory_9144',['get_category',['../classvg_1_1subcommand_1_1Subcommand.html#a252c8946e450ba4a194b7da6ece5ba2c',1,'vg::subcommand::Subcommand']]],
+ ['get_5fcc_5fin_5fwg_9145',['get_cc_in_wg',['../classvg_1_1FlowSort.html#a27df1607587f1f1e1f03ab8369c34ebe',1,'vg::FlowSort']]],
+ ['get_5fcenter_9146',['get_center',['../classvg_1_1VariantAdder.html#a2949d0ea5c46f477813df8f5162fe013',1,'vg::VariantAdder']]],
+ ['get_5fcenter_5fand_5fradius_9147',['get_center_and_radius',['../classvg_1_1VariantAdder.html#a29a14a6579197519b35653f542d5c1ec',1,'vg::VariantAdder']]],
+ ['get_5fchain_5fcode_9148',['get_chain_code',['../classvg_1_1ZipCode.html#aa0f40a265733bd4adfb920006fd9f57a',1,'vg::ZipCode']]],
+ ['get_5fchain_5fcomponent_9149',['get_chain_component',['../classvg_1_1ZipCode.html#af85179af0d75add0b10023343c2a407a',1,'vg::ZipCode::get_chain_component()'],['../structvg_1_1ZipCode_1_1node__code__t.html#a52e72d7ff49bcb809cac2f7ab85ad004',1,'vg::ZipCode::node_code_t::get_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a5dcd90a391b2382723f3b303687ca1c8',1,'vg::ZipCode::snarl_code_t::get_chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#adc51b5f6e09b00eb41964c902d7eb033',1,'vg::ZipCodeForest::sort_value_t::get_chain_component()']]],
+ ['get_5fchild_5fcount_9150',['get_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a315c9998b34918303feb08d5143fba7c',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fchild_5fsupport_9151',['get_child_support',['../classvg_1_1TraversalSupportFinder.html#ac46ef820b2a05e8b331677deb80871a9',1,'vg::TraversalSupportFinder::get_child_support()'],['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af112bf57cc9a16c9dc35f6578a3b1c14',1,'vg::NestedCachedPackedTraversalSupportFinder::get_child_support()']]],
+ ['get_5fclipped_5fposition_9152',['get_clipped_position',['../classvg_1_1Filter.html#a5cc119894a6baeb450c31dc7c6b75bed',1,'vg::Filter']]],
+ ['get_5fclipped_5fref_5fposition_9153',['get_clipped_ref_position',['../classvg_1_1Filter.html#ab1a309b366e677b179772e9bebd9f78f',1,'vg::Filter']]],
+ ['get_5fclipped_5fseq_9154',['get_clipped_seq',['../classvg_1_1Filter.html#a4c29ccf736113bb95328467d22f98ad8',1,'vg::Filter']]],
+ ['get_5fcluster_5fpairs_9155',['get_cluster_pairs',['../classvg_1_1MultipathMapper.html#a49fdf1a2efedda808c2d3a7bda5a7f98',1,'vg::MultipathMapper']]],
+ ['get_5fclusters_9156',['get_clusters',['../classvg_1_1MultipathMapper.html#a0a588e4f282d38add8626debe86c455d',1,'vg::MultipathMapper']]],
+ ['get_5fcode_5ftype_9157',['get_code_type',['../classvg_1_1ZipCode.html#ac91d59c7100fefc2011cda07996ed71a',1,'vg::ZipCode::get_code_type()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a0d7f3c9052df0ced4949b909d1ed20b5',1,'vg::ZipCode::snarl_code_t::get_code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a9959da3b3a6e98968794073dc049eb0b',1,'vg::ZipCodeForest::sort_value_t::get_code_type()']]],
+ ['get_5fcodename_9158',['get_codename',['../classvg_1_1Version.html#a0bab20984ed75b2df12c3ef4a409f922',1,'vg::Version']]],
+ ['get_5fconnected_5fcomponents_9159',['get_connected_components',['../classvg_1_1MultipathAlignmentGraph.html#af4fc215d24f20c5ddc3916024c7ab62b',1,'vg::MultipathAlignmentGraph']]],
+ ['get_5fconnectivity_9160',['get_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a0b28eb090f0d0f7b1b408a5e772b3105',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fcontained_5forientations_9161',['get_contained_orientations',['../structvg_1_1PathIndex.html#a6a7f7bbcd256a2ed34a58b8abefff712',1,'vg::PathIndex']]],
+ ['get_5fcontext_9162',['get_context',['../classvg_1_1Deconstructor.html#a049890802f6b6036a779eb3645bb1307',1,'vg::Deconstructor']]],
+ ['get_5fcorrelation_9163',['get_correlation',['../classvg_1_1ZipCodeForest.html#ab939e5ee856a9ac2531d0d8ac14e7cbe',1,'vg::ZipCodeForest']]],
+ ['get_5fcount_9164',['get_count',['../classvg_1_1NoAlignmentInBandException.html#a4b5f7f90a2be571131fb12484a9b4c18',1,'vg::NoAlignmentInBandException']]],
+ ['get_5fcreate_5fpath_9165',['get_create_path',['../classvg_1_1Paths.html#a4e79d7915cd2f68e55573bcc50c1d417',1,'vg::Paths']]],
+ ['get_5fcreated_5fhandle_9166',['get_created_handle',['../classvg_1_1ExtraNodeGraph.html#aac84ee8139e0aa885b87f02ad9ccf8ef',1,'vg::ExtraNodeGraph']]],
+ ['get_5fcurrent_5fcolumn_9167',['get_current_column',['../structhaplo_1_1haplo__DP.html#a0061c97ecd2330efdcf0fbabb69d808d',1,'haplo::haplo_DP']]],
+ ['get_5fcurrent_5fvmem_5fkb_9168',['get_current_vmem_kb',['../namespacevg.html#a8cd30aaebcab130194ac375f23e6f098',1,'vg']]],
+ ['get_5fcut_5fsegments_9169',['get_cut_segments',['../classvg_1_1MultipathAlignmentGraph.html#aaa64dbf4207ebe2fe75044d60be1d07e',1,'vg::MultipathAlignmentGraph']]],
+ ['get_5fcyclic_5fsnarl_5fintervals_9170',['get_cyclic_snarl_intervals',['../classvg_1_1ZipCodeForest.html#ad32664318549a51d8727204d665a2bc6',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const interval_state_t &snarl_interval, const interval_state_t &parent_interval, const forward_list< interval_state_t > &child_intervals, forward_list< interval_state_t > &next_intervals) const'],['../classvg_1_1ZipCodeForest.html#a72304772e60e79909b71f8a51e65d6a5',1,'vg::ZipCodeForest::get_cyclic_snarl_intervals(forest_growing_state_t &forest_state, const VectorView< Minimizer > &minimizers, const ZipCodeForest::interval_state_t &snarl_interval, const ZipCodeForest::interval_state_t &parent_interval, const forward_list< ZipCodeForest::interval_state_t > &child_intervals, forward_list< ZipCodeForest::interval_state_t > &next_intervals) const']]],
+ ['get_5fdefault_5flong_5fgiraffe_5findexes_9171',['get_default_long_giraffe_indexes',['../structvg_1_1VGIndexes.html#a8caf19bd7436cd7f9df4f9792aa86483',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fmap_5findexes_9172',['get_default_map_indexes',['../structvg_1_1VGIndexes.html#afcc2119cd690b16f57d4b9d137af58fe',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fmpmap_5findexes_9173',['get_default_mpmap_indexes',['../structvg_1_1VGIndexes.html#a9377b325c6e0f8bbca1368379ad60a0c',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5frpvg_5findexes_9174',['get_default_rpvg_indexes',['../structvg_1_1VGIndexes.html#ae56d5009377fed32d392fcff5ac02f7f',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fshort_5fgiraffe_5findexes_9175',['get_default_short_giraffe_indexes',['../structvg_1_1VGIndexes.html#ab0f962c74f9633fe27b0d59f9774358c',1,'vg::VGIndexes']]],
+ ['get_5fdefault_5fthreads_9176',['get_default_threads',['../minimizer__main_8cpp.html#a849308cddbd36f5fc06c5e1289112bae',1,'minimizer_main.cpp']]],
+ ['get_5fdefault_5fvalue_9177',['get_default_value',['../classvg_1_1OptionInterface.html#ade1ab38610fecb31821e13e5e296454c',1,'vg::OptionInterface::get_default_value()'],['../classvg_1_1BaseOption.html#af13c01c387907bb386b591bff8bbb5e9',1,'vg::BaseOption::get_default_value()']]],
+ ['get_5fdegree_9178',['get_degree',['../classvg_1_1ExtraNodeGraph.html#a0cc5cb40e81623b3a3e11bea359e41c5',1,'vg::ExtraNodeGraph::get_degree()'],['../classvg_1_1IncrementalSubgraph.html#ae3365d87d1cd6bfe12d3433197d06a85',1,'vg::IncrementalSubgraph::get_degree()'],['../classvg_1_1SourceSinkOverlay.html#a8bfc476463b487d42c77bda6bdfe2a7d',1,'vg::SourceSinkOverlay::get_degree()'],['../classvg_1_1VG.html#afc0ac00267e00156e04c849a10b1cb74',1,'vg::VG::get_degree()'],['../classhandlegraph_1_1HandleGraph.html#ab259e3aba0da47b0ef1c9b5e43c7d209',1,'handlegraph::HandleGraph::get_degree()']]],
+ ['get_5fdepth_5ffrom_5findex_9179',['get_depth_from_index',['../namespacevg_1_1algorithms.html#a4152fa019243d9fd4c41c73fafce2241',1,'vg::algorithms']]],
+ ['get_5fdescription_9180',['get_description',['../classvg_1_1OptionInterface.html#aa53deb39285f0045257083eb38d703cd',1,'vg::OptionInterface::get_description()'],['../classvg_1_1BaseOption.html#a4343a02a0967d6f79c0b8ae83c6a0795',1,'vg::BaseOption::get_description()'],['../classvg_1_1subcommand_1_1Subcommand.html#aca3e8621a4002b48b733211c3adc52b5',1,'vg::subcommand::Subcommand::get_description()']]],
+ ['get_5fdiagonals_9181',['get_diagonals',['../classvg_1_1WFATree.html#a2bd4732a5815c365d3790b76b9230973',1,'vg::WFATree']]],
+ ['get_5fdir_9182',['get_dir',['../namespacevg_1_1temp__file.html#ab1b0884547b4f3403e8cde0ca8b75b7c',1,'vg::temp_file::get_dir()'],['../namespacexg_1_1temp__file.html#a1cef40a1b0f27d1693d827db9773c020',1,'xg::temp_file::get_dir()']]],
+ ['get_5fdisjoint_5fsets_9183',['get_disjoint_sets',['../classvg_1_1ContractingGraph.html#acd929119b9b11170f1eb4893a7032fe6',1,'vg::ContractingGraph']]],
+ ['get_5fdistance_9184',['get_distance',['../classvg_1_1HaplotypePartitioner.html#a8d98335b0032014b1e033a6610fb644d',1,'vg::HaplotypePartitioner']]],
+ ['get_5fdistance_5fend_5fleft_9185',['get_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ad3e98278c0ca79470bc1a58e3fdcf370',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5fend_5fright_9186',['get_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa5d11da32ad7be1dfa88674efd4fa422',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5findex_5faddress_9187',['get_distance_index_address',['../classvg_1_1ZipCode.html#a6cc3964efc186615dab6bdd8bc52fbfb',1,'vg::ZipCode']]],
+ ['get_5fdistance_5flimit_9188',['get_distance_limit',['../classvg_1_1MinimizerMapper.html#a27798cd4a1bee171ec38713d402e8793',1,'vg::MinimizerMapper']]],
+ ['get_5fdistance_5fmeasurer_9189',['get_distance_measurer',['../classvg_1_1MultipathMapper.html#a56e1c69cfba7c1eebb4cae0af59a018d',1,'vg::MultipathMapper']]],
+ ['get_5fdistance_5fstart_5fleft_9190',['get_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a678e476d61bcf781b1461cedb8801c68',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5fstart_5fright_9191',['get_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aedb473ac00ffbd480c09fd04e44fcbb8',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fdistance_5fto_5fsnarl_5fbound_9192',['get_distance_to_snarl_bound',['../classvg_1_1ZipCode.html#ad39662d894fe714c1d8596b0343557f6',1,'vg::ZipCode']]],
+ ['get_5fdistance_5fvalue_9193',['get_distance_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a2a427abecffc91c8f56b715de43a43b3',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['get_5fduplicate_5fhandle_9194',['get_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#af51998490e3eac92e0d106b791eebbce',1,'vg::DozeuPinningOverlay']]],
+ ['get_5fedge_9195',['get_edge',['../classvg_1_1VG.html#a8668ddc84b9abe4fe9cb5acb3efd877b',1,'vg::VG::get_edge(const NodeSide &side1, const NodeSide &side2)'],['../classvg_1_1VG.html#a227023072262f46f7c423d30cf8bc443',1,'vg::VG::get_edge(const pair< NodeSide, NodeSide > &sides)'],['../classvg_1_1VG.html#af63d7ba7b69594ee99f3ad99dd394171',1,'vg::VG::get_edge(const NodeTraversal &left, const NodeTraversal &right)']]],
+ ['get_5fedge_5fcount_9196',['get_edge_count',['../classvg_1_1IncrementalSubgraph.html#aeab323f77d0363867dc60be6dafe73ce',1,'vg::IncrementalSubgraph::get_edge_count()'],['../classvg_1_1VG.html#ad4577be9213932c313efd3d016b88a31',1,'vg::VG::get_edge_count()'],['../classxg_1_1XG.html#aa624840475fc83351c00ef2728480355',1,'xg::XG::get_edge_count()'],['../classhandlegraph_1_1HandleGraph.html#a20ff62014d7f0f0c01ada8a3d40a278d',1,'handlegraph::HandleGraph::get_edge_count()']]],
+ ['get_5fedge_5flength_9197',['get_edge_length',['../classvg_1_1TraversalSupportFinder.html#a4902b9dcdaa53f74f45a394265163311',1,'vg::TraversalSupportFinder']]],
+ ['get_5fedge_5fsupport_9198',['get_edge_support',['../classvg_1_1TraversalSupportFinder.html#a8b497d8e282da9696d2ae5df86664069',1,'vg::TraversalSupportFinder::get_edge_support(const edge_t &edge) const =0'],['../classvg_1_1TraversalSupportFinder.html#a958a20d44167e8c29f677e12b950b5fa',1,'vg::TraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const =0'],['../classvg_1_1PackedTraversalSupportFinder.html#a394485c49fb5d8043d9f98385dab1b4a',1,'vg::PackedTraversalSupportFinder::get_edge_support(const edge_t &edge) const'],['../classvg_1_1PackedTraversalSupportFinder.html#a5cfa1254fae043f9920761a533d63480',1,'vg::PackedTraversalSupportFinder::get_edge_support(id_t from, bool from_reverse, id_t to, bool to_reverse) const'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#a72ae391a14cf1625286d8c3aff3cd7a5',1,'vg::CachedPackedTraversalSupportFinder::get_edge_support()']]],
+ ['get_5fedges_9199',['get_edges',['../classvg_1_1ContractingGraph.html#a9faff1ddfb92cfa26ba59803899148e7',1,'vg::ContractingGraph']]],
+ ['get_5fend_9200',['get_end',['../classvg_1_1NetGraph.html#acccdda49a6444e96292b90218e273942',1,'vg::NetGraph']]],
+ ['get_5fend_5fbound_9201',['get_end_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a4c500f039a8740ff6e771ddf4bf693ad',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fend_5fmatches_9202',['get_end_matches',['../classvg_1_1ReadFilter.html#a3cd3ee44928526e27e42e059b693ba76',1,'vg::ReadFilter::get_end_matches(const Read &read) const'],['../classvg_1_1ReadFilter.html#a1e40faa7aa74f7b17390b06da6ad32e4',1,'vg::ReadFilter::get_end_matches(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#a45116be7bd52bfd9fb40e30f08aee97f',1,'vg::ReadFilter::get_end_matches(const Alignment &read) const']]],
+ ['get_5fend_5fof_9203',['get_end_of',['../namespacevg.html#af76e8a5e74f67093a40ed5f2cd15ff28',1,'vg']]],
+ ['get_5fendpoints_9204',['get_endpoints',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a9e3d20d5ab60eb99688d6346a788d308',1,'vg::GraphSynchronizer::Lock']]],
+ ['get_5fexon_5fhaplotypes_9205',['get_exon_haplotypes',['../classvg_1_1Transcriptome.html#a2753baecefb5f065854fd9fbc1a24dc9',1,'vg::Transcriptome']]],
+ ['get_5ffeatures_9206',['get_features',['../classvg_1_1FeatureSet.html#a55b389aa1c68efddb28a188a757568fc',1,'vg::FeatureSet']]],
+ ['get_5ffile_5fsize_9207',['get_file_size',['../namespacevg.html#a53098c7c826c3d8d2aab804ba5500fd5',1,'vg']]],
+ ['get_5ffilenames_9208',['get_filenames',['../classvg_1_1IndexFile.html#a5833162264de6ce5f2a0d882b4b12839',1,'vg::IndexFile']]],
+ ['get_5ffirst_5fnode_5fhandle_9209',['get_first_node_handle',['../structvg_1_1EditedTranscriptPath.html#aec08731a5fd5989db7721a3ecf0859e7',1,'vg::EditedTranscriptPath::get_first_node_handle()'],['../structvg_1_1CompletedTranscriptPath.html#af48eb44f24298e5f3efa4641eb91d813',1,'vg::CompletedTranscriptPath::get_first_node_handle()']]],
+ ['get_5ffraction_5fof_5fns_9210',['get_fraction_of_ns',['../namespacevg.html#af8f8da6eb179ba0199fc2fdfe676fde7',1,'vg']]],
+ ['get_5ffragment_5flength_5fmean_9211',['get_fragment_length_mean',['../classvg_1_1MinimizerMapper.html#a1e08dfa10f620ef44d102123b38b8fe8',1,'vg::MinimizerMapper']]],
+ ['get_5ffragment_5flength_5fsample_5fsize_9212',['get_fragment_length_sample_size',['../classvg_1_1MinimizerMapper.html#ab4c62a806ad7b64072a770c9b4db3417',1,'vg::MinimizerMapper']]],
+ ['get_5ffragment_5flength_5fstdev_9213',['get_fragment_length_stdev',['../classvg_1_1MinimizerMapper.html#ae048c4929acb22eabd55f54ac3cc6f18',1,'vg::MinimizerMapper']]],
+ ['get_5fg_5fiv_5fsize_9214',['get_g_iv_size',['../classxg_1_1XG.html#a1162be39bbe491975cd47c56fc044489',1,'xg::XG']]],
+ ['get_5fgbwt_9215',['get_gbwt',['../classvg_1_1GBWTTraversalFinder.html#a07c5e06ec89e54f2efc2d84974b71ca3',1,'vg::GBWTTraversalFinder::get_gbwt()'],['../namespacevg.html#a571047c58b73b78d02a767c3ab6ec222',1,'vg::get_gbwt()']]],
+ ['get_5fgenotype_5flog_5flikelihood_9216',['get_genotype_log_likelihood',['../classvg_1_1Genotyper.html#a9071cdf5ae591b478feaac025b069772',1,'vg::Genotyper']]],
+ ['get_5fgenotype_5flog_5fprior_9217',['get_genotype_log_prior',['../classvg_1_1Genotyper.html#a5fc66cb05c4ba80e39d078af9ddce715',1,'vg::Genotyper']]],
+ ['get_5fgenotypes_9218',['get_genotypes',['../classvg_1_1Deconstructor.html#abed056375d448eeffebcf1b15633fe79',1,'vg::Deconstructor']]],
+ ['get_5fgraph_9219',['get_graph',['../classvg_1_1Packer.html#a19b5aa3c38b65c9e35e2ab7604bdbec4',1,'vg::Packer::get_graph()'],['../classvg_1_1VariantAdder.html#a1271c6d39e6387bac452d9bf80689ed5',1,'vg::VariantAdder::get_graph()'],['../structGraphHandler.html#ab0c19a482787b623d946746f33b2fb80',1,'GraphHandler::get_graph()']]],
+ ['get_5fgraph_5fdistance_9220',['get_graph_distance',['../namespacevg_1_1algorithms.html#a0b788763f4e6747ba55e5340de9da855',1,'vg::algorithms']]],
+ ['get_5fhandle_9221',['get_handle',['../classvg_1_1DagifiedGraph.html#a57e727b78f3eac1ee34b5dabf08a278f',1,'vg::DagifiedGraph::get_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a78c76b68997b94da8bb714ad87b6ce55',1,'vg::DozeuPinningOverlay::get_handle()'],['../classvg_1_1ExtraNodeGraph.html#a76226cecc78c23a95db06f2765138e6f',1,'vg::ExtraNodeGraph::get_handle()'],['../classvg_1_1GaplessExtender.html#ace7698779da48ed9216169b935b0287c',1,'vg::GaplessExtender::get_handle()'],['../classvg_1_1SnarlGraph.html#a8c06fedda57c3e031d8d3b7fbcb696a8',1,'vg::SnarlGraph::get_handle()'],['../classvg_1_1IdentityOverlay.html#a3fc814950bd9b0b003b82637be9c1d06',1,'vg::IdentityOverlay::get_handle()'],['../classvg_1_1IncrementalSubgraph.html#ac2d018cb5a59b4f43e24a4f30643e0f1',1,'vg::IncrementalSubgraph::get_handle()'],['../classvg_1_1IndexedVG.html#ad9779976b07decd5b593b7a097cac44e',1,'vg::IndexedVG::get_handle()'],['../classvg_1_1MemoizingGraph.html#aa0b891348a82fe4fad7f60ab87fbd4b4',1,'vg::MemoizingGraph::get_handle()'],['../classvg_1_1NullMaskingGraph.html#aea8062f2a253f0397a91005b3924475e',1,'vg::NullMaskingGraph::get_handle()'],['../classvg_1_1PathSubgraph.html#a9d2fc4747e6c86125ba149c90041abcd',1,'vg::PathSubgraph::get_handle()'],['../classvg_1_1ReverseGraph.html#a34a79e8c3f5d5f029d5a1427ca10cfbd',1,'vg::ReverseGraph::get_handle()'],['../classvg_1_1NetGraph.html#a639a1a278626238fe98568320590c64f',1,'vg::NetGraph::get_handle()'],['../classvg_1_1SourceSinkOverlay.html#a7cc144d829750cfb85341d42bd4f7e4a',1,'vg::SourceSinkOverlay::get_handle()'],['../classvg_1_1JoinedSpliceGraph.html#a17636cfa63438f4b5941d54b7632d64b',1,'vg::JoinedSpliceGraph::get_handle()'],['../classvg_1_1StrandSplitGraph.html#a97db8ec5efb4280bfe358b0859e96659',1,'vg::StrandSplitGraph::get_handle()'],['../classvg_1_1SubHandleGraph.html#a4cf66400a93dee8a1e49fcc88ab24eb5',1,'vg::SubHandleGraph::get_handle()'],['../classvg_1_1SubgraphOverlay.html#ab36d552e3882740962729d19069f9ddc',1,'vg::SubgraphOverlay::get_handle()'],['../classvg_1_1SubpathOverlay.html#a3871270e3d47a023f27f9bac6959983b',1,'vg::SubpathOverlay::get_handle()'],['../classvg_1_1TreeSubgraph.html#ab7b56b78b8750cc6453180e7e531d925',1,'vg::TreeSubgraph::get_handle()'],['../classvg_1_1VG.html#a70f50e6766af9262c732de26243658f5',1,'vg::VG::get_handle()'],['../classxg_1_1XG.html#adc5660ffe20948888aeca0c6e6bba90a',1,'xg::XG::get_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0a950e73c94a514de69f95be80f96b7e',1,'handlegraph::algorithms::SubHandleGraph::get_handle()'],['../classhandlegraph_1_1HandleGraph.html#a6dd9d70931835f5c75518b23a780b744',1,'handlegraph::HandleGraph::get_handle()'],['../classhandlegraph_1_1SnarlDecomposition.html#a94e6360cbad97a084d6ec3a6a461e20c',1,'handlegraph::SnarlDecomposition::get_handle()']]],
+ ['get_5fhandle_5ffrom_5finward_5fbacking_5fhandle_9222',['get_handle_from_inward_backing_handle',['../classvg_1_1NetGraph.html#a62b87ba5400e8c6d3f6335fc2198cc38',1,'vg::NetGraph']]],
+ ['get_5fhandle_5fof_5fstep_9223',['get_handle_of_step',['../classvg_1_1MemoizingGraph.html#a2b4cd0c4ebef4dcefd5bbafcd1ab3e54',1,'vg::MemoizingGraph::get_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a05ce3d84e3e774a89d4d61a70381cee2',1,'vg::PathSubgraphOverlay::get_handle_of_step()'],['../classvg_1_1VG.html#acb73599cc743a392650a7002c8dc2906',1,'vg::VG::get_handle_of_step()'],['../classxg_1_1XG.html#abbfaa6afca08ec2aca7f2fd550221793',1,'xg::XG::get_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a339e690ce3e2bb8280dd1f3ea45abe42',1,'handlegraph::PathHandleGraph::get_handle_of_step()']]],
+ ['get_5fhaplotype_9224',['get_haplotype',['../classhandlegraph_1_1PathMetadata.html#a8ea83e700d11830e7eb695b8a11cb17f',1,'handlegraph::PathMetadata::get_haplotype()'],['../haplotypes__main_8cpp.html#ada326bf02798916f16c46f5d308ebc5b',1,'get_haplotype(): haplotypes_main.cpp']]],
+ ['get_5fhaplotype_5falt_5fcontents_9225',['get_haplotype_alt_contents',['../classvg_1_1VCFTraversalFinder.html#a3ce22629a99aae20002c43c7e581c2fb',1,'vg::VCFTraversalFinder']]],
+ ['get_5fhaplotype_5fcount_9226',['get_haplotype_count',['../classhaplo_1_1ScoreProvider.html#aac21ae0e24c45170e81b4880f8c21f8d',1,'haplo::ScoreProvider::get_haplotype_count()'],['../classhaplo_1_1GBWTScoreProvider.html#a8aedfce11f295af0fba3ae7f17f20c9b',1,'haplo::GBWTScoreProvider::get_haplotype_count()']]],
+ ['get_5fhaplotypes_5fwith_5fsnarl_9227',['get_haplotypes_with_snarl',['../classvg_1_1PhasedGenome.html#a81cff23c8687f759dd464fca51cf306e',1,'vg::PhasedGenome']]],
+ ['get_5fhelp_9228',['get_help',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a9880c67cbeb3f5b7ba3bad714844702c',1,'vg::subcommand::BaseOptionGroup::get_help()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a958199095b53020a85a5abc2ae1f0a91',1,'vg::subcommand::OptionGroup::get_help()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a01f89740d89e82cf12c204c28ec01fd2',1,'vg::subcommand::GroupedOptionGroup::get_help()']]],
+ ['get_5fid_9229',['get_id',['../classvg_1_1DagifiedGraph.html#ae510cacf154e272f63b37a3207046c96',1,'vg::DagifiedGraph::get_id()'],['../classvg_1_1DozeuPinningOverlay.html#ad84aae5d9cce852e254d5da05da40fa8',1,'vg::DozeuPinningOverlay::get_id()'],['../classvg_1_1ExtraNodeGraph.html#aef3ca5fb2071fdb33a7a8f663473de32',1,'vg::ExtraNodeGraph::get_id()'],['../classvg_1_1SnarlGraph.html#aba421b2e2cd40a7d489c13e0ab81f179',1,'vg::SnarlGraph::get_id()'],['../classvg_1_1IdentityOverlay.html#ab144f5ecbf4a5f49a5ffbea80ebd56ec',1,'vg::IdentityOverlay::get_id()'],['../classvg_1_1IncrementalSubgraph.html#a825edf9eddd3fa6093f2045656ae98f1',1,'vg::IncrementalSubgraph::get_id()'],['../classvg_1_1IndexedVG.html#ad23ba69aad4d8c94f58319bb657e3235',1,'vg::IndexedVG::get_id()'],['../classvg_1_1MemoizingGraph.html#a23b6df961f0e8253fba88423f2bcf128',1,'vg::MemoizingGraph::get_id()'],['../classvg_1_1NullMaskingGraph.html#a541f81de46db62d5e8f37e3cfc51f08e',1,'vg::NullMaskingGraph::get_id()'],['../classvg_1_1PathSubgraph.html#a47ff1fe374dccd07542ed1523327553e',1,'vg::PathSubgraph::get_id()'],['../classvg_1_1ReverseGraph.html#aef09dbb8dd08735bdd123b2a9d0066e0',1,'vg::ReverseGraph::get_id()'],['../classvg_1_1NetGraph.html#a9964476cfff61404eeb9d65cc182aa4a',1,'vg::NetGraph::get_id()'],['../classvg_1_1SourceSinkOverlay.html#a9c10b6562749e62bc1038ef23e8b9b28',1,'vg::SourceSinkOverlay::get_id()'],['../classvg_1_1JoinedSpliceGraph.html#a716f0b44bb48b6148617dc772d66959c',1,'vg::JoinedSpliceGraph::get_id()'],['../classvg_1_1StrandSplitGraph.html#a07bd24e1ed6a14843ddb87108a11c7f8',1,'vg::StrandSplitGraph::get_id()'],['../classvg_1_1SubHandleGraph.html#af40f7f453c71d4e52273479d0b600612',1,'vg::SubHandleGraph::get_id()'],['../classvg_1_1SubgraphOverlay.html#a301c8016ac2769d041c611cebd738c1e',1,'vg::SubgraphOverlay::get_id()'],['../classvg_1_1SubpathOverlay.html#ab58cd06e1330b752ad55e32878e8e64e',1,'vg::SubpathOverlay::get_id()'],['../classvg_1_1TreeSubgraph.html#ae48a59a93737e729ada7660a39fafa50',1,'vg::TreeSubgraph::get_id()'],['../classvg_1_1VG.html#a6f4b9ac16f23eb0420544ce8357736a3',1,'vg::VG::get_id()'],['../classxg_1_1XG.html#a0a9d6bce054a3ebf14807869883e9b98',1,'xg::XG::get_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a8150ada3f96723110a2ec7c1ed16323b',1,'handlegraph::algorithms::SubHandleGraph::get_id()'],['../classhandlegraph_1_1HandleGraph.html#adb7f6e144bf2a59679f7b2eddad934eb',1,'handlegraph::HandleGraph::get_id()'],['../namespacevg.html#ae4370b5cb4b42e8556b0fbc793fbdfc0',1,'vg::get_id()'],['../namespacexg.html#a5aab54915cd81fa71fd2ebc3b9e52fb8',1,'xg::get_id()']]],
+ ['get_5fidentifier_9230',['get_identifier',['../classvg_1_1IndexFile.html#a0dde670fabfa3890d26c9e89c8564429',1,'vg::IndexFile::get_identifier()'],['../classvg_1_1ZipCode.html#a9cb3141131af81b42741bc9e7349e58b',1,'vg::ZipCode::get_identifier()']]],
+ ['get_5findex_9231',['get_index',['../classvg_1_1IndexRegistry.html#a3738a3916a17ca5a2716e7530b10c434',1,'vg::IndexRegistry::get_index(const IndexName &identifier)'],['../classvg_1_1IndexRegistry.html#a2cde822432825ea731fed5318bd94152',1,'vg::IndexRegistry::get_index(const IndexName &identifier) const']]],
+ ['get_5findexes_9232',['get_indexes',['../classvg_1_1RewindPlanException.html#a80a898014c62738052c18e85a0403a24',1,'vg::RewindPlanException']]],
+ ['get_5finput_5ffile_9233',['get_input_file',['../namespacevg.html#ab1b8b686ef6eca09515be1abe566c013',1,'vg::get_input_file(int &optind, int argc, char **argv, function< void(istream &)> callback)'],['../namespacevg.html#a09969fef23098c7729a2f190cecb4694',1,'vg::get_input_file(const string &file_name, function< void(istream &)> callback)']]],
+ ['get_5finput_5ffile_5fname_9234',['get_input_file_name',['../namespacevg.html#a5026b599b1094a6c8e157f23b204b09b',1,'vg']]],
+ ['get_5finward_5fbacking_5fhandle_9235',['get_inward_backing_handle',['../classvg_1_1NetGraph.html#adc4841db50e7f3073cad16d59426ba5a',1,'vg::NetGraph']]],
+ ['get_5firregular_5fsnarl_5fcode_9236',['get_irregular_snarl_code',['../classvg_1_1ZipCode.html#a2057ff4f25f04aa76066c3c5a83239fc',1,'vg::ZipCode']]],
+ ['get_5fis_5fcircular_9237',['get_is_circular',['../classvg_1_1MemoizingGraph.html#a2fb48c82bc92aa1fa263a4be92e21891',1,'vg::MemoizingGraph::get_is_circular()'],['../classvg_1_1PathSubgraphOverlay.html#ac33d15bc06e31045d07ecf22e018f0a8',1,'vg::PathSubgraphOverlay::get_is_circular()'],['../classvg_1_1VG.html#a1463f13c63b965a3663932e6fa87537e',1,'vg::VG::get_is_circular()'],['../classxg_1_1XG.html#a841e1c50686d3ea941fb9a01d9639784',1,'xg::XG::get_is_circular()'],['../classhandlegraph_1_1PathHandleGraph.html#a9391c34d9f0c16b21d5bb3bb7ec772e4',1,'handlegraph::PathHandleGraph::get_is_circular()']]],
+ ['get_5fis_5flooping_5fchain_9238',['get_is_looping_chain',['../classvg_1_1ZipCode.html#a2c0fa7d7130b57bee9b557750eb97eab',1,'vg::ZipCode::get_is_looping_chain()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#ac917c5b03c10bd9e57b344a708c6b033',1,'vg::ZipCode::chain_code_t::get_is_looping_chain()']]],
+ ['get_5fis_5fpaired_9239',['get_is_paired',['../classvg_1_1ReadFilter.html#a8b78c03c1379b1ed5576db5c6772adb3',1,'vg::ReadFilter::get_is_paired(const Read &read) const'],['../classvg_1_1ReadFilter.html#aaf6db93c73e3030a098aa54a21416cd7',1,'vg::ReadFilter::get_is_paired(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#a1aa38e8c41e26d7932caa918cfcfe76e',1,'vg::ReadFilter::get_is_paired(const MultipathAlignment &mp_aln) const']]],
+ ['get_5fis_5frev_9240',['get_is_rev',['../namespacevg.html#a1919abd090eae3a01120e0859d434ed9',1,'vg::get_is_rev()'],['../namespacexg.html#aca811d060bb9ddd2ff278e107c882e49',1,'xg::get_is_rev()']]],
+ ['get_5fis_5freverse_9241',['get_is_reverse',['../classvg_1_1DagifiedGraph.html#a0a5fa33f94733bb8470ccbc49e608a0d',1,'vg::DagifiedGraph::get_is_reverse()'],['../classvg_1_1DozeuPinningOverlay.html#a02b35f6198096c08f660df1170d556b4',1,'vg::DozeuPinningOverlay::get_is_reverse()'],['../classvg_1_1ExtraNodeGraph.html#ab3b496b4e1d8067cd7ed0e0ae9fb0aa9',1,'vg::ExtraNodeGraph::get_is_reverse()'],['../classvg_1_1SnarlGraph.html#a9deed0e8a0312d6ff12868e86c83cc0f',1,'vg::SnarlGraph::get_is_reverse()'],['../classvg_1_1IdentityOverlay.html#aa7bba299ded8eb2fff2af0adeb52000b',1,'vg::IdentityOverlay::get_is_reverse()'],['../classvg_1_1IncrementalSubgraph.html#ad4282dc0e503dc17e3724a41dbb0462c',1,'vg::IncrementalSubgraph::get_is_reverse()'],['../classvg_1_1IndexedVG.html#acf50f1ad8e40ac18d8a5469d63155a50',1,'vg::IndexedVG::get_is_reverse()'],['../classvg_1_1MemoizingGraph.html#aac8372783c6657f5473b1d33b4495e7c',1,'vg::MemoizingGraph::get_is_reverse()'],['../classvg_1_1NullMaskingGraph.html#ab99a483165208a4aabc1e2275f126a18',1,'vg::NullMaskingGraph::get_is_reverse()'],['../classvg_1_1PathSubgraph.html#a5305f2276ec4eecae4a59a4892cb63ab',1,'vg::PathSubgraph::get_is_reverse()'],['../classvg_1_1ReverseGraph.html#aaa65f6a0677677af70608a0294ec36f5',1,'vg::ReverseGraph::get_is_reverse()'],['../classvg_1_1NetGraph.html#a4581f8ffa5738a409e9e856f15c48a99',1,'vg::NetGraph::get_is_reverse()'],['../classvg_1_1SourceSinkOverlay.html#a274359d605130e8efec7c14791d5044b',1,'vg::SourceSinkOverlay::get_is_reverse()'],['../classvg_1_1JoinedSpliceGraph.html#a7179e1f5120aebb9670120b6cddf51ca',1,'vg::JoinedSpliceGraph::get_is_reverse()'],['../classvg_1_1StrandSplitGraph.html#a2882b925a09ba0ee35cdf8bdac0c4605',1,'vg::StrandSplitGraph::get_is_reverse()'],['../classvg_1_1SubHandleGraph.html#a050d46f68a21d9169d17a6e9580a542f',1,'vg::SubHandleGraph::get_is_reverse()'],['../classvg_1_1SubgraphOverlay.html#a797e1524539c9c96ef96dc5454d35c3a',1,'vg::SubgraphOverlay::get_is_reverse()'],['../classvg_1_1SubpathOverlay.html#ae1560abd95e0a6e64306622a68f7e6ac',1,'vg::SubpathOverlay::get_is_reverse()'],['../classvg_1_1TreeSubgraph.html#aa581eda84f6ae51edb0363b76075fe47',1,'vg::TreeSubgraph::get_is_reverse()'],['../classvg_1_1VG.html#a53e796617804bffe0203e422f2a23148',1,'vg::VG::get_is_reverse()'],['../classxg_1_1XG.html#a7a52d5c8396e40930cfed5f79ea9c201',1,'xg::XG::get_is_reverse()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade72d1d3264d1022227c44edc9329a26',1,'handlegraph::algorithms::SubHandleGraph::get_is_reverse()'],['../classhandlegraph_1_1HandleGraph.html#a92773f90eb58f18adb9418a4440223c1',1,'handlegraph::HandleGraph::get_is_reverse()']]],
+ ['get_5fis_5freversed_9242',['get_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#ae65abc62608f0643537bacfa78e0e7aa',1,'vg::ZipCode::node_code_t::get_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae6b247dcfb508636f982df6b3353001e',1,'vg::ZipCode::snarl_code_t::get_is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#a79691714f5f3bb06aed0d1a7a4b646ee',1,'vg::ZipCodeTree::tree_item_t::get_is_reversed()']]],
+ ['get_5fis_5freversed_5fin_5fparent_9243',['get_is_reversed_in_parent',['../classvg_1_1ZipCode.html#af27a1ca0026e32e588d0bb3b62a5bade',1,'vg::ZipCode']]],
+ ['get_5fitem_9244',['get_item',['../classvg_1_1Funnel.html#a5f8f988df65fc91adc7da9dd8d4446ef',1,'vg::Funnel']]],
+ ['get_5fitem_5fat_5findex_9245',['get_item_at_index',['../classvg_1_1ZipCodeTree.html#a66ff501bf5fa0044978550b188691068',1,'vg::ZipCodeTree']]],
+ ['get_5fiterator_9246',['get_iterator',['../structvg_1_1subcommand_1_1TickChainLink.html#aa21e2c735dba10a3b97c739d66008937',1,'vg::subcommand::TickChainLink']]],
+ ['get_5flast_5fchain_5fcomponent_9247',['get_last_chain_component',['../classvg_1_1ZipCode.html#aaf980083db4440866ee59d2a1b89e957',1,'vg::ZipCode']]],
+ ['get_5flast_5fcomponent_9248',['get_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa98d04c4d61201facf9e01c189b44f43',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fleaves_9249',['get_leaves',['../classvg_1_1WFATree.html#adea6d9333092f49afcc26f34e4bfc016',1,'vg::WFATree']]],
+ ['get_5flength_9250',['get_length',['../classvg_1_1DagifiedGraph.html#a5feaa48467ad288848fb2d1ffcd29fc1',1,'vg::DagifiedGraph::get_length()'],['../classvg_1_1DozeuPinningOverlay.html#a0d9fc0dbb4e18cfe9d7496b72d0f63fb',1,'vg::DozeuPinningOverlay::get_length()'],['../classvg_1_1ExtraNodeGraph.html#ab4385934c980deef266d30118b83a4df',1,'vg::ExtraNodeGraph::get_length()'],['../classvg_1_1SnarlGraph.html#ac521452a597e9159b8c281cc49239ccb',1,'vg::SnarlGraph::get_length()'],['../classvg_1_1IdentityOverlay.html#a659b0f5b71286479ef910bd984c525e6',1,'vg::IdentityOverlay::get_length()'],['../classvg_1_1IncrementalSubgraph.html#a84ee16f64d60195d6ead2a57933af720',1,'vg::IncrementalSubgraph::get_length()'],['../classvg_1_1IndexedVG.html#a235824616974770831a2ce006a954bbe',1,'vg::IndexedVG::get_length()'],['../classvg_1_1MemoizingGraph.html#ab5f66c5dae9ddc74750cb86595fef07e',1,'vg::MemoizingGraph::get_length()'],['../classvg_1_1NullMaskingGraph.html#a2144c791b97d05bf625a50442649def2',1,'vg::NullMaskingGraph::get_length()'],['../classvg_1_1PathSubgraph.html#a777f23f7156addc72dd508d08f069cc7',1,'vg::PathSubgraph::get_length()'],['../classvg_1_1ReadFilter.html#ae2ef22beb751d9415759fc1985da1946',1,'vg::ReadFilter::get_length()'],['../classvg_1_1ReverseGraph.html#a54f7adad266466143efaa59270432d8f',1,'vg::ReverseGraph::get_length()'],['../classvg_1_1NetGraph.html#a8170045aa0032b33628858c0717cc74a',1,'vg::NetGraph::get_length()'],['../classvg_1_1SourceSinkOverlay.html#a03f1de876e4731012b5e7168556d5236',1,'vg::SourceSinkOverlay::get_length()'],['../classvg_1_1JoinedSpliceGraph.html#aafba33cc8aa854fb9dc8d654bb2a3325',1,'vg::JoinedSpliceGraph::get_length()'],['../classvg_1_1StrandSplitGraph.html#a46c7611ab9f71f86e3192a34406860b4',1,'vg::StrandSplitGraph::get_length()'],['../classvg_1_1SubHandleGraph.html#a829ddac36b7fcb67ca87c058fe691a88',1,'vg::SubHandleGraph::get_length()'],['../classvg_1_1SubgraphOverlay.html#a5bc6640c35b21807f14332a51f84a2d9',1,'vg::SubgraphOverlay::get_length()'],['../classvg_1_1SubpathOverlay.html#ae15f1a187d3bf9a590f173fdf4bd8f9b',1,'vg::SubpathOverlay::get_length()'],['../classvg_1_1TreeSubgraph.html#ac6d8e68e5bff645f58f741291a810abe',1,'vg::TreeSubgraph::get_length()'],['../classvg_1_1VG.html#aff75e522e40559f5a5257a5cef776cdc',1,'vg::VG::get_length()'],['../classvg_1_1ZipCode.html#a8a5fd40be34ed83736e027a3ca6d9889',1,'vg::ZipCode::get_length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#ad67b89184b6f5d83cb888b5f14647ae3',1,'vg::ZipCode::node_code_t::get_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a214243244b7e99dfe24df8665860dbb2',1,'vg::ZipCode::chain_code_t::get_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa80045f926e1bfde2fb07e2c2e442732',1,'vg::ZipCode::snarl_code_t::get_length()'],['../classxg_1_1XG.html#aa52bb123eca4dbff84b316a7f56a98cc',1,'xg::XG::get_length()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af858e2c9467b674d836879d39f049a05',1,'handlegraph::algorithms::SubHandleGraph::get_length()'],['../classhandlegraph_1_1HandleGraph.html#a569ff35fb85c725b0b6b6933ed303e49',1,'handlegraph::HandleGraph::get_length()']]],
+ ['get_5flocus_5fname_9251',['get_locus_name',['../classhandlegraph_1_1PathMetadata.html#aeea07376b756bc5410dacf86f2c3983d',1,'handlegraph::PathMetadata']]],
+ ['get_5flog10_5fprob_5fof_5fdisruption_5fin_5finterval_9252',['get_log10_prob_of_disruption_in_interval',['../classvg_1_1MinimizerMapper.html#a4a680ca76191f68a70d17af1e0548f60',1,'vg::MinimizerMapper']]],
+ ['get_5flong_9253',['get_long',['../classvg_1_1Version.html#a5132823f48bf6019f1b94ace3a479de4',1,'vg::Version']]],
+ ['get_5flong_5foption_9254',['get_long_option',['../classvg_1_1OptionInterface.html#afba994fe31561a26b7495e78d9423679',1,'vg::OptionInterface::get_long_option()'],['../classvg_1_1BaseOption.html#ad990f7324262866fbc67f6e8adeeecfd',1,'vg::BaseOption::get_long_option()']]],
+ ['get_5fmagic_5fnumber_9255',['get_magic_number',['../classvg_1_1ZipCodeCollection.html#a59d0bd8bac747766d3471225e5a6ae05',1,'vg::ZipCodeCollection::get_magic_number()'],['../classxg_1_1XG.html#ac8ed9c987e2693c548ad834b39df7a80',1,'xg::XG::get_magic_number()'],['../classhandlegraph_1_1Serializable.html#a8879f13f2204a80a6c428883187961db',1,'handlegraph::Serializable::get_magic_number()']]],
+ ['get_5fmagic_5fnumber_5fas_5fstring_9256',['get_magic_number_as_string',['../classvg_1_1ZipCodeCollection.html#a6ee9653e5766e260ca6c903ca0920265',1,'vg::ZipCodeCollection']]],
+ ['get_5fmain_9257',['get_main',['../classvg_1_1subcommand_1_1Subcommand.html#a5a7af092ca69792ed2543bbcc3847ad4',1,'vg::subcommand::Subcommand']]],
+ ['get_5fmapping_9258',['get_mapping',['../classvg_1_1PhaseUnfolder.html#aae984d6ac43200dc82e6ef3066e01f15',1,'vg::PhaseUnfolder']]],
+ ['get_5fmapq_9259',['get_mapq',['../classvg_1_1ReadFilter.html#a0550e932f7becd1fbccd46787b580216',1,'vg::ReadFilter']]],
+ ['get_5fmax_5frss_5fkb_9260',['get_max_rss_kb',['../namespacevg.html#a546b60e87f7fc326074f6dcf2cdd0659',1,'vg']]],
+ ['get_5fmax_5fvmem_5fkb_9261',['get_max_vmem_kb',['../namespacevg.html#a917d8892f93a31e2d8c3161de264fea1',1,'vg']]],
+ ['get_5fmetavar_9262',['get_metavar',['../namespacevg_1_1subcommand.html#accfa400696eb815cf8c43d0909c0350f',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20bool_20_3e_9263',['get_metavar< bool >',['../namespacevg_1_1subcommand.html#a901fbf8366695921cb7844ee2da2d2a2',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20double_20_3e_9264',['get_metavar< double >',['../namespacevg_1_1subcommand.html#a6ab814763fe6f21091083e68bcf47a92',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20int_20_3e_9265',['get_metavar< int >',['../namespacevg_1_1subcommand.html#ac4cbf20c4fbaa1109469f8a358e1a213',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20int8_5ft_20_3e_9266',['get_metavar< int8_t >',['../namespacevg_1_1subcommand.html#a4945a3300d2d189e4c7fa6ad5d27ddf6',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20size_5ft_20_3e_9267',['get_metavar< size_t >',['../namespacevg_1_1subcommand.html#aebb27d4a98b972c03f63c8715bbd706c',1,'vg::subcommand']]],
+ ['get_5fmetavar_3c_20std_3a_3astring_20_3e_9268',['get_metavar< std::string >',['../namespacevg_1_1subcommand.html#a1615e3bd0398f56dfcdd1c9dfb864ec9',1,'vg::subcommand']]],
+ ['get_5fmin_5fbase_5fqual_5ffraction_9269',['get_min_base_qual_fraction',['../classvg_1_1ReadFilter.html#ad2ca26c062585494f69520f9997d34eb',1,'vg::ReadFilter']]],
+ ['get_5fmin_5fnode_5fsupport_9270',['get_min_node_support',['../classvg_1_1TraversalSupportFinder.html#ad166403d1a92690fe10e976d9789c065',1,'vg::TraversalSupportFinder::get_min_node_support()'],['../classvg_1_1PackedTraversalSupportFinder.html#a5a19f9777ecf01f0e8ea86870a993aea',1,'vg::PackedTraversalSupportFinder::get_min_node_support()'],['../classvg_1_1CachedPackedTraversalSupportFinder.html#aeeb7ecc5e9a3fa6f5030d3d41a436c59',1,'vg::CachedPackedTraversalSupportFinder::get_min_node_support()']]],
+ ['get_5fmin_5fposition_9271',['get_min_position',['../classvg_1_1StreamSorter.html#a4240a47a167f22d3815de6fe976420b5',1,'vg::StreamSorter']]],
+ ['get_5fmin_5ftotal_5fsupport_5ffor_5fcall_9272',['get_min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#ac7e36771ace6cf84d9f4f732cdbc692f',1,'vg::SupportBasedSnarlCaller']]],
+ ['get_5fmutable_9273',['get_mutable',['../structvg_1_1Annotation.html#a065db30c6b14ca2938254d603777e5c8',1,'vg::Annotation']]],
+ ['get_5fn_5fbins_9274',['get_n_bins',['../classvg_1_1Packer.html#a01716de1dc4501804d81fc38256dd2b5',1,'vg::Packer']]],
+ ['get_5fname_9275',['get_name',['../classvg_1_1Configurable.html#aee830d6a5cdcf8e7a2896a443bcc80cc',1,'vg::Configurable::get_name()'],['../structvg_1_1TranscriptPath.html#a0adaddaa3b952ed1f06bd7029673d2aa',1,'vg::TranscriptPath::get_name()'],['../classvg_1_1subcommand_1_1Subcommand.html#ab6c41ce3fe77e286f2caa1672b553293',1,'vg::subcommand::Subcommand::get_name()'],['../haplotypes__main_8cpp.html#a3781abae7c3253f254c4e795863d0c09',1,'get_name(): haplotypes_main.cpp']]],
+ ['get_5fnet_9276',['get_net',['../classhandlegraph_1_1SnarlDecomposition.html#a84b4951e1bf931d03539ac6e048fdb98',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fnet_5fgraph_9277',['get_net_graph',['../classvg_1_1GenomeState.html#ad07741efc2a949dd69aee266dbb4500b',1,'vg::GenomeState']]],
+ ['get_5fnet_5fhandle_9278',['get_net_handle',['../classvg_1_1ZipCode.html#a051a9144646b660f213fe44d5b123d77',1,'vg::ZipCode']]],
+ ['get_5fnet_5fhandle_5fslow_9279',['get_net_handle_slow',['../classvg_1_1ZipCode.html#ad1d40ef72bc5fa0f9e0e933add4265a2',1,'vg::ZipCode']]],
+ ['get_5fnext_5falignment_5ffrom_5ffastq_9280',['get_next_alignment_from_fastq',['../namespacevg.html#aca76d8e219f90833fdabe3528c3c6441',1,'vg']]],
+ ['get_5fnext_5falignment_5fpair_5ffrom_5ffastqs_9281',['get_next_alignment_pair_from_fastqs',['../namespacevg.html#a3255bd8bf9846a34da799947f7642dc7',1,'vg']]],
+ ['get_5fnext_5finterleaved_5falignment_5fpair_5ffrom_5ffastq_9282',['get_next_interleaved_alignment_pair_from_fastq',['../namespacevg.html#ab58cf3da638d7e8833a14ef801c7e2db',1,'vg']]],
+ ['get_5fnext_5finterleaved_5frecord_5fpair_5ffrom_5fgaf_9283',['get_next_interleaved_record_pair_from_gaf',['../namespacevg_1_1io.html#a0f27b2a472320e0e45a130b73827d1fd',1,'vg::io']]],
+ ['get_5fnext_5fintervals_9284',['get_next_intervals',['../classvg_1_1ZipCodeForest.html#a2c9a60acfcb3f8521eeb7bbf5e36007b',1,'vg::ZipCodeForest']]],
+ ['get_5fnext_5fnode_5frecalc_5fdegrees_9285',['get_next_node_recalc_degrees',['../classvg_1_1FlowSort.html#a1fac8545c184446eee5cae0f55567b1f',1,'vg::FlowSort']]],
+ ['get_5fnext_5frank_9286',['get_next_rank',['../classvg_1_1Paths.html#aad2977756f0166a341fb488cd5c6a9b0',1,'vg::Paths']]],
+ ['get_5fnext_5frecord_5ffrom_5fgaf_9287',['get_next_record_from_gaf',['../namespacevg_1_1io.html#aa357ed5eaa447e495149c7bd7df356b9',1,'vg::io']]],
+ ['get_5fnext_5frecord_5fpair_5ffrom_5fgaf_9288',['get_next_record_pair_from_gaf',['../namespacevg_1_1io.html#ab11e877e850b127b8004e7223cc77247',1,'vg::io']]],
+ ['get_5fnext_5fstep_9289',['get_next_step',['../classvg_1_1MemoizingGraph.html#a91e5d4f1ce3028d58c162adf8d19e70f',1,'vg::MemoizingGraph::get_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a2e18088c831f6757a4eafa7d862d0329',1,'vg::PathSubgraphOverlay::get_next_step()'],['../classvg_1_1VG.html#a144fb8b69eb2274b8dcea914898919f0',1,'vg::VG::get_next_step()'],['../classxg_1_1XG.html#a6595e2654ee4955763a08ab51780941a',1,'xg::XG::get_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a209786f5c9e2c0210b383f2022ee221f',1,'handlegraph::PathHandleGraph::get_next_step()']]],
+ ['get_5fnode_9290',['get_node',['../classvg_1_1VG.html#a95223ec6984efc003e5cac69acd43445',1,'vg::VG::get_node(nid_t id)'],['../classvg_1_1VG.html#aa264e9386b98b57c3549a56870d8e29e',1,'vg::VG::get_node(nid_t id) const']]],
+ ['get_5fnode_5fat_5fnucleotide_9291',['get_node_at_nucleotide',['../classvg_1_1VG.html#a07462d3f895e77cb407695e6c8e85727',1,'vg::VG']]],
+ ['get_5fnode_5fby_5fid_9292',['get_node_by_id',['../structvg_1_1algorithms_1_1Graph.html#a6113178f0138c18d19ed32a08a4a474e',1,'vg::algorithms::Graph']]],
+ ['get_5fnode_5fcode_9293',['get_node_code',['../classvg_1_1ZipCode.html#a1a37e35bfbd8910f64b95906f2930e28',1,'vg::ZipCode']]],
+ ['get_5fnode_5fcount_9294',['get_node_count',['../classvg_1_1DagifiedGraph.html#a46afdba1fbffa6ffebce5966a1829918',1,'vg::DagifiedGraph::get_node_count()'],['../classvg_1_1DozeuPinningOverlay.html#ab324121c34fdc2ab5edfaf742f26280d',1,'vg::DozeuPinningOverlay::get_node_count()'],['../classvg_1_1ExtraNodeGraph.html#a0c55bc093996c9148a3b6c4e46634759',1,'vg::ExtraNodeGraph::get_node_count()'],['../classvg_1_1SnarlGraph.html#aa797abb0b6518ca38b557759d074cd33',1,'vg::SnarlGraph::get_node_count()'],['../classvg_1_1IdentityOverlay.html#a9a58eb7938308dad847ded70b1abec56',1,'vg::IdentityOverlay::get_node_count()'],['../classvg_1_1IncrementalSubgraph.html#a076dbda3b4b724157cad61f5f7b76b2b',1,'vg::IncrementalSubgraph::get_node_count()'],['../classvg_1_1IndexedVG.html#aa275aa5b547bf464b95ce162e9a2fcd5',1,'vg::IndexedVG::get_node_count()'],['../classvg_1_1MemoizingGraph.html#a4276a59439fc7edc984fe6e666e3b69e',1,'vg::MemoizingGraph::get_node_count()'],['../classvg_1_1NullMaskingGraph.html#a7a7eeb58c5787789e6b8ae8a9e58101b',1,'vg::NullMaskingGraph::get_node_count()'],['../classvg_1_1PathSubgraph.html#a52f431143ff624475a16629fa46898f0',1,'vg::PathSubgraph::get_node_count()'],['../classvg_1_1ReverseGraph.html#a075661952d5a567b1e09ad9a5624c5a7',1,'vg::ReverseGraph::get_node_count()'],['../classvg_1_1NetGraph.html#a49f4b9958557920e8b81c3f6b6c62de2',1,'vg::NetGraph::get_node_count()'],['../classvg_1_1SourceSinkOverlay.html#ac49954276cde4384262f3501f4ed70ce',1,'vg::SourceSinkOverlay::get_node_count()'],['../classvg_1_1JoinedSpliceGraph.html#a15ac4bff9b6862ec0d7c6cefabb916c9',1,'vg::JoinedSpliceGraph::get_node_count()'],['../classvg_1_1StrandSplitGraph.html#a2a4f01cb39da9b46431a7ea3b46f540f',1,'vg::StrandSplitGraph::get_node_count()'],['../classvg_1_1SubHandleGraph.html#a0ea741c8d98e8c12b9f83b3427bee115',1,'vg::SubHandleGraph::get_node_count()'],['../classvg_1_1SubgraphOverlay.html#a40d036bc03e5bb02b1b0fe657b283b2b',1,'vg::SubgraphOverlay::get_node_count()'],['../classvg_1_1SubpathOverlay.html#a1d0208a9cfe646b6d25741c2bbfbd4b3',1,'vg::SubpathOverlay::get_node_count()'],['../classvg_1_1TreeSubgraph.html#a63dd0c1a1fce7a59a563be0448085246',1,'vg::TreeSubgraph::get_node_count()'],['../classvg_1_1VG.html#a495649c1646b865d6c88b8dc126589b0',1,'vg::VG::get_node_count()'],['../classxg_1_1XG.html#ae7b3b8008c6779aafb72b8e2fc47d4a1',1,'xg::XG::get_node_count()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a0c17ba8c59000d2562fb0318a1faaa7c',1,'handlegraph::algorithms::SubHandleGraph::get_node_count()'],['../classhandlegraph_1_1HandleGraph.html#a9f95108e6c3f68f404fa93bd3306e4c6',1,'handlegraph::HandleGraph::get_node_count()']]],
+ ['get_5fnode_5fdegree_9295',['get_node_degree',['../classvg_1_1FlowSort.html#a033cbc4da28f5ad6c3be63374eb55ac3',1,'vg::FlowSort']]],
+ ['get_5fnode_5fids_9296',['get_node_ids',['../structvg_1_1algorithms_1_1Graph.html#afe478cbb3ccb5f5125b59467db143b59',1,'vg::algorithms::Graph']]],
+ ['get_5fnode_5flength_9297',['get_node_length',['../classvg_1_1Mapper.html#a99717b5d61b6db599c177b8bafcb6dd8',1,'vg::Mapper']]],
+ ['get_5fnode_5fmapping_9298',['get_node_mapping',['../classvg_1_1Paths.html#a6314d7f8036a65b31d4dfac643bc3598',1,'vg::Paths::get_node_mapping(Node *n)'],['../classvg_1_1Paths.html#a7fa795ccee1427d6cac6e44fafe41e1e',1,'vg::Paths::get_node_mapping(id_t id)'],['../classvg_1_1Paths.html#a99f8491f18c0ccaf1bb7b7bf45500517',1,'vg::Paths::get_node_mapping(id_t id) const']]],
+ ['get_5fnode_5fmapping_5fby_5fpath_5fname_9299',['get_node_mapping_by_path_name',['../classvg_1_1Paths.html#a9c9cf2b7f26c788195812e2b8170a6ce',1,'vg::Paths::get_node_mapping_by_path_name(Node *n)'],['../classvg_1_1Paths.html#a72c6a29a41521996fd3454170b1a76f6',1,'vg::Paths::get_node_mapping_by_path_name(id_t id)']]],
+ ['get_5fnode_5fmapping_5fcopies_5fby_5frank_9300',['get_node_mapping_copies_by_rank',['../classvg_1_1Paths.html#a36a26abe18d10e17e273fa658be9d5c6',1,'vg::Paths']]],
+ ['get_5fnode_5fmappings_5fby_5frank_9301',['get_node_mappings_by_rank',['../classvg_1_1Paths.html#a5a40b701389bcc2c513083b02f17b4f4',1,'vg::Paths']]],
+ ['get_5fnode_5fnid_5fto_5fvariant_9302',['get_node_nid_to_variant',['../classvg_1_1VG.html#a52fa15aebd7d190eb743311f31037e55',1,'vg::VG']]],
+ ['get_5fnode_5foffset_9303',['get_node_offset',['../classvg_1_1GaplessExtender.html#a12663a32f4bc41137eb372c845f0eafe',1,'vg::GaplessExtender']]],
+ ['get_5fnodes_9304',['get_nodes',['../classvg_1_1ContractingGraph.html#a9c960fb16e62bc152fcf2f4230eead9c',1,'vg::ContractingGraph::get_nodes()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a932649a134317ad387ee70adc03d4474',1,'vg::SnarlDistanceIndexClusterer::get_nodes()']]],
+ ['get_5fnon_5fhts_5falignment_5femitter_9305',['get_non_hts_alignment_emitter',['../namespacevg_1_1io.html#a2f9f4db8b0374c57d2963881784c40d3',1,'vg::io']]],
+ ['get_5fnonoverlapping_9306',['get_nonoverlapping',['../classvg_1_1WindowedVcfBuffer.html#a63b89391977d77c5320003d0e0f70469',1,'vg::WindowedVcfBuffer']]],
+ ['get_5fnum_5fsamples_9307',['get_num_samples',['../namespacevg.html#afe9d79548464e7842327275008447299',1,'vg']]],
+ ['get_5foffset_9308',['get_offset',['../namespacevg.html#af826519a2b2e0cf58394e35d7ab7b84c',1,'vg::get_offset()'],['../namespacexg.html#a6e76d42101c987bf595a807522766cfa',1,'xg::get_offset()']]],
+ ['get_5foffset_5fin_5fchain_9309',['get_offset_in_chain',['../classvg_1_1ZipCode.html#a5d8b333ee954fa9a513b6190e1910843',1,'vg::ZipCode']]],
+ ['get_5fon_5fstrand_5fdistance_5ftree_9310',['get_on_strand_distance_tree',['../classvg_1_1OrientedDistanceClusterer.html#a736cd908b11ed3a000698291c541bbc0',1,'vg::OrientedDistanceClusterer']]],
+ ['get_5foption_5fid_9311',['get_option_id',['../namespacevg_1_1subcommand.html#a7e03678789f1a34608294f43e1047457',1,'vg::subcommand']]],
+ ['get_5foption_5fstruct_9312',['get_option_struct',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a58bddced5eb3503314ae1f7ef2bd60d1',1,'vg::subcommand::BaseArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#aeeb773f962b7de9459a67f2b74cce151',1,'vg::subcommand::ValueArgSpec::get_option_struct()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#a4287432c965cf788c3619aa13634c613',1,'vg::subcommand::FlagArgSpec::get_option_struct()']]],
+ ['get_5foption_5fvalue_9313',['get_option_value',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#af234d02566c656202396f78df73d35d7',1,'vg::subcommand::BaseOptionGroup']]],
+ ['get_5foptions_9314',['get_options',['../classvg_1_1Configurable.html#a553f14c4f4a19bb51d40ffb211945b3a',1,'vg::Configurable']]],
+ ['get_5for_5festimate_5fcoverage_9315',['get_or_estimate_coverage',['../namespacevg.html#aba3f6bc9cc27f9c6bb91dc27c7fb28b8',1,'vg']]],
+ ['get_5for_5fmake_5fvariant_5fid_9316',['get_or_make_variant_id',['../namespacevg.html#ae9fc5855bb49062ce72e56c805e1545a',1,'vg']]],
+ ['get_5foutput_5ffile_5fname_9317',['get_output_file_name',['../namespacevg.html#ae2a0425675c4a85289b230eef2c985b8',1,'vg']]],
+ ['get_5foverhang_9318',['get_overhang',['../classvg_1_1ReadFilter.html#a71bb794016b2f59d6495a98b9716e0b5',1,'vg::ReadFilter::get_overhang(const Read &read) const'],['../classvg_1_1ReadFilter.html#a50797c8911ec77ac3a392370a1c91cbe',1,'vg::ReadFilter::get_overhang(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#ab3bff405c9a8994993ea71e0c03b8772',1,'vg::ReadFilter::get_overhang(const MultipathAlignment &mp_aln) const']]],
+ ['get_5foverlay_5fhandle_9319',['get_overlay_handle',['../classvg_1_1StrandSplitGraph.html#ab60c1d256ba23abea598861ca7cf7f42',1,'vg::StrandSplitGraph']]],
+ ['get_5fparent_9320',['get_parent',['../classhandlegraph_1_1SnarlDecomposition.html#afb665da6af9e2ccfc10e6e667254b91d',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fparent_5fidentifier_9321',['get_parent_identifier',['../classvg_1_1ZipCode.html#a487d7a307e6b728df95581d6d261d526',1,'vg::ZipCode']]],
+ ['get_5fparent_5ftraversal_9322',['get_parent_traversal',['../classhandlegraph_1_1SnarlDecomposition.html#a2738b92f35c61666df57cd6088f3def1',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fparsed_5fgenotypes_9323',['get_parsed_genotypes',['../classvg_1_1WindowedVcfBuffer.html#a8970a1ba82342645b319a1f7091c6cea',1,'vg::WindowedVcfBuffer']]],
+ ['get_5fpath_9324',['get_path',['../classvg_1_1Paths.html#a386fefa3ef22c69bdfa06711ec43ca93',1,'vg::Paths::get_path()'],['../classxg_1_1XG.html#a79017177d025a7608c76a7901da5a463',1,'xg::XG::get_path()'],['../namespacevg.html#a3d972910bf64084a1ee50ca4350c5b59',1,'vg::get_path(const std::vector< handle_t > &first, handle_t second)'],['../namespacevg.html#aa5fc35eee866d216357a5818cd1fb927',1,'vg::get_path(handle_t first, const std::vector< handle_t > &second)'],['../namespacevg.html#a162ed4c8f358ca4c33ab05a27f8349cb',1,'vg::get_path(const std::vector< handle_t > &first, gbwt::node_type second)'],['../namespacevg.html#a66796444cb3b92c35ebeddbb7a9bc6bf',1,'vg::get_path(gbwt::node_type reverse_first, const std::vector< handle_t > &second)']]],
+ ['get_5fpath_5fbase_5fname_9325',['get_path_base_name',['../namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65',1,'vg']]],
+ ['get_5fpath_5fcount_9326',['get_path_count',['../classvg_1_1MemoizingGraph.html#ae0625c7cd87213ce030e03d7373c7216',1,'vg::MemoizingGraph::get_path_count()'],['../classvg_1_1PathSubgraphOverlay.html#a589dea47ddf887c61f88d4ef2f9110a2',1,'vg::PathSubgraphOverlay::get_path_count()'],['../classvg_1_1VG.html#a7b20ecaa6a8a3155b5abb90a3139f6de',1,'vg::VG::get_path_count()'],['../classxg_1_1XG.html#af7b58d4d10af78ac88675a40661967c2',1,'xg::XG::get_path_count()'],['../classhandlegraph_1_1PathHandleGraph.html#acd5df753593ecdfb7aa8c411b98ebad9',1,'handlegraph::PathHandleGraph::get_path_count()']]],
+ ['get_5fpath_5fedge_5findex_9327',['get_path_edge_index',['../classvg_1_1PathChunker.html#aef30dd2569597b64d36b19824ebee37f',1,'vg::PathChunker']]],
+ ['get_5fpath_5fedges_9328',['get_path_edges',['../classvg_1_1VG.html#a26f160750dfed33c16a257bd5cbecddf',1,'vg::VG']]],
+ ['get_5fpath_5fhandle_9329',['get_path_handle',['../classvg_1_1MemoizingGraph.html#ad26dd5209b1364601acf977df6cc52dc',1,'vg::MemoizingGraph::get_path_handle()'],['../classvg_1_1PathSubgraphOverlay.html#a45c63b93ee36ea86ce966aa2f6fc1530',1,'vg::PathSubgraphOverlay::get_path_handle()'],['../classvg_1_1VG.html#a6261550a7c6bbe7eb6ee0976639bc1d7',1,'vg::VG::get_path_handle()'],['../classxg_1_1XG.html#a0cca09a102d01c9f952b857f23f165e1',1,'xg::XG::get_path_handle()'],['../classhandlegraph_1_1PathHandleGraph.html#a5d6059d716882a80e3982de17011866e',1,'handlegraph::PathHandleGraph::get_path_handle()']]],
+ ['get_5fpath_5fhandle_5fof_5fstep_9330',['get_path_handle_of_step',['../classvg_1_1MemoizingGraph.html#a7a7ec48fc32e5798b58216b3f8fc2624',1,'vg::MemoizingGraph::get_path_handle_of_step()'],['../classvg_1_1PathSubgraphOverlay.html#a8a369e743f3f797db333ef04505bb292',1,'vg::PathSubgraphOverlay::get_path_handle_of_step()'],['../classvg_1_1VG.html#aae55721d38d4db3068ca93b4aac8e962',1,'vg::VG::get_path_handle_of_step()'],['../classxg_1_1XG.html#ab12dcc61dc8227d5dfde03b0f6b5ef16',1,'xg::XG::get_path_handle_of_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a1d1ca9865da585257709f54769f5d6a9',1,'handlegraph::PathHandleGraph::get_path_handle_of_step()'],['../classhandlegraph_1_1PathMetadata.html#a38041ec30b5c66bd94f951f4e61b8bab',1,'handlegraph::PathMetadata::get_path_handle_of_step()']]],
+ ['get_5fpath_5fid_9331',['get_path_id',['../classvg_1_1Paths.html#a8fba2fa812589af544a4a0406f78cca7',1,'vg::Paths']]],
+ ['get_5fpath_5findex_9332',['get_path_index',['../classvg_1_1GraphSynchronizer.html#aa13b46c21814ff09172452e28a4da71d',1,'vg::GraphSynchronizer']]],
+ ['get_5fpath_5flength_9333',['get_path_length',['../classvg_1_1MemoizingGraph.html#a34c10df2b34669fffd3c036636f4f608',1,'vg::MemoizingGraph::get_path_length()'],['../classxg_1_1XG.html#a458bf40b2282e7bd4743781d20f7072b',1,'xg::XG::get_path_length()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#ab71f007638c65db10efbe198f923413b',1,'handlegraph::PathPositionHandleGraph::get_path_length()']]],
+ ['get_5fpath_5fname_9334',['get_path_name',['../classvg_1_1MemoizingGraph.html#ad6e5c2da620079ff9fc488a282cb88f9',1,'vg::MemoizingGraph::get_path_name()'],['../classvg_1_1Paths.html#a56b39299430400066796a0332492f7a5',1,'vg::Paths::get_path_name()'],['../classvg_1_1PathSubgraphOverlay.html#a4331971206c3b9cb069b01abad5d965c',1,'vg::PathSubgraphOverlay::get_path_name()'],['../classvg_1_1VG.html#a8ad62c3977b6f38f0b570ea78251dc6d',1,'vg::VG::get_path_name()'],['../classxg_1_1XG.html#acc895561f10e41d82329a45e78bcdbac',1,'xg::XG::get_path_name()'],['../classhandlegraph_1_1PathHandleGraph.html#a565f4312a42dfe77ae14c1ee9ed9f2ba',1,'handlegraph::PathHandleGraph::get_path_name()'],['../classhandlegraph_1_1PathMetadata.html#acf37917fbe8c308de24264854b535018',1,'handlegraph::PathMetadata::get_path_name()']]],
+ ['get_5fpath_5fsequence_9335',['get_path_sequence',['../classvg_1_1GraphSynchronizer.html#ac33a770c7ce8206e4649133062333898',1,'vg::GraphSynchronizer']]],
+ ['get_5fpayload_5ffrom_5fzip_9336',['get_payload_from_zip',['../classvg_1_1ZipCode.html#a05895f989a23d97b08bd0c1c56bbc3bc',1,'vg::ZipCode']]],
+ ['get_5fpayload_5ffrom_5fzipcode_9337',['get_payload_from_zipcode',['../classvg_1_1ZipCode.html#ae9a95e07dd615b3692fe7742990c6c8b',1,'vg::ZipCode']]],
+ ['get_5fperipheral_5fattachments_9338',['get_peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#afbd7c2ce70efdcc6c25c20cc7710faa0',1,'vg::GraphSynchronizer::Lock']]],
+ ['get_5fphase_5fblock_9339',['get_phase_block',['../classhandlegraph_1_1PathMetadata.html#aadcc53d7a55b54eb2499b66a02500065',1,'handlegraph::PathMetadata']]],
+ ['get_5fpos_9340',['get_pos',['../classvg_1_1GaplessExtender.html#a92241e0a9691fc7b06f5258a21d1c9c4',1,'vg::GaplessExtender']]],
+ ['get_5fposition_5fof_5fstep_9341',['get_position_of_step',['../classvg_1_1MemoizingGraph.html#ade585496ff8b0d082500a1a76c2b187b',1,'vg::MemoizingGraph::get_position_of_step()'],['../classxg_1_1XG.html#ab6e8ce09a0ed201a56b9f8bd387b4e4d',1,'xg::XG::get_position_of_step()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#a473d58ac35a06551e06ae7f5ad5073be',1,'handlegraph::PathPositionHandleGraph::get_position_of_step()']]],
+ ['get_5fpositions_9342',['get_positions',['../classvg_1_1Funnel.html#a617af9590f607720de6a87dfcddbe553',1,'vg::Funnel']]],
+ ['get_5fpossible_5ffilenames_9343',['get_possible_filenames',['../classvg_1_1IndexRegistry.html#a6dc3fd500ab65621ad72ae968cedecf0',1,'vg::IndexRegistry']]],
+ ['get_5fprefix_9344',['get_prefix',['../classvg_1_1IndexRegistry.html#aa3748affd87c03e3a883ccb9d913eb73',1,'vg::IndexRegistry::get_prefix()'],['../classvg_1_1PhaseUnfolder.html#abae52ee7605f03c82622c63c55463db7',1,'vg::PhaseUnfolder::get_prefix()']]],
+ ['get_5fprefix_5fsum_5for_5fidentifier_9345',['get_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#ab2390c393bb641b64ca80183686df54a',1,'vg::ZipCode::node_code_t::get_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a34832c0fc381d48cb1424a224f8d9dae',1,'vg::ZipCode::snarl_code_t::get_prefix_sum_or_identifier()']]],
+ ['get_5fprevious_5fstep_9346',['get_previous_step',['../classvg_1_1MemoizingGraph.html#a2ceee67be1ab5744fe53de6e1fa5e718',1,'vg::MemoizingGraph::get_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#a5b3b4cb54c2f5fedc9fc4d765c6f8b3a',1,'vg::PathSubgraphOverlay::get_previous_step()'],['../classvg_1_1VG.html#a95d4b19a83f11ac6244855f86555fe76',1,'vg::VG::get_previous_step()'],['../classxg_1_1XG.html#aedec198c2181d7f729c10317e5ca8089',1,'xg::XG::get_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a71040226b29aa5046f4cc04c8c9aa9fb',1,'handlegraph::PathHandleGraph::get_previous_step()']]],
+ ['get_5fpriority_9347',['get_priority',['../classvg_1_1subcommand_1_1Subcommand.html#a4dccbaf1dc530dc55b57e1dd9dbc09e1',1,'vg::subcommand::Subcommand']]],
+ ['get_5fprob_5fof_5fdisruption_5fin_5fcolumn_9348',['get_prob_of_disruption_in_column',['../classvg_1_1MinimizerMapper.html#a6d4969130b9f7cb75efec316774b8e82',1,'vg::MinimizerMapper']]],
+ ['get_5fproc_5fstatus_5fvalue_9349',['get_proc_status_value',['../namespacevg.html#a9fb67697fd1e49bcb389a735ba9fa8f2',1,'vg']]],
+ ['get_5fprotobuf_5ftag_9350',['get_protobuf_tag',['../classvg_1_1io_1_1Registry.html#a9ccb7ac94bdb24687992af702d387620',1,'vg::io::Registry']]],
+ ['get_5fpruned_5falt_5falleles_9351',['get_pruned_alt_alleles',['../classvg_1_1VCFTraversalFinder.html#a116466101f77d992e54bb3328a42c90b',1,'vg::VCFTraversalFinder']]],
+ ['get_5fqual_5fadj_5faligner_9352',['get_qual_adj_aligner',['../classvg_1_1AlignerClient.html#aa84332f52915c20b2f2db1e060736fb5',1,'vg::AlignerClient']]],
+ ['get_5fqualities_5fin_5fsnarl_9353',['get_qualities_in_snarl',['../classvg_1_1Genotyper.html#af6518141a6e6f122e5f534c041d16918',1,'vg::Genotyper']]],
+ ['get_5fradius_9354',['get_radius',['../classvg_1_1VariantAdder.html#ae974fd5d06287893b0b1f8690624d18f',1,'vg::VariantAdder']]],
+ ['get_5frank_5fin_5fsnarl_9355',['get_rank_in_snarl',['../classvg_1_1ZipCode.html#a32750209d049ac9e5fea67c97be1f151',1,'vg::ZipCode']]],
+ ['get_5fraw_5fchain_5fcomponent_9356',['get_raw_chain_component',['../structvg_1_1ZipCode_1_1node__code__t.html#a0ab97119fa36e9682bb28118190cb8e4',1,'vg::ZipCode::node_code_t::get_raw_chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#af202024a5bb84df848c92b06535682c4',1,'vg::ZipCode::snarl_code_t::get_raw_chain_component()']]],
+ ['get_5fraw_5fchild_5fcount_9357',['get_raw_child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#af740b35df2d7b5cd84b3ab439440e492',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fcode_5ftype_9358',['get_raw_code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#abca762bde40792cc01251c5372cd8b61',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fconnectivity_9359',['get_raw_connectivity',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4f3a37a0ed45286df4f4d3cf254ac376',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fraw_5fdistance_5fend_5fleft_9360',['get_raw_distance_end_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a2619d7eccb0849542a6c8a86bb7937c1',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fdistance_5fend_5fright_9361',['get_raw_distance_end_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a1fe89643eb1a0f051e5ac71465984a71',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fdistance_5fstart_5fleft_9362',['get_raw_distance_start_left',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a39806103fa11d9969668f75045732bec',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fdistance_5fstart_5fright_9363',['get_raw_distance_start_right',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a168236545b3436928b1099c1fe572379',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fis_5freversed_9364',['get_raw_is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a5009106b8ce3273a9db11d5c177e5760',1,'vg::ZipCode::node_code_t::get_raw_is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa00b0cb7326f1fabc61bc7330936f0ee',1,'vg::ZipCode::snarl_code_t::get_raw_is_reversed()']]],
+ ['get_5fraw_5flast_5fcomponent_9365',['get_raw_last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#aa3fc8437a85ebad068b816cb2c04d0e3',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fraw_5flength_9366',['get_raw_length',['../structvg_1_1ZipCode_1_1node__code__t.html#a7ac1eeeb4a44eec49317c89ec69ec5e0',1,'vg::ZipCode::node_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a31621cf955a3423ca4fa85b440597df2',1,'vg::ZipCode::chain_code_t::get_raw_length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aabb9e23dfe383bcf8d241675975a80d6',1,'vg::ZipCode::snarl_code_t::get_raw_length()']]],
+ ['get_5fraw_5fprefix_5fsum_5for_5fidentifier_9367',['get_raw_prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#a2382df4c7c2f34b2e538edd9c2c27c66',1,'vg::ZipCode::node_code_t::get_raw_prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#adfcdf800c56ed38d46c5d2db8f291e62',1,'vg::ZipCode::snarl_code_t::get_raw_prefix_sum_or_identifier()']]],
+ ['get_5fraw_5frecord_5foffset_9368',['get_raw_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a04bf6c411365529b20b893c2b30b9f8e',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fraw_5fsnarl_5frank_5for_5fidentifier_9369',['get_raw_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#af4bfbe05a99156b9cc18446647c88830',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fread_5fcoverage_9370',['get_read_coverage',['../classvg_1_1MinimizerMapper.html#a59563aa4a1d0f00d909edd4cf8b8aa7a',1,'vg::MinimizerMapper']]],
+ ['get_5fread_5fdistance_9371',['get_read_distance',['../namespacevg_1_1algorithms.html#a5d8762b533e64039ce1a917b047097d8',1,'vg::algorithms']]],
+ ['get_5fread_5ffn_9372',['get_read_fn',['../classvg_1_1io_1_1JSONStreamHelper.html#a549e248d11b13f164c871cbf3ccbf935',1,'vg::io::JSONStreamHelper']]],
+ ['get_5fread_5fname_9373',['get_read_name',['../classvg_1_1NGSSimulator.html#a44c1fcd6a665cc7804e561a7c8700a04',1,'vg::NGSSimulator']]],
+ ['get_5fread_5foffset_9374',['get_read_offset',['../classvg_1_1GaplessExtender.html#a5c568cad31cb0cc1007ef05183c197ab',1,'vg::GaplessExtender']]],
+ ['get_5frecipe_9375',['get_recipe',['../classvg_1_1IndexRegistry.html#a1f378b76124b73c85111a81be74f92b3',1,'vg::IndexRegistry']]],
+ ['get_5frecord_5foffset_9376',['get_record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#ae3dde9ebd7b44658b083f4bd372e823f',1,'vg::ZipCode::snarl_code_t']]],
+ ['get_5fref_5ffollowing_9377',['get_ref_following',['../structhaplo_1_1linear__haplo__structure.html#a2e9ec5540a31571c3daba83abf03d18d',1,'haplo::linear_haplo_structure']]],
+ ['get_5fref_5finterval_9378',['get_ref_interval',['../classvg_1_1VCFOutputCaller.html#ab382edfcd67f4f3e73fe032cf8f96b04',1,'vg::VCFOutputCaller']]],
+ ['get_5fref_5foffsets_9379',['get_ref_offsets',['../classvg_1_1RatioSupportSnarlCaller.html#a7f838a459153e23e7963a2bd779711de',1,'vg::RatioSupportSnarlCaller::get_ref_offsets()'],['../classvg_1_1TraversalSupportFinder.html#a437e9478fc7551f23246d954af4b0d90',1,'vg::TraversalSupportFinder::get_ref_offsets()']]],
+ ['get_5fref_5fposition_9380',['get_ref_position',['../classvg_1_1VCFOutputCaller.html#a9398350530fc4df45918dc1a14eed549',1,'vg::VCFOutputCaller::get_ref_position()'],['../classvg_1_1MCMCCaller.html#a368d2f5dbd85941acceec2a1d7d44d41',1,'vg::MCMCCaller::get_ref_position()']]],
+ ['get_5fref_5fpositions_9381',['get_ref_positions',['../classvg_1_1VCFGenotyper.html#a60af53e97463c30ff180d3c1b8356df7',1,'vg::VCFGenotyper']]],
+ ['get_5freference_5ftraversal_9382',['get_reference_traversal',['../classvg_1_1LegacyCaller.html#a6d00fa81c7923b88b886f87f28984184',1,'vg::LegacyCaller']]],
+ ['get_5fregistry_9383',['get_registry',['../classvg_1_1subcommand_1_1Subcommand.html#a0e3707f1f4e9ce445faea71fddd61a00',1,'vg::subcommand::Subcommand']]],
+ ['get_5fregular_5faligner_9384',['get_regular_aligner',['../classvg_1_1AlignerClient.html#a60d4602ba9be4861136af507f8eacaec',1,'vg::AlignerClient']]],
+ ['get_5fregular_5fsnarl_5fcode_9385',['get_regular_snarl_code',['../classvg_1_1ZipCode.html#a13c0515e594e7da8c54e29314b1af6a6',1,'vg::ZipCode']]],
+ ['get_5frelease_9386',['get_release',['../classvg_1_1Version.html#a3e99ae82ab6bcc07d982012d731e7091',1,'vg::Version']]],
+ ['get_5fresolver_9387',['get_resolver',['../classvg_1_1io_1_1Registry.html#a45f5ca692e2d85618f2081e7aa967730',1,'vg::io::Registry']]],
+ ['get_5froot_9388',['get_root',['../classvg_1_1TreeSubgraph.html#a16b12e54e0c87d9a84f4d3a809a8171b',1,'vg::TreeSubgraph::get_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#af94fd9c82aaa2742123b25b0ec95311f',1,'handlegraph::SnarlDecomposition::get_root()']]],
+ ['get_5frr_5fmemo_9389',['get_rr_memo',['../classvg_1_1MultipathMapper.html#a42169ca0715c4c784584ba3d2a5d34bb',1,'vg::MultipathMapper']]],
+ ['get_5fsample_5fname_9390',['get_sample_name',['../classhandlegraph_1_1PathMetadata.html#ada7fda320c3b28c0fb642d7e4a789045',1,'handlegraph::PathMetadata']]],
+ ['get_5fscore_9391',['get_score',['../classvg_1_1ReadFilter.html#a3e168659158cf4372fc11b8cda05883d',1,'vg::ReadFilter::get_score()'],['../classvg_1_1Surjector.html#a42d2fa6bd9590a02329f31666fbe0cd5',1,'vg::Surjector::get_score()'],['../classvg_1_1ReadFilter.html#a2144e5b768ebd71768d37265c07deda2',1,'vg::ReadFilter::get_score(const Alignment &aln) const'],['../classvg_1_1ReadFilter.html#af800d67aa469136b6318c02e282c5a30',1,'vg::ReadFilter::get_score(const MultipathAlignment &read) const'],['../classvg_1_1Surjector.html#aafe9672e0a82c6540c4d1360070725ec',1,'vg::Surjector::get_score(const Alignment &aln)'],['../classvg_1_1Surjector.html#a4df48f23da07159bb99bc6577d992938',1,'vg::Surjector::get_score(const multipath_alignment_t &mp_aln)']]],
+ ['get_5fscores_9392',['get_scores',['../structhaplo_1_1haplo__DP__column.html#a784a7e41856ad01f9bdd88ca59dfb146',1,'haplo::haplo_DP_column']]],
+ ['get_5fseed_5fpos_9393',['get_seed_pos',['../classvg_1_1SpliceRegion.html#ab79a29d07732a726cffffea140af98c4',1,'vg::SpliceRegion']]],
+ ['get_5fsense_9394',['get_sense',['../classhandlegraph_1_1PathMetadata.html#a6cf06655af059252487f9581cad0dc4a',1,'handlegraph::PathMetadata']]],
+ ['get_5fsequence_9395',['get_sequence',['../classvg_1_1DagifiedGraph.html#a5d47d90eeaac4f0a6f1e12f0ed2d197e',1,'vg::DagifiedGraph::get_sequence()'],['../classvg_1_1DozeuPinningOverlay.html#ab7eabd260a4585f04809d8da64b7f2f4',1,'vg::DozeuPinningOverlay::get_sequence()'],['../classvg_1_1ExtraNodeGraph.html#a4b9d7578f0f601b186295d365cf7e487',1,'vg::ExtraNodeGraph::get_sequence()'],['../classvg_1_1SnarlGraph.html#a4a97ed146e23b853fd66a0ad827823e5',1,'vg::SnarlGraph::get_sequence()'],['../classvg_1_1IdentityOverlay.html#ada02cf10738e4fc81c7bb21ecf5d4b56',1,'vg::IdentityOverlay::get_sequence()'],['../classvg_1_1IncrementalSubgraph.html#a61eef0cd10c65efae0cac12816084bb2',1,'vg::IncrementalSubgraph::get_sequence()'],['../classvg_1_1IndexedVG.html#a64c03afcfd0c1c210e8b84a9b78a06dc',1,'vg::IndexedVG::get_sequence()'],['../classvg_1_1MemoizingGraph.html#a841433ccb7c64a657e43130c81c47c39',1,'vg::MemoizingGraph::get_sequence()'],['../classvg_1_1NullMaskingGraph.html#a7a92b5f2747dca58d2fe63368e1294d4',1,'vg::NullMaskingGraph::get_sequence()'],['../classvg_1_1PathSubgraph.html#a1549c36d974dfc4e8bcc54e0e9950646',1,'vg::PathSubgraph::get_sequence()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af008e59ecc555d391149053284ca0cbb',1,'vg::Haplotypes::Subchain::get_sequence()'],['../classvg_1_1ReverseGraph.html#ad815813ebd0d2b33515473bc974c53ad',1,'vg::ReverseGraph::get_sequence()'],['../classvg_1_1NetGraph.html#a4278d3e414d6e5b8e8055d7bdf87c7ac',1,'vg::NetGraph::get_sequence()'],['../classvg_1_1SourceSinkOverlay.html#a4a3eb7401c1b90b33d97672f50a17d39',1,'vg::SourceSinkOverlay::get_sequence()'],['../classvg_1_1JoinedSpliceGraph.html#a6b4f089ed86cdb7ff6ba9177d1187066',1,'vg::JoinedSpliceGraph::get_sequence()'],['../classvg_1_1StrandSplitGraph.html#a878c4be6f6ad6652d3b33f2691bbb570',1,'vg::StrandSplitGraph::get_sequence()'],['../classvg_1_1SubHandleGraph.html#ae9915dd52c55a51616822713509afab0',1,'vg::SubHandleGraph::get_sequence()'],['../classvg_1_1SubgraphOverlay.html#af924de823a9ef5c1a846136eb34637f4',1,'vg::SubgraphOverlay::get_sequence()'],['../classvg_1_1SubpathOverlay.html#a425e89bc05405ef207305c302c18a259',1,'vg::SubpathOverlay::get_sequence()'],['../classvg_1_1TreeSubgraph.html#ae9859d1486d3023b44ab83b3f8c5438c',1,'vg::TreeSubgraph::get_sequence()'],['../classvg_1_1VG.html#a353df9b2449ac859804359632283078b',1,'vg::VG::get_sequence()'],['../classxg_1_1XG.html#ad748df5f6e521774c1d5871ab3519bd8',1,'xg::XG::get_sequence()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a4c93978f2d225b926991b34b27528bfd',1,'handlegraph::algorithms::SubHandleGraph::get_sequence()'],['../classhandlegraph_1_1HandleGraph.html#a8cc2ab8a1292e30ba5e167a823f66d92',1,'handlegraph::HandleGraph::get_sequence()']]],
+ ['get_5fsequence_5fdictionary_9396',['get_sequence_dictionary',['../namespacevg.html#a2e23f130325e05c894696771e50f2636',1,'vg']]],
+ ['get_5fsequence_5fvisits_9397',['get_sequence_visits',['../classvg_1_1HaplotypePartitioner.html#acbe0f7f081cf6db06a894e451d8915b6',1,'vg::HaplotypePartitioner']]],
+ ['get_5fsequences_9398',['get_sequences',['../classvg_1_1HaplotypePartitioner.html#a8bdd15927542e95eb536fc9e9bb69aa7',1,'vg::HaplotypePartitioner::get_sequences(handle_t handle) const'],['../classvg_1_1HaplotypePartitioner.html#af88d6e4839d697b5780c453441d3abb0',1,'vg::HaplotypePartitioner::get_sequences(Subchain subchain) const']]],
+ ['get_5fshort_9399',['get_short',['../classvg_1_1Version.html#a8105cc0ae9049ca2daf91fbce5efa5e9',1,'vg::Version']]],
+ ['get_5fshort_5foptions_9400',['get_short_options',['../classvg_1_1OptionInterface.html#a7c1a8f1f6a3071a502362d9765c94add',1,'vg::OptionInterface::get_short_options()'],['../classvg_1_1BaseOption.html#a5b77fd0a8211f8cabd07b14db491fb64',1,'vg::BaseOption::get_short_options()']]],
+ ['get_5fsink_5fhandle_9401',['get_sink_handle',['../classvg_1_1SourceSinkOverlay.html#a71ce03b168ed695659a6ed61a946d089',1,'vg::SourceSinkOverlay']]],
+ ['get_5fsize_9402',['get_size',['../structvg_1_1algorithms_1_1Graph.html#ae7a493be0a453a3e82c7c36f0ad70e07',1,'vg::algorithms::Graph']]],
+ ['get_5fsizes_9403',['get_sizes',['../structhaplo_1_1haplo__DP__column.html#aa2c307962df62885eaca8caa4723d8a4',1,'haplo::haplo_DP_column']]],
+ ['get_5fskip_5fallele_5ffn_9404',['get_skip_allele_fn',['../classvg_1_1SnarlCaller.html#acbc3b71e19fca0c018ff9dd713f2b052',1,'vg::SnarlCaller::get_skip_allele_fn()'],['../classvg_1_1SupportBasedSnarlCaller.html#aa702e223a90771c4090511c23b7c55a7',1,'vg::SupportBasedSnarlCaller::get_skip_allele_fn()']]],
+ ['get_5fsnarl_5fchild_5fcount_9405',['get_snarl_child_count',['../classvg_1_1ZipCode.html#ad6d78deca4d723ac8d5ede306abd5578',1,'vg::ZipCode']]],
+ ['get_5fsnarl_5frank_5for_5fidentifier_9406',['get_snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a078386aa48caae9dda52e73c2975f8b7',1,'vg::ZipCode::chain_code_t']]],
+ ['get_5fsnarl_5freference_5fbounds_9407',['get_snarl_reference_bounds',['../classvg_1_1Genotyper.html#a29a6f2fd20161c9313498760578c091a',1,'vg::Genotyper']]],
+ ['get_5fsnarl_5ftraversals_9408',['get_snarl_traversals',['../classvg_1_1Genotyper.html#a7a14f1e259fe612b944aadf701ca1585',1,'vg::Genotyper']]],
+ ['get_5fsnp_5fref_5fposition_9409',['get_SNP_ref_position',['../structhaplo_1_1linear__haplo__structure.html#a312a7a7a748cc4acd3c4b75717db1fe6',1,'haplo::linear_haplo_structure']]],
+ ['get_5fsnv_5fallele_9410',['get_SNV_allele',['../structhaplo_1_1linear__haplo__structure.html#a353eefc81d042a96f98980b7cb2a72aa',1,'haplo::linear_haplo_structure']]],
+ ['get_5fsort_5fvalue_9411',['get_sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aae5b7a35573e7133c368eb6bf4678aab',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['get_5fsource_5fhandle_9412',['get_source_handle',['../classvg_1_1SourceSinkOverlay.html#a4126d6851b442614cb115668eaeeb89f',1,'vg::SourceSinkOverlay']]],
+ ['get_5fspanning_5fhaplotypes_9413',['get_spanning_haplotypes',['../classvg_1_1GBWTTraversalFinder.html#a88b35f62878ceab005faf07f7386691c',1,'vg::GBWTTraversalFinder']]],
+ ['get_5fstart_9414',['get_start',['../classvg_1_1NetGraph.html#a35e17fbdc2bade4b5b0195d03cb0dc22',1,'vg::NetGraph']]],
+ ['get_5fstart_5fbound_9415',['get_start_bound',['../classhandlegraph_1_1SnarlDecomposition.html#a63eea99ca9840f16ef358ee664ecda23',1,'handlegraph::SnarlDecomposition']]],
+ ['get_5fstart_5fof_9416',['get_start_of',['../namespacevg.html#afa918cf29c1c8238d88f2bbc94b6abef',1,'vg']]],
+ ['get_5fstep_5fat_5fposition_9417',['get_step_at_position',['../classvg_1_1MemoizingGraph.html#acbae8703ecc85597b33e36d5208a4f1e',1,'vg::MemoizingGraph::get_step_at_position()'],['../classxg_1_1XG.html#a087db8dbe184e5a22dda11d61f8fff6a',1,'xg::XG::get_step_at_position()'],['../classhandlegraph_1_1PathPositionHandleGraph.html#aefbae4c3392c32ec13534a44bcc21136',1,'handlegraph::PathPositionHandleGraph::get_step_at_position()']]],
+ ['get_5fstep_5fcount_9418',['get_step_count',['../classvg_1_1MemoizingGraph.html#ae0bc7232272e70adab6333dbe3718f46',1,'vg::MemoizingGraph::get_step_count()'],['../classvg_1_1PathSubgraphOverlay.html#ae2df84b76bcec7b4899838a99d3799f5',1,'vg::PathSubgraphOverlay::get_step_count()'],['../classvg_1_1VG.html#a3efe30807d096a6175373bc3f4863dd7',1,'vg::VG::get_step_count()'],['../classxg_1_1XG.html#a0609241ee4795d7c9dd2a2b5cc8ce3a4',1,'xg::XG::get_step_count()'],['../classhandlegraph_1_1PathHandleGraph.html#add91075c3490f8dc5acf667f2b26832c',1,'handlegraph::PathHandleGraph::get_step_count(const path_handle_t &path_handle) const =0'],['../classhandlegraph_1_1PathHandleGraph.html#a6d3a31f0c19054cd2908525119869b80',1,'handlegraph::PathHandleGraph::get_step_count(const handle_t &handle) const']]],
+ ['get_5fsteps_9419',['get_steps',['../classvg_1_1IndexingPlan.html#a52c631c507d1cd0f0451ce7de71f2091',1,'vg::IndexingPlan']]],
+ ['get_5fstream_5flength_9420',['get_stream_length',['../namespacevg_1_1io.html#aff18a599bd6affc6e2709cb2cff9154c',1,'vg::io']]],
+ ['get_5fstream_5fposition_9421',['get_stream_position',['../namespacevg_1_1io.html#aca3b265c558db37b69a837668d2fdf12',1,'vg::io']]],
+ ['get_5fsubchains_9422',['get_subchains',['../classvg_1_1HaplotypePartitioner.html#a27be1484d044a8f872083ea6e98d9786',1,'vg::HaplotypePartitioner']]],
+ ['get_5fsubgraph_9423',['get_subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a8754c28fbea6df69e6204a9128912a20',1,'vg::GraphSynchronizer::Lock::get_subgraph()'],['../classvg_1_1SpliceRegion.html#ae10fef3784f1d382cb8f3973e1c9ff1b',1,'vg::SpliceRegion::get_subgraph()']]],
+ ['get_5fsubrange_9424',['get_subrange',['../classhandlegraph_1_1PathMetadata.html#a80f47deffdb584fa74ea43dad580cce7',1,'handlegraph::PathMetadata']]],
+ ['get_5fsubsequence_9425',['get_subsequence',['../classvg_1_1IncrementalSubgraph.html#a258698c76e4d96ecefd38505894f778b',1,'vg::IncrementalSubgraph::get_subsequence()'],['../classvg_1_1JoinedSpliceGraph.html#a2348c9a3357615ce0eea301366344376',1,'vg::JoinedSpliceGraph::get_subsequence()'],['../classvg_1_1VG.html#a45075c22efc7cfb1ed06a8996fec119c',1,'vg::VG::get_subsequence()'],['../classxg_1_1XG.html#a0368861cc6c99d2a1d40c059db62c2a9',1,'xg::XG::get_subsequence()'],['../classhandlegraph_1_1HandleGraph.html#a74c6fcda357516b1160996c63ed40d63',1,'handlegraph::HandleGraph::get_subsequence()']]],
+ ['get_5fsuffix_9426',['get_suffix',['../classvg_1_1IndexFile.html#ac81438a82e18b86b443e7d853245d599',1,'vg::IndexFile::get_suffix()'],['../classvg_1_1PhaseUnfolder.html#a97128de268b43c9ccf9dd117829adedf',1,'vg::PhaseUnfolder::get_suffix()']]],
+ ['get_5fsupport_9427',['get_support',['../structvg_1_1AugmentedGraph.html#ad239a8516427304ef304e944f7d20c00',1,'vg::AugmentedGraph::get_support(id_t node)'],['../structvg_1_1AugmentedGraph.html#a87c6ed55516068757be3b1ad54a6cfd0',1,'vg::AugmentedGraph::get_support(edge_t edge)'],['../structvg_1_1SupportAugmentedGraph.html#a0ffa85683b46b7f8d6b64da42ba19fbb',1,'vg::SupportAugmentedGraph::get_support(id_t node)'],['../structvg_1_1SupportAugmentedGraph.html#a4c86be41ce8680c5473080c704ddcc10',1,'vg::SupportAugmentedGraph::get_support(edge_t edge)']]],
+ ['get_5fsupport_5ffinder_9428',['get_support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a04ebbd23ec0162a72c959351131e17ba',1,'vg::SupportBasedSnarlCaller']]],
+ ['get_5fsymbolic_5fbounds_9429',['get_symbolic_bounds',['../classvg_1_1Constructor.html#a31a7837804bd45819ab249687a858fbb',1,'vg::Constructor']]],
+ ['get_5fsystem_5fmemory_9430',['get_system_memory',['../classvg_1_1IndexRegistry.html#a1f03f21a783cad871997b03bcd0c8dff',1,'vg::IndexRegistry']]],
+ ['get_5ftables_9431',['get_tables',['../classvg_1_1io_1_1Registry.html#aa9f3d682e2b43bfdc3fc30e252a716b9',1,'vg::io::Registry']]],
+ ['get_5ftail_5fforest_9432',['get_tail_forest',['../classvg_1_1MinimizerMapper.html#afdbaa5b2938d0050476d078d336286cf',1,'vg::MinimizerMapper']]],
+ ['get_5ftarget_5fmemory_5fusage_9433',['get_target_memory_usage',['../classvg_1_1IndexRegistry.html#aa8aae29f234def70dc6de5f1a291cbc0',1,'vg::IndexRegistry']]],
+ ['get_5fthread_5fcount_9434',['get_thread_count',['../namespacevg.html#ade988dd38efaa705be15ba17500fe219',1,'vg::get_thread_count()'],['../namespacexg.html#a025cd6958c94d7ce14c1be1425792161',1,'xg::get_thread_count()']]],
+ ['get_5fthread_5fstream_9435',['get_thread_stream',['../classvg_1_1io_1_1StreamMultiplexer.html#a749ab082e0364d470d84978c9757ef76',1,'vg::io::StreamMultiplexer']]],
+ ['get_5ftop_5flevel_5fchain_5foffset_9436',['get_top_level_chain_offset',['../classvg_1_1ZipCode.html#a304ce8419239ce69dfb69e85e50d3c8c',1,'vg::ZipCode']]],
+ ['get_5ftopological_5forder_9437',['get_topological_order',['../classvg_1_1PathSubgraph.html#a591e8f29ef3f356a38aca18e466ae954',1,'vg::PathSubgraph::get_topological_order()'],['../classvg_1_1TreeSubgraph.html#a850f30c11c28ab61148215970b5c6129',1,'vg::TreeSubgraph::get_topological_order()']]],
+ ['get_5ftotal_5flength_9438',['get_total_length',['../classxg_1_1XG.html#a4437293fdec75f15a296fb545a6d539d',1,'xg::XG::get_total_length()'],['../classhandlegraph_1_1HandleGraph.html#a4c98da99e0d32ebcc9fd31be4b779e29',1,'handlegraph::HandleGraph::get_total_length()']]],
+ ['get_5ftranslation_9439',['get_translation',['../classvg_1_1Translator.html#ac76452dc0c74164d2bcfa25f53ca9828',1,'vg::Translator']]],
+ ['get_5ftraversal_5fgenotype_5fsupport_9440',['get_traversal_genotype_support',['../classvg_1_1TraversalSupportFinder.html#a1b818e6111dd2eec62067a562ecc2078',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fmapqs_9441',['get_traversal_mapqs',['../classvg_1_1TraversalSupportFinder.html#a1a7ce9dabeac1835ce0c9765301fcafd',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fof_5fsnarl_9442',['get_traversal_of_snarl',['../namespacevg.html#a871d5cdd29e1806636314021d0b6d451',1,'vg']]],
+ ['get_5ftraversal_5forder_9443',['get_traversal_order',['../namespacevg.html#aaa05224d1b8daa421ebfb9320fc1d2d1',1,'vg']]],
+ ['get_5ftraversal_5fset_5fsupport_9444',['get_traversal_set_support',['../classvg_1_1TraversalSupportFinder.html#aead4beb53b5148baa538c6481be8700d',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fsizes_9445',['get_traversal_sizes',['../classvg_1_1TraversalSupportFinder.html#a95944f27ca78da63466f5623ad646ee4',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversal_5fsupport_9446',['get_traversal_support',['../classvg_1_1TraversalSupportFinder.html#a28c6f9088f6c28d64855d6cac9a65322',1,'vg::TraversalSupportFinder']]],
+ ['get_5ftraversals_9447',['get_traversals',['../classvg_1_1Deconstructor.html#ad58319907ec3f7bf3e6d130f6469a9a9',1,'vg::Deconstructor']]],
+ ['get_5ftree_5fsize_9448',['get_tree_size',['../classvg_1_1ZipCodeTree.html#a1207ebf8f31cd6f17593f100be3c7f00',1,'vg::ZipCodeTree']]],
+ ['get_5ftype_9449',['get_type',['../structhaplo_1_1linear__haplo__structure.html#ac0dcdb90717d1585bbc847206746e293',1,'haplo::linear_haplo_structure::get_type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#aef1abc2e62fd2ebcc722e26978bb56b7',1,'vg::ZipCodeTree::tree_item_t::get_type()']]],
+ ['get_5funderlying_5fhandle_9450',['get_underlying_handle',['../classvg_1_1DagifiedGraph.html#aea86fce4d0f22943935bad1e5cc17f48',1,'vg::DagifiedGraph::get_underlying_handle()'],['../classvg_1_1DozeuPinningOverlay.html#a5cfe7e76c343f768037c84df85037ace',1,'vg::DozeuPinningOverlay::get_underlying_handle()'],['../classvg_1_1IdentityOverlay.html#a5bfd0bebd074847b5504b9ad3f968836',1,'vg::IdentityOverlay::get_underlying_handle()'],['../classvg_1_1IncrementalSubgraph.html#a6b3e5f09eb2a9edb698eb08c55cc9486',1,'vg::IncrementalSubgraph::get_underlying_handle()'],['../classvg_1_1NullMaskingGraph.html#aa903d2c61cf2ba035aac11a3015c2cab',1,'vg::NullMaskingGraph::get_underlying_handle()'],['../classvg_1_1PathSubgraph.html#aa6c521d9a3770f20483f3f16b0686eeb',1,'vg::PathSubgraph::get_underlying_handle()'],['../classvg_1_1ReverseGraph.html#a246e5d5c82508b512fb4c041bfe38892',1,'vg::ReverseGraph::get_underlying_handle()'],['../classvg_1_1SourceSinkOverlay.html#abe2d0e58471d1ab7840618a02958fc96',1,'vg::SourceSinkOverlay::get_underlying_handle()'],['../classvg_1_1StrandSplitGraph.html#aa6379c95c71b6a6682311733de098d1f',1,'vg::StrandSplitGraph::get_underlying_handle()'],['../classvg_1_1SubHandleGraph.html#a434e6cd60bb278307df255a43681e08a',1,'vg::SubHandleGraph::get_underlying_handle()'],['../classvg_1_1SubpathOverlay.html#a595889f41331fbbc8a049ae56ba29624',1,'vg::SubpathOverlay::get_underlying_handle()'],['../classvg_1_1TreeSubgraph.html#a2d88a6edb6d6d586b6fe26a88e13248f',1,'vg::TreeSubgraph::get_underlying_handle()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ada7dab5b4c9e55607563d1bcf546d401',1,'handlegraph::algorithms::SubHandleGraph::get_underlying_handle()'],['../classhandlegraph_1_1ExpandingOverlayGraph.html#aacfa30b0166f91f1aa80f0fd566d2b65',1,'handlegraph::ExpandingOverlayGraph::get_underlying_handle()']]],
+ ['get_5funderlying_5fid_9451',['get_underlying_id',['../classvg_1_1DagifiedGraph.html#ae8707e0886baf125d0c0a25a3cc3a4cc',1,'vg::DagifiedGraph::get_underlying_id()'],['../classvg_1_1DozeuPinningOverlay.html#a45047bf7a55843a4099d9db6b83e2d17',1,'vg::DozeuPinningOverlay::get_underlying_id()']]],
+ ['get_5funique_5fhaplotypes_9452',['get_unique_haplotypes',['../classvg_1_1VariantAdder.html#aa9ae7b7fa8ad3ac6bec72ada43a3d4b7',1,'vg::VariantAdder']]],
+ ['get_5fvalue_9453',['get_value',['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#adf719dd5d99dd4b31952df3af1911ed1',1,'vg::ZipCodeTree::tree_item_t::get_value()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a6d28a735e7c8a6a0cc8b11675fb8d261',1,'vg::subcommand::ArgSpec::get_value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#acb802adcf83734cc84ee4745ed4ee505',1,'vg::subcommand::ValueArgSpec::get_value()']]],
+ ['get_5fvalue_5fand_5fnext_5findex_9454',['get_value_and_next_index',['../structvg_1_1varint__vector__t.html#afee3663cabce117ecf7b114b0179ae31',1,'vg::varint_vector_t']]],
+ ['get_5fvariants_5fin_5fsite_9455',['get_variants_in_site',['../classvg_1_1VCFTraversalFinder.html#ae45b4f713e847be11c4aa07482de3e12',1,'vg::VCFTraversalFinder']]],
+ ['get_5fvcf_5fheader_9456',['get_vcf_header',['../classvg_1_1Deconstructor.html#a6c14aa01fabc63b945bc69550335408b',1,'vg::Deconstructor']]],
+ ['get_5fversion_9457',['get_version',['../classvg_1_1Version.html#aa6e698d728ebd5e3318511dfde778eaf',1,'vg::Version']]],
+ ['get_5fvg_5findex_5fregistry_9458',['get_vg_index_registry',['../structvg_1_1VGIndexes.html#a4291997834048ac385331f19390889c0',1,'vg::VGIndexes']]],
+ ['get_5fweight_5fusing_5fother_9459',['get_weight_using_other',['../structvg_1_1algorithms_1_1Graph.html#ad0741db7b09040c706ffaffbb7337098',1,'vg::algorithms::Graph']]],
+ ['get_5fwork_5fdir_9460',['get_work_dir',['../classvg_1_1IndexRegistry.html#ac587073860174b6c074d2be7ad53e103',1,'vg::IndexRegistry']]],
+ ['getreachablebridges_9461',['getReachableBridges',['../namespacevg.html#af601021f7ec2c0b0d7404030ee7271c9',1,'vg']]],
+ ['getreachablebridges2_9462',['getReachableBridges2',['../namespacevg.html#a2dc613a63afb3f23851c96494006630d',1,'vg']]],
+ ['gfa_5fhas_5fhaplotypes_9463',['gfa_has_haplotypes',['../classvg_1_1IndexRegistry.html#a019e2efc800d3280acdce7814db8b096',1,'vg::IndexRegistry']]],
+ ['gfa_5fto_5fhandle_5fgraph_9464',['gfa_to_handle_graph',['../namespacevg_1_1algorithms.html#aedfca626dc003dc3fee77c6bbfcde297',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, GFAIDMapInfo *translation)'],['../namespacevg_1_1algorithms.html#adca14b7dcba0bb21f3fdb0c98d867c72',1,'vg::algorithms::gfa_to_handle_graph(const string &filename, MutableHandleGraph *graph, const string &translation_filename)'],['../namespacevg_1_1algorithms.html#a031cb6d0db20a6aaee020c5a6909ba80',1,'vg::algorithms::gfa_to_handle_graph(istream &in, MutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr)']]],
+ ['gfa_5fto_5fpath_5fhandle_5fgraph_9465',['gfa_to_path_handle_graph',['../namespacevg_1_1algorithms.html#a9f5c41c06269c778d2c97f39cbc79de8',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a61f2c7006c531ad5dd319ea30ec0087f',1,'vg::algorithms::gfa_to_path_handle_graph(const string &filename, MutablePathMutableHandleGraph *graph, int64_t max_rgfa_rank, const string &translation_filename, unordered_set< PathSense > *ignore_sense=nullptr)'],['../namespacevg_1_1algorithms.html#a8baa82611439357dc02996ba17ce6aa9',1,'vg::algorithms::gfa_to_path_handle_graph(istream &in, MutablePathMutableHandleGraph *graph, GFAIDMapInfo *translation=nullptr, int64_t max_rgfa_rank=numeric_limits< int64_t >::max(), unordered_set< PathSense > *ignore_sense=nullptr)']]],
+ ['gfaduplicatepatherror_9466',['GFADuplicatePathError',['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#aa815b9f84fdf80d9bf29c38d3d68408c',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name)'],['../structvg_1_1algorithms_1_1GFADuplicatePathError.html#a05dd140439b17113dec810a3cdc26bab',1,'vg::algorithms::GFADuplicatePathError::GFADuplicatePathError(const std::string &path_name, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
+ ['gfaformaterror_9467',['GFAFormatError',['../structvg_1_1algorithms_1_1GFAFormatError.html#add2d72c679e2b69e1c9f9c481228e0fb',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message)'],['../structvg_1_1algorithms_1_1GFAFormatError.html#afdf6dea244cc33a30ae5d9446199bea2',1,'vg::algorithms::GFAFormatError::GFAFormatError(const string &message, const GFAParser::cursor_t &position, const char *parsing_state=nullptr)']]],
+ ['gfahandlegraph_9468',['GFAHandleGraph',['../classvg_1_1GFAHandleGraph.html#aeffc2278ffcad22cd6950f3fa831f60d',1,'vg::GFAHandleGraph']]],
+ ['gffreader_9469',['GFFReader',['../classvg_1_1GFFReader.html#a886d9cf2d287f8d0f6c87b206c26d893',1,'vg::GFFReader']]],
+ ['gffrecord_9470',['GFFRecord',['../structvg_1_1GFFRecord.html#a8fc2a234093eccb6ed958325887e0f08',1,'vg::GFFRecord']]],
+ ['golden_5fsection_5fsearch_9471',['golden_section_search',['../namespacevg.html#a314ff925fad534d112e4531617e408fa',1,'vg']]],
+ ['graph_9472',['graph',['../classvg_1_1Transcriptome.html#aee456b8b8e3acaf836914c987d89a16a',1,'vg::Transcriptome']]],
+ ['graph_5fcigar_9473',['graph_cigar',['../classvg_1_1GSSWAligner.html#a429c1cbb1e166acba4e29a8dc172da7d',1,'vg::GSSWAligner']]],
+ ['graph_5fend_9474',['graph_end',['../classvg_1_1algorithms_1_1Anchor.html#a3ddb866c3cb925619705602580076942',1,'vg::algorithms::Anchor']]],
+ ['graph_5finterval_5fto_5fstring_9475',['graph_interval_to_string',['../namespacevg.html#aeade23d997b1899023cfe7f560cc6bc1',1,'vg']]],
+ ['graph_5fmixed_5fdistance_5festimate_9476',['graph_mixed_distance_estimate',['../classvg_1_1Mapper.html#a67fb2b4bc540b81be063075ce5593569',1,'vg::Mapper']]],
+ ['graph_5fpos_5fat_5fpath_5fposition_9477',['graph_pos_at_path_position',['../classxg_1_1XG.html#a85c47feeb19e96486140c5e1b8184bc7',1,'xg::XG::graph_pos_at_path_position(const path_handle_t &path, size_t path_pos) const'],['../classxg_1_1XG.html#a31c733ed1c2045b1e2a7e9f343dc9296',1,'xg::XG::graph_pos_at_path_position(const std::string &name, size_t path_pos) const']]],
+ ['graph_5fstart_9478',['graph_start',['../classvg_1_1algorithms_1_1Anchor.html#ac7bd5f21e10bae0f6dacb3fcc623752f',1,'vg::algorithms::Anchor']]],
+ ['graph_5fto_5fgfa_9479',['graph_to_gfa',['../namespacevg.html#ad8c4a075bb9301c8050d89ed8e6a33b9',1,'vg']]],
+ ['graph_5fto_5fxg_5fadjusting_5fpaths_9480',['graph_to_xg_adjusting_paths',['../convert__main_8cpp.html#afe37e7186bce3c6128d32b210f99a9a5',1,'convert_main.cpp']]],
+ ['graphcaller_9481',['GraphCaller',['../classvg_1_1GraphCaller.html#a621386ff80a0fe3289719c75c282bc5a',1,'vg::GraphCaller']]],
+ ['graphsynchronizer_9482',['GraphSynchronizer',['../classvg_1_1GraphSynchronizer.html#addf1e96558546d4f5e708827b9eb4d67',1,'vg::GraphSynchronizer']]],
+ ['greedymindistanceclusterer_9483',['GreedyMinDistanceClusterer',['../classvg_1_1GreedyMinDistanceClusterer.html#a603a74649e16204cace3e714ebe67a74',1,'vg::GreedyMinDistanceClusterer']]],
+ ['groom_5fcomponents_9484',['groom_components',['../classvg_1_1FlowSort.html#a2a52b4d445acf50ebfd8f7dc3a07d044',1,'vg::FlowSort']]],
+ ['group_9485',['group',['../classvg_1_1SparseUnionFind.html#af91351abb606a1bc16c1cbb5f1b668ab',1,'vg::SparseUnionFind']]],
+ ['group_5fmapping_5fquality_5fexact_9486',['group_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#a7e03bd79bceb8a8034ae57ba640069bc',1,'vg::GSSWAligner']]],
+ ['group_5fsize_9487',['group_size',['../classvg_1_1SparseUnionFind.html#aff34e4252e15a68b1e8e79c8cef27a66',1,'vg::SparseUnionFind']]],
+ ['groupedoptiongroup_9488',['GroupedOptionGroup',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a6da6deb7ccf8697e84db1c266dd9180f',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup()=default'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af4f06c1eff0303d1c982b0c2d34c2b55',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(const GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#ab1c7b6f34e8d53cf4536625ea6709e80',1,'vg::subcommand::GroupedOptionGroup::GroupedOptionGroup(GroupedOptionGroup &&other)=delete']]],
+ ['growth_9489',['Growth',['../structvg_1_1FlowSort_1_1Growth.html#aa156ae24695e73aee936d00a7ef70d22',1,'vg::FlowSort::Growth']]],
+ ['gssw_5fmapping_5fto_5falignment_9490',['gssw_mapping_to_alignment',['../classvg_1_1GSSWAligner.html#ab45f7399b68bdc980499d4384515b9b7',1,'vg::GSSWAligner']]],
+ ['gsswaligner_9491',['GSSWAligner',['../classvg_1_1GSSWAligner.html#a02c1c427118eb1a8244274d852684c79',1,'vg::GSSWAligner::GSSWAligner()=default'],['../classvg_1_1GSSWAligner.html#a6c3f1338e6a66850b779e8331a65a61c',1,'vg::GSSWAligner::GSSWAligner(const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int8_t _full_length_bonus, double _gc_content)']]],
+ ['guess_5fparallel_5fgbwt_5fjobs_9492',['guess_parallel_gbwt_jobs',['../namespacevg.html#a70ebd70e5b26c5fefe30895fa313f3b9',1,'vg']]]
];
diff --git a/search/functions_8.js b/search/functions_8.js
index 490d759b49..73a94f2b60 100644
--- a/search/functions_8.js
+++ b/search/functions_8.js
@@ -1,142 +1,142 @@
var searchData=
[
- ['halt_9489',['halt',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aeabcba66f2745dd0e6a4793e954aa23d',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['handle_9490',['handle',['../classxg_1_1XGPath.html#a93ab3c3284afd4d780368ab03d51ee43',1,'xg::XGPath::handle()'],['../classvg_1_1io_1_1MessageIterator.html#a4b3ba16717c1900a0638518bd33a4a59',1,'vg::io::MessageIterator::handle()'],['../classvg_1_1io_1_1ProtobufEmitter.html#afb457287f96e5ed57d53f91fd5247ec7',1,'vg::io::ProtobufEmitter::handle()']]],
- ['handle_5fat_5forder_9491',['handle_at_order',['../classvg_1_1IncrementalSubgraph.html#a8c2059a01cfda921bd8c5f91bd3763c7',1,'vg::IncrementalSubgraph']]],
- ['handle_5fat_5fpath_5fposition_9492',['handle_at_path_position',['../classxg_1_1XG.html#a63e8b7be4676a9fb4c77e16f0c76b5a8',1,'xg::XG']]],
- ['handle_5fat_5fposition_9493',['handle_at_position',['../classxg_1_1XGPath.html#ac3dac0fefe450c561f44dadd3ac00487',1,'xg::XGPath']]],
- ['handle_5fbuffer_9494',['handle_buffer',['../classvg_1_1VcfBuffer.html#a1d8968beb2952113ea8a724dad1e1752',1,'vg::VcfBuffer']]],
- ['handle_5ffull_5flength_9495',['handle_full_length',['../namespacevg.html#a536dfd4326c17ad4d072d2c9021e4b7c',1,'vg']]],
- ['handle_5fgraph_5fto_5fcactus_9496',['handle_graph_to_cactus',['../namespacevg.html#a3d4e7ee3d7394e2318e874dc98dd8320',1,'vg']]],
- ['handle_5frank_9497',['handle_rank',['../classxg_1_1XG.html#a2e8f51499dd0ba67d52100bf380b0936',1,'xg::XG']]],
- ['handle_5fstart_9498',['handle_start',['../classxg_1_1XGPath.html#a5a62bf71a4a85c9617402504a2be01a4',1,'xg::XGPath']]],
- ['handle_5fto_5fgbwt_9499',['handle_to_gbwt',['../namespacevg.html#a1fa5cc80bff735a8803aa9f564c29994',1,'vg']]],
- ['handle_5fto_5frank_9500',['handle_to_rank',['../classhandlegraph_1_1RankedHandleGraph.html#a6a21763bef01676efd4dd10767681bfc',1,'handlegraph::RankedHandleGraph']]],
- ['handlegraphnodeset_9501',['HandleGraphNodeSet',['../classvg_1_1HandleGraphNodeSet.html#af257f6c350350577cc2bef059a133837',1,'vg::HandleGraphNodeSet']]],
- ['handlegraphsnarlfinder_9502',['HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html#a8fb53057585d8e64313485c02a15cec5',1,'vg::HandleGraphSnarlFinder']]],
- ['haplo_5fdp_9503',['haplo_DP',['../structhaplo_1_1haplo__DP.html#a35035e7b00f8d5503ae3582afebbac50',1,'haplo::haplo_DP']]],
- ['haplo_5fdp_5fcolumn_9504',['haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html#a15c9d8c26ba9eba47510eaac32b49eb8',1,'haplo::haplo_DP_column']]],
- ['haplo_5fdp_5frectangle_9505',['haplo_DP_rectangle',['../structhaplo_1_1haplo__DP__rectangle.html#a54e3de46211170326d89ee11f9d61fab',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle()'],['../structhaplo_1_1haplo__DP__rectangle.html#a5e2a880c7d8974ac08021256994a51e2',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle(bool inclusive_interval)']]],
- ['haplotype_9506',['Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html#aba98c5b032e48cf1a83b21cae31966a0',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversal node_traversal)'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a61d6bf4127d5e607eccca43b730b8d74',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversalIterator first, NodeTraversalIterator last)']]],
- ['haplotype_5fconsistent_5falignments_9507',['haplotype_consistent_alignments',['../namespacevg.html#ab5a2adbf9370dc37be337d927341f9db',1,'vg']]],
- ['haplotype_5fto_5fstring_9508',['haplotype_to_string',['../classvg_1_1VariantAdder.html#a86108ed47c5e85a23d31fe380ae2670d',1,'vg::VariantAdder']]],
- ['haplotype_5ftranscript_5fpaths_9509',['haplotype_transcript_paths',['../classvg_1_1Transcriptome.html#a8103dfe99f0bb36e806cab44d2e21d54',1,'vg::Transcriptome']]],
- ['haplotypeindexer_9510',['HaplotypeIndexer',['../classvg_1_1HaplotypeIndexer.html#ae0b8cbfe64f32152ceefa57daf9ece72',1,'vg::HaplotypeIndexer']]],
- ['haplotypenode_9511',['HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a584a6b469c7f9709ea7da34f867f49aa',1,'vg::PhasedGenome::HaplotypeNode']]],
- ['haplotypepartitioner_9512',['HaplotypePartitioner',['../classvg_1_1HaplotypePartitioner.html#a6faa6da8cc4a62f7cabc8d66e19e9ac1',1,'vg::HaplotypePartitioner']]],
- ['haplotypesconfig_9513',['HaplotypesConfig',['../structHaplotypesConfig.html#a45bef8cdfe50758d06d6d078b5a6a13f',1,'HaplotypesConfig']]],
- ['has_5fannotation_9514',['has_annotation',['../classvg_1_1multipath__alignment__t.html#a6b60350a3dada734b919bdf15f41bf82',1,'vg::multipath_alignment_t::has_annotation()'],['../namespacevg.html#a34f4e73b242fa5b34d30ecc4da496835',1,'vg::has_annotation()']]],
- ['has_5fargument_9515',['has_argument',['../classvg_1_1OptionInterface.html#a29383428b6a6e40109fb4949286f07f7',1,'vg::OptionInterface::has_argument()'],['../classvg_1_1OptionValueParser.html#af8d6268a6cec527dd0e117aef58cbd63',1,'vg::OptionValueParser::has_argument()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a104c6803a28a2528b33759ac8ad69175',1,'vg::OptionValueParser< vector< Item > >::has_argument()'],['../classvg_1_1BaseOption.html#a3aa53d25627ae95383edce8f6e001caa',1,'vg::BaseOption::has_argument()'],['../classvg_1_1OptionValueParser.html#aabf09c8e0e807fb19debad284331387d',1,'vg::OptionValueParser::has_argument()']]],
- ['has_5fbase_5fgraph_9516',['has_base_graph',['../structvg_1_1AugmentedGraph.html#ae1b8b8c8246ccfe1f2d56250a3361177',1,'vg::AugmentedGraph']]],
- ['has_5fconnection_9517',['has_connection',['../classvg_1_1subpath__t.html#a972d307d386a636cc2dc1fc170f56df3',1,'vg::subpath_t']]],
- ['has_5fcurrent_9518',['has_current',['../classvg_1_1io_1_1MessageIterator.html#abcbec4e2b7376ae5ca8bbd4e05d9103a',1,'vg::io::MessageIterator::has_current()'],['../classvg_1_1io_1_1ProtobufIterator.html#a59294f819b65352528da9224ea39d973',1,'vg::io::ProtobufIterator::has_current()']]],
- ['has_5fedge_9519',['has_edge',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a6fd765d7a5623bef825effc7fdf46b87',1,'haplo::hDP_gbwt_graph_accessor::has_edge()'],['../classvg_1_1VG.html#a501886a0c593ac3231cfcc6989911ced',1,'vg::VG::has_edge(const handle_t &left, const handle_t &right) const'],['../classvg_1_1VG.html#a447d717e83131c526d26e6d2f0a091a6',1,'vg::VG::has_edge(const NodeSide &side1, const NodeSide &side2) const'],['../classvg_1_1VG.html#a1c7ff3b6f9cfca2c21e1a8d1c848fc01',1,'vg::VG::has_edge(const pair< NodeSide, NodeSide > &sides) const'],['../classvg_1_1VG.html#aa69701fcb4bf9e8b593681ba1d818571',1,'vg::VG::has_edge(Edge *edge) const'],['../classvg_1_1VG.html#ab2c85fad61f57260c913bc565a549832',1,'vg::VG::has_edge(const Edge &edge) const'],['../classhandlegraph_1_1HandleGraph.html#a069448fbe58665b9ff531ad0b8c5af57',1,'handlegraph::HandleGraph::has_edge(const handle_t &left, const handle_t &right) const'],['../classhandlegraph_1_1HandleGraph.html#a6171cdd6036c73623c96656f8b44fe9d',1,'handlegraph::HandleGraph::has_edge(const edge_t &edge) const']]],
- ['has_5fend_9520',['has_end',['../structvg_1_1Haplotypes_1_1Subchain.html#ae9fbddda11e52d6e9b98156a50224a73',1,'vg::Haplotypes::Subchain::has_end()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a0aa037691bcf20d78faad42eea3c8f57',1,'vg::HaplotypePartitioner::Subchain::has_end()']]],
- ['has_5fexcluded_5frefpos_9521',['has_excluded_refpos',['../classvg_1_1ReadFilter.html#ac772c0651477027191108e64ab7c53cb',1,'vg::ReadFilter::has_excluded_refpos(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab609cc20f1e49dc1001e71fe82c5ead4',1,'vg::ReadFilter::has_excluded_refpos(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#aca79c3eda85a8f4fafcd25a243b7efd4',1,'vg::ReadFilter::has_excluded_refpos(const Alignment &aln) const']]],
- ['has_5fexcuded_5ffeature_9522',['has_excuded_feature',['../classvg_1_1ReadFilter.html#a2d30291c0c609d58670f40e2eb9661e4',1,'vg::ReadFilter']]],
- ['has_5ffixed_5ffragment_5flength_5fdistr_9523',['has_fixed_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ad0a2d836cfcaddae8569bf1a024aa56b',1,'vg::PairedEndMapper']]],
- ['has_5fincorrect_5forder_5fexons_9524',['has_incorrect_order_exons',['../classvg_1_1Transcriptome.html#a4cba921dae9fe3eae2361b0b7391b7b3',1,'vg::Transcriptome']]],
- ['has_5fincremental_5fsearch_9525',['has_incremental_search',['../classhaplo_1_1ScoreProvider.html#a1455c3ccb6a9d03e5d79636e79be301a',1,'haplo::ScoreProvider::has_incremental_search()'],['../classhaplo_1_1GBWTScoreProvider.html#abe35e78c1d11af952b27dc8c36c1909f',1,'haplo::GBWTScoreProvider::has_incremental_search()']]],
- ['has_5finversion_9526',['has_inversion',['../namespacevg.html#a1b545f6474c6e528176031149a8bc570',1,'vg']]],
- ['has_5finverting_5fedge_9527',['has_inverting_edge',['../classvg_1_1VG.html#a49fb4de3494407b800c3efda254851cf',1,'vg::VG']]],
- ['has_5finverting_5fedge_5ffrom_9528',['has_inverting_edge_from',['../classvg_1_1VG.html#a7b7bbf066c6608211e7527ba50b23e48',1,'vg::VG']]],
- ['has_5finverting_5fedge_5fto_9529',['has_inverting_edge_to',['../classvg_1_1VG.html#a63088ee0039a8e1f5cf6b5a3b23f745a',1,'vg::VG']]],
- ['has_5finverting_5fedges_9530',['has_inverting_edges',['../classvg_1_1VG.html#a8d1dbb49df52e016746829776ca0f952',1,'vg::VG']]],
- ['has_5fmapping_9531',['has_mapping',['../classvg_1_1Paths.html#a32ecf6382d9fa9c9826cb59f8e79349e',1,'vg::Paths']]],
- ['has_5fnext_9532',['has_next',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a376e3ac5d3d820bd4b5ac55f1ad0d69b',1,'vg::BandedGlobalAligner::AltTracebackStack::has_next()'],['../classvg_1_1subpath__t.html#acb3834a6661d55a407a58cff5cd539c3',1,'vg::subpath_t::has_next()']]],
- ['has_5fnext_5fstep_9533',['has_next_step',['../classvg_1_1MemoizingGraph.html#a3c6e172a85dd0c03a290bf4b5b04792e',1,'vg::MemoizingGraph::has_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a56d9a8eb9dfbbac174ed677e4f22f14d',1,'vg::PathSubgraphOverlay::has_next_step()'],['../classvg_1_1VG.html#add23d09d2925d505f793979f7fe35921',1,'vg::VG::has_next_step()'],['../classxg_1_1XG.html#ad193420b3ab85a6d2b47f305779d6b5c',1,'xg::XG::has_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a81bf54cb4d07a0d47c84862ecebc349d',1,'handlegraph::PathHandleGraph::has_next_step()']]],
- ['has_5fnode_9534',['has_node',['../classvg_1_1DagifiedGraph.html#ad6c8a0d0a6c21fee9c10065927d4ba97',1,'vg::DagifiedGraph::has_node()'],['../classvg_1_1DozeuPinningOverlay.html#a696d9ff9c1731e98d7235a637d794174',1,'vg::DozeuPinningOverlay::has_node()'],['../classvg_1_1ExtraNodeGraph.html#a89299bba0acddf6e2bb2a8d6cb561b86',1,'vg::ExtraNodeGraph::has_node()'],['../classvg_1_1SnarlGraph.html#a43e8f719e0d3b9814e3328d14c28c85e',1,'vg::SnarlGraph::has_node()'],['../classvg_1_1IdentityOverlay.html#a56aabb0a049d7bbf9079733d7824e0db',1,'vg::IdentityOverlay::has_node()'],['../classvg_1_1IncrementalSubgraph.html#a29fe9b69774ab975e3b6fe15900d1c9e',1,'vg::IncrementalSubgraph::has_node()'],['../classvg_1_1IndexedVG.html#a184b4de54cd807fc818091c56bac41a8',1,'vg::IndexedVG::has_node()'],['../classvg_1_1MemoizingGraph.html#a5e5fea73aaa5c9b403b7e63318e15702',1,'vg::MemoizingGraph::has_node()'],['../classvg_1_1NullMaskingGraph.html#a550edf96fd717710f5051804d0d1bafe',1,'vg::NullMaskingGraph::has_node()'],['../classvg_1_1PathSubgraph.html#ad13f4f28e024ac0d43991cb9d162420f',1,'vg::PathSubgraph::has_node()'],['../classvg_1_1ReverseGraph.html#a98c0e584e6cb8246c9b2deb65d92e370',1,'vg::ReverseGraph::has_node()'],['../classvg_1_1NetGraph.html#a99ddd8990ab25cd314618321a5837ff9',1,'vg::NetGraph::has_node()'],['../classvg_1_1SourceSinkOverlay.html#ad2e4740b5a84271e053840e6b60fc53c',1,'vg::SourceSinkOverlay::has_node()'],['../classvg_1_1JoinedSpliceGraph.html#af167d082a5c148792ae9a533eac068f0',1,'vg::JoinedSpliceGraph::has_node()'],['../classvg_1_1StrandSplitGraph.html#aad17d3113bdc3f8ec03327a16ccfadd9',1,'vg::StrandSplitGraph::has_node()'],['../classvg_1_1SubHandleGraph.html#a66e144a38ed8437cbf71a186a6e8afa0',1,'vg::SubHandleGraph::has_node()'],['../classvg_1_1SubgraphOverlay.html#aaa8aca387ac5ba4f962d03da956979a2',1,'vg::SubgraphOverlay::has_node()'],['../classvg_1_1SubpathOverlay.html#a7c9a83697a1f3041e3dfbcb10f3a831b',1,'vg::SubpathOverlay::has_node()'],['../classvg_1_1TreeSubgraph.html#a84c11ffd899e018587d6ccb25dd1211b',1,'vg::TreeSubgraph::has_node()'],['../classvg_1_1VG.html#ac9339913ecff654569a9c81ae091ebfe',1,'vg::VG::has_node(nid_t id) const'],['../classvg_1_1VG.html#a049bd863e2ac7e93aec79404d56b4a34',1,'vg::VG::has_node(const Node *node) const'],['../classvg_1_1VG.html#ab000649761c7201555284390dd8a4fa0',1,'vg::VG::has_node(const Node &node) const'],['../classxg_1_1XG.html#a60dd1cf3ec755863aabc99e6948011e0',1,'xg::XG::has_node()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a29475639dafe548f44b4c0e995005083',1,'handlegraph::algorithms::SubHandleGraph::has_node()'],['../classhandlegraph_1_1HandleGraph.html#a6e58a79001cd7d839ac1f1adaff34dfb',1,'handlegraph::HandleGraph::has_node()']]],
- ['has_5fnode_5fmapping_9535',['has_node_mapping',['../classvg_1_1Paths.html#a4f744ed09e266781a366dd11a73993b8',1,'vg::Paths::has_node_mapping(id_t id) const'],['../classvg_1_1Paths.html#a48f74571d94bdd9845ff761d51701034',1,'vg::Paths::has_node_mapping(Node *n) const']]],
- ['has_5fnovel_5fexon_5fboundaries_9536',['has_novel_exon_boundaries',['../classvg_1_1Transcriptome.html#aaf34b6da5110fa44f787994be4ea2791',1,'vg::Transcriptome']]],
- ['has_5foverlapping_5fexons_9537',['has_overlapping_exons',['../classvg_1_1Transcriptome.html#a405f6a2b87ab7d919d0cb8780b1362a5',1,'vg::Transcriptome']]],
- ['has_5foverlay_5fnode_5ffor_9538',['has_overlay_node_for',['../classvg_1_1StrandSplitGraph.html#a66d77e125b056b19273bb037fef6012c',1,'vg::StrandSplitGraph']]],
- ['has_5fpath_9539',['has_path',['../classvg_1_1MemoizingGraph.html#a62559a9038db86f33b149616dd6c5d27',1,'vg::MemoizingGraph::has_path()'],['../classvg_1_1subpath__t.html#a55a56773ae505e410262b8954d34fc3c',1,'vg::subpath_t::has_path()'],['../classvg_1_1Paths.html#a38cd0087925c24ea1bf8a22755c30cbf',1,'vg::Paths::has_path()'],['../classvg_1_1PathSubgraphOverlay.html#a284e49aa618e321cc8402f4b98c9b41b',1,'vg::PathSubgraphOverlay::has_path()'],['../classvg_1_1VG.html#a0328316df2438f0006349c71206810e6',1,'vg::VG::has_path()'],['../classxg_1_1XG.html#a243d2c25b54008f0f79c480b5ff9429c',1,'xg::XG::has_path()'],['../classhandlegraph_1_1PathHandleGraph.html#ab7de11c1e994bc104378c4b798013430',1,'handlegraph::PathHandleGraph::has_path()']]],
- ['has_5fprevious_5fstep_9540',['has_previous_step',['../classvg_1_1MemoizingGraph.html#aed383459047e290a94817d010361a24f',1,'vg::MemoizingGraph::has_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#aa21af9591c2d1e457c32aaa703cda785',1,'vg::PathSubgraphOverlay::has_previous_step()'],['../classvg_1_1VG.html#ac5f9ec61fe7a32e3756e4b7fc77939ba',1,'vg::VG::has_previous_step()'],['../classxg_1_1XG.html#af833a0ffe45757002869b5802c8d3747',1,'xg::XG::has_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a93a1ee451e750cb82f1711fd6c3db8cc',1,'handlegraph::PathHandleGraph::has_previous_step()']]],
- ['has_5fqualities_9541',['has_qualities',['../classvg_1_1Packer.html#ae00e614a5cb879210690e3b94e2dcc6e',1,'vg::Packer']]],
- ['has_5frepeat_9542',['has_repeat',['../classvg_1_1ReadFilter.html#a9aecb91c19bb44bb9be32c4f30c44538',1,'vg::ReadFilter']]],
- ['has_5fstart_9543',['has_start',['../classvg_1_1multipath__alignment__t.html#af56553f4ec379201916081cba150781b',1,'vg::multipath_alignment_t::has_start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#ac1b3268f8305395fc8e35530d900b230',1,'vg::Haplotypes::Subchain::has_start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#ab13d2b1ae3f525cea9be92630f32c3e9',1,'vg::HaplotypePartitioner::Subchain::has_start()']]],
- ['has_5fsupports_9544',['has_supports',['../structvg_1_1AugmentedGraph.html#a5519dec3147cb54da3e32cdb2f6c1428',1,'vg::AugmentedGraph::has_supports()'],['../structvg_1_1SupportAugmentedGraph.html#a32dc8f5559a750e393b8cedfb42cbf83',1,'vg::SupportAugmentedGraph::has_supports()']]],
- ['has_5ftabix_9545',['has_tabix',['../classvg_1_1VcfBuffer.html#ae0a4db2dd14b0a00545ef726879a0951',1,'vg::VcfBuffer::has_tabix()'],['../classvg_1_1WindowedVcfBuffer.html#a84bbabd4f6b5b948ce6d2d0aa5fa7ff4',1,'vg::WindowedVcfBuffer::has_tabix()']]],
- ['has_5ftranslation_9546',['has_translation',['../classvg_1_1Translator.html#ae6ccab957bfb3f7eba512f7021a4052b',1,'vg::Translator']]],
- ['hash_9547',['hash',['../classvg_1_1VG.html#a2b75ca400f858be77b0716ab7c68dfcb',1,'vg::VG']]],
- ['hash_5falignment_9548',['hash_alignment',['../namespacevg.html#a94f469aebb2be5b0028c337108d253fb',1,'vg']]],
- ['hash_5fto_5frgb_9549',['hash_to_rgb',['../namespacevg.html#a8bc1d89bbcee041956e59895ed605ca3',1,'vg']]],
- ['hashed_9550',['hashed',['../classvg_1_1Colors.html#a9c14e90e97e7fd193b25461a40ff6235',1,'vg::Colors::hashed()'],['../classvg_1_1Pictographs.html#a42c157819fffed93d2bfa730c5517e56',1,'vg::Pictographs::hashed()']]],
- ['hashed_5fchar_9551',['hashed_char',['../classvg_1_1Pictographs.html#a91309563adbfaaf7eab19a51623d66c2',1,'vg::Pictographs']]],
- ['have_5finput_5ffile_9552',['have_input_file',['../namespacevg.html#a7c950dca7cd25a5ce9846be2a6b93e13',1,'vg']]],
- ['hdp_5fgbwt_5fgraph_5faccessor_9553',['hDP_gbwt_graph_accessor',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a63ed5e1c48904968ae61ff21f411c0db',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type old_node, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a7a8d1f9ad8428fe0ff0b6071dc6f47ef',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)']]],
- ['head_5fnodes_9554',['head_nodes',['../classvg_1_1VG.html#a7eecc0bd555c31d1c541c3ce44b421c3',1,'vg::VG::head_nodes(vector< Node * > &nodes)'],['../classvg_1_1VG.html#a3a44c415fb5882c184e2f35bb3999700',1,'vg::VG::head_nodes(void)'],['../namespacehandlegraph_1_1algorithms.html#a3d26728fa655f872ccac738a2bcb6166',1,'handlegraph::algorithms::head_nodes()']]],
- ['help_5fadd_9555',['help_add',['../add__main_8cpp.html#ad49fa30ce6a9b619ad5df1cfa8621d9a',1,'add_main.cpp']]],
- ['help_5falign_9556',['help_align',['../align__main_8cpp.html#ac749b2692aaca8eeaa6b48d7b44e167d',1,'align_main.cpp']]],
- ['help_5fannotate_9557',['help_annotate',['../annotate__main_8cpp.html#a6957d47b527eacd587f20f9d11ccd333',1,'annotate_main.cpp']]],
- ['help_5faugment_9558',['help_augment',['../augment__main_8cpp.html#a7cf03aa52fd6e8d75e480d4d0632b71c',1,'augment_main.cpp']]],
- ['help_5fautoindex_9559',['help_autoindex',['../autoindex__main_8cpp.html#a4a3c7ba0d785194a42444bdedac4db50',1,'autoindex_main.cpp']]],
- ['help_5fbenchmark_9560',['help_benchmark',['../benchmark__main_8cpp.html#a1e3da44e3dcc6fea154d15a1986ade1b',1,'benchmark_main.cpp']]],
- ['help_5fcall_9561',['help_call',['../call__main_8cpp.html#ab92ccd67b3c20b7be7c46281c4cabfb3',1,'call_main.cpp']]],
- ['help_5fchain_9562',['help_chain',['../chain__main_8cpp.html#a88894e89fc3e50d33042f88c993a0e0c',1,'chain_main.cpp']]],
- ['help_5fchunk_9563',['help_chunk',['../chunk__main_8cpp.html#a502600dcc3e4e15a338642fe554fbf8d',1,'chunk_main.cpp']]],
- ['help_5fcircularize_9564',['help_circularize',['../circularize__main_8cpp.html#a0613e20e02d0fbb56d7270a7b268ffb3',1,'circularize_main.cpp']]],
- ['help_5fclip_9565',['help_clip',['../clip__main_8cpp.html#a451b2ddc17b7d65f1bac0fcd7cac810c',1,'clip_main.cpp']]],
- ['help_5fcluster_9566',['help_cluster',['../cluster__main_8cpp.html#a4099bc0f1cb9fecb87c903e578ff2a17',1,'cluster_main.cpp']]],
- ['help_5fcombine_9567',['help_combine',['../combine__main_8cpp.html#a14fa4eb501b75ae37a166fb633cda8dd',1,'combine_main.cpp']]],
- ['help_5fconcat_9568',['help_concat',['../concat__main_8cpp.html#a795aaef3bab6d86036c1362ba5b76ac0',1,'concat_main.cpp']]],
- ['help_5fconstruct_9569',['help_construct',['../construct__main_8cpp.html#a0c8b1d02948ee021399fef93344a9def',1,'construct_main.cpp']]],
- ['help_5fconvert_9570',['help_convert',['../convert__main_8cpp.html#a61c2208fb6645c58f794c57e1851a194',1,'convert_main.cpp']]],
- ['help_5fdeconstruct_9571',['help_deconstruct',['../deconstruct__main_8cpp.html#a32554f3b30e86c414a7c6940beb660e3',1,'deconstruct_main.cpp']]],
- ['help_5fdepth_9572',['help_depth',['../depth__main_8cpp.html#aa182528e1e692b2b6ea79e3ed6a36661',1,'depth_main.cpp']]],
- ['help_5fdotplot_9573',['help_dotplot',['../dotplot__main_8cpp.html#a628ebfce6d823f9dca7722f0721a5a3b',1,'dotplot_main.cpp']]],
- ['help_5fexplode_9574',['help_explode',['../explode__main_8cpp.html#a5ed55d49ef3d15ac39e1e275e6792907',1,'explode_main.cpp']]],
- ['help_5ffilter_9575',['help_filter',['../filter__main_8cpp.html#a9072d5dfad52adc43da1d2a700be313b',1,'filter_main.cpp']]],
- ['help_5ffind_9576',['help_find',['../find__main_8cpp.html#a61f46a85b426fbf3e48cdffc07d107f8',1,'find_main.cpp']]],
- ['help_5fgamcompare_9577',['help_gamcompare',['../gamcompare__main_8cpp.html#a33c9728d9a784c1ae54baae635b6e56d',1,'gamcompare_main.cpp']]],
- ['help_5fgampcompare_9578',['help_gampcompare',['../gampcompare__main_8cpp.html#a4eb570f78fda3fc79752c40fccb794d9',1,'gampcompare_main.cpp']]],
- ['help_5fgamsort_9579',['help_gamsort',['../gamsort__main_8cpp.html#ab37435867b2e79dc2fd17af9f6b3667b',1,'gamsort_main.cpp']]],
- ['help_5fgbwt_9580',['help_gbwt',['../gbwt__main_8cpp.html#a73013ddacba7ab20beed9e8022b2b57b',1,'gbwt_main.cpp']]],
- ['help_5fgenotype_9581',['help_genotype',['../genotype__main_8cpp.html#a7d9960cb294ff9984b99ed7816f06323',1,'genotype_main.cpp']]],
- ['help_5fgiraffe_9582',['help_giraffe',['../giraffe__main_8cpp.html#aa6d5c2140d259252f3cad8b7bf6b4b1a',1,'giraffe_main.cpp']]],
- ['help_5fhaplotypes_9583',['help_haplotypes',['../haplotypes__main_8cpp.html#a06899318e624a0766060720e2403f380',1,'haplotypes_main.cpp']]],
- ['help_5fhelp_9584',['help_help',['../help__main_8cpp.html#abbe09b0c0e2e4abc339997cd4b8c1bf7',1,'help_main.cpp']]],
- ['help_5fids_9585',['help_ids',['../ids__main_8cpp.html#ae3e40ed9a49e6e00fe241abf728c11ea',1,'ids_main.cpp']]],
- ['help_5findex_9586',['help_index',['../index__main_8cpp.html#a24afe767ac485cebbc2f2b47ef515274',1,'index_main.cpp']]],
- ['help_5finject_9587',['help_inject',['../inject__main_8cpp.html#a10c867b9f97d3e0d6a1396bad277880a',1,'inject_main.cpp']]],
- ['help_5fjoin_9588',['help_join',['../join__main_8cpp.html#af6a676c62773f02853c583961fe3a59d',1,'join_main.cpp']]],
- ['help_5fkmers_9589',['help_kmers',['../kmers__main_8cpp.html#ab5e392cd094049b8b9a863d2ce1acdb4',1,'kmers_main.cpp']]],
- ['help_5fmap_9590',['help_map',['../map__main_8cpp.html#afec224c846352e16703d590d52bad501',1,'map_main.cpp']]],
- ['help_5fmask_9591',['help_mask',['../mask__main_8cpp.html#a0502efe715f6be3e9b8abd1514c3faae',1,'mask_main.cpp']]],
- ['help_5fmcmc_9592',['help_mcmc',['../mcmc__main_8cpp.html#a2d01e9b5436c54c18299e579f8f850e9',1,'mcmc_main.cpp']]],
- ['help_5fminimizer_9593',['help_minimizer',['../minimizer__main_8cpp.html#a45dc67f0fe9ce978202fda58585b6b52',1,'minimizer_main.cpp']]],
- ['help_5fmod_9594',['help_mod',['../mod__main_8cpp.html#a7ff398c2ef9439dc08f0d318693c9b0b',1,'mod_main.cpp']]],
- ['help_5fmpmap_9595',['help_mpmap',['../mpmap__main_8cpp.html#ad68f4a7fc19b061a16fe9d7fb2810133',1,'mpmap_main.cpp']]],
- ['help_5fmsga_9596',['help_msga',['../msga__main_8cpp.html#a75ed90adae627c02a0d46998bb73ee99',1,'msga_main.cpp']]],
- ['help_5fpack_9597',['help_pack',['../pack__main_8cpp.html#aadaeba7e32c73f9093b262830bd2541e',1,'pack_main.cpp']]],
- ['help_5fpaths_9598',['help_paths',['../paths__main_8cpp.html#a290bac84a159c7e6ab2a9abca73f7000',1,'paths_main.cpp']]],
- ['help_5fprune_9599',['help_prune',['../prune__main_8cpp.html#a4da6cb650889066af17a6223ba1bfa81',1,'prune_main.cpp']]],
- ['help_5frna_9600',['help_rna',['../rna__main_8cpp.html#a703e9ebf973bfcd363ce619ccaff160b',1,'rna_main.cpp']]],
- ['help_5fsift_9601',['help_sift',['../sift__main_8cpp.html#ad82567fc886ab61b4c209226f45b0d8f',1,'sift_main.cpp']]],
- ['help_5fsim_9602',['help_sim',['../sim__main_8cpp.html#ab2368d74cf2fb693982eeb4676e6b534',1,'sim_main.cpp']]],
- ['help_5fsimplify_9603',['help_simplify',['../simplify__main_8cpp.html#a6fbde48f0c083d661e2e8e8b2b0a17e7',1,'simplify_main.cpp']]],
- ['help_5fsnarl_9604',['help_snarl',['../snarls__main_8cpp.html#a4f8c80c7a187ae51a198f3ec42d85f26',1,'snarls_main.cpp']]],
- ['help_5fsort_9605',['help_sort',['../sort__main_8cpp.html#aa2e0a3c74cb1ee9a7278b5399da39a1b',1,'sort_main.cpp']]],
- ['help_5fstats_9606',['help_stats',['../stats__main_8cpp.html#a8a996696d6e2c9ecca6dffd6fbc8bf26',1,'stats_main.cpp']]],
- ['help_5fsurject_9607',['help_surject',['../surject__main_8cpp.html#a9d8217a048300f2a321bfe032e31c769',1,'surject_main.cpp']]],
- ['help_5ftrace_9608',['help_trace',['../trace__main_8cpp.html#a1e6c8dca8a2b0b1ba628313be3a56fe8',1,'trace_main.cpp']]],
- ['help_5ftranslate_9609',['help_translate',['../translate__main_8cpp.html#ad94d99f9e08a28731eb6f4d42d64b553',1,'translate_main.cpp']]],
- ['help_5fvalidate_9610',['help_validate',['../validate__main_8cpp.html#ab89c45aa2e33410d5c76183fd5148cff',1,'validate_main.cpp']]],
- ['help_5fvectorize_9611',['help_vectorize',['../vectorize__main_8cpp.html#a66888bb2b18d743f2ada4c879d2999da',1,'vectorize_main.cpp']]],
- ['help_5fversion_9612',['help_version',['../version__main_8cpp.html#a5c4af51f2cb117ca875b8b1c6be39639',1,'version_main.cpp']]],
- ['help_5fview_9613',['help_view',['../view__main_8cpp.html#a764409d4876e90847c2d8635194f0a3e',1,'view_main.cpp']]],
- ['help_5fviz_9614',['help_viz',['../viz__main_8cpp.html#a81fc7d050b03830c81c731e0ceb98bd1',1,'viz_main.cpp']]],
- ['help_5fzipcode_9615',['help_zipcode',['../zipcode__main_8cpp.html#abc97cba8ea07b911b9c5da9defcc81d8',1,'zipcode_main.cpp']]],
- ['hex2bin_9616',['hex2bin',['../bin2ascii_8h.html#a63db266c863090d6b7c179df1ea160f1',1,'bin2ascii.h']]],
- ['hfile_5finit_9617',['hfile_init',['../hfile__internal_8hpp.html#abf020a8f3a695c1848cb3671855383b8',1,'hfile_internal.hpp']]],
- ['hfile_5fwrap_9618',['hfile_wrap',['../namespacevg_1_1io.html#a62b10a042ea08faa5da35ff07183d49b',1,'vg::io::hfile_wrap(std::istream &input)'],['../namespacevg_1_1io.html#a4fa9b57a79b55cf4eeb10806be649ede',1,'vg::io::hfile_wrap(std::ostream &output)']]],
- ['hitedge_9619',['HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html#adfc12ed7c93d550e05882555d0004235',1,'vg::MEMClusterer::HitEdge::HitEdge(size_t to_idx, int32_t weight, int64_t distance)'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a16766cbf34e0ec89d8bbdcd7f9d42988',1,'vg::MEMClusterer::HitEdge::HitEdge()=default']]],
- ['hitgraph_9620',['HitGraph',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a9895e95cdaa1b95876c79c07d29fe852',1,'vg::MEMClusterer::HitGraph']]],
- ['hitnode_9621',['HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html#a3156b62ac2208fdac8d0b12475011472',1,'vg::MEMClusterer::HitNode::HitNode(const MaximalExactMatch &mem, pos_t start_pos, int32_t score)'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aaeb6e6e2bb1c2ce2cda76adce19a40d6',1,'vg::MEMClusterer::HitNode::HitNode()=default']]],
- ['hts_5ffile_5fheader_9622',['hts_file_header',['../namespacevg.html#a0676eec9e08d9589fe286cabdd16ffb3',1,'vg']]],
- ['hts_5ffor_5feach_9623',['hts_for_each',['../namespacevg.html#a1f1e53242cb6ccf3d567c73c0895c4ca',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#ad7abb14966c1c20cff85c5744a47de0e',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda)']]],
- ['hts_5ffor_5feach_5fparallel_9624',['hts_for_each_parallel',['../namespacevg.html#a7c0d37c85747f2bce6ba3356a813524a',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#a59c6c494c2e7663fb14e40c978b4f9e5',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda)']]],
- ['hts_5fstring_5fheader_9625',['hts_string_header',['../namespacevg.html#abc01af3a6e386a06a2971c17a0e6d1b1',1,'vg::hts_string_header(string &header, const map< string, int64_t > &path_length, const map< string, string > &rg_sample)'],['../namespacevg.html#aeb8cd62602cb90541b2270a79aed7595',1,'vg::hts_string_header(string &header, const vector< pair< string, int64_t >> &path_order_and_length, const map< string, string > &rg_sample)']]],
- ['htsalignmentemitter_9626',['HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html#acc9b5714c55e4b644216066eda386dbd',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSAlignmentEmitter.html#a0c76946bf064ecac88e21a2467ea2410',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a780156f43d54cf16906948ad8286c20f',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(HTSAlignmentEmitter &&other)=delete']]],
- ['htswriter_9627',['HTSWriter',['../classvg_1_1HTSWriter.html#a8257b1e35ac5abf92b43b8a823c66aa5',1,'vg::HTSWriter::HTSWriter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSWriter.html#ae2fc6b2a60e3bc9441956faf87ff6a07',1,'vg::HTSWriter::HTSWriter(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a0a23221d8449a4b4e0b1278995ad0207',1,'vg::HTSWriter::HTSWriter(HTSWriter &&other)=delete']]]
+ ['halt_9493',['halt',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aeabcba66f2745dd0e6a4793e954aa23d',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['handle_9494',['handle',['../classxg_1_1XGPath.html#a93ab3c3284afd4d780368ab03d51ee43',1,'xg::XGPath::handle()'],['../classvg_1_1io_1_1MessageIterator.html#a4b3ba16717c1900a0638518bd33a4a59',1,'vg::io::MessageIterator::handle()'],['../classvg_1_1io_1_1ProtobufEmitter.html#afb457287f96e5ed57d53f91fd5247ec7',1,'vg::io::ProtobufEmitter::handle()']]],
+ ['handle_5fat_5forder_9495',['handle_at_order',['../classvg_1_1IncrementalSubgraph.html#a8c2059a01cfda921bd8c5f91bd3763c7',1,'vg::IncrementalSubgraph']]],
+ ['handle_5fat_5fpath_5fposition_9496',['handle_at_path_position',['../classxg_1_1XG.html#a63e8b7be4676a9fb4c77e16f0c76b5a8',1,'xg::XG']]],
+ ['handle_5fat_5fposition_9497',['handle_at_position',['../classxg_1_1XGPath.html#ac3dac0fefe450c561f44dadd3ac00487',1,'xg::XGPath']]],
+ ['handle_5fbuffer_9498',['handle_buffer',['../classvg_1_1VcfBuffer.html#a1d8968beb2952113ea8a724dad1e1752',1,'vg::VcfBuffer']]],
+ ['handle_5ffull_5flength_9499',['handle_full_length',['../namespacevg.html#a536dfd4326c17ad4d072d2c9021e4b7c',1,'vg']]],
+ ['handle_5fgraph_5fto_5fcactus_9500',['handle_graph_to_cactus',['../namespacevg.html#a3d4e7ee3d7394e2318e874dc98dd8320',1,'vg']]],
+ ['handle_5frank_9501',['handle_rank',['../classxg_1_1XG.html#a2e8f51499dd0ba67d52100bf380b0936',1,'xg::XG']]],
+ ['handle_5fstart_9502',['handle_start',['../classxg_1_1XGPath.html#a5a62bf71a4a85c9617402504a2be01a4',1,'xg::XGPath']]],
+ ['handle_5fto_5fgbwt_9503',['handle_to_gbwt',['../namespacevg.html#a1fa5cc80bff735a8803aa9f564c29994',1,'vg']]],
+ ['handle_5fto_5frank_9504',['handle_to_rank',['../classhandlegraph_1_1RankedHandleGraph.html#a6a21763bef01676efd4dd10767681bfc',1,'handlegraph::RankedHandleGraph']]],
+ ['handlegraphnodeset_9505',['HandleGraphNodeSet',['../classvg_1_1HandleGraphNodeSet.html#af257f6c350350577cc2bef059a133837',1,'vg::HandleGraphNodeSet']]],
+ ['handlegraphsnarlfinder_9506',['HandleGraphSnarlFinder',['../classvg_1_1HandleGraphSnarlFinder.html#a8fb53057585d8e64313485c02a15cec5',1,'vg::HandleGraphSnarlFinder']]],
+ ['haplo_5fdp_9507',['haplo_DP',['../structhaplo_1_1haplo__DP.html#a35035e7b00f8d5503ae3582afebbac50',1,'haplo::haplo_DP']]],
+ ['haplo_5fdp_5fcolumn_9508',['haplo_DP_column',['../structhaplo_1_1haplo__DP__column.html#a15c9d8c26ba9eba47510eaac32b49eb8',1,'haplo::haplo_DP_column']]],
+ ['haplo_5fdp_5frectangle_9509',['haplo_DP_rectangle',['../structhaplo_1_1haplo__DP__rectangle.html#a54e3de46211170326d89ee11f9d61fab',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle()'],['../structhaplo_1_1haplo__DP__rectangle.html#a5e2a880c7d8974ac08021256994a51e2',1,'haplo::haplo_DP_rectangle::haplo_DP_rectangle(bool inclusive_interval)']]],
+ ['haplotype_9510',['Haplotype',['../classvg_1_1PhasedGenome_1_1Haplotype.html#aba98c5b032e48cf1a83b21cae31966a0',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversal node_traversal)'],['../classvg_1_1PhasedGenome_1_1Haplotype.html#a61d6bf4127d5e607eccca43b730b8d74',1,'vg::PhasedGenome::Haplotype::Haplotype(NodeTraversalIterator first, NodeTraversalIterator last)']]],
+ ['haplotype_5fconsistent_5falignments_9511',['haplotype_consistent_alignments',['../namespacevg.html#ab5a2adbf9370dc37be337d927341f9db',1,'vg']]],
+ ['haplotype_5fto_5fstring_9512',['haplotype_to_string',['../classvg_1_1VariantAdder.html#a86108ed47c5e85a23d31fe380ae2670d',1,'vg::VariantAdder']]],
+ ['haplotype_5ftranscript_5fpaths_9513',['haplotype_transcript_paths',['../classvg_1_1Transcriptome.html#a8103dfe99f0bb36e806cab44d2e21d54',1,'vg::Transcriptome']]],
+ ['haplotypeindexer_9514',['HaplotypeIndexer',['../classvg_1_1HaplotypeIndexer.html#ae0b8cbfe64f32152ceefa57daf9ece72',1,'vg::HaplotypeIndexer']]],
+ ['haplotypenode_9515',['HaplotypeNode',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a584a6b469c7f9709ea7da34f867f49aa',1,'vg::PhasedGenome::HaplotypeNode']]],
+ ['haplotypepartitioner_9516',['HaplotypePartitioner',['../classvg_1_1HaplotypePartitioner.html#a6faa6da8cc4a62f7cabc8d66e19e9ac1',1,'vg::HaplotypePartitioner']]],
+ ['haplotypesconfig_9517',['HaplotypesConfig',['../structHaplotypesConfig.html#a45bef8cdfe50758d06d6d078b5a6a13f',1,'HaplotypesConfig']]],
+ ['has_5fannotation_9518',['has_annotation',['../classvg_1_1multipath__alignment__t.html#a6b60350a3dada734b919bdf15f41bf82',1,'vg::multipath_alignment_t::has_annotation()'],['../namespacevg.html#a34f4e73b242fa5b34d30ecc4da496835',1,'vg::has_annotation()']]],
+ ['has_5fargument_9519',['has_argument',['../classvg_1_1OptionInterface.html#a29383428b6a6e40109fb4949286f07f7',1,'vg::OptionInterface::has_argument()'],['../classvg_1_1OptionValueParser.html#af8d6268a6cec527dd0e117aef58cbd63',1,'vg::OptionValueParser::has_argument()'],['../classvg_1_1OptionValueParser_3_01vector_3_01Item_01_4_01_4.html#a104c6803a28a2528b33759ac8ad69175',1,'vg::OptionValueParser< vector< Item > >::has_argument()'],['../classvg_1_1BaseOption.html#a3aa53d25627ae95383edce8f6e001caa',1,'vg::BaseOption::has_argument()'],['../classvg_1_1OptionValueParser.html#aabf09c8e0e807fb19debad284331387d',1,'vg::OptionValueParser::has_argument()']]],
+ ['has_5fbase_5fgraph_9520',['has_base_graph',['../structvg_1_1AugmentedGraph.html#ae1b8b8c8246ccfe1f2d56250a3361177',1,'vg::AugmentedGraph']]],
+ ['has_5fconnection_9521',['has_connection',['../classvg_1_1subpath__t.html#a972d307d386a636cc2dc1fc170f56df3',1,'vg::subpath_t']]],
+ ['has_5fcurrent_9522',['has_current',['../classvg_1_1io_1_1MessageIterator.html#abcbec4e2b7376ae5ca8bbd4e05d9103a',1,'vg::io::MessageIterator::has_current()'],['../classvg_1_1io_1_1ProtobufIterator.html#a59294f819b65352528da9224ea39d973',1,'vg::io::ProtobufIterator::has_current()']]],
+ ['has_5fedge_9523',['has_edge',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a6fd765d7a5623bef825effc7fdf46b87',1,'haplo::hDP_gbwt_graph_accessor::has_edge()'],['../classvg_1_1VG.html#a501886a0c593ac3231cfcc6989911ced',1,'vg::VG::has_edge(const handle_t &left, const handle_t &right) const'],['../classvg_1_1VG.html#a447d717e83131c526d26e6d2f0a091a6',1,'vg::VG::has_edge(const NodeSide &side1, const NodeSide &side2) const'],['../classvg_1_1VG.html#a1c7ff3b6f9cfca2c21e1a8d1c848fc01',1,'vg::VG::has_edge(const pair< NodeSide, NodeSide > &sides) const'],['../classvg_1_1VG.html#aa69701fcb4bf9e8b593681ba1d818571',1,'vg::VG::has_edge(Edge *edge) const'],['../classvg_1_1VG.html#ab2c85fad61f57260c913bc565a549832',1,'vg::VG::has_edge(const Edge &edge) const'],['../classhandlegraph_1_1HandleGraph.html#a069448fbe58665b9ff531ad0b8c5af57',1,'handlegraph::HandleGraph::has_edge(const handle_t &left, const handle_t &right) const'],['../classhandlegraph_1_1HandleGraph.html#a6171cdd6036c73623c96656f8b44fe9d',1,'handlegraph::HandleGraph::has_edge(const edge_t &edge) const']]],
+ ['has_5fend_9524',['has_end',['../structvg_1_1Haplotypes_1_1Subchain.html#ae9fbddda11e52d6e9b98156a50224a73',1,'vg::Haplotypes::Subchain::has_end()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a0aa037691bcf20d78faad42eea3c8f57',1,'vg::HaplotypePartitioner::Subchain::has_end()']]],
+ ['has_5fexcluded_5frefpos_9525',['has_excluded_refpos',['../classvg_1_1ReadFilter.html#ac772c0651477027191108e64ab7c53cb',1,'vg::ReadFilter::has_excluded_refpos(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab609cc20f1e49dc1001e71fe82c5ead4',1,'vg::ReadFilter::has_excluded_refpos(const MultipathAlignment &read) const'],['../classvg_1_1ReadFilter.html#aca79c3eda85a8f4fafcd25a243b7efd4',1,'vg::ReadFilter::has_excluded_refpos(const Alignment &aln) const']]],
+ ['has_5fexcuded_5ffeature_9526',['has_excuded_feature',['../classvg_1_1ReadFilter.html#a2d30291c0c609d58670f40e2eb9661e4',1,'vg::ReadFilter']]],
+ ['has_5ffixed_5ffragment_5flength_5fdistr_9527',['has_fixed_fragment_length_distr',['../classvg_1_1PairedEndMapper.html#ad0a2d836cfcaddae8569bf1a024aa56b',1,'vg::PairedEndMapper']]],
+ ['has_5fincorrect_5forder_5fexons_9528',['has_incorrect_order_exons',['../classvg_1_1Transcriptome.html#a4cba921dae9fe3eae2361b0b7391b7b3',1,'vg::Transcriptome']]],
+ ['has_5fincremental_5fsearch_9529',['has_incremental_search',['../classhaplo_1_1ScoreProvider.html#a1455c3ccb6a9d03e5d79636e79be301a',1,'haplo::ScoreProvider::has_incremental_search()'],['../classhaplo_1_1GBWTScoreProvider.html#abe35e78c1d11af952b27dc8c36c1909f',1,'haplo::GBWTScoreProvider::has_incremental_search()']]],
+ ['has_5finversion_9530',['has_inversion',['../namespacevg.html#a1b545f6474c6e528176031149a8bc570',1,'vg']]],
+ ['has_5finverting_5fedge_9531',['has_inverting_edge',['../classvg_1_1VG.html#a49fb4de3494407b800c3efda254851cf',1,'vg::VG']]],
+ ['has_5finverting_5fedge_5ffrom_9532',['has_inverting_edge_from',['../classvg_1_1VG.html#a7b7bbf066c6608211e7527ba50b23e48',1,'vg::VG']]],
+ ['has_5finverting_5fedge_5fto_9533',['has_inverting_edge_to',['../classvg_1_1VG.html#a63088ee0039a8e1f5cf6b5a3b23f745a',1,'vg::VG']]],
+ ['has_5finverting_5fedges_9534',['has_inverting_edges',['../classvg_1_1VG.html#a8d1dbb49df52e016746829776ca0f952',1,'vg::VG']]],
+ ['has_5fmapping_9535',['has_mapping',['../classvg_1_1Paths.html#a32ecf6382d9fa9c9826cb59f8e79349e',1,'vg::Paths']]],
+ ['has_5fnext_9536',['has_next',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a376e3ac5d3d820bd4b5ac55f1ad0d69b',1,'vg::BandedGlobalAligner::AltTracebackStack::has_next()'],['../classvg_1_1subpath__t.html#acb3834a6661d55a407a58cff5cd539c3',1,'vg::subpath_t::has_next()']]],
+ ['has_5fnext_5fstep_9537',['has_next_step',['../classvg_1_1MemoizingGraph.html#a3c6e172a85dd0c03a290bf4b5b04792e',1,'vg::MemoizingGraph::has_next_step()'],['../classvg_1_1PathSubgraphOverlay.html#a56d9a8eb9dfbbac174ed677e4f22f14d',1,'vg::PathSubgraphOverlay::has_next_step()'],['../classvg_1_1VG.html#add23d09d2925d505f793979f7fe35921',1,'vg::VG::has_next_step()'],['../classxg_1_1XG.html#ad193420b3ab85a6d2b47f305779d6b5c',1,'xg::XG::has_next_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a81bf54cb4d07a0d47c84862ecebc349d',1,'handlegraph::PathHandleGraph::has_next_step()']]],
+ ['has_5fnode_9538',['has_node',['../classvg_1_1DagifiedGraph.html#ad6c8a0d0a6c21fee9c10065927d4ba97',1,'vg::DagifiedGraph::has_node()'],['../classvg_1_1DozeuPinningOverlay.html#a696d9ff9c1731e98d7235a637d794174',1,'vg::DozeuPinningOverlay::has_node()'],['../classvg_1_1ExtraNodeGraph.html#a89299bba0acddf6e2bb2a8d6cb561b86',1,'vg::ExtraNodeGraph::has_node()'],['../classvg_1_1SnarlGraph.html#a43e8f719e0d3b9814e3328d14c28c85e',1,'vg::SnarlGraph::has_node()'],['../classvg_1_1IdentityOverlay.html#a56aabb0a049d7bbf9079733d7824e0db',1,'vg::IdentityOverlay::has_node()'],['../classvg_1_1IncrementalSubgraph.html#a29fe9b69774ab975e3b6fe15900d1c9e',1,'vg::IncrementalSubgraph::has_node()'],['../classvg_1_1IndexedVG.html#a184b4de54cd807fc818091c56bac41a8',1,'vg::IndexedVG::has_node()'],['../classvg_1_1MemoizingGraph.html#a5e5fea73aaa5c9b403b7e63318e15702',1,'vg::MemoizingGraph::has_node()'],['../classvg_1_1NullMaskingGraph.html#a550edf96fd717710f5051804d0d1bafe',1,'vg::NullMaskingGraph::has_node()'],['../classvg_1_1PathSubgraph.html#ad13f4f28e024ac0d43991cb9d162420f',1,'vg::PathSubgraph::has_node()'],['../classvg_1_1ReverseGraph.html#a98c0e584e6cb8246c9b2deb65d92e370',1,'vg::ReverseGraph::has_node()'],['../classvg_1_1NetGraph.html#a99ddd8990ab25cd314618321a5837ff9',1,'vg::NetGraph::has_node()'],['../classvg_1_1SourceSinkOverlay.html#ad2e4740b5a84271e053840e6b60fc53c',1,'vg::SourceSinkOverlay::has_node()'],['../classvg_1_1JoinedSpliceGraph.html#af167d082a5c148792ae9a533eac068f0',1,'vg::JoinedSpliceGraph::has_node()'],['../classvg_1_1StrandSplitGraph.html#aad17d3113bdc3f8ec03327a16ccfadd9',1,'vg::StrandSplitGraph::has_node()'],['../classvg_1_1SubHandleGraph.html#a66e144a38ed8437cbf71a186a6e8afa0',1,'vg::SubHandleGraph::has_node()'],['../classvg_1_1SubgraphOverlay.html#aaa8aca387ac5ba4f962d03da956979a2',1,'vg::SubgraphOverlay::has_node()'],['../classvg_1_1SubpathOverlay.html#a7c9a83697a1f3041e3dfbcb10f3a831b',1,'vg::SubpathOverlay::has_node()'],['../classvg_1_1TreeSubgraph.html#a84c11ffd899e018587d6ccb25dd1211b',1,'vg::TreeSubgraph::has_node()'],['../classvg_1_1VG.html#ac9339913ecff654569a9c81ae091ebfe',1,'vg::VG::has_node(nid_t id) const'],['../classvg_1_1VG.html#a049bd863e2ac7e93aec79404d56b4a34',1,'vg::VG::has_node(const Node *node) const'],['../classvg_1_1VG.html#ab000649761c7201555284390dd8a4fa0',1,'vg::VG::has_node(const Node &node) const'],['../classxg_1_1XG.html#a60dd1cf3ec755863aabc99e6948011e0',1,'xg::XG::has_node()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a29475639dafe548f44b4c0e995005083',1,'handlegraph::algorithms::SubHandleGraph::has_node()'],['../classhandlegraph_1_1HandleGraph.html#a6e58a79001cd7d839ac1f1adaff34dfb',1,'handlegraph::HandleGraph::has_node()']]],
+ ['has_5fnode_5fmapping_9539',['has_node_mapping',['../classvg_1_1Paths.html#a4f744ed09e266781a366dd11a73993b8',1,'vg::Paths::has_node_mapping(id_t id) const'],['../classvg_1_1Paths.html#a48f74571d94bdd9845ff761d51701034',1,'vg::Paths::has_node_mapping(Node *n) const']]],
+ ['has_5fnovel_5fexon_5fboundaries_9540',['has_novel_exon_boundaries',['../classvg_1_1Transcriptome.html#aaf34b6da5110fa44f787994be4ea2791',1,'vg::Transcriptome']]],
+ ['has_5foverlapping_5fexons_9541',['has_overlapping_exons',['../classvg_1_1Transcriptome.html#a405f6a2b87ab7d919d0cb8780b1362a5',1,'vg::Transcriptome']]],
+ ['has_5foverlay_5fnode_5ffor_9542',['has_overlay_node_for',['../classvg_1_1StrandSplitGraph.html#a66d77e125b056b19273bb037fef6012c',1,'vg::StrandSplitGraph']]],
+ ['has_5fpath_9543',['has_path',['../classvg_1_1MemoizingGraph.html#a62559a9038db86f33b149616dd6c5d27',1,'vg::MemoizingGraph::has_path()'],['../classvg_1_1subpath__t.html#a55a56773ae505e410262b8954d34fc3c',1,'vg::subpath_t::has_path()'],['../classvg_1_1Paths.html#a38cd0087925c24ea1bf8a22755c30cbf',1,'vg::Paths::has_path()'],['../classvg_1_1PathSubgraphOverlay.html#a284e49aa618e321cc8402f4b98c9b41b',1,'vg::PathSubgraphOverlay::has_path()'],['../classvg_1_1VG.html#a0328316df2438f0006349c71206810e6',1,'vg::VG::has_path()'],['../classxg_1_1XG.html#a243d2c25b54008f0f79c480b5ff9429c',1,'xg::XG::has_path()'],['../classhandlegraph_1_1PathHandleGraph.html#ab7de11c1e994bc104378c4b798013430',1,'handlegraph::PathHandleGraph::has_path()']]],
+ ['has_5fprevious_5fstep_9544',['has_previous_step',['../classvg_1_1MemoizingGraph.html#aed383459047e290a94817d010361a24f',1,'vg::MemoizingGraph::has_previous_step()'],['../classvg_1_1PathSubgraphOverlay.html#aa21af9591c2d1e457c32aaa703cda785',1,'vg::PathSubgraphOverlay::has_previous_step()'],['../classvg_1_1VG.html#ac5f9ec61fe7a32e3756e4b7fc77939ba',1,'vg::VG::has_previous_step()'],['../classxg_1_1XG.html#af833a0ffe45757002869b5802c8d3747',1,'xg::XG::has_previous_step()'],['../classhandlegraph_1_1PathHandleGraph.html#a93a1ee451e750cb82f1711fd6c3db8cc',1,'handlegraph::PathHandleGraph::has_previous_step()']]],
+ ['has_5fqualities_9545',['has_qualities',['../classvg_1_1Packer.html#ae00e614a5cb879210690e3b94e2dcc6e',1,'vg::Packer']]],
+ ['has_5frepeat_9546',['has_repeat',['../classvg_1_1ReadFilter.html#a9aecb91c19bb44bb9be32c4f30c44538',1,'vg::ReadFilter']]],
+ ['has_5fstart_9547',['has_start',['../classvg_1_1multipath__alignment__t.html#af56553f4ec379201916081cba150781b',1,'vg::multipath_alignment_t::has_start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#ac1b3268f8305395fc8e35530d900b230',1,'vg::Haplotypes::Subchain::has_start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#ab13d2b1ae3f525cea9be92630f32c3e9',1,'vg::HaplotypePartitioner::Subchain::has_start()']]],
+ ['has_5fsupports_9548',['has_supports',['../structvg_1_1AugmentedGraph.html#a5519dec3147cb54da3e32cdb2f6c1428',1,'vg::AugmentedGraph::has_supports()'],['../structvg_1_1SupportAugmentedGraph.html#a32dc8f5559a750e393b8cedfb42cbf83',1,'vg::SupportAugmentedGraph::has_supports()']]],
+ ['has_5ftabix_9549',['has_tabix',['../classvg_1_1VcfBuffer.html#ae0a4db2dd14b0a00545ef726879a0951',1,'vg::VcfBuffer::has_tabix()'],['../classvg_1_1WindowedVcfBuffer.html#a84bbabd4f6b5b948ce6d2d0aa5fa7ff4',1,'vg::WindowedVcfBuffer::has_tabix()']]],
+ ['has_5ftranslation_9550',['has_translation',['../classvg_1_1Translator.html#ae6ccab957bfb3f7eba512f7021a4052b',1,'vg::Translator']]],
+ ['hash_9551',['hash',['../classvg_1_1VG.html#a2b75ca400f858be77b0716ab7c68dfcb',1,'vg::VG']]],
+ ['hash_5falignment_9552',['hash_alignment',['../namespacevg.html#a94f469aebb2be5b0028c337108d253fb',1,'vg']]],
+ ['hash_5fto_5frgb_9553',['hash_to_rgb',['../namespacevg.html#a8bc1d89bbcee041956e59895ed605ca3',1,'vg']]],
+ ['hashed_9554',['hashed',['../classvg_1_1Colors.html#a9c14e90e97e7fd193b25461a40ff6235',1,'vg::Colors::hashed()'],['../classvg_1_1Pictographs.html#a42c157819fffed93d2bfa730c5517e56',1,'vg::Pictographs::hashed()']]],
+ ['hashed_5fchar_9555',['hashed_char',['../classvg_1_1Pictographs.html#a91309563adbfaaf7eab19a51623d66c2',1,'vg::Pictographs']]],
+ ['have_5finput_5ffile_9556',['have_input_file',['../namespacevg.html#a7c950dca7cd25a5ce9846be2a6b93e13',1,'vg']]],
+ ['hdp_5fgbwt_5fgraph_5faccessor_9557',['hDP_gbwt_graph_accessor',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a63ed5e1c48904968ae61ff21f411c0db',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type old_node, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a7a8d1f9ad8428fe0ff0b6071dc6f47ef',1,'haplo::hDP_gbwt_graph_accessor::hDP_gbwt_graph_accessor(GBWTType &graph, gbwt::node_type new_node, size_t new_length, haploMath::RRMemo &memo)']]],
+ ['head_5fnodes_9558',['head_nodes',['../classvg_1_1VG.html#a7eecc0bd555c31d1c541c3ce44b421c3',1,'vg::VG::head_nodes(vector< Node * > &nodes)'],['../classvg_1_1VG.html#a3a44c415fb5882c184e2f35bb3999700',1,'vg::VG::head_nodes(void)'],['../namespacehandlegraph_1_1algorithms.html#a3d26728fa655f872ccac738a2bcb6166',1,'handlegraph::algorithms::head_nodes()']]],
+ ['help_5fadd_9559',['help_add',['../add__main_8cpp.html#ad49fa30ce6a9b619ad5df1cfa8621d9a',1,'add_main.cpp']]],
+ ['help_5falign_9560',['help_align',['../align__main_8cpp.html#ac749b2692aaca8eeaa6b48d7b44e167d',1,'align_main.cpp']]],
+ ['help_5fannotate_9561',['help_annotate',['../annotate__main_8cpp.html#a6957d47b527eacd587f20f9d11ccd333',1,'annotate_main.cpp']]],
+ ['help_5faugment_9562',['help_augment',['../augment__main_8cpp.html#a7cf03aa52fd6e8d75e480d4d0632b71c',1,'augment_main.cpp']]],
+ ['help_5fautoindex_9563',['help_autoindex',['../autoindex__main_8cpp.html#a4a3c7ba0d785194a42444bdedac4db50',1,'autoindex_main.cpp']]],
+ ['help_5fbenchmark_9564',['help_benchmark',['../benchmark__main_8cpp.html#a1e3da44e3dcc6fea154d15a1986ade1b',1,'benchmark_main.cpp']]],
+ ['help_5fcall_9565',['help_call',['../call__main_8cpp.html#ab92ccd67b3c20b7be7c46281c4cabfb3',1,'call_main.cpp']]],
+ ['help_5fchain_9566',['help_chain',['../chain__main_8cpp.html#a88894e89fc3e50d33042f88c993a0e0c',1,'chain_main.cpp']]],
+ ['help_5fchunk_9567',['help_chunk',['../chunk__main_8cpp.html#a502600dcc3e4e15a338642fe554fbf8d',1,'chunk_main.cpp']]],
+ ['help_5fcircularize_9568',['help_circularize',['../circularize__main_8cpp.html#a0613e20e02d0fbb56d7270a7b268ffb3',1,'circularize_main.cpp']]],
+ ['help_5fclip_9569',['help_clip',['../clip__main_8cpp.html#a451b2ddc17b7d65f1bac0fcd7cac810c',1,'clip_main.cpp']]],
+ ['help_5fcluster_9570',['help_cluster',['../cluster__main_8cpp.html#a4099bc0f1cb9fecb87c903e578ff2a17',1,'cluster_main.cpp']]],
+ ['help_5fcombine_9571',['help_combine',['../combine__main_8cpp.html#a14fa4eb501b75ae37a166fb633cda8dd',1,'combine_main.cpp']]],
+ ['help_5fconcat_9572',['help_concat',['../concat__main_8cpp.html#a795aaef3bab6d86036c1362ba5b76ac0',1,'concat_main.cpp']]],
+ ['help_5fconstruct_9573',['help_construct',['../construct__main_8cpp.html#a0c8b1d02948ee021399fef93344a9def',1,'construct_main.cpp']]],
+ ['help_5fconvert_9574',['help_convert',['../convert__main_8cpp.html#a61c2208fb6645c58f794c57e1851a194',1,'convert_main.cpp']]],
+ ['help_5fdeconstruct_9575',['help_deconstruct',['../deconstruct__main_8cpp.html#a32554f3b30e86c414a7c6940beb660e3',1,'deconstruct_main.cpp']]],
+ ['help_5fdepth_9576',['help_depth',['../depth__main_8cpp.html#aa182528e1e692b2b6ea79e3ed6a36661',1,'depth_main.cpp']]],
+ ['help_5fdotplot_9577',['help_dotplot',['../dotplot__main_8cpp.html#a628ebfce6d823f9dca7722f0721a5a3b',1,'dotplot_main.cpp']]],
+ ['help_5fexplode_9578',['help_explode',['../explode__main_8cpp.html#a5ed55d49ef3d15ac39e1e275e6792907',1,'explode_main.cpp']]],
+ ['help_5ffilter_9579',['help_filter',['../filter__main_8cpp.html#a9072d5dfad52adc43da1d2a700be313b',1,'filter_main.cpp']]],
+ ['help_5ffind_9580',['help_find',['../find__main_8cpp.html#a61f46a85b426fbf3e48cdffc07d107f8',1,'find_main.cpp']]],
+ ['help_5fgamcompare_9581',['help_gamcompare',['../gamcompare__main_8cpp.html#a33c9728d9a784c1ae54baae635b6e56d',1,'gamcompare_main.cpp']]],
+ ['help_5fgampcompare_9582',['help_gampcompare',['../gampcompare__main_8cpp.html#a4eb570f78fda3fc79752c40fccb794d9',1,'gampcompare_main.cpp']]],
+ ['help_5fgamsort_9583',['help_gamsort',['../gamsort__main_8cpp.html#ab37435867b2e79dc2fd17af9f6b3667b',1,'gamsort_main.cpp']]],
+ ['help_5fgbwt_9584',['help_gbwt',['../gbwt__main_8cpp.html#a73013ddacba7ab20beed9e8022b2b57b',1,'gbwt_main.cpp']]],
+ ['help_5fgenotype_9585',['help_genotype',['../genotype__main_8cpp.html#a7d9960cb294ff9984b99ed7816f06323',1,'genotype_main.cpp']]],
+ ['help_5fgiraffe_9586',['help_giraffe',['../giraffe__main_8cpp.html#aa6d5c2140d259252f3cad8b7bf6b4b1a',1,'giraffe_main.cpp']]],
+ ['help_5fhaplotypes_9587',['help_haplotypes',['../haplotypes__main_8cpp.html#a06899318e624a0766060720e2403f380',1,'haplotypes_main.cpp']]],
+ ['help_5fhelp_9588',['help_help',['../help__main_8cpp.html#abbe09b0c0e2e4abc339997cd4b8c1bf7',1,'help_main.cpp']]],
+ ['help_5fids_9589',['help_ids',['../ids__main_8cpp.html#ae3e40ed9a49e6e00fe241abf728c11ea',1,'ids_main.cpp']]],
+ ['help_5findex_9590',['help_index',['../index__main_8cpp.html#a24afe767ac485cebbc2f2b47ef515274',1,'index_main.cpp']]],
+ ['help_5finject_9591',['help_inject',['../inject__main_8cpp.html#a10c867b9f97d3e0d6a1396bad277880a',1,'inject_main.cpp']]],
+ ['help_5fjoin_9592',['help_join',['../join__main_8cpp.html#af6a676c62773f02853c583961fe3a59d',1,'join_main.cpp']]],
+ ['help_5fkmers_9593',['help_kmers',['../kmers__main_8cpp.html#ab5e392cd094049b8b9a863d2ce1acdb4',1,'kmers_main.cpp']]],
+ ['help_5fmap_9594',['help_map',['../map__main_8cpp.html#afec224c846352e16703d590d52bad501',1,'map_main.cpp']]],
+ ['help_5fmask_9595',['help_mask',['../mask__main_8cpp.html#a0502efe715f6be3e9b8abd1514c3faae',1,'mask_main.cpp']]],
+ ['help_5fmcmc_9596',['help_mcmc',['../mcmc__main_8cpp.html#a2d01e9b5436c54c18299e579f8f850e9',1,'mcmc_main.cpp']]],
+ ['help_5fminimizer_9597',['help_minimizer',['../minimizer__main_8cpp.html#a45dc67f0fe9ce978202fda58585b6b52',1,'minimizer_main.cpp']]],
+ ['help_5fmod_9598',['help_mod',['../mod__main_8cpp.html#a7ff398c2ef9439dc08f0d318693c9b0b',1,'mod_main.cpp']]],
+ ['help_5fmpmap_9599',['help_mpmap',['../mpmap__main_8cpp.html#ad68f4a7fc19b061a16fe9d7fb2810133',1,'mpmap_main.cpp']]],
+ ['help_5fmsga_9600',['help_msga',['../msga__main_8cpp.html#a75ed90adae627c02a0d46998bb73ee99',1,'msga_main.cpp']]],
+ ['help_5fpack_9601',['help_pack',['../pack__main_8cpp.html#aadaeba7e32c73f9093b262830bd2541e',1,'pack_main.cpp']]],
+ ['help_5fpaths_9602',['help_paths',['../paths__main_8cpp.html#a290bac84a159c7e6ab2a9abca73f7000',1,'paths_main.cpp']]],
+ ['help_5fprune_9603',['help_prune',['../prune__main_8cpp.html#a4da6cb650889066af17a6223ba1bfa81',1,'prune_main.cpp']]],
+ ['help_5frna_9604',['help_rna',['../rna__main_8cpp.html#a703e9ebf973bfcd363ce619ccaff160b',1,'rna_main.cpp']]],
+ ['help_5fsift_9605',['help_sift',['../sift__main_8cpp.html#ad82567fc886ab61b4c209226f45b0d8f',1,'sift_main.cpp']]],
+ ['help_5fsim_9606',['help_sim',['../sim__main_8cpp.html#ab2368d74cf2fb693982eeb4676e6b534',1,'sim_main.cpp']]],
+ ['help_5fsimplify_9607',['help_simplify',['../simplify__main_8cpp.html#a6fbde48f0c083d661e2e8e8b2b0a17e7',1,'simplify_main.cpp']]],
+ ['help_5fsnarl_9608',['help_snarl',['../snarls__main_8cpp.html#a4f8c80c7a187ae51a198f3ec42d85f26',1,'snarls_main.cpp']]],
+ ['help_5fsort_9609',['help_sort',['../sort__main_8cpp.html#aa2e0a3c74cb1ee9a7278b5399da39a1b',1,'sort_main.cpp']]],
+ ['help_5fstats_9610',['help_stats',['../stats__main_8cpp.html#a8a996696d6e2c9ecca6dffd6fbc8bf26',1,'stats_main.cpp']]],
+ ['help_5fsurject_9611',['help_surject',['../surject__main_8cpp.html#a9d8217a048300f2a321bfe032e31c769',1,'surject_main.cpp']]],
+ ['help_5ftrace_9612',['help_trace',['../trace__main_8cpp.html#a1e6c8dca8a2b0b1ba628313be3a56fe8',1,'trace_main.cpp']]],
+ ['help_5ftranslate_9613',['help_translate',['../translate__main_8cpp.html#ad94d99f9e08a28731eb6f4d42d64b553',1,'translate_main.cpp']]],
+ ['help_5fvalidate_9614',['help_validate',['../validate__main_8cpp.html#ab89c45aa2e33410d5c76183fd5148cff',1,'validate_main.cpp']]],
+ ['help_5fvectorize_9615',['help_vectorize',['../vectorize__main_8cpp.html#a66888bb2b18d743f2ada4c879d2999da',1,'vectorize_main.cpp']]],
+ ['help_5fversion_9616',['help_version',['../version__main_8cpp.html#a5c4af51f2cb117ca875b8b1c6be39639',1,'version_main.cpp']]],
+ ['help_5fview_9617',['help_view',['../view__main_8cpp.html#a764409d4876e90847c2d8635194f0a3e',1,'view_main.cpp']]],
+ ['help_5fviz_9618',['help_viz',['../viz__main_8cpp.html#a81fc7d050b03830c81c731e0ceb98bd1',1,'viz_main.cpp']]],
+ ['help_5fzipcode_9619',['help_zipcode',['../zipcode__main_8cpp.html#abc97cba8ea07b911b9c5da9defcc81d8',1,'zipcode_main.cpp']]],
+ ['hex2bin_9620',['hex2bin',['../bin2ascii_8h.html#a63db266c863090d6b7c179df1ea160f1',1,'bin2ascii.h']]],
+ ['hfile_5finit_9621',['hfile_init',['../hfile__internal_8hpp.html#abf020a8f3a695c1848cb3671855383b8',1,'hfile_internal.hpp']]],
+ ['hfile_5fwrap_9622',['hfile_wrap',['../namespacevg_1_1io.html#a62b10a042ea08faa5da35ff07183d49b',1,'vg::io::hfile_wrap(std::istream &input)'],['../namespacevg_1_1io.html#a4fa9b57a79b55cf4eeb10806be649ede',1,'vg::io::hfile_wrap(std::ostream &output)']]],
+ ['hitedge_9623',['HitEdge',['../classvg_1_1MEMClusterer_1_1HitEdge.html#adfc12ed7c93d550e05882555d0004235',1,'vg::MEMClusterer::HitEdge::HitEdge(size_t to_idx, int32_t weight, int64_t distance)'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a16766cbf34e0ec89d8bbdcd7f9d42988',1,'vg::MEMClusterer::HitEdge::HitEdge()=default']]],
+ ['hitgraph_9624',['HitGraph',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a9895e95cdaa1b95876c79c07d29fe852',1,'vg::MEMClusterer::HitGraph']]],
+ ['hitnode_9625',['HitNode',['../classvg_1_1MEMClusterer_1_1HitNode.html#a3156b62ac2208fdac8d0b12475011472',1,'vg::MEMClusterer::HitNode::HitNode(const MaximalExactMatch &mem, pos_t start_pos, int32_t score)'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aaeb6e6e2bb1c2ce2cda76adce19a40d6',1,'vg::MEMClusterer::HitNode::HitNode()=default']]],
+ ['hts_5ffile_5fheader_9626',['hts_file_header',['../namespacevg.html#a0676eec9e08d9589fe286cabdd16ffb3',1,'vg']]],
+ ['hts_5ffor_5feach_9627',['hts_for_each',['../namespacevg.html#a1f1e53242cb6ccf3d567c73c0895c4ca',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#ad7abb14966c1c20cff85c5744a47de0e',1,'vg::hts_for_each(string &filename, function< void(Alignment &)> lambda)']]],
+ ['hts_5ffor_5feach_5fparallel_9628',['hts_for_each_parallel',['../namespacevg.html#a7c0d37c85747f2bce6ba3356a813524a',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda, const PathPositionHandleGraph *graph)'],['../namespacevg.html#a59c6c494c2e7663fb14e40c978b4f9e5',1,'vg::hts_for_each_parallel(string &filename, function< void(Alignment &)> lambda)']]],
+ ['hts_5fstring_5fheader_9629',['hts_string_header',['../namespacevg.html#abc01af3a6e386a06a2971c17a0e6d1b1',1,'vg::hts_string_header(string &header, const map< string, int64_t > &path_length, const map< string, string > &rg_sample)'],['../namespacevg.html#aeb8cd62602cb90541b2270a79aed7595',1,'vg::hts_string_header(string &header, const vector< pair< string, int64_t >> &path_order_and_length, const map< string, string > &rg_sample)']]],
+ ['htsalignmentemitter_9630',['HTSAlignmentEmitter',['../classvg_1_1HTSAlignmentEmitter.html#acc9b5714c55e4b644216066eda386dbd',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSAlignmentEmitter.html#a0c76946bf064ecac88e21a2467ea2410',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a780156f43d54cf16906948ad8286c20f',1,'vg::HTSAlignmentEmitter::HTSAlignmentEmitter(HTSAlignmentEmitter &&other)=delete']]],
+ ['htswriter_9631',['HTSWriter',['../classvg_1_1HTSWriter.html#a8257b1e35ac5abf92b43b8a823c66aa5',1,'vg::HTSWriter::HTSWriter(const string &filename, const string &format, const vector< pair< string, int64_t >> &path_order_and_length, const unordered_map< string, int64_t > &subpath_to_length, size_t max_threads)'],['../classvg_1_1HTSWriter.html#ae2fc6b2a60e3bc9441956faf87ff6a07',1,'vg::HTSWriter::HTSWriter(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a0a23221d8449a4b4e0b1278995ad0207',1,'vg::HTSWriter::HTSWriter(HTSWriter &&other)=delete']]]
];
diff --git a/search/functions_9.js b/search/functions_9.js
index b4712180a6..86f81d1656 100644
--- a/search/functions_9.js
+++ b/search/functions_9.js
@@ -1,150 +1,150 @@
var searchData=
[
- ['i_9628',['I',['../structhaplo_1_1haplo__DP__rectangle.html#ad961ad4ab25e6d0358b58dc44b3c0319',1,'haplo::haplo_DP_rectangle']]],
- ['id_9629',['id',['../namespacevg.html#a9f6602b7e7a46c19819c8f362147b315',1,'vg::id()'],['../namespacexg.html#a7bfa373a28253072de64785adc9b1188',1,'xg::id()']]],
- ['id_5fmap_9630',['id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a22e20a6a984b3dd5def4ad22836b15b9',1,'vg::algorithms::GFAParser']]],
- ['id_5forder_9631',['id_order',['../namespacevg_1_1algorithms.html#a54730e9452c2609633da201ba85a8bca',1,'vg::algorithms']]],
- ['id_5fsort_9632',['id_sort',['../classvg_1_1VG.html#ab1aecdffe7759a1e14248e00f2866b84',1,'vg::VG']]],
- ['id_5fto_5fprefix_9633',['id_to_prefix',['../classvg_1_1StreamIndexBase.html#a4b0e44b8cb40b33c5ef4db47a8a89272',1,'vg::StreamIndexBase']]],
- ['id_5fto_5frank_9634',['id_to_rank',['../classvg_1_1Viz.html#a2474cd8505ed561cd414648438fedb5e',1,'vg::Viz::id_to_rank()'],['../classxg_1_1XG.html#a39172dc94153da745dd765f3c45ceeea',1,'xg::XG::id_to_rank()'],['../classhandlegraph_1_1RankedHandleGraph.html#a4c919e31efff422d9a29fa264290836c',1,'handlegraph::RankedHandleGraph::id_to_rank()']]],
- ['identify_5faligned_5fsplice_5fcandidates_9635',['identify_aligned_splice_candidates',['../classvg_1_1MultipathMapper.html#aa97ce2f7dcd38916169b78483b7c21ec',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< multipath_alignment_t > &multipath_alns, const vector< size_t > &cluster_idxs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const'],['../classvg_1_1MultipathMapper.html#a63fc3e0fac9b46faf4c28fe47c88c784',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool read_1, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, const vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const']]],
- ['identify_5fpinning_5fpoints_9636',['identify_pinning_points',['../classvg_1_1GSSWAligner.html#a4cd705824a3926a510fea64f883cab66',1,'vg::GSSWAligner']]],
- ['identify_5fsources_5fand_5fsinks_9637',['identify_sources_and_sinks',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aff810bb5affe3201fccf437be3290fde',1,'vg::MEMClusterer::HitGraph']]],
- ['identify_5fstart_5fsubpaths_9638',['identify_start_subpaths',['../namespacevg.html#a0844cc3c2da56dfed0e9436d7f0dd7de',1,'vg']]],
- ['identify_5funaligned_5fsplice_5fcandidates_9639',['identify_unaligned_splice_candidates',['../classvg_1_1MultipathMapper.html#a50f4e1e71c3fb6272009297f1e012493',1,'vg::MultipathMapper']]],
- ['identity_9640',['identity',['../namespacevg.html#ab3c5c7a407962a8c735c1d533cc0b186',1,'vg']]],
- ['identity_5ftranslation_9641',['identity_translation',['../classvg_1_1VG.html#ab015755dc8b427f4e226f920eb26c428',1,'vg::VG']]],
- ['identityoverlay_9642',['IdentityOverlay',['../classvg_1_1IdentityOverlay.html#ab287d9dd0b6b6c0832dc725a2cdb6740',1,'vg::IdentityOverlay::IdentityOverlay(const HandleGraph *graph)'],['../classvg_1_1IdentityOverlay.html#a8a699d8689c9d93e72a7e78023cc3413',1,'vg::IdentityOverlay::IdentityOverlay()=default']]],
- ['immutable_5fpath_5ffrom_5flength_9643',['immutable_path_from_length',['../classvg_1_1MinimizerMapper.html#ab3008803e2ce57d5bbcd6a077f9dcde6',1,'vg::MinimizerMapper']]],
- ['in_5fnontrivial_5fchain_9644',['in_nontrivial_chain',['../classvg_1_1SnarlManager.html#a92c63ede9881ce261258540ceb40fddb',1,'vg::SnarlManager']]],
- ['in_5fplace_5fsubvector_9645',['in_place_subvector',['../namespacevg.html#a62239efefb85e451fcec6519644186d1',1,'vg']]],
- ['include_9646',['include',['../classvg_1_1VG.html#a66e4dac76edcf0218f9749352c19acae',1,'vg::VG']]],
- ['inclusive_5finterval_9647',['inclusive_interval',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af66a44ac51fe4a01ce0b24e0490b657b',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['increment_5fcoverage_9648',['increment_coverage',['../classvg_1_1Packer.html#ab97f6f0bb52c3641aceb5ffe4359492d',1,'vg::Packer::increment_coverage(size_t i)'],['../classvg_1_1Packer.html#a4da9199584ad1279a1e0a54aea12c6c1',1,'vg::Packer::increment_coverage(size_t i, size_t v)']]],
- ['increment_5fedge_5fcoverage_9649',['increment_edge_coverage',['../classvg_1_1Packer.html#a7e2313be4468ea83a3e8b6a75b00cd7c',1,'vg::Packer::increment_edge_coverage(size_t i)'],['../classvg_1_1Packer.html#abdc73870b8a141908a21eb7ff7c31d4f',1,'vg::Packer::increment_edge_coverage(size_t i, size_t v)']]],
- ['increment_5fnode_5fids_9650',['increment_node_ids',['../classvg_1_1Paths.html#a8a9b275a5979218a784105364248b5ba',1,'vg::Paths::increment_node_ids()'],['../classvg_1_1VG.html#a86b3ecdf29d100a8d43f6aaccd6f2e0e',1,'vg::VG::increment_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a902b211a1f86645818b3da1cb64af0be',1,'handlegraph::MutableHandleGraph::increment_node_ids(nid_t increment)'],['../classhandlegraph_1_1MutableHandleGraph.html#a877dc8c0ae9a584907d45328512720cc',1,'handlegraph::MutableHandleGraph::increment_node_ids(long increment)']]],
- ['increment_5fnode_5fmapping_5fids_9651',['increment_node_mapping_ids',['../namespacevg.html#a9fa6175557c33cd572b8726222cf6547',1,'vg']]],
- ['increment_5fnode_5fquality_9652',['increment_node_quality',['../classvg_1_1Packer.html#a0195e9186f8162fc4fab673fbd65b0a8',1,'vg::Packer']]],
- ['increment_5fprogress_9653',['increment_progress',['../classvg_1_1Progressive.html#ab1de11917caf25974a02e2f5c3946280',1,'vg::Progressive']]],
- ['incremental_5fextend_9654',['incremental_extend',['../classhaplo_1_1ScoreProvider.html#a834b5b57b025ae27cc2c668869ee9b13',1,'haplo::ScoreProvider::incremental_extend()'],['../classhaplo_1_1GBWTScoreProvider.html#af52bee39ffe97d84ba020c49f7fbf7a6',1,'haplo::GBWTScoreProvider::incremental_extend()']]],
- ['incremental_5ffind_9655',['incremental_find',['../classhaplo_1_1ScoreProvider.html#a6272d9bca95e7846807ef2e71d616a9c',1,'haplo::ScoreProvider::incremental_find()'],['../classhaplo_1_1GBWTScoreProvider.html#a540105f41d66c4b536fda44fce248680',1,'haplo::GBWTScoreProvider::incremental_find()']]],
- ['incrementalsubgraph_9656',['IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html#ab942f4d62b91144afce73896b8004609',1,'vg::IncrementalSubgraph::IncrementalSubgraph(const HandleGraph &graph, const pos_t &starting_position, bool extract_left, int64_t max_distance=numeric_limits< int64_t >::max(), size_t frontier_copy_limit=numeric_limits< size_t >::max(), size_t max_num_nodes=numeric_limits< size_t >::max())'],['../classvg_1_1IncrementalSubgraph.html#a4c8f5a87dfcf68630d645a9469e75837',1,'vg::IncrementalSubgraph::IncrementalSubgraph()=default']]],
- ['incrementiter_9657',['IncrementIter',['../structvg_1_1IncrementIter.html#a1231b6b6c0fde0c7ae6cf69b9cfe9a6b',1,'vg::IncrementIter']]],
- ['index_9658',['index',['../classvg_1_1StreamIndex.html#a8ee1930510b5d02e9a00ba1a246ba146',1,'vg::StreamIndex']]],
- ['index_5fedge_5fby_5fnode_5fsides_9659',['index_edge_by_node_sides',['../classvg_1_1VG.html#a53ff7033966852f5fb3852716cab21a9',1,'vg::VG']]],
- ['index_5fnode_5fto_5fpath_9660',['index_node_to_path',['../classxg_1_1XG.html#a4599310a72acd2ccfbe9d6041cc51dd1',1,'xg::XG']]],
- ['index_5fpath_5fnames_9661',['index_path_names',['../classxg_1_1XG.html#aff97dc01cda8460ebeb98a4b789e3485',1,'xg::XG']]],
- ['index_5fto_5fnode_9662',['index_to_node',['../classvg_1_1Packer.html#a967dcbe2cbcb6df4c7e2d938f7cd11fa',1,'vg::Packer']]],
- ['indexedvg_9663',['IndexedVG',['../classvg_1_1IndexedVG.html#a89030b52047b0e005a5c86b7f9a206f6',1,'vg::IndexedVG::IndexedVG(string graph_filename)'],['../classvg_1_1IndexedVG.html#a0972bd3bf8d93bfa8b41aff828aab070',1,'vg::IndexedVG::IndexedVG(const IndexedVG &other)=delete']]],
- ['indexfile_9664',['IndexFile',['../classvg_1_1IndexFile.html#ae22fd6ea5fd4419ca8ed2070410638ca',1,'vg::IndexFile']]],
- ['indexingplan_9665',['IndexingPlan',['../classvg_1_1IndexingPlan.html#a5e6231a7a515964589ea8e55e8e2d5fe',1,'vg::IndexingPlan']]],
- ['indexrecipe_9666',['IndexRecipe',['../structvg_1_1IndexRecipe.html#a11948f5026c5aff21e22775446e419b6',1,'vg::IndexRecipe']]],
- ['indexregistry_9667',['IndexRegistry',['../classvg_1_1IndexRegistry.html#a0a0debbd6d61db053403e7cbca69d4c2',1,'vg::IndexRegistry::IndexRegistry()=default'],['../classvg_1_1IndexRegistry.html#aec3008292713502924fcf3cc51253e4f',1,'vg::IndexRegistry::IndexRegistry(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#aa4f9837b4beb749a06b3dcb3150475b0',1,'vg::IndexRegistry::IndexRegistry(IndexRegistry &&other)']]],
- ['init_9668',['init',['../classvg_1_1SpliceStats.html#afd5923a5cd636a140697cad2605fc415',1,'vg::SpliceStats::init()'],['../classvg_1_1VG.html#aafd0f191fe33bd4590f15f309d0fd89c',1,'vg::VG::init()'],['../classvg_1_1Viz.html#aad7ceb7896288f2d4444b10cceb946d8',1,'vg::Viz::init()']]],
- ['init_5fcoverage_5fbin_9669',['init_coverage_bin',['../classvg_1_1Packer.html#abdd9bd13b38dced4c61d78e5baf3c0fb',1,'vg::Packer']]],
- ['init_5fedge_5fcoverage_5fbin_9670',['init_edge_coverage_bin',['../classvg_1_1Packer.html#a693598b3d8227598075e02fbc8124789',1,'vg::Packer']]],
- ['init_5fmapper_9671',['init_mapper',['../classvg_1_1Filter.html#abd9fa5045b867b20e1b20e3d74d77e4b',1,'vg::Filter']]],
- ['init_5fnode_5fquality_5fbin_9672',['init_node_quality_bin',['../classvg_1_1Packer.html#aff44bf5abf4eacda46958eeb436eb2e4',1,'vg::Packer']]],
- ['init_5fsnarls_9673',['init_snarls',['../classvg_1_1Masker.html#a28b4317d6319672c9b9fa02b0e515335',1,'vg::Masker']]],
- ['init_5fstate_9674',['init_state',['../classvg_1_1DinucleotideMachine.html#a35193673a88abc7f0933d2f65fd7f2ea',1,'vg::DinucleotideMachine']]],
- ['init_5ftraceback_5findexes_9675',['init_traceback_indexes',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ab251d4ff6f6b7f351f29c5dd29ead002',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['initial_5fposition_9676',['initial_position',['../namespacevg.html#acd31d3a8dc67801f147d0ba1b0059c3f',1,'vg::initial_position(const Path &path)'],['../namespacevg.html#a5273bbd5e5d0f9bbf639c19c962a58dd',1,'vg::initial_position(const path_t &path)']]],
- ['initialize_5fsam_5ffile_9677',['initialize_sam_file',['../classvg_1_1HTSWriter.html#a3063999c0e6b467c7717edfb53040166',1,'vg::HTSWriter']]],
- ['input_5fgroup_9678',['input_group',['../structvg_1_1IndexRecipe.html#aa22beac92907ecf99b821ee6bfed4e33',1,'vg::IndexRecipe']]],
- ['inputstream_9679',['inputStream',['../namespacevg_1_1io.html#a857cf3810d138ef43e25aa37f147ac25',1,'vg::io']]],
- ['ins_5fpredecessor_9680',['ins_predecessor',['../classvg_1_1WFATree.html#a8ab38ec2797b5119eb9ffd213bdb957e',1,'vg::WFATree']]],
- ['insert_9681',['insert',['../classvg_1_1SnarlState.html#a428e616c3ef0bab94325edbd728819e3',1,'vg::SnarlState::insert(const vector< pair< handle_t, size_t >> &haplotype)'],['../classvg_1_1SnarlState.html#a8489b6496d77d037d0ee2f0367119a3a',1,'vg::SnarlState::insert(size_t overall_lane, const vector< handle_t > &haplotype, bool backward=false)'],['../classvg_1_1HandleGraphNodeSet.html#a2c8d82e307853b75c099422d8e5e717c',1,'vg::HandleGraphNodeSet::insert()'],['../structvg_1_1RecombinatorHaplotype.html#a370a97d18bca8d1448eb359eee91be6e',1,'vg::RecombinatorHaplotype::insert()'],['../classvg_1_1SmallBitset.html#a9336d107ad4a8f98005ecfcf313e1334',1,'vg::SmallBitset::insert()'],['../classvg_1_1BitStringTree.html#ac323a5f006f9ad739facc0f306b1b6ed',1,'vg::BitStringTree::insert()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#a1658df8b5e184e15cce3b5e70bc2769c',1,'vg::BitStringTree::TreeNode::insert()'],['../structjob__type.html#a28737e853741fb1798c718e3637070b0',1,'job_type::insert()']]],
- ['insert_5fgbwt_5fpath_9682',['insert_gbwt_path',['../namespacevg.html#a9bf4a7dd2a81bb5b873127156a2dfb33',1,'vg']]],
- ['insert_5fhandles_9683',['insert_handles',['../classvg_1_1GenomeState.html#aa85289ade641db44976ac969c5fb6750',1,'vg::GenomeState']]],
- ['insert_5fhaplotype_9684',['insert_haplotype',['../classvg_1_1GenomeState.html#a371e13f6d644e9979fa0e5177ffaadba',1,'vg::GenomeState']]],
- ['insert_5fleft_9685',['insert_left',['../classvg_1_1PhasedGenome.html#a02e624546cf3f5675fbfa128c080c75d',1,'vg::PhasedGenome']]],
- ['insert_5fmapping_9686',['insert_mapping',['../classvg_1_1Paths.html#aa6e0eb5748713837711612e5e347f8cb',1,'vg::Paths']]],
- ['insert_5fpath_9687',['insert_path',['../classvg_1_1PhaseUnfolder.html#a28e7cee8d0922cf0aac91dba0d86f1c3',1,'vg::PhaseUnfolder']]],
- ['insert_5fright_9688',['insert_right',['../classvg_1_1PhasedGenome.html#adfbd6242bff1445e5210f4046150fc85',1,'vg::PhasedGenome']]],
- ['insert_5fsize_5ffilter_9689',['insert_size_filter',['../classvg_1_1Filter.html#a198243f4ffebc1b1442ca4521542ac99',1,'vg::Filter']]],
- ['insert_5ftraceback_9690',['insert_traceback',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#aa6db44fa8e957169e11fd1a7853d2a19',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['insertion_5ffilter_9691',['insertion_filter',['../classvg_1_1Filter.html#a02bb368759eef77f7f7aa3753b23469e',1,'vg::Filter']]],
- ['insufficientinputexception_9692',['InsufficientInputException',['../classvg_1_1InsufficientInputException.html#a2361f9743d9c5f2af8bb170a6240b891',1,'vg::InsufficientInputException::InsufficientInputException()=delete'],['../classvg_1_1InsufficientInputException.html#af9014e0e82772828f66dc699e2eb8734',1,'vg::InsufficientInputException::InsufficientInputException(const IndexName &target, const IndexRegistry ®istry) noexcept']]],
- ['int_5fto_5fstring_9693',['int_to_string',['../namespacegafkluge.html#ad9c7bb306be39ddca425533a3583d71e',1,'gafkluge']]],
- ['int_5fweighted_5fsum_9694',['int_weighted_sum',['../namespacehaplo_1_1haploMath.html#a5bc2868874173d377a55c788f21796ef',1,'haplo::haploMath::int_weighted_sum(double *values, int64_t *counts, size_t n_values)'],['../namespacehaplo_1_1haploMath.html#ab17ccf8a6fa509f269bdaf1c69e4f6bc',1,'haplo::haploMath::int_weighted_sum(vector< double > values, vector< int64_t > counts)']]],
- ['integer_5fpower_9695',['integer_power',['../namespacevg.html#aca4239af1a9e3eb1283f78bf5cc1411a',1,'vg::integer_power(uint64_t base, uint64_t exponent)'],['../namespacevg.html#aa7c32d1e90ec006624a7ee03655f3c35',1,'vg::integer_power(size_t x, size_t power)']]],
- ['integratedsnarlfinder_9696',['IntegratedSnarlFinder',['../classvg_1_1IntegratedSnarlFinder.html#a888085d87664c7e58ad4f988091c62f5',1,'vg::IntegratedSnarlFinder']]],
- ['interchromosomal_5ffilter_9697',['interchromosomal_filter',['../classvg_1_1Filter.html#a1f1daa97b40d6ca6b2a3f37950f4f117',1,'vg::Filter']]],
- ['intersect_5fpath_5foffsets_9698',['intersect_path_offsets',['../namespacevg_1_1algorithms.html#a9ce4dabb6661657c7d72593afc3f41df',1,'vg::algorithms']]],
- ['intersection_9699',['intersection',['../structhaplo_1_1int__itvl__t.html#ade4051b750fcce428be13a69663ec035',1,'haplo::int_itvl_t']]],
- ['interval_5flength_9700',['interval_length',['../namespacevg.html#a9467900ec651b93d47190413208cdf6f',1,'vg']]],
- ['interval_5fsize_9701',['interval_size',['../structhaplo_1_1haplo__DP__rectangle.html#a751f03ab1d68636c47340dbd376b66a8',1,'haplo::haplo_DP_rectangle']]],
- ['interval_5fstate_5ft_9702',['interval_state_t',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#aa86bab20d96ef26dc66afadf5dd22195',1,'vg::ZipCodeForest::interval_state_t']]],
- ['into_5fcutting_5fsnarl_9703',['into_cutting_snarl',['../classvg_1_1MultipathAlignmentGraph.html#a44bd7328dd8ea140223226ae4da8afff',1,'vg::MultipathAlignmentGraph']]],
- ['into_5fwhich_5fsnarl_9704',['into_which_snarl',['../classvg_1_1SnarlManager.html#ac08074e3073ecd2ef72a57116b459577',1,'vg::SnarlManager::into_which_snarl(int64_t id, bool reverse) const'],['../classvg_1_1SnarlManager.html#a852f930d4e68e9bbd664ebe5a73a4669',1,'vg::SnarlManager::into_which_snarl(const Visit &visit) const']]],
- ['introduce_9705',['introduce',['../classvg_1_1Funnel.html#adfe8a13519ae236c400f3ad68980e16c',1,'vg::Funnel']]],
- ['intron_5flength_5flog_5flikelihood_9706',['intron_length_log_likelihood',['../classvg_1_1SpliceStats.html#ad61aebd450e01500b86d1fec55b8ccd9',1,'vg::SpliceStats']]],
- ['intron_5flength_5fscore_9707',['intron_length_score',['../classvg_1_1SpliceStats.html#aedf26f015ecfb06f71aadbca66c81935',1,'vg::SpliceStats']]],
- ['inversion_5ffilter_9708',['inversion_filter',['../classvg_1_1Filter.html#a5503147c786a4d9bfb18fc081630b5f6',1,'vg::Filter']]],
- ['invert_9709',['invert',['../structvg_1_1Counts.html#a3a4cf08069fb263d89a96b86313a04a2',1,'vg::Counts']]],
- ['invert_5ftranslation_9710',['invert_translation',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#abeffeb079b7f3997db8cfbb9a701f63c',1,'vg::algorithms::GFAIDMapInfo']]],
- ['is_5fa_5fduplicate_5fhandle_9711',['is_a_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#a3089cf35214f919d15030e029df3f6eb',1,'vg::DozeuPinningOverlay']]],
- ['is_5fa_5fduplicate_5fid_9712',['is_a_duplicate_id',['../classvg_1_1DozeuPinningOverlay.html#ab549aa4693c8425cd1df8d04a04a178f',1,'vg::DozeuPinningOverlay']]],
- ['is_5facyclic_9713',['is_acyclic',['../namespacehandlegraph_1_1algorithms.html#a03c1bfbc47b88a0bd18ca2cc93a1b0b3',1,'handlegraph::algorithms']]],
- ['is_5fall_5fn_9714',['is_all_n',['../namespacevg.html#abe6f7955b97d8537da2133a47f37f462',1,'vg']]],
- ['is_5fancestor_5fnext_9715',['is_ancestor_next',['../classvg_1_1VG.html#a7903acd7a977a85fdd78d306f2063252',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ab919097a72a96dada04310b2aaf019f8',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
- ['is_5fancestor_5fprev_9716',['is_ancestor_prev',['../classvg_1_1VG.html#a25215a67c3eac7570e2ab62e825ae169',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ae6699fe9d747f761f6efae39c3c0501c',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
- ['is_5fany_5fpainted_9717',['is_any_painted',['../structvg_1_1Funnel_1_1PaintableSpace.html#ab42e113d364cfa7da4e7b0c76ba448f1',1,'vg::Funnel::PaintableSpace']]],
- ['is_5fchain_9718',['is_chain',['../classhandlegraph_1_1SnarlDecomposition.html#ad383774992bf6a3acc5fd34dc8cd9770',1,'handlegraph::SnarlDecomposition']]],
- ['is_5fchild_9719',['is_child',['../classvg_1_1NetGraph.html#a25dbff454e5c9aa081c354f05523a512',1,'vg::NetGraph']]],
- ['is_5fconsistent_9720',['is_consistent',['../classvg_1_1MultipathMapper.html#a76742066028c14330177d74d9cd0286c',1,'vg::MultipathMapper']]],
- ['is_5fcorrect_9721',['is_correct',['../classvg_1_1Funnel.html#a4296184811926cf97a42d52aaf3fc6f6',1,'vg::Funnel']]],
- ['is_5fcorrectly_5fmapped_9722',['is_correctly_mapped',['../classvg_1_1ReadFilter.html#ac5da32515034e6669d9e14de3c748122',1,'vg::ReadFilter::is_correctly_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab76d4dc77becdaf866f724d5b88dcdb5',1,'vg::ReadFilter::is_correctly_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a053397b20bc378d11f11b365e6d68032',1,'vg::ReadFilter::is_correctly_mapped(const MultipathAlignment &alignment) const']]],
- ['is_5fdirected_5facyclic_9723',['is_directed_acyclic',['../namespacehandlegraph_1_1algorithms.html#afe81ab458644253f1064ffa3c73783a3',1,'handlegraph::algorithms']]],
- ['is_5fdynamic_9724',['is_dynamic',['../classvg_1_1Packer.html#a370e8ef56ffd369c6a498aa36ed9c570',1,'vg::Packer']]],
- ['is_5fempty_9725',['is_empty',['../structhaplo_1_1haplo__DP__column.html#af8bc221754159aa83d44d9373359939c',1,'haplo::haplo_DP_column::is_empty()'],['../classvg_1_1MemoizingGraph.html#a4596372ebc27c5e849127f4f09d9ae6b',1,'vg::MemoizingGraph::is_empty()'],['../classhandlegraph_1_1PathHandleGraph.html#aef3f2c04d1e315e485460dcd902467cb',1,'handlegraph::PathHandleGraph::is_empty()'],['../namespacevg.html#a3620df68e5af61a8eb660e4a4838ea06',1,'vg::is_empty()'],['../namespacexg.html#a9ef9c7147d5ae7c20d60ec17581d81bb',1,'xg::is_empty()']]],
- ['is_5fequal_9726',['is_equal',['../classvg_1_1ZipCode.html#a38f2c794e04f2ad21447358fd7b93665',1,'vg::ZipCode']]],
- ['is_5fextendable_9727',['is_extendable',['../classvg_1_1IncrementalSubgraph.html#ada07715a97931d98157e8fc5aba697a9',1,'vg::IncrementalSubgraph']]],
- ['is_5fexternally_5fend_5fend_5fconnected_9728',['is_externally_end_end_connected',['../classvg_1_1ZipCode.html#ac59bc5911574a1fa356cac4f90471324',1,'vg::ZipCode']]],
- ['is_5fexternally_5fstart_5fend_5fconnected_9729',['is_externally_start_end_connected',['../classvg_1_1ZipCode.html#a28d318606661f6e99b2374b5a87f370f',1,'vg::ZipCode']]],
- ['is_5fexternally_5fstart_5fstart_5fconnected_9730',['is_externally_start_start_connected',['../classvg_1_1ZipCode.html#a842b8118dd218d6451199c1fd5f2e04b',1,'vg::ZipCode']]],
- ['is_5ffarther_5fthan_9731',['is_farther_than',['../classvg_1_1ZipCode.html#a967a3c40a7c49674c6d14883b6b02e71',1,'vg::ZipCode']]],
- ['is_5ffinalized_9732',['is_finalized',['../classvg_1_1FragmentLengthDistribution.html#a4f1fa1f539e504fdd0f92467b81e9172',1,'vg::FragmentLengthDistribution']]],
- ['is_5ffinished_9733',['is_finished',['../classvg_1_1IndexFile.html#a80f432755770a31c2c1fa4c41d404f8b',1,'vg::IndexFile']]],
- ['is_5fgzipped_9734',['is_gzipped',['../namespacevg.html#a8f065676bdbe54b44e45961d7d40d8a5',1,'vg']]],
- ['is_5fhead_5fnode_9735',['is_head_node',['../classvg_1_1VG.html#a80438f4ab98e10b68caab27fdece09ab',1,'vg::VG::is_head_node(nid_t id)'],['../classvg_1_1VG.html#a1bc3866468d5eb941fa6ba010ccce2ec',1,'vg::VG::is_head_node(Node *node)'],['../namespacevg_1_1algorithms.html#aa4cb6665721af1f7c749ca8f73472d6c',1,'vg::algorithms::is_head_node()']]],
- ['is_5fhead_5for_5ftail_5fnode_9736',['is_head_or_tail_node',['../classvg_1_1Paths.html#afec902ce6a22b7aa3aeee25f20eb1386',1,'vg::Paths']]],
- ['is_5fid_5fsortable_9737',['is_id_sortable',['../namespacevg.html#a5570a5685bef6eee6ac2697920ebc6c0',1,'vg']]],
- ['is_5fin_5frange_9738',['is_in_range',['../classvg_1_1StreamIndexBase.html#ab2b832d8cca9dee3c38d452dc47da0e3',1,'vg::StreamIndexBase']]],
- ['is_5fintermediate_9739',['is_intermediate',['../classvg_1_1IndexingPlan.html#ae04def089761ea2ef65532fabd909794',1,'vg::IndexingPlan']]],
- ['is_5fleaf_9740',['is_leaf',['../structvg_1_1WFANode.html#af75c62d0086aaa47baa79808601cf4f0',1,'vg::WFANode::is_leaf()'],['../classvg_1_1SnarlManager.html#aef63882ba4ef5e098890b1eeb3bbb985',1,'vg::SnarlManager::is_leaf()']]],
- ['is_5fleft_5fclipped_9741',['is_left_clipped',['../classvg_1_1Filter.html#a08ace85cd60850045415e5e6640b0038',1,'vg::Filter']]],
- ['is_5fmapped_9742',['is_mapped',['../classvg_1_1ReadFilter.html#a1acad05129d0a6146416f596903216a8',1,'vg::ReadFilter::is_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#acf05b0ded409cd19894c24b6fe9412bf',1,'vg::ReadFilter::is_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#ad1fe573ba370f839adb1cd28350cac81',1,'vg::ReadFilter::is_mapped(const MultipathAlignment &mp_alignment) const']]],
- ['is_5fmatch_9743',['is_match',['../namespacevg.html#a52292dfd3869a811170f7c5c0d9da564',1,'vg']]],
- ['is_5fmissing_9744',['is_missing',['../namespacegafkluge.html#a190e58cca553fe5b7b67dac6f7aad7d4',1,'gafkluge::is_missing(const std::string &s)'],['../namespacegafkluge.html#ae093534cbdd3fda37e3a75ea91a0f6b2',1,'gafkluge::is_missing(int64_t i)']]],
- ['is_5fnew_9745',['is_new',['../structhaplo_1_1haplo__DP__rectangle.html#a509976d09905bfe9312bc855641a7a59',1,'haplo::haplo_DP_rectangle']]],
- ['is_5fnode_9746',['is_node',['../classhandlegraph_1_1SnarlDecomposition.html#a6f410ac594c7ed44a7cc9b6e44077900',1,'handlegraph::SnarlDecomposition']]],
- ['is_5fnovel_5fedge_9747',['is_novel_edge',['../structvg_1_1AugmentedGraph.html#ab0dd61392dacbee763cea6297d95f876',1,'vg::AugmentedGraph']]],
- ['is_5fnovel_5fnode_9748',['is_novel_node',['../structvg_1_1AugmentedGraph.html#ac6f4df5e0f80b0509ff3ec26b685d5c9',1,'vg::AugmentedGraph']]],
- ['is_5fnumber_9749',['is_number',['../namespacevg.html#af051490e6e94b4c476695610472cdf5b',1,'vg::is_number(const std::string &s)'],['../namespacevg.html#a97c44463adc7ddcc77ac9664692a62b8',1,'vg::is_number(const string &s)']]],
- ['is_5fours_9750',['is_ours',['../classvg_1_1ExtraNodeGraph.html#a16421769feafbfb95e2466391a6fa97c',1,'vg::ExtraNodeGraph::is_ours()'],['../classvg_1_1SourceSinkOverlay.html#abe7c1c7dcdf76a6116f500654e73fb89',1,'vg::SourceSinkOverlay::is_ours()']]],
- ['is_5fproper_5fpair_9751',['is_proper_pair',['../classvg_1_1ReadFilter.html#ad5ebb80a71eaf7c765f33b306ab230d8',1,'vg::ReadFilter']]],
- ['is_5frev_9752',['is_rev',['../namespacevg.html#aac725dd44bc5a8f540554d4b1882c1fe',1,'vg::is_rev()'],['../namespacexg.html#a92c2e7f37dfa3b8b8dbb07d80e5482be',1,'xg::is_rev()']]],
- ['is_5freverse_9753',['is_reverse',['../classvg_1_1mapping__t.html#a26eda6f4c9bc3da9376c2e0f5569aa62',1,'vg::mapping_t::is_reverse()'],['../classvg_1_1position__t.html#a7028d95b6cc9c55db816e9500949283b',1,'vg::position_t::is_reverse()'],['../classxg_1_1XGPath.html#a89bfa5d4417fea7455c520e6817108e7',1,'xg::XGPath::is_reverse()']]],
- ['is_5froot_9754',['is_root',['../classvg_1_1WFATree.html#af1ad9e8285b7a9414d8af9ec257add49',1,'vg::WFATree::is_root()'],['../classvg_1_1SnarlManager.html#a294ce522d34dadb5288d6115c88dfa89',1,'vg::SnarlManager::is_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#afef6c85a6564d6d3ec65bfb245e1f38c',1,'handlegraph::SnarlDecomposition::is_root()']]],
- ['is_5fsecondary_9755',['is_secondary',['../classvg_1_1ReadFilter.html#a947155b6ed467a8ea83ac80db6e11a63',1,'vg::ReadFilter::is_secondary(const Read &read) const'],['../classvg_1_1ReadFilter.html#a44451e4c12ff1a923221d019c31c610c',1,'vg::ReadFilter::is_secondary(const MultipathAlignment &mp_aln) const'],['../classvg_1_1ReadFilter.html#ab4ae201744c8abc543d60afb24b294eb',1,'vg::ReadFilter::is_secondary(const Alignment &aln) const']]],
- ['is_5fself_5flooping_9756',['is_self_looping',['../classvg_1_1VG.html#ad09549b6cfab8e1097dd207e01e57812',1,'vg::VG']]],
- ['is_5fsentinel_9757',['is_sentinel',['../classhandlegraph_1_1SnarlDecomposition.html#af3ce2079f249448a8c8a829daedd1678',1,'handlegraph::SnarlDecomposition']]],
- ['is_5fsingle_5fstranded_9758',['is_single_stranded',['../namespacehandlegraph_1_1algorithms.html#afbca1e7b54575bfce7f0844dbda83c6f',1,'handlegraph::algorithms']]],
- ['is_5fskippable_9759',['is_skippable',['../classvg_1_1algorithms_1_1Anchor.html#a002732eac1459215244c89710a4ef2e3',1,'vg::algorithms::Anchor']]],
- ['is_5fsnarl_9760',['is_snarl',['../classhandlegraph_1_1SnarlDecomposition.html#a32b29fc153b3a355cae8b15008ec8c1b',1,'handlegraph::SnarlDecomposition']]],
- ['is_5fsnarl_5fsmaller_5fthan_5freads_9761',['is_snarl_smaller_than_reads',['../classvg_1_1Genotyper.html#a7c7f091482612f6b0cd2baf0c19c45fb',1,'vg::Genotyper']]],
- ['is_5fsnv_9762',['is_snv',['../structhaplo_1_1linear__haplo__structure.html#aa95f64d55f6bf7b1239396ba4a722a05',1,'haplo::linear_haplo_structure']]],
- ['is_5fsolitary_5fref_9763',['is_solitary_ref',['../structhaplo_1_1linear__haplo__structure.html#a5909bdd11b10437a4d70af1fda222a85',1,'haplo::linear_haplo_structure']]],
- ['is_5fsplit_9764',['is_split',['../classvg_1_1ReadFilter.html#a34d313741dcfe8c009dfcc380d1293ad',1,'vg::ReadFilter::is_split(const Read &read) const'],['../classvg_1_1ReadFilter.html#a956bc9e366bb25f9544dbb3d8573b5b5',1,'vg::ReadFilter::is_split(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a3fcb1771035304240c7a0401d84ef60b',1,'vg::ReadFilter::is_split(const MultipathAlignment &mp_aln) const']]],
- ['is_5fstatic_9765',['is_static',['../structvg_1_1subcommand_1_1TickChainLink.html#aae7e5f61e0f577ae29fd404c6f0a9482',1,'vg::subcommand::TickChainLink::is_static()'],['../structvg_1_1Range.html#a07b020e2621ac7d0a6cc636384242c73',1,'vg::Range::is_static()'],['../structvg_1_1subcommand_1_1RangeArgSpec.html#a20410637df207e212fee01c268624d85',1,'vg::subcommand::RangeArgSpec::is_static()']]],
- ['is_5ftail_5fnode_9766',['is_tail_node',['../classvg_1_1VG.html#a660692b8769618259f69be25bfed0bc3',1,'vg::VG::is_tail_node(nid_t id)'],['../classvg_1_1VG.html#af58b227f21324d30be531088ed49b0f1',1,'vg::VG::is_tail_node(Node *node)'],['../namespacevg_1_1algorithms.html#ac8e4eb795d14d441c4b2944c070a1d78',1,'vg::algorithms::is_tail_node()']]],
- ['is_5ftraversable_9767',['is_traversable',['../classvg_1_1LegacyCaller.html#a369827412ee13857083444776aa240c7',1,'vg::LegacyCaller::is_traversable()'],['../classvg_1_1MCMCCaller.html#a1e632e1f6e31cd559ec0a6c3cff1db7c',1,'vg::MCMCCaller::is_traversable()']]],
- ['is_5ftrivial_9768',['is_trivial',['../classvg_1_1SnarlManager.html#a5fdc8b210fa5339485b1e0a8ab1683b6',1,'vg::SnarlManager']]],
- ['is_5fvalid_9769',['is_valid',['../classvg_1_1Sampler.html#a6f979036816c6f3657c98193b9b1e22d',1,'vg::Sampler::is_valid()'],['../classvg_1_1VG.html#aa77d93fdf76698460ce509ea5dcde954',1,'vg::VG::is_valid()'],['../structvg_1_1Range.html#a15b962d68b5743aa9ba5f8a487007a83',1,'vg::Range::is_valid()']]],
- ['is_5fvalid_5ftag_9770',['is_valid_tag',['../classvg_1_1io_1_1Registry.html#a4985634eed56438635dfbe0999103305',1,'vg::io::Registry']]],
- ['is_5fweakly_5fconnected_9771',['is_weakly_connected',['../namespacehandlegraph_1_1algorithms.html#a99bd1e8b398ce2df3530cc47baef8818',1,'handlegraph::algorithms']]],
- ['isatgc_9772',['isATGC',['../namespacevg.html#a92c923774a6526b7bfc7f06ae4ae7a18',1,'vg']]],
- ['isbgzf_9773',['IsBGZF',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a1eb2633e42ca1b50ab167497e581e6bd',1,'vg::io::BlockedGzipInputStream']]],
- ['iterator_9774',['iterator',['../classvg_1_1ShuffledPairs_1_1iterator.html#ade5cfb8f4e824c4d02c51df5ca396096',1,'vg::ShuffledPairs::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ShuffledPairs_1_1iterator.html#a3b52dd39c46e409ef1bfd67ab8ee76e4',1,'vg::ShuffledPairs::iterator::iterator(const ShuffledPairs &iteratee, size_t start_at)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0f330d79400d74c3da0c81e4af73d441',1,'vg::PhasedGenome::iterator::iterator(size_t rank, int haplotype_number, HaplotypeNode *haplo_node)'],['../classvg_1_1PhasedGenome_1_1iterator.html#ac8ddc9db361c6f07887fdc36b5484bcf',1,'vg::PhasedGenome::iterator::iterator()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a03bdcb94d8ed8b6e895ff003412185e4',1,'vg::PhasedGenome::iterator::iterator(const iterator &other)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aba25925d1c05e690d672b69ff66a3beb',1,'vg::ZipCodeTree::iterator::iterator(vector< tree_item_t >::const_iterator begin, vector< tree_item_t >::const_iterator end)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a51bef2f0839b26694742584b8a6dbedd',1,'vg::ZipCodeTree::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a171cb654dcd53b1bf78670b4002ba988',1,'vg::ZipCodeTree::iterator::iterator(iterator &&other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac02b7134a97591fcd4a821093a0a4ab4',1,'handlegraph::PathForEachSocket::iterator::iterator(const iterator &other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aed3d6dd2502cf236a6a55ed29e8c41dc',1,'handlegraph::PathForEachSocket::iterator::iterator()=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#af854ca3bd6cdbcfc8af01f7879f85106',1,'handlegraph::PathForEachSocket::iterator::iterator(const step_handle_t &step, bool force_unequal, const PathHandleGraph *graph)']]]
+ ['i_9632',['I',['../structhaplo_1_1haplo__DP__rectangle.html#ad961ad4ab25e6d0358b58dc44b3c0319',1,'haplo::haplo_DP_rectangle']]],
+ ['id_9633',['id',['../namespacevg.html#a9f6602b7e7a46c19819c8f362147b315',1,'vg::id()'],['../namespacexg.html#a7bfa373a28253072de64785adc9b1188',1,'xg::id()']]],
+ ['id_5fmap_9634',['id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a22e20a6a984b3dd5def4ad22836b15b9',1,'vg::algorithms::GFAParser']]],
+ ['id_5forder_9635',['id_order',['../namespacevg_1_1algorithms.html#a54730e9452c2609633da201ba85a8bca',1,'vg::algorithms']]],
+ ['id_5fsort_9636',['id_sort',['../classvg_1_1VG.html#ab1aecdffe7759a1e14248e00f2866b84',1,'vg::VG']]],
+ ['id_5fto_5fprefix_9637',['id_to_prefix',['../classvg_1_1StreamIndexBase.html#a4b0e44b8cb40b33c5ef4db47a8a89272',1,'vg::StreamIndexBase']]],
+ ['id_5fto_5frank_9638',['id_to_rank',['../classvg_1_1Viz.html#a2474cd8505ed561cd414648438fedb5e',1,'vg::Viz::id_to_rank()'],['../classxg_1_1XG.html#a39172dc94153da745dd765f3c45ceeea',1,'xg::XG::id_to_rank()'],['../classhandlegraph_1_1RankedHandleGraph.html#a4c919e31efff422d9a29fa264290836c',1,'handlegraph::RankedHandleGraph::id_to_rank()']]],
+ ['identify_5faligned_5fsplice_5fcandidates_9639',['identify_aligned_splice_candidates',['../classvg_1_1MultipathMapper.html#aa97ce2f7dcd38916169b78483b7c21ec',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< multipath_alignment_t > &multipath_alns, const vector< size_t > &cluster_idxs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const'],['../classvg_1_1MultipathMapper.html#a63fc3e0fac9b46faf4c28fe47c88c784',1,'vg::MultipathMapper::identify_aligned_splice_candidates(const Alignment &alignment, bool read_1, bool search_left, const pair< int64_t, int64_t > &primary_interval, const vector< pair< multipath_alignment_t, multipath_alignment_t >> &multipath_aln_pairs, const vector< pair< pair< size_t, size_t >, int64_t >> &cluster_pairs, const vector< int64_t > ¤t_index, int64_t anchor, unordered_set< size_t > &clusters_used_out, vector< size_t > &mp_aln_candidates_out) const']]],
+ ['identify_5fpinning_5fpoints_9640',['identify_pinning_points',['../classvg_1_1GSSWAligner.html#a4cd705824a3926a510fea64f883cab66',1,'vg::GSSWAligner']]],
+ ['identify_5fsources_5fand_5fsinks_9641',['identify_sources_and_sinks',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aff810bb5affe3201fccf437be3290fde',1,'vg::MEMClusterer::HitGraph']]],
+ ['identify_5fstart_5fsubpaths_9642',['identify_start_subpaths',['../namespacevg.html#a0844cc3c2da56dfed0e9436d7f0dd7de',1,'vg']]],
+ ['identify_5funaligned_5fsplice_5fcandidates_9643',['identify_unaligned_splice_candidates',['../classvg_1_1MultipathMapper.html#a50f4e1e71c3fb6272009297f1e012493',1,'vg::MultipathMapper']]],
+ ['identity_9644',['identity',['../namespacevg.html#ab3c5c7a407962a8c735c1d533cc0b186',1,'vg']]],
+ ['identity_5ftranslation_9645',['identity_translation',['../classvg_1_1VG.html#ab015755dc8b427f4e226f920eb26c428',1,'vg::VG']]],
+ ['identityoverlay_9646',['IdentityOverlay',['../classvg_1_1IdentityOverlay.html#ab287d9dd0b6b6c0832dc725a2cdb6740',1,'vg::IdentityOverlay::IdentityOverlay(const HandleGraph *graph)'],['../classvg_1_1IdentityOverlay.html#a8a699d8689c9d93e72a7e78023cc3413',1,'vg::IdentityOverlay::IdentityOverlay()=default']]],
+ ['immutable_5fpath_5ffrom_5flength_9647',['immutable_path_from_length',['../classvg_1_1MinimizerMapper.html#ab3008803e2ce57d5bbcd6a077f9dcde6',1,'vg::MinimizerMapper']]],
+ ['in_5fnontrivial_5fchain_9648',['in_nontrivial_chain',['../classvg_1_1SnarlManager.html#a92c63ede9881ce261258540ceb40fddb',1,'vg::SnarlManager']]],
+ ['in_5fplace_5fsubvector_9649',['in_place_subvector',['../namespacevg.html#a62239efefb85e451fcec6519644186d1',1,'vg']]],
+ ['include_9650',['include',['../classvg_1_1VG.html#a66e4dac76edcf0218f9749352c19acae',1,'vg::VG']]],
+ ['inclusive_5finterval_9651',['inclusive_interval',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af66a44ac51fe4a01ce0b24e0490b657b',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['increment_5fcoverage_9652',['increment_coverage',['../classvg_1_1Packer.html#ab97f6f0bb52c3641aceb5ffe4359492d',1,'vg::Packer::increment_coverage(size_t i)'],['../classvg_1_1Packer.html#a4da9199584ad1279a1e0a54aea12c6c1',1,'vg::Packer::increment_coverage(size_t i, size_t v)']]],
+ ['increment_5fedge_5fcoverage_9653',['increment_edge_coverage',['../classvg_1_1Packer.html#a7e2313be4468ea83a3e8b6a75b00cd7c',1,'vg::Packer::increment_edge_coverage(size_t i)'],['../classvg_1_1Packer.html#abdc73870b8a141908a21eb7ff7c31d4f',1,'vg::Packer::increment_edge_coverage(size_t i, size_t v)']]],
+ ['increment_5fnode_5fids_9654',['increment_node_ids',['../classvg_1_1Paths.html#a8a9b275a5979218a784105364248b5ba',1,'vg::Paths::increment_node_ids()'],['../classvg_1_1VG.html#a86b3ecdf29d100a8d43f6aaccd6f2e0e',1,'vg::VG::increment_node_ids()'],['../classhandlegraph_1_1MutableHandleGraph.html#a902b211a1f86645818b3da1cb64af0be',1,'handlegraph::MutableHandleGraph::increment_node_ids(nid_t increment)'],['../classhandlegraph_1_1MutableHandleGraph.html#a877dc8c0ae9a584907d45328512720cc',1,'handlegraph::MutableHandleGraph::increment_node_ids(long increment)']]],
+ ['increment_5fnode_5fmapping_5fids_9655',['increment_node_mapping_ids',['../namespacevg.html#a9fa6175557c33cd572b8726222cf6547',1,'vg']]],
+ ['increment_5fnode_5fquality_9656',['increment_node_quality',['../classvg_1_1Packer.html#a0195e9186f8162fc4fab673fbd65b0a8',1,'vg::Packer']]],
+ ['increment_5fprogress_9657',['increment_progress',['../classvg_1_1Progressive.html#ab1de11917caf25974a02e2f5c3946280',1,'vg::Progressive']]],
+ ['incremental_5fextend_9658',['incremental_extend',['../classhaplo_1_1ScoreProvider.html#a834b5b57b025ae27cc2c668869ee9b13',1,'haplo::ScoreProvider::incremental_extend()'],['../classhaplo_1_1GBWTScoreProvider.html#af52bee39ffe97d84ba020c49f7fbf7a6',1,'haplo::GBWTScoreProvider::incremental_extend()']]],
+ ['incremental_5ffind_9659',['incremental_find',['../classhaplo_1_1ScoreProvider.html#a6272d9bca95e7846807ef2e71d616a9c',1,'haplo::ScoreProvider::incremental_find()'],['../classhaplo_1_1GBWTScoreProvider.html#a540105f41d66c4b536fda44fce248680',1,'haplo::GBWTScoreProvider::incremental_find()']]],
+ ['incrementalsubgraph_9660',['IncrementalSubgraph',['../classvg_1_1IncrementalSubgraph.html#ab942f4d62b91144afce73896b8004609',1,'vg::IncrementalSubgraph::IncrementalSubgraph(const HandleGraph &graph, const pos_t &starting_position, bool extract_left, int64_t max_distance=numeric_limits< int64_t >::max(), size_t frontier_copy_limit=numeric_limits< size_t >::max(), size_t max_num_nodes=numeric_limits< size_t >::max())'],['../classvg_1_1IncrementalSubgraph.html#a4c8f5a87dfcf68630d645a9469e75837',1,'vg::IncrementalSubgraph::IncrementalSubgraph()=default']]],
+ ['incrementiter_9661',['IncrementIter',['../structvg_1_1IncrementIter.html#a1231b6b6c0fde0c7ae6cf69b9cfe9a6b',1,'vg::IncrementIter']]],
+ ['index_9662',['index',['../classvg_1_1StreamIndex.html#a8ee1930510b5d02e9a00ba1a246ba146',1,'vg::StreamIndex']]],
+ ['index_5fedge_5fby_5fnode_5fsides_9663',['index_edge_by_node_sides',['../classvg_1_1VG.html#a53ff7033966852f5fb3852716cab21a9',1,'vg::VG']]],
+ ['index_5fnode_5fto_5fpath_9664',['index_node_to_path',['../classxg_1_1XG.html#a4599310a72acd2ccfbe9d6041cc51dd1',1,'xg::XG']]],
+ ['index_5fpath_5fnames_9665',['index_path_names',['../classxg_1_1XG.html#aff97dc01cda8460ebeb98a4b789e3485',1,'xg::XG']]],
+ ['index_5fto_5fnode_9666',['index_to_node',['../classvg_1_1Packer.html#a967dcbe2cbcb6df4c7e2d938f7cd11fa',1,'vg::Packer']]],
+ ['indexedvg_9667',['IndexedVG',['../classvg_1_1IndexedVG.html#a89030b52047b0e005a5c86b7f9a206f6',1,'vg::IndexedVG::IndexedVG(string graph_filename)'],['../classvg_1_1IndexedVG.html#a0972bd3bf8d93bfa8b41aff828aab070',1,'vg::IndexedVG::IndexedVG(const IndexedVG &other)=delete']]],
+ ['indexfile_9668',['IndexFile',['../classvg_1_1IndexFile.html#ae22fd6ea5fd4419ca8ed2070410638ca',1,'vg::IndexFile']]],
+ ['indexingplan_9669',['IndexingPlan',['../classvg_1_1IndexingPlan.html#a5e6231a7a515964589ea8e55e8e2d5fe',1,'vg::IndexingPlan']]],
+ ['indexrecipe_9670',['IndexRecipe',['../structvg_1_1IndexRecipe.html#a11948f5026c5aff21e22775446e419b6',1,'vg::IndexRecipe']]],
+ ['indexregistry_9671',['IndexRegistry',['../classvg_1_1IndexRegistry.html#a0a0debbd6d61db053403e7cbca69d4c2',1,'vg::IndexRegistry::IndexRegistry()=default'],['../classvg_1_1IndexRegistry.html#aec3008292713502924fcf3cc51253e4f',1,'vg::IndexRegistry::IndexRegistry(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#aa4f9837b4beb749a06b3dcb3150475b0',1,'vg::IndexRegistry::IndexRegistry(IndexRegistry &&other)']]],
+ ['init_9672',['init',['../classvg_1_1SpliceStats.html#afd5923a5cd636a140697cad2605fc415',1,'vg::SpliceStats::init()'],['../classvg_1_1VG.html#aafd0f191fe33bd4590f15f309d0fd89c',1,'vg::VG::init()'],['../classvg_1_1Viz.html#aad7ceb7896288f2d4444b10cceb946d8',1,'vg::Viz::init()']]],
+ ['init_5fcoverage_5fbin_9673',['init_coverage_bin',['../classvg_1_1Packer.html#abdd9bd13b38dced4c61d78e5baf3c0fb',1,'vg::Packer']]],
+ ['init_5fedge_5fcoverage_5fbin_9674',['init_edge_coverage_bin',['../classvg_1_1Packer.html#a693598b3d8227598075e02fbc8124789',1,'vg::Packer']]],
+ ['init_5fmapper_9675',['init_mapper',['../classvg_1_1Filter.html#abd9fa5045b867b20e1b20e3d74d77e4b',1,'vg::Filter']]],
+ ['init_5fnode_5fquality_5fbin_9676',['init_node_quality_bin',['../classvg_1_1Packer.html#aff44bf5abf4eacda46958eeb436eb2e4',1,'vg::Packer']]],
+ ['init_5fsnarls_9677',['init_snarls',['../classvg_1_1Masker.html#a28b4317d6319672c9b9fa02b0e515335',1,'vg::Masker']]],
+ ['init_5fstate_9678',['init_state',['../classvg_1_1DinucleotideMachine.html#a35193673a88abc7f0933d2f65fd7f2ea',1,'vg::DinucleotideMachine']]],
+ ['init_5ftraceback_5findexes_9679',['init_traceback_indexes',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ab251d4ff6f6b7f351f29c5dd29ead002',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['initial_5fposition_9680',['initial_position',['../namespacevg.html#acd31d3a8dc67801f147d0ba1b0059c3f',1,'vg::initial_position(const Path &path)'],['../namespacevg.html#a5273bbd5e5d0f9bbf639c19c962a58dd',1,'vg::initial_position(const path_t &path)']]],
+ ['initialize_5fsam_5ffile_9681',['initialize_sam_file',['../classvg_1_1HTSWriter.html#a3063999c0e6b467c7717edfb53040166',1,'vg::HTSWriter']]],
+ ['input_5fgroup_9682',['input_group',['../structvg_1_1IndexRecipe.html#aa22beac92907ecf99b821ee6bfed4e33',1,'vg::IndexRecipe']]],
+ ['inputstream_9683',['inputStream',['../namespacevg_1_1io.html#a857cf3810d138ef43e25aa37f147ac25',1,'vg::io']]],
+ ['ins_5fpredecessor_9684',['ins_predecessor',['../classvg_1_1WFATree.html#a8ab38ec2797b5119eb9ffd213bdb957e',1,'vg::WFATree']]],
+ ['insert_9685',['insert',['../classvg_1_1SnarlState.html#a428e616c3ef0bab94325edbd728819e3',1,'vg::SnarlState::insert(const vector< pair< handle_t, size_t >> &haplotype)'],['../classvg_1_1SnarlState.html#a8489b6496d77d037d0ee2f0367119a3a',1,'vg::SnarlState::insert(size_t overall_lane, const vector< handle_t > &haplotype, bool backward=false)'],['../classvg_1_1HandleGraphNodeSet.html#a2c8d82e307853b75c099422d8e5e717c',1,'vg::HandleGraphNodeSet::insert()'],['../structvg_1_1RecombinatorHaplotype.html#a370a97d18bca8d1448eb359eee91be6e',1,'vg::RecombinatorHaplotype::insert()'],['../classvg_1_1SmallBitset.html#a9336d107ad4a8f98005ecfcf313e1334',1,'vg::SmallBitset::insert()'],['../classvg_1_1BitStringTree.html#ac323a5f006f9ad739facc0f306b1b6ed',1,'vg::BitStringTree::insert()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#a1658df8b5e184e15cce3b5e70bc2769c',1,'vg::BitStringTree::TreeNode::insert()'],['../structjob__type.html#a28737e853741fb1798c718e3637070b0',1,'job_type::insert()']]],
+ ['insert_5fgbwt_5fpath_9686',['insert_gbwt_path',['../namespacevg.html#a9bf4a7dd2a81bb5b873127156a2dfb33',1,'vg']]],
+ ['insert_5fhandles_9687',['insert_handles',['../classvg_1_1GenomeState.html#aa85289ade641db44976ac969c5fb6750',1,'vg::GenomeState']]],
+ ['insert_5fhaplotype_9688',['insert_haplotype',['../classvg_1_1GenomeState.html#a371e13f6d644e9979fa0e5177ffaadba',1,'vg::GenomeState']]],
+ ['insert_5fleft_9689',['insert_left',['../classvg_1_1PhasedGenome.html#a02e624546cf3f5675fbfa128c080c75d',1,'vg::PhasedGenome']]],
+ ['insert_5fmapping_9690',['insert_mapping',['../classvg_1_1Paths.html#aa6e0eb5748713837711612e5e347f8cb',1,'vg::Paths']]],
+ ['insert_5fpath_9691',['insert_path',['../classvg_1_1PhaseUnfolder.html#a28e7cee8d0922cf0aac91dba0d86f1c3',1,'vg::PhaseUnfolder']]],
+ ['insert_5fright_9692',['insert_right',['../classvg_1_1PhasedGenome.html#adfbd6242bff1445e5210f4046150fc85',1,'vg::PhasedGenome']]],
+ ['insert_5fsize_5ffilter_9693',['insert_size_filter',['../classvg_1_1Filter.html#a198243f4ffebc1b1442ca4521542ac99',1,'vg::Filter']]],
+ ['insert_5ftraceback_9694',['insert_traceback',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#aa6db44fa8e957169e11fd1a7853d2a19',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['insertion_5ffilter_9695',['insertion_filter',['../classvg_1_1Filter.html#a02bb368759eef77f7f7aa3753b23469e',1,'vg::Filter']]],
+ ['insufficientinputexception_9696',['InsufficientInputException',['../classvg_1_1InsufficientInputException.html#a2361f9743d9c5f2af8bb170a6240b891',1,'vg::InsufficientInputException::InsufficientInputException()=delete'],['../classvg_1_1InsufficientInputException.html#af9014e0e82772828f66dc699e2eb8734',1,'vg::InsufficientInputException::InsufficientInputException(const IndexName &target, const IndexRegistry ®istry) noexcept']]],
+ ['int_5fto_5fstring_9697',['int_to_string',['../namespacegafkluge.html#ad9c7bb306be39ddca425533a3583d71e',1,'gafkluge']]],
+ ['int_5fweighted_5fsum_9698',['int_weighted_sum',['../namespacehaplo_1_1haploMath.html#a5bc2868874173d377a55c788f21796ef',1,'haplo::haploMath::int_weighted_sum(double *values, int64_t *counts, size_t n_values)'],['../namespacehaplo_1_1haploMath.html#ab17ccf8a6fa509f269bdaf1c69e4f6bc',1,'haplo::haploMath::int_weighted_sum(vector< double > values, vector< int64_t > counts)']]],
+ ['integer_5fpower_9699',['integer_power',['../namespacevg.html#aca4239af1a9e3eb1283f78bf5cc1411a',1,'vg::integer_power(uint64_t base, uint64_t exponent)'],['../namespacevg.html#aa7c32d1e90ec006624a7ee03655f3c35',1,'vg::integer_power(size_t x, size_t power)']]],
+ ['integratedsnarlfinder_9700',['IntegratedSnarlFinder',['../classvg_1_1IntegratedSnarlFinder.html#a888085d87664c7e58ad4f988091c62f5',1,'vg::IntegratedSnarlFinder']]],
+ ['interchromosomal_5ffilter_9701',['interchromosomal_filter',['../classvg_1_1Filter.html#a1f1daa97b40d6ca6b2a3f37950f4f117',1,'vg::Filter']]],
+ ['intersect_5fpath_5foffsets_9702',['intersect_path_offsets',['../namespacevg_1_1algorithms.html#a9ce4dabb6661657c7d72593afc3f41df',1,'vg::algorithms']]],
+ ['intersection_9703',['intersection',['../structhaplo_1_1int__itvl__t.html#ade4051b750fcce428be13a69663ec035',1,'haplo::int_itvl_t']]],
+ ['interval_5flength_9704',['interval_length',['../namespacevg.html#a9467900ec651b93d47190413208cdf6f',1,'vg']]],
+ ['interval_5fsize_9705',['interval_size',['../structhaplo_1_1haplo__DP__rectangle.html#a751f03ab1d68636c47340dbd376b66a8',1,'haplo::haplo_DP_rectangle']]],
+ ['interval_5fstate_5ft_9706',['interval_state_t',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#aa86bab20d96ef26dc66afadf5dd22195',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['into_5fcutting_5fsnarl_9707',['into_cutting_snarl',['../classvg_1_1MultipathAlignmentGraph.html#a44bd7328dd8ea140223226ae4da8afff',1,'vg::MultipathAlignmentGraph']]],
+ ['into_5fwhich_5fsnarl_9708',['into_which_snarl',['../classvg_1_1SnarlManager.html#ac08074e3073ecd2ef72a57116b459577',1,'vg::SnarlManager::into_which_snarl(int64_t id, bool reverse) const'],['../classvg_1_1SnarlManager.html#a852f930d4e68e9bbd664ebe5a73a4669',1,'vg::SnarlManager::into_which_snarl(const Visit &visit) const']]],
+ ['introduce_9709',['introduce',['../classvg_1_1Funnel.html#adfe8a13519ae236c400f3ad68980e16c',1,'vg::Funnel']]],
+ ['intron_5flength_5flog_5flikelihood_9710',['intron_length_log_likelihood',['../classvg_1_1SpliceStats.html#ad61aebd450e01500b86d1fec55b8ccd9',1,'vg::SpliceStats']]],
+ ['intron_5flength_5fscore_9711',['intron_length_score',['../classvg_1_1SpliceStats.html#aedf26f015ecfb06f71aadbca66c81935',1,'vg::SpliceStats']]],
+ ['inversion_5ffilter_9712',['inversion_filter',['../classvg_1_1Filter.html#a5503147c786a4d9bfb18fc081630b5f6',1,'vg::Filter']]],
+ ['invert_9713',['invert',['../structvg_1_1Counts.html#a3a4cf08069fb263d89a96b86313a04a2',1,'vg::Counts']]],
+ ['invert_5ftranslation_9714',['invert_translation',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#abeffeb079b7f3997db8cfbb9a701f63c',1,'vg::algorithms::GFAIDMapInfo']]],
+ ['is_5fa_5fduplicate_5fhandle_9715',['is_a_duplicate_handle',['../classvg_1_1DozeuPinningOverlay.html#a3089cf35214f919d15030e029df3f6eb',1,'vg::DozeuPinningOverlay']]],
+ ['is_5fa_5fduplicate_5fid_9716',['is_a_duplicate_id',['../classvg_1_1DozeuPinningOverlay.html#ab549aa4693c8425cd1df8d04a04a178f',1,'vg::DozeuPinningOverlay']]],
+ ['is_5facyclic_9717',['is_acyclic',['../namespacehandlegraph_1_1algorithms.html#a03c1bfbc47b88a0bd18ca2cc93a1b0b3',1,'handlegraph::algorithms']]],
+ ['is_5fall_5fn_9718',['is_all_n',['../namespacevg.html#abe6f7955b97d8537da2133a47f37f462',1,'vg']]],
+ ['is_5fancestor_5fnext_9719',['is_ancestor_next',['../classvg_1_1VG.html#a7903acd7a977a85fdd78d306f2063252',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ab919097a72a96dada04310b2aaf019f8',1,'vg::VG::is_ancestor_next(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
+ ['is_5fancestor_5fprev_9720',['is_ancestor_prev',['../classvg_1_1VG.html#a25215a67c3eac7570e2ab62e825ae169',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id)'],['../classvg_1_1VG.html#ae6699fe9d747f761f6efae39c3c0501c',1,'vg::VG::is_ancestor_prev(nid_t node_id, nid_t candidate_id, set< nid_t > &seen, size_t steps=64)']]],
+ ['is_5fany_5fpainted_9721',['is_any_painted',['../structvg_1_1Funnel_1_1PaintableSpace.html#ab42e113d364cfa7da4e7b0c76ba448f1',1,'vg::Funnel::PaintableSpace']]],
+ ['is_5fchain_9722',['is_chain',['../classhandlegraph_1_1SnarlDecomposition.html#ad383774992bf6a3acc5fd34dc8cd9770',1,'handlegraph::SnarlDecomposition']]],
+ ['is_5fchild_9723',['is_child',['../classvg_1_1NetGraph.html#a25dbff454e5c9aa081c354f05523a512',1,'vg::NetGraph']]],
+ ['is_5fconsistent_9724',['is_consistent',['../classvg_1_1MultipathMapper.html#a76742066028c14330177d74d9cd0286c',1,'vg::MultipathMapper']]],
+ ['is_5fcorrect_9725',['is_correct',['../classvg_1_1Funnel.html#a4296184811926cf97a42d52aaf3fc6f6',1,'vg::Funnel']]],
+ ['is_5fcorrectly_5fmapped_9726',['is_correctly_mapped',['../classvg_1_1ReadFilter.html#ac5da32515034e6669d9e14de3c748122',1,'vg::ReadFilter::is_correctly_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#ab76d4dc77becdaf866f724d5b88dcdb5',1,'vg::ReadFilter::is_correctly_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a053397b20bc378d11f11b365e6d68032',1,'vg::ReadFilter::is_correctly_mapped(const MultipathAlignment &alignment) const']]],
+ ['is_5fdirected_5facyclic_9727',['is_directed_acyclic',['../namespacehandlegraph_1_1algorithms.html#afe81ab458644253f1064ffa3c73783a3',1,'handlegraph::algorithms']]],
+ ['is_5fdynamic_9728',['is_dynamic',['../classvg_1_1Packer.html#a370e8ef56ffd369c6a498aa36ed9c570',1,'vg::Packer']]],
+ ['is_5fempty_9729',['is_empty',['../structhaplo_1_1haplo__DP__column.html#af8bc221754159aa83d44d9373359939c',1,'haplo::haplo_DP_column::is_empty()'],['../classvg_1_1MemoizingGraph.html#a4596372ebc27c5e849127f4f09d9ae6b',1,'vg::MemoizingGraph::is_empty()'],['../classhandlegraph_1_1PathHandleGraph.html#aef3f2c04d1e315e485460dcd902467cb',1,'handlegraph::PathHandleGraph::is_empty()'],['../namespacevg.html#a3620df68e5af61a8eb660e4a4838ea06',1,'vg::is_empty()'],['../namespacexg.html#a9ef9c7147d5ae7c20d60ec17581d81bb',1,'xg::is_empty()']]],
+ ['is_5fequal_9730',['is_equal',['../classvg_1_1ZipCode.html#a38f2c794e04f2ad21447358fd7b93665',1,'vg::ZipCode']]],
+ ['is_5fextendable_9731',['is_extendable',['../classvg_1_1IncrementalSubgraph.html#ada07715a97931d98157e8fc5aba697a9',1,'vg::IncrementalSubgraph']]],
+ ['is_5fexternally_5fend_5fend_5fconnected_9732',['is_externally_end_end_connected',['../classvg_1_1ZipCode.html#ac59bc5911574a1fa356cac4f90471324',1,'vg::ZipCode']]],
+ ['is_5fexternally_5fstart_5fend_5fconnected_9733',['is_externally_start_end_connected',['../classvg_1_1ZipCode.html#a28d318606661f6e99b2374b5a87f370f',1,'vg::ZipCode']]],
+ ['is_5fexternally_5fstart_5fstart_5fconnected_9734',['is_externally_start_start_connected',['../classvg_1_1ZipCode.html#a842b8118dd218d6451199c1fd5f2e04b',1,'vg::ZipCode']]],
+ ['is_5ffarther_5fthan_9735',['is_farther_than',['../classvg_1_1ZipCode.html#a967a3c40a7c49674c6d14883b6b02e71',1,'vg::ZipCode']]],
+ ['is_5ffinalized_9736',['is_finalized',['../classvg_1_1FragmentLengthDistribution.html#a4f1fa1f539e504fdd0f92467b81e9172',1,'vg::FragmentLengthDistribution']]],
+ ['is_5ffinished_9737',['is_finished',['../classvg_1_1IndexFile.html#a80f432755770a31c2c1fa4c41d404f8b',1,'vg::IndexFile']]],
+ ['is_5fgzipped_9738',['is_gzipped',['../namespacevg.html#a8f065676bdbe54b44e45961d7d40d8a5',1,'vg']]],
+ ['is_5fhead_5fnode_9739',['is_head_node',['../classvg_1_1VG.html#a80438f4ab98e10b68caab27fdece09ab',1,'vg::VG::is_head_node(nid_t id)'],['../classvg_1_1VG.html#a1bc3866468d5eb941fa6ba010ccce2ec',1,'vg::VG::is_head_node(Node *node)'],['../namespacevg_1_1algorithms.html#aa4cb6665721af1f7c749ca8f73472d6c',1,'vg::algorithms::is_head_node()']]],
+ ['is_5fhead_5for_5ftail_5fnode_9740',['is_head_or_tail_node',['../classvg_1_1Paths.html#afec902ce6a22b7aa3aeee25f20eb1386',1,'vg::Paths']]],
+ ['is_5fid_5fsortable_9741',['is_id_sortable',['../namespacevg.html#a5570a5685bef6eee6ac2697920ebc6c0',1,'vg']]],
+ ['is_5fin_5frange_9742',['is_in_range',['../classvg_1_1StreamIndexBase.html#ab2b832d8cca9dee3c38d452dc47da0e3',1,'vg::StreamIndexBase']]],
+ ['is_5fintermediate_9743',['is_intermediate',['../classvg_1_1IndexingPlan.html#ae04def089761ea2ef65532fabd909794',1,'vg::IndexingPlan']]],
+ ['is_5fleaf_9744',['is_leaf',['../structvg_1_1WFANode.html#af75c62d0086aaa47baa79808601cf4f0',1,'vg::WFANode::is_leaf()'],['../classvg_1_1SnarlManager.html#aef63882ba4ef5e098890b1eeb3bbb985',1,'vg::SnarlManager::is_leaf()']]],
+ ['is_5fleft_5fclipped_9745',['is_left_clipped',['../classvg_1_1Filter.html#a08ace85cd60850045415e5e6640b0038',1,'vg::Filter']]],
+ ['is_5fmapped_9746',['is_mapped',['../classvg_1_1ReadFilter.html#a1acad05129d0a6146416f596903216a8',1,'vg::ReadFilter::is_mapped(const Read &read) const'],['../classvg_1_1ReadFilter.html#acf05b0ded409cd19894c24b6fe9412bf',1,'vg::ReadFilter::is_mapped(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#ad1fe573ba370f839adb1cd28350cac81',1,'vg::ReadFilter::is_mapped(const MultipathAlignment &mp_alignment) const']]],
+ ['is_5fmatch_9747',['is_match',['../namespacevg.html#a52292dfd3869a811170f7c5c0d9da564',1,'vg']]],
+ ['is_5fmissing_9748',['is_missing',['../namespacegafkluge.html#a190e58cca553fe5b7b67dac6f7aad7d4',1,'gafkluge::is_missing(const std::string &s)'],['../namespacegafkluge.html#ae093534cbdd3fda37e3a75ea91a0f6b2',1,'gafkluge::is_missing(int64_t i)']]],
+ ['is_5fnew_9749',['is_new',['../structhaplo_1_1haplo__DP__rectangle.html#a509976d09905bfe9312bc855641a7a59',1,'haplo::haplo_DP_rectangle']]],
+ ['is_5fnode_9750',['is_node',['../classhandlegraph_1_1SnarlDecomposition.html#a6f410ac594c7ed44a7cc9b6e44077900',1,'handlegraph::SnarlDecomposition']]],
+ ['is_5fnovel_5fedge_9751',['is_novel_edge',['../structvg_1_1AugmentedGraph.html#ab0dd61392dacbee763cea6297d95f876',1,'vg::AugmentedGraph']]],
+ ['is_5fnovel_5fnode_9752',['is_novel_node',['../structvg_1_1AugmentedGraph.html#ac6f4df5e0f80b0509ff3ec26b685d5c9',1,'vg::AugmentedGraph']]],
+ ['is_5fnumber_9753',['is_number',['../namespacevg.html#af051490e6e94b4c476695610472cdf5b',1,'vg::is_number(const std::string &s)'],['../namespacevg.html#a97c44463adc7ddcc77ac9664692a62b8',1,'vg::is_number(const string &s)']]],
+ ['is_5fours_9754',['is_ours',['../classvg_1_1ExtraNodeGraph.html#a16421769feafbfb95e2466391a6fa97c',1,'vg::ExtraNodeGraph::is_ours()'],['../classvg_1_1SourceSinkOverlay.html#abe7c1c7dcdf76a6116f500654e73fb89',1,'vg::SourceSinkOverlay::is_ours()']]],
+ ['is_5fproper_5fpair_9755',['is_proper_pair',['../classvg_1_1ReadFilter.html#ad5ebb80a71eaf7c765f33b306ab230d8',1,'vg::ReadFilter']]],
+ ['is_5frev_9756',['is_rev',['../namespacevg.html#aac725dd44bc5a8f540554d4b1882c1fe',1,'vg::is_rev()'],['../namespacexg.html#a92c2e7f37dfa3b8b8dbb07d80e5482be',1,'xg::is_rev()']]],
+ ['is_5freverse_9757',['is_reverse',['../classvg_1_1mapping__t.html#a26eda6f4c9bc3da9376c2e0f5569aa62',1,'vg::mapping_t::is_reverse()'],['../classvg_1_1position__t.html#a7028d95b6cc9c55db816e9500949283b',1,'vg::position_t::is_reverse()'],['../classxg_1_1XGPath.html#a89bfa5d4417fea7455c520e6817108e7',1,'xg::XGPath::is_reverse()']]],
+ ['is_5froot_9758',['is_root',['../classvg_1_1WFATree.html#af1ad9e8285b7a9414d8af9ec257add49',1,'vg::WFATree::is_root()'],['../classvg_1_1SnarlManager.html#a294ce522d34dadb5288d6115c88dfa89',1,'vg::SnarlManager::is_root()'],['../classhandlegraph_1_1SnarlDecomposition.html#afef6c85a6564d6d3ec65bfb245e1f38c',1,'handlegraph::SnarlDecomposition::is_root()']]],
+ ['is_5fsecondary_9759',['is_secondary',['../classvg_1_1ReadFilter.html#a947155b6ed467a8ea83ac80db6e11a63',1,'vg::ReadFilter::is_secondary(const Read &read) const'],['../classvg_1_1ReadFilter.html#a44451e4c12ff1a923221d019c31c610c',1,'vg::ReadFilter::is_secondary(const MultipathAlignment &mp_aln) const'],['../classvg_1_1ReadFilter.html#ab4ae201744c8abc543d60afb24b294eb',1,'vg::ReadFilter::is_secondary(const Alignment &aln) const']]],
+ ['is_5fself_5flooping_9760',['is_self_looping',['../classvg_1_1VG.html#ad09549b6cfab8e1097dd207e01e57812',1,'vg::VG']]],
+ ['is_5fsentinel_9761',['is_sentinel',['../classhandlegraph_1_1SnarlDecomposition.html#af3ce2079f249448a8c8a829daedd1678',1,'handlegraph::SnarlDecomposition']]],
+ ['is_5fsingle_5fstranded_9762',['is_single_stranded',['../namespacehandlegraph_1_1algorithms.html#afbca1e7b54575bfce7f0844dbda83c6f',1,'handlegraph::algorithms']]],
+ ['is_5fskippable_9763',['is_skippable',['../classvg_1_1algorithms_1_1Anchor.html#a002732eac1459215244c89710a4ef2e3',1,'vg::algorithms::Anchor']]],
+ ['is_5fsnarl_9764',['is_snarl',['../classhandlegraph_1_1SnarlDecomposition.html#a32b29fc153b3a355cae8b15008ec8c1b',1,'handlegraph::SnarlDecomposition']]],
+ ['is_5fsnarl_5fsmaller_5fthan_5freads_9765',['is_snarl_smaller_than_reads',['../classvg_1_1Genotyper.html#a7c7f091482612f6b0cd2baf0c19c45fb',1,'vg::Genotyper']]],
+ ['is_5fsnv_9766',['is_snv',['../structhaplo_1_1linear__haplo__structure.html#aa95f64d55f6bf7b1239396ba4a722a05',1,'haplo::linear_haplo_structure']]],
+ ['is_5fsolitary_5fref_9767',['is_solitary_ref',['../structhaplo_1_1linear__haplo__structure.html#a5909bdd11b10437a4d70af1fda222a85',1,'haplo::linear_haplo_structure']]],
+ ['is_5fsplit_9768',['is_split',['../classvg_1_1ReadFilter.html#a34d313741dcfe8c009dfcc380d1293ad',1,'vg::ReadFilter::is_split(const Read &read) const'],['../classvg_1_1ReadFilter.html#a956bc9e366bb25f9544dbb3d8573b5b5',1,'vg::ReadFilter::is_split(const Alignment &alignment) const'],['../classvg_1_1ReadFilter.html#a3fcb1771035304240c7a0401d84ef60b',1,'vg::ReadFilter::is_split(const MultipathAlignment &mp_aln) const']]],
+ ['is_5fstatic_9769',['is_static',['../structvg_1_1subcommand_1_1TickChainLink.html#aae7e5f61e0f577ae29fd404c6f0a9482',1,'vg::subcommand::TickChainLink::is_static()'],['../structvg_1_1Range.html#a07b020e2621ac7d0a6cc636384242c73',1,'vg::Range::is_static()'],['../structvg_1_1subcommand_1_1RangeArgSpec.html#a20410637df207e212fee01c268624d85',1,'vg::subcommand::RangeArgSpec::is_static()']]],
+ ['is_5ftail_5fnode_9770',['is_tail_node',['../classvg_1_1VG.html#a660692b8769618259f69be25bfed0bc3',1,'vg::VG::is_tail_node(nid_t id)'],['../classvg_1_1VG.html#af58b227f21324d30be531088ed49b0f1',1,'vg::VG::is_tail_node(Node *node)'],['../namespacevg_1_1algorithms.html#ac8e4eb795d14d441c4b2944c070a1d78',1,'vg::algorithms::is_tail_node()']]],
+ ['is_5ftraversable_9771',['is_traversable',['../classvg_1_1LegacyCaller.html#a369827412ee13857083444776aa240c7',1,'vg::LegacyCaller::is_traversable()'],['../classvg_1_1MCMCCaller.html#a1e632e1f6e31cd559ec0a6c3cff1db7c',1,'vg::MCMCCaller::is_traversable()']]],
+ ['is_5ftrivial_9772',['is_trivial',['../classvg_1_1SnarlManager.html#a5fdc8b210fa5339485b1e0a8ab1683b6',1,'vg::SnarlManager']]],
+ ['is_5fvalid_9773',['is_valid',['../classvg_1_1Sampler.html#a6f979036816c6f3657c98193b9b1e22d',1,'vg::Sampler::is_valid()'],['../classvg_1_1VG.html#aa77d93fdf76698460ce509ea5dcde954',1,'vg::VG::is_valid()'],['../structvg_1_1Range.html#a15b962d68b5743aa9ba5f8a487007a83',1,'vg::Range::is_valid()']]],
+ ['is_5fvalid_5ftag_9774',['is_valid_tag',['../classvg_1_1io_1_1Registry.html#a4985634eed56438635dfbe0999103305',1,'vg::io::Registry']]],
+ ['is_5fweakly_5fconnected_9775',['is_weakly_connected',['../namespacehandlegraph_1_1algorithms.html#a99bd1e8b398ce2df3530cc47baef8818',1,'handlegraph::algorithms']]],
+ ['isatgc_9776',['isATGC',['../namespacevg.html#a92c923774a6526b7bfc7f06ae4ae7a18',1,'vg']]],
+ ['isbgzf_9777',['IsBGZF',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a1eb2633e42ca1b50ab167497e581e6bd',1,'vg::io::BlockedGzipInputStream']]],
+ ['iterator_9778',['iterator',['../classvg_1_1ShuffledPairs_1_1iterator.html#ade5cfb8f4e824c4d02c51df5ca396096',1,'vg::ShuffledPairs::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ShuffledPairs_1_1iterator.html#a3b52dd39c46e409ef1bfd67ab8ee76e4',1,'vg::ShuffledPairs::iterator::iterator(const ShuffledPairs &iteratee, size_t start_at)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0f330d79400d74c3da0c81e4af73d441',1,'vg::PhasedGenome::iterator::iterator(size_t rank, int haplotype_number, HaplotypeNode *haplo_node)'],['../classvg_1_1PhasedGenome_1_1iterator.html#ac8ddc9db361c6f07887fdc36b5484bcf',1,'vg::PhasedGenome::iterator::iterator()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a03bdcb94d8ed8b6e895ff003412185e4',1,'vg::PhasedGenome::iterator::iterator(const iterator &other)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aba25925d1c05e690d672b69ff66a3beb',1,'vg::ZipCodeTree::iterator::iterator(vector< tree_item_t >::const_iterator begin, vector< tree_item_t >::const_iterator end)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a51bef2f0839b26694742584b8a6dbedd',1,'vg::ZipCodeTree::iterator::iterator(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a171cb654dcd53b1bf78670b4002ba988',1,'vg::ZipCodeTree::iterator::iterator(iterator &&other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac02b7134a97591fcd4a821093a0a4ab4',1,'handlegraph::PathForEachSocket::iterator::iterator(const iterator &other)=default'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aed3d6dd2502cf236a6a55ed29e8c41dc',1,'handlegraph::PathForEachSocket::iterator::iterator()=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#af854ca3bd6cdbcfc8af01f7879f85106',1,'handlegraph::PathForEachSocket::iterator::iterator(const step_handle_t &step, bool force_unequal, const PathHandleGraph *graph)']]]
];
diff --git a/search/functions_a.js b/search/functions_a.js
index 577594a86c..ec00e647a3 100644
--- a/search/functions_a.js
+++ b/search/functions_a.js
@@ -1,17 +1,17 @@
var searchData=
[
- ['j2pb_5ferror_9775',['j2pb_error',['../classj2pb__error.html#af314b5998280a0298ef786b0d3e50765',1,'j2pb_error::j2pb_error(const std::string &e)'],['../classj2pb__error.html#a8276d8df905431fe862af63d9e2eb09a',1,'j2pb_error::j2pb_error(const FieldDescriptor *field, const std::string &e)']]],
- ['jaccard_5fcoefficient_9776',['jaccard_coefficient',['../namespacevg.html#aff10785a6df2466c851785b406172e89',1,'vg']]],
- ['jitter_5fhomopolymer_5fends_9777',['jitter_homopolymer_ends',['../classvg_1_1MultipathAlignmentGraph.html#a406e1b266f46b28d5d7b4e2041a9210d',1,'vg::MultipathAlignmentGraph']]],
- ['jobs_9778',['jobs',['../classvg_1_1Haplotypes.html#af1b40bc51ea14870df84ab86ca71c0ce',1,'vg::Haplotypes']]],
- ['jobschedule_9779',['JobSchedule',['../classvg_1_1JobSchedule.html#a3a959781a3d2b43dba66483468b27401',1,'vg::JobSchedule']]],
- ['join_9780',['join',['../structvg_1_1WFAAlignment.html#af2ab05c29ced20c7ad917e83a8b8c71a',1,'vg::WFAAlignment']]],
- ['join_5fheads_9781',['join_heads',['../classvg_1_1VG.html#a817384b8d147371448ad60e1db097b52',1,'vg::VG::join_heads(void)'],['../classvg_1_1VG.html#adc40377520118436b729cd68be16d0ba',1,'vg::VG::join_heads(Node *node, bool from_start=false)']]],
- ['join_5ftails_9782',['join_tails',['../classvg_1_1VG.html#a33e3f7942afd3ca82bfb78083c245146',1,'vg::VG']]],
- ['joinedsplicegraph_9783',['JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html#ac9f9c336a88b2c291c348cff4c30d563',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph(const HandleGraph &parent_graph, const IncrementalSubgraph &left_subgraph, handle_t left_splice_node, size_t left_splice_offset, const IncrementalSubgraph &right_subgraph, handle_t right_splice_node, size_t right_splice_offset)'],['../classvg_1_1JoinedSpliceGraph.html#a994fd7ad86bf77793da9a6ee2612cabc',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph()=default']]],
- ['json2graph_9784',['json2graph',['../namespacevg_1_1io.html#a550ead63070ee82e14eb16659099755b',1,'vg::io']]],
- ['json2pb_9785',['json2pb',['../json2pb_8cpp.html#a2eb37967f22b379b956fe97f7c974203',1,'json2pb(Message &msg, const char *buf, size_t size): json2pb.cpp'],['../json2pb_8cpp.html#a947740c497c7efcc20241ca8dcd890c5',1,'json2pb(Message &msg, FILE *fp): json2pb.cpp'],['../json2pb_8cpp.html#a3b3ae0b9e33187a31a408a4e4e82898b',1,'json2pb(Message &msg, const std::string &data): json2pb.cpp'],['../json2pb_8h.html#aee640ab0597802043d3778f2f8d251ab',1,'json2pb(google::protobuf::Message &msg, const char *buf, size_t size): json2pb.h'],['../json2pb_8h.html#ad3edc7550a299bb85558377c35581364',1,'json2pb(google::protobuf::Message &msg, FILE *fp): json2pb.h'],['../json2pb_8h.html#ae83324c05726c12f6a3602a6aa7b2182',1,'json2pb(google::protobuf::Message &msg, const std::string &data): json2pb.h']]],
- ['json_5fautoptr_9786',['json_autoptr',['../structjson__autoptr.html#a3879742fd5ef3183006f93ebc6e57678',1,'json_autoptr']]],
- ['jsonstreamhelper_9787',['JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html#ad795787bc270c5cfe737535f2e242aa6',1,'vg::io::JSONStreamHelper']]],
- ['jump_5falong_5fclosest_5fpath_9788',['jump_along_closest_path',['../namespacevg_1_1algorithms.html#a633a1600c6a7e447c040fefb1432e508',1,'vg::algorithms']]]
+ ['j2pb_5ferror_9779',['j2pb_error',['../classj2pb__error.html#af314b5998280a0298ef786b0d3e50765',1,'j2pb_error::j2pb_error(const std::string &e)'],['../classj2pb__error.html#a8276d8df905431fe862af63d9e2eb09a',1,'j2pb_error::j2pb_error(const FieldDescriptor *field, const std::string &e)']]],
+ ['jaccard_5fcoefficient_9780',['jaccard_coefficient',['../namespacevg.html#aff10785a6df2466c851785b406172e89',1,'vg']]],
+ ['jitter_5fhomopolymer_5fends_9781',['jitter_homopolymer_ends',['../classvg_1_1MultipathAlignmentGraph.html#a406e1b266f46b28d5d7b4e2041a9210d',1,'vg::MultipathAlignmentGraph']]],
+ ['jobs_9782',['jobs',['../classvg_1_1Haplotypes.html#af1b40bc51ea14870df84ab86ca71c0ce',1,'vg::Haplotypes']]],
+ ['jobschedule_9783',['JobSchedule',['../classvg_1_1JobSchedule.html#a3a959781a3d2b43dba66483468b27401',1,'vg::JobSchedule']]],
+ ['join_9784',['join',['../structvg_1_1WFAAlignment.html#af2ab05c29ced20c7ad917e83a8b8c71a',1,'vg::WFAAlignment']]],
+ ['join_5fheads_9785',['join_heads',['../classvg_1_1VG.html#a817384b8d147371448ad60e1db097b52',1,'vg::VG::join_heads(void)'],['../classvg_1_1VG.html#adc40377520118436b729cd68be16d0ba',1,'vg::VG::join_heads(Node *node, bool from_start=false)']]],
+ ['join_5ftails_9786',['join_tails',['../classvg_1_1VG.html#a33e3f7942afd3ca82bfb78083c245146',1,'vg::VG']]],
+ ['joinedsplicegraph_9787',['JoinedSpliceGraph',['../classvg_1_1JoinedSpliceGraph.html#ac9f9c336a88b2c291c348cff4c30d563',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph(const HandleGraph &parent_graph, const IncrementalSubgraph &left_subgraph, handle_t left_splice_node, size_t left_splice_offset, const IncrementalSubgraph &right_subgraph, handle_t right_splice_node, size_t right_splice_offset)'],['../classvg_1_1JoinedSpliceGraph.html#a994fd7ad86bf77793da9a6ee2612cabc',1,'vg::JoinedSpliceGraph::JoinedSpliceGraph()=default']]],
+ ['json2graph_9788',['json2graph',['../namespacevg_1_1io.html#a550ead63070ee82e14eb16659099755b',1,'vg::io']]],
+ ['json2pb_9789',['json2pb',['../json2pb_8cpp.html#a2eb37967f22b379b956fe97f7c974203',1,'json2pb(Message &msg, const char *buf, size_t size): json2pb.cpp'],['../json2pb_8cpp.html#a947740c497c7efcc20241ca8dcd890c5',1,'json2pb(Message &msg, FILE *fp): json2pb.cpp'],['../json2pb_8cpp.html#a3b3ae0b9e33187a31a408a4e4e82898b',1,'json2pb(Message &msg, const std::string &data): json2pb.cpp'],['../json2pb_8h.html#aee640ab0597802043d3778f2f8d251ab',1,'json2pb(google::protobuf::Message &msg, const char *buf, size_t size): json2pb.h'],['../json2pb_8h.html#ad3edc7550a299bb85558377c35581364',1,'json2pb(google::protobuf::Message &msg, FILE *fp): json2pb.h'],['../json2pb_8h.html#ae83324c05726c12f6a3602a6aa7b2182',1,'json2pb(google::protobuf::Message &msg, const std::string &data): json2pb.h']]],
+ ['json_5fautoptr_9790',['json_autoptr',['../structjson__autoptr.html#a3879742fd5ef3183006f93ebc6e57678',1,'json_autoptr']]],
+ ['jsonstreamhelper_9791',['JSONStreamHelper',['../classvg_1_1io_1_1JSONStreamHelper.html#ad795787bc270c5cfe737535f2e242aa6',1,'vg::io::JSONStreamHelper']]],
+ ['jump_5falong_5fclosest_5fpath_9792',['jump_along_closest_path',['../namespacevg_1_1algorithms.html#a633a1600c6a7e447c040fefb1432e508',1,'vg::algorithms']]]
];
diff --git a/search/functions_b.js b/search/functions_b.js
index b71db5a01f..acc1f1495c 100644
--- a/search/functions_b.js
+++ b/search/functions_b.js
@@ -1,27 +1,27 @@
var searchData=
[
- ['k_9789',['k',['../classvg_1_1Haplotypes.html#af081161e7b2e1867d83aef6427082cd5',1,'vg::Haplotypes::k()'],['../namespacehaplotypes__defaults.html#a53866dde2f0b53eb6e41923c4e3eb9ff',1,'haplotypes_defaults::k()']]],
- ['karger_5fstein_9790',['karger_stein',['../classvg_1_1MCMCGenotyper.html#ae04571da16e2129ef7d56aea9cc899b5',1,'vg::MCMCGenotyper']]],
- ['kargers_5fmin_5fcut_9791',['kargers_min_cut',['../namespacevg_1_1algorithms.html#a0820d23864c46dc1bc71ec68aee4e55e',1,'vg::algorithms']]],
- ['keep_9792',['keep',['../structvg_1_1Counts.html#a4ffc0e936d50a5bce649cc973f8cbe98',1,'vg::Counts']]],
- ['keep_5fpath_9793',['keep_path',['../classvg_1_1VG.html#a65cc16f52f478a25e84c6f1fc2805915',1,'vg::VG']]],
- ['keep_5fpaths_9794',['keep_paths',['../classvg_1_1Paths.html#a4ed60968ce4b7d6e4bd7f3d24c895f94',1,'vg::Paths::keep_paths()'],['../classvg_1_1VG.html#ac2aa9d438bcec4d7facbfcc44abea8fd',1,'vg::VG::keep_paths()']]],
- ['key_9795',['key',['../classvg_1_1ProblemDumpExplainer.html#a40a9715e80632f9e2e70b4d54f749579',1,'vg::ProblemDumpExplainer::key()'],['../structvg_1_1WFAPoint.html#ae19b5b586bb269c2e465d6a8e87c0041',1,'vg::WFAPoint::key()']]],
- ['kff_5fbytes_9796',['kff_bytes',['../namespacevg.html#ae8290bb0f46f4410bd8d19a9214f42d9',1,'vg']]],
- ['kff_5fdecode_9797',['kff_decode',['../namespacevg.html#adbd931ab5e8c6d8549262292b5fd1bdb',1,'vg::kff_decode(uint8_t byte, size_t chars, const std::string &decoding, std::string &output)'],['../namespacevg.html#a508b66314d777de73b671860cc1ba66f',1,'vg::kff_decode(const uint8_t *kmer, size_t k, const std::string &decoding)']]],
- ['kff_5fencode_9798',['kff_encode',['../namespacevg.html#a703f0e894fc3faab71d1f56963a1b1f2',1,'vg::kff_encode(const std::string &kmer, size_t start, size_t limit, const uint8_t *encoding)'],['../namespacevg.html#ad8ec52a5e105f9ff5dc0ee6a882f11ef',1,'vg::kff_encode(const std::string &kmer, const uint8_t *encoding)']]],
- ['kff_5fget_9799',['kff_get',['../namespacevg.html#a971fa4f581aa13c4d3a29728485a496a',1,'vg']]],
- ['kff_5finvert_9800',['kff_invert',['../namespacevg.html#afff8c68e07248aa6b304c3b9f45f8e4b',1,'vg']]],
- ['kff_5fis_5ftrivial_9801',['kff_is_trivial',['../namespacevg.html#ab293dcf09c223de43976346c70763cd8',1,'vg']]],
- ['kff_5fparse_9802',['kff_parse',['../namespacevg.html#ac3021a605be981221a7454ed41329abb',1,'vg']]],
- ['kff_5frecode_9803',['kff_recode',['../namespacevg.html#a1d573b735cb520c77d373fe1231fb94d',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, size_t chars, const uint8_t *encoding)'],['../namespacevg.html#acc31374a96e3cd653324ab57eb9714ff',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, const uint8_t *encoding)'],['../namespacevg.html#ab6b770ea79c9b74e89ecff6f5e347bf6',1,'vg::kff_recode(const uint8_t *kmer, size_t k, kff_recoding_t recoding)'],['../namespacevg.html#a92ba361b3ec6a01bac17e71af08d2223',1,'vg::kff_recode(const uint8_t *kmers, size_t n, size_t k, kff_recoding_t recoding)']]],
- ['kff_5frecode_5ftrivial_9804',['kff_recode_trivial',['../namespacevg.html#ad52eac0801905a9d5f2ba805f1387213',1,'vg']]],
- ['kff_5frecoding_9805',['kff_recoding',['../namespacevg.html#a1429f1c00018d575e753609329896f31',1,'vg']]],
- ['kff_5freverse_5fcomplement_9806',['kff_reverse_complement',['../namespacevg.html#a213d22fbc9d8056efb8082e529ab0f22',1,'vg']]],
- ['kff_5fset_9807',['kff_set',['../namespacevg.html#ad78d3175e64e6a9c019275b5b3e17fe5',1,'vg']]],
- ['kmer_5fcounts_9808',['kmer_counts',['../classvg_1_1Haplotypes.html#a48ed72eff81d77df7a4159afd0c6d20e',1,'vg::Haplotypes']]],
- ['kmer_5ft_9809',['kmer_t',['../structvg_1_1kmer__t.html#a83d1946c92dcdc9c6adbc03b4da30312',1,'vg::kmer_t::kmer_t()'],['../structvg_1_1algorithms_1_1kmer__t.html#ae029bc309fbd34a7dd7391f9a74f79f5',1,'vg::algorithms::kmer_t::kmer_t()']]],
- ['kmer_5fto_5fgcsa_5fkmers_9810',['kmer_to_gcsa_kmers',['../namespacevg.html#a661fc17618ee9ff7bd9d469c74c63369',1,'vg']]],
- ['kmers_9811',['kmers',['../classvg_1_1Haplotypes.html#a85b9a6d31a3485f0ccf925023543414b',1,'vg::Haplotypes']]],
- ['kmp_5fsearch_9812',['kmp_search',['../namespacevg.html#a4f32c345e847a3627afcee659116730c',1,'vg']]]
+ ['k_9793',['k',['../classvg_1_1Haplotypes.html#af081161e7b2e1867d83aef6427082cd5',1,'vg::Haplotypes::k()'],['../namespacehaplotypes__defaults.html#a53866dde2f0b53eb6e41923c4e3eb9ff',1,'haplotypes_defaults::k()']]],
+ ['karger_5fstein_9794',['karger_stein',['../classvg_1_1MCMCGenotyper.html#ae04571da16e2129ef7d56aea9cc899b5',1,'vg::MCMCGenotyper']]],
+ ['kargers_5fmin_5fcut_9795',['kargers_min_cut',['../namespacevg_1_1algorithms.html#a0820d23864c46dc1bc71ec68aee4e55e',1,'vg::algorithms']]],
+ ['keep_9796',['keep',['../structvg_1_1Counts.html#a4ffc0e936d50a5bce649cc973f8cbe98',1,'vg::Counts']]],
+ ['keep_5fpath_9797',['keep_path',['../classvg_1_1VG.html#a65cc16f52f478a25e84c6f1fc2805915',1,'vg::VG']]],
+ ['keep_5fpaths_9798',['keep_paths',['../classvg_1_1Paths.html#a4ed60968ce4b7d6e4bd7f3d24c895f94',1,'vg::Paths::keep_paths()'],['../classvg_1_1VG.html#ac2aa9d438bcec4d7facbfcc44abea8fd',1,'vg::VG::keep_paths()']]],
+ ['key_9799',['key',['../classvg_1_1ProblemDumpExplainer.html#a40a9715e80632f9e2e70b4d54f749579',1,'vg::ProblemDumpExplainer::key()'],['../structvg_1_1WFAPoint.html#ae19b5b586bb269c2e465d6a8e87c0041',1,'vg::WFAPoint::key()']]],
+ ['kff_5fbytes_9800',['kff_bytes',['../namespacevg.html#ae8290bb0f46f4410bd8d19a9214f42d9',1,'vg']]],
+ ['kff_5fdecode_9801',['kff_decode',['../namespacevg.html#adbd931ab5e8c6d8549262292b5fd1bdb',1,'vg::kff_decode(uint8_t byte, size_t chars, const std::string &decoding, std::string &output)'],['../namespacevg.html#a508b66314d777de73b671860cc1ba66f',1,'vg::kff_decode(const uint8_t *kmer, size_t k, const std::string &decoding)']]],
+ ['kff_5fencode_9802',['kff_encode',['../namespacevg.html#a703f0e894fc3faab71d1f56963a1b1f2',1,'vg::kff_encode(const std::string &kmer, size_t start, size_t limit, const uint8_t *encoding)'],['../namespacevg.html#ad8ec52a5e105f9ff5dc0ee6a882f11ef',1,'vg::kff_encode(const std::string &kmer, const uint8_t *encoding)']]],
+ ['kff_5fget_9803',['kff_get',['../namespacevg.html#a971fa4f581aa13c4d3a29728485a496a',1,'vg']]],
+ ['kff_5finvert_9804',['kff_invert',['../namespacevg.html#afff8c68e07248aa6b304c3b9f45f8e4b',1,'vg']]],
+ ['kff_5fis_5ftrivial_9805',['kff_is_trivial',['../namespacevg.html#ab293dcf09c223de43976346c70763cd8',1,'vg']]],
+ ['kff_5fparse_9806',['kff_parse',['../namespacevg.html#ac3021a605be981221a7454ed41329abb',1,'vg']]],
+ ['kff_5frecode_9807',['kff_recode',['../namespacevg.html#a1d573b735cb520c77d373fe1231fb94d',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, size_t chars, const uint8_t *encoding)'],['../namespacevg.html#acc31374a96e3cd653324ab57eb9714ff',1,'vg::kff_recode(gbwtgraph::Key64::value_type kmer, size_t k, const uint8_t *encoding)'],['../namespacevg.html#ab6b770ea79c9b74e89ecff6f5e347bf6',1,'vg::kff_recode(const uint8_t *kmer, size_t k, kff_recoding_t recoding)'],['../namespacevg.html#a92ba361b3ec6a01bac17e71af08d2223',1,'vg::kff_recode(const uint8_t *kmers, size_t n, size_t k, kff_recoding_t recoding)']]],
+ ['kff_5frecode_5ftrivial_9808',['kff_recode_trivial',['../namespacevg.html#ad52eac0801905a9d5f2ba805f1387213',1,'vg']]],
+ ['kff_5frecoding_9809',['kff_recoding',['../namespacevg.html#a1429f1c00018d575e753609329896f31',1,'vg']]],
+ ['kff_5freverse_5fcomplement_9810',['kff_reverse_complement',['../namespacevg.html#a213d22fbc9d8056efb8082e529ab0f22',1,'vg']]],
+ ['kff_5fset_9811',['kff_set',['../namespacevg.html#ad78d3175e64e6a9c019275b5b3e17fe5',1,'vg']]],
+ ['kmer_5fcounts_9812',['kmer_counts',['../classvg_1_1Haplotypes.html#a48ed72eff81d77df7a4159afd0c6d20e',1,'vg::Haplotypes']]],
+ ['kmer_5ft_9813',['kmer_t',['../structvg_1_1kmer__t.html#a83d1946c92dcdc9c6adbc03b4da30312',1,'vg::kmer_t::kmer_t()'],['../structvg_1_1algorithms_1_1kmer__t.html#ae029bc309fbd34a7dd7391f9a74f79f5',1,'vg::algorithms::kmer_t::kmer_t()']]],
+ ['kmer_5fto_5fgcsa_5fkmers_9814',['kmer_to_gcsa_kmers',['../namespacevg.html#a661fc17618ee9ff7bd9d469c74c63369',1,'vg']]],
+ ['kmers_9815',['kmers',['../classvg_1_1Haplotypes.html#a85b9a6d31a3485f0ccf925023543414b',1,'vg::Haplotypes']]],
+ ['kmp_5fsearch_9816',['kmp_search',['../namespacevg.html#a4f32c345e847a3627afcee659116730c',1,'vg']]]
];
diff --git a/search/functions_c.js b/search/functions_c.js
index 558110b9ec..9df028ab83 100644
--- a/search/functions_c.js
+++ b/search/functions_c.js
@@ -1,85 +1,85 @@
var searchData=
[
- ['last_5fcorrect_5fstage_9813',['last_correct_stage',['../classvg_1_1Funnel.html#a996005ebe76091bbba404bf4a2a9a405',1,'vg::Funnel']]],
- ['last_5fpath_5fposition_9814',['last_path_position',['../namespacevg.html#aa1c1e5b8ce9f9607976913317102d6dc',1,'vg']]],
- ['last_5ftagged_5fstage_9815',['last_tagged_stage',['../classvg_1_1Funnel.html#ab53e816bd740407417b0bd8d14d5237c',1,'vg::Funnel']]],
- ['latest_9816',['latest',['../classvg_1_1Funnel.html#a933c8a296c5a680aa96b0b913c465250',1,'vg::Funnel']]],
- ['layout_5forder_5fof_5fhandle_9817',['layout_order_of_handle',['../classvg_1_1DagifiedGraph.html#af364d952c459117f871368bcc9d33573',1,'vg::DagifiedGraph']]],
- ['lazier_5ftopological_5forder_9818',['lazier_topological_order',['../namespacehandlegraph_1_1algorithms.html#a26e0547c886eede7d3c0766907f39645',1,'handlegraph::algorithms']]],
- ['lazy_5ftopological_5forder_9819',['lazy_topological_order',['../namespacehandlegraph_1_1algorithms.html#ac9c0542f382080d1af3914714a62b9b6',1,'handlegraph::algorithms']]],
- ['lazy_5ftopological_5forder_5finternal_9820',['lazy_topological_order_internal',['../namespacehandlegraph_1_1algorithms.html#a53c98a2b062e6b5e92757945788b2e91',1,'handlegraph::algorithms']]],
- ['lazyrng_9821',['LazyRNG',['../classvg_1_1LazyRNG.html#a34ef87c442913becab5f596f50bd850e',1,'vg::LazyRNG']]],
- ['left_5fdegree_9822',['left_degree',['../classvg_1_1VG.html#af9ac6e61dfa9350459dbb9586088c4a5',1,'vg::VG']]],
- ['left_5fseed_5fnode_9823',['left_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a8152492345122b0db73d6242b2958b45',1,'vg::JoinedSpliceGraph']]],
- ['left_5fsplice_5fnode_9824',['left_splice_node',['../classvg_1_1JoinedSpliceGraph.html#a37860d9de2993abb60cdf2fecce96c22',1,'vg::JoinedSpliceGraph']]],
- ['legacycaller_9825',['LegacyCaller',['../classvg_1_1LegacyCaller.html#a7c9d6aa80ac330f844aedc80d267c6dc',1,'vg::LegacyCaller']]],
- ['length_9826',['length',['../structvg_1_1WFANode.html#a9f70c59baed78d97644100b45cf865cd',1,'vg::WFANode::length()'],['../structvg_1_1GaplessExtension.html#a9c16f9e41fdfafb22a6a64c1e852bb9c',1,'vg::GaplessExtension::length()'],['../classvg_1_1MaximalExactMatch.html#a8f70425ec532b9c43694efbd40d2d587',1,'vg::MaximalExactMatch::length()'],['../classvg_1_1MEMAccelerator.html#a32cb183aeee38c64432c8ea66ff167d6',1,'vg::MEMAccelerator::length()'],['../classvg_1_1BitString.html#a07225c6d00ba670f2dd0b3d6dd83bf70',1,'vg::BitString::length()'],['../classvg_1_1VG.html#a23641dedefa2b6d573939515fcf5974c',1,'vg::VG::length()'],['../classvg_1_1algorithms_1_1Anchor.html#a2fbd6d0440d796d4feb855488bab5b24',1,'vg::algorithms::Anchor::length()'],['../classvg_1_1algorithms_1_1GFAParser.html#aea0cfcb22ae0987ea37f64c5cd547322',1,'vg::algorithms::GFAParser::length()'],['../structReferenceInterval.html#ae74cc528a4962e5049a5028f3d2fd416',1,'ReferenceInterval::length()']]],
- ['less_5fthan_9827',['less_than',['../classvg_1_1StreamSorter.html#a4ebd8489bcf1ea8c3155c1aa202ab2e2',1,'vg::StreamSorter::less_than(const Message &a, const Message &b) const'],['../classvg_1_1StreamSorter.html#a243723f25750130a537550ac111be9ed',1,'vg::StreamSorter::less_than(const Position &a, const Position &b) const']]],
- ['likelihoods_9828',['likelihoods',['../classvg_1_1VG.html#ada5821862279a350885f5368a54a5cba',1,'vg::VG']]],
- ['likely_5fmate_5fpositions_9829',['likely_mate_positions',['../classvg_1_1Mapper.html#a77e11337e9d2aed7a7ffdbb01e1ddd01',1,'vg::Mapper']]],
- ['likely_5fmismapping_9830',['likely_mismapping',['../classvg_1_1MultipathMapper.html#a30d9d4d69c937777d844baf2d60aed45',1,'vg::MultipathMapper']]],
- ['likely_5fmisrescue_9831',['likely_misrescue',['../classvg_1_1MultipathMapper.html#af0f679cfdca87e7a4d150c4f4c2b329a',1,'vg::MultipathMapper']]],
- ['limit_9832',['limit',['../structMappingRun.html#a3000c865dac9811ac82dc54c8073f553',1,'MappingRun']]],
- ['line_9833',['line',['../classvg_1_1TSVExplainer.html#a4d5e63408088dcb1185b613fb57bab04',1,'vg::TSVExplainer']]],
- ['linear_5fhaplo_5fstructure_9834',['linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html#abde17ce1452b109275975bf0e4f2d51c',1,'haplo::linear_haplo_structure']]],
- ['linearscoreprovider_9835',['LinearScoreProvider',['../classhaplo_1_1LinearScoreProvider.html#a096c19ba7e847bdeb344e79d487ba675',1,'haplo::LinearScoreProvider']]],
- ['list_5fhaplotypes_9836',['list_haplotypes',['../namespacevg.html#abe3c447c811f77c28669a36c4d3376b9',1,'vg']]],
- ['literal_5ftarget_5fmemory_5fusage_9837',['literal_target_memory_usage',['../classvg_1_1IndexingPlan.html#a93541f9db06d755f91d420072fe733e4',1,'vg::IndexingPlan']]],
- ['ln_5fto_5flog10_9838',['ln_to_log10',['../namespacevg.html#a664ec3301c226596ad971b97a8e1fa65',1,'vg']]],
- ['load_9839',['load',['../classvg_1_1Packer.html#aa85311440b3cd054439b59d64581a58a',1,'vg::Packer::load()'],['../classvg_1_1Packers.html#a66b45adedcd2fb5da8cd8aaf8bd43abc',1,'vg::Packers::load()'],['../classvg_1_1Paths.html#ab8a32e29f758ec6b62e0dc87e7f8018d',1,'vg::Paths::load()'],['../classvg_1_1StreamIndexBase.html#af30b1923f99ff4946103625f90ea1d9c',1,'vg::StreamIndexBase::load()'],['../classvg_1_1Translator.html#aec046a08186a8235a9dec5e844e30536',1,'vg::Translator::load()'],['../classxg_1_1XGPath.html#aeeb9f00d9af56f7f4aae8981f9dafe35',1,'xg::XGPath::load()']]],
- ['load_5falignments_9840',['load_alignments',['../classvg_1_1MSAConverter.html#aa03dea64fc16011eb69d212deb115446',1,'vg::MSAConverter']]],
- ['load_5fbed_9841',['load_bed',['../classvg_1_1FeatureSet.html#a373be59592f7f4f8c98f6d76563051ef',1,'vg::FeatureSet']]],
- ['load_5ffrom_5ffile_9842',['load_from_file',['../classvg_1_1Packer.html#a55b21208921e13f2399f4475d4d02b32',1,'vg::Packer']]],
- ['load_5ffrom_5fold_5fversion_9843',['load_from_old_version',['../classxg_1_1XGPath.html#ac67bde23d92b8720ece6d1176e09a103',1,'xg::XGPath']]],
- ['load_5fgbwt_9844',['load_gbwt',['../namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e',1,'vg::load_gbwt(gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a5197b188ae631a5adcd9689a18138042',1,'vg::load_gbwt(gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
- ['load_5fgbwtgraph_9845',['load_gbwtgraph',['../structGraphHandler.html#aa04b99afe3ef6c536a14f0aa371d4f4b',1,'GraphHandler::load_gbwtgraph()'],['../namespacevg.html#af83417b41cb483c6cad692b718c2bc02',1,'vg::load_gbwtgraph()']]],
- ['load_5fgbz_9846',['load_gbz',['../structGraphHandler.html#a74c5a92b327a6cfef23afac62eb413a5',1,'GraphHandler::load_gbz()'],['../namespacevg.html#a7f775d6f61207052e3c157e5ad6cfcf0',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a142177e721683d3e4d428f6cb8f22981',1,'vg::load_gbz(gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a1bd12c27c337a889da2db07d54d2e1d6',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
- ['load_5fgcsa_9847',['load_gcsa',['../namespacevg.html#afb0e46d1a71de77dddab10d147ac0538',1,'vg']]],
- ['load_5flcp_9848',['load_lcp',['../namespacevg.html#a0679feb8bafbf4be20c4bffa633223c6',1,'vg']]],
- ['load_5fminimizer_9849',['load_minimizer',['../namespacevg.html#a649b144d7ce85a247af73055577c4d91',1,'vg']]],
- ['load_5fone_9850',['load_one',['../classvg_1_1io_1_1VPKG.html#affd67a72df658a50228c6cae7efe7753',1,'vg::io::VPKG::load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a60cacf98de761eab29ed168ee56e8e39',1,'vg::io::VPKG::load_one(const string &filename)']]],
- ['load_5fpack_5fas_5fsupports_9851',['load_pack_as_supports',['../structvg_1_1SupportAugmentedGraph.html#ac7374e695e572eb9eace645005992ec9',1,'vg::SupportAugmentedGraph']]],
- ['load_5fproto_5fto_5fgraph_9852',['load_proto_to_graph',['../namespacevg_1_1io.html#aeef1360dbaeba693008f3ee0d39dde30',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const vg::io::message_sender_function_t &for_each_message)'],['../namespacevg_1_1io.html#ad96a1414b35d7f181ddbb3194d6dcf6c',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const function< void(const function< void(Graph &)> &)> &chunk_sender)']]],
- ['load_5fr_5findex_9853',['load_r_index',['../namespacevg.html#a4ab05fd111751cbf31c3a6a5189a76ff',1,'vg']]],
- ['load_5fsubchain_5fheader_9854',['load_subchain_header',['../namespacevg.html#a4d9b75e74f770318a088011e478c5400',1,'vg']]],
- ['load_5fsubchain_5fkmers_5fpresent_9855',['load_subchain_kmers_present',['../namespacevg.html#a76469b7556e38a779309eeaf9e92ba75',1,'vg']]],
- ['load_5fsupports_9856',['load_supports',['../structvg_1_1SupportAugmentedGraph.html#a1aef5debe026648525732be7bc6cc4b1',1,'vg::SupportAugmentedGraph']]],
- ['load_5ftranslation_5fback_5fmap_9857',['load_translation_back_map',['../namespacevg.html#a3cde90cbb8b1fc46d2b830bf87dba997',1,'vg::load_translation_back_map(HandleGraph &graph, ifstream &input_stream)'],['../namespacevg.html#a0b717077a15106d70c8ce4cc035ca890',1,'vg::load_translation_back_map(const gbwtgraph::GBWTGraph &graph)']]],
- ['load_5ftranslation_5fmap_9858',['load_translation_map',['../namespacevg.html#a11a634196a7420547646dc30d2c57b18',1,'vg::load_translation_map(ifstream &input_stream)'],['../namespacevg.html#a709e93bb1c0dbdcdbc928960e42688ec',1,'vg::load_translation_map(const gbwtgraph::GBWTGraph &graph)']]],
- ['load_5ftranslations_9859',['load_translations',['../structvg_1_1AugmentedGraph.html#af86dc51d58ee0cfa4513602dccc373cd',1,'vg::AugmentedGraph']]],
- ['load_5fv1_9860',['load_v1',['../structvg_1_1Haplotypes_1_1Subchain.html#aacfeb074e57aa98d8ab342114af74e56',1,'vg::Haplotypes::Subchain::load_v1()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a1ace0bf2f790aec2cc6be94bd751009f',1,'vg::Haplotypes::TopLevelChain::load_v1()']]],
- ['load_5fv2_9861',['load_v2',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ab6639ac2e85e25e7e5a4e854e0960708',1,'vg::Haplotypes::TopLevelChain']]],
- ['local_5fhandle_9862',['local_handle',['../classxg_1_1XGPath.html#a6a9566f974aebd3c74fc00ee9dc0c5f0',1,'xg::XGPath']]],
- ['locally_5fexpand_5fgraph_9863',['locally_expand_graph',['../namespacevg_1_1algorithms.html#aa015cfde6842fff0d0dcd81f7130c659',1,'vg::algorithms']]],
- ['lock_9864',['Lock',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a62805a6582a0280c58509f232079b416',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t path_offset, size_t context_bases, bool reflect)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a64972da675bb40fbbaec55470aeebdc4',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t start, size_t past_end)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1a6ed95994cc497481d3338986a30e49',1,'vg::GraphSynchronizer::Lock::lock()']]],
- ['locus_5fto_5fvariant_9865',['locus_to_variant',['../classvg_1_1Genotyper.html#a55c456d612728331007f2f6c4307195f',1,'vg::Genotyper']]],
- ['log10_5fadd_5fone_9866',['log10_add_one',['../namespacevg.html#a16b2b6e110a2f72a871c309b888b013c',1,'vg']]],
- ['log10_5fto_5fln_9867',['log10_to_ln',['../namespacevg.html#a48d9ec9295afc7457506af4ddaf44217',1,'vg']]],
- ['log_5falignment_9868',['log_alignment',['../classvg_1_1MinimizerMapper.html#ab02245901b7ec1710512eab20aec3a48',1,'vg::MinimizerMapper::log_alignment(const Alignment &aln)'],['../classvg_1_1MinimizerMapper.html#aed8f32c63a79281d8693c19f6d6d5521',1,'vg::MinimizerMapper::log_alignment(const Path &path, bool force_condensed=false)']]],
- ['log_5fbits_9869',['log_bits',['../classvg_1_1MinimizerMapper.html#a8d6f418b719d4a4671562c9eeb998601',1,'vg::MinimizerMapper']]],
- ['log_5fcontinue_5ffactor_9870',['log_continue_factor',['../structhaplo_1_1haploMath_1_1RRMemo.html#a4a3dacc819f40fd7e5063821b133028d',1,'haplo::haploMath::RRMemo']]],
- ['log_5fname_9871',['log_name',['../classvg_1_1MinimizerMapper.html#ad49858579fbcd962383387351e2b0183',1,'vg::MinimizerMapper']]],
- ['log_5fpopulation_5fsize_9872',['log_population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#a27a02a4732a9e50c9a1cb9f0b7d7ac3b',1,'haplo::haploMath::RRMemo']]],
- ['log_5frecombination_5fpenalty_9873',['log_recombination_penalty',['../structhaplo_1_1haploMath_1_1RRMemo.html#aa33b509ee804234be1fb33061b3a9f76',1,'haplo::haploMath::RRMemo']]],
- ['log_5ftarget_9874',['log_target',['../classvg_1_1MCMCGenotyper.html#a4622c5efee68d8f148b961a92a1abc62',1,'vg::MCMCGenotyper']]],
- ['logdiff_9875',['logdiff',['../namespacehaplo_1_1haploMath.html#af0182b1e73c64ac6ef0be9d621cce576',1,'haplo::haploMath']]],
- ['lognormal_5fpdf_9876',['lognormal_pdf',['../namespacevg.html#afe6b7d44806f0d50d79f7de39800495d',1,'vg']]],
- ['logprob_5fadd_9877',['logprob_add',['../namespacevg.html#a64b25a99232585c5e76baf01d1ef5520',1,'vg']]],
- ['logprob_5fgeometric_5fmean_9878',['logprob_geometric_mean',['../namespacevg.html#a0f8a1a81a5402187152a97ca6293b4f1',1,'vg']]],
- ['logprob_5finvert_9879',['logprob_invert',['../namespacevg.html#a1056422cd0697f2bbdcf8a085486793a',1,'vg']]],
- ['logprob_5fsum_9880',['logprob_sum',['../namespacevg.html#a93d81b5193ecfc9600990bd427337adf',1,'vg']]],
- ['logprob_5fto_5fphred_9881',['logprob_to_phred',['../namespacevg.html#a66d295b4b0f83393ce621b44d88680a6',1,'vg']]],
- ['logprob_5fto_5fprob_9882',['logprob_to_prob',['../namespacevg.html#aea77a4ed92d78c48a08fce58cf319c4d',1,'vg']]],
- ['logrrdiff_9883',['logRRDiff',['../structhaplo_1_1haploMath_1_1RRMemo.html#a770235503ce0b9bc84f8ec5585f7d328',1,'haplo::haploMath::RRMemo']]],
- ['logs_9884',['logS',['../structhaplo_1_1haploMath_1_1RRMemo.html#a3c54d778760482c2bc80935ceefb0f61',1,'haplo::haploMath::RRMemo']]],
- ['logsum_9885',['logsum',['../namespacehaplo_1_1haploMath.html#a5bc510bf3fca2eeaba726ababf32678f',1,'haplo::haploMath']]],
- ['logt_9886',['logT',['../structhaplo_1_1haploMath_1_1RRMemo.html#ac74af8f5adda75809d2995a37ca79317',1,'haplo::haploMath::RRMemo']]],
- ['longest_5fcommon_5fprefix_9887',['longest_common_prefix',['../namespacevg.html#a2d872af86508016fe8b78d61a190e90a',1,'vg']]],
- ['longest_5fdetectable_5fgap_9888',['longest_detectable_gap',['../classvg_1_1GSSWAligner.html#a9a0d0245bdab8420b4f760d818a3d9cc',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment, const string::const_iterator &read_pos) const'],['../classvg_1_1GSSWAligner.html#a6c803e19e479e8310fda8976ac30eb3a',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length, size_t read_pos) const'],['../classvg_1_1GSSWAligner.html#a00852660c55c381bdcc3546bdb2b1a93',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment) const'],['../classvg_1_1GSSWAligner.html#a6f2bbbc1b2c955874ad531cab3bf4879',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length) const']]],
- ['longest_5fdetectable_5fgap_5fin_5frange_9889',['longest_detectable_gap_in_range',['../classvg_1_1MinimizerMapper.html#aa0f917b2d622c95d9f8bc65186cb898f',1,'vg::MinimizerMapper']]],
- ['longest_5fpaths_5fin_5fforest_9890',['longest_paths_in_forest',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a98105712f44db6c5fadc3b9bd64f97f0',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['look_5fback_9891',['look_back',['../classvg_1_1ZipCodeTree.html#aefac261dda914b102fa57dd504af15d5',1,'vg::ZipCodeTree']]],
- ['lookback_5ftransition_5fiterator_9892',['lookback_transition_iterator',['../namespacevg_1_1algorithms.html#ac8e2917f0a06c55852e4ef044548f2bb',1,'vg::algorithms']]],
- ['lookup_5ffor_5fread_5fin_9893',['lookup_for_read_in',['../structvg_1_1read__alignment__index__t.html#add622e2d97706e4ad842ed27d2a93726',1,'vg::read_alignment_index_t']]],
- ['lookup_5fin_9894',['lookup_in',['../structvg_1_1alignment__index__t.html#a96d88d8fc53918a02c51b6ba811e88be',1,'vg::alignment_index_t']]]
+ ['last_5fcorrect_5fstage_9817',['last_correct_stage',['../classvg_1_1Funnel.html#a996005ebe76091bbba404bf4a2a9a405',1,'vg::Funnel']]],
+ ['last_5fpath_5fposition_9818',['last_path_position',['../namespacevg.html#aa1c1e5b8ce9f9607976913317102d6dc',1,'vg']]],
+ ['last_5ftagged_5fstage_9819',['last_tagged_stage',['../classvg_1_1Funnel.html#ab53e816bd740407417b0bd8d14d5237c',1,'vg::Funnel']]],
+ ['latest_9820',['latest',['../classvg_1_1Funnel.html#a933c8a296c5a680aa96b0b913c465250',1,'vg::Funnel']]],
+ ['layout_5forder_5fof_5fhandle_9821',['layout_order_of_handle',['../classvg_1_1DagifiedGraph.html#af364d952c459117f871368bcc9d33573',1,'vg::DagifiedGraph']]],
+ ['lazier_5ftopological_5forder_9822',['lazier_topological_order',['../namespacehandlegraph_1_1algorithms.html#a26e0547c886eede7d3c0766907f39645',1,'handlegraph::algorithms']]],
+ ['lazy_5ftopological_5forder_9823',['lazy_topological_order',['../namespacehandlegraph_1_1algorithms.html#ac9c0542f382080d1af3914714a62b9b6',1,'handlegraph::algorithms']]],
+ ['lazy_5ftopological_5forder_5finternal_9824',['lazy_topological_order_internal',['../namespacehandlegraph_1_1algorithms.html#a53c98a2b062e6b5e92757945788b2e91',1,'handlegraph::algorithms']]],
+ ['lazyrng_9825',['LazyRNG',['../classvg_1_1LazyRNG.html#a34ef87c442913becab5f596f50bd850e',1,'vg::LazyRNG']]],
+ ['left_5fdegree_9826',['left_degree',['../classvg_1_1VG.html#af9ac6e61dfa9350459dbb9586088c4a5',1,'vg::VG']]],
+ ['left_5fseed_5fnode_9827',['left_seed_node',['../classvg_1_1JoinedSpliceGraph.html#a8152492345122b0db73d6242b2958b45',1,'vg::JoinedSpliceGraph']]],
+ ['left_5fsplice_5fnode_9828',['left_splice_node',['../classvg_1_1JoinedSpliceGraph.html#a37860d9de2993abb60cdf2fecce96c22',1,'vg::JoinedSpliceGraph']]],
+ ['legacycaller_9829',['LegacyCaller',['../classvg_1_1LegacyCaller.html#a7c9d6aa80ac330f844aedc80d267c6dc',1,'vg::LegacyCaller']]],
+ ['length_9830',['length',['../structvg_1_1WFANode.html#a9f70c59baed78d97644100b45cf865cd',1,'vg::WFANode::length()'],['../structvg_1_1GaplessExtension.html#a9c16f9e41fdfafb22a6a64c1e852bb9c',1,'vg::GaplessExtension::length()'],['../classvg_1_1MaximalExactMatch.html#a8f70425ec532b9c43694efbd40d2d587',1,'vg::MaximalExactMatch::length()'],['../classvg_1_1MEMAccelerator.html#a32cb183aeee38c64432c8ea66ff167d6',1,'vg::MEMAccelerator::length()'],['../classvg_1_1BitString.html#a07225c6d00ba670f2dd0b3d6dd83bf70',1,'vg::BitString::length()'],['../classvg_1_1VG.html#a23641dedefa2b6d573939515fcf5974c',1,'vg::VG::length()'],['../classvg_1_1algorithms_1_1Anchor.html#a2fbd6d0440d796d4feb855488bab5b24',1,'vg::algorithms::Anchor::length()'],['../classvg_1_1algorithms_1_1GFAParser.html#aea0cfcb22ae0987ea37f64c5cd547322',1,'vg::algorithms::GFAParser::length()'],['../structReferenceInterval.html#ae74cc528a4962e5049a5028f3d2fd416',1,'ReferenceInterval::length()']]],
+ ['less_5fthan_9831',['less_than',['../classvg_1_1StreamSorter.html#a4ebd8489bcf1ea8c3155c1aa202ab2e2',1,'vg::StreamSorter::less_than(const Message &a, const Message &b) const'],['../classvg_1_1StreamSorter.html#a243723f25750130a537550ac111be9ed',1,'vg::StreamSorter::less_than(const Position &a, const Position &b) const']]],
+ ['likelihoods_9832',['likelihoods',['../classvg_1_1VG.html#ada5821862279a350885f5368a54a5cba',1,'vg::VG']]],
+ ['likely_5fmate_5fpositions_9833',['likely_mate_positions',['../classvg_1_1Mapper.html#a77e11337e9d2aed7a7ffdbb01e1ddd01',1,'vg::Mapper']]],
+ ['likely_5fmismapping_9834',['likely_mismapping',['../classvg_1_1MultipathMapper.html#a30d9d4d69c937777d844baf2d60aed45',1,'vg::MultipathMapper']]],
+ ['likely_5fmisrescue_9835',['likely_misrescue',['../classvg_1_1MultipathMapper.html#af0f679cfdca87e7a4d150c4f4c2b329a',1,'vg::MultipathMapper']]],
+ ['limit_9836',['limit',['../structMappingRun.html#a3000c865dac9811ac82dc54c8073f553',1,'MappingRun']]],
+ ['line_9837',['line',['../classvg_1_1TSVExplainer.html#a4d5e63408088dcb1185b613fb57bab04',1,'vg::TSVExplainer']]],
+ ['linear_5fhaplo_5fstructure_9838',['linear_haplo_structure',['../structhaplo_1_1linear__haplo__structure.html#abde17ce1452b109275975bf0e4f2d51c',1,'haplo::linear_haplo_structure']]],
+ ['linearscoreprovider_9839',['LinearScoreProvider',['../classhaplo_1_1LinearScoreProvider.html#a096c19ba7e847bdeb344e79d487ba675',1,'haplo::LinearScoreProvider']]],
+ ['list_5fhaplotypes_9840',['list_haplotypes',['../namespacevg.html#abe3c447c811f77c28669a36c4d3376b9',1,'vg']]],
+ ['literal_5ftarget_5fmemory_5fusage_9841',['literal_target_memory_usage',['../classvg_1_1IndexingPlan.html#a93541f9db06d755f91d420072fe733e4',1,'vg::IndexingPlan']]],
+ ['ln_5fto_5flog10_9842',['ln_to_log10',['../namespacevg.html#a664ec3301c226596ad971b97a8e1fa65',1,'vg']]],
+ ['load_9843',['load',['../classvg_1_1Packer.html#aa85311440b3cd054439b59d64581a58a',1,'vg::Packer::load()'],['../classvg_1_1Packers.html#a66b45adedcd2fb5da8cd8aaf8bd43abc',1,'vg::Packers::load()'],['../classvg_1_1Paths.html#ab8a32e29f758ec6b62e0dc87e7f8018d',1,'vg::Paths::load()'],['../classvg_1_1StreamIndexBase.html#af30b1923f99ff4946103625f90ea1d9c',1,'vg::StreamIndexBase::load()'],['../classvg_1_1Translator.html#aec046a08186a8235a9dec5e844e30536',1,'vg::Translator::load()'],['../classxg_1_1XGPath.html#aeeb9f00d9af56f7f4aae8981f9dafe35',1,'xg::XGPath::load()']]],
+ ['load_5falignments_9844',['load_alignments',['../classvg_1_1MSAConverter.html#aa03dea64fc16011eb69d212deb115446',1,'vg::MSAConverter']]],
+ ['load_5fbed_9845',['load_bed',['../classvg_1_1FeatureSet.html#a373be59592f7f4f8c98f6d76563051ef',1,'vg::FeatureSet']]],
+ ['load_5ffrom_5ffile_9846',['load_from_file',['../classvg_1_1Packer.html#a55b21208921e13f2399f4475d4d02b32',1,'vg::Packer']]],
+ ['load_5ffrom_5fold_5fversion_9847',['load_from_old_version',['../classxg_1_1XGPath.html#ac67bde23d92b8720ece6d1176e09a103',1,'xg::XGPath']]],
+ ['load_5fgbwt_9848',['load_gbwt',['../namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e',1,'vg::load_gbwt(gbwt::GBWT &index, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a5197b188ae631a5adcd9689a18138042',1,'vg::load_gbwt(gbwt::DynamicGBWT &index, const std::string &filename, bool show_progress=false)']]],
+ ['load_5fgbwtgraph_9849',['load_gbwtgraph',['../structGraphHandler.html#aa04b99afe3ef6c536a14f0aa371d4f4b',1,'GraphHandler::load_gbwtgraph()'],['../namespacevg.html#af83417b41cb483c6cad692b718c2bc02',1,'vg::load_gbwtgraph()']]],
+ ['load_5fgbz_9850',['load_gbz',['../structGraphHandler.html#a74c5a92b327a6cfef23afac62eb413a5',1,'GraphHandler::load_gbz()'],['../namespacevg.html#a7f775d6f61207052e3c157e5ad6cfcf0',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a142177e721683d3e4d428f6cb8f22981',1,'vg::load_gbz(gbwt::GBWT &index, gbwtgraph::GBWTGraph &graph, const std::string &filename, bool show_progress=false)'],['../namespacevg.html#a1bd12c27c337a889da2db07d54d2e1d6',1,'vg::load_gbz(gbwtgraph::GBZ &gbz, const std::string &gbwt_name, const std::string &graph_name, bool show_progress=false)']]],
+ ['load_5fgcsa_9851',['load_gcsa',['../namespacevg.html#afb0e46d1a71de77dddab10d147ac0538',1,'vg']]],
+ ['load_5flcp_9852',['load_lcp',['../namespacevg.html#a0679feb8bafbf4be20c4bffa633223c6',1,'vg']]],
+ ['load_5fminimizer_9853',['load_minimizer',['../namespacevg.html#a649b144d7ce85a247af73055577c4d91',1,'vg']]],
+ ['load_5fone_9854',['load_one',['../classvg_1_1io_1_1VPKG.html#affd67a72df658a50228c6cae7efe7753',1,'vg::io::VPKG::load_one(istream &in, const string &filename="")'],['../classvg_1_1io_1_1VPKG.html#a60cacf98de761eab29ed168ee56e8e39',1,'vg::io::VPKG::load_one(const string &filename)']]],
+ ['load_5fpack_5fas_5fsupports_9855',['load_pack_as_supports',['../structvg_1_1SupportAugmentedGraph.html#ac7374e695e572eb9eace645005992ec9',1,'vg::SupportAugmentedGraph']]],
+ ['load_5fproto_5fto_5fgraph_9856',['load_proto_to_graph',['../namespacevg_1_1io.html#aeef1360dbaeba693008f3ee0d39dde30',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const vg::io::message_sender_function_t &for_each_message)'],['../namespacevg_1_1io.html#ad96a1414b35d7f181ddbb3194d6dcf6c',1,'vg::io::load_proto_to_graph(vg::MutablePathMutableHandleGraph *destination, const function< void(const function< void(Graph &)> &)> &chunk_sender)']]],
+ ['load_5fr_5findex_9857',['load_r_index',['../namespacevg.html#a4ab05fd111751cbf31c3a6a5189a76ff',1,'vg']]],
+ ['load_5fsubchain_5fheader_9858',['load_subchain_header',['../namespacevg.html#a4d9b75e74f770318a088011e478c5400',1,'vg']]],
+ ['load_5fsubchain_5fkmers_5fpresent_9859',['load_subchain_kmers_present',['../namespacevg.html#a76469b7556e38a779309eeaf9e92ba75',1,'vg']]],
+ ['load_5fsupports_9860',['load_supports',['../structvg_1_1SupportAugmentedGraph.html#a1aef5debe026648525732be7bc6cc4b1',1,'vg::SupportAugmentedGraph']]],
+ ['load_5ftranslation_5fback_5fmap_9861',['load_translation_back_map',['../namespacevg.html#a3cde90cbb8b1fc46d2b830bf87dba997',1,'vg::load_translation_back_map(HandleGraph &graph, ifstream &input_stream)'],['../namespacevg.html#a0b717077a15106d70c8ce4cc035ca890',1,'vg::load_translation_back_map(const gbwtgraph::GBWTGraph &graph)']]],
+ ['load_5ftranslation_5fmap_9862',['load_translation_map',['../namespacevg.html#a11a634196a7420547646dc30d2c57b18',1,'vg::load_translation_map(ifstream &input_stream)'],['../namespacevg.html#a709e93bb1c0dbdcdbc928960e42688ec',1,'vg::load_translation_map(const gbwtgraph::GBWTGraph &graph)']]],
+ ['load_5ftranslations_9863',['load_translations',['../structvg_1_1AugmentedGraph.html#af86dc51d58ee0cfa4513602dccc373cd',1,'vg::AugmentedGraph']]],
+ ['load_5fv1_9864',['load_v1',['../structvg_1_1Haplotypes_1_1Subchain.html#aacfeb074e57aa98d8ab342114af74e56',1,'vg::Haplotypes::Subchain::load_v1()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a1ace0bf2f790aec2cc6be94bd751009f',1,'vg::Haplotypes::TopLevelChain::load_v1()']]],
+ ['load_5fv2_9865',['load_v2',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ab6639ac2e85e25e7e5a4e854e0960708',1,'vg::Haplotypes::TopLevelChain']]],
+ ['local_5fhandle_9866',['local_handle',['../classxg_1_1XGPath.html#a6a9566f974aebd3c74fc00ee9dc0c5f0',1,'xg::XGPath']]],
+ ['locally_5fexpand_5fgraph_9867',['locally_expand_graph',['../namespacevg_1_1algorithms.html#aa015cfde6842fff0d0dcd81f7130c659',1,'vg::algorithms']]],
+ ['lock_9868',['Lock',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a62805a6582a0280c58509f232079b416',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t path_offset, size_t context_bases, bool reflect)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a64972da675bb40fbbaec55470aeebdc4',1,'vg::GraphSynchronizer::Lock::Lock(GraphSynchronizer &synchronizer, const string &path_name, size_t start, size_t past_end)'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#a1a6ed95994cc497481d3338986a30e49',1,'vg::GraphSynchronizer::Lock::lock()']]],
+ ['locus_5fto_5fvariant_9869',['locus_to_variant',['../classvg_1_1Genotyper.html#a55c456d612728331007f2f6c4307195f',1,'vg::Genotyper']]],
+ ['log10_5fadd_5fone_9870',['log10_add_one',['../namespacevg.html#a16b2b6e110a2f72a871c309b888b013c',1,'vg']]],
+ ['log10_5fto_5fln_9871',['log10_to_ln',['../namespacevg.html#a48d9ec9295afc7457506af4ddaf44217',1,'vg']]],
+ ['log_5falignment_9872',['log_alignment',['../classvg_1_1MinimizerMapper.html#ab02245901b7ec1710512eab20aec3a48',1,'vg::MinimizerMapper::log_alignment(const Alignment &aln)'],['../classvg_1_1MinimizerMapper.html#aed8f32c63a79281d8693c19f6d6d5521',1,'vg::MinimizerMapper::log_alignment(const Path &path, bool force_condensed=false)']]],
+ ['log_5fbits_9873',['log_bits',['../classvg_1_1MinimizerMapper.html#a8d6f418b719d4a4671562c9eeb998601',1,'vg::MinimizerMapper']]],
+ ['log_5fcontinue_5ffactor_9874',['log_continue_factor',['../structhaplo_1_1haploMath_1_1RRMemo.html#a4a3dacc819f40fd7e5063821b133028d',1,'haplo::haploMath::RRMemo']]],
+ ['log_5fname_9875',['log_name',['../classvg_1_1MinimizerMapper.html#ad49858579fbcd962383387351e2b0183',1,'vg::MinimizerMapper']]],
+ ['log_5fpopulation_5fsize_9876',['log_population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#a27a02a4732a9e50c9a1cb9f0b7d7ac3b',1,'haplo::haploMath::RRMemo']]],
+ ['log_5frecombination_5fpenalty_9877',['log_recombination_penalty',['../structhaplo_1_1haploMath_1_1RRMemo.html#aa33b509ee804234be1fb33061b3a9f76',1,'haplo::haploMath::RRMemo']]],
+ ['log_5ftarget_9878',['log_target',['../classvg_1_1MCMCGenotyper.html#a4622c5efee68d8f148b961a92a1abc62',1,'vg::MCMCGenotyper']]],
+ ['logdiff_9879',['logdiff',['../namespacehaplo_1_1haploMath.html#af0182b1e73c64ac6ef0be9d621cce576',1,'haplo::haploMath']]],
+ ['lognormal_5fpdf_9880',['lognormal_pdf',['../namespacevg.html#afe6b7d44806f0d50d79f7de39800495d',1,'vg']]],
+ ['logprob_5fadd_9881',['logprob_add',['../namespacevg.html#a64b25a99232585c5e76baf01d1ef5520',1,'vg']]],
+ ['logprob_5fgeometric_5fmean_9882',['logprob_geometric_mean',['../namespacevg.html#a0f8a1a81a5402187152a97ca6293b4f1',1,'vg']]],
+ ['logprob_5finvert_9883',['logprob_invert',['../namespacevg.html#a1056422cd0697f2bbdcf8a085486793a',1,'vg']]],
+ ['logprob_5fsum_9884',['logprob_sum',['../namespacevg.html#a93d81b5193ecfc9600990bd427337adf',1,'vg']]],
+ ['logprob_5fto_5fphred_9885',['logprob_to_phred',['../namespacevg.html#a66d295b4b0f83393ce621b44d88680a6',1,'vg']]],
+ ['logprob_5fto_5fprob_9886',['logprob_to_prob',['../namespacevg.html#aea77a4ed92d78c48a08fce58cf319c4d',1,'vg']]],
+ ['logrrdiff_9887',['logRRDiff',['../structhaplo_1_1haploMath_1_1RRMemo.html#a770235503ce0b9bc84f8ec5585f7d328',1,'haplo::haploMath::RRMemo']]],
+ ['logs_9888',['logS',['../structhaplo_1_1haploMath_1_1RRMemo.html#a3c54d778760482c2bc80935ceefb0f61',1,'haplo::haploMath::RRMemo']]],
+ ['logsum_9889',['logsum',['../namespacehaplo_1_1haploMath.html#a5bc510bf3fca2eeaba726ababf32678f',1,'haplo::haploMath']]],
+ ['logt_9890',['logT',['../structhaplo_1_1haploMath_1_1RRMemo.html#ac74af8f5adda75809d2995a37ca79317',1,'haplo::haploMath::RRMemo']]],
+ ['longest_5fcommon_5fprefix_9891',['longest_common_prefix',['../namespacevg.html#a2d872af86508016fe8b78d61a190e90a',1,'vg']]],
+ ['longest_5fdetectable_5fgap_9892',['longest_detectable_gap',['../classvg_1_1GSSWAligner.html#a9a0d0245bdab8420b4f760d818a3d9cc',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment, const string::const_iterator &read_pos) const'],['../classvg_1_1GSSWAligner.html#a6c803e19e479e8310fda8976ac30eb3a',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length, size_t read_pos) const'],['../classvg_1_1GSSWAligner.html#a00852660c55c381bdcc3546bdb2b1a93',1,'vg::GSSWAligner::longest_detectable_gap(const Alignment &alignment) const'],['../classvg_1_1GSSWAligner.html#a6f2bbbc1b2c955874ad531cab3bf4879',1,'vg::GSSWAligner::longest_detectable_gap(size_t read_length) const']]],
+ ['longest_5fdetectable_5fgap_5fin_5frange_9893',['longest_detectable_gap_in_range',['../classvg_1_1MinimizerMapper.html#aa0f917b2d622c95d9f8bc65186cb898f',1,'vg::MinimizerMapper']]],
+ ['longest_5fpaths_5fin_5fforest_9894',['longest_paths_in_forest',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a98105712f44db6c5fadc3b9bd64f97f0',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['look_5fback_9895',['look_back',['../classvg_1_1ZipCodeTree.html#aefac261dda914b102fa57dd504af15d5',1,'vg::ZipCodeTree']]],
+ ['lookback_5ftransition_5fiterator_9896',['lookback_transition_iterator',['../namespacevg_1_1algorithms.html#ac8e2917f0a06c55852e4ef044548f2bb',1,'vg::algorithms']]],
+ ['lookup_5ffor_5fread_5fin_9897',['lookup_for_read_in',['../structvg_1_1read__alignment__index__t.html#add622e2d97706e4ad842ed27d2a93726',1,'vg::read_alignment_index_t']]],
+ ['lookup_5fin_9898',['lookup_in',['../structvg_1_1alignment__index__t.html#a96d88d8fc53918a02c51b6ba811e88be',1,'vg::alignment_index_t']]]
];
diff --git a/search/functions_d.js b/search/functions_d.js
index 8256c14bf8..f53b486d3e 100644
--- a/search/functions_d.js
+++ b/search/functions_d.js
@@ -1,260 +1,260 @@
var searchData=
[
- ['main_9895',['main',['../main_8cpp.html#a813f1942a22b88bf4ff8686af6c643bd',1,'main(int argc, char *argv[]) VG_PREFLIGHT_EVERYWHERE: main.cpp'],['../main_8cpp.html#a3c04138a5bfe5d72780bb7e82a18e627',1,'main(int argc, char **argv): main.cpp']]],
- ['main_5fadd_9896',['main_add',['../add__main_8cpp.html#a70f2a72c5f1d86661c78534083fbe668',1,'add_main.cpp']]],
- ['main_5falign_9897',['main_align',['../align__main_8cpp.html#acc3c08d6346e0538c36aa20a0af338f2',1,'align_main.cpp']]],
- ['main_5fannotate_9898',['main_annotate',['../annotate__main_8cpp.html#ae4b460c351b8e163410fbacf4244f7f2',1,'annotate_main.cpp']]],
- ['main_5faugment_9899',['main_augment',['../augment__main_8cpp.html#a39b28115682b22f672ec0f6932d0f259',1,'augment_main.cpp']]],
- ['main_5fautoindex_9900',['main_autoindex',['../autoindex__main_8cpp.html#a0c5af200c1937f0b3c5723ce0220a7bf',1,'autoindex_main.cpp']]],
- ['main_5fbenchmark_9901',['main_benchmark',['../benchmark__main_8cpp.html#add0702a6210234f5e42ee9c301265d6a',1,'benchmark_main.cpp']]],
- ['main_5fcall_9902',['main_call',['../call__main_8cpp.html#ac255329e18ef1a778298cd5fdc5d3050',1,'call_main.cpp']]],
- ['main_5fchain_9903',['main_chain',['../chain__main_8cpp.html#af61d7259730b08c0c8ff61629e51d78a',1,'chain_main.cpp']]],
- ['main_5fchunk_9904',['main_chunk',['../chunk__main_8cpp.html#aa34cae934dcb31ac7653f079d0d4bf93',1,'chunk_main.cpp']]],
- ['main_5fcircularize_9905',['main_circularize',['../circularize__main_8cpp.html#a1d21512b4c5eb417fa6a1b20a72c1195',1,'circularize_main.cpp']]],
- ['main_5fclip_9906',['main_clip',['../clip__main_8cpp.html#af09a429b96343cf918b8fdea5ebf1a4b',1,'clip_main.cpp']]],
- ['main_5fcluster_9907',['main_cluster',['../cluster__main_8cpp.html#a88693148489c263b15047d96976b9b94',1,'cluster_main.cpp']]],
- ['main_5fcombine_9908',['main_combine',['../combine__main_8cpp.html#a7f4bcb1d0c551b46ed39797df9d0da60',1,'combine_main.cpp']]],
- ['main_5fconcat_9909',['main_concat',['../concat__main_8cpp.html#a22a9b545fc267c18654f312d4fa8d701',1,'concat_main.cpp']]],
- ['main_5fconstruct_9910',['main_construct',['../construct__main_8cpp.html#a385574d21007babb8ef7fa73c9b39cee',1,'construct_main.cpp']]],
- ['main_5fconvert_9911',['main_convert',['../convert__main_8cpp.html#abd9dc3a752930342a8096088f2d4b742',1,'convert_main.cpp']]],
- ['main_5fdeconstruct_9912',['main_deconstruct',['../deconstruct__main_8cpp.html#a80a32834c987861cb4c90d124e0aba12',1,'deconstruct_main.cpp']]],
- ['main_5fdepth_9913',['main_depth',['../depth__main_8cpp.html#a7db982076303bea19c79ee8df88e086f',1,'depth_main.cpp']]],
- ['main_5fdotplot_9914',['main_dotplot',['../dotplot__main_8cpp.html#a74751264f7ead208e151be5408766053',1,'dotplot_main.cpp']]],
- ['main_5fexplode_9915',['main_explode',['../explode__main_8cpp.html#a0448cf7f521dde683e09f6c57df48d67',1,'explode_main.cpp']]],
- ['main_5ffilter_9916',['main_filter',['../filter__main_8cpp.html#af14726647fef6f08e5f916f8a1b4ae0e',1,'filter_main.cpp']]],
- ['main_5ffind_9917',['main_find',['../find__main_8cpp.html#a35569e011de224c166556ea563a4861e',1,'find_main.cpp']]],
- ['main_5fgamcompare_9918',['main_gamcompare',['../gamcompare__main_8cpp.html#a0685b1cc8cff4ca811a199eb1746ddf7',1,'gamcompare_main.cpp']]],
- ['main_5fgampcompare_9919',['main_gampcompare',['../gampcompare__main_8cpp.html#a4b081154219461589d0978c7d993d547',1,'gampcompare_main.cpp']]],
- ['main_5fgamsort_9920',['main_gamsort',['../gamsort__main_8cpp.html#a0aa266bac1f77e7c3625c293f1050108',1,'gamsort_main.cpp']]],
- ['main_5fgbwt_9921',['main_gbwt',['../gbwt__main_8cpp.html#a2018904e4679a19c52921f97afab4592',1,'gbwt_main.cpp']]],
- ['main_5fgenotype_9922',['main_genotype',['../genotype__main_8cpp.html#a04819bc8264065b3aadb2b7bf3a923fa',1,'genotype_main.cpp']]],
- ['main_5fgiraffe_9923',['main_giraffe',['../giraffe__main_8cpp.html#a03a19bdd804f12c23f77bb885e91df4a',1,'giraffe_main.cpp']]],
- ['main_5fhaplotypes_9924',['main_haplotypes',['../haplotypes__main_8cpp.html#ae8ab8ef2233eb016b7b7f0c2bd5c9411',1,'haplotypes_main.cpp']]],
- ['main_5fhelp_9925',['main_help',['../help__main_8cpp.html#ad13a4a4aadfb1314983f35c8cca2e5c7',1,'help_main.cpp']]],
- ['main_5fids_9926',['main_ids',['../ids__main_8cpp.html#aaefd32fe84e813daa1089df0d0bd955f',1,'ids_main.cpp']]],
- ['main_5findex_9927',['main_index',['../index__main_8cpp.html#a7a9da678374c285546cdf243a185b15e',1,'index_main.cpp']]],
- ['main_5finject_9928',['main_inject',['../inject__main_8cpp.html#a214bda0795dc475a91ffd32752b2ee8e',1,'inject_main.cpp']]],
- ['main_5fjoin_9929',['main_join',['../join__main_8cpp.html#a904b50e94b5426c0bb0a39523aada064',1,'join_main.cpp']]],
- ['main_5fkmers_9930',['main_kmers',['../kmers__main_8cpp.html#af32e430824ef93e29253ec42f2edb21e',1,'kmers_main.cpp']]],
- ['main_5fmap_9931',['main_map',['../map__main_8cpp.html#ac963a6cd2cd103405e86f088d5c8358a',1,'map_main.cpp']]],
- ['main_5fmask_9932',['main_mask',['../mask__main_8cpp.html#a66e6db9d20d50a757d7ab70d7ca458f8',1,'mask_main.cpp']]],
- ['main_5fmcmc_9933',['main_mcmc',['../mcmc__main_8cpp.html#a7a702ad991c4285feaeee55461c95a63',1,'mcmc_main.cpp']]],
- ['main_5fminimizer_9934',['main_minimizer',['../minimizer__main_8cpp.html#a5a43d1ef287159cce46f07df1b8b088d',1,'minimizer_main.cpp']]],
- ['main_5fmod_9935',['main_mod',['../mod__main_8cpp.html#ab561b57168cf02964d1a14e024108f2e',1,'mod_main.cpp']]],
- ['main_5fmpmap_9936',['main_mpmap',['../mpmap__main_8cpp.html#a8deece908ee37e2d38e61b2c921e508f',1,'mpmap_main.cpp']]],
- ['main_5fmsga_9937',['main_msga',['../msga__main_8cpp.html#a60a999194e7689bb509442f1caa2354e',1,'msga_main.cpp']]],
- ['main_5fpack_9938',['main_pack',['../pack__main_8cpp.html#a0b3d5bb3cabcd119b839dded9853de23',1,'pack_main.cpp']]],
- ['main_5fpaths_9939',['main_paths',['../paths__main_8cpp.html#a6357ea987a573514a31781145d74cd61',1,'paths_main.cpp']]],
- ['main_5fprune_9940',['main_prune',['../prune__main_8cpp.html#a5b6c70447534213ea13f56ad785d881b',1,'prune_main.cpp']]],
- ['main_5frna_9941',['main_rna',['../rna__main_8cpp.html#a6d06f637eb10cfbb38bb55619ceb3c00',1,'rna_main.cpp']]],
- ['main_5fsift_9942',['main_sift',['../sift__main_8cpp.html#a5c78b9bf77f34696d562b5abffb7a1ef',1,'sift_main.cpp']]],
- ['main_5fsim_9943',['main_sim',['../sim__main_8cpp.html#a1926f81c841475ca54d3100d6340d468',1,'sim_main.cpp']]],
- ['main_5fsimplify_9944',['main_simplify',['../simplify__main_8cpp.html#a16ebf24b0dce88509b5e97fc2fc777b8',1,'simplify_main.cpp']]],
- ['main_5fsnarl_9945',['main_snarl',['../snarls__main_8cpp.html#a4bda7d45d00c828d1e8555573c1c3caf',1,'snarls_main.cpp']]],
- ['main_5fsort_9946',['main_sort',['../sort__main_8cpp.html#a40dc673c2ce8bc4c8ae1496857641885',1,'sort_main.cpp']]],
- ['main_5fstats_9947',['main_stats',['../stats__main_8cpp.html#a6e64cedc2b30a69dea5b727edded704d',1,'stats_main.cpp']]],
- ['main_5fsurject_9948',['main_surject',['../surject__main_8cpp.html#a51d014c6923a46c0f34ca4deb59d11b0',1,'surject_main.cpp']]],
- ['main_5ftest_9949',['main_test',['../test__main_8cpp.html#abd8de8d504f1b1aa53207643a7b553b4',1,'test_main.cpp']]],
- ['main_5ftrace_9950',['main_trace',['../trace__main_8cpp.html#a7bc03098058581a46cba55a13de823e9',1,'trace_main.cpp']]],
- ['main_5ftranslate_9951',['main_translate',['../translate__main_8cpp.html#a2578e3814e52126bf55e62054a01ec7d',1,'translate_main.cpp']]],
- ['main_5fvalidate_9952',['main_validate',['../validate__main_8cpp.html#a8249f1e29a84af534ef5116f778267fb',1,'validate_main.cpp']]],
- ['main_5fvectorize_9953',['main_vectorize',['../vectorize__main_8cpp.html#a8e4da879b5896dd1e13ee84e310870ea',1,'vectorize_main.cpp']]],
- ['main_5fversion_9954',['main_version',['../version__main_8cpp.html#a972dc6662988df17dcc0b4cc0abf6e54',1,'version_main.cpp']]],
- ['main_5fview_9955',['main_view',['../view__main_8cpp.html#a868d2fd8e59794e18a2ecee28f838143',1,'view_main.cpp']]],
- ['main_5fviz_9956',['main_viz',['../viz__main_8cpp.html#a9e415066b5a221e559f9a402b85f386d',1,'viz_main.cpp']]],
- ['main_5fzipcode_9957',['main_zipcode',['../zipcode__main_8cpp.html#a8b81469e01a40dbf9eefbdf90e0c0427',1,'zipcode_main.cpp']]],
- ['make_5fbands_9958',['make_bands',['../classvg_1_1Mapper.html#aafecbaf352024b2847928860fe6c1168',1,'vg::Mapper']]],
- ['make_5fcircular_9959',['make_circular',['../classvg_1_1Paths.html#a1e8760e2c86dd64141c2d0df35926430',1,'vg::Paths']]],
- ['make_5fcompact_9960',['make_compact',['../classvg_1_1Packer.html#a66e266fca00d4e74b7bda1ddbcf384e3',1,'vg::Packer']]],
- ['make_5fdynamic_9961',['make_dynamic',['../classvg_1_1Packer.html#ac3ab6cab2e0cf0ae4e65663db73184e8',1,'vg::Packer']]],
- ['make_5fedge_9962',['make_edge',['../classvg_1_1PhaseUnfolder.html#a82b0a653c98ead9bc4c31d283583d102',1,'vg::PhaseUnfolder']]],
- ['make_5fempty_9963',['make_empty',['../structvg_1_1WFAAlignment.html#ae54f9060454a45ea9a2131a9b5b81c38',1,'vg::WFAAlignment']]],
- ['make_5fgraph_9964',['make_graph',['../classvg_1_1MSAConverter.html#aa4556065637b908e37d2cbf7534b930a',1,'vg::MSAConverter']]],
- ['make_5fhit_5fgraph_9965',['make_hit_graph',['../classvg_1_1MEMClusterer.html#ac65c43448463ef346199437b073c1467',1,'vg::MEMClusterer::make_hit_graph()'],['../classvg_1_1NullClusterer.html#a4e7540aadd3d1eb3d4616cf0d268b3f0',1,'vg::NullClusterer::make_hit_graph()'],['../classvg_1_1OrientedDistanceClusterer.html#af520fdf27e87d46d3a7a5976ec6179c2',1,'vg::OrientedDistanceClusterer::make_hit_graph()'],['../classvg_1_1TVSClusterer.html#a33dff32277c63fa9dc42969c01094900',1,'vg::TVSClusterer::make_hit_graph()'],['../classvg_1_1MinDistanceClusterer.html#a8f3bd899d336e3a30f77e2985eaceb81',1,'vg::MinDistanceClusterer::make_hit_graph()'],['../classvg_1_1GreedyMinDistanceClusterer.html#ad5a3eda064089d19eec2338ccc82e515',1,'vg::GreedyMinDistanceClusterer::make_hit_graph()'],['../classvg_1_1ComponentMinDistanceClusterer.html#afe8b8bc133b5ef94999264dabb3452b8',1,'vg::ComponentMinDistanceClusterer::make_hit_graph()']]],
- ['make_5findexes_9966',['make_indexes',['../classvg_1_1IndexRegistry.html#a4c954dbadbab6cdcd3e81b438864668d',1,'vg::IndexRegistry']]],
- ['make_5flinear_9967',['make_linear',['../classvg_1_1Paths.html#aa82bcbd02b83a9f0781c3696ef46d371',1,'vg::Paths']]],
- ['make_5flong_5foptions_9968',['make_long_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aec2fb8fe7d2b574993b33658440227e0',1,'vg::subcommand::BaseOptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8db74c059e0822c3b25ea7d05bcce340',1,'vg::subcommand::OptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af521b678294674ffcd04b670b5cde737',1,'vg::subcommand::GroupedOptionGroup::make_long_options()']]],
- ['make_5fnontrivial_5fmultipath_5falignment_9969',['make_nontrivial_multipath_alignment',['../classvg_1_1MultipathMapper.html#a4e4be08a92493e0e3b865783b4701cd7',1,'vg::MultipathMapper']]],
- ['make_5fnull_5falignment_9970',['make_null_alignment',['../classvg_1_1Surjector.html#a139ffe849fc1164217e45ea5755fc518',1,'vg::Surjector']]],
- ['make_5fnull_5fmp_5falignment_9971',['make_null_mp_alignment',['../classvg_1_1Surjector.html#a7db137631f3315ede2f6887334a161b4',1,'vg::Surjector']]],
- ['make_5fplan_9972',['make_plan',['../classvg_1_1IndexRegistry.html#ab31ecdcf8f9d50a1310667d23c6410e2',1,'vg::IndexRegistry']]],
- ['make_5fpos_5ft_9973',['make_pos_t',['../namespacevg.html#a2d9f0a2379194fb00d706e90d373b378',1,'vg::make_pos_t(const Position &pos)'],['../namespacevg.html#a1b348dcfac955a7030a3721f436e7d5d',1,'vg::make_pos_t(const position_t &pos)'],['../namespacevg.html#afc066dab7543192bf782959ef160f2d4',1,'vg::make_pos_t(gcsa::node_type node)'],['../namespacevg.html#a1d85d380ba4b936ac8a715a72062866c',1,'vg::make_pos_t(id_t id, bool is_rev, offset_t off)'],['../namespacexg.html#aace66781c520f719a1f8f64ab24f2589',1,'xg::make_pos_t()']]],
- ['make_5fposition_9974',['make_position',['../namespacevg.html#a6247de8deb27aaabf2bc0d6fc755f693',1,'vg::make_position(const pos_t &pos)'],['../namespacevg.html#ac6af3d55800703f7534ca07a84450580',1,'vg::make_position(id_t id, bool is_rev, offset_t off)'],['../namespacevg.html#a4cdd9b08b7b6d6e15d00536554f3ca56',1,'vg::make_position(gcsa::node_type node)']]],
- ['make_5fprefix_5fsuffix_5ftable_9975',['make_prefix_suffix_table',['../namespacevg.html#a3ff1638bd636bb4b9746545dc261aea1',1,'vg']]],
- ['make_5fshort_5foptions_9976',['make_short_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a0a5933555ce227565029122dfd6f15e9',1,'vg::subcommand::BaseOptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8ef56a59e757ab9cd808cf9112e1f64b',1,'vg::subcommand::OptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3f2f2249f4edee37552c77bce6c4a42c',1,'vg::subcommand::GroupedOptionGroup::make_short_options()']]],
- ['make_5fshuffle_5fseed_9977',['make_shuffle_seed',['../namespacevg.html#aeca2b8e2d5730b1d5b94c1d3861757d7',1,'vg::make_shuffle_seed(const multipath_alignment_t &aln)'],['../namespacevg.html#acc312d814d6a06a4a5159c7943675bbe',1,'vg::make_shuffle_seed(const Alignment &aln)'],['../namespacevg.html#a2ec8fc79a1f84c6ef4a02c9d7c7a2850',1,'vg::make_shuffle_seed(const T *ptr)'],['../namespacevg.html#a04ebc20fd2965b1932e27958dd0c602c',1,'vg::make_shuffle_seed(const pair< T1, T2 > &p)']]],
- ['make_5fsingle_5fstranded_9978',['make_single_stranded',['../namespacehandlegraph_1_1algorithms.html#a8cac1e5f4dc0c5e0e501ebb9fc58fca3',1,'handlegraph::algorithms']]],
- ['make_5fsnarl_5fgraph_9979',['make_snarl_graph',['../classvg_1_1MCMCGenotyper.html#abbbf0c2625e4039f5a79b8b360515b41',1,'vg::MCMCGenotyper']]],
- ['make_5fsnarl_5fmap_9980',['make_snarl_map',['../classvg_1_1MCMCGenotyper.html#a5e31dd64fad5dfb14d38be487fc14e59',1,'vg::MCMCGenotyper']]],
- ['make_5fsubset_5fgraph_9981',['make_subset_graph',['../classvg_1_1Genotyper.html#ab11a87f5f21d3a7122ec85f6d853f336',1,'vg::Genotyper']]],
- ['make_5fsupport_9982',['make_support',['../namespacevg.html#a1c0ae5cc687e77bb7cee28e975a005b3',1,'vg']]],
- ['make_5ftemporary_5fdistance_5findex_9983',['make_temporary_distance_index',['../namespacevg.html#ae55954f00a00c8b34d20966f7d9fe72a',1,'vg']]],
- ['make_5ftranslation_9984',['make_translation',['../namespacevg.html#a028aa842a68b6993a37a82c7645e0633',1,'vg']]],
- ['make_5funlocalized_5finsertion_9985',['make_unlocalized_insertion',['../structvg_1_1WFAAlignment.html#aee475e8a07f1e06f61411f581813252e',1,'vg::WFAAlignment']]],
- ['make_5fvariant_5fid_9986',['make_variant_id',['../namespacevg.html#aa74ef603900cf05ce35dbab813d21deb',1,'vg']]],
- ['manage_9987',['manage',['../classvg_1_1SnarlManager.html#adb68da18eef20aa324c498444a9ed77f',1,'vg::SnarlManager']]],
- ['map_9988',['map',['../classvg_1_1MinimizerMapper.html#a4c955e7607a1c07d2ca2b22a065e8b91',1,'vg::MinimizerMapper::map(Alignment &aln, AlignmentEmitter &alignment_emitter)'],['../classvg_1_1MinimizerMapper.html#a182c026fcc4e3a8dea5de373d1a79bbb',1,'vg::MinimizerMapper::map(Alignment &aln)']]],
- ['map_5ffrom_5fchains_9989',['map_from_chains',['../classvg_1_1MinimizerMapper.html#af098e417ff3df9ff70d18cd4cd12555b',1,'vg::MinimizerMapper']]],
- ['map_5ffrom_5fextensions_9990',['map_from_extensions',['../classvg_1_1MinimizerMapper.html#aaaaff0f62d2003bd8814c3fd90dd8226',1,'vg::MinimizerMapper']]],
- ['map_5fkeys_5fto_5fset_9991',['map_keys_to_set',['../namespacevg.html#ace99283a6b34f0891dc0b49f0cd60eea',1,'vg']]],
- ['map_5fover_9992',['map_over',['../namespacevg.html#a4833086451a8b97af4709aa6c7385177',1,'vg']]],
- ['map_5fpaired_9993',['map_paired',['../classvg_1_1MinimizerMapper.html#a5c90ef4f961998cc7904e78225b36f50',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer)'],['../classvg_1_1MinimizerMapper.html#ab5f4c707ec44ba8f742c79bb0153c157',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2)']]],
- ['map_5fstage_5fresults_5fto_5fprevious_5fstage_9994',['map_stage_results_to_previous_stage',['../classvg_1_1Funnel.html#aeca18258bb42790609df5f17d2394135',1,'vg::Funnel']]],
- ['map_5fvariants_9995',['map_variants',['../haplotypes__main_8cpp.html#a1e43abd4f18210a8a4e131afbc8d182d',1,'haplotypes_main.cpp']]],
- ['mapper_9996',['Mapper',['../classvg_1_1Mapper.html#a1d808071bd518202414fba56f5ec333e',1,'vg::Mapper::Mapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr)'],['../classvg_1_1Mapper.html#ae47e4e50adf1a5132656e9dd9a227628',1,'vg::Mapper::Mapper(void)']]],
- ['mapping_9997',['mapping',['../classvg_1_1path__t.html#ab7f2f4df754fec9f8631c8388cbe4aad',1,'vg::path_t::mapping() const'],['../classvg_1_1path__t.html#a07af6243d1650ddef63ed19804da8071',1,'vg::path_t::mapping(size_t i) const']]],
- ['mapping_5fagainst_5fpath_9998',['mapping_against_path',['../namespacevg.html#ad2e7730a993652e18d80ca77dac73713',1,'vg']]],
- ['mapping_5fcigar_9999',['mapping_cigar',['../namespacevg.html#a5a0bb992cac134b2eed1e7b84eaecc2c',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char >> &cigar, char mismatch_operation)'],['../namespacevg.html#a642736d2f652e5ab522e1f26b874e097',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char > > &cigar, char mismatch_operation='M')']]],
- ['mapping_5fends_5fin_5fdeletion_10000',['mapping_ends_in_deletion',['../namespacevg.html#afeef6a4c023183ead5725398b14d443c',1,'vg']]],
- ['mapping_5fenters_5fside_10001',['mapping_enters_side',['../classvg_1_1Genotyper.html#aa2b4d94f59265c107895c48a26b107a6',1,'vg::Genotyper']]],
- ['mapping_5fexits_5fside_10002',['mapping_exits_side',['../classvg_1_1Genotyper.html#a8b054a94fb2ceb4c65731188227b0cf8',1,'vg::Genotyper']]],
- ['mapping_5ffrom_5flength_10003',['mapping_from_length',['../namespacevg.html#aa2aa77c6d4db628d13488c0bd82538ed',1,'vg::mapping_from_length(const Mapping &m)'],['../namespacevg.html#a151a868062bd12ac34b9aea68dc8d4f0',1,'vg::mapping_from_length(const path_mapping_t &mapping)']]],
- ['mapping_5fis_5fmatch_10004',['mapping_is_match',['../namespacevg.html#a78ea8a2cf04759a3cfecbe4bf3e926c2',1,'vg']]],
- ['mapping_5fis_5fsimple_5fmatch_10005',['mapping_is_simple_match',['../namespacevg.html#ae8ba5042b838f859a078cf014f1a0871',1,'vg']]],
- ['mapping_5fis_5ftotal_5fdeletion_10006',['mapping_is_total_deletion',['../namespacevg.html#a6d10b5bc5677fdb0ae164f79848bb1bb',1,'vg']]],
- ['mapping_5fis_5ftotal_5finsertion_10007',['mapping_is_total_insertion',['../namespacevg.html#a54cdb9b97e741de6ced9fefbc2bf48f3',1,'vg']]],
- ['mapping_5fis_5ftotal_5fmatch_10008',['mapping_is_total_match',['../classvg_1_1VG.html#acd555e66c8fa99984c8cb24aef0ab6f9',1,'vg::VG']]],
- ['mapping_5flikelihoods_10009',['mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a9c55acfb3c1116daeba543b42303ce7d',1,'vg::MultipathMapper']]],
- ['mapping_5fpath_5fid_10010',['mapping_path_id',['../classvg_1_1Paths.html#abb58996e669d1b9271772a929f6bebe2',1,'vg::Paths']]],
- ['mapping_5fpath_5fname_10011',['mapping_path_name',['../classvg_1_1Paths.html#ab520f6e02a5a9b2e11f10a6455be5bdd',1,'vg::Paths']]],
- ['mapping_5fquality_10012',['mapping_quality',['../classvg_1_1multipath__alignment__t.html#a7a9fd028a082d666d19522d27ea5aa2c',1,'vg::multipath_alignment_t']]],
- ['mapping_5fquality_5fscore_5fdiff_10013',['mapping_quality_score_diff',['../classvg_1_1GSSWAligner.html#a1c341fd9f6dd51131b714d580f5ccfea',1,'vg::GSSWAligner']]],
- ['mapping_5fsequence_10014',['mapping_sequence',['../namespacevg.html#a2b648cd1a51584623d6618565d3ca9c6',1,'vg::mapping_sequence(const Mapping &mp, const string &node_seq)'],['../namespacevg.html#ac23702705b681eacdfd1b3bcbc5254b5',1,'vg::mapping_sequence(const Mapping &mp, const Node &n)']]],
- ['mapping_5fsize_10015',['mapping_size',['../classvg_1_1path__t.html#aa3e09b61e5f2b803461ac3e20df6117c',1,'vg::path_t']]],
- ['mapping_5fstarts_5fin_5fdeletion_10016',['mapping_starts_in_deletion',['../namespacevg.html#aa377b3e776e312c717aedec842216f48',1,'vg']]],
- ['mapping_5fstring_10017',['mapping_string',['../namespacevg.html#ad993b1f289a57f3413b85840984b459c',1,'vg']]],
- ['mapping_5ft_10018',['mapping_t',['../classvg_1_1mapping__t.html#aa47429bfca4c4120a2e5c116d6d54450',1,'vg::mapping_t::mapping_t(void)'],['../classvg_1_1mapping__t.html#a6c9be43df27053b2bc5599faad299513',1,'vg::mapping_t::mapping_t(const Mapping &m)']]],
- ['mapping_5fto_5fgbwt_10019',['mapping_to_gbwt',['../namespacevg.html#ace1a7180fda8bb98abba24fb19183e9d',1,'vg']]],
- ['mapping_5fto_5fhandle_10020',['mapping_to_handle',['../namespacevg.html#acdaa29c218d5d55e76fe4ab168f7a14b',1,'vg']]],
- ['mapping_5fto_5flength_10021',['mapping_to_length',['../namespacevg.html#a9ef1ccef545dfc30f9123eba61267b4a',1,'vg::mapping_to_length(const Mapping &m)'],['../namespacevg.html#a3f709a91987a7d669b3974fa00aa8ecd',1,'vg::mapping_to_length(const path_mapping_t &mapping)']]],
- ['mappings_5fequivalent_10022',['mappings_equivalent',['../namespacevg.html#af26a23818c9426d77ef25b07bbaaf605',1,'vg']]],
- ['maps_5fto_5fnode_10023',['maps_to_node',['../namespacevg.html#a242b97c26d74e9fc05ad16c31b21dcca',1,'vg']]],
- ['mark_5fdfs_10024',['mark_dfs',['../classvg_1_1FlowSort.html#a498b6d9f0a37f2588e4ad08b6c35a0ff',1,'vg::FlowSort']]],
- ['mark_5fsmallvariant_5falignments_10025',['mark_smallVariant_alignments',['../classvg_1_1Filter.html#a2ab59f83f673047f5c2106456c4426c3',1,'vg::Filter']]],
- ['mark_5fsv_5falignments_10026',['mark_sv_alignments',['../classvg_1_1Filter.html#a267d55220fcf5239f12dcc852586bc71',1,'vg::Filter']]],
- ['markovdistribution_10027',['MarkovDistribution',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#aef78cda42fffdef670a3ceb7e4877ee9',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['mask_5fsequences_10028',['mask_sequences',['../classvg_1_1Masker.html#a18d454c702ded8fdb3436f90135631ed',1,'vg::Masker']]],
- ['masker_10029',['Masker',['../classvg_1_1Masker.html#a0c3817b4839ee4b2dd6d38d193cd61e8',1,'vg::Masker::Masker(gbwtgraph::GBWTGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#ab302923c0d437d4e997e1c11d35125ac',1,'vg::Masker::Masker(MutablePathDeletableHandleGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#a5398d6fdb929425966c9b71c0c9dc2fd',1,'vg::Masker::Masker()=default'],['../classvg_1_1Masker.html#aae42512f78c75af240e164d16a3445e1',1,'vg::Masker::Masker(Masker &&other)=default']]],
- ['match_5fbackward_10030',['match_backward',['../namespacevg.html#a3495eb8e73ceeece9957079280edc921',1,'vg']]],
- ['match_5fforward_10031',['match_forward',['../structvg_1_1WFANode.html#a368dbe3b756f08e21718cbfac97978fd',1,'vg::WFANode::match_forward()'],['../namespacevg.html#abcb300141666ec86856482f6a59cec4c',1,'vg::match_forward()']]],
- ['match_5finitial_10032',['match_initial',['../namespacevg.html#a4b1defb1ef0b163389ff84745294d1d0',1,'vg']]],
- ['match_5fpredecessor_10033',['match_predecessor',['../classvg_1_1WFATree.html#a4242e9739a9f789386354f4582dea547',1,'vg::WFATree']]],
- ['matches_10034',['matches',['../classvg_1_1DinucleotideMachine.html#a2250f97747bf0e9390ed7326d357c557',1,'vg::DinucleotideMachine::matches(uint32_t state, const char *dinucleotide) const'],['../classvg_1_1DinucleotideMachine.html#aa30db9eff5e43b78cd23094f3d7edce5',1,'vg::DinucleotideMachine::matches(uint32_t state, const string &dinucleotide) const']]],
- ['matches_5fannotation_10035',['matches_annotation',['../classvg_1_1ReadFilter.html#a95d1165f7c3901772a70ba863d1fc983',1,'vg::ReadFilter']]],
- ['matches_5fname_10036',['matches_name',['../classvg_1_1ReadFilter.html#ab72c4fd96eedcb4bcd6aa565e97dfe4d',1,'vg::ReadFilter']]],
- ['matchpos_10037',['MatchPos',['../structvg_1_1MatchPos.html#ab44cfadd41dfc2ec79266e4fe204458f',1,'vg::MatchPos::MatchPos()'],['../structvg_1_1MatchPos.html#a167922796c04609cdf6a129c7135f869',1,'vg::MatchPos::MatchPos(uint32_t seq_offset, uint32_t node_offset, const PathList &path)']]],
- ['matrix_5finvert_10038',['matrix_invert',['../namespacevg.html#a7effc13e3f877e676d65d9164a44b4a6',1,'vg']]],
- ['matrix_5fmultiply_10039',['matrix_multiply',['../namespacevg.html#a02d66ca193142fb4825a62b300d60697',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< vector< double >> &B)'],['../namespacevg.html#a9a1927488f1b7b82758828d5a53ca845',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< double > &b)']]],
- ['max_10040',['max',['../classvg_1_1WideningPRNG.html#a3083db737b68cc80dacad05c9e1ae1ee',1,'vg::WideningPRNG::max()'],['../namespacestd.html#a032e2e35689ce96dfb488db853f83334',1,'std::max()']]],
- ['max_5fdepth_10041',['max_depth',['../classvg_1_1ZipCode.html#aa9b8e3ee702697e3692a83e2307d9084',1,'vg::ZipCode']]],
- ['max_5fdistance_5ffrom_5fstart_10042',['max_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#a0d573babd81fa2d0c209c75afec6c91d',1,'vg::IncrementalSubgraph']]],
- ['max_5fexponential_5fcdf_10043',['max_exponential_cdf',['../namespacevg.html#a82dc203eaecb442a26d8f1a3db773dda',1,'vg']]],
- ['max_5fexponential_5flog_5flikelihood_10044',['max_exponential_log_likelihood',['../namespacevg.html#a617472d242ff7aad1126a6b70e70a7a8',1,'vg']]],
- ['max_5fflow_5fsort_10045',['max_flow_sort',['../classvg_1_1FlowSort.html#a8a5d0ba61635331b2107ad3df4972ff1',1,'vg::FlowSort']]],
- ['max_5fin_10046',['max_in',['../classvg_1_1algorithms_1_1TracedScore.html#a8d01a37cedeb1e7e7667f05bdb8f67e9',1,'vg::algorithms::TracedScore']]],
- ['max_5flink_5flength_10047',['max_link_length',['../classvg_1_1JoinedSpliceGraph.html#a25612fe4db491aa5cbcc06f5816bd5bd',1,'vg::JoinedSpliceGraph']]],
- ['max_5fnode_5fid_10048',['max_node_id',['../classvg_1_1DagifiedGraph.html#a511c81e2e65250eeeac52936bfe3ae0e',1,'vg::DagifiedGraph::max_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#a4962a5c38f363db65a1b0083a05bcfcc',1,'vg::DozeuPinningOverlay::max_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ab7384a54f90e4351cb7e6d0a99f3290d',1,'vg::ExtraNodeGraph::max_node_id()'],['../classvg_1_1SnarlGraph.html#a69ce6bde5f346eb5926b6db093122be1',1,'vg::SnarlGraph::max_node_id()'],['../classvg_1_1IdentityOverlay.html#a5aba68df4094870dd2324613d2db1d63',1,'vg::IdentityOverlay::max_node_id()'],['../classvg_1_1IncrementalSubgraph.html#aa92bb84a3ea785a09c814932ae56a5a8',1,'vg::IncrementalSubgraph::max_node_id()'],['../classvg_1_1IndexedVG.html#ab7e6f41fefb23702e708d23a0dcec9d0',1,'vg::IndexedVG::max_node_id()'],['../classvg_1_1MemoizingGraph.html#a7a9052b566d4062493432265aa1c9e70',1,'vg::MemoizingGraph::max_node_id()'],['../classvg_1_1NullMaskingGraph.html#a768717b98ae295bb52a68028db0145ec',1,'vg::NullMaskingGraph::max_node_id()'],['../classvg_1_1PathSubgraph.html#a7d5368e9b40989fa3e1ecd020468a1da',1,'vg::PathSubgraph::max_node_id()'],['../classvg_1_1ReverseGraph.html#ac276a2df66a605842304eec2d9ef340c',1,'vg::ReverseGraph::max_node_id()'],['../classvg_1_1NetGraph.html#abb16fbc7ae88f61e3ce9076d2e2a3817',1,'vg::NetGraph::max_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ab9be77971160f356b0ba0721ed17983e',1,'vg::SourceSinkOverlay::max_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#abbf5f65b4f075efb985c0978cead8513',1,'vg::JoinedSpliceGraph::max_node_id()'],['../classvg_1_1StrandSplitGraph.html#a83194bc2415f2f0fa2e23ce970d2f932',1,'vg::StrandSplitGraph::max_node_id()'],['../classvg_1_1SubHandleGraph.html#afd0e51c2e81f5b51f4e21167e3e691f3',1,'vg::SubHandleGraph::max_node_id()'],['../classvg_1_1SubgraphOverlay.html#ab2858c7e55226d9754eb388654da88ab',1,'vg::SubgraphOverlay::max_node_id()'],['../classvg_1_1SubpathOverlay.html#aa5b627c97bac0914a4b77e289a1f888b',1,'vg::SubpathOverlay::max_node_id()'],['../classvg_1_1TreeSubgraph.html#ae8f3ebca4f5d097fe9b5081cdc1f7a96',1,'vg::TreeSubgraph::max_node_id()'],['../classvg_1_1VG.html#a5a03ad90e03794944c5e0d4d61780652',1,'vg::VG::max_node_id()'],['../classvg_1_1VGset.html#a31691223aa51fca983dd145b5896cad7',1,'vg::VGset::max_node_id()'],['../classxg_1_1XG.html#ac991d9094b1959ff503d9a94d0a9ed4c',1,'xg::XG::max_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a599303e41c6f9913424933778893f1c6',1,'handlegraph::algorithms::SubHandleGraph::max_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a5a2e2b1ea6a29b3f4b34a6abcb6dbc50',1,'handlegraph::HandleGraph::max_node_id()']]],
- ['max_5fnode_5frank_10049',['max_node_rank',['../classxg_1_1XG.html#a1bc4d756800a8e55ddb33abf49865956',1,'xg::XG']]],
- ['max_5fpath_5frank_10050',['max_path_rank',['../classxg_1_1XG.html#acd75e4cc0ccf977505a5c6bda03ddb73',1,'xg::XG']]],
- ['max_5fpossible_5fmapping_5fquality_10051',['max_possible_mapping_quality',['../classvg_1_1GSSWAligner.html#a0058c97d1dbe2be7643e9f75cee15bab',1,'vg::GSSWAligner::max_possible_mapping_quality()'],['../classvg_1_1Mapper.html#a1799afefa90f9fbfd7de41626bdb460c',1,'vg::Mapper::max_possible_mapping_quality()']]],
- ['max_5fsample_5fsize_10052',['max_sample_size',['../classvg_1_1FragmentLengthDistribution.html#ae5f1b666c1bee15996ad997eb4c9505e',1,'vg::FragmentLengthDistribution']]],
- ['max_5fshift_10053',['max_shift',['../classvg_1_1MultipathAlignmentGraph.html#a50ff4a1c2bc2b997c28af99527e595dd',1,'vg::MultipathAlignmentGraph']]],
- ['max_5fvertex_10054',['max_vertex',['../classvg_1_1MEMChainModel.html#abc9cf4a87ae1b38488bcf96c0a09b853',1,'vg::MEMChainModel::max_vertex()'],['../classvg_1_1AlignmentChainModel.html#a79f49cd995d623a0dae8b704ad57432e',1,'vg::AlignmentChainModel::max_vertex()']]],
- ['maximalexactmatch_10055',['MaximalExactMatch',['../classvg_1_1MaximalExactMatch.html#a0eb93e97b671cbafb0de7aa5827fa5f0',1,'vg::MaximalExactMatch::MaximalExactMatch(string::const_iterator b, string::const_iterator e, gcsa::range_type r, size_t m=0)'],['../classvg_1_1MaximalExactMatch.html#aab0c8e120398563dfa7dae32a92b2fa9',1,'vg::MaximalExactMatch::MaximalExactMatch(void)=default'],['../classvg_1_1MaximalExactMatch.html#a058f43692dd5943fa4e4ecc1b5fc68c0',1,'vg::MaximalExactMatch::MaximalExactMatch(const MaximalExactMatch &)=default'],['../classvg_1_1MaximalExactMatch.html#a9b0816ee01550f8ce43d32984d6fc333',1,'vg::MaximalExactMatch::MaximalExactMatch(MaximalExactMatch &&)=default']]],
- ['maximum_5fdistance_10056',['maximum_distance',['../namespacevg.html#a004ed92d4db665ce8ec4e527f150a7c4',1,'vg']]],
- ['maximum_5fmapping_5fquality_5fapprox_10057',['maximum_mapping_quality_approx',['../classvg_1_1GSSWAligner.html#a3104dc6ddfd6a15e1ed02950006a4063',1,'vg::GSSWAligner']]],
- ['maximum_5fmapping_5fquality_5fexact_10058',['maximum_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#ac17619c1908446d3e61a882c879f2eb1',1,'vg::GSSWAligner']]],
- ['mcmccaller_10059',['MCMCCaller',['../classvg_1_1MCMCCaller.html#add4fcb2e5a2a8633e659a986bb347c40',1,'vg::MCMCCaller']]],
- ['mcmcgenotyper_10060',['MCMCGenotyper',['../classvg_1_1MCMCGenotyper.html#abb6ddf1a8e99fc5c183ec188ae87bb22',1,'vg::MCMCGenotyper']]],
- ['mean_10061',['mean',['../classvg_1_1FragmentLengthDistribution.html#abe1b685c70bdafff09e089038ae68971',1,'vg::FragmentLengthDistribution::mean()'],['../classvg_1_1normal__distribution.html#a8b5bd06d0c3589eab21131a033bd706a',1,'vg::normal_distribution::mean()'],['../classvg_1_1truncated__normal__distribution.html#ad842920993df04cbcc18cc4182f9d005',1,'vg::truncated_normal_distribution::mean()']]],
- ['mean_5fnode_5flength_10062',['mean_node_length',['../classvg_1_1Transcriptome.html#af173c32d4ccfa7f94f68220e7e564895',1,'vg::Transcriptome']]],
- ['measurements_5fbegin_10063',['measurements_begin',['../classvg_1_1FragmentLengthDistribution.html#a9a57a0e4a86983fc13a87d5ee4c5b8a7',1,'vg::FragmentLengthDistribution']]],
- ['measurements_5fend_10064',['measurements_end',['../classvg_1_1FragmentLengthDistribution.html#a929562555917920f58a5d3692cd14fb4',1,'vg::FragmentLengthDistribution']]],
- ['median_10065',['median',['../namespacevg.html#a6eef175773ce8532826ba78eee0cece5',1,'vg']]],
- ['median_5fmem_5fcoverage_10066',['median_mem_coverage',['../classvg_1_1MEMClusterer_1_1HitGraph.html#abe3be52c11df5f9b5fc131cfe9460d5a',1,'vg::MEMClusterer::HitGraph']]],
- ['mem_5fmin_5foriented_5fdistances_10067',['mem_min_oriented_distances',['../namespacevg.html#ae1678438e6011469b88ddf3b54023013',1,'vg']]],
- ['mem_5fnode_5fstart_5fpositions_10068',['mem_node_start_positions',['../namespacevg.html#aa65ea58e40ea30264407f9fdbce2a83d',1,'vg']]],
- ['mem_5fusage_5fstring_10069',['mem_usage_string',['../autoindex__main_8cpp.html#a95ea1f250ba974749a30b213bede7969',1,'autoindex_main.cpp']]],
- ['memaccelerator_10070',['MEMAccelerator',['../classvg_1_1MEMAccelerator.html#af51ef34773bca8cc723fb3ef0bfe87c8',1,'vg::MEMAccelerator::MEMAccelerator()=default'],['../classvg_1_1MEMAccelerator.html#a3928fe622799f9ac33ba7e2e5d4b3568',1,'vg::MEMAccelerator::MEMAccelerator(const gcsa::GCSA &gcsa_index, size_t k)']]],
- ['memchainmodel_10071',['MEMChainModel',['../classvg_1_1MEMChainModel.html#ae612545bdf38bad27b4fc18e19d38eff',1,'vg::MEMChainModel']]],
- ['memchainmodelvertex_10072',['MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html#a9ec1a9cd36b3328911409e598109c1c9',1,'vg::MEMChainModelVertex::MEMChainModelVertex(void)=default'],['../classvg_1_1MEMChainModelVertex.html#a01ed669199f3319be51dbd2aafc268de',1,'vg::MEMChainModelVertex::MEMChainModelVertex(const MEMChainModelVertex &)=default'],['../classvg_1_1MEMChainModelVertex.html#adb5651ba734c5700f334b0074dfaaca8',1,'vg::MEMChainModelVertex::MEMChainModelVertex(MEMChainModelVertex &&)=default']]],
- ['memclusterer_10073',['MEMClusterer',['../classvg_1_1MEMClusterer.html#ae035e62365ff4617433e18d102bec452',1,'vg::MEMClusterer']]],
- ['memoized_5flf_10074',['memoized_LF',['../classvg_1_1MEMAccelerator.html#a89dfd34874f065088799dfce96c11649',1,'vg::MEMAccelerator']]],
- ['memoizinggraph_10075',['MemoizingGraph',['../classvg_1_1MemoizingGraph.html#aef84e6abc0084e0f910bc99edc760345',1,'vg::MemoizingGraph::MemoizingGraph(const PathPositionHandleGraph *graph)'],['../classvg_1_1MemoizingGraph.html#aa6030fdc5e73a8d88059bc31f1886746',1,'vg::MemoizingGraph::MemoizingGraph()=default']]],
- ['mems_5fid_5fclusters_5fto_5falignments_10076',['mems_id_clusters_to_alignments',['../classvg_1_1Mapper.html#a0dc4c04ebad76435afafe9cec62a5eaa',1,'vg::Mapper']]],
- ['mems_5foverlap_10077',['mems_overlap',['../namespacevg.html#aa412de4741b61d2a8b863f50f31209e0',1,'vg']]],
- ['mems_5foverlap_5flength_10078',['mems_overlap_length',['../namespacevg.html#af5d04132733b3487e3dab20729645850',1,'vg']]],
- ['mems_5fto_5fjson_10079',['mems_to_json',['../namespacevg.html#ab0bec9992b4441128754ac4ed1a330e8',1,'vg']]],
- ['merge_10080',['merge',['../classvg_1_1Funnel.html#ae75f133fdc545176a27f0121a61a98e4',1,'vg::Funnel::merge()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a658429a7896e87dc276f749f5ba8dc27',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::merge()'],['../classvg_1_1VG.html#a0abc84684faea29b49032ec254d5e13b',1,'vg::VG::merge(Graph &g)'],['../classvg_1_1VG.html#a40f22f6bb4a3e7a2aea7b3887237faec',1,'vg::VG::merge(VG &g)'],['../namespacevg_1_1algorithms.html#a91a6bbd822f6380421a973f75036c3d3',1,'vg::algorithms::merge()']]],
- ['merge_5fadjacent_5fedits_10081',['merge_adjacent_edits',['../namespacevg.html#a30a83a9e127a0c7d75118dc14a8985f6',1,'vg::merge_adjacent_edits(const Mapping &m)'],['../namespacevg.html#a2c9985bf70965bd36bb54f910ab74e3b',1,'vg::merge_adjacent_edits(const Path &m)']]],
- ['merge_5falignments_10082',['merge_alignments',['../namespacevg.html#afa2d2a5d955cff1e7a99369055ebe75d',1,'vg::merge_alignments(const vector< Alignment > &alns)'],['../namespacevg.html#a9d71527a132d7e6bf364d2108b269e09',1,'vg::merge_alignments(const Alignment &a1, const Alignment &a2, bool debug)']]],
- ['merge_5fedits_5fin_5fplace_10083',['merge_edits_in_place',['../namespacevg.html#a20ebf02d59df03f906550e695a1aa00d',1,'vg']]],
- ['merge_5fequivalent_5ftraversals_5fin_5fgraph_10084',['merge_equivalent_traversals_in_graph',['../namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1',1,'vg']]],
- ['merge_5ffrom_5fdynamic_10085',['merge_from_dynamic',['../classvg_1_1Packer.html#a79ce5d54645f6d124c710b86b666f5d7',1,'vg::Packer']]],
- ['merge_5ffrom_5ffiles_10086',['merge_from_files',['../classvg_1_1Packer.html#af857449c08a56dd66c6a4bc0402231cb',1,'vg::Packer']]],
- ['merge_5fgroup_10087',['merge_group',['../classvg_1_1Funnel.html#a585c5484ef877a1ede56ed4467e32312',1,'vg::Funnel']]],
- ['merge_5fgroups_10088',['merge_groups',['../classvg_1_1Funnel.html#a44fcff7c06cb79e43cc1aa2fc73a8da6',1,'vg::Funnel']]],
- ['merge_5fid_5fspace_10089',['merge_id_space',['../classvg_1_1VGset.html#a968fb68f13f91ea8ded32d02c6ea683a',1,'vg::VGset']]],
- ['merge_5fnodes_10090',['merge_nodes',['../classvg_1_1VG.html#a2e506d51db427b617cc334a791c7f594',1,'vg::VG']]],
- ['merge_5fnon_5fbranching_5fsubpaths_10091',['merge_non_branching_subpaths',['../namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43',1,'vg']]],
- ['merge_5fpartially_5fredundant_5fmatch_5fnodes_10092',['merge_partially_redundant_match_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a9f8ca4f9936aa6abcc8681e91dae3f43',1,'vg::MultipathAlignmentGraph']]],
- ['merge_5frescued_5fmappings_10093',['merge_rescued_mappings',['../classvg_1_1MultipathMapper.html#a525152a98c905ba789a0454c70336c3e',1,'vg::MultipathMapper']]],
- ['merge_5fstate_10094',['merge_state',['../classvg_1_1DinucleotideMachine.html#ab28bcc9f016d8df680d6f17b5957fc57',1,'vg::DinucleotideMachine']]],
- ['merge_5funion_10095',['merge_union',['../classvg_1_1VG.html#a5aff716eee0bf720b3836caa761d48be',1,'vg::VG']]],
- ['mergedadjacencygraph_10096',['MergedAdjacencyGraph',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#aa09eaec5fd36cfe50b4313a38ba01fe1',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const RankedHandleGraph *graph)'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ab8d7ea6f475144c3779568d9d552c1c7',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const MergedAdjacencyGraph &other)']]],
- ['mergegraphs_10097',['mergeGraphs',['../namespacevg_1_1io.html#a09b6c55dd368ec0c3e85f51a87321ba2',1,'vg::io']]],
- ['mergenodeobjects_10098',['mergeNodeObjects',['../namespacevg.html#aa539af4f481d4e955ede26ee85c320c5',1,'vg']]],
- ['messageemitter_10099',['MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html#a674e6dee23ee5d3a5b49e56ff6dad2c1',1,'vg::io::MessageEmitter::MessageEmitter(ostream &out, bool compress=false, size_t max_group_size=1000)'],['../classvg_1_1io_1_1MessageEmitter.html#a4e9dd0179e7e2b815fcbf3175fd5a030',1,'vg::io::MessageEmitter::MessageEmitter(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#af48941a2e4e66c513e169d29f120d511',1,'vg::io::MessageEmitter::MessageEmitter(MessageEmitter &&other)=default']]],
- ['messageiterator_10100',['MessageIterator',['../classvg_1_1io_1_1MessageIterator.html#a44eabe49bb3f28067f8ba3396915ee64',1,'vg::io::MessageIterator::MessageIterator(istream &in, bool verbose=false, size_t thread_count=0)'],['../classvg_1_1io_1_1MessageIterator.html#ae7ddb87951881f58221acd0a1beeb32f',1,'vg::io::MessageIterator::MessageIterator(unique_ptr< BlockedGzipInputStream > &&bgzf, bool verbose=false)'],['../classvg_1_1io_1_1MessageIterator.html#a46b16972d489742f42922fd9cb9b85af',1,'vg::io::MessageIterator::MessageIterator()=default']]],
- ['middle_5fsignature_10101',['middle_signature',['../namespacevg.html#a7848d492a243a93f37b1ac52a541a96a',1,'vg::middle_signature(const Alignment &aln, int len)'],['../namespacevg.html#af64c67658563ff567bc0b103ef1d8af4',1,'vg::middle_signature(const Alignment &aln1, const Alignment &aln2, int len)']]],
- ['min_10102',['min',['../classvg_1_1WideningPRNG.html#a3cd7defb4589ed56c43b27f5d7bd36fe',1,'vg::WideningPRNG']]],
- ['min_5fapprox_5fpath_5fdistance_10103',['min_approx_path_distance',['../classxg_1_1XG.html#ae92433487bc35ef856ee592137937a98',1,'xg::XG::min_approx_path_distance()'],['../namespacevg_1_1algorithms.html#ae18b50d29d9accb763b44d6e065dac58',1,'vg::algorithms::min_approx_path_distance()']]],
- ['min_5fcut_10104',['min_cut',['../classvg_1_1FlowSort.html#aa489e8c6bbf375d149410afe0a35d58b',1,'vg::FlowSort']]],
- ['min_5fcut_5fdecomposition_10105',['min_cut_decomposition',['../namespacevg_1_1algorithms.html#a5cd4d23b1a702613134895c2d5618154',1,'vg::algorithms']]],
- ['min_5fdistance_5ffrom_5fstart_10106',['min_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#ab859980ced41bcd382cd5961ff3b8475',1,'vg::IncrementalSubgraph']]],
- ['min_5fdists_10107',['min_dists',['../classvg_1_1DeletionAligner.html#a42b9fef2da830c0912fb4141701c501e',1,'vg::DeletionAligner']]],
- ['min_5flink_5flength_10108',['min_link_length',['../classvg_1_1JoinedSpliceGraph.html#a92c8438c7a1efd3f0c5351a59b519a38',1,'vg::JoinedSpliceGraph']]],
- ['min_5fnode_5fid_10109',['min_node_id',['../classvg_1_1DagifiedGraph.html#a59e1c5556c2f5a984d9680cdaf8be41d',1,'vg::DagifiedGraph::min_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#ac48d1492dd478af9811307c52954e517',1,'vg::DozeuPinningOverlay::min_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ae07290cc251f0843de41551e25ffd4bf',1,'vg::ExtraNodeGraph::min_node_id()'],['../classvg_1_1SnarlGraph.html#a6e61014fadcbc2703a8fe3b208132ee4',1,'vg::SnarlGraph::min_node_id()'],['../classvg_1_1IdentityOverlay.html#a9a689ba99fa1452b5434a8a523e142c1',1,'vg::IdentityOverlay::min_node_id()'],['../classvg_1_1IncrementalSubgraph.html#a2d34ac8b129c82511c38f267644918d5',1,'vg::IncrementalSubgraph::min_node_id()'],['../classvg_1_1IndexedVG.html#ac496219064127ecd533ab41f77fc5da6',1,'vg::IndexedVG::min_node_id()'],['../classvg_1_1MemoizingGraph.html#afcbf2c9b526deaddee36140a362f4640',1,'vg::MemoizingGraph::min_node_id()'],['../classvg_1_1NullMaskingGraph.html#ab970c84b4caea2d00fd43a77f0826a95',1,'vg::NullMaskingGraph::min_node_id()'],['../classvg_1_1PathSubgraph.html#a472e93221aa3a728984d07aa6b7f0cc0',1,'vg::PathSubgraph::min_node_id()'],['../classvg_1_1ReverseGraph.html#adf486245a2201f1685e2af41a57a98f3',1,'vg::ReverseGraph::min_node_id()'],['../classvg_1_1NetGraph.html#a9b3c2b7f61f5c0133e844fa5edc4ea6d',1,'vg::NetGraph::min_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ad91d6241e1a962eaf4b4f1c92f2d94c8',1,'vg::SourceSinkOverlay::min_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#aa92df9f1002415710b4ffa4e6074cb5b',1,'vg::JoinedSpliceGraph::min_node_id()'],['../classvg_1_1StrandSplitGraph.html#aaeaf9231d44d7e0260ef5439f49e5e40',1,'vg::StrandSplitGraph::min_node_id()'],['../classvg_1_1SubHandleGraph.html#a180704728aa79aaf37189c644995cf91',1,'vg::SubHandleGraph::min_node_id()'],['../classvg_1_1SubgraphOverlay.html#a0d876d83943a078f6d9114bd08216086',1,'vg::SubgraphOverlay::min_node_id()'],['../classvg_1_1SubpathOverlay.html#a3d0fc1b94bdd931b4bd72197a07d6510',1,'vg::SubpathOverlay::min_node_id()'],['../classvg_1_1TreeSubgraph.html#a1ac845e3e2d75d7da5ff81b79aba3d08',1,'vg::TreeSubgraph::min_node_id()'],['../classvg_1_1VG.html#ac27674d67445ddc135c3c8ab4d3d5231',1,'vg::VG::min_node_id()'],['../classxg_1_1XG.html#a9195d1b18542de3b89b80bb14ce1ca0a',1,'xg::XG::min_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af944543089a7fae6c052decc4ff0a4c4',1,'handlegraph::algorithms::SubHandleGraph::min_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a85c52fe4b5f483504ed142d0ad94a969',1,'handlegraph::HandleGraph::min_node_id()']]],
- ['min_5foriented_5fdistances_10110',['min_oriented_distances',['../namespacevg.html#a973bf2647d54324bc63c323a0aa29a35',1,'vg']]],
- ['min_5fpair_5ffragment_5flength_10111',['min_pair_fragment_length',['../classvg_1_1Mapper.html#a3682f47407c7feddc2f8a22cd546a4ec',1,'vg::Mapper']]],
- ['min_5fsupport_5fin_5fpath_10112',['min_support_in_path',['../classvg_1_1NestedTraversalFinder.html#a3021b0689285b7c73f8201dcea103dac',1,'vg::NestedTraversalFinder::min_support_in_path()'],['../classvg_1_1RepresentativeTraversalFinder.html#acdea076c1d46ca2b92b338bd023c081b',1,'vg::RepresentativeTraversalFinder::min_support_in_path()']]],
- ['mindistanceclusterer_10113',['MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html#a8fe5349edbec12f8f15465249b8e6726',1,'vg::MinDistanceClusterer']]],
- ['minimizer_5freverse_5fcomplement_10114',['minimizer_reverse_complement',['../namespacevg.html#ae4b8625853b4a17f731c9fbd5a040fd7',1,'vg']]],
- ['minimizermapper_10115',['MinimizerMapper',['../classvg_1_1MinimizerMapper.html#ae2ecef3023c1cd374f0c7b1a3ac6ac5d',1,'vg::MinimizerMapper']]],
- ['minimum_5fdistance_10116',['minimum_distance',['../namespacevg.html#abcbcd550b51078ae43f2b1d87941e1a0',1,'vg']]],
- ['minimum_5fdistance_5fbetween_10117',['minimum_distance_between',['../classvg_1_1ZipCode.html#a3f0f330d338d949d04dbe14fd606e838',1,'vg::ZipCode']]],
- ['mismatches_10118',['mismatches',['../structvg_1_1GaplessExtension.html#a4898e2fabc109703f497e19f10bb164a',1,'vg::GaplessExtension']]],
- ['mode_5fname_10119',['mode_name',['../prune__main_8cpp.html#a9b89c7a3b7a8efd51b246bc312140bb8',1,'prune_main.cpp']]],
- ['modular_5fexponent_10120',['modular_exponent',['../namespacevg.html#abc8f8791be2575164e6070e1cef39b4e',1,'vg']]],
- ['motif_5ffrequency_10121',['motif_frequency',['../classvg_1_1SpliceStats.html#aeb0d77ba4fc7a6767eff466a6ba8ed9e',1,'vg::SpliceStats']]],
- ['motif_5fis_5freverse_10122',['motif_is_reverse',['../classvg_1_1SpliceStats.html#afc22a25e939fa725d3808430f9a62007',1,'vg::SpliceStats']]],
- ['motif_5fscore_10123',['motif_score',['../classvg_1_1SpliceStats.html#a7da67978c875a8e9bc1fac31fdb8277b',1,'vg::SpliceStats']]],
- ['motif_5fsize_10124',['motif_size',['../classvg_1_1SpliceStats.html#aae5310e0728aebc36703641a566242e3',1,'vg::SpliceStats']]],
- ['move_10125',['move',['../classvg_1_1SmallBitset.html#a5c80c7e3d6d92c7c5e58463771a2a341',1,'vg::SmallBitset']]],
- ['msaconverter_10126',['MSAConverter',['../classvg_1_1MSAConverter.html#ac6e82d70cf93d7b8a75750b40dd89277',1,'vg::MSAConverter']]],
- ['multi_5fsurject_10127',['multi_surject',['../classvg_1_1Surjector.html#a0ed6215f3860203803deb2f3078d93b4',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#ab8b34cbb819829cd493bdc901a6e3060',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a943158332e4865de071dca68454a4d77',1,'vg::Surjector::multi_surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
- ['multinomial_5fcensored_5fsampling_5fprob_5fln_10128',['multinomial_censored_sampling_prob_ln',['../namespacevg.html#a074fcebfeb68fc970b5b2a0db3722f01',1,'vg']]],
- ['multinomial_5fchoose_5fln_10129',['multinomial_choose_ln',['../namespacevg.html#a15f09f05f7894863e9cd852c63266078',1,'vg']]],
- ['multinomial_5fsampling_5fprob_5fln_10130',['multinomial_sampling_prob_ln',['../namespacevg.html#af4d69cf9a7d7e6272960fcb9f0a0a00c',1,'vg']]],
- ['multipath_5falign_10131',['multipath_align',['../classvg_1_1MultipathMapper.html#a7af0cb7af3f7a3e3ab60627f3793aa0a',1,'vg::MultipathMapper']]],
- ['multipath_5falignment_5fpath_5foffsets_10132',['multipath_alignment_path_offsets',['../namespacevg_1_1algorithms.html#ad0cecedaa8dd475e634b513af5be028b',1,'vg::algorithms']]],
- ['multipath_5falignment_5ft_10133',['multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html#ae7f715f63023d3043c01ed29193ea6a1',1,'vg::multipath_alignment_t::multipath_alignment_t()'],['../classvg_1_1multipath__alignment__t.html#a55b4c1fee893c4b596f0a654a624bccc',1,'vg::multipath_alignment_t::multipath_alignment_t(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ad4de932d4f01d8d44a76095605294470',1,'vg::multipath_alignment_t::multipath_alignment_t(multipath_alignment_t &&other)']]],
- ['multipath_5fmap_10134',['multipath_map',['../classvg_1_1MultipathMapper.html#a9ea318c04336aa79020b7c012e468ef8',1,'vg::MultipathMapper']]],
- ['multipath_5fmap_5fpaired_10135',['multipath_map_paired',['../classvg_1_1MultipathMapper.html#a240c4502e41aa0e5961772a12b1b42a8',1,'vg::MultipathMapper']]],
- ['multipathalignmentemitter_10136',['MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html#a022247fcbd889aeb51b35b0cae1c3622',1,'vg::MultipathAlignmentEmitter']]],
- ['multipathalignmentgraph_10137',['MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html#a058e6120cb359e2566c1c2d7961c608e',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a51e7308dc1c0c96d1e576970211b7705',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#afd75ac7afd23901c4b8f38eb126bdba0',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a74eec86f754011999dc6caed5d1f6c8a',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a366ddb07faadad371e896d3f453e147c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a4289e77bb6d76abfbb1d3c02d89a2586',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#ac8f4ae19921529920157bcbbf9a2f5c3',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a10f9b18c8aa4db1b80bf54ccc5dcc09c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const unordered_map< id_t, pair< id_t, bool >> &projection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a89b441f028fd26c177a9ce8d8188b7c1',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project)']]],
- ['multipathmapper_10138',['MultipathMapper',['../classvg_1_1MultipathMapper.html#a4d3a7e85dfc2d7cda41912a4f87fd5ac',1,'vg::MultipathMapper']]],
- ['multipathproblem_10139',['MultipathProblem',['../structvg_1_1MultipathProblem.html#ac97d55858c86d218c380fd43e115d18a',1,'vg::MultipathProblem']]],
- ['mutable_5fconnection_10140',['mutable_connection',['../classvg_1_1subpath__t.html#a271236a46bdb6105f216a630c0c67a74',1,'vg::subpath_t::mutable_connection()'],['../classvg_1_1subpath__t.html#aa967fceb620f92e73e965345d4cd0b67',1,'vg::subpath_t::mutable_connection(size_t i)']]],
- ['mutable_5fedit_10141',['mutable_edit',['../classvg_1_1path__mapping__t.html#aeb9d50accda37c8829c49cd8567f72bc',1,'vg::path_mapping_t::mutable_edit()'],['../classvg_1_1path__mapping__t.html#a56c059138a051e7889f4083a74c5401f',1,'vg::path_mapping_t::mutable_edit(size_t i)']]],
- ['mutable_5fmapping_10142',['mutable_mapping',['../classvg_1_1path__t.html#ab3f1eeeefe1c604dacdeff019488ff07',1,'vg::path_t::mutable_mapping()'],['../classvg_1_1path__t.html#aac0ad10ace8970358d471d779061b22d',1,'vg::path_t::mutable_mapping(size_t i)']]],
- ['mutable_5fnext_10143',['mutable_next',['../classvg_1_1subpath__t.html#ae1331c79838d972ccb8be4e98ac87954',1,'vg::subpath_t']]],
- ['mutable_5fpath_10144',['mutable_path',['../classvg_1_1subpath__t.html#aa5f32fe1e7167d09187d4a69c091bde5',1,'vg::subpath_t']]],
- ['mutable_5fposition_10145',['mutable_position',['../classvg_1_1path__mapping__t.html#a87ef119207623109aea694cd5432421d',1,'vg::path_mapping_t']]],
- ['mutable_5fquality_10146',['mutable_quality',['../classvg_1_1multipath__alignment__t.html#a5d62a17eb3aad07f05f5580aa7f9dfbd',1,'vg::multipath_alignment_t']]],
- ['mutable_5fsequence_10147',['mutable_sequence',['../classvg_1_1multipath__alignment__t.html#a11d22790dc8b9cc631a237ef00b6e0e4',1,'vg::multipath_alignment_t::mutable_sequence()'],['../classvg_1_1edit__t.html#aa5e639217215d8d67bfe1ec2a07105fb',1,'vg::edit_t::mutable_sequence()']]],
- ['mutable_5fstart_10148',['mutable_start',['../classvg_1_1multipath__alignment__t.html#a43e30d76e7ac0596fc15c868fbbd603c',1,'vg::multipath_alignment_t']]],
- ['mutable_5fsubpath_10149',['mutable_subpath',['../classvg_1_1multipath__alignment__t.html#a65ee05140e26b51a60f7d33a7b9b9c54',1,'vg::multipath_alignment_t::mutable_subpath()'],['../classvg_1_1multipath__alignment__t.html#a727e5e6bc04955e46efe83bc5d668bdf',1,'vg::multipath_alignment_t::mutable_subpath(size_t i)']]],
- ['mutate_10150',['mutate',['../classvg_1_1Sampler.html#a8f148dac7598a3465202371511e53f2a',1,'vg::Sampler']]],
- ['mutate_5fedit_10151',['mutate_edit',['../classvg_1_1Sampler.html#ad372d6fdcac5af601bdb0729f94a7e7d',1,'vg::Sampler']]]
+ ['main_9899',['main',['../main_8cpp.html#a813f1942a22b88bf4ff8686af6c643bd',1,'main(int argc, char *argv[]) VG_PREFLIGHT_EVERYWHERE: main.cpp'],['../main_8cpp.html#a3c04138a5bfe5d72780bb7e82a18e627',1,'main(int argc, char **argv): main.cpp']]],
+ ['main_5fadd_9900',['main_add',['../add__main_8cpp.html#a70f2a72c5f1d86661c78534083fbe668',1,'add_main.cpp']]],
+ ['main_5falign_9901',['main_align',['../align__main_8cpp.html#acc3c08d6346e0538c36aa20a0af338f2',1,'align_main.cpp']]],
+ ['main_5fannotate_9902',['main_annotate',['../annotate__main_8cpp.html#ae4b460c351b8e163410fbacf4244f7f2',1,'annotate_main.cpp']]],
+ ['main_5faugment_9903',['main_augment',['../augment__main_8cpp.html#a39b28115682b22f672ec0f6932d0f259',1,'augment_main.cpp']]],
+ ['main_5fautoindex_9904',['main_autoindex',['../autoindex__main_8cpp.html#a0c5af200c1937f0b3c5723ce0220a7bf',1,'autoindex_main.cpp']]],
+ ['main_5fbenchmark_9905',['main_benchmark',['../benchmark__main_8cpp.html#add0702a6210234f5e42ee9c301265d6a',1,'benchmark_main.cpp']]],
+ ['main_5fcall_9906',['main_call',['../call__main_8cpp.html#ac255329e18ef1a778298cd5fdc5d3050',1,'call_main.cpp']]],
+ ['main_5fchain_9907',['main_chain',['../chain__main_8cpp.html#af61d7259730b08c0c8ff61629e51d78a',1,'chain_main.cpp']]],
+ ['main_5fchunk_9908',['main_chunk',['../chunk__main_8cpp.html#aa34cae934dcb31ac7653f079d0d4bf93',1,'chunk_main.cpp']]],
+ ['main_5fcircularize_9909',['main_circularize',['../circularize__main_8cpp.html#a1d21512b4c5eb417fa6a1b20a72c1195',1,'circularize_main.cpp']]],
+ ['main_5fclip_9910',['main_clip',['../clip__main_8cpp.html#af09a429b96343cf918b8fdea5ebf1a4b',1,'clip_main.cpp']]],
+ ['main_5fcluster_9911',['main_cluster',['../cluster__main_8cpp.html#a88693148489c263b15047d96976b9b94',1,'cluster_main.cpp']]],
+ ['main_5fcombine_9912',['main_combine',['../combine__main_8cpp.html#a7f4bcb1d0c551b46ed39797df9d0da60',1,'combine_main.cpp']]],
+ ['main_5fconcat_9913',['main_concat',['../concat__main_8cpp.html#a22a9b545fc267c18654f312d4fa8d701',1,'concat_main.cpp']]],
+ ['main_5fconstruct_9914',['main_construct',['../construct__main_8cpp.html#a385574d21007babb8ef7fa73c9b39cee',1,'construct_main.cpp']]],
+ ['main_5fconvert_9915',['main_convert',['../convert__main_8cpp.html#abd9dc3a752930342a8096088f2d4b742',1,'convert_main.cpp']]],
+ ['main_5fdeconstruct_9916',['main_deconstruct',['../deconstruct__main_8cpp.html#a80a32834c987861cb4c90d124e0aba12',1,'deconstruct_main.cpp']]],
+ ['main_5fdepth_9917',['main_depth',['../depth__main_8cpp.html#a7db982076303bea19c79ee8df88e086f',1,'depth_main.cpp']]],
+ ['main_5fdotplot_9918',['main_dotplot',['../dotplot__main_8cpp.html#a74751264f7ead208e151be5408766053',1,'dotplot_main.cpp']]],
+ ['main_5fexplode_9919',['main_explode',['../explode__main_8cpp.html#a0448cf7f521dde683e09f6c57df48d67',1,'explode_main.cpp']]],
+ ['main_5ffilter_9920',['main_filter',['../filter__main_8cpp.html#af14726647fef6f08e5f916f8a1b4ae0e',1,'filter_main.cpp']]],
+ ['main_5ffind_9921',['main_find',['../find__main_8cpp.html#a35569e011de224c166556ea563a4861e',1,'find_main.cpp']]],
+ ['main_5fgamcompare_9922',['main_gamcompare',['../gamcompare__main_8cpp.html#a0685b1cc8cff4ca811a199eb1746ddf7',1,'gamcompare_main.cpp']]],
+ ['main_5fgampcompare_9923',['main_gampcompare',['../gampcompare__main_8cpp.html#a4b081154219461589d0978c7d993d547',1,'gampcompare_main.cpp']]],
+ ['main_5fgamsort_9924',['main_gamsort',['../gamsort__main_8cpp.html#a0aa266bac1f77e7c3625c293f1050108',1,'gamsort_main.cpp']]],
+ ['main_5fgbwt_9925',['main_gbwt',['../gbwt__main_8cpp.html#a2018904e4679a19c52921f97afab4592',1,'gbwt_main.cpp']]],
+ ['main_5fgenotype_9926',['main_genotype',['../genotype__main_8cpp.html#a04819bc8264065b3aadb2b7bf3a923fa',1,'genotype_main.cpp']]],
+ ['main_5fgiraffe_9927',['main_giraffe',['../giraffe__main_8cpp.html#a03a19bdd804f12c23f77bb885e91df4a',1,'giraffe_main.cpp']]],
+ ['main_5fhaplotypes_9928',['main_haplotypes',['../haplotypes__main_8cpp.html#ae8ab8ef2233eb016b7b7f0c2bd5c9411',1,'haplotypes_main.cpp']]],
+ ['main_5fhelp_9929',['main_help',['../help__main_8cpp.html#ad13a4a4aadfb1314983f35c8cca2e5c7',1,'help_main.cpp']]],
+ ['main_5fids_9930',['main_ids',['../ids__main_8cpp.html#aaefd32fe84e813daa1089df0d0bd955f',1,'ids_main.cpp']]],
+ ['main_5findex_9931',['main_index',['../index__main_8cpp.html#a7a9da678374c285546cdf243a185b15e',1,'index_main.cpp']]],
+ ['main_5finject_9932',['main_inject',['../inject__main_8cpp.html#a214bda0795dc475a91ffd32752b2ee8e',1,'inject_main.cpp']]],
+ ['main_5fjoin_9933',['main_join',['../join__main_8cpp.html#a904b50e94b5426c0bb0a39523aada064',1,'join_main.cpp']]],
+ ['main_5fkmers_9934',['main_kmers',['../kmers__main_8cpp.html#af32e430824ef93e29253ec42f2edb21e',1,'kmers_main.cpp']]],
+ ['main_5fmap_9935',['main_map',['../map__main_8cpp.html#ac963a6cd2cd103405e86f088d5c8358a',1,'map_main.cpp']]],
+ ['main_5fmask_9936',['main_mask',['../mask__main_8cpp.html#a66e6db9d20d50a757d7ab70d7ca458f8',1,'mask_main.cpp']]],
+ ['main_5fmcmc_9937',['main_mcmc',['../mcmc__main_8cpp.html#a7a702ad991c4285feaeee55461c95a63',1,'mcmc_main.cpp']]],
+ ['main_5fminimizer_9938',['main_minimizer',['../minimizer__main_8cpp.html#a5a43d1ef287159cce46f07df1b8b088d',1,'minimizer_main.cpp']]],
+ ['main_5fmod_9939',['main_mod',['../mod__main_8cpp.html#ab561b57168cf02964d1a14e024108f2e',1,'mod_main.cpp']]],
+ ['main_5fmpmap_9940',['main_mpmap',['../mpmap__main_8cpp.html#a8deece908ee37e2d38e61b2c921e508f',1,'mpmap_main.cpp']]],
+ ['main_5fmsga_9941',['main_msga',['../msga__main_8cpp.html#a60a999194e7689bb509442f1caa2354e',1,'msga_main.cpp']]],
+ ['main_5fpack_9942',['main_pack',['../pack__main_8cpp.html#a0b3d5bb3cabcd119b839dded9853de23',1,'pack_main.cpp']]],
+ ['main_5fpaths_9943',['main_paths',['../paths__main_8cpp.html#a6357ea987a573514a31781145d74cd61',1,'paths_main.cpp']]],
+ ['main_5fprune_9944',['main_prune',['../prune__main_8cpp.html#a5b6c70447534213ea13f56ad785d881b',1,'prune_main.cpp']]],
+ ['main_5frna_9945',['main_rna',['../rna__main_8cpp.html#a6d06f637eb10cfbb38bb55619ceb3c00',1,'rna_main.cpp']]],
+ ['main_5fsift_9946',['main_sift',['../sift__main_8cpp.html#a5c78b9bf77f34696d562b5abffb7a1ef',1,'sift_main.cpp']]],
+ ['main_5fsim_9947',['main_sim',['../sim__main_8cpp.html#a1926f81c841475ca54d3100d6340d468',1,'sim_main.cpp']]],
+ ['main_5fsimplify_9948',['main_simplify',['../simplify__main_8cpp.html#a16ebf24b0dce88509b5e97fc2fc777b8',1,'simplify_main.cpp']]],
+ ['main_5fsnarl_9949',['main_snarl',['../snarls__main_8cpp.html#a4bda7d45d00c828d1e8555573c1c3caf',1,'snarls_main.cpp']]],
+ ['main_5fsort_9950',['main_sort',['../sort__main_8cpp.html#a40dc673c2ce8bc4c8ae1496857641885',1,'sort_main.cpp']]],
+ ['main_5fstats_9951',['main_stats',['../stats__main_8cpp.html#a6e64cedc2b30a69dea5b727edded704d',1,'stats_main.cpp']]],
+ ['main_5fsurject_9952',['main_surject',['../surject__main_8cpp.html#a51d014c6923a46c0f34ca4deb59d11b0',1,'surject_main.cpp']]],
+ ['main_5ftest_9953',['main_test',['../test__main_8cpp.html#abd8de8d504f1b1aa53207643a7b553b4',1,'test_main.cpp']]],
+ ['main_5ftrace_9954',['main_trace',['../trace__main_8cpp.html#a7bc03098058581a46cba55a13de823e9',1,'trace_main.cpp']]],
+ ['main_5ftranslate_9955',['main_translate',['../translate__main_8cpp.html#a2578e3814e52126bf55e62054a01ec7d',1,'translate_main.cpp']]],
+ ['main_5fvalidate_9956',['main_validate',['../validate__main_8cpp.html#a8249f1e29a84af534ef5116f778267fb',1,'validate_main.cpp']]],
+ ['main_5fvectorize_9957',['main_vectorize',['../vectorize__main_8cpp.html#a8e4da879b5896dd1e13ee84e310870ea',1,'vectorize_main.cpp']]],
+ ['main_5fversion_9958',['main_version',['../version__main_8cpp.html#a972dc6662988df17dcc0b4cc0abf6e54',1,'version_main.cpp']]],
+ ['main_5fview_9959',['main_view',['../view__main_8cpp.html#a868d2fd8e59794e18a2ecee28f838143',1,'view_main.cpp']]],
+ ['main_5fviz_9960',['main_viz',['../viz__main_8cpp.html#a9e415066b5a221e559f9a402b85f386d',1,'viz_main.cpp']]],
+ ['main_5fzipcode_9961',['main_zipcode',['../zipcode__main_8cpp.html#a8b81469e01a40dbf9eefbdf90e0c0427',1,'zipcode_main.cpp']]],
+ ['make_5fbands_9962',['make_bands',['../classvg_1_1Mapper.html#aafecbaf352024b2847928860fe6c1168',1,'vg::Mapper']]],
+ ['make_5fcircular_9963',['make_circular',['../classvg_1_1Paths.html#a1e8760e2c86dd64141c2d0df35926430',1,'vg::Paths']]],
+ ['make_5fcompact_9964',['make_compact',['../classvg_1_1Packer.html#a66e266fca00d4e74b7bda1ddbcf384e3',1,'vg::Packer']]],
+ ['make_5fdynamic_9965',['make_dynamic',['../classvg_1_1Packer.html#ac3ab6cab2e0cf0ae4e65663db73184e8',1,'vg::Packer']]],
+ ['make_5fedge_9966',['make_edge',['../classvg_1_1PhaseUnfolder.html#a82b0a653c98ead9bc4c31d283583d102',1,'vg::PhaseUnfolder']]],
+ ['make_5fempty_9967',['make_empty',['../structvg_1_1WFAAlignment.html#ae54f9060454a45ea9a2131a9b5b81c38',1,'vg::WFAAlignment']]],
+ ['make_5fgraph_9968',['make_graph',['../classvg_1_1MSAConverter.html#aa4556065637b908e37d2cbf7534b930a',1,'vg::MSAConverter']]],
+ ['make_5fhit_5fgraph_9969',['make_hit_graph',['../classvg_1_1MEMClusterer.html#ac65c43448463ef346199437b073c1467',1,'vg::MEMClusterer::make_hit_graph()'],['../classvg_1_1NullClusterer.html#a4e7540aadd3d1eb3d4616cf0d268b3f0',1,'vg::NullClusterer::make_hit_graph()'],['../classvg_1_1OrientedDistanceClusterer.html#af520fdf27e87d46d3a7a5976ec6179c2',1,'vg::OrientedDistanceClusterer::make_hit_graph()'],['../classvg_1_1TVSClusterer.html#a33dff32277c63fa9dc42969c01094900',1,'vg::TVSClusterer::make_hit_graph()'],['../classvg_1_1MinDistanceClusterer.html#a8f3bd899d336e3a30f77e2985eaceb81',1,'vg::MinDistanceClusterer::make_hit_graph()'],['../classvg_1_1GreedyMinDistanceClusterer.html#ad5a3eda064089d19eec2338ccc82e515',1,'vg::GreedyMinDistanceClusterer::make_hit_graph()'],['../classvg_1_1ComponentMinDistanceClusterer.html#afe8b8bc133b5ef94999264dabb3452b8',1,'vg::ComponentMinDistanceClusterer::make_hit_graph()']]],
+ ['make_5findexes_9970',['make_indexes',['../classvg_1_1IndexRegistry.html#a4c954dbadbab6cdcd3e81b438864668d',1,'vg::IndexRegistry']]],
+ ['make_5flinear_9971',['make_linear',['../classvg_1_1Paths.html#aa82bcbd02b83a9f0781c3696ef46d371',1,'vg::Paths']]],
+ ['make_5flong_5foptions_9972',['make_long_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#aec2fb8fe7d2b574993b33658440227e0',1,'vg::subcommand::BaseOptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8db74c059e0822c3b25ea7d05bcce340',1,'vg::subcommand::OptionGroup::make_long_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#af521b678294674ffcd04b670b5cde737',1,'vg::subcommand::GroupedOptionGroup::make_long_options()']]],
+ ['make_5fnontrivial_5fmultipath_5falignment_9973',['make_nontrivial_multipath_alignment',['../classvg_1_1MultipathMapper.html#a4e4be08a92493e0e3b865783b4701cd7',1,'vg::MultipathMapper']]],
+ ['make_5fnull_5falignment_9974',['make_null_alignment',['../classvg_1_1Surjector.html#a139ffe849fc1164217e45ea5755fc518',1,'vg::Surjector']]],
+ ['make_5fnull_5fmp_5falignment_9975',['make_null_mp_alignment',['../classvg_1_1Surjector.html#a7db137631f3315ede2f6887334a161b4',1,'vg::Surjector']]],
+ ['make_5fplan_9976',['make_plan',['../classvg_1_1IndexRegistry.html#ab31ecdcf8f9d50a1310667d23c6410e2',1,'vg::IndexRegistry']]],
+ ['make_5fpos_5ft_9977',['make_pos_t',['../namespacevg.html#a2d9f0a2379194fb00d706e90d373b378',1,'vg::make_pos_t(const Position &pos)'],['../namespacevg.html#a1b348dcfac955a7030a3721f436e7d5d',1,'vg::make_pos_t(const position_t &pos)'],['../namespacevg.html#afc066dab7543192bf782959ef160f2d4',1,'vg::make_pos_t(gcsa::node_type node)'],['../namespacevg.html#a1d85d380ba4b936ac8a715a72062866c',1,'vg::make_pos_t(id_t id, bool is_rev, offset_t off)'],['../namespacexg.html#aace66781c520f719a1f8f64ab24f2589',1,'xg::make_pos_t()']]],
+ ['make_5fposition_9978',['make_position',['../namespacevg.html#a6247de8deb27aaabf2bc0d6fc755f693',1,'vg::make_position(const pos_t &pos)'],['../namespacevg.html#ac6af3d55800703f7534ca07a84450580',1,'vg::make_position(id_t id, bool is_rev, offset_t off)'],['../namespacevg.html#a4cdd9b08b7b6d6e15d00536554f3ca56',1,'vg::make_position(gcsa::node_type node)']]],
+ ['make_5fprefix_5fsuffix_5ftable_9979',['make_prefix_suffix_table',['../namespacevg.html#a3ff1638bd636bb4b9746545dc261aea1',1,'vg']]],
+ ['make_5fshort_5foptions_9980',['make_short_options',['../structvg_1_1subcommand_1_1BaseOptionGroup.html#a0a5933555ce227565029122dfd6f15e9',1,'vg::subcommand::BaseOptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1OptionGroup.html#a8ef56a59e757ab9cd808cf9112e1f64b',1,'vg::subcommand::OptionGroup::make_short_options()'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3f2f2249f4edee37552c77bce6c4a42c',1,'vg::subcommand::GroupedOptionGroup::make_short_options()']]],
+ ['make_5fshuffle_5fseed_9981',['make_shuffle_seed',['../namespacevg.html#aeca2b8e2d5730b1d5b94c1d3861757d7',1,'vg::make_shuffle_seed(const multipath_alignment_t &aln)'],['../namespacevg.html#acc312d814d6a06a4a5159c7943675bbe',1,'vg::make_shuffle_seed(const Alignment &aln)'],['../namespacevg.html#a2ec8fc79a1f84c6ef4a02c9d7c7a2850',1,'vg::make_shuffle_seed(const T *ptr)'],['../namespacevg.html#a04ebc20fd2965b1932e27958dd0c602c',1,'vg::make_shuffle_seed(const pair< T1, T2 > &p)']]],
+ ['make_5fsingle_5fstranded_9982',['make_single_stranded',['../namespacehandlegraph_1_1algorithms.html#a8cac1e5f4dc0c5e0e501ebb9fc58fca3',1,'handlegraph::algorithms']]],
+ ['make_5fsnarl_5fgraph_9983',['make_snarl_graph',['../classvg_1_1MCMCGenotyper.html#abbbf0c2625e4039f5a79b8b360515b41',1,'vg::MCMCGenotyper']]],
+ ['make_5fsnarl_5fmap_9984',['make_snarl_map',['../classvg_1_1MCMCGenotyper.html#a5e31dd64fad5dfb14d38be487fc14e59',1,'vg::MCMCGenotyper']]],
+ ['make_5fsubset_5fgraph_9985',['make_subset_graph',['../classvg_1_1Genotyper.html#ab11a87f5f21d3a7122ec85f6d853f336',1,'vg::Genotyper']]],
+ ['make_5fsupport_9986',['make_support',['../namespacevg.html#a1c0ae5cc687e77bb7cee28e975a005b3',1,'vg']]],
+ ['make_5ftemporary_5fdistance_5findex_9987',['make_temporary_distance_index',['../namespacevg.html#ae55954f00a00c8b34d20966f7d9fe72a',1,'vg']]],
+ ['make_5ftranslation_9988',['make_translation',['../namespacevg.html#a028aa842a68b6993a37a82c7645e0633',1,'vg']]],
+ ['make_5funlocalized_5finsertion_9989',['make_unlocalized_insertion',['../structvg_1_1WFAAlignment.html#aee475e8a07f1e06f61411f581813252e',1,'vg::WFAAlignment']]],
+ ['make_5fvariant_5fid_9990',['make_variant_id',['../namespacevg.html#aa74ef603900cf05ce35dbab813d21deb',1,'vg']]],
+ ['manage_9991',['manage',['../classvg_1_1SnarlManager.html#adb68da18eef20aa324c498444a9ed77f',1,'vg::SnarlManager']]],
+ ['map_9992',['map',['../classvg_1_1MinimizerMapper.html#a4c955e7607a1c07d2ca2b22a065e8b91',1,'vg::MinimizerMapper::map(Alignment &aln, AlignmentEmitter &alignment_emitter)'],['../classvg_1_1MinimizerMapper.html#a182c026fcc4e3a8dea5de373d1a79bbb',1,'vg::MinimizerMapper::map(Alignment &aln)']]],
+ ['map_5ffrom_5fchains_9993',['map_from_chains',['../classvg_1_1MinimizerMapper.html#af098e417ff3df9ff70d18cd4cd12555b',1,'vg::MinimizerMapper']]],
+ ['map_5ffrom_5fextensions_9994',['map_from_extensions',['../classvg_1_1MinimizerMapper.html#aaaaff0f62d2003bd8814c3fd90dd8226',1,'vg::MinimizerMapper']]],
+ ['map_5fkeys_5fto_5fset_9995',['map_keys_to_set',['../namespacevg.html#ace99283a6b34f0891dc0b49f0cd60eea',1,'vg']]],
+ ['map_5fover_9996',['map_over',['../namespacevg.html#a4833086451a8b97af4709aa6c7385177',1,'vg']]],
+ ['map_5fpaired_9997',['map_paired',['../classvg_1_1MinimizerMapper.html#a5c90ef4f961998cc7904e78225b36f50',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2, vector< pair< Alignment, Alignment >> &ambiguous_pair_buffer)'],['../classvg_1_1MinimizerMapper.html#ab5f4c707ec44ba8f742c79bb0153c157',1,'vg::MinimizerMapper::map_paired(Alignment &aln1, Alignment &aln2)']]],
+ ['map_5fstage_5fresults_5fto_5fprevious_5fstage_9998',['map_stage_results_to_previous_stage',['../classvg_1_1Funnel.html#aeca18258bb42790609df5f17d2394135',1,'vg::Funnel']]],
+ ['map_5fvariants_9999',['map_variants',['../haplotypes__main_8cpp.html#a1e43abd4f18210a8a4e131afbc8d182d',1,'haplotypes_main.cpp']]],
+ ['mapper_10000',['Mapper',['../classvg_1_1Mapper.html#a1d808071bd518202414fba56f5ec333e',1,'vg::Mapper::Mapper(PathPositionHandleGraph *xidex, gcsa::GCSA *g, gcsa::LCPArray *a, haplo::ScoreProvider *haplo_score_provider=nullptr)'],['../classvg_1_1Mapper.html#ae47e4e50adf1a5132656e9dd9a227628',1,'vg::Mapper::Mapper(void)']]],
+ ['mapping_10001',['mapping',['../classvg_1_1path__t.html#ab7f2f4df754fec9f8631c8388cbe4aad',1,'vg::path_t::mapping() const'],['../classvg_1_1path__t.html#a07af6243d1650ddef63ed19804da8071',1,'vg::path_t::mapping(size_t i) const']]],
+ ['mapping_5fagainst_5fpath_10002',['mapping_against_path',['../namespacevg.html#ad2e7730a993652e18d80ca77dac73713',1,'vg']]],
+ ['mapping_5fcigar_10003',['mapping_cigar',['../namespacevg.html#a5a0bb992cac134b2eed1e7b84eaecc2c',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char >> &cigar, char mismatch_operation)'],['../namespacevg.html#a642736d2f652e5ab522e1f26b874e097',1,'vg::mapping_cigar(const Mapping &mapping, vector< pair< int, char > > &cigar, char mismatch_operation='M')']]],
+ ['mapping_5fends_5fin_5fdeletion_10004',['mapping_ends_in_deletion',['../namespacevg.html#afeef6a4c023183ead5725398b14d443c',1,'vg']]],
+ ['mapping_5fenters_5fside_10005',['mapping_enters_side',['../classvg_1_1Genotyper.html#aa2b4d94f59265c107895c48a26b107a6',1,'vg::Genotyper']]],
+ ['mapping_5fexits_5fside_10006',['mapping_exits_side',['../classvg_1_1Genotyper.html#a8b054a94fb2ceb4c65731188227b0cf8',1,'vg::Genotyper']]],
+ ['mapping_5ffrom_5flength_10007',['mapping_from_length',['../namespacevg.html#aa2aa77c6d4db628d13488c0bd82538ed',1,'vg::mapping_from_length(const Mapping &m)'],['../namespacevg.html#a151a868062bd12ac34b9aea68dc8d4f0',1,'vg::mapping_from_length(const path_mapping_t &mapping)']]],
+ ['mapping_5fis_5fmatch_10008',['mapping_is_match',['../namespacevg.html#a78ea8a2cf04759a3cfecbe4bf3e926c2',1,'vg']]],
+ ['mapping_5fis_5fsimple_5fmatch_10009',['mapping_is_simple_match',['../namespacevg.html#ae8ba5042b838f859a078cf014f1a0871',1,'vg']]],
+ ['mapping_5fis_5ftotal_5fdeletion_10010',['mapping_is_total_deletion',['../namespacevg.html#a6d10b5bc5677fdb0ae164f79848bb1bb',1,'vg']]],
+ ['mapping_5fis_5ftotal_5finsertion_10011',['mapping_is_total_insertion',['../namespacevg.html#a54cdb9b97e741de6ced9fefbc2bf48f3',1,'vg']]],
+ ['mapping_5fis_5ftotal_5fmatch_10012',['mapping_is_total_match',['../classvg_1_1VG.html#acd555e66c8fa99984c8cb24aef0ab6f9',1,'vg::VG']]],
+ ['mapping_5flikelihoods_10013',['mapping_likelihoods',['../classvg_1_1MultipathMapper.html#a9c55acfb3c1116daeba543b42303ce7d',1,'vg::MultipathMapper']]],
+ ['mapping_5fpath_5fid_10014',['mapping_path_id',['../classvg_1_1Paths.html#abb58996e669d1b9271772a929f6bebe2',1,'vg::Paths']]],
+ ['mapping_5fpath_5fname_10015',['mapping_path_name',['../classvg_1_1Paths.html#ab520f6e02a5a9b2e11f10a6455be5bdd',1,'vg::Paths']]],
+ ['mapping_5fquality_10016',['mapping_quality',['../classvg_1_1multipath__alignment__t.html#a7a9fd028a082d666d19522d27ea5aa2c',1,'vg::multipath_alignment_t']]],
+ ['mapping_5fquality_5fscore_5fdiff_10017',['mapping_quality_score_diff',['../classvg_1_1GSSWAligner.html#a1c341fd9f6dd51131b714d580f5ccfea',1,'vg::GSSWAligner']]],
+ ['mapping_5fsequence_10018',['mapping_sequence',['../namespacevg.html#a2b648cd1a51584623d6618565d3ca9c6',1,'vg::mapping_sequence(const Mapping &mp, const string &node_seq)'],['../namespacevg.html#ac23702705b681eacdfd1b3bcbc5254b5',1,'vg::mapping_sequence(const Mapping &mp, const Node &n)']]],
+ ['mapping_5fsize_10019',['mapping_size',['../classvg_1_1path__t.html#aa3e09b61e5f2b803461ac3e20df6117c',1,'vg::path_t']]],
+ ['mapping_5fstarts_5fin_5fdeletion_10020',['mapping_starts_in_deletion',['../namespacevg.html#aa377b3e776e312c717aedec842216f48',1,'vg']]],
+ ['mapping_5fstring_10021',['mapping_string',['../namespacevg.html#ad993b1f289a57f3413b85840984b459c',1,'vg']]],
+ ['mapping_5ft_10022',['mapping_t',['../classvg_1_1mapping__t.html#aa47429bfca4c4120a2e5c116d6d54450',1,'vg::mapping_t::mapping_t(void)'],['../classvg_1_1mapping__t.html#a6c9be43df27053b2bc5599faad299513',1,'vg::mapping_t::mapping_t(const Mapping &m)']]],
+ ['mapping_5fto_5fgbwt_10023',['mapping_to_gbwt',['../namespacevg.html#ace1a7180fda8bb98abba24fb19183e9d',1,'vg']]],
+ ['mapping_5fto_5fhandle_10024',['mapping_to_handle',['../namespacevg.html#acdaa29c218d5d55e76fe4ab168f7a14b',1,'vg']]],
+ ['mapping_5fto_5flength_10025',['mapping_to_length',['../namespacevg.html#a9ef1ccef545dfc30f9123eba61267b4a',1,'vg::mapping_to_length(const Mapping &m)'],['../namespacevg.html#a3f709a91987a7d669b3974fa00aa8ecd',1,'vg::mapping_to_length(const path_mapping_t &mapping)']]],
+ ['mappings_5fequivalent_10026',['mappings_equivalent',['../namespacevg.html#af26a23818c9426d77ef25b07bbaaf605',1,'vg']]],
+ ['maps_5fto_5fnode_10027',['maps_to_node',['../namespacevg.html#a242b97c26d74e9fc05ad16c31b21dcca',1,'vg']]],
+ ['mark_5fdfs_10028',['mark_dfs',['../classvg_1_1FlowSort.html#a498b6d9f0a37f2588e4ad08b6c35a0ff',1,'vg::FlowSort']]],
+ ['mark_5fsmallvariant_5falignments_10029',['mark_smallVariant_alignments',['../classvg_1_1Filter.html#a2ab59f83f673047f5c2106456c4426c3',1,'vg::Filter']]],
+ ['mark_5fsv_5falignments_10030',['mark_sv_alignments',['../classvg_1_1Filter.html#a267d55220fcf5239f12dcc852586bc71',1,'vg::Filter']]],
+ ['markovdistribution_10031',['MarkovDistribution',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#aef78cda42fffdef670a3ceb7e4877ee9',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['mask_5fsequences_10032',['mask_sequences',['../classvg_1_1Masker.html#a18d454c702ded8fdb3436f90135631ed',1,'vg::Masker']]],
+ ['masker_10033',['Masker',['../classvg_1_1Masker.html#a0c3817b4839ee4b2dd6d38d193cd61e8',1,'vg::Masker::Masker(gbwtgraph::GBWTGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#ab302923c0d437d4e997e1c11d35125ac',1,'vg::Masker::Masker(MutablePathDeletableHandleGraph &graph, const SnarlManager *snarl_manager=nullptr)'],['../classvg_1_1Masker.html#a5398d6fdb929425966c9b71c0c9dc2fd',1,'vg::Masker::Masker()=default'],['../classvg_1_1Masker.html#aae42512f78c75af240e164d16a3445e1',1,'vg::Masker::Masker(Masker &&other)=default']]],
+ ['match_5fbackward_10034',['match_backward',['../namespacevg.html#a3495eb8e73ceeece9957079280edc921',1,'vg']]],
+ ['match_5fforward_10035',['match_forward',['../structvg_1_1WFANode.html#a368dbe3b756f08e21718cbfac97978fd',1,'vg::WFANode::match_forward()'],['../namespacevg.html#abcb300141666ec86856482f6a59cec4c',1,'vg::match_forward()']]],
+ ['match_5finitial_10036',['match_initial',['../namespacevg.html#a4b1defb1ef0b163389ff84745294d1d0',1,'vg']]],
+ ['match_5fpredecessor_10037',['match_predecessor',['../classvg_1_1WFATree.html#a4242e9739a9f789386354f4582dea547',1,'vg::WFATree']]],
+ ['matches_10038',['matches',['../classvg_1_1DinucleotideMachine.html#a2250f97747bf0e9390ed7326d357c557',1,'vg::DinucleotideMachine::matches(uint32_t state, const char *dinucleotide) const'],['../classvg_1_1DinucleotideMachine.html#aa30db9eff5e43b78cd23094f3d7edce5',1,'vg::DinucleotideMachine::matches(uint32_t state, const string &dinucleotide) const']]],
+ ['matches_5fannotation_10039',['matches_annotation',['../classvg_1_1ReadFilter.html#a95d1165f7c3901772a70ba863d1fc983',1,'vg::ReadFilter']]],
+ ['matches_5fname_10040',['matches_name',['../classvg_1_1ReadFilter.html#ab72c4fd96eedcb4bcd6aa565e97dfe4d',1,'vg::ReadFilter']]],
+ ['matchpos_10041',['MatchPos',['../structvg_1_1MatchPos.html#ab44cfadd41dfc2ec79266e4fe204458f',1,'vg::MatchPos::MatchPos()'],['../structvg_1_1MatchPos.html#a167922796c04609cdf6a129c7135f869',1,'vg::MatchPos::MatchPos(uint32_t seq_offset, uint32_t node_offset, const PathList &path)']]],
+ ['matrix_5finvert_10042',['matrix_invert',['../namespacevg.html#a7effc13e3f877e676d65d9164a44b4a6',1,'vg']]],
+ ['matrix_5fmultiply_10043',['matrix_multiply',['../namespacevg.html#a02d66ca193142fb4825a62b300d60697',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< vector< double >> &B)'],['../namespacevg.html#a9a1927488f1b7b82758828d5a53ca845',1,'vg::matrix_multiply(const vector< vector< double >> &A, const vector< double > &b)']]],
+ ['max_10044',['max',['../classvg_1_1WideningPRNG.html#a3083db737b68cc80dacad05c9e1ae1ee',1,'vg::WideningPRNG::max()'],['../namespacestd.html#a032e2e35689ce96dfb488db853f83334',1,'std::max()']]],
+ ['max_5fdepth_10045',['max_depth',['../classvg_1_1ZipCode.html#aa9b8e3ee702697e3692a83e2307d9084',1,'vg::ZipCode']]],
+ ['max_5fdistance_5ffrom_5fstart_10046',['max_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#a0d573babd81fa2d0c209c75afec6c91d',1,'vg::IncrementalSubgraph']]],
+ ['max_5fexponential_5fcdf_10047',['max_exponential_cdf',['../namespacevg.html#a82dc203eaecb442a26d8f1a3db773dda',1,'vg']]],
+ ['max_5fexponential_5flog_5flikelihood_10048',['max_exponential_log_likelihood',['../namespacevg.html#a617472d242ff7aad1126a6b70e70a7a8',1,'vg']]],
+ ['max_5fflow_5fsort_10049',['max_flow_sort',['../classvg_1_1FlowSort.html#a8a5d0ba61635331b2107ad3df4972ff1',1,'vg::FlowSort']]],
+ ['max_5fin_10050',['max_in',['../classvg_1_1algorithms_1_1TracedScore.html#a8d01a37cedeb1e7e7667f05bdb8f67e9',1,'vg::algorithms::TracedScore']]],
+ ['max_5flink_5flength_10051',['max_link_length',['../classvg_1_1JoinedSpliceGraph.html#a25612fe4db491aa5cbcc06f5816bd5bd',1,'vg::JoinedSpliceGraph']]],
+ ['max_5fnode_5fid_10052',['max_node_id',['../classvg_1_1DagifiedGraph.html#a511c81e2e65250eeeac52936bfe3ae0e',1,'vg::DagifiedGraph::max_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#a4962a5c38f363db65a1b0083a05bcfcc',1,'vg::DozeuPinningOverlay::max_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ab7384a54f90e4351cb7e6d0a99f3290d',1,'vg::ExtraNodeGraph::max_node_id()'],['../classvg_1_1SnarlGraph.html#a69ce6bde5f346eb5926b6db093122be1',1,'vg::SnarlGraph::max_node_id()'],['../classvg_1_1IdentityOverlay.html#a5aba68df4094870dd2324613d2db1d63',1,'vg::IdentityOverlay::max_node_id()'],['../classvg_1_1IncrementalSubgraph.html#aa92bb84a3ea785a09c814932ae56a5a8',1,'vg::IncrementalSubgraph::max_node_id()'],['../classvg_1_1IndexedVG.html#ab7e6f41fefb23702e708d23a0dcec9d0',1,'vg::IndexedVG::max_node_id()'],['../classvg_1_1MemoizingGraph.html#a7a9052b566d4062493432265aa1c9e70',1,'vg::MemoizingGraph::max_node_id()'],['../classvg_1_1NullMaskingGraph.html#a768717b98ae295bb52a68028db0145ec',1,'vg::NullMaskingGraph::max_node_id()'],['../classvg_1_1PathSubgraph.html#a7d5368e9b40989fa3e1ecd020468a1da',1,'vg::PathSubgraph::max_node_id()'],['../classvg_1_1ReverseGraph.html#ac276a2df66a605842304eec2d9ef340c',1,'vg::ReverseGraph::max_node_id()'],['../classvg_1_1NetGraph.html#abb16fbc7ae88f61e3ce9076d2e2a3817',1,'vg::NetGraph::max_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ab9be77971160f356b0ba0721ed17983e',1,'vg::SourceSinkOverlay::max_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#abbf5f65b4f075efb985c0978cead8513',1,'vg::JoinedSpliceGraph::max_node_id()'],['../classvg_1_1StrandSplitGraph.html#a83194bc2415f2f0fa2e23ce970d2f932',1,'vg::StrandSplitGraph::max_node_id()'],['../classvg_1_1SubHandleGraph.html#afd0e51c2e81f5b51f4e21167e3e691f3',1,'vg::SubHandleGraph::max_node_id()'],['../classvg_1_1SubgraphOverlay.html#ab2858c7e55226d9754eb388654da88ab',1,'vg::SubgraphOverlay::max_node_id()'],['../classvg_1_1SubpathOverlay.html#aa5b627c97bac0914a4b77e289a1f888b',1,'vg::SubpathOverlay::max_node_id()'],['../classvg_1_1TreeSubgraph.html#ae8f3ebca4f5d097fe9b5081cdc1f7a96',1,'vg::TreeSubgraph::max_node_id()'],['../classvg_1_1VG.html#a5a03ad90e03794944c5e0d4d61780652',1,'vg::VG::max_node_id()'],['../classvg_1_1VGset.html#a31691223aa51fca983dd145b5896cad7',1,'vg::VGset::max_node_id()'],['../classxg_1_1XG.html#ac991d9094b1959ff503d9a94d0a9ed4c',1,'xg::XG::max_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a599303e41c6f9913424933778893f1c6',1,'handlegraph::algorithms::SubHandleGraph::max_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a5a2e2b1ea6a29b3f4b34a6abcb6dbc50',1,'handlegraph::HandleGraph::max_node_id()']]],
+ ['max_5fnode_5frank_10053',['max_node_rank',['../classxg_1_1XG.html#a1bc4d756800a8e55ddb33abf49865956',1,'xg::XG']]],
+ ['max_5fpath_5frank_10054',['max_path_rank',['../classxg_1_1XG.html#acd75e4cc0ccf977505a5c6bda03ddb73',1,'xg::XG']]],
+ ['max_5fpossible_5fmapping_5fquality_10055',['max_possible_mapping_quality',['../classvg_1_1GSSWAligner.html#a0058c97d1dbe2be7643e9f75cee15bab',1,'vg::GSSWAligner::max_possible_mapping_quality()'],['../classvg_1_1Mapper.html#a1799afefa90f9fbfd7de41626bdb460c',1,'vg::Mapper::max_possible_mapping_quality()']]],
+ ['max_5fsample_5fsize_10056',['max_sample_size',['../classvg_1_1FragmentLengthDistribution.html#ae5f1b666c1bee15996ad997eb4c9505e',1,'vg::FragmentLengthDistribution']]],
+ ['max_5fshift_10057',['max_shift',['../classvg_1_1MultipathAlignmentGraph.html#a50ff4a1c2bc2b997c28af99527e595dd',1,'vg::MultipathAlignmentGraph']]],
+ ['max_5fvertex_10058',['max_vertex',['../classvg_1_1MEMChainModel.html#abc9cf4a87ae1b38488bcf96c0a09b853',1,'vg::MEMChainModel::max_vertex()'],['../classvg_1_1AlignmentChainModel.html#a79f49cd995d623a0dae8b704ad57432e',1,'vg::AlignmentChainModel::max_vertex()']]],
+ ['maximalexactmatch_10059',['MaximalExactMatch',['../classvg_1_1MaximalExactMatch.html#a0eb93e97b671cbafb0de7aa5827fa5f0',1,'vg::MaximalExactMatch::MaximalExactMatch(string::const_iterator b, string::const_iterator e, gcsa::range_type r, size_t m=0)'],['../classvg_1_1MaximalExactMatch.html#aab0c8e120398563dfa7dae32a92b2fa9',1,'vg::MaximalExactMatch::MaximalExactMatch(void)=default'],['../classvg_1_1MaximalExactMatch.html#a058f43692dd5943fa4e4ecc1b5fc68c0',1,'vg::MaximalExactMatch::MaximalExactMatch(const MaximalExactMatch &)=default'],['../classvg_1_1MaximalExactMatch.html#a9b0816ee01550f8ce43d32984d6fc333',1,'vg::MaximalExactMatch::MaximalExactMatch(MaximalExactMatch &&)=default']]],
+ ['maximum_5fdistance_10060',['maximum_distance',['../namespacevg.html#a004ed92d4db665ce8ec4e527f150a7c4',1,'vg']]],
+ ['maximum_5fmapping_5fquality_5fapprox_10061',['maximum_mapping_quality_approx',['../classvg_1_1GSSWAligner.html#a3104dc6ddfd6a15e1ed02950006a4063',1,'vg::GSSWAligner']]],
+ ['maximum_5fmapping_5fquality_5fexact_10062',['maximum_mapping_quality_exact',['../classvg_1_1GSSWAligner.html#ac17619c1908446d3e61a882c879f2eb1',1,'vg::GSSWAligner']]],
+ ['mcmccaller_10063',['MCMCCaller',['../classvg_1_1MCMCCaller.html#add4fcb2e5a2a8633e659a986bb347c40',1,'vg::MCMCCaller']]],
+ ['mcmcgenotyper_10064',['MCMCGenotyper',['../classvg_1_1MCMCGenotyper.html#abb6ddf1a8e99fc5c183ec188ae87bb22',1,'vg::MCMCGenotyper']]],
+ ['mean_10065',['mean',['../classvg_1_1FragmentLengthDistribution.html#abe1b685c70bdafff09e089038ae68971',1,'vg::FragmentLengthDistribution::mean()'],['../classvg_1_1normal__distribution.html#a8b5bd06d0c3589eab21131a033bd706a',1,'vg::normal_distribution::mean()'],['../classvg_1_1truncated__normal__distribution.html#ad842920993df04cbcc18cc4182f9d005',1,'vg::truncated_normal_distribution::mean()']]],
+ ['mean_5fnode_5flength_10066',['mean_node_length',['../classvg_1_1Transcriptome.html#af173c32d4ccfa7f94f68220e7e564895',1,'vg::Transcriptome']]],
+ ['measurements_5fbegin_10067',['measurements_begin',['../classvg_1_1FragmentLengthDistribution.html#a9a57a0e4a86983fc13a87d5ee4c5b8a7',1,'vg::FragmentLengthDistribution']]],
+ ['measurements_5fend_10068',['measurements_end',['../classvg_1_1FragmentLengthDistribution.html#a929562555917920f58a5d3692cd14fb4',1,'vg::FragmentLengthDistribution']]],
+ ['median_10069',['median',['../namespacevg.html#a6eef175773ce8532826ba78eee0cece5',1,'vg']]],
+ ['median_5fmem_5fcoverage_10070',['median_mem_coverage',['../classvg_1_1MEMClusterer_1_1HitGraph.html#abe3be52c11df5f9b5fc131cfe9460d5a',1,'vg::MEMClusterer::HitGraph']]],
+ ['mem_5fmin_5foriented_5fdistances_10071',['mem_min_oriented_distances',['../namespacevg.html#ae1678438e6011469b88ddf3b54023013',1,'vg']]],
+ ['mem_5fnode_5fstart_5fpositions_10072',['mem_node_start_positions',['../namespacevg.html#aa65ea58e40ea30264407f9fdbce2a83d',1,'vg']]],
+ ['mem_5fusage_5fstring_10073',['mem_usage_string',['../autoindex__main_8cpp.html#a95ea1f250ba974749a30b213bede7969',1,'autoindex_main.cpp']]],
+ ['memaccelerator_10074',['MEMAccelerator',['../classvg_1_1MEMAccelerator.html#af51ef34773bca8cc723fb3ef0bfe87c8',1,'vg::MEMAccelerator::MEMAccelerator()=default'],['../classvg_1_1MEMAccelerator.html#a3928fe622799f9ac33ba7e2e5d4b3568',1,'vg::MEMAccelerator::MEMAccelerator(const gcsa::GCSA &gcsa_index, size_t k)']]],
+ ['memchainmodel_10075',['MEMChainModel',['../classvg_1_1MEMChainModel.html#ae612545bdf38bad27b4fc18e19d38eff',1,'vg::MEMChainModel']]],
+ ['memchainmodelvertex_10076',['MEMChainModelVertex',['../classvg_1_1MEMChainModelVertex.html#a9ec1a9cd36b3328911409e598109c1c9',1,'vg::MEMChainModelVertex::MEMChainModelVertex(void)=default'],['../classvg_1_1MEMChainModelVertex.html#a01ed669199f3319be51dbd2aafc268de',1,'vg::MEMChainModelVertex::MEMChainModelVertex(const MEMChainModelVertex &)=default'],['../classvg_1_1MEMChainModelVertex.html#adb5651ba734c5700f334b0074dfaaca8',1,'vg::MEMChainModelVertex::MEMChainModelVertex(MEMChainModelVertex &&)=default']]],
+ ['memclusterer_10077',['MEMClusterer',['../classvg_1_1MEMClusterer.html#ae035e62365ff4617433e18d102bec452',1,'vg::MEMClusterer']]],
+ ['memoized_5flf_10078',['memoized_LF',['../classvg_1_1MEMAccelerator.html#a89dfd34874f065088799dfce96c11649',1,'vg::MEMAccelerator']]],
+ ['memoizinggraph_10079',['MemoizingGraph',['../classvg_1_1MemoizingGraph.html#aef84e6abc0084e0f910bc99edc760345',1,'vg::MemoizingGraph::MemoizingGraph(const PathPositionHandleGraph *graph)'],['../classvg_1_1MemoizingGraph.html#aa6030fdc5e73a8d88059bc31f1886746',1,'vg::MemoizingGraph::MemoizingGraph()=default']]],
+ ['mems_5fid_5fclusters_5fto_5falignments_10080',['mems_id_clusters_to_alignments',['../classvg_1_1Mapper.html#a0dc4c04ebad76435afafe9cec62a5eaa',1,'vg::Mapper']]],
+ ['mems_5foverlap_10081',['mems_overlap',['../namespacevg.html#aa412de4741b61d2a8b863f50f31209e0',1,'vg']]],
+ ['mems_5foverlap_5flength_10082',['mems_overlap_length',['../namespacevg.html#af5d04132733b3487e3dab20729645850',1,'vg']]],
+ ['mems_5fto_5fjson_10083',['mems_to_json',['../namespacevg.html#ab0bec9992b4441128754ac4ed1a330e8',1,'vg']]],
+ ['merge_10084',['merge',['../classvg_1_1Funnel.html#ae75f133fdc545176a27f0121a61a98e4',1,'vg::Funnel::merge()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a658429a7896e87dc276f749f5ba8dc27',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::merge()'],['../classvg_1_1VG.html#a0abc84684faea29b49032ec254d5e13b',1,'vg::VG::merge(Graph &g)'],['../classvg_1_1VG.html#a40f22f6bb4a3e7a2aea7b3887237faec',1,'vg::VG::merge(VG &g)'],['../namespacevg_1_1algorithms.html#a91a6bbd822f6380421a973f75036c3d3',1,'vg::algorithms::merge()']]],
+ ['merge_5fadjacent_5fedits_10085',['merge_adjacent_edits',['../namespacevg.html#a30a83a9e127a0c7d75118dc14a8985f6',1,'vg::merge_adjacent_edits(const Mapping &m)'],['../namespacevg.html#a2c9985bf70965bd36bb54f910ab74e3b',1,'vg::merge_adjacent_edits(const Path &m)']]],
+ ['merge_5falignments_10086',['merge_alignments',['../namespacevg.html#afa2d2a5d955cff1e7a99369055ebe75d',1,'vg::merge_alignments(const vector< Alignment > &alns)'],['../namespacevg.html#a9d71527a132d7e6bf364d2108b269e09',1,'vg::merge_alignments(const Alignment &a1, const Alignment &a2, bool debug)']]],
+ ['merge_5fedits_5fin_5fplace_10087',['merge_edits_in_place',['../namespacevg.html#a20ebf02d59df03f906550e695a1aa00d',1,'vg']]],
+ ['merge_5fequivalent_5ftraversals_5fin_5fgraph_10088',['merge_equivalent_traversals_in_graph',['../namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1',1,'vg']]],
+ ['merge_5ffrom_5fdynamic_10089',['merge_from_dynamic',['../classvg_1_1Packer.html#a79ce5d54645f6d124c710b86b666f5d7',1,'vg::Packer']]],
+ ['merge_5ffrom_5ffiles_10090',['merge_from_files',['../classvg_1_1Packer.html#af857449c08a56dd66c6a4bc0402231cb',1,'vg::Packer']]],
+ ['merge_5fgroup_10091',['merge_group',['../classvg_1_1Funnel.html#a585c5484ef877a1ede56ed4467e32312',1,'vg::Funnel']]],
+ ['merge_5fgroups_10092',['merge_groups',['../classvg_1_1Funnel.html#a44fcff7c06cb79e43cc1aa2fc73a8da6',1,'vg::Funnel']]],
+ ['merge_5fid_5fspace_10093',['merge_id_space',['../classvg_1_1VGset.html#a968fb68f13f91ea8ded32d02c6ea683a',1,'vg::VGset']]],
+ ['merge_5fnodes_10094',['merge_nodes',['../classvg_1_1VG.html#a2e506d51db427b617cc334a791c7f594',1,'vg::VG']]],
+ ['merge_5fnon_5fbranching_5fsubpaths_10095',['merge_non_branching_subpaths',['../namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43',1,'vg']]],
+ ['merge_5fpartially_5fredundant_5fmatch_5fnodes_10096',['merge_partially_redundant_match_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a9f8ca4f9936aa6abcc8681e91dae3f43',1,'vg::MultipathAlignmentGraph']]],
+ ['merge_5frescued_5fmappings_10097',['merge_rescued_mappings',['../classvg_1_1MultipathMapper.html#a525152a98c905ba789a0454c70336c3e',1,'vg::MultipathMapper']]],
+ ['merge_5fstate_10098',['merge_state',['../classvg_1_1DinucleotideMachine.html#ab28bcc9f016d8df680d6f17b5957fc57',1,'vg::DinucleotideMachine']]],
+ ['merge_5funion_10099',['merge_union',['../classvg_1_1VG.html#a5aff716eee0bf720b3836caa761d48be',1,'vg::VG']]],
+ ['mergedadjacencygraph_10100',['MergedAdjacencyGraph',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#aa09eaec5fd36cfe50b4313a38ba01fe1',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const RankedHandleGraph *graph)'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#ab8d7ea6f475144c3779568d9d552c1c7',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::MergedAdjacencyGraph(const MergedAdjacencyGraph &other)']]],
+ ['mergegraphs_10101',['mergeGraphs',['../namespacevg_1_1io.html#a09b6c55dd368ec0c3e85f51a87321ba2',1,'vg::io']]],
+ ['mergenodeobjects_10102',['mergeNodeObjects',['../namespacevg.html#aa539af4f481d4e955ede26ee85c320c5',1,'vg']]],
+ ['messageemitter_10103',['MessageEmitter',['../classvg_1_1io_1_1MessageEmitter.html#a674e6dee23ee5d3a5b49e56ff6dad2c1',1,'vg::io::MessageEmitter::MessageEmitter(ostream &out, bool compress=false, size_t max_group_size=1000)'],['../classvg_1_1io_1_1MessageEmitter.html#a4e9dd0179e7e2b815fcbf3175fd5a030',1,'vg::io::MessageEmitter::MessageEmitter(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#af48941a2e4e66c513e169d29f120d511',1,'vg::io::MessageEmitter::MessageEmitter(MessageEmitter &&other)=default']]],
+ ['messageiterator_10104',['MessageIterator',['../classvg_1_1io_1_1MessageIterator.html#a44eabe49bb3f28067f8ba3396915ee64',1,'vg::io::MessageIterator::MessageIterator(istream &in, bool verbose=false, size_t thread_count=0)'],['../classvg_1_1io_1_1MessageIterator.html#ae7ddb87951881f58221acd0a1beeb32f',1,'vg::io::MessageIterator::MessageIterator(unique_ptr< BlockedGzipInputStream > &&bgzf, bool verbose=false)'],['../classvg_1_1io_1_1MessageIterator.html#a46b16972d489742f42922fd9cb9b85af',1,'vg::io::MessageIterator::MessageIterator()=default']]],
+ ['middle_5fsignature_10105',['middle_signature',['../namespacevg.html#a7848d492a243a93f37b1ac52a541a96a',1,'vg::middle_signature(const Alignment &aln, int len)'],['../namespacevg.html#af64c67658563ff567bc0b103ef1d8af4',1,'vg::middle_signature(const Alignment &aln1, const Alignment &aln2, int len)']]],
+ ['min_10106',['min',['../classvg_1_1WideningPRNG.html#a3cd7defb4589ed56c43b27f5d7bd36fe',1,'vg::WideningPRNG']]],
+ ['min_5fapprox_5fpath_5fdistance_10107',['min_approx_path_distance',['../classxg_1_1XG.html#ae92433487bc35ef856ee592137937a98',1,'xg::XG::min_approx_path_distance()'],['../namespacevg_1_1algorithms.html#ae18b50d29d9accb763b44d6e065dac58',1,'vg::algorithms::min_approx_path_distance()']]],
+ ['min_5fcut_10108',['min_cut',['../classvg_1_1FlowSort.html#aa489e8c6bbf375d149410afe0a35d58b',1,'vg::FlowSort']]],
+ ['min_5fcut_5fdecomposition_10109',['min_cut_decomposition',['../namespacevg_1_1algorithms.html#a5cd4d23b1a702613134895c2d5618154',1,'vg::algorithms']]],
+ ['min_5fdistance_5ffrom_5fstart_10110',['min_distance_from_start',['../classvg_1_1IncrementalSubgraph.html#ab859980ced41bcd382cd5961ff3b8475',1,'vg::IncrementalSubgraph']]],
+ ['min_5fdists_10111',['min_dists',['../classvg_1_1DeletionAligner.html#a42b9fef2da830c0912fb4141701c501e',1,'vg::DeletionAligner']]],
+ ['min_5flink_5flength_10112',['min_link_length',['../classvg_1_1JoinedSpliceGraph.html#a92c8438c7a1efd3f0c5351a59b519a38',1,'vg::JoinedSpliceGraph']]],
+ ['min_5fnode_5fid_10113',['min_node_id',['../classvg_1_1DagifiedGraph.html#a59e1c5556c2f5a984d9680cdaf8be41d',1,'vg::DagifiedGraph::min_node_id()'],['../classvg_1_1DozeuPinningOverlay.html#ac48d1492dd478af9811307c52954e517',1,'vg::DozeuPinningOverlay::min_node_id()'],['../classvg_1_1ExtraNodeGraph.html#ae07290cc251f0843de41551e25ffd4bf',1,'vg::ExtraNodeGraph::min_node_id()'],['../classvg_1_1SnarlGraph.html#a6e61014fadcbc2703a8fe3b208132ee4',1,'vg::SnarlGraph::min_node_id()'],['../classvg_1_1IdentityOverlay.html#a9a689ba99fa1452b5434a8a523e142c1',1,'vg::IdentityOverlay::min_node_id()'],['../classvg_1_1IncrementalSubgraph.html#a2d34ac8b129c82511c38f267644918d5',1,'vg::IncrementalSubgraph::min_node_id()'],['../classvg_1_1IndexedVG.html#ac496219064127ecd533ab41f77fc5da6',1,'vg::IndexedVG::min_node_id()'],['../classvg_1_1MemoizingGraph.html#afcbf2c9b526deaddee36140a362f4640',1,'vg::MemoizingGraph::min_node_id()'],['../classvg_1_1NullMaskingGraph.html#ab970c84b4caea2d00fd43a77f0826a95',1,'vg::NullMaskingGraph::min_node_id()'],['../classvg_1_1PathSubgraph.html#a472e93221aa3a728984d07aa6b7f0cc0',1,'vg::PathSubgraph::min_node_id()'],['../classvg_1_1ReverseGraph.html#adf486245a2201f1685e2af41a57a98f3',1,'vg::ReverseGraph::min_node_id()'],['../classvg_1_1NetGraph.html#a9b3c2b7f61f5c0133e844fa5edc4ea6d',1,'vg::NetGraph::min_node_id()'],['../classvg_1_1SourceSinkOverlay.html#ad91d6241e1a962eaf4b4f1c92f2d94c8',1,'vg::SourceSinkOverlay::min_node_id()'],['../classvg_1_1JoinedSpliceGraph.html#aa92df9f1002415710b4ffa4e6074cb5b',1,'vg::JoinedSpliceGraph::min_node_id()'],['../classvg_1_1StrandSplitGraph.html#aaeaf9231d44d7e0260ef5439f49e5e40',1,'vg::StrandSplitGraph::min_node_id()'],['../classvg_1_1SubHandleGraph.html#a180704728aa79aaf37189c644995cf91',1,'vg::SubHandleGraph::min_node_id()'],['../classvg_1_1SubgraphOverlay.html#a0d876d83943a078f6d9114bd08216086',1,'vg::SubgraphOverlay::min_node_id()'],['../classvg_1_1SubpathOverlay.html#a3d0fc1b94bdd931b4bd72197a07d6510',1,'vg::SubpathOverlay::min_node_id()'],['../classvg_1_1TreeSubgraph.html#a1ac845e3e2d75d7da5ff81b79aba3d08',1,'vg::TreeSubgraph::min_node_id()'],['../classvg_1_1VG.html#ac27674d67445ddc135c3c8ab4d3d5231',1,'vg::VG::min_node_id()'],['../classxg_1_1XG.html#a9195d1b18542de3b89b80bb14ce1ca0a',1,'xg::XG::min_node_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af944543089a7fae6c052decc4ff0a4c4',1,'handlegraph::algorithms::SubHandleGraph::min_node_id()'],['../classhandlegraph_1_1HandleGraph.html#a85c52fe4b5f483504ed142d0ad94a969',1,'handlegraph::HandleGraph::min_node_id()']]],
+ ['min_5foriented_5fdistances_10114',['min_oriented_distances',['../namespacevg.html#a973bf2647d54324bc63c323a0aa29a35',1,'vg']]],
+ ['min_5fpair_5ffragment_5flength_10115',['min_pair_fragment_length',['../classvg_1_1Mapper.html#a3682f47407c7feddc2f8a22cd546a4ec',1,'vg::Mapper']]],
+ ['min_5fsupport_5fin_5fpath_10116',['min_support_in_path',['../classvg_1_1NestedTraversalFinder.html#a3021b0689285b7c73f8201dcea103dac',1,'vg::NestedTraversalFinder::min_support_in_path()'],['../classvg_1_1RepresentativeTraversalFinder.html#acdea076c1d46ca2b92b338bd023c081b',1,'vg::RepresentativeTraversalFinder::min_support_in_path()']]],
+ ['mindistanceclusterer_10117',['MinDistanceClusterer',['../classvg_1_1MinDistanceClusterer.html#a8fe5349edbec12f8f15465249b8e6726',1,'vg::MinDistanceClusterer']]],
+ ['minimizer_5freverse_5fcomplement_10118',['minimizer_reverse_complement',['../namespacevg.html#ae4b8625853b4a17f731c9fbd5a040fd7',1,'vg']]],
+ ['minimizermapper_10119',['MinimizerMapper',['../classvg_1_1MinimizerMapper.html#ae2ecef3023c1cd374f0c7b1a3ac6ac5d',1,'vg::MinimizerMapper']]],
+ ['minimum_5fdistance_10120',['minimum_distance',['../namespacevg.html#abcbcd550b51078ae43f2b1d87941e1a0',1,'vg']]],
+ ['minimum_5fdistance_5fbetween_10121',['minimum_distance_between',['../classvg_1_1ZipCode.html#a3f0f330d338d949d04dbe14fd606e838',1,'vg::ZipCode']]],
+ ['mismatches_10122',['mismatches',['../structvg_1_1GaplessExtension.html#a4898e2fabc109703f497e19f10bb164a',1,'vg::GaplessExtension']]],
+ ['mode_5fname_10123',['mode_name',['../prune__main_8cpp.html#a9b89c7a3b7a8efd51b246bc312140bb8',1,'prune_main.cpp']]],
+ ['modular_5fexponent_10124',['modular_exponent',['../namespacevg.html#abc8f8791be2575164e6070e1cef39b4e',1,'vg']]],
+ ['motif_5ffrequency_10125',['motif_frequency',['../classvg_1_1SpliceStats.html#aeb0d77ba4fc7a6767eff466a6ba8ed9e',1,'vg::SpliceStats']]],
+ ['motif_5fis_5freverse_10126',['motif_is_reverse',['../classvg_1_1SpliceStats.html#afc22a25e939fa725d3808430f9a62007',1,'vg::SpliceStats']]],
+ ['motif_5fscore_10127',['motif_score',['../classvg_1_1SpliceStats.html#a7da67978c875a8e9bc1fac31fdb8277b',1,'vg::SpliceStats']]],
+ ['motif_5fsize_10128',['motif_size',['../classvg_1_1SpliceStats.html#aae5310e0728aebc36703641a566242e3',1,'vg::SpliceStats']]],
+ ['move_10129',['move',['../classvg_1_1SmallBitset.html#a5c80c7e3d6d92c7c5e58463771a2a341',1,'vg::SmallBitset']]],
+ ['msaconverter_10130',['MSAConverter',['../classvg_1_1MSAConverter.html#ac6e82d70cf93d7b8a75750b40dd89277',1,'vg::MSAConverter']]],
+ ['multi_5fsurject_10131',['multi_surject',['../classvg_1_1Surjector.html#a0ed6215f3860203803deb2f3078d93b4',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#ab8b34cbb819829cd493bdc901a6e3060',1,'vg::Surjector::multi_surject(const Alignment &source, const unordered_set< path_handle_t > &paths, bool allow_negative_scores=false, bool preserve_deletions=false) const'],['../classvg_1_1Surjector.html#a943158332e4865de071dca68454a4d77',1,'vg::Surjector::multi_surject(const multipath_alignment_t &source, const unordered_set< path_handle_t > &paths, vector< tuple< string, int64_t, bool >> &positions_out, bool allow_negative_scores=false, bool preserve_deletions=false) const']]],
+ ['multinomial_5fcensored_5fsampling_5fprob_5fln_10132',['multinomial_censored_sampling_prob_ln',['../namespacevg.html#a074fcebfeb68fc970b5b2a0db3722f01',1,'vg']]],
+ ['multinomial_5fchoose_5fln_10133',['multinomial_choose_ln',['../namespacevg.html#a15f09f05f7894863e9cd852c63266078',1,'vg']]],
+ ['multinomial_5fsampling_5fprob_5fln_10134',['multinomial_sampling_prob_ln',['../namespacevg.html#af4d69cf9a7d7e6272960fcb9f0a0a00c',1,'vg']]],
+ ['multipath_5falign_10135',['multipath_align',['../classvg_1_1MultipathMapper.html#a7af0cb7af3f7a3e3ab60627f3793aa0a',1,'vg::MultipathMapper']]],
+ ['multipath_5falignment_5fpath_5foffsets_10136',['multipath_alignment_path_offsets',['../namespacevg_1_1algorithms.html#ad0cecedaa8dd475e634b513af5be028b',1,'vg::algorithms']]],
+ ['multipath_5falignment_5ft_10137',['multipath_alignment_t',['../classvg_1_1multipath__alignment__t.html#ae7f715f63023d3043c01ed29193ea6a1',1,'vg::multipath_alignment_t::multipath_alignment_t()'],['../classvg_1_1multipath__alignment__t.html#a55b4c1fee893c4b596f0a654a624bccc',1,'vg::multipath_alignment_t::multipath_alignment_t(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ad4de932d4f01d8d44a76095605294470',1,'vg::multipath_alignment_t::multipath_alignment_t(multipath_alignment_t &&other)']]],
+ ['multipath_5fmap_10138',['multipath_map',['../classvg_1_1MultipathMapper.html#a9ea318c04336aa79020b7c012e468ef8',1,'vg::MultipathMapper']]],
+ ['multipath_5fmap_5fpaired_10139',['multipath_map_paired',['../classvg_1_1MultipathMapper.html#a240c4502e41aa0e5961772a12b1b42a8',1,'vg::MultipathMapper']]],
+ ['multipathalignmentemitter_10140',['MultipathAlignmentEmitter',['../classvg_1_1MultipathAlignmentEmitter.html#a022247fcbd889aeb51b35b0cae1c3622',1,'vg::MultipathAlignmentEmitter']]],
+ ['multipathalignmentgraph_10141',['MultipathAlignmentGraph',['../classvg_1_1MultipathAlignmentGraph.html#a058e6120cb359e2566c1c2d7961c608e',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a51e7308dc1c0c96d1e576970211b7705',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#afd75ac7afd23901c4b8f38eb126bdba0',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, MultipathMapper::memcluster_t &hits, const function< pair< id_t, bool >(id_t)> &project, vector< size_t > &path_node_provenance, size_t max_branch_trim_length=0, gcsa::GCSA *gcsa=nullptr, const MultipathMapper::match_fanouts_t *fanout_breaks=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a74eec86f754011999dc6caed5d1f6c8a',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a366ddb07faadad371e896d3f453e147c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const unordered_map< id_t, pair< id_t, bool >> &projection_trans, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#a4289e77bb6d76abfbb1d3c02d89a2586',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const vector< pair< pair< string::const_iterator, string::const_iterator >, path_t >> &path_chunks, const Alignment &alignment, const function< pair< id_t, bool >(id_t)> &project, bool realign_Ns=true, bool preserve_tail_anchors=false, vector< size_t > *path_node_provenance=nullptr)'],['../classvg_1_1MultipathAlignmentGraph.html#ac8f4ae19921529920157bcbbf9a2f5c3',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a10f9b18c8aa4db1b80bf54ccc5dcc09c',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const unordered_map< id_t, pair< id_t, bool >> &projection_trans)'],['../classvg_1_1MultipathAlignmentGraph.html#a89b441f028fd26c177a9ce8d8188b7c1',1,'vg::MultipathAlignmentGraph::MultipathAlignmentGraph(const HandleGraph &graph, const Alignment &alignment, SnarlManager *snarl_manager, SnarlDistanceIndex *dist_index, size_t max_snarl_cut_size, const function< pair< id_t, bool >(id_t)> &project)']]],
+ ['multipathmapper_10142',['MultipathMapper',['../classvg_1_1MultipathMapper.html#a4d3a7e85dfc2d7cda41912a4f87fd5ac',1,'vg::MultipathMapper']]],
+ ['multipathproblem_10143',['MultipathProblem',['../structvg_1_1MultipathProblem.html#ac97d55858c86d218c380fd43e115d18a',1,'vg::MultipathProblem']]],
+ ['mutable_5fconnection_10144',['mutable_connection',['../classvg_1_1subpath__t.html#a271236a46bdb6105f216a630c0c67a74',1,'vg::subpath_t::mutable_connection()'],['../classvg_1_1subpath__t.html#aa967fceb620f92e73e965345d4cd0b67',1,'vg::subpath_t::mutable_connection(size_t i)']]],
+ ['mutable_5fedit_10145',['mutable_edit',['../classvg_1_1path__mapping__t.html#aeb9d50accda37c8829c49cd8567f72bc',1,'vg::path_mapping_t::mutable_edit()'],['../classvg_1_1path__mapping__t.html#a56c059138a051e7889f4083a74c5401f',1,'vg::path_mapping_t::mutable_edit(size_t i)']]],
+ ['mutable_5fmapping_10146',['mutable_mapping',['../classvg_1_1path__t.html#ab3f1eeeefe1c604dacdeff019488ff07',1,'vg::path_t::mutable_mapping()'],['../classvg_1_1path__t.html#aac0ad10ace8970358d471d779061b22d',1,'vg::path_t::mutable_mapping(size_t i)']]],
+ ['mutable_5fnext_10147',['mutable_next',['../classvg_1_1subpath__t.html#ae1331c79838d972ccb8be4e98ac87954',1,'vg::subpath_t']]],
+ ['mutable_5fpath_10148',['mutable_path',['../classvg_1_1subpath__t.html#aa5f32fe1e7167d09187d4a69c091bde5',1,'vg::subpath_t']]],
+ ['mutable_5fposition_10149',['mutable_position',['../classvg_1_1path__mapping__t.html#a87ef119207623109aea694cd5432421d',1,'vg::path_mapping_t']]],
+ ['mutable_5fquality_10150',['mutable_quality',['../classvg_1_1multipath__alignment__t.html#a5d62a17eb3aad07f05f5580aa7f9dfbd',1,'vg::multipath_alignment_t']]],
+ ['mutable_5fsequence_10151',['mutable_sequence',['../classvg_1_1multipath__alignment__t.html#a11d22790dc8b9cc631a237ef00b6e0e4',1,'vg::multipath_alignment_t::mutable_sequence()'],['../classvg_1_1edit__t.html#aa5e639217215d8d67bfe1ec2a07105fb',1,'vg::edit_t::mutable_sequence()']]],
+ ['mutable_5fstart_10152',['mutable_start',['../classvg_1_1multipath__alignment__t.html#a43e30d76e7ac0596fc15c868fbbd603c',1,'vg::multipath_alignment_t']]],
+ ['mutable_5fsubpath_10153',['mutable_subpath',['../classvg_1_1multipath__alignment__t.html#a65ee05140e26b51a60f7d33a7b9b9c54',1,'vg::multipath_alignment_t::mutable_subpath()'],['../classvg_1_1multipath__alignment__t.html#a727e5e6bc04955e46efe83bc5d668bdf',1,'vg::multipath_alignment_t::mutable_subpath(size_t i)']]],
+ ['mutate_10154',['mutate',['../classvg_1_1Sampler.html#a8f148dac7598a3465202371511e53f2a',1,'vg::Sampler']]],
+ ['mutate_5fedit_10155',['mutate_edit',['../classvg_1_1Sampler.html#ad372d6fdcac5af601bdb0729f94a7e7d',1,'vg::Sampler']]]
];
diff --git a/search/functions_e.js b/search/functions_e.js
index 8b2126c066..2aafb27268 100644
--- a/search/functions_e.js
+++ b/search/functions_e.js
@@ -1,79 +1,79 @@
var searchData=
[
- ['n_10152',['n',['../namespacehaplotypes__defaults.html#a08f2ff580a81523291eed7ef0d644bd2',1,'haplotypes_defaults']]],
- ['nearest_5foffsets_5fin_5fpaths_10153',['nearest_offsets_in_paths',['../classxg_1_1XG.html#ab885cecf687ffb8583fb95cce8ca34b2',1,'xg::XG::nearest_offsets_in_paths()'],['../namespacevg_1_1algorithms.html#a477330d3ab29cbd3c48e4830d51b3e0f',1,'vg::algorithms::nearest_offsets_in_paths()']]],
- ['nearest_5fpath_5fnode_10154',['nearest_path_node',['../classxg_1_1XG.html#a03f2f8a4cc3d06e4f1748474082efdb9',1,'xg::XG']]],
- ['nestedcachedpackedtraversalsupportfinder_10155',['NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#a6893d620886b1bb326f735e36757f6e2',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
- ['nestedflowcaller_10156',['NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html#ab56c3d2fe181450dc33167539bc8f74c',1,'vg::NestedFlowCaller']]],
- ['nestedtraversalfinder_10157',['NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html#a0ab18d1355be2772f9ca78c5eb269e6c',1,'vg::NestedTraversalFinder']]],
- ['net_5fgraph_5fof_10158',['net_graph_of',['../classvg_1_1SnarlManager.html#aa8872188679a5ad4d0da08c1235f2019',1,'vg::SnarlManager']]],
- ['netgraph_10159',['NetGraph',['../classvg_1_1NetGraph.html#a9059c913779ce4095224a5ae6638a27d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains_mixed, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#a29abf89e03eedc7ac2af4682a1b5bb04',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains, const SnarlContainer &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aa1e17ccb08d595123db3d8cd6e2593b2',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const vector< vector< pair< Snarl, bool >>> &child_chains, const vector< Snarl > &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aba1479f586d07f276ba6925cfc1a8e6d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const HandleGraph *graph, bool use_internal_connectivity=false)']]],
- ['new_5fheight_10160',['new_height',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae444abfaf71eedae674fb4703e910248',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['new_5flength_10161',['new_length',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a9d8c1bf7222ee28236691c30185194d3',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['new_5foutput_5fgraph_10162',['new_output_graph',['../namespacevg_1_1io.html#a4b6ad53e3fc9e4c143221b213932db70',1,'vg::io']]],
- ['new_5fside_10163',['new_side',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af0ea102c59fcbcb1a5387ea5b465e950',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['next_10164',['Next',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a91e4dc4f48957737a80e99a8ad32ba53',1,'vg::io::BlockedGzipInputStream::Next()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a0c3e80161a999b884abf3965dd0a5a39',1,'vg::io::BlockedGzipOutputStream::Next()'],['../classvg_1_1WFATree.html#acec4f54d7784d6c7310418ddec2716b9',1,'vg::WFATree::next()'],['../classvg_1_1connection__t.html#a18d278044df80b1334542e6d25043a32',1,'vg::connection_t::next()'],['../classvg_1_1subpath__t.html#a60a4ec0114c307ae532ea307128bfe24',1,'vg::subpath_t::next() const'],['../classvg_1_1subpath__t.html#aabe3e1337325511c83d7e949195fdf37',1,'vg::subpath_t::next(size_t i) const'],['../classvg_1_1WindowedVcfBuffer.html#a0d66b5a177f55cb726122577840d8911',1,'vg::WindowedVcfBuffer::next()']]],
- ['next_5fempty_5falignment_10165',['next_empty_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a08e8eed8f95a621c9786bca1b0850dd2',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['next_5fis_5fempty_10166',['next_is_empty',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a016150b6b6f4551ee3eb7600d7037b67',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['next_5fpath_5fposition_10167',['next_path_position',['../classxg_1_1XG.html#ae973d41358ddab92f0a2dca094806102',1,'xg::XG']]],
- ['next_5fpos_5fchars_10168',['next_pos_chars',['../classvg_1_1Sampler.html#ab5455f8f6faf176b418e3dbcb6bf1ce8',1,'vg::Sampler::next_pos_chars()'],['../namespacevg_1_1algorithms.html#a22d03c4f50c51d0d537811ba88895688',1,'vg::algorithms::next_pos_chars()']]],
- ['next_5fscore_10169',['next_score',['../classvg_1_1WFATree.html#aba63fbf6ca1e1382e62727ea95c4b0af',1,'vg::WFATree']]],
- ['next_5fsize_10170',['next_size',['../classvg_1_1subpath__t.html#aab697710ebd5e8f968bed5c5262bbe2a',1,'vg::subpath_t']]],
- ['next_5fsnarl_10171',['next_snarl',['../classvg_1_1SnarlManager.html#afcca3b74e960b6931598188e0b9ae7a8',1,'vg::SnarlManager']]],
- ['next_5ftraceback_5falignment_10172',['next_traceback_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a8d6cbc921387724da8db3c8c0f20f363',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['ngssimulator_10173',['NGSSimulator',['../classvg_1_1NGSSimulator.html#a51e3a4117f9339b3195d73f2c6cf560e',1,'vg::NGSSimulator::NGSSimulator(PathPositionHandleGraph &graph, const string &ngs_fastq_file, const string &ngs_paired_fastq_file="", bool interleaved_fastq=false, const vector< string > &source_paths={}, const vector< double > &source_path_ploidies={}, const vector< pair< string, double >> &transcript_expressions={}, const vector< tuple< string, string, size_t >> &haplotype_transcripts={}, double substition_polymorphism_rate=0.001, double indel_polymorphism_rate=0.0002, double indel_error_proportion=0.01, double fragment_length_mean=300.0, double fragment_length_stdev=50.0, double error_multiplier=1.0, bool retry_on_Ns=true, bool sample_unsheared_paths=false, uint64_t seed=0)'],['../classvg_1_1NGSSimulator.html#a5417af00068600ab1e6d0acb24836698',1,'vg::NGSSimulator::NGSSimulator(void)=delete']]],
- ['no_5fchain_5finfo_10174',['no_chain_info',['../classvg_1_1MinimizerMapper.html#a3b9a4518b171aa85909da6ccde88e0a8',1,'vg::MinimizerMapper']]],
- ['no_5fmultiple_5fcover_5ftypes_10175',['no_multiple_cover_types',['../gbwt__main_8cpp.html#a0124aac03621e82b84ef0de974a08574',1,'gbwt_main.cpp']]],
- ['no_5fmultiple_5finput_5ftypes_10176',['no_multiple_input_types',['../gbwt__main_8cpp.html#ae1c5768186dc339c157bf4b72517b5ab',1,'gbwt_main.cpp']]],
- ['no_5fmultiple_5finputs_10177',['no_multiple_inputs',['../convert__main_8cpp.html#aca425ac5df78dde7681385a5341abb1b',1,'convert_main.cpp']]],
- ['no_5fpos_10178',['no_pos',['../classvg_1_1WFATree.html#ad0383cee94782b3f0e8d48078d4d2348',1,'vg::WFATree']]],
- ['node_10179',['node',['../structvg_1_1MatchPos.html#abd73a2a9a1d86e1747631f89b045e4fd',1,'vg::MatchPos::node()'],['../classxg_1_1XGPath.html#a621253a080fdb8b81eb5efe2359b93a8',1,'xg::XGPath::node()']]],
- ['node_5fat_5fvector_5foffset_10180',['node_at_vector_offset',['../classxg_1_1XG.html#a2f2c0b014af5d0032f9beaefb074cc59',1,'xg::XG::node_at_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a3095e541eee436a9f49ef0846539ef44',1,'handlegraph::VectorizableHandleGraph::node_at_vector_offset()']]],
- ['node_5fcount_10181',['node_count',['../classvg_1_1VG.html#abb3e9e655bcaad0bc522307743acd6a0',1,'vg::VG']]],
- ['node_5fcount_5fnext_10182',['node_count_next',['../classvg_1_1VG.html#a4c614759c77b4b0a95b25360c2fa1fa0',1,'vg::VG']]],
- ['node_5fcount_5fprev_10183',['node_count_prev',['../classvg_1_1VG.html#a1091113608fae5b9cbafc87cf4cf82a2',1,'vg::VG']]],
- ['node_5fend_10184',['node_end',['../namespacevg.html#a434e32ac84fd027508a6506e80107331',1,'vg']]],
- ['node_5fgraph_5fidx_10185',['node_graph_idx',['../classxg_1_1XG.html#a191b03b4ada2d076ae6cc53a5a0f5b3d',1,'xg::XG']]],
- ['node_5fid_10186',['node_id',['../classvg_1_1mapping__t.html#a878754e2bea167b11b7cb83af5556a6f',1,'vg::mapping_t::node_id()'],['../classvg_1_1position__t.html#a241b513ec1180294fc6e43f7df1935a7',1,'vg::position_t::node_id()']]],
- ['node_5findex_10187',['node_index',['../classvg_1_1Packer.html#abc210cd0133e161824e80c366738d158',1,'vg::Packer']]],
- ['node_5fis_5fin_5fcyclic_5fsnarl_10188',['node_is_in_cyclic_snarl',['../classvg_1_1ZipCodeTree.html#aadc6866376dcdda602ff117838ced129',1,'vg::ZipCodeTree']]],
- ['node_5fis_5finvalid_10189',['node_is_invalid',['../classvg_1_1ZipCodeTree.html#ad12d46904662a2f622a2ec83567177f3',1,'vg::ZipCodeTree']]],
- ['node_5flength_10190',['node_length',['../structvg_1_1PathIndex.html#a398380d0a0f4b4fefc15eef8b37cd2f3',1,'vg::PathIndex::node_length()'],['../classvg_1_1Sampler.html#a490f1a1d093d2c8bf4369c32ad2c257e',1,'vg::Sampler::node_length()']]],
- ['node_5foffset_10191',['node_offset',['../classvg_1_1Viz.html#aa4fc0be6ae2f6acc7fe790e5f50f67f5',1,'vg::Viz']]],
- ['node_5fpath_5ftraversal_5fcounts_10192',['node_path_traversal_counts',['../classvg_1_1Paths.html#a787ba9aa7f693c4a92c5e17957bb0877',1,'vg::Paths']]],
- ['node_5fpath_5ftraversals_10193',['node_path_traversals',['../classvg_1_1Paths.html#a6856b1b2f59defaeccedc1e31a8a88d3',1,'vg::Paths']]],
- ['node_5fquality_5fbin_5foffset_10194',['node_quality_bin_offset',['../classvg_1_1Packer.html#ac3f39972f863ff761e8c32dee7702296',1,'vg::Packer']]],
- ['node_5fquality_5fbin_5fsize_10195',['node_quality_bin_size',['../classvg_1_1Packer.html#a1526efc7e55974a7f3b009f769900dda',1,'vg::Packer']]],
- ['node_5fquality_5fvector_5fsize_10196',['node_quality_vector_size',['../classvg_1_1Packer.html#ada965622937baaf933fd36cd84315cde',1,'vg::Packer']]],
- ['node_5frank_10197',['node_rank',['../classvg_1_1VG.html#a0202180fa7153f464c3b1d3ff70dc9cb',1,'vg::VG::node_rank(Node *node)'],['../classvg_1_1VG.html#ad7ac4861a64a07f344c21cf2f41b91f1',1,'vg::VG::node_rank(nid_t id)']]],
- ['node_5fstart_10198',['node_start',['../namespacevg.html#a30f5b0dc3732e48a6d9b8d1c895cd8d1',1,'vg']]],
- ['node_5fstart_5fat_5fpath_5fposition_10199',['node_start_at_path_position',['../classxg_1_1XG.html#aa9b17c02171a7073eeb9d4614e619f34',1,'xg::XG']]],
- ['node_5fstarts_5fin_5fpath_10200',['node_starts_in_path',['../classvg_1_1VG.html#a093f4e4dffe0d03806df32edc33cdb9a',1,'vg::VG::node_starts_in_path(const list< NodeTraversal > &path, map< Node *, int > &node_start)'],['../classvg_1_1VG.html#ac27c591957478a17605c2453749f7d20',1,'vg::VG::node_starts_in_path(list< NodeTraversal > &path, map< NodeTraversal *, int > &node_start)']]],
- ['node_5fto_5fsnarl_10201',['node_to_snarl',['../classvg_1_1SnarlGraph.html#afccf2e9cf0326a49a9d2226869e11c5f',1,'vg::SnarlGraph']]],
- ['node_5fvector_5foffset_10202',['node_vector_offset',['../classxg_1_1XG.html#abc79b8d077e089d9a847a6a4a4be70cc',1,'xg::XG::node_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a8666da4a9f55361893544fbb4eff76ce',1,'handlegraph::VectorizableHandleGraph::node_vector_offset()']]],
- ['nodelength_10203',['nodelength',['../structhaplo_1_1gbwt__thread__t.html#afcc24f78011916b909ac56b22c8f82c3',1,'haplo::gbwt_thread_t']]],
- ['nodes_5fare_5fperfect_5fpath_5fneighbors_10204',['nodes_are_perfect_path_neighbors',['../namespacehandlegraph_1_1algorithms.html#afbf906cc6a283954093403396ee5ce0e',1,'handlegraph::algorithms']]],
- ['nodes_5fbefore_5foffset_10205',['nodes_before_offset',['../classvg_1_1Viz.html#aa315096c3932839c5cf98b28da52b078',1,'vg::Viz']]],
- ['nodes_5fnext_10206',['nodes_next',['../classvg_1_1VG.html#a0b084d958fd8069839884dc3a01ed745',1,'vg::VG::nodes_next(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a62f1bb7fa27d4d4312017b113aab099a',1,'vg::VG::nodes_next(NodeTraversal n)']]],
- ['nodes_5fprev_10207',['nodes_prev',['../classvg_1_1VG.html#ac08e778396904ad3b3f20f605f54628d',1,'vg::VG::nodes_prev(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a0f3e69ced0c3135f3f363c14bf752aad',1,'vg::VG::nodes_prev(NodeTraversal n)']]],
- ['nodeside_10208',['NodeSide',['../classvg_1_1NodeSide.html#ac4bde3f59ff17ea8c7415fcd9fdd4a0b',1,'vg::NodeSide::NodeSide(id_t node, bool is_end=false)'],['../classvg_1_1NodeSide.html#a3ecb3102be6a85788a003754925c5872',1,'vg::NodeSide::NodeSide()']]],
- ['nodetraversal_10209',['NodeTraversal',['../classvg_1_1NodeTraversal.html#afca10c8751d4d0f0a86da02277d11513',1,'vg::NodeTraversal::NodeTraversal(Node *node, bool backward=false)'],['../classvg_1_1NodeTraversal.html#a795cce0d085b9113a41fc187e0669f12',1,'vg::NodeTraversal::NodeTraversal()']]],
- ['non_5fintermediate_5faliases_10210',['non_intermediate_aliases',['../classvg_1_1AliasGraph.html#ac400ab0ecb048175fc460f69820204e8',1,'vg::AliasGraph']]],
- ['non_5fmatch_5fend_10211',['non_match_end',['../namespacevg.html#a3ec2e2ef9679291d966bc348a47c3537',1,'vg']]],
- ['non_5fmatch_5fstart_10212',['non_match_start',['../namespacevg.html#ae838e7d89edc59dd87747238cee49b49',1,'vg']]],
- ['nonatgcnton_10213',['nonATGCNtoN',['../namespacevg.html#a453b457823e1ddf916ebf298befb4512',1,'vg']]],
- ['nondisjoint_10214',['nondisjoint',['../structhaplo_1_1int__itvl__t.html#af18e576db32fb19f602ed249e07567a7',1,'haplo::int_itvl_t']]],
- ['nonoverlapping_5fnode_5fcontext_5fwithout_5fpaths_10215',['nonoverlapping_node_context_without_paths',['../classvg_1_1VG.html#a44edad9ba2a6df332234b43715dd71db',1,'vg::VG']]],
- ['normal_5fdistribution_10216',['normal_distribution',['../classvg_1_1normal__distribution.html#a7c7bb2c253ac80e0752fd2ba2f84ed56',1,'vg::normal_distribution']]],
- ['normal_5fpdf_10217',['normal_pdf',['../namespacevg.html#ae825181ee40a5f0d5087fc657db9a7db',1,'vg']]],
- ['normalize_10218',['normalize',['../namespacevg_1_1algorithms.html#afb6a93eb17739d744908d61ca6650f4c',1,'vg::algorithms']]],
- ['normalize_5falignment_10219',['normalize_alignment',['../namespacevg.html#afa0c54720b2b1007ae540dc70b5b8024',1,'vg']]],
- ['nowhere_10220',['nowhere',['../classvg_1_1algorithms_1_1TracedScore.html#ad2f398d1d22f2a027a870182e7fd26d4',1,'vg::algorithms::TracedScore']]],
- ['nth_5fcopy_5fof_5fhandle_10221',['nth_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a716193b4f3dcecfd26de15acf83964b9',1,'vg::DagifiedGraph']]],
- ['nullclusterer_10222',['NullClusterer',['../classvg_1_1NullClusterer.html#a63ae2e8bfe748f6557df52cddf4b41e8',1,'vg::NullClusterer']]],
- ['nullmaskinggraph_10223',['NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html#a2d348fa5aa3bd9216fc4133d320575ef',1,'vg::NullMaskingGraph::NullMaskingGraph(const HandleGraph *graph)'],['../classvg_1_1NullMaskingGraph.html#addeb1ab4002f516c686a5af59018597f',1,'vg::NullMaskingGraph::NullMaskingGraph()=default']]],
- ['num_5fcomponents_10224',['num_components',['../namespacevg_1_1algorithms.html#aa84bd9740e748431857b5fd8a0397183',1,'vg::algorithms']]],
- ['num_5fconnected_5fcomponents_10225',['num_connected_components',['../namespacevg.html#a1ac45a06bc04f88ba6c2321d7af304c6',1,'vg']]],
- ['num_5fhaplotypes_10226',['num_haplotypes',['../classvg_1_1PhasedGenome.html#af17e5f99a07028d41f94885480cdddf7',1,'vg::PhasedGenome']]],
- ['num_5fsnarls_10227',['num_snarls',['../classvg_1_1SnarlManager.html#a727734d76e892a3fc0d421c6382349a1',1,'vg::SnarlManager']]]
+ ['n_10156',['n',['../namespacehaplotypes__defaults.html#a08f2ff580a81523291eed7ef0d644bd2',1,'haplotypes_defaults']]],
+ ['nearest_5foffsets_5fin_5fpaths_10157',['nearest_offsets_in_paths',['../classxg_1_1XG.html#ab885cecf687ffb8583fb95cce8ca34b2',1,'xg::XG::nearest_offsets_in_paths()'],['../namespacevg_1_1algorithms.html#a477330d3ab29cbd3c48e4830d51b3e0f',1,'vg::algorithms::nearest_offsets_in_paths()']]],
+ ['nearest_5fpath_5fnode_10158',['nearest_path_node',['../classxg_1_1XG.html#a03f2f8a4cc3d06e4f1748474082efdb9',1,'xg::XG']]],
+ ['nestedcachedpackedtraversalsupportfinder_10159',['NestedCachedPackedTraversalSupportFinder',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#a6893d620886b1bb326f735e36757f6e2',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
+ ['nestedflowcaller_10160',['NestedFlowCaller',['../classvg_1_1NestedFlowCaller.html#ab56c3d2fe181450dc33167539bc8f74c',1,'vg::NestedFlowCaller']]],
+ ['nestedtraversalfinder_10161',['NestedTraversalFinder',['../classvg_1_1NestedTraversalFinder.html#a0ab18d1355be2772f9ca78c5eb269e6c',1,'vg::NestedTraversalFinder']]],
+ ['net_5fgraph_5fof_10162',['net_graph_of',['../classvg_1_1SnarlManager.html#aa8872188679a5ad4d0da08c1235f2019',1,'vg::SnarlManager']]],
+ ['netgraph_10163',['NetGraph',['../classvg_1_1NetGraph.html#a9059c913779ce4095224a5ae6638a27d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains_mixed, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#a29abf89e03eedc7ac2af4682a1b5bb04',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const ChainContainer &child_chains, const SnarlContainer &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aa1e17ccb08d595123db3d8cd6e2593b2',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const vector< vector< pair< Snarl, bool >>> &child_chains, const vector< Snarl > &child_unary_snarls, const HandleGraph *graph, bool use_internal_connectivity=false)'],['../classvg_1_1NetGraph.html#aba1479f586d07f276ba6925cfc1a8e6d',1,'vg::NetGraph::NetGraph(const Visit &start, const Visit &end, const HandleGraph *graph, bool use_internal_connectivity=false)']]],
+ ['new_5fheight_10164',['new_height',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ae444abfaf71eedae674fb4703e910248',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['new_5flength_10165',['new_length',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a9d8c1bf7222ee28236691c30185194d3',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['new_5foutput_5fgraph_10166',['new_output_graph',['../namespacevg_1_1io.html#a4b6ad53e3fc9e4c143221b213932db70',1,'vg::io']]],
+ ['new_5fside_10167',['new_side',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#af0ea102c59fcbcb1a5387ea5b465e950',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['next_10168',['Next',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a91e4dc4f48957737a80e99a8ad32ba53',1,'vg::io::BlockedGzipInputStream::Next()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a0c3e80161a999b884abf3965dd0a5a39',1,'vg::io::BlockedGzipOutputStream::Next()'],['../classvg_1_1WFATree.html#acec4f54d7784d6c7310418ddec2716b9',1,'vg::WFATree::next()'],['../classvg_1_1connection__t.html#a18d278044df80b1334542e6d25043a32',1,'vg::connection_t::next()'],['../classvg_1_1subpath__t.html#a60a4ec0114c307ae532ea307128bfe24',1,'vg::subpath_t::next() const'],['../classvg_1_1subpath__t.html#aabe3e1337325511c83d7e949195fdf37',1,'vg::subpath_t::next(size_t i) const'],['../classvg_1_1WindowedVcfBuffer.html#a0d66b5a177f55cb726122577840d8911',1,'vg::WindowedVcfBuffer::next()']]],
+ ['next_5fempty_5falignment_10169',['next_empty_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a08e8eed8f95a621c9786bca1b0850dd2',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['next_5fis_5fempty_10170',['next_is_empty',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a016150b6b6f4551ee3eb7600d7037b67',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['next_5fpath_5fposition_10171',['next_path_position',['../classxg_1_1XG.html#ae973d41358ddab92f0a2dca094806102',1,'xg::XG']]],
+ ['next_5fpos_5fchars_10172',['next_pos_chars',['../classvg_1_1Sampler.html#ab5455f8f6faf176b418e3dbcb6bf1ce8',1,'vg::Sampler::next_pos_chars()'],['../namespacevg_1_1algorithms.html#a22d03c4f50c51d0d537811ba88895688',1,'vg::algorithms::next_pos_chars()']]],
+ ['next_5fscore_10173',['next_score',['../classvg_1_1WFATree.html#aba63fbf6ca1e1382e62727ea95c4b0af',1,'vg::WFATree']]],
+ ['next_5fsize_10174',['next_size',['../classvg_1_1subpath__t.html#aab697710ebd5e8f968bed5c5262bbe2a',1,'vg::subpath_t']]],
+ ['next_5fsnarl_10175',['next_snarl',['../classvg_1_1SnarlManager.html#afcca3b74e960b6931598188e0b9ae7a8',1,'vg::SnarlManager']]],
+ ['next_5ftraceback_5falignment_10176',['next_traceback_alignment',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a8d6cbc921387724da8db3c8c0f20f363',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['ngssimulator_10177',['NGSSimulator',['../classvg_1_1NGSSimulator.html#a51e3a4117f9339b3195d73f2c6cf560e',1,'vg::NGSSimulator::NGSSimulator(PathPositionHandleGraph &graph, const string &ngs_fastq_file, const string &ngs_paired_fastq_file="", bool interleaved_fastq=false, const vector< string > &source_paths={}, const vector< double > &source_path_ploidies={}, const vector< pair< string, double >> &transcript_expressions={}, const vector< tuple< string, string, size_t >> &haplotype_transcripts={}, double substition_polymorphism_rate=0.001, double indel_polymorphism_rate=0.0002, double indel_error_proportion=0.01, double fragment_length_mean=300.0, double fragment_length_stdev=50.0, double error_multiplier=1.0, bool retry_on_Ns=true, bool sample_unsheared_paths=false, uint64_t seed=0)'],['../classvg_1_1NGSSimulator.html#a5417af00068600ab1e6d0acb24836698',1,'vg::NGSSimulator::NGSSimulator(void)=delete']]],
+ ['no_5fchain_5finfo_10178',['no_chain_info',['../classvg_1_1MinimizerMapper.html#a3b9a4518b171aa85909da6ccde88e0a8',1,'vg::MinimizerMapper']]],
+ ['no_5fmultiple_5fcover_5ftypes_10179',['no_multiple_cover_types',['../gbwt__main_8cpp.html#a0124aac03621e82b84ef0de974a08574',1,'gbwt_main.cpp']]],
+ ['no_5fmultiple_5finput_5ftypes_10180',['no_multiple_input_types',['../gbwt__main_8cpp.html#ae1c5768186dc339c157bf4b72517b5ab',1,'gbwt_main.cpp']]],
+ ['no_5fmultiple_5finputs_10181',['no_multiple_inputs',['../convert__main_8cpp.html#aca425ac5df78dde7681385a5341abb1b',1,'convert_main.cpp']]],
+ ['no_5fpos_10182',['no_pos',['../classvg_1_1WFATree.html#ad0383cee94782b3f0e8d48078d4d2348',1,'vg::WFATree']]],
+ ['node_10183',['node',['../structvg_1_1MatchPos.html#abd73a2a9a1d86e1747631f89b045e4fd',1,'vg::MatchPos::node()'],['../classxg_1_1XGPath.html#a621253a080fdb8b81eb5efe2359b93a8',1,'xg::XGPath::node()']]],
+ ['node_5fat_5fvector_5foffset_10184',['node_at_vector_offset',['../classxg_1_1XG.html#a2f2c0b014af5d0032f9beaefb074cc59',1,'xg::XG::node_at_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a3095e541eee436a9f49ef0846539ef44',1,'handlegraph::VectorizableHandleGraph::node_at_vector_offset()']]],
+ ['node_5fcount_10185',['node_count',['../classvg_1_1VG.html#abb3e9e655bcaad0bc522307743acd6a0',1,'vg::VG']]],
+ ['node_5fcount_5fnext_10186',['node_count_next',['../classvg_1_1VG.html#a4c614759c77b4b0a95b25360c2fa1fa0',1,'vg::VG']]],
+ ['node_5fcount_5fprev_10187',['node_count_prev',['../classvg_1_1VG.html#a1091113608fae5b9cbafc87cf4cf82a2',1,'vg::VG']]],
+ ['node_5fend_10188',['node_end',['../namespacevg.html#a434e32ac84fd027508a6506e80107331',1,'vg']]],
+ ['node_5fgraph_5fidx_10189',['node_graph_idx',['../classxg_1_1XG.html#a191b03b4ada2d076ae6cc53a5a0f5b3d',1,'xg::XG']]],
+ ['node_5fid_10190',['node_id',['../classvg_1_1mapping__t.html#a878754e2bea167b11b7cb83af5556a6f',1,'vg::mapping_t::node_id()'],['../classvg_1_1position__t.html#a241b513ec1180294fc6e43f7df1935a7',1,'vg::position_t::node_id()']]],
+ ['node_5findex_10191',['node_index',['../classvg_1_1Packer.html#abc210cd0133e161824e80c366738d158',1,'vg::Packer']]],
+ ['node_5fis_5fin_5fcyclic_5fsnarl_10192',['node_is_in_cyclic_snarl',['../classvg_1_1ZipCodeTree.html#aadc6866376dcdda602ff117838ced129',1,'vg::ZipCodeTree']]],
+ ['node_5fis_5finvalid_10193',['node_is_invalid',['../classvg_1_1ZipCodeTree.html#ad12d46904662a2f622a2ec83567177f3',1,'vg::ZipCodeTree']]],
+ ['node_5flength_10194',['node_length',['../structvg_1_1PathIndex.html#a398380d0a0f4b4fefc15eef8b37cd2f3',1,'vg::PathIndex::node_length()'],['../classvg_1_1Sampler.html#a490f1a1d093d2c8bf4369c32ad2c257e',1,'vg::Sampler::node_length()']]],
+ ['node_5foffset_10195',['node_offset',['../classvg_1_1Viz.html#aa4fc0be6ae2f6acc7fe790e5f50f67f5',1,'vg::Viz']]],
+ ['node_5fpath_5ftraversal_5fcounts_10196',['node_path_traversal_counts',['../classvg_1_1Paths.html#a787ba9aa7f693c4a92c5e17957bb0877',1,'vg::Paths']]],
+ ['node_5fpath_5ftraversals_10197',['node_path_traversals',['../classvg_1_1Paths.html#a6856b1b2f59defaeccedc1e31a8a88d3',1,'vg::Paths']]],
+ ['node_5fquality_5fbin_5foffset_10198',['node_quality_bin_offset',['../classvg_1_1Packer.html#ac3f39972f863ff761e8c32dee7702296',1,'vg::Packer']]],
+ ['node_5fquality_5fbin_5fsize_10199',['node_quality_bin_size',['../classvg_1_1Packer.html#a1526efc7e55974a7f3b009f769900dda',1,'vg::Packer']]],
+ ['node_5fquality_5fvector_5fsize_10200',['node_quality_vector_size',['../classvg_1_1Packer.html#ada965622937baaf933fd36cd84315cde',1,'vg::Packer']]],
+ ['node_5frank_10201',['node_rank',['../classvg_1_1VG.html#a0202180fa7153f464c3b1d3ff70dc9cb',1,'vg::VG::node_rank(Node *node)'],['../classvg_1_1VG.html#ad7ac4861a64a07f344c21cf2f41b91f1',1,'vg::VG::node_rank(nid_t id)']]],
+ ['node_5fstart_10202',['node_start',['../namespacevg.html#a30f5b0dc3732e48a6d9b8d1c895cd8d1',1,'vg']]],
+ ['node_5fstart_5fat_5fpath_5fposition_10203',['node_start_at_path_position',['../classxg_1_1XG.html#aa9b17c02171a7073eeb9d4614e619f34',1,'xg::XG']]],
+ ['node_5fstarts_5fin_5fpath_10204',['node_starts_in_path',['../classvg_1_1VG.html#a093f4e4dffe0d03806df32edc33cdb9a',1,'vg::VG::node_starts_in_path(const list< NodeTraversal > &path, map< Node *, int > &node_start)'],['../classvg_1_1VG.html#ac27c591957478a17605c2453749f7d20',1,'vg::VG::node_starts_in_path(list< NodeTraversal > &path, map< NodeTraversal *, int > &node_start)']]],
+ ['node_5fto_5fsnarl_10205',['node_to_snarl',['../classvg_1_1SnarlGraph.html#afccf2e9cf0326a49a9d2226869e11c5f',1,'vg::SnarlGraph']]],
+ ['node_5fvector_5foffset_10206',['node_vector_offset',['../classxg_1_1XG.html#abc79b8d077e089d9a847a6a4a4be70cc',1,'xg::XG::node_vector_offset()'],['../classhandlegraph_1_1VectorizableHandleGraph.html#a8666da4a9f55361893544fbb4eff76ce',1,'handlegraph::VectorizableHandleGraph::node_vector_offset()']]],
+ ['nodelength_10207',['nodelength',['../structhaplo_1_1gbwt__thread__t.html#afcc24f78011916b909ac56b22c8f82c3',1,'haplo::gbwt_thread_t']]],
+ ['nodes_5fare_5fperfect_5fpath_5fneighbors_10208',['nodes_are_perfect_path_neighbors',['../namespacehandlegraph_1_1algorithms.html#afbf906cc6a283954093403396ee5ce0e',1,'handlegraph::algorithms']]],
+ ['nodes_5fbefore_5foffset_10209',['nodes_before_offset',['../classvg_1_1Viz.html#aa315096c3932839c5cf98b28da52b078',1,'vg::Viz']]],
+ ['nodes_5fnext_10210',['nodes_next',['../classvg_1_1VG.html#a0b084d958fd8069839884dc3a01ed745',1,'vg::VG::nodes_next(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a62f1bb7fa27d4d4312017b113aab099a',1,'vg::VG::nodes_next(NodeTraversal n)']]],
+ ['nodes_5fprev_10211',['nodes_prev',['../classvg_1_1VG.html#ac08e778396904ad3b3f20f605f54628d',1,'vg::VG::nodes_prev(NodeTraversal n, vector< NodeTraversal > &nodes)'],['../classvg_1_1VG.html#a0f3e69ced0c3135f3f363c14bf752aad',1,'vg::VG::nodes_prev(NodeTraversal n)']]],
+ ['nodeside_10212',['NodeSide',['../classvg_1_1NodeSide.html#ac4bde3f59ff17ea8c7415fcd9fdd4a0b',1,'vg::NodeSide::NodeSide(id_t node, bool is_end=false)'],['../classvg_1_1NodeSide.html#a3ecb3102be6a85788a003754925c5872',1,'vg::NodeSide::NodeSide()']]],
+ ['nodetraversal_10213',['NodeTraversal',['../classvg_1_1NodeTraversal.html#afca10c8751d4d0f0a86da02277d11513',1,'vg::NodeTraversal::NodeTraversal(Node *node, bool backward=false)'],['../classvg_1_1NodeTraversal.html#a795cce0d085b9113a41fc187e0669f12',1,'vg::NodeTraversal::NodeTraversal()']]],
+ ['non_5fintermediate_5faliases_10214',['non_intermediate_aliases',['../classvg_1_1AliasGraph.html#ac400ab0ecb048175fc460f69820204e8',1,'vg::AliasGraph']]],
+ ['non_5fmatch_5fend_10215',['non_match_end',['../namespacevg.html#a3ec2e2ef9679291d966bc348a47c3537',1,'vg']]],
+ ['non_5fmatch_5fstart_10216',['non_match_start',['../namespacevg.html#ae838e7d89edc59dd87747238cee49b49',1,'vg']]],
+ ['nonatgcnton_10217',['nonATGCNtoN',['../namespacevg.html#a453b457823e1ddf916ebf298befb4512',1,'vg']]],
+ ['nondisjoint_10218',['nondisjoint',['../structhaplo_1_1int__itvl__t.html#af18e576db32fb19f602ed249e07567a7',1,'haplo::int_itvl_t']]],
+ ['nonoverlapping_5fnode_5fcontext_5fwithout_5fpaths_10219',['nonoverlapping_node_context_without_paths',['../classvg_1_1VG.html#a44edad9ba2a6df332234b43715dd71db',1,'vg::VG']]],
+ ['normal_5fdistribution_10220',['normal_distribution',['../classvg_1_1normal__distribution.html#a7c7bb2c253ac80e0752fd2ba2f84ed56',1,'vg::normal_distribution']]],
+ ['normal_5fpdf_10221',['normal_pdf',['../namespacevg.html#ae825181ee40a5f0d5087fc657db9a7db',1,'vg']]],
+ ['normalize_10222',['normalize',['../namespacevg_1_1algorithms.html#afb6a93eb17739d744908d61ca6650f4c',1,'vg::algorithms']]],
+ ['normalize_5falignment_10223',['normalize_alignment',['../namespacevg.html#afa0c54720b2b1007ae540dc70b5b8024',1,'vg']]],
+ ['nowhere_10224',['nowhere',['../classvg_1_1algorithms_1_1TracedScore.html#ad2f398d1d22f2a027a870182e7fd26d4',1,'vg::algorithms::TracedScore']]],
+ ['nth_5fcopy_5fof_5fhandle_10225',['nth_copy_of_handle',['../classvg_1_1DagifiedGraph.html#a716193b4f3dcecfd26de15acf83964b9',1,'vg::DagifiedGraph']]],
+ ['nullclusterer_10226',['NullClusterer',['../classvg_1_1NullClusterer.html#a63ae2e8bfe748f6557df52cddf4b41e8',1,'vg::NullClusterer']]],
+ ['nullmaskinggraph_10227',['NullMaskingGraph',['../classvg_1_1NullMaskingGraph.html#a2d348fa5aa3bd9216fc4133d320575ef',1,'vg::NullMaskingGraph::NullMaskingGraph(const HandleGraph *graph)'],['../classvg_1_1NullMaskingGraph.html#addeb1ab4002f516c686a5af59018597f',1,'vg::NullMaskingGraph::NullMaskingGraph()=default']]],
+ ['num_5fcomponents_10228',['num_components',['../namespacevg_1_1algorithms.html#aa84bd9740e748431857b5fd8a0397183',1,'vg::algorithms']]],
+ ['num_5fconnected_5fcomponents_10229',['num_connected_components',['../namespacevg.html#a1ac45a06bc04f88ba6c2321d7af304c6',1,'vg']]],
+ ['num_5fhaplotypes_10230',['num_haplotypes',['../classvg_1_1PhasedGenome.html#af17e5f99a07028d41f94885480cdddf7',1,'vg::PhasedGenome']]],
+ ['num_5fsnarls_10231',['num_snarls',['../classvg_1_1SnarlManager.html#a727734d76e892a3fc0d421c6382349a1',1,'vg::SnarlManager']]]
];
diff --git a/search/functions_f.js b/search/functions_f.js
index 05c1184391..2fe219e45f 100644
--- a/search/functions_f.js
+++ b/search/functions_f.js
@@ -1,66 +1,66 @@
var searchData=
[
- ['object_5fend_10228',['object_end',['../classvg_1_1ProblemDumpExplainer.html#adb13795992af2eafcbfe0f6716a127f9',1,'vg::ProblemDumpExplainer']]],
- ['object_5fstart_10229',['object_start',['../classvg_1_1ProblemDumpExplainer.html#a5ebde44f8627a596cdb75267a55f887d',1,'vg::ProblemDumpExplainer']]],
- ['of_5fnode_10230',['of_node',['../classvg_1_1Paths.html#abda01c563a3455d491b152a23b22a27a',1,'vg::Paths']]],
- ['offset_10231',['offset',['../classvg_1_1position__t.html#a8de3e2b8d4801ca2951d4c21d57bd404',1,'vg::position_t::offset()'],['../namespacevg.html#ad48a54a3ddd5e6ffd8e3e6296fb9c037',1,'vg::offset()'],['../namespacexg.html#ac689f45eccbedaba6fab410913961f8c',1,'xg::offset()']]],
- ['offsets_5fin_5fpaths_10232',['offsets_in_paths',['../classxg_1_1XG.html#af77c93c34b8009c590fa4ee2b01fd64e',1,'xg::XG::offsets_in_paths()'],['../namespacevg_1_1algorithms.html#aef24fa77dadb09d5920ec94b88af2128',1,'vg::algorithms::offsets_in_paths()']]],
- ['on_5fgroup_10233',['on_group',['../classvg_1_1io_1_1MessageEmitter.html#a5b5f11b2f9b08a870fc68a980c91f1e4',1,'vg::io::MessageEmitter::on_group()'],['../classvg_1_1io_1_1ProtobufEmitter.html#af22328bc428af2be817a7a0d097ca370',1,'vg::io::ProtobufEmitter::on_group()']]],
- ['on_5fmessage_10234',['on_message',['../classvg_1_1io_1_1ProtobufEmitter.html#a6a3a16550dcd7dd7a320109125d4e2a1',1,'vg::io::ProtobufEmitter']]],
- ['on_5fpath_5fedit_10235',['on_path_edit',['../classvg_1_1FeatureSet.html#a72b47862b3121905222f7662c4ff65ca',1,'vg::FeatureSet']]],
- ['one_5fend_5fanchored_5ffilter_10236',['one_end_anchored_filter',['../classvg_1_1Filter.html#adf0ea872057dafedc321b256ec072b8c',1,'vg::Filter']]],
- ['open_5fall_10237',['open_all',['../classvg_1_1StreamSorter.html#a112c5a39918bb37f4aa3bf1413d31b37',1,'vg::StreamSorter']]],
- ['open_5fchain_10238',['open_chain',['../classvg_1_1ZipCodeForest.html#a56fb93ecb975f5f6c12deeef5b1f9b20',1,'vg::ZipCodeForest']]],
- ['open_5ffd_10239',['open_fd',['../classhandlegraph_1_1TriviallySerializable.html#aa1f5b9cdb957540dfea7e0e4b478e9b2',1,'handlegraph::TriviallySerializable']]],
- ['open_5fsnarl_10240',['open_snarl',['../classvg_1_1ZipCodeForest.html#ab219e010a4e80804f7c5f6ada581f18d',1,'vg::ZipCodeForest']]],
- ['operator_20bool_10241',['operator bool',['../structvg_1_1AlignmentValidity.html#a2f6b53f193bad40111118e3293ad361c',1,'vg::AlignmentValidity::operator bool()'],['../classvg_1_1Explainer.html#aeca40f040dd309c5f457e8ea0bd8627f',1,'vg::Explainer::operator bool()'],['../structvg_1_1WFAAlignment.html#a7f1464e6b2a86671cdf376137409eeeb',1,'vg::WFAAlignment::operator bool()']]],
- ['operator_20number_10242',['operator Number',['../structvg_1_1Range.html#acb0f6ebb720df6227410bf9403079a32',1,'vg::Range']]],
- ['operator_20value_20_26_10243',['operator Value &',['../classvg_1_1BaseOption.html#a760720e496d3058589d34d823f61566b',1,'vg::BaseOption']]],
- ['operator_21_3d_10244',['operator!=',['../classvg_1_1ShuffledPairs_1_1iterator.html#a2714f2334dae600fc66c3508ecd4494a',1,'vg::ShuffledPairs::iterator::operator!=()'],['../structvg_1_1GaplessExtension.html#a5fc94cd2cfd5898459cac75c65be55a5',1,'vg::GaplessExtension::operator!=()'],['../structvg_1_1read__alignment__index__t.html#ac967a7e4d2339bf2ab83208991b0ce69',1,'vg::read_alignment_index_t::operator!=()'],['../structvg_1_1alignment__index__t.html#ab09e271d0c6eb6f08fd1bde411c6c5f7',1,'vg::alignment_index_t::operator!=()'],['../classvg_1_1NodeSide.html#a48481b0155b782c27644080c98d20656',1,'vg::NodeSide::operator!=()'],['../classvg_1_1NodeTraversal.html#aaa81c382e219ed6f832b1401872fe898',1,'vg::NodeTraversal::operator!=()'],['../classvg_1_1edit__t.html#ac6b81fe1407a1ae901f72ed555a30dae',1,'vg::edit_t::operator!=()'],['../classvg_1_1path__mapping__t.html#a78466c5a9e83d7367bd70799dfd4a76b',1,'vg::path_mapping_t::operator!=()'],['../classvg_1_1path__t.html#a5a0f6368c497cfe5eac4025080c20bc1',1,'vg::path_t::operator!=()'],['../classvg_1_1PhasedGenome_1_1iterator.html#aff3ae0b92ca06496a22d1aad89016737',1,'vg::PhasedGenome::iterator::operator!=()'],['../classvg_1_1position__t.html#a9011acaf2ade42c99a74596214196fa8',1,'vg::position_t::operator!=()'],['../structvg_1_1ChainIterator.html#aec215507b5b43e388afb2933d25c21d0',1,'vg::ChainIterator::operator!=()'],['../classvg_1_1BitString.html#a57b03c3b055ab267c199bd429ff5e4c6',1,'vg::BitString::operator!=()'],['../structvg_1_1VectorView_1_1const__iterator.html#a620b2bd9b99aff0ab077ce6d9441b684',1,'vg::VectorView::const_iterator::operator!=()'],['../structvg_1_1IncrementIter.html#a97c041dbf0473d997321d19072fe85e6',1,'vg::IncrementIter::operator!=()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#aced4d93ad8d1fb3b5b530ff0dd912912',1,'vg::ZipCodeTree::oriented_seed_t::operator!=()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#ac730025c4f3c9144cd742a6c0b15f3d3',1,'vg::ZipCodeTree::seed_result_t::operator!=()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a1eddeaefb5ff95cbde90e0112efa2433',1,'vg::ZipCodeTree::iterator::operator!=()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4925ff71b13d15855904e7e7497b295b',1,'vg::ZipCodeTree::reverse_iterator::operator!=()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4a74c0a77c2df092ecc5d2be1a4b793c',1,'vg::algorithms::TracedScore::operator!=()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a2c24b07521aa704e517c386e1369d227',1,'handlegraph::PathForEachSocket::iterator::operator!=()'],['../classvg_1_1io_1_1MessageIterator.html#ad6a23c45ab954ce158faec0b8935cd90',1,'vg::io::MessageIterator::operator!=()'],['../classvg_1_1io_1_1ProtobufIterator.html#a1f67a6fcda4cfa7d6d1b37bcdb74c0ac',1,'vg::io::ProtobufIterator::operator!=()'],['../namespacevg.html#abb6063b76b70947010198b46c053b578',1,'vg::operator!=(const Visit &a, const Visit &b)'],['../namespacevg.html#a24e1e38ea29c615b2c5f5cd8dbaeeb2a',1,'vg::operator!=(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a654eca8448629e42ae87cadd893ee10e',1,'vg::operator!=(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a22cb5c700c1dee4fec8d3af77057ea2a',1,'vg::operator!=(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#a4f594795be32cb04b7baf0ef71ad77b0',1,'vg::operator!=(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a581944f1e71285f8c4887c2f5ce1467f',1,'vg::operator!=(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a67115fb742d1bf6d7e4e489fda99b78e',1,'vg::operator!=(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#a913cf04aa9946eebf68cc319d7929f11',1,'handlegraph::operator!=(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a18f417ab023834f355f735c2baa18324',1,'handlegraph::operator!=(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#acbbe7b08c190039a0a3700e078818aa5',1,'handlegraph::operator!=(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#acc5274f38cf004b29d2bf398a96f4da5',1,'handlegraph::operator!=(const net_handle_t &a, const net_handle_t &b)']]],
- ['operator_26_3d_10245',['operator&=',['../classvg_1_1SmallBitset.html#a44c58c409898c13b98b3937669bf7b8f',1,'vg::SmallBitset']]],
- ['operator_28_29_10246',['operator()',['../structvg_1_1BBEdgeHash.html#af0c713bc536e343b416520dd0f14732b',1,'vg::BBEdgeHash::operator()()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a748c3131cdb69751197546f36a1298bb',1,'vg::MEMClusterer::DPScoreComparator::operator()()'],['../classvg_1_1DistanceHeuristic.html#afb17aa7db222de3ef43a70115c7eec6a',1,'vg::DistanceHeuristic::operator()()'],['../classvg_1_1SnarlMinDistance.html#a4a87d093a5ee90f158ce5e5a1fdc8fd4',1,'vg::SnarlMinDistance::operator()()'],['../classvg_1_1TipAnchoredMaxDistance.html#a165cc0f3d3e70810f72bd7ad49b9416e',1,'vg::TipAnchoredMaxDistance::operator()()'],['../structvg_1_1state__hash.html#a5ddcb7dd42852b3f35fd414663677e8c',1,'vg::state_hash::operator()()'],['../classvg_1_1ReadMasker.html#a8d7a36b958e3405106494e93fffcda5f',1,'vg::ReadMasker::operator()()'],['../structvg_1_1Genotyper_1_1hash__node__traversal.html#a62f374bedac308110f484df59f6c905f',1,'vg::Genotyper::hash_node_traversal::operator()()'],['../structvg_1_1Genotyper_1_1hash__oriented__edge.html#a070a16b42f8aeace08dfee4f22badc8d',1,'vg::Genotyper::hash_oriented_edge::operator()()'],['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html#a44aad1a7e112842dc576fd9cbebdbbfc',1,'vg::Genotyper::hash_ambiguous_allele_set::operator()()'],['../structvg_1_1wang__hash_3_01handle__t_01_4.html#a2abb45aa397420108850ce590f7f3bf7',1,'vg::wang_hash< handle_t >::operator()()'],['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html#a5a9ad96629401a307c94b17a2d91fc53',1,'vg::wang_hash< path_handle_t >::operator()()'],['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html#a847da6dc45718131135dba8e17aa93a6',1,'std::hash< pair< A, B > >::operator()()'],['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html#afdf58525bd44e80be2af8355db0eba2e',1,'std::hash< std::tuple< TT... > >::operator()()'],['../structvg_1_1wang__hash_3_01T_01_5_01_4.html#a55ef00b42c8f6103e78eb7f7b7597984',1,'vg::wang_hash< T * >::operator()()'],['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html#a87443673fa41e2f7a7ee5cf4e2bd533c',1,'vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >::operator()()'],['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html#af62856c68653d586e53d842a16e54cf7',1,'vg::wang_hash< std::pair< A, B > >::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1FCmp.html#a65b7021e0e5237b4b7f0fbb34a8f99ec',1,'vg::IncrementalSubgraph::FCmp::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html#a9a34770a4c767bf069601106bbdde191',1,'vg::IncrementalSubgraph::IterFCmp::operator()()'],['../structvg_1_1wang__hash_3_01NodeSide_01_4.html#a7880d169d8ebf669908ae4262c49c7b8',1,'vg::wang_hash< NodeSide >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html#a7db7a7f185329bda1e74c4fb99e2d7ed',1,'std::hash< vg::NodeSide >::operator()()'],['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html#ae175f5bef4a05d469ebec4341ff47062',1,'vg::wang_hash< NodeTraversal >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html#a0286ba89a52b8479c5bb4f0e474add3e',1,'std::hash< vg::NodeTraversal >::operator()()'],['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html#a14d9633d19737075532f81dc0a97cb0c',1,'vg::wang_hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html#a16e12560069fba289b6e248fb1534347',1,'std::hash< const vg::Snarl >::operator()()'],['../classvg_1_1uniform__real__distribution.html#a2943db49f42d531d7358b64dbbd87d66',1,'vg::uniform_real_distribution::operator()()'],['../classvg_1_1normal__distribution.html#a022c67bb09abf48906156257c76f0ce0',1,'vg::normal_distribution::operator()()'],['../classvg_1_1truncated__normal__distribution.html#a594bdf20c6d6ce7088dde9b1bdb8ae16',1,'vg::truncated_normal_distribution::operator()()'],['../classvg_1_1WideningPRNG.html#a6d58ed2b6a9704e40e751974d5f77927',1,'vg::WideningPRNG::operator()()'],['../classvg_1_1uniform__int__distribution.html#a51f168ff739db2810fc443c8a17a7981',1,'vg::uniform_int_distribution::operator()()'],['../classvg_1_1discrete__distribution.html#a9f9d62f067a25f9a996367d6d187638b',1,'vg::discrete_distribution::operator()()'],['../structvg_1_1MappingHash.html#ab4877c05349b1d70a4fc9fc1d91bfabf',1,'vg::MappingHash::operator()()'],['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html#a5593776feee196b357efe27af34375dd',1,'vg::NestedCachedPackedTraversalSupportFinder::snarl_less::operator()()'],['../classvg_1_1LazyRNG.html#a76642be6e0b23e61b217e22256faccce',1,'vg::LazyRNG::operator()()'],['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html#a43c26f94ae3a429cd5f02e164fbc8893',1,'vg::wang_hash< net_identifier_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html#a267e3d69b89d37dbfc9d6aee50403bfe',1,'std::hash< vg::ZipCodeTree::oriented_seed_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html#a2db521dc14ad90c29f532932a2cb116f',1,'std::hash< vg::ZipCodeTree::seed_result_t >::operator()()'],['../structcompare__gaf.html#abd0df39e112998e5f3cd4e8fc145454c',1,'compare_gaf::operator()()'],['../structgreater__gaffile.html#af92140ef197df65a58d0687a93f4194e',1,'greater_gaffile::operator()()'],['../classvg_1_1subcommand_1_1Subcommand.html#a2a236ec06c3d6d7ff148712a2ae2e492',1,'vg::subcommand::Subcommand::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html#a825db1e0338e86d296b57cd96a8e0899',1,'std::hash< handlegraph::handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html#a6ad769a3d7b2f71b5696eb33bc977d76',1,'std::hash< handlegraph::path_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html#a4dfc6072381e899f6771b7fef4a1df96',1,'std::hash< handlegraph::step_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html#a9530041f163d977cee6147e78e7f3458',1,'std::hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html#ae02ac63af6a68ca8788a3d16e0d282dc',1,'std::hash< handlegraph::edge_t >::operator()()']]],
- ['operator_2a_10247',['operator*',['../classvg_1_1ShuffledPairs_1_1iterator.html#a7a364e5a3933631209f6356bcbab4195',1,'vg::ShuffledPairs::iterator::operator*()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a6f0c09512af20809ebd66342e0b48e72',1,'vg::PhasedGenome::iterator::operator*()'],['../structvg_1_1ChainIterator.html#a4026eb3698271db72e04c8bf189a7638',1,'vg::ChainIterator::operator*()'],['../classvg_1_1count__back__inserter.html#a23ab94b37972f651d60dc06aea28f567',1,'vg::count_back_inserter::operator*()'],['../structvg_1_1VectorView_1_1const__iterator.html#a6c46dcd71c5b170627061551c7ce0755',1,'vg::VectorView::const_iterator::operator*()'],['../structvg_1_1IncrementIter.html#a5a174a8f85492d7242b52cf1531d50e1',1,'vg::IncrementIter::operator*()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aabf844f9503fb882498e9ad7348644c0',1,'vg::ZipCodeTree::iterator::operator*()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a952c338af40fc2b3c6ab3dda1e36991a',1,'vg::ZipCodeTree::reverse_iterator::operator*()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a9e1c7bf243cdf38e9844e6e253b4f48e',1,'handlegraph::PathForEachSocket::iterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#af9bd6f7d8acd6b65d86ace13aae12a49',1,'vg::io::MessageIterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#a1bde69631cd194d596192908e5a70f0a',1,'vg::io::MessageIterator::operator*() const'],['../classvg_1_1io_1_1ProtobufIterator.html#ab75942ce88acea7c4766895033c51c6f',1,'vg::io::ProtobufIterator::operator*()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6df5500c6398933f60d761188c68895b',1,'vg::io::ProtobufIterator::operator*() const'],['../namespacevg.html#a84dfc966c7511b05c234d215e3b6aec7',1,'vg::operator*(const Support &support, const Scalar &scale)'],['../namespacevg.html#a10844a7c14d7ff54051bad20c75d012e',1,'vg::operator*(const Scalar &scale, const Support &support)']]],
- ['operator_2a_3d_10248',['operator*=',['../namespacevg.html#abe7831ba6fe294e8be36fa0359a63848',1,'vg']]],
- ['operator_2b_10249',['operator+',['../structvg_1_1VectorView_1_1const__iterator.html#aa97c1950851a2eb9d5731c12340b81ff',1,'vg::VectorView::const_iterator::operator+()'],['../namespacevg.html#a27dd5c8f7c6d984a396665cbab5eba01',1,'vg::operator+(const Support &one, const Support &other)'],['../namespacevg.html#a64380ba1816d3fd97847a6dc6b2665d8',1,'vg::operator+(typename VectorView< Item >::const_iterator::difference_type a, const typename VectorView< Item >::const_iterator &b)']]],
- ['operator_2b_2b_10250',['operator++',['../classvg_1_1ShuffledPairs_1_1iterator.html#a1b39b43991061c9b38c0f66be116aa07',1,'vg::ShuffledPairs::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ae7af24b8cfca1872c3b7ecd34cc691b4',1,'vg::PhasedGenome::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a5d6220ad0e3ce9c6fad9c7bd33cd10c2',1,'vg::PhasedGenome::iterator::operator++(int)'],['../structvg_1_1ChainIterator.html#a93335ca3360cd50d0561ad1d4691d017',1,'vg::ChainIterator::operator++()'],['../classvg_1_1count__back__inserter.html#a58b46f86e84878928184f16cd71d2025',1,'vg::count_back_inserter::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab5b2928f08fa931ca8a3da78b9a6e540',1,'vg::VectorView::const_iterator::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#aadee453c16ff3359ea59c37123b1a684',1,'vg::VectorView::const_iterator::operator++(int)'],['../structvg_1_1IncrementIter.html#aa6e20c55ec21957277f5cf07d13ad04d',1,'vg::IncrementIter::operator++()'],['../structvg_1_1IncrementIter.html#a3e40dfadfa140aa600d2bc98ad7a7f90',1,'vg::IncrementIter::operator++(int)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a4fc98efef75fa50606213903af2ec146',1,'vg::ZipCodeTree::iterator::operator++()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa47b19eb964a614f69c6dc2326ed6c83',1,'vg::ZipCodeTree::reverse_iterator::operator++()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#abf9ece90b8080b6f93cbfc516777eac2',1,'handlegraph::PathForEachSocket::iterator::operator++()'],['../classvg_1_1io_1_1MessageIterator.html#a89872d57d9e7d9e49f38b6700e40c99d',1,'vg::io::MessageIterator::operator++()'],['../classvg_1_1io_1_1ProtobufIterator.html#a513fd9e86996eda664b8e5eef5d532e9',1,'vg::io::ProtobufIterator::operator++()']]],
- ['operator_2b_3d_10251',['operator+=',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a54b9cf8b8a2f6c13c1dfce6e73c203e8',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const double &value)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#aff1c525641da64850545049b20a485fb',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const stat_collection_t &other)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a180b0b1ea0fd2c5a3a2c1a1aa2cbbc94',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t::operator+=()'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af3eb35c3215c0b4cdd6628bcfc896c71',1,'vg::MinimizerMapper::aligner_stats_t::operator+=()'],['../structvg_1_1Counts.html#a0bfb40ac3e3eafe2606af33f8c4fde06',1,'vg::Counts::operator+=()'],['../structvg_1_1VectorView_1_1const__iterator.html#ac0ff4c93cb85429b2436b93a0500ab8c',1,'vg::VectorView::const_iterator::operator+=()'],['../namespacevg.html#a4f550213560bfa3c3ad8446478be24d8',1,'vg::operator+=()']]],
- ['operator_2d_10252',['operator-',['../structvg_1_1VectorView_1_1const__iterator.html#a5950d800357a74c5df1a46f3fee1e690',1,'vg::VectorView::const_iterator::operator-(const difference_type &difference) const'],['../structvg_1_1VectorView_1_1const__iterator.html#a6ca91702bea775756791a2505fec98a4',1,'vg::VectorView::const_iterator::operator-(const const_iterator &other) const'],['../classvg_1_1algorithms_1_1TracedScore.html#ade52d5662380757204b3a9eb7e632b5f',1,'vg::algorithms::TracedScore::operator-()']]],
- ['operator_2d_2d_10253',['operator--',['../structvg_1_1VectorView_1_1const__iterator.html#a3f07387c29c6f82c4cb7aa6102e2ff83',1,'vg::VectorView::const_iterator::operator--()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab04cc90a3cb13d7e5a08d51be8cadf0c',1,'vg::VectorView::const_iterator::operator--(int)']]],
- ['operator_2d_3d_10254',['operator-=',['../structvg_1_1VectorView_1_1const__iterator.html#a5da176cea2552046f8080d5be2dc67f7',1,'vg::VectorView::const_iterator']]],
- ['operator_2d_3e_10255',['operator->',['../structvg_1_1ChainIterator.html#a2e521810ed86af3b3bfcbd47285236bb',1,'vg::ChainIterator::operator->()'],['../structvg_1_1VectorView_1_1const__iterator.html#a4029e7dd6c859ed5019bb9169211e235',1,'vg::VectorView::const_iterator::operator->()']]],
- ['operator_2f_10256',['operator/',['../namespacevg.html#a5a9eefddbec41755309a378fb150071c',1,'vg']]],
- ['operator_2f_3d_10257',['operator/=',['../namespacevg.html#a1807752a0b6b83fd5952d36cc64b758d',1,'vg']]],
- ['operator_3c_10258',['operator<',['../structvg_1_1MatchPos.html#a91c8cec7a4cf39616157279004751d56',1,'vg::MatchPos::operator<()'],['../structvg_1_1WFAPoint.html#a4c1eb3733361639c504e79502946747a',1,'vg::WFAPoint::operator<()'],['../structvg_1_1GaplessExtension.html#a60ac9a1eba5b7ca5a0bd1f196a8dc94d',1,'vg::GaplessExtension::operator<()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a94ddd290e4408f2a758083d2022b6c46',1,'vg::MinimizerMapper::Minimizer::operator<()'],['../classvg_1_1NodeSide.html#aa567438110aee30bceb1c00a2c6d4eec',1,'vg::NodeSide::operator<()'],['../classvg_1_1NodeTraversal.html#aaf0141ddf2587f8284bd4c111d6cdff2',1,'vg::NodeTraversal::operator<()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4e460a44f0c5027a3864e5b1b65beee8',1,'vg::algorithms::TracedScore::operator<()'],['../structjob__type.html#aed73e63d2b1d652b075a3346c5f36335',1,'job_type::operator<()'],['../namespacevg.html#ab554a977204c1f756bd0e2738a797447',1,'vg::operator<(const Support &a, const Support &b)'],['../namespacevg.html#ac476fcc21a47f34d00b4a449b28c686b',1,'vg::operator<(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a9d2e2066b3b4534b62cde6e4423efd81',1,'vg::operator<(const Visit &a, const Visit &b)'],['../namespacevg.html#aea87c61d2cc1d5acf1af1d2d351bdb75',1,'vg::operator<(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a0fd908e60f72bd98dcba364a16ab7190',1,'vg::operator<(const Snarl &a, const Snarl &b)'],['../namespacevg.html#ad29d63c9b09132ab0457b3d28ea704ff',1,'vg::operator<(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ad3728100975bea667f2f60fdc1df2dd1',1,'vg::operator<(const Transcript &lhs, const Transcript &rhs)'],['../namespacehandlegraph.html#a3e16d241ab6863b8954754d42c9a0764',1,'handlegraph::operator<(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#abe4f45c9fe64c8cf37fe277b870cf56b',1,'handlegraph::operator<(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a8fc5f1eb104107d55fb043c2a24321aa',1,'handlegraph::operator<(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a926cfa5c0852fd9dfe7685d6eec73fe9',1,'handlegraph::operator<(const net_handle_t &a, const net_handle_t &b)']]],
- ['operator_3c_3c_10259',['operator<<',['../namespacevg.html#a7cc9c4d4d792e1e7f38c2c6009207706',1,'vg::operator<<(ostream &out, const BenchmarkResult &result)'],['../namespacevg.html#a3caa19999a88016c7aedf3fefb8ca69c',1,'vg::operator<<(std::ostream &out, const Funnel::State &state)'],['../namespacevg.html#a1fbb5dfd532a055d9e8251d2dcab3e58',1,'vg::operator<<(std::ostream &out, const WFAAlignment::Edit &edit)'],['../namespacevg.html#a141fbf9c40f389909c5c46132ab6c615',1,'vg::operator<<(ostream &stream, const Support &support)'],['../namespacevg.html#a0e459d4a7dda13edf5b79ea8996cfd82',1,'vg::operator<<(ostream &out, const kmer_t &kmer)'],['../namespacevg.html#af0a4b11db620d43a7e20886d5563e5b8',1,'vg::operator<<(ostream &out, const MaximalExactMatch &mem)'],['../namespacevg.html#a9b4bea48392e7bb9e745b3b04e5bf223',1,'vg::operator<<(ostream &out, const NodeSide &nodeside)'],['../namespacevg.html#ad1bdeb550c6f5fa632ad61454321e001',1,'vg::operator<<(ostream &out, const NodeTraversal &nodetraversal)'],['../namespacevg.html#a81357f8477c9ed2c3839489e0ada1ced',1,'vg::operator<<(ostream &out, mapping_t mapping)'],['../namespacevg.html#a1e7a5fc9017560cc1b505641cc4ef6d0',1,'vg::operator<<(std::ostream &out, PathBranch branch)'],['../namespacevg.html#a35d8d71a9d6d51760cc7354910d029e9',1,'vg::operator<<(ostream &os, const Counts &counts)'],['../namespacevg.html#ab38d6991537581f9ce3f4c549f966a33',1,'vg::operator<<(ostream &out, const Visit &visit)'],['../namespacevg.html#ae0744fdee12e0f4136de643a91c15f77',1,'vg::operator<<(ostream &out, const Snarl &snarl)'],['../namespacevg.html#ac5fc02ee1a5713060cd5f4b33e2eaaab',1,'vg::operator<<(ostream &out, const BitString &bs)'],['../namespacevg.html#a19349c6c73bac7da9651ee91c4272156',1,'vg::operator<<(std::ostream &out, const pos_t &pos)'],['../namespacevg.html#a848f547eaaa9c1ec84809d5ad3bd6871',1,'vg::operator<<(std::ostream &out, const ZipCode &zip)'],['../namespacevg.html#a796e339855648a7b8bdee41619eed23b',1,'vg::operator<<(std::ostream &out, const ZipCode::code_type_t &type)'],['../namespacevg.html#afacdb481e4a38366ce65c39efcb5af49',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::tree_item_type_t &type)'],['../namespacevg.html#a047b1758c707866aceb6c39b2503d5c6',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::reverse_iterator::State &state)'],['../namespacevg_1_1algorithms.html#aafbc78daa41b0c018cd39b7cccbaf53a',1,'vg::algorithms::operator<<(ostream &out, const Anchor &anchor)'],['../namespacevg_1_1algorithms.html#a503ad2215490c5c599530d7331a70120',1,'vg::algorithms::operator<<(ostream &out, const TracedScore &value)'],['../namespacevg_1_1algorithms.html#a3961418e3f3af94c4275118e4693a2fe',1,'vg::algorithms::operator<<(std::ostream &out, const kmer_t &kmer)'],['../namespacevg_1_1algorithms.html#a58ec8c8d09fde1a6e83194ec7126ed4e',1,'vg::algorithms::operator<<(std::ostream &out, const walk_t &walk)'],['../namespacevg_1_1subcommand.html#af9ff4f2d2051fd67f272a581e17dd668',1,'vg::subcommand::operator<<()'],['../namespacexg.html#a72b16c0bf83f5b1d0a1bfd3773d4eb77',1,'xg::operator<<()'],['../namespacegafkluge.html#a226812c098c373a50d825916b4c92a7c',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)'],['../namespacegafkluge.html#a098de1edfb3f22da8638f01e76d9ae2a',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)']]],
- ['operator_3d_10260',['operator=',['../classvg_1_1MEMChainModelVertex.html#a607061ec174e1ea4ed0829c86e1d23de',1,'vg::MEMChainModelVertex::operator=(const MEMChainModelVertex &) &=default'],['../classvg_1_1MEMChainModelVertex.html#ac83963d8e6a0ae78e048910f7441c83a',1,'vg::MEMChainModelVertex::operator=(MEMChainModelVertex &&) &=default'],['../classvg_1_1XdropAligner.html#a5bb2cfcbd85802990c1386827ac98192',1,'vg::XdropAligner::operator=(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a39627c50a6e60a7f065332fbd99fdcba',1,'vg::XdropAligner::operator=(XdropAligner &&other)'],['../classvg_1_1QualAdjXdropAligner.html#ab68a1dff1baf74e2275c5db0c7ac4d39',1,'vg::QualAdjXdropAligner::operator=(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a55c6307a0d16cb7ac32e25f1c4f19e6f',1,'vg::QualAdjXdropAligner::operator=(QualAdjXdropAligner &&other)'],['../classvg_1_1HTSWriter.html#aaa299cc70e86ed6fe1dd1eefef0a23f5',1,'vg::HTSWriter::operator=(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a2ec4df6ab5d9c7d4b1557e9cb04ef30d',1,'vg::HTSWriter::operator=(HTSWriter &&other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#aadcc0b64b3f9178c7e30bb15cccc4e21',1,'vg::HTSAlignmentEmitter::operator=(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a19eafc506789bd80e235ebc63e2bbe7f',1,'vg::HTSAlignmentEmitter::operator=(HTSAlignmentEmitter &&other)=delete'],['../classvg_1_1IndexRegistry.html#a50fcb23d815a8eb3da616c9284157ada',1,'vg::IndexRegistry::operator=(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#a6d96c08dbecf5d59154715bb5010f1f2',1,'vg::IndexRegistry::operator=(IndexRegistry &&other)'],['../structvg_1_1IndexedVG_1_1CacheEntry.html#a6b657674e880f1c5a8026617818f19ed',1,'vg::IndexedVG::CacheEntry::operator=()'],['../classvg_1_1ParallelKFFReader.html#ae7be7ffcc93e64e55d82f9dd4983fc04',1,'vg::ParallelKFFReader::operator=()'],['../classvg_1_1AlignmentChainModelVertex.html#a6f6558dec94cc641a412c130a024a4a2',1,'vg::AlignmentChainModelVertex::operator=(const AlignmentChainModelVertex &) &=default'],['../classvg_1_1AlignmentChainModelVertex.html#af47223eaba279b5018abd209fd9a16e8',1,'vg::AlignmentChainModelVertex::operator=(AlignmentChainModelVertex &&) &=default'],['../classvg_1_1Masker.html#ae04eeec74cbbee249846d138668a2b12',1,'vg::Masker::operator=()'],['../classvg_1_1MaximalExactMatch.html#af5383e1741bfcd3f7a9d41018bc4b7e1',1,'vg::MaximalExactMatch::operator=(const MaximalExactMatch &) &=default'],['../classvg_1_1MaximalExactMatch.html#ab2fbcdac0244023338ff7958a650c8dd',1,'vg::MaximalExactMatch::operator=(MaximalExactMatch &&) &=default'],['../classvg_1_1connection__t.html#a1af38cdb2b71e4ad441e427494c9548f',1,'vg::connection_t::operator=(const connection_t &)=default'],['../classvg_1_1connection__t.html#a9326a4bf2490223f72fbd90ac2805203',1,'vg::connection_t::operator=(connection_t &&)=default'],['../classvg_1_1subpath__t.html#a23ccc424b12615a3121c733470f5329d',1,'vg::subpath_t::operator=(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a3e18ac17337fa05ed3fc58fd69b55589',1,'vg::subpath_t::operator=(subpath_t &&)=default'],['../classvg_1_1multipath__alignment__t.html#aa0528d2e50e3d355b33a4e82f1c4fd3a',1,'vg::multipath_alignment_t::operator=(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ac68c86f5c5ffa82b45aa047f020c8296',1,'vg::multipath_alignment_t::operator=(multipath_alignment_t &&other)'],['../classvg_1_1BaseOption.html#acc23a4aa53f5aadc0524d2b4abc0fe5c',1,'vg::BaseOption::operator=(const BaseOption< Value, Parser > &other)=default'],['../classvg_1_1BaseOption.html#a37b2e13a4c48f8ee49ebc5d034d88ce4',1,'vg::BaseOption::operator=(const Value &other)'],['../classvg_1_1Paths.html#a42b45e7dcb60d7f744566ea2f1e8a6ba',1,'vg::Paths::operator=(const Paths &other)'],['../classvg_1_1Paths.html#a298a38346fff38db91b2a42a56c1b9ea',1,'vg::Paths::operator=(Paths &&other) noexcept'],['../classvg_1_1edit__t.html#ad1c13528b7936c7129ea96a96c6e8671',1,'vg::edit_t::operator=(const edit_t &other)=default'],['../classvg_1_1edit__t.html#a0fc702abc036cbc6448f7129d332082d',1,'vg::edit_t::operator=(edit_t &&other)=default'],['../classvg_1_1path__mapping__t.html#a7e04cd691817a0ba29c45e08caabc1c4',1,'vg::path_mapping_t::operator=(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a572fc6feefb1ca777a6920691d08fb4d',1,'vg::path_mapping_t::operator=(path_mapping_t &&other)=default'],['../classvg_1_1path__t.html#a48b9304e0a7dd08c9593c8cbbcf1954e',1,'vg::path_t::operator=(const path_t &other)=default'],['../classvg_1_1path__t.html#acff4daba9b88bec84475641ebbd07221',1,'vg::path_t::operator=(path_t &&other)=default'],['../classvg_1_1PhasedGenome.html#aa4f75b660fd6b1fe8528a10289621d01',1,'vg::PhasedGenome::operator=(PhasedGenome &&phased_genome)=delete'],['../classvg_1_1PhasedGenome.html#af2bcd75ffe10fee6c1af5456b229c752',1,'vg::PhasedGenome::operator=(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a2802e8904098e873bf6d261dc93bc9ec',1,'vg::PhasedGenome::iterator::operator=()'],['../classvg_1_1position__t.html#a8d39338541d93824d9bc488798e5d0b7',1,'vg::position_t::operator=(const position_t &other)=default'],['../classvg_1_1position__t.html#ae75f741879494ab27fd07a6d3085a8ca',1,'vg::position_t::operator=(position_t &&other)=default'],['../classvg_1_1SmallBitset.html#a2e0933ff70a59061ccb2a20e826364e9',1,'vg::SmallBitset::operator=(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#adb79e0c1d451eb3f54e0051c2c2ede3d',1,'vg::SmallBitset::operator=(SmallBitset &&another)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a8c84bbff732b6fa701659482136d123b',1,'vg::SnarlDistanceIndexClusterer::Seed::operator=()'],['../classvg_1_1SnarlManager.html#a08acef6ec793e011aa7537f9ccb4dcfe',1,'vg::SnarlManager::operator=(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#af6f0f956456ef8ec76616fc47bc74428',1,'vg::SnarlManager::operator=(SnarlManager &&other)=default'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ad230c1701326adfb7d3bbcb57628be43',1,'vg::SnarlManager::SnarlRecord::operator=()'],['../classvg_1_1BitString.html#a0754865910378300b6b17a76df6cfa7b',1,'vg::BitString::operator=(const BitString &other)=default'],['../classvg_1_1BitString.html#ac7bb86ec9ba1b684056abea6da960d73',1,'vg::BitString::operator=(BitString &&other)=default'],['../classvg_1_1StreamIndexBase.html#ab0ac239e55d7748226a6a2d08480e026',1,'vg::StreamIndexBase::operator=()'],['../classvg_1_1count__back__inserter.html#aeb34352656680f80cb53fdec6cd2c554',1,'vg::count_back_inserter::operator=()'],['../structvg_1_1VectorView.html#acd9cb0c00656475140021a97275b66f8',1,'vg::VectorView::operator=(const VectorView &other)=default'],['../structvg_1_1VectorView.html#a4818009b7d0a655c23e8f132c9ba65c5',1,'vg::VectorView::operator=(VectorView &&other)=default'],['../structvg_1_1IncrementIter.html#a985cc14fcad953ece4e532342778929f',1,'vg::IncrementIter::operator=()'],['../classvg_1_1VcfBuffer.html#ae0157d603d27d962a8dbd83d12e0fad6',1,'vg::VcfBuffer::operator=()'],['../classvg_1_1WindowedVcfBuffer.html#ab26fcdb650d9ca250827fa4db733fdd6',1,'vg::WindowedVcfBuffer::operator=()'],['../classvg_1_1VG.html#a46f1fe88897cfe4d62625cffd3db5ebb',1,'vg::VG::operator=(const VG &other)'],['../classvg_1_1VG.html#a3b3efbadb9fd3923bbc7e8f0b73c524f',1,'vg::VG::operator=(VG &&other) noexcept'],['../classvg_1_1Watchdog.html#a05ee3b04abde016d4dad666372a38bbb',1,'vg::Watchdog::operator=(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a46119cc28dee74f545eaa3befa3ff149',1,'vg::Watchdog::operator=(Watchdog &&other)=delete'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a393cad2bfd5329385620d1f8434f1092',1,'vg::ZipCodeTree::iterator::operator=(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a3ad6d9e6a4753a9b15df622ee3ec15ec',1,'vg::ZipCodeTree::iterator::operator=(iterator &&other)=default'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4d35f9d95c053c5941706dd3c02ac8b2',1,'vg::ZipCodeTree::reverse_iterator::operator=(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a6ca3e5d86a90780d082cdb07392096fe',1,'vg::ZipCodeTree::reverse_iterator::operator=(reverse_iterator &&other)'],['../classvg_1_1algorithms_1_1Anchor.html#a8774c392a8da56c5510d47fd418cf696',1,'vg::algorithms::Anchor::operator=(const Anchor &other)=default'],['../classvg_1_1algorithms_1_1Anchor.html#a380a35dbb36f866a533c9b4ee9571850',1,'vg::algorithms::Anchor::operator=(Anchor &&other)=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a6af8d418d16c2e2bdee3389929845669',1,'vg::subcommand::TickChainLink::operator=(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#a367346c43d55fc270b39edf46be3cf29',1,'vg::subcommand::TickChainLink::operator=(TickChainLink &&other)=delete'],['../structvg_1_1Range.html#a4880259b13fcdda9fa55abf2faf6a38c',1,'vg::Range::operator=(const Range &other)'],['../structvg_1_1Range.html#ac25f332d4f29872e1e785317dc35fe00',1,'vg::Range::operator=(Range &&other)'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3d9ea843f0b9e571bd4fe01b27f8c466',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a4c926b0df4f6b70d0b4665aedbd9256c',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &&other)=delete'],['../classxg_1_1XG.html#a5dc0f63bc2e56b29638a7a4fc89bbacb',1,'xg::XG::operator=(const XG &other)=delete'],['../classxg_1_1XG.html#aa06dbf48d0e060ddec20000e4242ed5a',1,'xg::XG::operator=(XG &&other)=delete'],['../classxg_1_1XGPath.html#a2386595dfbd819402d30a76b83b3b65d',1,'xg::XGPath::operator=(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a08310ec2e3e6e968b3d412329a9fc4ad',1,'xg::XGPath::operator=(XGPath &&other)=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a3fd64baf9dcc05eceb2a653b225ed325',1,'handlegraph::PathForEachSocket::iterator::operator=()'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#aaae753008929cd78c3ece15f1e73826d',1,'vg::io::BlockedGzipInputStream::operator=(const BlockedGzipInputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#ab978351afc9df57f66dfcbaf11932c17',1,'vg::io::BlockedGzipInputStream::operator=(BlockedGzipInputStream &&other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a26746003c36d4c51964fe291412c48a0',1,'vg::io::BlockedGzipOutputStream::operator=(const BlockedGzipOutputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae54f16684d6a1f7ea66cf57ab0a481f9',1,'vg::io::BlockedGzipOutputStream::operator=(BlockedGzipOutputStream &&other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a8cc7250b2785917930d88f92d66058cb',1,'vg::io::MessageEmitter::operator=(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a7c0f2a53bd5e382b5543eb5ccf7acb3b',1,'vg::io::MessageEmitter::operator=(MessageEmitter &&other)=default'],['../classvg_1_1io_1_1ProtobufEmitter.html#ad81cc27d627747dc34683bb2e0500ff6',1,'vg::io::ProtobufEmitter::operator=(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#a7d4c3a9c587971479a5b9a2a6c50db74',1,'vg::io::ProtobufEmitter::operator=(ProtobufEmitter &&other)=default'],['../classvg_1_1io_1_1StreamMultiplexer.html#af986451d89174a2947be32aaefba6f94',1,'vg::io::StreamMultiplexer::operator=(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#aa0426a0e605e8375e1716dfb28b6482e',1,'vg::io::StreamMultiplexer::operator=(StreamMultiplexer &&other)=delete']]],
- ['operator_3d_3d_10261',['operator==',['../classvg_1_1ShuffledPairs_1_1iterator.html#a35842cde2d948d93e9919b267410a8da',1,'vg::ShuffledPairs::iterator::operator==()'],['../structvg_1_1GaplessExtension.html#af2acf967c1b81204f8f5cea754ae1ae1',1,'vg::GaplessExtension::operator==()'],['../structvg_1_1read__alignment__index__t.html#a194c254826c92dcbf90f2d08fb805245',1,'vg::read_alignment_index_t::operator==()'],['../structvg_1_1alignment__index__t.html#aca2a478078ae34cef69bd3ba0e404a08',1,'vg::alignment_index_t::operator==()'],['../classvg_1_1NodeSide.html#af011a5aeaffe705507a89ed91032ad3e',1,'vg::NodeSide::operator==()'],['../classvg_1_1NodeTraversal.html#a07c1f0b8bdc0c6b851f158e0a1cbd5b5',1,'vg::NodeTraversal::operator==()'],['../classvg_1_1edit__t.html#a2ea672c3e9e8a4a4c2332d117bf85461',1,'vg::edit_t::operator==()'],['../classvg_1_1path__mapping__t.html#a40d364000efb3da1660dede1c3762d65',1,'vg::path_mapping_t::operator==()'],['../classvg_1_1path__t.html#a1aadea895d6ca0a94f5f038809308ef9',1,'vg::path_t::operator==()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0a2ad098ff6d931f04fee951eb50b80a',1,'vg::PhasedGenome::iterator::operator==()'],['../classvg_1_1position__t.html#ad53946ea84a94a664810e7bd67689f3c',1,'vg::position_t::operator==()'],['../structvg_1_1ChainIterator.html#a87ca4ac16d01af9741d45c5c7f391c2c',1,'vg::ChainIterator::operator==()'],['../classvg_1_1BitString.html#a0e19002b533b25e6258ae9e2b7b6bd4e',1,'vg::BitString::operator==()'],['../structvg_1_1VectorView_1_1const__iterator.html#a10426612008a0eb5a74ed91193ecbb96',1,'vg::VectorView::const_iterator::operator==()'],['../structvg_1_1IncrementIter.html#ae67e82103cdee625555eced2c8f51d69',1,'vg::IncrementIter::operator==()'],['../structvg_1_1varint__vector__t.html#ada0c0ea0373d2eb784f4c8459153701f',1,'vg::varint_vector_t::operator==()'],['../classvg_1_1ZipCode.html#a0b983931fc8219fafc6cde9357b553b0',1,'vg::ZipCode::operator==()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a09179a35995161986e2a2db97f5f59c1',1,'vg::ZipCode::decoder_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a4483a326cb25512a552a1594232d3fdd',1,'vg::ZipCodeTree::oriented_seed_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#a015179ff6e9a5e02cc9dfe4af73ff32e',1,'vg::ZipCodeTree::seed_result_t::operator==()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a431bbe58e47281666f1bbd7d0db511a2',1,'vg::ZipCodeTree::iterator::operator==()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ab8ad33ac681c64fafec59409e1fcdce1',1,'vg::ZipCodeTree::reverse_iterator::operator==()'],['../classvg_1_1algorithms_1_1TracedScore.html#af8d42e525e16257aa99b6965a6d6ad4c',1,'vg::algorithms::TracedScore::operator==()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aaa1690bd6bf9f463589b8c953940741c',1,'handlegraph::PathForEachSocket::iterator::operator==()'],['../classvg_1_1io_1_1MessageIterator.html#a870adfdc044f57202d26d5fb2109b425',1,'vg::io::MessageIterator::operator==()'],['../classvg_1_1io_1_1ProtobufIterator.html#ad57a7afe6c7759074d1c9ffd3c31a4e0',1,'vg::io::ProtobufIterator::operator==()'],['../namespacevg.html#af94d73312bfd787493e87d207398d73a',1,'vg::operator==(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a87b890a4bc73725bbea08984d7510df4',1,'vg::operator==(const Visit &a, const Visit &b)'],['../namespacevg.html#a845213e6efb7204868c05afcae9c926f',1,'vg::operator==(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a387ff1f8cefcf4feb705b0f1225d16c7',1,'vg::operator==(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a6ace94ff076945069d22aa548b6e0bf6',1,'vg::operator==(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ace8e1de0bfe604d8da5537fd86e251ee',1,'vg::operator==(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a8e2505b73c51b9659c94950d2f283eec',1,'vg::operator==(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a92e719e28c0d3f7d6dfa354824220211',1,'vg::operator==(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#aadbc38098e019cace58583b35000d19f',1,'handlegraph::operator==(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a5a7206835ea412fabb928f106b291349',1,'handlegraph::operator==(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a4e83573fadcc147c475d0a7678ffbe98',1,'handlegraph::operator==(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a3b87d2ae8d5a93f67ddacb95a5fd791f',1,'handlegraph::operator==(const net_handle_t &a, const net_handle_t &b)'],['../namespacevg_1_1io.html#a05438ce01e149360e263cb83346a5261',1,'vg::io::operator==()']]],
- ['operator_3e_10262',['operator>',['../classvg_1_1algorithms_1_1TracedScore.html#ad7b72c45ce0349b96aae49d2a1cc8eec',1,'vg::algorithms::TracedScore::operator>()'],['../namespacevg.html#a955d56fb4c95213de77c1fcce44c77b8',1,'vg::operator>()']]],
- ['operator_5b_5d_10263',['operator[]',['../structhaplo_1_1gbwt__thread__t.html#a9dd1cb0268973121f00304ae34c7688d',1,'haplo::gbwt_thread_t::operator[](size_t i)'],['../structhaplo_1_1gbwt__thread__t.html#a0ebbbd89e60564e347b1bc441230786c',1,'haplo::gbwt_thread_t::operator[](size_t i) const'],['../structvg_1_1VectorView.html#aa89f493da3bd725632dd1dfb02479c0d',1,'vg::VectorView::operator[]()'],['../classvg_1_1VectorViewInverse.html#a6943170a05ddc962f61fa7ab4fed926d',1,'vg::VectorViewInverse::operator[]()']]],
- ['operator_7c_3d_10264',['operator|=',['../classvg_1_1SmallBitset.html#a541303f562fa1579b94ceda2eda95927',1,'vg::SmallBitset']]],
- ['optimal_5falignment_10265',['optimal_alignment',['../namespacevg.html#a4e3c0f0d0f60a6a6ef1c301b63e9a21e',1,'vg']]],
- ['optimal_5falignment_5finternal_10266',['optimal_alignment_internal',['../namespacevg.html#a3caee9d564f3a803a6ad69642269c5b6',1,'vg']]],
- ['optimal_5falignment_5fscore_10267',['optimal_alignment_score',['../namespacevg.html#ad3548ef9766130a155ba65420c0e7c0e',1,'vg']]],
- ['optimal_5falignments_10268',['optimal_alignments',['../namespacevg.html#ada4d6b6771c5d7e5b2367b18ca8f76f3',1,'vg']]],
- ['optimal_5falignments_5fwith_5fdisjoint_5fsubpaths_10269',['optimal_alignments_with_disjoint_subpaths',['../namespacevg.html#af711577f7d293ffc1c8002c868081bb1',1,'vg']]],
- ['optimal_5fscore_5fon_5fgenome_10270',['optimal_score_on_genome',['../classvg_1_1PhasedGenome.html#a4f8838611a252e9a574a33af3965ad4c',1,'vg::PhasedGenome']]],
- ['optimize_10271',['optimize',['../classvg_1_1VG.html#a0b4fa1970f08f3e4d0cf2f8c33a967a5',1,'vg::VG::optimize()'],['../classhandlegraph_1_1MutableHandleGraph.html#a195c81fa446b62d94fda8841eaa3bb85',1,'handlegraph::MutableHandleGraph::optimize()']]],
- ['option_10272',['Option',['../classvg_1_1Option.html#a636f83c45d4a863e53dcb2f9d1d753aa',1,'vg::Option::Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#aa01cfc188e53cf0fb37a6ccc9b4b0043',1,'vg::Option< vector< Item >, Parser >::Option()']]],
- ['optiongroup_10273',['OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html#a1e4abb9a235dcfe1d50809bbb36b40a8',1,'vg::subcommand::OptionGroup']]],
- ['order_5fof_10274',['order_of',['../classvg_1_1IncrementalSubgraph.html#afe160f21d5b4a7964c1bceef47ca54a4',1,'vg::IncrementalSubgraph']]],
- ['orderedgraph_10275',['OrderedGraph',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a321fef7bca4632cec8f2ed02f8294ad8',1,'vg::DozeuInterface::OrderedGraph']]],
- ['orientation_5ffrom_5fold_5fedge_5ftype_10276',['orientation_from_old_edge_type',['../classxg_1_1XG.html#a6383f68a1f2f9150a0649c6db1c43891',1,'xg::XG']]],
- ['oriented_5fdistance_10277',['oriented_distance',['../classvg_1_1OrientedDistanceMeasurer.html#af6551e771deca01e6af9054a1ad3d30e',1,'vg::OrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a8ec77086bfe160d85961a509725b529f',1,'vg::PathOrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a8f8081d5bb9b0f5526935e2691f52dc3',1,'vg::SnarlOrientedDistanceMeasurer::oriented_distance()']]],
- ['oriented_5fmotif_10278',['oriented_motif',['../classvg_1_1SpliceStats.html#a0568cd8d7b986fdd703bd4021dbb41a1',1,'vg::SpliceStats']]],
- ['orienteddistanceclusterer_10279',['OrientedDistanceClusterer',['../classvg_1_1OrientedDistanceClusterer.html#a0bab84127f018db9467240db290113b4',1,'vg::OrientedDistanceClusterer']]],
- ['output_5ffilepath_10280',['output_filepath',['../classvg_1_1IndexingPlan.html#a405ede5620e8a7263fbb734f656c9971',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier) const'],['../classvg_1_1IndexingPlan.html#a5ef2f8275a2f997e94d178089107502a',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier, size_t chunk, size_t num_chunks) const']]],
- ['output_5fgraph_5fwith_5fembedded_5fpaths_10281',['output_graph_with_embedded_paths',['../namespacevg.html#ae62ff63e415416fd298c6f59c8f2da47',1,'vg::output_graph_with_embedded_paths(vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source)'],['../namespacevg.html#a134ccba76916d6d94e59581932f1b595',1,'vg::output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json)']]],
- ['output_5fhaplotype_5fcounts_10282',['output_haplotype_counts',['../namespacevg.html#ae2d79bdac899f70214959ef92dbbad2f',1,'vg']]],
- ['output_5fwabbit_5fmap_10283',['output_wabbit_map',['../classVectorizer.html#a788aaec704ce78d29f55459ff2eaedb4',1,'Vectorizer']]],
- ['outputstream_10284',['outputStream',['../namespacevg_1_1io.html#a477841175891d3e770995307eea45f38',1,'vg::io']]],
- ['over_5fdirected_5fedge_10285',['over_directed_edge',['../classvg_1_1Paths.html#a8d1fde70db5d5c4d1e26821d4f03ba7a',1,'vg::Paths']]],
- ['over_5fedge_10286',['over_edge',['../classvg_1_1Paths.html#ae7cd0d9291a31a63aa80e9d4d578575e',1,'vg::Paths']]],
- ['overflow_10287',['overflow',['../classvg_1_1io_1_1fdoutbuf.html#aa0b27dbd39a3ad9452f0d4c0d8ca11a1',1,'vg::io::fdoutbuf']]],
- ['overlap_10288',['overlap',['../structvg_1_1BREAKPOINT.html#a8843c2775e6cc15ef2739e13a02b2c86',1,'vg::BREAKPOINT::overlap()'],['../structvg_1_1GaplessExtension.html#ae13cbdb46d6375425a2f82e75daadb66',1,'vg::GaplessExtension::overlap()'],['../namespacevg.html#aaac70d8b120ca61591561cba307dcc1b',1,'vg::overlap()']]],
- ['overlay_10289',['overlay',['../classvg_1_1Translator.html#a91965cec764734c35ace2ecb0c643d5c',1,'vg::Translator']]],
- ['overlay_5fnode_5ftranslations_10290',['overlay_node_translations',['../classvg_1_1VG.html#ae9b314bb2021525e60a0ad23e99fb994',1,'vg::VG::overlay_node_translations()'],['../namespacevg.html#a86d5f690fe272c74949e080aca561467',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#a7816225a17a671ff849a79f064770ebb',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#af224cfdc27efec675771ba4cc5143a3f',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, id_t > &under)'],['../namespacevg.html#ae996017b379b1178d5e588b96a7c7f3f',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, id_t > &under)']]]
+ ['object_5fend_10232',['object_end',['../classvg_1_1ProblemDumpExplainer.html#adb13795992af2eafcbfe0f6716a127f9',1,'vg::ProblemDumpExplainer']]],
+ ['object_5fstart_10233',['object_start',['../classvg_1_1ProblemDumpExplainer.html#a5ebde44f8627a596cdb75267a55f887d',1,'vg::ProblemDumpExplainer']]],
+ ['of_5fnode_10234',['of_node',['../classvg_1_1Paths.html#abda01c563a3455d491b152a23b22a27a',1,'vg::Paths']]],
+ ['offset_10235',['offset',['../classvg_1_1position__t.html#a8de3e2b8d4801ca2951d4c21d57bd404',1,'vg::position_t::offset()'],['../namespacevg.html#ad48a54a3ddd5e6ffd8e3e6296fb9c037',1,'vg::offset()'],['../namespacexg.html#ac689f45eccbedaba6fab410913961f8c',1,'xg::offset()']]],
+ ['offsets_5fin_5fpaths_10236',['offsets_in_paths',['../classxg_1_1XG.html#af77c93c34b8009c590fa4ee2b01fd64e',1,'xg::XG::offsets_in_paths()'],['../namespacevg_1_1algorithms.html#aef24fa77dadb09d5920ec94b88af2128',1,'vg::algorithms::offsets_in_paths()']]],
+ ['on_5fgroup_10237',['on_group',['../classvg_1_1io_1_1MessageEmitter.html#a5b5f11b2f9b08a870fc68a980c91f1e4',1,'vg::io::MessageEmitter::on_group()'],['../classvg_1_1io_1_1ProtobufEmitter.html#af22328bc428af2be817a7a0d097ca370',1,'vg::io::ProtobufEmitter::on_group()']]],
+ ['on_5fmessage_10238',['on_message',['../classvg_1_1io_1_1ProtobufEmitter.html#a6a3a16550dcd7dd7a320109125d4e2a1',1,'vg::io::ProtobufEmitter']]],
+ ['on_5fpath_5fedit_10239',['on_path_edit',['../classvg_1_1FeatureSet.html#a72b47862b3121905222f7662c4ff65ca',1,'vg::FeatureSet']]],
+ ['one_5fend_5fanchored_5ffilter_10240',['one_end_anchored_filter',['../classvg_1_1Filter.html#adf0ea872057dafedc321b256ec072b8c',1,'vg::Filter']]],
+ ['open_5fall_10241',['open_all',['../classvg_1_1StreamSorter.html#a112c5a39918bb37f4aa3bf1413d31b37',1,'vg::StreamSorter']]],
+ ['open_5fchain_10242',['open_chain',['../classvg_1_1ZipCodeForest.html#a56fb93ecb975f5f6c12deeef5b1f9b20',1,'vg::ZipCodeForest']]],
+ ['open_5ffd_10243',['open_fd',['../classhandlegraph_1_1TriviallySerializable.html#aa1f5b9cdb957540dfea7e0e4b478e9b2',1,'handlegraph::TriviallySerializable']]],
+ ['open_5fsnarl_10244',['open_snarl',['../classvg_1_1ZipCodeForest.html#ab219e010a4e80804f7c5f6ada581f18d',1,'vg::ZipCodeForest']]],
+ ['operator_20bool_10245',['operator bool',['../structvg_1_1AlignmentValidity.html#a2f6b53f193bad40111118e3293ad361c',1,'vg::AlignmentValidity::operator bool()'],['../classvg_1_1Explainer.html#aeca40f040dd309c5f457e8ea0bd8627f',1,'vg::Explainer::operator bool()'],['../structvg_1_1WFAAlignment.html#a7f1464e6b2a86671cdf376137409eeeb',1,'vg::WFAAlignment::operator bool()']]],
+ ['operator_20number_10246',['operator Number',['../structvg_1_1Range.html#acb0f6ebb720df6227410bf9403079a32',1,'vg::Range']]],
+ ['operator_20value_20_26_10247',['operator Value &',['../classvg_1_1BaseOption.html#a760720e496d3058589d34d823f61566b',1,'vg::BaseOption']]],
+ ['operator_21_3d_10248',['operator!=',['../classvg_1_1ShuffledPairs_1_1iterator.html#a2714f2334dae600fc66c3508ecd4494a',1,'vg::ShuffledPairs::iterator::operator!=()'],['../structvg_1_1GaplessExtension.html#a5fc94cd2cfd5898459cac75c65be55a5',1,'vg::GaplessExtension::operator!=()'],['../structvg_1_1read__alignment__index__t.html#ac967a7e4d2339bf2ab83208991b0ce69',1,'vg::read_alignment_index_t::operator!=()'],['../structvg_1_1alignment__index__t.html#ab09e271d0c6eb6f08fd1bde411c6c5f7',1,'vg::alignment_index_t::operator!=()'],['../classvg_1_1NodeSide.html#a48481b0155b782c27644080c98d20656',1,'vg::NodeSide::operator!=()'],['../classvg_1_1NodeTraversal.html#aaa81c382e219ed6f832b1401872fe898',1,'vg::NodeTraversal::operator!=()'],['../classvg_1_1edit__t.html#ac6b81fe1407a1ae901f72ed555a30dae',1,'vg::edit_t::operator!=()'],['../classvg_1_1path__mapping__t.html#a78466c5a9e83d7367bd70799dfd4a76b',1,'vg::path_mapping_t::operator!=()'],['../classvg_1_1path__t.html#a5a0f6368c497cfe5eac4025080c20bc1',1,'vg::path_t::operator!=()'],['../classvg_1_1PhasedGenome_1_1iterator.html#aff3ae0b92ca06496a22d1aad89016737',1,'vg::PhasedGenome::iterator::operator!=()'],['../classvg_1_1position__t.html#a9011acaf2ade42c99a74596214196fa8',1,'vg::position_t::operator!=()'],['../structvg_1_1ChainIterator.html#aec215507b5b43e388afb2933d25c21d0',1,'vg::ChainIterator::operator!=()'],['../classvg_1_1BitString.html#a57b03c3b055ab267c199bd429ff5e4c6',1,'vg::BitString::operator!=()'],['../structvg_1_1VectorView_1_1const__iterator.html#a620b2bd9b99aff0ab077ce6d9441b684',1,'vg::VectorView::const_iterator::operator!=()'],['../structvg_1_1IncrementIter.html#a97c041dbf0473d997321d19072fe85e6',1,'vg::IncrementIter::operator!=()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#aced4d93ad8d1fb3b5b530ff0dd912912',1,'vg::ZipCodeTree::oriented_seed_t::operator!=()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#ac730025c4f3c9144cd742a6c0b15f3d3',1,'vg::ZipCodeTree::seed_result_t::operator!=()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a1eddeaefb5ff95cbde90e0112efa2433',1,'vg::ZipCodeTree::iterator::operator!=()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4925ff71b13d15855904e7e7497b295b',1,'vg::ZipCodeTree::reverse_iterator::operator!=()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4a74c0a77c2df092ecc5d2be1a4b793c',1,'vg::algorithms::TracedScore::operator!=()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a2c24b07521aa704e517c386e1369d227',1,'handlegraph::PathForEachSocket::iterator::operator!=()'],['../classvg_1_1io_1_1MessageIterator.html#ad6a23c45ab954ce158faec0b8935cd90',1,'vg::io::MessageIterator::operator!=()'],['../classvg_1_1io_1_1ProtobufIterator.html#a1f67a6fcda4cfa7d6d1b37bcdb74c0ac',1,'vg::io::ProtobufIterator::operator!=()'],['../namespacevg.html#abb6063b76b70947010198b46c053b578',1,'vg::operator!=(const Visit &a, const Visit &b)'],['../namespacevg.html#a24e1e38ea29c615b2c5f5cd8dbaeeb2a',1,'vg::operator!=(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a654eca8448629e42ae87cadd893ee10e',1,'vg::operator!=(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a22cb5c700c1dee4fec8d3af77057ea2a',1,'vg::operator!=(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#a4f594795be32cb04b7baf0ef71ad77b0',1,'vg::operator!=(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a581944f1e71285f8c4887c2f5ce1467f',1,'vg::operator!=(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a67115fb742d1bf6d7e4e489fda99b78e',1,'vg::operator!=(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#a913cf04aa9946eebf68cc319d7929f11',1,'handlegraph::operator!=(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a18f417ab023834f355f735c2baa18324',1,'handlegraph::operator!=(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#acbbe7b08c190039a0a3700e078818aa5',1,'handlegraph::operator!=(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#acc5274f38cf004b29d2bf398a96f4da5',1,'handlegraph::operator!=(const net_handle_t &a, const net_handle_t &b)']]],
+ ['operator_26_3d_10249',['operator&=',['../classvg_1_1SmallBitset.html#a44c58c409898c13b98b3937669bf7b8f',1,'vg::SmallBitset']]],
+ ['operator_28_29_10250',['operator()',['../structvg_1_1BBEdgeHash.html#af0c713bc536e343b416520dd0f14732b',1,'vg::BBEdgeHash::operator()()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a748c3131cdb69751197546f36a1298bb',1,'vg::MEMClusterer::DPScoreComparator::operator()()'],['../classvg_1_1DistanceHeuristic.html#afb17aa7db222de3ef43a70115c7eec6a',1,'vg::DistanceHeuristic::operator()()'],['../classvg_1_1SnarlMinDistance.html#a4a87d093a5ee90f158ce5e5a1fdc8fd4',1,'vg::SnarlMinDistance::operator()()'],['../classvg_1_1TipAnchoredMaxDistance.html#a165cc0f3d3e70810f72bd7ad49b9416e',1,'vg::TipAnchoredMaxDistance::operator()()'],['../structvg_1_1state__hash.html#a5ddcb7dd42852b3f35fd414663677e8c',1,'vg::state_hash::operator()()'],['../classvg_1_1ReadMasker.html#a8d7a36b958e3405106494e93fffcda5f',1,'vg::ReadMasker::operator()()'],['../structvg_1_1Genotyper_1_1hash__node__traversal.html#a62f374bedac308110f484df59f6c905f',1,'vg::Genotyper::hash_node_traversal::operator()()'],['../structvg_1_1Genotyper_1_1hash__oriented__edge.html#a070a16b42f8aeace08dfee4f22badc8d',1,'vg::Genotyper::hash_oriented_edge::operator()()'],['../structvg_1_1Genotyper_1_1hash__ambiguous__allele__set.html#a44aad1a7e112842dc576fd9cbebdbbfc',1,'vg::Genotyper::hash_ambiguous_allele_set::operator()()'],['../structvg_1_1wang__hash_3_01handle__t_01_4.html#a2abb45aa397420108850ce590f7f3bf7',1,'vg::wang_hash< handle_t >::operator()()'],['../structvg_1_1wang__hash_3_01path__handle__t_01_4.html#a5a9ad96629401a307c94b17a2d91fc53',1,'vg::wang_hash< path_handle_t >::operator()()'],['../structstd_1_1hash_3_01pair_3_01A_00_01B_01_4_01_4.html#a847da6dc45718131135dba8e17aa93a6',1,'std::hash< pair< A, B > >::operator()()'],['../structstd_1_1hash_3_01std_1_1tuple_3_01TT_8_8_8_01_4_01_4.html#afdf58525bd44e80be2af8355db0eba2e',1,'std::hash< std::tuple< TT... > >::operator()()'],['../structvg_1_1wang__hash_3_01T_01_5_01_4.html#a55ef00b42c8f6103e78eb7f7b7597984',1,'vg::wang_hash< T * >::operator()()'],['../structvg_1_1wang__hash_3_01T_00_01typename_01std_1_1enable__if_3_01std_1_1is__integral_3_01T_01_4_1_1value_01_4_1_1type_01_4.html#a87443673fa41e2f7a7ee5cf4e2bd533c',1,'vg::wang_hash< T, typename std::enable_if< std::is_integral< T >::value >::type >::operator()()'],['../structvg_1_1wang__hash_3_01std_1_1pair_3_01A_00_01B_01_4_01_4.html#af62856c68653d586e53d842a16e54cf7',1,'vg::wang_hash< std::pair< A, B > >::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1FCmp.html#a65b7021e0e5237b4b7f0fbb34a8f99ec',1,'vg::IncrementalSubgraph::FCmp::operator()()'],['../structvg_1_1IncrementalSubgraph_1_1IterFCmp.html#a9a34770a4c767bf069601106bbdde191',1,'vg::IncrementalSubgraph::IterFCmp::operator()()'],['../structvg_1_1wang__hash_3_01NodeSide_01_4.html#a7880d169d8ebf669908ae4262c49c7b8',1,'vg::wang_hash< NodeSide >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeSide_01_4.html#a7db7a7f185329bda1e74c4fb99e2d7ed',1,'std::hash< vg::NodeSide >::operator()()'],['../structvg_1_1wang__hash_3_01NodeTraversal_01_4.html#ae175f5bef4a05d469ebec4341ff47062',1,'vg::wang_hash< NodeTraversal >::operator()()'],['../structstd_1_1hash_3_01vg_1_1NodeTraversal_01_4.html#a0286ba89a52b8479c5bb4f0e474add3e',1,'std::hash< vg::NodeTraversal >::operator()()'],['../structvg_1_1wang__hash_3_01handlegraph_1_1net__handle__t_01_4.html#a14d9633d19737075532f81dc0a97cb0c',1,'vg::wang_hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01const_01vg_1_1Snarl_01_4.html#a16e12560069fba289b6e248fb1534347',1,'std::hash< const vg::Snarl >::operator()()'],['../classvg_1_1uniform__real__distribution.html#a2943db49f42d531d7358b64dbbd87d66',1,'vg::uniform_real_distribution::operator()()'],['../classvg_1_1normal__distribution.html#a022c67bb09abf48906156257c76f0ce0',1,'vg::normal_distribution::operator()()'],['../classvg_1_1truncated__normal__distribution.html#a594bdf20c6d6ce7088dde9b1bdb8ae16',1,'vg::truncated_normal_distribution::operator()()'],['../classvg_1_1WideningPRNG.html#a6d58ed2b6a9704e40e751974d5f77927',1,'vg::WideningPRNG::operator()()'],['../classvg_1_1uniform__int__distribution.html#a51f168ff739db2810fc443c8a17a7981',1,'vg::uniform_int_distribution::operator()()'],['../classvg_1_1discrete__distribution.html#a9f9d62f067a25f9a996367d6d187638b',1,'vg::discrete_distribution::operator()()'],['../structvg_1_1MappingHash.html#ab4877c05349b1d70a4fc9fc1d91bfabf',1,'vg::MappingHash::operator()()'],['../structvg_1_1NestedCachedPackedTraversalSupportFinder_1_1snarl__less.html#a5593776feee196b357efe27af34375dd',1,'vg::NestedCachedPackedTraversalSupportFinder::snarl_less::operator()()'],['../classvg_1_1LazyRNG.html#a76642be6e0b23e61b217e22256faccce',1,'vg::LazyRNG::operator()()'],['../structvg_1_1wang__hash_3_01net__identifier__t_01_4.html#a43c26f94ae3a429cd5f02e164fbc8893',1,'vg::wang_hash< net_identifier_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1oriented__seed__t_01_4.html#a267e3d69b89d37dbfc9d6aee50403bfe',1,'std::hash< vg::ZipCodeTree::oriented_seed_t >::operator()()'],['../structstd_1_1hash_3_01vg_1_1ZipCodeTree_1_1seed__result__t_01_4.html#a2db521dc14ad90c29f532932a2cb116f',1,'std::hash< vg::ZipCodeTree::seed_result_t >::operator()()'],['../structcompare__gaf.html#abd0df39e112998e5f3cd4e8fc145454c',1,'compare_gaf::operator()()'],['../structgreater__gaffile.html#af92140ef197df65a58d0687a93f4194e',1,'greater_gaffile::operator()()'],['../classvg_1_1subcommand_1_1Subcommand.html#a2a236ec06c3d6d7ff148712a2ae2e492',1,'vg::subcommand::Subcommand::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1handle__t_01_4.html#a825db1e0338e86d296b57cd96a8e0899',1,'std::hash< handlegraph::handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1path__handle__t_01_4.html#a6ad769a3d7b2f71b5696eb33bc977d76',1,'std::hash< handlegraph::path_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1step__handle__t_01_4.html#a4dfc6072381e899f6771b7fef4a1df96',1,'std::hash< handlegraph::step_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1net__handle__t_01_4.html#a9530041f163d977cee6147e78e7f3458',1,'std::hash< handlegraph::net_handle_t >::operator()()'],['../structstd_1_1hash_3_01handlegraph_1_1edge__t_01_4.html#ae02ac63af6a68ca8788a3d16e0d282dc',1,'std::hash< handlegraph::edge_t >::operator()()']]],
+ ['operator_2a_10251',['operator*',['../classvg_1_1ShuffledPairs_1_1iterator.html#a7a364e5a3933631209f6356bcbab4195',1,'vg::ShuffledPairs::iterator::operator*()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a6f0c09512af20809ebd66342e0b48e72',1,'vg::PhasedGenome::iterator::operator*()'],['../structvg_1_1ChainIterator.html#a4026eb3698271db72e04c8bf189a7638',1,'vg::ChainIterator::operator*()'],['../classvg_1_1count__back__inserter.html#a23ab94b37972f651d60dc06aea28f567',1,'vg::count_back_inserter::operator*()'],['../structvg_1_1VectorView_1_1const__iterator.html#a6c46dcd71c5b170627061551c7ce0755',1,'vg::VectorView::const_iterator::operator*()'],['../structvg_1_1IncrementIter.html#a5a174a8f85492d7242b52cf1531d50e1',1,'vg::IncrementIter::operator*()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aabf844f9503fb882498e9ad7348644c0',1,'vg::ZipCodeTree::iterator::operator*()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a952c338af40fc2b3c6ab3dda1e36991a',1,'vg::ZipCodeTree::reverse_iterator::operator*()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a9e1c7bf243cdf38e9844e6e253b4f48e',1,'handlegraph::PathForEachSocket::iterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#af9bd6f7d8acd6b65d86ace13aae12a49',1,'vg::io::MessageIterator::operator*()'],['../classvg_1_1io_1_1MessageIterator.html#a1bde69631cd194d596192908e5a70f0a',1,'vg::io::MessageIterator::operator*() const'],['../classvg_1_1io_1_1ProtobufIterator.html#ab75942ce88acea7c4766895033c51c6f',1,'vg::io::ProtobufIterator::operator*()'],['../classvg_1_1io_1_1ProtobufIterator.html#a6df5500c6398933f60d761188c68895b',1,'vg::io::ProtobufIterator::operator*() const'],['../namespacevg.html#a84dfc966c7511b05c234d215e3b6aec7',1,'vg::operator*(const Support &support, const Scalar &scale)'],['../namespacevg.html#a10844a7c14d7ff54051bad20c75d012e',1,'vg::operator*(const Scalar &scale, const Support &support)']]],
+ ['operator_2a_3d_10252',['operator*=',['../namespacevg.html#abe7831ba6fe294e8be36fa0359a63848',1,'vg']]],
+ ['operator_2b_10253',['operator+',['../structvg_1_1VectorView_1_1const__iterator.html#aa97c1950851a2eb9d5731c12340b81ff',1,'vg::VectorView::const_iterator::operator+()'],['../namespacevg.html#a27dd5c8f7c6d984a396665cbab5eba01',1,'vg::operator+(const Support &one, const Support &other)'],['../namespacevg.html#a64380ba1816d3fd97847a6dc6b2665d8',1,'vg::operator+(typename VectorView< Item >::const_iterator::difference_type a, const typename VectorView< Item >::const_iterator &b)']]],
+ ['operator_2b_2b_10254',['operator++',['../classvg_1_1ShuffledPairs_1_1iterator.html#a1b39b43991061c9b38c0f66be116aa07',1,'vg::ShuffledPairs::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ae7af24b8cfca1872c3b7ecd34cc691b4',1,'vg::PhasedGenome::iterator::operator++()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a5d6220ad0e3ce9c6fad9c7bd33cd10c2',1,'vg::PhasedGenome::iterator::operator++(int)'],['../structvg_1_1ChainIterator.html#a93335ca3360cd50d0561ad1d4691d017',1,'vg::ChainIterator::operator++()'],['../classvg_1_1count__back__inserter.html#a58b46f86e84878928184f16cd71d2025',1,'vg::count_back_inserter::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab5b2928f08fa931ca8a3da78b9a6e540',1,'vg::VectorView::const_iterator::operator++()'],['../structvg_1_1VectorView_1_1const__iterator.html#aadee453c16ff3359ea59c37123b1a684',1,'vg::VectorView::const_iterator::operator++(int)'],['../structvg_1_1IncrementIter.html#aa6e20c55ec21957277f5cf07d13ad04d',1,'vg::IncrementIter::operator++()'],['../structvg_1_1IncrementIter.html#a3e40dfadfa140aa600d2bc98ad7a7f90',1,'vg::IncrementIter::operator++(int)'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a4fc98efef75fa50606213903af2ec146',1,'vg::ZipCodeTree::iterator::operator++()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#aa47b19eb964a614f69c6dc2326ed6c83',1,'vg::ZipCodeTree::reverse_iterator::operator++()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#abf9ece90b8080b6f93cbfc516777eac2',1,'handlegraph::PathForEachSocket::iterator::operator++()'],['../classvg_1_1io_1_1MessageIterator.html#a89872d57d9e7d9e49f38b6700e40c99d',1,'vg::io::MessageIterator::operator++()'],['../classvg_1_1io_1_1ProtobufIterator.html#a513fd9e86996eda664b8e5eef5d532e9',1,'vg::io::ProtobufIterator::operator++()']]],
+ ['operator_2b_3d_10255',['operator+=',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a54b9cf8b8a2f6c13c1dfce6e73c203e8',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const double &value)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#aff1c525641da64850545049b20a485fb',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t::operator+=(const stat_collection_t &other)'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a180b0b1ea0fd2c5a3a2c1a1aa2cbbc94',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t::operator+=()'],['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af3eb35c3215c0b4cdd6628bcfc896c71',1,'vg::MinimizerMapper::aligner_stats_t::operator+=()'],['../structvg_1_1Counts.html#a0bfb40ac3e3eafe2606af33f8c4fde06',1,'vg::Counts::operator+=()'],['../structvg_1_1VectorView_1_1const__iterator.html#ac0ff4c93cb85429b2436b93a0500ab8c',1,'vg::VectorView::const_iterator::operator+=()'],['../namespacevg.html#a4f550213560bfa3c3ad8446478be24d8',1,'vg::operator+=()']]],
+ ['operator_2d_10256',['operator-',['../structvg_1_1VectorView_1_1const__iterator.html#a5950d800357a74c5df1a46f3fee1e690',1,'vg::VectorView::const_iterator::operator-(const difference_type &difference) const'],['../structvg_1_1VectorView_1_1const__iterator.html#a6ca91702bea775756791a2505fec98a4',1,'vg::VectorView::const_iterator::operator-(const const_iterator &other) const'],['../classvg_1_1algorithms_1_1TracedScore.html#ade52d5662380757204b3a9eb7e632b5f',1,'vg::algorithms::TracedScore::operator-()']]],
+ ['operator_2d_2d_10257',['operator--',['../structvg_1_1VectorView_1_1const__iterator.html#a3f07387c29c6f82c4cb7aa6102e2ff83',1,'vg::VectorView::const_iterator::operator--()'],['../structvg_1_1VectorView_1_1const__iterator.html#ab04cc90a3cb13d7e5a08d51be8cadf0c',1,'vg::VectorView::const_iterator::operator--(int)']]],
+ ['operator_2d_3d_10258',['operator-=',['../structvg_1_1VectorView_1_1const__iterator.html#a5da176cea2552046f8080d5be2dc67f7',1,'vg::VectorView::const_iterator']]],
+ ['operator_2d_3e_10259',['operator->',['../structvg_1_1ChainIterator.html#a2e521810ed86af3b3bfcbd47285236bb',1,'vg::ChainIterator::operator->()'],['../structvg_1_1VectorView_1_1const__iterator.html#a4029e7dd6c859ed5019bb9169211e235',1,'vg::VectorView::const_iterator::operator->()']]],
+ ['operator_2f_10260',['operator/',['../namespacevg.html#a5a9eefddbec41755309a378fb150071c',1,'vg']]],
+ ['operator_2f_3d_10261',['operator/=',['../namespacevg.html#a1807752a0b6b83fd5952d36cc64b758d',1,'vg']]],
+ ['operator_3c_10262',['operator<',['../structvg_1_1MatchPos.html#a91c8cec7a4cf39616157279004751d56',1,'vg::MatchPos::operator<()'],['../structvg_1_1WFAPoint.html#a4c1eb3733361639c504e79502946747a',1,'vg::WFAPoint::operator<()'],['../structvg_1_1GaplessExtension.html#a60ac9a1eba5b7ca5a0bd1f196a8dc94d',1,'vg::GaplessExtension::operator<()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a94ddd290e4408f2a758083d2022b6c46',1,'vg::MinimizerMapper::Minimizer::operator<()'],['../classvg_1_1NodeSide.html#aa567438110aee30bceb1c00a2c6d4eec',1,'vg::NodeSide::operator<()'],['../classvg_1_1NodeTraversal.html#aaf0141ddf2587f8284bd4c111d6cdff2',1,'vg::NodeTraversal::operator<()'],['../classvg_1_1algorithms_1_1TracedScore.html#a4e460a44f0c5027a3864e5b1b65beee8',1,'vg::algorithms::TracedScore::operator<()'],['../structjob__type.html#aed73e63d2b1d652b075a3346c5f36335',1,'job_type::operator<()'],['../namespacevg.html#ab554a977204c1f756bd0e2738a797447',1,'vg::operator<(const Support &a, const Support &b)'],['../namespacevg.html#ac476fcc21a47f34d00b4a449b28c686b',1,'vg::operator<(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a9d2e2066b3b4534b62cde6e4423efd81',1,'vg::operator<(const Visit &a, const Visit &b)'],['../namespacevg.html#aea87c61d2cc1d5acf1af1d2d351bdb75',1,'vg::operator<(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a0fd908e60f72bd98dcba364a16ab7190',1,'vg::operator<(const Snarl &a, const Snarl &b)'],['../namespacevg.html#ad29d63c9b09132ab0457b3d28ea704ff',1,'vg::operator<(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ad3728100975bea667f2f60fdc1df2dd1',1,'vg::operator<(const Transcript &lhs, const Transcript &rhs)'],['../namespacehandlegraph.html#a3e16d241ab6863b8954754d42c9a0764',1,'handlegraph::operator<(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#abe4f45c9fe64c8cf37fe277b870cf56b',1,'handlegraph::operator<(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a8fc5f1eb104107d55fb043c2a24321aa',1,'handlegraph::operator<(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a926cfa5c0852fd9dfe7685d6eec73fe9',1,'handlegraph::operator<(const net_handle_t &a, const net_handle_t &b)']]],
+ ['operator_3c_3c_10263',['operator<<',['../namespacevg.html#a7cc9c4d4d792e1e7f38c2c6009207706',1,'vg::operator<<(ostream &out, const BenchmarkResult &result)'],['../namespacevg.html#a3caa19999a88016c7aedf3fefb8ca69c',1,'vg::operator<<(std::ostream &out, const Funnel::State &state)'],['../namespacevg.html#a1fbb5dfd532a055d9e8251d2dcab3e58',1,'vg::operator<<(std::ostream &out, const WFAAlignment::Edit &edit)'],['../namespacevg.html#a141fbf9c40f389909c5c46132ab6c615',1,'vg::operator<<(ostream &stream, const Support &support)'],['../namespacevg.html#a0e459d4a7dda13edf5b79ea8996cfd82',1,'vg::operator<<(ostream &out, const kmer_t &kmer)'],['../namespacevg.html#af0a4b11db620d43a7e20886d5563e5b8',1,'vg::operator<<(ostream &out, const MaximalExactMatch &mem)'],['../namespacevg.html#a9b4bea48392e7bb9e745b3b04e5bf223',1,'vg::operator<<(ostream &out, const NodeSide &nodeside)'],['../namespacevg.html#ad1bdeb550c6f5fa632ad61454321e001',1,'vg::operator<<(ostream &out, const NodeTraversal &nodetraversal)'],['../namespacevg.html#a81357f8477c9ed2c3839489e0ada1ced',1,'vg::operator<<(ostream &out, mapping_t mapping)'],['../namespacevg.html#a1e7a5fc9017560cc1b505641cc4ef6d0',1,'vg::operator<<(std::ostream &out, PathBranch branch)'],['../namespacevg.html#a35d8d71a9d6d51760cc7354910d029e9',1,'vg::operator<<(ostream &os, const Counts &counts)'],['../namespacevg.html#ab38d6991537581f9ce3f4c549f966a33',1,'vg::operator<<(ostream &out, const Visit &visit)'],['../namespacevg.html#ae0744fdee12e0f4136de643a91c15f77',1,'vg::operator<<(ostream &out, const Snarl &snarl)'],['../namespacevg.html#ac5fc02ee1a5713060cd5f4b33e2eaaab',1,'vg::operator<<(ostream &out, const BitString &bs)'],['../namespacevg.html#a19349c6c73bac7da9651ee91c4272156',1,'vg::operator<<(std::ostream &out, const pos_t &pos)'],['../namespacevg.html#a848f547eaaa9c1ec84809d5ad3bd6871',1,'vg::operator<<(std::ostream &out, const ZipCode &zip)'],['../namespacevg.html#a796e339855648a7b8bdee41619eed23b',1,'vg::operator<<(std::ostream &out, const ZipCode::code_type_t &type)'],['../namespacevg.html#afacdb481e4a38366ce65c39efcb5af49',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::tree_item_type_t &type)'],['../namespacevg.html#a047b1758c707866aceb6c39b2503d5c6',1,'vg::operator<<(std::ostream &out, const ZipCodeTree::reverse_iterator::State &state)'],['../namespacevg_1_1algorithms.html#aafbc78daa41b0c018cd39b7cccbaf53a',1,'vg::algorithms::operator<<(ostream &out, const Anchor &anchor)'],['../namespacevg_1_1algorithms.html#a503ad2215490c5c599530d7331a70120',1,'vg::algorithms::operator<<(ostream &out, const TracedScore &value)'],['../namespacevg_1_1algorithms.html#a3961418e3f3af94c4275118e4693a2fe',1,'vg::algorithms::operator<<(std::ostream &out, const kmer_t &kmer)'],['../namespacevg_1_1algorithms.html#a58ec8c8d09fde1a6e83194ec7126ed4e',1,'vg::algorithms::operator<<(std::ostream &out, const walk_t &walk)'],['../namespacevg_1_1subcommand.html#af9ff4f2d2051fd67f272a581e17dd668',1,'vg::subcommand::operator<<()'],['../namespacexg.html#a72b16c0bf83f5b1d0a1bfd3773d4eb77',1,'xg::operator<<()'],['../namespacegafkluge.html#a226812c098c373a50d825916b4c92a7c',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafStep &gaf_step)'],['../namespacegafkluge.html#a098de1edfb3f22da8638f01e76d9ae2a',1,'gafkluge::operator<<(std::ostream &os, const gafkluge::GafRecord &gaf_record)']]],
+ ['operator_3d_10264',['operator=',['../classvg_1_1MEMChainModelVertex.html#a607061ec174e1ea4ed0829c86e1d23de',1,'vg::MEMChainModelVertex::operator=(const MEMChainModelVertex &) &=default'],['../classvg_1_1MEMChainModelVertex.html#ac83963d8e6a0ae78e048910f7441c83a',1,'vg::MEMChainModelVertex::operator=(MEMChainModelVertex &&) &=default'],['../classvg_1_1XdropAligner.html#a5bb2cfcbd85802990c1386827ac98192',1,'vg::XdropAligner::operator=(const XdropAligner &other)'],['../classvg_1_1XdropAligner.html#a39627c50a6e60a7f065332fbd99fdcba',1,'vg::XdropAligner::operator=(XdropAligner &&other)'],['../classvg_1_1QualAdjXdropAligner.html#ab68a1dff1baf74e2275c5db0c7ac4d39',1,'vg::QualAdjXdropAligner::operator=(const QualAdjXdropAligner &other)'],['../classvg_1_1QualAdjXdropAligner.html#a55c6307a0d16cb7ac32e25f1c4f19e6f',1,'vg::QualAdjXdropAligner::operator=(QualAdjXdropAligner &&other)'],['../classvg_1_1HTSWriter.html#aaa299cc70e86ed6fe1dd1eefef0a23f5',1,'vg::HTSWriter::operator=(const HTSWriter &other)=delete'],['../classvg_1_1HTSWriter.html#a2ec4df6ab5d9c7d4b1557e9cb04ef30d',1,'vg::HTSWriter::operator=(HTSWriter &&other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#aadcc0b64b3f9178c7e30bb15cccc4e21',1,'vg::HTSAlignmentEmitter::operator=(const HTSAlignmentEmitter &other)=delete'],['../classvg_1_1HTSAlignmentEmitter.html#a19eafc506789bd80e235ebc63e2bbe7f',1,'vg::HTSAlignmentEmitter::operator=(HTSAlignmentEmitter &&other)=delete'],['../classvg_1_1IndexRegistry.html#a50fcb23d815a8eb3da616c9284157ada',1,'vg::IndexRegistry::operator=(const IndexRegistry &other)=delete'],['../classvg_1_1IndexRegistry.html#a6d96c08dbecf5d59154715bb5010f1f2',1,'vg::IndexRegistry::operator=(IndexRegistry &&other)'],['../structvg_1_1IndexedVG_1_1CacheEntry.html#a6b657674e880f1c5a8026617818f19ed',1,'vg::IndexedVG::CacheEntry::operator=()'],['../classvg_1_1ParallelKFFReader.html#ae7be7ffcc93e64e55d82f9dd4983fc04',1,'vg::ParallelKFFReader::operator=()'],['../classvg_1_1AlignmentChainModelVertex.html#a6f6558dec94cc641a412c130a024a4a2',1,'vg::AlignmentChainModelVertex::operator=(const AlignmentChainModelVertex &) &=default'],['../classvg_1_1AlignmentChainModelVertex.html#af47223eaba279b5018abd209fd9a16e8',1,'vg::AlignmentChainModelVertex::operator=(AlignmentChainModelVertex &&) &=default'],['../classvg_1_1Masker.html#ae04eeec74cbbee249846d138668a2b12',1,'vg::Masker::operator=()'],['../classvg_1_1MaximalExactMatch.html#af5383e1741bfcd3f7a9d41018bc4b7e1',1,'vg::MaximalExactMatch::operator=(const MaximalExactMatch &) &=default'],['../classvg_1_1MaximalExactMatch.html#ab2fbcdac0244023338ff7958a650c8dd',1,'vg::MaximalExactMatch::operator=(MaximalExactMatch &&) &=default'],['../classvg_1_1connection__t.html#a1af38cdb2b71e4ad441e427494c9548f',1,'vg::connection_t::operator=(const connection_t &)=default'],['../classvg_1_1connection__t.html#a9326a4bf2490223f72fbd90ac2805203',1,'vg::connection_t::operator=(connection_t &&)=default'],['../classvg_1_1subpath__t.html#a23ccc424b12615a3121c733470f5329d',1,'vg::subpath_t::operator=(const subpath_t &)=default'],['../classvg_1_1subpath__t.html#a3e18ac17337fa05ed3fc58fd69b55589',1,'vg::subpath_t::operator=(subpath_t &&)=default'],['../classvg_1_1multipath__alignment__t.html#aa0528d2e50e3d355b33a4e82f1c4fd3a',1,'vg::multipath_alignment_t::operator=(const multipath_alignment_t &other)'],['../classvg_1_1multipath__alignment__t.html#ac68c86f5c5ffa82b45aa047f020c8296',1,'vg::multipath_alignment_t::operator=(multipath_alignment_t &&other)'],['../classvg_1_1BaseOption.html#acc23a4aa53f5aadc0524d2b4abc0fe5c',1,'vg::BaseOption::operator=(const BaseOption< Value, Parser > &other)=default'],['../classvg_1_1BaseOption.html#a37b2e13a4c48f8ee49ebc5d034d88ce4',1,'vg::BaseOption::operator=(const Value &other)'],['../classvg_1_1Paths.html#a42b45e7dcb60d7f744566ea2f1e8a6ba',1,'vg::Paths::operator=(const Paths &other)'],['../classvg_1_1Paths.html#a298a38346fff38db91b2a42a56c1b9ea',1,'vg::Paths::operator=(Paths &&other) noexcept'],['../classvg_1_1edit__t.html#ad1c13528b7936c7129ea96a96c6e8671',1,'vg::edit_t::operator=(const edit_t &other)=default'],['../classvg_1_1edit__t.html#a0fc702abc036cbc6448f7129d332082d',1,'vg::edit_t::operator=(edit_t &&other)=default'],['../classvg_1_1path__mapping__t.html#a7e04cd691817a0ba29c45e08caabc1c4',1,'vg::path_mapping_t::operator=(const path_mapping_t &other)=default'],['../classvg_1_1path__mapping__t.html#a572fc6feefb1ca777a6920691d08fb4d',1,'vg::path_mapping_t::operator=(path_mapping_t &&other)=default'],['../classvg_1_1path__t.html#a48b9304e0a7dd08c9593c8cbbcf1954e',1,'vg::path_t::operator=(const path_t &other)=default'],['../classvg_1_1path__t.html#acff4daba9b88bec84475641ebbd07221',1,'vg::path_t::operator=(path_t &&other)=default'],['../classvg_1_1PhasedGenome.html#aa4f75b660fd6b1fe8528a10289621d01',1,'vg::PhasedGenome::operator=(PhasedGenome &&phased_genome)=delete'],['../classvg_1_1PhasedGenome.html#af2bcd75ffe10fee6c1af5456b229c752',1,'vg::PhasedGenome::operator=(PhasedGenome &phased_genome)'],['../classvg_1_1PhasedGenome_1_1iterator.html#a2802e8904098e873bf6d261dc93bc9ec',1,'vg::PhasedGenome::iterator::operator=()'],['../classvg_1_1position__t.html#a8d39338541d93824d9bc488798e5d0b7',1,'vg::position_t::operator=(const position_t &other)=default'],['../classvg_1_1position__t.html#ae75f741879494ab27fd07a6d3085a8ca',1,'vg::position_t::operator=(position_t &&other)=default'],['../classvg_1_1SmallBitset.html#a2e0933ff70a59061ccb2a20e826364e9',1,'vg::SmallBitset::operator=(const SmallBitset &another)'],['../classvg_1_1SmallBitset.html#adb79e0c1d451eb3f54e0051c2c2ede3d',1,'vg::SmallBitset::operator=(SmallBitset &&another)'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a8c84bbff732b6fa701659482136d123b',1,'vg::SnarlDistanceIndexClusterer::Seed::operator=()'],['../classvg_1_1SnarlManager.html#a08acef6ec793e011aa7537f9ccb4dcfe',1,'vg::SnarlManager::operator=(const SnarlManager &other)=delete'],['../classvg_1_1SnarlManager.html#af6f0f956456ef8ec76616fc47bc74428',1,'vg::SnarlManager::operator=(SnarlManager &&other)=default'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ad230c1701326adfb7d3bbcb57628be43',1,'vg::SnarlManager::SnarlRecord::operator=()'],['../classvg_1_1BitString.html#a0754865910378300b6b17a76df6cfa7b',1,'vg::BitString::operator=(const BitString &other)=default'],['../classvg_1_1BitString.html#ac7bb86ec9ba1b684056abea6da960d73',1,'vg::BitString::operator=(BitString &&other)=default'],['../classvg_1_1StreamIndexBase.html#ab0ac239e55d7748226a6a2d08480e026',1,'vg::StreamIndexBase::operator=()'],['../classvg_1_1count__back__inserter.html#aeb34352656680f80cb53fdec6cd2c554',1,'vg::count_back_inserter::operator=()'],['../structvg_1_1VectorView.html#acd9cb0c00656475140021a97275b66f8',1,'vg::VectorView::operator=(const VectorView &other)=default'],['../structvg_1_1VectorView.html#a4818009b7d0a655c23e8f132c9ba65c5',1,'vg::VectorView::operator=(VectorView &&other)=default'],['../structvg_1_1IncrementIter.html#a985cc14fcad953ece4e532342778929f',1,'vg::IncrementIter::operator=()'],['../classvg_1_1VcfBuffer.html#ae0157d603d27d962a8dbd83d12e0fad6',1,'vg::VcfBuffer::operator=()'],['../classvg_1_1WindowedVcfBuffer.html#ab26fcdb650d9ca250827fa4db733fdd6',1,'vg::WindowedVcfBuffer::operator=()'],['../classvg_1_1VG.html#a46f1fe88897cfe4d62625cffd3db5ebb',1,'vg::VG::operator=(const VG &other)'],['../classvg_1_1VG.html#a3b3efbadb9fd3923bbc7e8f0b73c524f',1,'vg::VG::operator=(VG &&other) noexcept'],['../classvg_1_1Watchdog.html#a05ee3b04abde016d4dad666372a38bbb',1,'vg::Watchdog::operator=(const Watchdog &other)=delete'],['../classvg_1_1Watchdog.html#a46119cc28dee74f545eaa3befa3ff149',1,'vg::Watchdog::operator=(Watchdog &&other)=delete'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a393cad2bfd5329385620d1f8434f1092',1,'vg::ZipCodeTree::iterator::operator=(const iterator &other)=default'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a3ad6d9e6a4753a9b15df622ee3ec15ec',1,'vg::ZipCodeTree::iterator::operator=(iterator &&other)=default'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a4d35f9d95c053c5941706dd3c02ac8b2',1,'vg::ZipCodeTree::reverse_iterator::operator=(const reverse_iterator &other)'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a6ca3e5d86a90780d082cdb07392096fe',1,'vg::ZipCodeTree::reverse_iterator::operator=(reverse_iterator &&other)'],['../classvg_1_1algorithms_1_1Anchor.html#a8774c392a8da56c5510d47fd418cf696',1,'vg::algorithms::Anchor::operator=(const Anchor &other)=default'],['../classvg_1_1algorithms_1_1Anchor.html#a380a35dbb36f866a533c9b4ee9571850',1,'vg::algorithms::Anchor::operator=(Anchor &&other)=default'],['../structvg_1_1subcommand_1_1TickChainLink.html#a6af8d418d16c2e2bdee3389929845669',1,'vg::subcommand::TickChainLink::operator=(const TickChainLink &other)=delete'],['../structvg_1_1subcommand_1_1TickChainLink.html#a367346c43d55fc270b39edf46be3cf29',1,'vg::subcommand::TickChainLink::operator=(TickChainLink &&other)=delete'],['../structvg_1_1Range.html#a4880259b13fcdda9fa55abf2faf6a38c',1,'vg::Range::operator=(const Range &other)'],['../structvg_1_1Range.html#ac25f332d4f29872e1e785317dc35fe00',1,'vg::Range::operator=(Range &&other)'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a3d9ea843f0b9e571bd4fe01b27f8c466',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &other)=delete'],['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a4c926b0df4f6b70d0b4665aedbd9256c',1,'vg::subcommand::GroupedOptionGroup::operator=(GroupedOptionGroup &&other)=delete'],['../classxg_1_1XG.html#a5dc0f63bc2e56b29638a7a4fc89bbacb',1,'xg::XG::operator=(const XG &other)=delete'],['../classxg_1_1XG.html#aa06dbf48d0e060ddec20000e4242ed5a',1,'xg::XG::operator=(XG &&other)=delete'],['../classxg_1_1XGPath.html#a2386595dfbd819402d30a76b83b3b65d',1,'xg::XGPath::operator=(const XGPath &other)=delete'],['../classxg_1_1XGPath.html#a08310ec2e3e6e968b3d412329a9fc4ad',1,'xg::XGPath::operator=(XGPath &&other)=delete'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a3fd64baf9dcc05eceb2a653b225ed325',1,'handlegraph::PathForEachSocket::iterator::operator=()'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#aaae753008929cd78c3ece15f1e73826d',1,'vg::io::BlockedGzipInputStream::operator=(const BlockedGzipInputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipInputStream.html#ab978351afc9df57f66dfcbaf11932c17',1,'vg::io::BlockedGzipInputStream::operator=(BlockedGzipInputStream &&other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a26746003c36d4c51964fe291412c48a0',1,'vg::io::BlockedGzipOutputStream::operator=(const BlockedGzipOutputStream &other)=delete'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae54f16684d6a1f7ea66cf57ab0a481f9',1,'vg::io::BlockedGzipOutputStream::operator=(BlockedGzipOutputStream &&other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a8cc7250b2785917930d88f92d66058cb',1,'vg::io::MessageEmitter::operator=(const MessageEmitter &other)=delete'],['../classvg_1_1io_1_1MessageEmitter.html#a7c0f2a53bd5e382b5543eb5ccf7acb3b',1,'vg::io::MessageEmitter::operator=(MessageEmitter &&other)=default'],['../classvg_1_1io_1_1ProtobufEmitter.html#ad81cc27d627747dc34683bb2e0500ff6',1,'vg::io::ProtobufEmitter::operator=(const ProtobufEmitter &other)=delete'],['../classvg_1_1io_1_1ProtobufEmitter.html#a7d4c3a9c587971479a5b9a2a6c50db74',1,'vg::io::ProtobufEmitter::operator=(ProtobufEmitter &&other)=default'],['../classvg_1_1io_1_1StreamMultiplexer.html#af986451d89174a2947be32aaefba6f94',1,'vg::io::StreamMultiplexer::operator=(const StreamMultiplexer &other)=delete'],['../classvg_1_1io_1_1StreamMultiplexer.html#aa0426a0e605e8375e1716dfb28b6482e',1,'vg::io::StreamMultiplexer::operator=(StreamMultiplexer &&other)=delete']]],
+ ['operator_3d_3d_10265',['operator==',['../classvg_1_1ShuffledPairs_1_1iterator.html#a35842cde2d948d93e9919b267410a8da',1,'vg::ShuffledPairs::iterator::operator==()'],['../structvg_1_1GaplessExtension.html#af2acf967c1b81204f8f5cea754ae1ae1',1,'vg::GaplessExtension::operator==()'],['../structvg_1_1read__alignment__index__t.html#a194c254826c92dcbf90f2d08fb805245',1,'vg::read_alignment_index_t::operator==()'],['../structvg_1_1alignment__index__t.html#aca2a478078ae34cef69bd3ba0e404a08',1,'vg::alignment_index_t::operator==()'],['../classvg_1_1NodeSide.html#af011a5aeaffe705507a89ed91032ad3e',1,'vg::NodeSide::operator==()'],['../classvg_1_1NodeTraversal.html#a07c1f0b8bdc0c6b851f158e0a1cbd5b5',1,'vg::NodeTraversal::operator==()'],['../classvg_1_1edit__t.html#a2ea672c3e9e8a4a4c2332d117bf85461',1,'vg::edit_t::operator==()'],['../classvg_1_1path__mapping__t.html#a40d364000efb3da1660dede1c3762d65',1,'vg::path_mapping_t::operator==()'],['../classvg_1_1path__t.html#a1aadea895d6ca0a94f5f038809308ef9',1,'vg::path_t::operator==()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a0a2ad098ff6d931f04fee951eb50b80a',1,'vg::PhasedGenome::iterator::operator==()'],['../classvg_1_1position__t.html#ad53946ea84a94a664810e7bd67689f3c',1,'vg::position_t::operator==()'],['../structvg_1_1ChainIterator.html#a87ca4ac16d01af9741d45c5c7f391c2c',1,'vg::ChainIterator::operator==()'],['../classvg_1_1BitString.html#a0e19002b533b25e6258ae9e2b7b6bd4e',1,'vg::BitString::operator==()'],['../structvg_1_1VectorView_1_1const__iterator.html#a10426612008a0eb5a74ed91193ecbb96',1,'vg::VectorView::const_iterator::operator==()'],['../structvg_1_1IncrementIter.html#ae67e82103cdee625555eced2c8f51d69',1,'vg::IncrementIter::operator==()'],['../structvg_1_1varint__vector__t.html#ada0c0ea0373d2eb784f4c8459153701f',1,'vg::varint_vector_t::operator==()'],['../classvg_1_1ZipCode.html#a0b983931fc8219fafc6cde9357b553b0',1,'vg::ZipCode::operator==()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a09179a35995161986e2a2db97f5f59c1',1,'vg::ZipCode::decoder_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a4483a326cb25512a552a1594232d3fdd',1,'vg::ZipCodeTree::oriented_seed_t::operator==()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#a015179ff6e9a5e02cc9dfe4af73ff32e',1,'vg::ZipCodeTree::seed_result_t::operator==()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#a431bbe58e47281666f1bbd7d0db511a2',1,'vg::ZipCodeTree::iterator::operator==()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ab8ad33ac681c64fafec59409e1fcdce1',1,'vg::ZipCodeTree::reverse_iterator::operator==()'],['../classvg_1_1algorithms_1_1TracedScore.html#af8d42e525e16257aa99b6965a6d6ad4c',1,'vg::algorithms::TracedScore::operator==()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#aaa1690bd6bf9f463589b8c953940741c',1,'handlegraph::PathForEachSocket::iterator::operator==()'],['../classvg_1_1io_1_1MessageIterator.html#a870adfdc044f57202d26d5fb2109b425',1,'vg::io::MessageIterator::operator==()'],['../classvg_1_1io_1_1ProtobufIterator.html#ad57a7afe6c7759074d1c9ffd3c31a4e0',1,'vg::io::ProtobufIterator::operator==()'],['../namespacevg.html#af94d73312bfd787493e87d207398d73a',1,'vg::operator==(const MaximalExactMatch &m1, const MaximalExactMatch &m2)'],['../namespacevg.html#a87b890a4bc73725bbea08984d7510df4',1,'vg::operator==(const Visit &a, const Visit &b)'],['../namespacevg.html#a845213e6efb7204868c05afcae9c926f',1,'vg::operator==(const SnarlTraversal &a, const SnarlTraversal &b)'],['../namespacevg.html#a387ff1f8cefcf4feb705b0f1225d16c7',1,'vg::operator==(const Snarl &a, const Snarl &b)'],['../namespacevg.html#a6ace94ff076945069d22aa548b6e0bf6',1,'vg::operator==(const Exon &lhs, const Exon &rhs)'],['../namespacevg.html#ace8e1de0bfe604d8da5537fd86e251ee',1,'vg::operator==(const Transcript &lhs, const Transcript &rhs)'],['../namespacevg.html#a8e2505b73c51b9659c94950d2f283eec',1,'vg::operator==(const Mapping &lhs, const Mapping &rhs)'],['../namespacevg.html#a92e719e28c0d3f7d6dfa354824220211',1,'vg::operator==(const Path &lhs, const Path &rhs)'],['../namespacehandlegraph.html#aadbc38098e019cace58583b35000d19f',1,'handlegraph::operator==(const handle_t &a, const handle_t &b)'],['../namespacehandlegraph.html#a5a7206835ea412fabb928f106b291349',1,'handlegraph::operator==(const path_handle_t &a, const path_handle_t &b)'],['../namespacehandlegraph.html#a4e83573fadcc147c475d0a7678ffbe98',1,'handlegraph::operator==(const step_handle_t &a, const step_handle_t &b)'],['../namespacehandlegraph.html#a3b87d2ae8d5a93f67ddacb95a5fd791f',1,'handlegraph::operator==(const net_handle_t &a, const net_handle_t &b)'],['../namespacevg_1_1io.html#a05438ce01e149360e263cb83346a5261',1,'vg::io::operator==()']]],
+ ['operator_3e_10266',['operator>',['../classvg_1_1algorithms_1_1TracedScore.html#ad7b72c45ce0349b96aae49d2a1cc8eec',1,'vg::algorithms::TracedScore::operator>()'],['../namespacevg.html#a955d56fb4c95213de77c1fcce44c77b8',1,'vg::operator>()']]],
+ ['operator_5b_5d_10267',['operator[]',['../structhaplo_1_1gbwt__thread__t.html#a9dd1cb0268973121f00304ae34c7688d',1,'haplo::gbwt_thread_t::operator[](size_t i)'],['../structhaplo_1_1gbwt__thread__t.html#a0ebbbd89e60564e347b1bc441230786c',1,'haplo::gbwt_thread_t::operator[](size_t i) const'],['../structvg_1_1VectorView.html#aa89f493da3bd725632dd1dfb02479c0d',1,'vg::VectorView::operator[]()'],['../classvg_1_1VectorViewInverse.html#a6943170a05ddc962f61fa7ab4fed926d',1,'vg::VectorViewInverse::operator[]()']]],
+ ['operator_7c_3d_10268',['operator|=',['../classvg_1_1SmallBitset.html#a541303f562fa1579b94ceda2eda95927',1,'vg::SmallBitset']]],
+ ['optimal_5falignment_10269',['optimal_alignment',['../namespacevg.html#a4e3c0f0d0f60a6a6ef1c301b63e9a21e',1,'vg']]],
+ ['optimal_5falignment_5finternal_10270',['optimal_alignment_internal',['../namespacevg.html#a3caee9d564f3a803a6ad69642269c5b6',1,'vg']]],
+ ['optimal_5falignment_5fscore_10271',['optimal_alignment_score',['../namespacevg.html#ad3548ef9766130a155ba65420c0e7c0e',1,'vg']]],
+ ['optimal_5falignments_10272',['optimal_alignments',['../namespacevg.html#ada4d6b6771c5d7e5b2367b18ca8f76f3',1,'vg']]],
+ ['optimal_5falignments_5fwith_5fdisjoint_5fsubpaths_10273',['optimal_alignments_with_disjoint_subpaths',['../namespacevg.html#af711577f7d293ffc1c8002c868081bb1',1,'vg']]],
+ ['optimal_5fscore_5fon_5fgenome_10274',['optimal_score_on_genome',['../classvg_1_1PhasedGenome.html#a4f8838611a252e9a574a33af3965ad4c',1,'vg::PhasedGenome']]],
+ ['optimize_10275',['optimize',['../classvg_1_1VG.html#a0b4fa1970f08f3e4d0cf2f8c33a967a5',1,'vg::VG::optimize()'],['../classhandlegraph_1_1MutableHandleGraph.html#a195c81fa446b62d94fda8841eaa3bb85',1,'handlegraph::MutableHandleGraph::optimize()']]],
+ ['option_10276',['Option',['../classvg_1_1Option.html#a636f83c45d4a863e53dcb2f9d1d753aa',1,'vg::Option::Option()'],['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#aa01cfc188e53cf0fb37a6ccc9b4b0043',1,'vg::Option< vector< Item >, Parser >::Option()']]],
+ ['optiongroup_10277',['OptionGroup',['../structvg_1_1subcommand_1_1OptionGroup.html#a1e4abb9a235dcfe1d50809bbb36b40a8',1,'vg::subcommand::OptionGroup']]],
+ ['order_5fof_10278',['order_of',['../classvg_1_1IncrementalSubgraph.html#afe160f21d5b4a7964c1bceef47ca54a4',1,'vg::IncrementalSubgraph']]],
+ ['orderedgraph_10279',['OrderedGraph',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a321fef7bca4632cec8f2ed02f8294ad8',1,'vg::DozeuInterface::OrderedGraph']]],
+ ['orientation_5ffrom_5fold_5fedge_5ftype_10280',['orientation_from_old_edge_type',['../classxg_1_1XG.html#a6383f68a1f2f9150a0649c6db1c43891',1,'xg::XG']]],
+ ['oriented_5fdistance_10281',['oriented_distance',['../classvg_1_1OrientedDistanceMeasurer.html#af6551e771deca01e6af9054a1ad3d30e',1,'vg::OrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a8ec77086bfe160d85961a509725b529f',1,'vg::PathOrientedDistanceMeasurer::oriented_distance()'],['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a8f8081d5bb9b0f5526935e2691f52dc3',1,'vg::SnarlOrientedDistanceMeasurer::oriented_distance()']]],
+ ['oriented_5fmotif_10282',['oriented_motif',['../classvg_1_1SpliceStats.html#a0568cd8d7b986fdd703bd4021dbb41a1',1,'vg::SpliceStats']]],
+ ['orienteddistanceclusterer_10283',['OrientedDistanceClusterer',['../classvg_1_1OrientedDistanceClusterer.html#a0bab84127f018db9467240db290113b4',1,'vg::OrientedDistanceClusterer']]],
+ ['output_5ffilepath_10284',['output_filepath',['../classvg_1_1IndexingPlan.html#a405ede5620e8a7263fbb734f656c9971',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier) const'],['../classvg_1_1IndexingPlan.html#a5ef2f8275a2f997e94d178089107502a',1,'vg::IndexingPlan::output_filepath(const IndexName &identifier, size_t chunk, size_t num_chunks) const']]],
+ ['output_5fgraph_5fwith_5fembedded_5fpaths_10285',['output_graph_with_embedded_paths',['../namespacevg.html#ae62ff63e415416fd298c6f59c8f2da47',1,'vg::output_graph_with_embedded_paths(vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source)'],['../namespacevg.html#a134ccba76916d6d94e59581932f1b595',1,'vg::output_graph_with_embedded_paths(ostream &subgraph_ostream, vector< pair< thread_t, int >> &haplotype_list, const HandleGraph &source, bool json)']]],
+ ['output_5fhaplotype_5fcounts_10286',['output_haplotype_counts',['../namespacevg.html#ae2d79bdac899f70214959ef92dbbad2f',1,'vg']]],
+ ['output_5fwabbit_5fmap_10287',['output_wabbit_map',['../classVectorizer.html#a788aaec704ce78d29f55459ff2eaedb4',1,'Vectorizer']]],
+ ['outputstream_10288',['outputStream',['../namespacevg_1_1io.html#a477841175891d3e770995307eea45f38',1,'vg::io']]],
+ ['over_5fdirected_5fedge_10289',['over_directed_edge',['../classvg_1_1Paths.html#a8d1fde70db5d5c4d1e26821d4f03ba7a',1,'vg::Paths']]],
+ ['over_5fedge_10290',['over_edge',['../classvg_1_1Paths.html#ae7cd0d9291a31a63aa80e9d4d578575e',1,'vg::Paths']]],
+ ['overflow_10291',['overflow',['../classvg_1_1io_1_1fdoutbuf.html#aa0b27dbd39a3ad9452f0d4c0d8ca11a1',1,'vg::io::fdoutbuf']]],
+ ['overlap_10292',['overlap',['../structvg_1_1BREAKPOINT.html#a8843c2775e6cc15ef2739e13a02b2c86',1,'vg::BREAKPOINT::overlap()'],['../structvg_1_1GaplessExtension.html#ae13cbdb46d6375425a2f82e75daadb66',1,'vg::GaplessExtension::overlap()'],['../namespacevg.html#aaac70d8b120ca61591561cba307dcc1b',1,'vg::overlap()']]],
+ ['overlay_10293',['overlay',['../classvg_1_1Translator.html#a91965cec764734c35ace2ecb0c643d5c',1,'vg::Translator']]],
+ ['overlay_5fnode_5ftranslations_10294',['overlay_node_translations',['../classvg_1_1VG.html#ae9b314bb2021525e60a0ad23e99fb994',1,'vg::VG::overlay_node_translations()'],['../namespacevg.html#a86d5f690fe272c74949e080aca561467',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#a7816225a17a671ff849a79f064770ebb',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, pair< id_t, bool >> &under)'],['../namespacevg.html#af224cfdc27efec675771ba4cc5143a3f',1,'vg::overlay_node_translations(const unordered_map< id_t, pair< id_t, bool >> &over, const unordered_map< id_t, id_t > &under)'],['../namespacevg.html#ae996017b379b1178d5e588b96a7c7f3f',1,'vg::overlay_node_translations(const unordered_map< id_t, id_t > &over, const unordered_map< id_t, id_t > &under)']]]
];
diff --git a/search/namespaces_0.js b/search/namespaces_0.js
index bbb150363c..879a68db6f 100644
--- a/search/namespaces_0.js
+++ b/search/namespaces_0.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['gafkluge_7395',['gafkluge',['../namespacegafkluge.html',1,'']]],
- ['google_7396',['google',['../namespacegoogle.html',1,'']]],
- ['protobuf_7397',['protobuf',['../namespacegoogle_1_1protobuf.html',1,'google']]]
+ ['gafkluge_7397',['gafkluge',['../namespacegafkluge.html',1,'']]],
+ ['google_7398',['google',['../namespacegoogle.html',1,'']]],
+ ['protobuf_7399',['protobuf',['../namespacegoogle_1_1protobuf.html',1,'google']]]
];
diff --git a/search/namespaces_1.js b/search/namespaces_1.js
index 606cea8165..4d1bdb8469 100644
--- a/search/namespaces_1.js
+++ b/search/namespaces_1.js
@@ -1,9 +1,9 @@
var searchData=
[
- ['algorithms_7398',['algorithms',['../namespacehandlegraph_1_1algorithms.html',1,'handlegraph']]],
- ['handlegraph_7399',['handlegraph',['../namespacehandlegraph.html',1,'']]],
- ['haplo_7400',['haplo',['../namespacehaplo.html',1,'']]],
- ['haplomath_7401',['haploMath',['../namespacehaplo_1_1haploMath.html',1,'haplo']]],
- ['haplotypes_5fdefaults_7402',['haplotypes_defaults',['../namespacehaplotypes__defaults.html',1,'']]],
- ['internal_7403',['internal',['../namespacehandlegraph_1_1algorithms_1_1internal.html',1,'handlegraph::algorithms']]]
+ ['algorithms_7400',['algorithms',['../namespacehandlegraph_1_1algorithms.html',1,'handlegraph']]],
+ ['handlegraph_7401',['handlegraph',['../namespacehandlegraph.html',1,'']]],
+ ['haplo_7402',['haplo',['../namespacehaplo.html',1,'']]],
+ ['haplomath_7403',['haploMath',['../namespacehaplo_1_1haploMath.html',1,'haplo']]],
+ ['haplotypes_5fdefaults_7404',['haplotypes_defaults',['../namespacehaplotypes__defaults.html',1,'']]],
+ ['internal_7405',['internal',['../namespacehandlegraph_1_1algorithms_1_1internal.html',1,'handlegraph::algorithms']]]
];
diff --git a/search/namespaces_2.js b/search/namespaces_2.js
index 6daba00113..6b3a617bc6 100644
--- a/search/namespaces_2.js
+++ b/search/namespaces_2.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['std_7404',['std',['../namespacestd.html',1,'']]]
+ ['std_7406',['std',['../namespacestd.html',1,'']]]
];
diff --git a/search/namespaces_3.js b/search/namespaces_3.js
index 6f44807def..1dfd1b5102 100644
--- a/search/namespaces_3.js
+++ b/search/namespaces_3.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['algorithms_7405',['algorithms',['../namespacevg_1_1algorithms.html',1,'vg']]],
- ['io_7406',['io',['../namespacevg_1_1io.html',1,'vg']]],
- ['subcommand_7407',['subcommand',['../namespacevg_1_1subcommand.html',1,'vg']]],
- ['temp_5ffile_7408',['temp_file',['../namespacevg_1_1temp__file.html',1,'vg']]],
- ['vg_7409',['vg',['../namespacevg.html',1,'']]]
+ ['algorithms_7407',['algorithms',['../namespacevg_1_1algorithms.html',1,'vg']]],
+ ['io_7408',['io',['../namespacevg_1_1io.html',1,'vg']]],
+ ['subcommand_7409',['subcommand',['../namespacevg_1_1subcommand.html',1,'vg']]],
+ ['temp_5ffile_7410',['temp_file',['../namespacevg_1_1temp__file.html',1,'vg']]],
+ ['vg_7411',['vg',['../namespacevg.html',1,'']]]
];
diff --git a/search/namespaces_4.js b/search/namespaces_4.js
index 5cbf6edd18..166954428f 100644
--- a/search/namespaces_4.js
+++ b/search/namespaces_4.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['temp_5ffile_7410',['temp_file',['../namespacexg_1_1temp__file.html',1,'xg']]],
- ['xg_7411',['xg',['../namespacexg.html',1,'']]]
+ ['temp_5ffile_7412',['temp_file',['../namespacexg_1_1temp__file.html',1,'xg']]],
+ ['xg_7413',['xg',['../namespacexg.html',1,'']]]
];
diff --git a/search/namespaces_5.js b/search/namespaces_5.js
index 45c4b39a9b..7946c49747 100644
--- a/search/namespaces_5.js
+++ b/search/namespaces_5.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['zstdutil_7412',['zstdutil',['../namespacezstdutil.html',1,'']]]
+ ['zstdutil_7414',['zstdutil',['../namespacezstdutil.html',1,'']]]
];
diff --git a/search/related_0.js b/search/related_0.js
index b8aa2a8a2b..f7ced9012d 100644
--- a/search/related_0.js
+++ b/search/related_0.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['alttracebackstack_14098',['AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#afb02520a42fa4bde2fefbf5b46e028c9',1,'vg::BandedGlobalAligner::BAMatrix']]]
+ ['alttracebackstack_14102',['AltTracebackStack',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#afb02520a42fa4bde2fefbf5b46e028c9',1,'vg::BandedGlobalAligner::BAMatrix']]]
];
diff --git a/search/related_1.js b/search/related_1.js
index bf3a2824bf..96c3a1f899 100644
--- a/search/related_1.js
+++ b/search/related_1.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['babuilder_14099',['BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a0e96e19808a2cdebe69caa967ca2ca5c',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['bandedglobalaligner_14100',['BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#aa1514e35f3c2194f569f60067c542ab9',1,'vg::BandedGlobalAligner::BAMatrix']]]
+ ['babuilder_14103',['BABuilder',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a0e96e19808a2cdebe69caa967ca2ca5c',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['bandedglobalaligner_14104',['BandedGlobalAligner',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#aa1514e35f3c2194f569f60067c542ab9',1,'vg::BandedGlobalAligner::BAMatrix']]]
];
diff --git a/search/related_2.js b/search/related_2.js
index eceb41123b..12867dc9b5 100644
--- a/search/related_2.js
+++ b/search/related_2.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['haplotype_14101',['Haplotype',['../classvg_1_1PhasedGenome_1_1iterator.html#a2a8d7bc98747d6a54dbeef69cc966afc',1,'vg::PhasedGenome::iterator']]],
- ['haplotypenode_14102',['HaplotypeNode',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a4f0160b2daeebec5d984b4fe1921887a',1,'vg::PhasedGenome::Haplotype']]]
+ ['haplotype_14105',['Haplotype',['../classvg_1_1PhasedGenome_1_1iterator.html#a2a8d7bc98747d6a54dbeef69cc966afc',1,'vg::PhasedGenome::iterator']]],
+ ['haplotypenode_14106',['HaplotypeNode',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a4f0160b2daeebec5d984b4fe1921887a',1,'vg::PhasedGenome::Haplotype']]]
];
diff --git a/search/related_3.js b/search/related_3.js
index a4b00114cc..144e42d444 100644
--- a/search/related_3.js
+++ b/search/related_3.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['indexingplan_14103',['IndexingPlan',['../classvg_1_1IndexRegistry.html#a490f2f891225b54cb14e32d593f30f5c',1,'vg::IndexRegistry']]],
- ['indexregistry_14104',['IndexRegistry',['../classvg_1_1IndexingPlan.html#a77ea72c93e5f6c8a5e65279ae52aec32',1,'vg::IndexingPlan']]]
+ ['indexingplan_14107',['IndexingPlan',['../classvg_1_1IndexRegistry.html#a490f2f891225b54cb14e32d593f30f5c',1,'vg::IndexRegistry']]],
+ ['indexregistry_14108',['IndexRegistry',['../classvg_1_1IndexingPlan.html#a77ea72c93e5f6c8a5e65279ae52aec32',1,'vg::IndexingPlan']]]
];
diff --git a/search/related_4.js b/search/related_4.js
index 29126489ca..fa0dacf8d8 100644
--- a/search/related_4.js
+++ b/search/related_4.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['operator_3c_14105',['operator<',['../classvg_1_1MaximalExactMatch.html#ace421d32490547fc94b4003484e97dcb',1,'vg::MaximalExactMatch']]],
- ['operator_3c_3c_14106',['operator<<',['../classvg_1_1MaximalExactMatch.html#a415b6e9f064006bb599e11971822669a',1,'vg::MaximalExactMatch']]],
- ['operator_3d_3d_14107',['operator==',['../classvg_1_1MaximalExactMatch.html#a19feb3f51f02208aa5161562991992dc',1,'vg::MaximalExactMatch']]]
+ ['operator_3c_14109',['operator<',['../classvg_1_1MaximalExactMatch.html#ace421d32490547fc94b4003484e97dcb',1,'vg::MaximalExactMatch']]],
+ ['operator_3c_3c_14110',['operator<<',['../classvg_1_1MaximalExactMatch.html#a415b6e9f064006bb599e11971822669a',1,'vg::MaximalExactMatch']]],
+ ['operator_3d_3d_14111',['operator==',['../classvg_1_1MaximalExactMatch.html#a19feb3f51f02208aa5161562991992dc',1,'vg::MaximalExactMatch']]]
];
diff --git a/search/related_5.js b/search/related_5.js
index c692bc48a7..c51f1f52d1 100644
--- a/search/related_5.js
+++ b/search/related_5.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['pathforeachsocket_14108',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ad5b94c4a72e3d6d48be27cb00bc41ca2',1,'handlegraph::PathForEachSocket::iterator']]],
- ['pathhandlegraph_14109',['PathHandleGraph',['../classhandlegraph_1_1PathForEachSocket.html#a4260787fbe094766e75485f7d7d9d0ca',1,'handlegraph::PathForEachSocket']]],
- ['phasedgenome_14110',['PhasedGenome',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::Haplotype::PhasedGenome()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::iterator::PhasedGenome()']]]
+ ['pathforeachsocket_14112',['PathForEachSocket',['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ad5b94c4a72e3d6d48be27cb00bc41ca2',1,'handlegraph::PathForEachSocket::iterator']]],
+ ['pathhandlegraph_14113',['PathHandleGraph',['../classhandlegraph_1_1PathForEachSocket.html#a4260787fbe094766e75485f7d7d9d0ca',1,'handlegraph::PathForEachSocket']]],
+ ['phasedgenome_14114',['PhasedGenome',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::Haplotype::PhasedGenome()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a9a2572c185819a46668ffbb59ff09008',1,'vg::PhasedGenome::iterator::PhasedGenome()']]]
];
diff --git a/search/related_6.js b/search/related_6.js
index 3eb58dfc56..bbe91e4e63 100644
--- a/search/related_6.js
+++ b/search/related_6.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['shuffledpairs_14111',['ShuffledPairs',['../classvg_1_1ShuffledPairs_1_1iterator.html#a716354d123e5197d160a8d6c4da7817d',1,'vg::ShuffledPairs::iterator']]]
+ ['shuffledpairs_14115',['ShuffledPairs',['../classvg_1_1ShuffledPairs_1_1iterator.html#a716354d123e5197d160a8d6c4da7817d',1,'vg::ShuffledPairs::iterator']]]
];
diff --git a/search/related_7.js b/search/related_7.js
index bf0237a46a..29e6d5aace 100644
--- a/search/related_7.js
+++ b/search/related_7.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['testminimizermapper_14112',['TestMinimizerMapper',['../classvg_1_1MinimizerMapper.html#a8239430f869fd4cc597359f38a1ab29e',1,'vg::MinimizerMapper']]]
+ ['testminimizermapper_14116',['TestMinimizerMapper',['../classvg_1_1MinimizerMapper.html#a8239430f869fd4cc597359f38a1ab29e',1,'vg::MinimizerMapper']]]
];
diff --git a/search/related_8.js b/search/related_8.js
index d1235f373c..d510e976a8 100644
--- a/search/related_8.js
+++ b/search/related_8.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['zipcodeforest_14113',['ZipCodeForest',['../classvg_1_1ZipCodeTree.html#ae954dd8e2c990674b2293ddd18ae6517',1,'vg::ZipCodeTree']]]
+ ['zipcodeforest_14117',['ZipCodeForest',['../classvg_1_1ZipCodeTree.html#ae954dd8e2c990674b2293ddd18ae6517',1,'vg::ZipCodeTree']]]
];
diff --git a/search/typedefs_0.js b/search/typedefs_0.js
index 91e26797a1..0fd515f208 100644
--- a/search/typedefs_0.js
+++ b/search/typedefs_0.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['annotation_5ft_13760',['annotation_t',['../classvg_1_1DiagramExplainer.html#ae004adcb43e886c401bff5708e53ce63',1,'vg::DiagramExplainer']]]
+ ['annotation_5ft_13764',['annotation_t',['../classvg_1_1DiagramExplainer.html#ae004adcb43e886c401bff5708e53ce63',1,'vg::DiagramExplainer']]]
];
diff --git a/search/typedefs_1.js b/search/typedefs_1.js
index 2b8a747707..f47b1205bd 100644
--- a/search/typedefs_1.js
+++ b/search/typedefs_1.js
@@ -1,9 +1,9 @@
var searchData=
[
- ['bare_5fload_5ffunction_5ft_13761',['bare_load_function_t',['../namespacevg_1_1io.html#a53e90871d34e2a1d10329d419f809cea',1,'vg::io']]],
- ['bare_5fload_5ffunction_5fwith_5ffilename_5ft_13762',['bare_load_function_with_filename_t',['../namespacevg_1_1io.html#a659a48880b52fc28b36e8cc51eb1ffd0',1,'vg::io']]],
- ['bare_5fsave_5ffunction_5ft_13763',['bare_save_function_t',['../namespacevg_1_1io.html#af8c1fde642062992c5179d67196ee4f2',1,'vg::io']]],
- ['benchtime_13764',['benchtime',['../namespacevg.html#a4ab10687f0a0cca11ecfd062d9bb0a07',1,'vg']]],
- ['bin_5ft_13765',['bin_t',['../classvg_1_1StreamIndexBase.html#a1de6fb384732cab26d21f38f133bc9e9',1,'vg::StreamIndexBase']]],
- ['binneddepthindex_13766',['BinnedDepthIndex',['../namespacevg_1_1algorithms.html#acf8cb40a8f834b42f1ec89af0ef140b9',1,'vg::algorithms']]]
+ ['bare_5fload_5ffunction_5ft_13765',['bare_load_function_t',['../namespacevg_1_1io.html#a53e90871d34e2a1d10329d419f809cea',1,'vg::io']]],
+ ['bare_5fload_5ffunction_5fwith_5ffilename_5ft_13766',['bare_load_function_with_filename_t',['../namespacevg_1_1io.html#a659a48880b52fc28b36e8cc51eb1ffd0',1,'vg::io']]],
+ ['bare_5fsave_5ffunction_5ft_13767',['bare_save_function_t',['../namespacevg_1_1io.html#af8c1fde642062992c5179d67196ee4f2',1,'vg::io']]],
+ ['benchtime_13768',['benchtime',['../namespacevg.html#a4ab10687f0a0cca11ecfd062d9bb0a07',1,'vg']]],
+ ['bin_5ft_13769',['bin_t',['../classvg_1_1StreamIndexBase.html#a1de6fb384732cab26d21f38f133bc9e9',1,'vg::StreamIndexBase']]],
+ ['binneddepthindex_13770',['BinnedDepthIndex',['../namespacevg_1_1algorithms.html#acf8cb40a8f834b42f1ec89af0ef140b9',1,'vg::algorithms']]]
];
diff --git a/search/typedefs_10.js b/search/typedefs_10.js
index 3152f2d4ca..7febfa4a7e 100644
--- a/search/typedefs_10.js
+++ b/search/typedefs_10.js
@@ -1,15 +1,15 @@
var searchData=
[
- ['save_5ffunction_5ft_13853',['save_function_t',['../namespacevg_1_1io.html#a161bd20a13c1fd9993bcddd7ea3cbe57',1,'vg::io']]],
- ['search_5ftype_13854',['search_type',['../classvg_1_1PhaseUnfolder.html#a7484966dc448f4c3b894a53233f46d9f',1,'vg::PhaseUnfolder']]],
- ['seed_13855',['Seed',['../classvg_1_1MinimizerMapper.html#ab964411462aea4fc777127a887a9a6f7',1,'vg::MinimizerMapper::Seed()'],['../classvg_1_1ZipCodeTree.html#a50817b343d4ad6368df659e16b9a7549',1,'vg::ZipCodeTree::Seed()'],['../classvg_1_1ZipCodeForest.html#a93f9eaa38dd8024a73a2aeca456e5156',1,'vg::ZipCodeForest::Seed()']]],
- ['seed_5ftype_13856',['seed_type',['../structvg_1_1GaplessExtension.html#a8c8a3d415e13a943e87b4c1e33347081',1,'vg::GaplessExtension::seed_type()'],['../classvg_1_1GaplessExtender.html#a8891a422c7921863c589850636d9f252',1,'vg::GaplessExtender::seed_type()']]],
- ['sequence_5ftype_13857',['sequence_type',['../structvg_1_1RecombinatorHaplotype.html#a20c784c55500a6e02c9ad4762be12176',1,'vg::RecombinatorHaplotype::sequence_type()'],['../classvg_1_1Haplotypes.html#aebc70f387d48bd0e5c8f0c607c496535',1,'vg::Haplotypes::sequence_type()'],['../classvg_1_1HaplotypePartitioner.html#aa06fc618c54377342c05b7306b8dec72',1,'vg::HaplotypePartitioner::sequence_type()'],['../classvg_1_1Recombinator.html#a8a1ad77c3ad37fbcfa48dc5f89f591af',1,'vg::Recombinator::sequence_type()']]],
- ['serializablehandlegraph_13858',['SerializableHandleGraph',['../namespacevg.html#a7378a177b4ed2e7be87e02a9bfcb7d4e',1,'vg']]],
- ['state_5ftype_13859',['state_type',['../classvg_1_1PhaseUnfolder.html#a95529e399d5ef61f6a426e1b5cfe9237',1,'vg::PhaseUnfolder']]],
- ['step_5fhandle_5ft_13860',['step_handle_t',['../namespacevg.html#a40b137bbd07d198ca2b77962eeeaf7c8',1,'vg::step_handle_t()'],['../namespacevg_1_1io.html#a5473f8a5ac351719453cfd62655beebb',1,'vg::io::step_handle_t()']]],
- ['stored_5fedge_5ft_13861',['stored_edge_t',['../classvg_1_1DiagramExplainer.html#a6eca0d51970a6782f49171a354aaeb74',1,'vg::DiagramExplainer']]],
- ['subrange_5ft_13862',['subrange_t',['../namespacevg.html#ae28b502adf2ce7302acbb3138280f06c',1,'vg::subrange_t()'],['../namespacehandlegraph.html#a097e656b1ffb02a80c0b530b1987984a',1,'handlegraph::subrange_t()']]],
- ['suggested_5fedge_5ft_13863',['suggested_edge_t',['../classvg_1_1DiagramExplainer.html#ae9907aa970a58c2c6a89829c6f3020ba',1,'vg::DiagramExplainer']]],
- ['supportmap_13864',['SupportMap',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af8ae65b6009d1f121c27fb3ab969ef90',1,'vg::NestedCachedPackedTraversalSupportFinder']]]
+ ['save_5ffunction_5ft_13857',['save_function_t',['../namespacevg_1_1io.html#a161bd20a13c1fd9993bcddd7ea3cbe57',1,'vg::io']]],
+ ['search_5ftype_13858',['search_type',['../classvg_1_1PhaseUnfolder.html#a7484966dc448f4c3b894a53233f46d9f',1,'vg::PhaseUnfolder']]],
+ ['seed_13859',['Seed',['../classvg_1_1MinimizerMapper.html#ab964411462aea4fc777127a887a9a6f7',1,'vg::MinimizerMapper::Seed()'],['../classvg_1_1ZipCodeTree.html#a50817b343d4ad6368df659e16b9a7549',1,'vg::ZipCodeTree::Seed()'],['../classvg_1_1ZipCodeForest.html#a93f9eaa38dd8024a73a2aeca456e5156',1,'vg::ZipCodeForest::Seed()']]],
+ ['seed_5ftype_13860',['seed_type',['../structvg_1_1GaplessExtension.html#a8c8a3d415e13a943e87b4c1e33347081',1,'vg::GaplessExtension::seed_type()'],['../classvg_1_1GaplessExtender.html#a8891a422c7921863c589850636d9f252',1,'vg::GaplessExtender::seed_type()']]],
+ ['sequence_5ftype_13861',['sequence_type',['../structvg_1_1RecombinatorHaplotype.html#a20c784c55500a6e02c9ad4762be12176',1,'vg::RecombinatorHaplotype::sequence_type()'],['../classvg_1_1Haplotypes.html#aebc70f387d48bd0e5c8f0c607c496535',1,'vg::Haplotypes::sequence_type()'],['../classvg_1_1HaplotypePartitioner.html#aa06fc618c54377342c05b7306b8dec72',1,'vg::HaplotypePartitioner::sequence_type()'],['../classvg_1_1Recombinator.html#a8a1ad77c3ad37fbcfa48dc5f89f591af',1,'vg::Recombinator::sequence_type()']]],
+ ['serializablehandlegraph_13862',['SerializableHandleGraph',['../namespacevg.html#a7378a177b4ed2e7be87e02a9bfcb7d4e',1,'vg']]],
+ ['state_5ftype_13863',['state_type',['../classvg_1_1PhaseUnfolder.html#a95529e399d5ef61f6a426e1b5cfe9237',1,'vg::PhaseUnfolder']]],
+ ['step_5fhandle_5ft_13864',['step_handle_t',['../namespacevg.html#a40b137bbd07d198ca2b77962eeeaf7c8',1,'vg::step_handle_t()'],['../namespacevg_1_1io.html#a5473f8a5ac351719453cfd62655beebb',1,'vg::io::step_handle_t()']]],
+ ['stored_5fedge_5ft_13865',['stored_edge_t',['../classvg_1_1DiagramExplainer.html#a6eca0d51970a6782f49171a354aaeb74',1,'vg::DiagramExplainer']]],
+ ['subrange_5ft_13866',['subrange_t',['../namespacevg.html#ae28b502adf2ce7302acbb3138280f06c',1,'vg::subrange_t()'],['../namespacehandlegraph.html#a097e656b1ffb02a80c0b530b1987984a',1,'handlegraph::subrange_t()']]],
+ ['suggested_5fedge_5ft_13867',['suggested_edge_t',['../classvg_1_1DiagramExplainer.html#ae9907aa970a58c2c6a89829c6f3020ba',1,'vg::DiagramExplainer']]],
+ ['supportmap_13868',['SupportMap',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#af8ae65b6009d1f121c27fb3ab969ef90',1,'vg::NestedCachedPackedTraversalSupportFinder']]]
];
diff --git a/search/typedefs_11.js b/search/typedefs_11.js
index 8716bb9989..dc17fd10e2 100644
--- a/search/typedefs_11.js
+++ b/search/typedefs_11.js
@@ -1,15 +1,15 @@
var searchData=
[
- ['t_13865',['T',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a830a224fa9ca0c0f9e4027f98537ddd0',1,'vg::subcommand::FlagArgSpec']]],
- ['tag_5flist_5ft_13866',['tag_list_t',['../classvg_1_1algorithms_1_1GFAParser.html#ad6ed4063154c14a6e348a5c646bae1f1',1,'vg::algorithms::GFAParser']]],
- ['taggedmessage_13867',['TaggedMessage',['../classvg_1_1io_1_1MessageIterator.html#ac914a651c928eedea34171366c9f62e8',1,'vg::io::MessageIterator']]],
- ['thread_5fids_5ft_13868',['thread_ids_t',['../namespacevg.html#a5c7b3ebb9ad8d6c01a0c54668b102c26',1,'vg']]],
- ['thread_5ft_13869',['thread_t',['../namespacevg.html#a31b8b476fb46de6667b26514b7b24fd2',1,'vg']]],
- ['time_5fpoint_13870',['time_point',['../classvg_1_1Funnel.html#a573543e4560aee58697f78cc266f22c7',1,'vg::Funnel::time_point()'],['../classvg_1_1Watchdog.html#adbdb9378ef086d2e9255f22ff9ef454d',1,'vg::Watchdog::time_point()']]],
- ['transition_5fiteratee_13871',['transition_iteratee',['../namespacevg_1_1algorithms.html#ad64245b7dca5a8144ae8720a92b65685',1,'vg::algorithms']]],
- ['transition_5fiterator_13872',['transition_iterator',['../namespacevg_1_1algorithms.html#a79c214c1e7f1d7cc5fe322b8c9fb260c',1,'vg::algorithms']]],
- ['traversal_13873',['Traversal',['../namespacevg.html#a4ea210eff71c5a1039378130f98de166',1,'vg']]],
- ['tree_5fitem_5ft_13874',['tree_item_t',['../classvg_1_1ZipCodeForest.html#a6f4d116fc7bbdf877de9a8968133f5d5',1,'vg::ZipCodeForest']]],
- ['tree_5fitem_5ftype_5ft_13875',['tree_item_type_t',['../classvg_1_1ZipCodeForest.html#a21bc3d5c8b89cd4260cdacbcd3e853df',1,'vg::ZipCodeForest']]],
- ['type_13876',['type',['../structvg_1_1Range.html#a5ea713fb16f3d49d94278914668503a9',1,'vg::Range::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html#ac5175c5d84e3de42bbf69d38196d8026',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...) const >::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html#aea61ef0da1a01e10576a705d6d1605ac',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...)>::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html#a579d806514cabd7b397ad5e0c1db94b4',1,'handlegraph::return_type_of< Returns(*)(Args...)>::type()']]]
+ ['t_13869',['T',['../structvg_1_1subcommand_1_1FlagArgSpec.html#a830a224fa9ca0c0f9e4027f98537ddd0',1,'vg::subcommand::FlagArgSpec']]],
+ ['tag_5flist_5ft_13870',['tag_list_t',['../classvg_1_1algorithms_1_1GFAParser.html#ad6ed4063154c14a6e348a5c646bae1f1',1,'vg::algorithms::GFAParser']]],
+ ['taggedmessage_13871',['TaggedMessage',['../classvg_1_1io_1_1MessageIterator.html#ac914a651c928eedea34171366c9f62e8',1,'vg::io::MessageIterator']]],
+ ['thread_5fids_5ft_13872',['thread_ids_t',['../namespacevg.html#a5c7b3ebb9ad8d6c01a0c54668b102c26',1,'vg']]],
+ ['thread_5ft_13873',['thread_t',['../namespacevg.html#a31b8b476fb46de6667b26514b7b24fd2',1,'vg']]],
+ ['time_5fpoint_13874',['time_point',['../classvg_1_1Funnel.html#a573543e4560aee58697f78cc266f22c7',1,'vg::Funnel::time_point()'],['../classvg_1_1Watchdog.html#adbdb9378ef086d2e9255f22ff9ef454d',1,'vg::Watchdog::time_point()']]],
+ ['transition_5fiteratee_13875',['transition_iteratee',['../namespacevg_1_1algorithms.html#ad64245b7dca5a8144ae8720a92b65685',1,'vg::algorithms']]],
+ ['transition_5fiterator_13876',['transition_iterator',['../namespacevg_1_1algorithms.html#a79c214c1e7f1d7cc5fe322b8c9fb260c',1,'vg::algorithms']]],
+ ['traversal_13877',['Traversal',['../namespacevg.html#a4ea210eff71c5a1039378130f98de166',1,'vg']]],
+ ['tree_5fitem_5ft_13878',['tree_item_t',['../classvg_1_1ZipCodeForest.html#a6f4d116fc7bbdf877de9a8968133f5d5',1,'vg::ZipCodeForest']]],
+ ['tree_5fitem_5ftype_5ft_13879',['tree_item_type_t',['../classvg_1_1ZipCodeForest.html#a21bc3d5c8b89cd4260cdacbcd3e853df',1,'vg::ZipCodeForest']]],
+ ['type_13880',['type',['../structvg_1_1Range.html#a5ea713fb16f3d49d94278914668503a9',1,'vg::Range::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_01const_01_4.html#ac5175c5d84e3de42bbf69d38196d8026',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...) const >::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07Owner_1_1_5_08_07Args_8_8_8_08_4.html#aea61ef0da1a01e10576a705d6d1605ac',1,'handlegraph::return_type_of< Returns(Owner::*)(Args...)>::type()'],['../structhandlegraph_1_1return__type__of_3_01Returns_07_5_08_07Args_8_8_8_08_4.html#a579d806514cabd7b397ad5e0c1db94b4',1,'handlegraph::return_type_of< Returns(*)(Args...)>::type()']]]
];
diff --git a/search/typedefs_12.js b/search/typedefs_12.js
index b72a615a5b..492df26ae6 100644
--- a/search/typedefs_12.js
+++ b/search/typedefs_12.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['validatorfunction_13877',['ValidatorFunction',['../namespacevg_1_1subcommand.html#a2b4313825cf18541121dd65b08b066e9',1,'vg::subcommand']]],
- ['value_13878',['Value',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a74a157bf3bce2696b04754f1c6dd72b9',1,'vg::Option< vector< Item >, Parser >']]],
- ['value_5ftype_13879',['value_type',['../structvg_1_1WFAPoint.html#a783bd5a58352f7be967ed9556c99f95b',1,'vg::WFAPoint::value_type()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a93f9129d2273ed4e7475456485be17b1',1,'vg::PhasedGenome::iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#a5d5cc51db9a7bee260aa4b303b8d593a',1,'std::iterator_traits< vg::PhasedGenome::iterator >::value_type()'],['../classvg_1_1SmallBitset.html#a424751e879964b97d81879b1c2ef2e25',1,'vg::SmallBitset::value_type()'],['../classvg_1_1count__back__inserter.html#a18a57c061e584b32ad1cc805c59b8a84',1,'vg::count_back_inserter::value_type()'],['../structvg_1_1VectorView_1_1const__iterator.html#a9dbd79edd9a90a030c98fe15df98749c',1,'vg::VectorView::const_iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#ae6286581a32d15a3a27ea7413e38cf4c',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a4864777b7b0405f28848b8a478867cb3',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::value_type()']]],
- ['vectorizablehandlegraph_13880',['VectorizableHandleGraph',['../namespacevg.html#a449aa64ac606119e59f71cecb8a3b218',1,'vg']]],
- ['verbosity_13881',['Verbosity',['../classvg_1_1HaplotypePartitioner.html#a7b5fa99a041f7c61f73644541dd926b1',1,'vg::HaplotypePartitioner::Verbosity()'],['../classvg_1_1Recombinator.html#a097faaea0512d01e5e7732dd1991f129',1,'vg::Recombinator::Verbosity()']]]
+ ['validatorfunction_13881',['ValidatorFunction',['../namespacevg_1_1subcommand.html#a2b4313825cf18541121dd65b08b066e9',1,'vg::subcommand']]],
+ ['value_13882',['Value',['../classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a74a157bf3bce2696b04754f1c6dd72b9',1,'vg::Option< vector< Item >, Parser >']]],
+ ['value_5ftype_13883',['value_type',['../structvg_1_1WFAPoint.html#a783bd5a58352f7be967ed9556c99f95b',1,'vg::WFAPoint::value_type()'],['../classvg_1_1PhasedGenome_1_1iterator.html#a93f9129d2273ed4e7475456485be17b1',1,'vg::PhasedGenome::iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#a5d5cc51db9a7bee260aa4b303b8d593a',1,'std::iterator_traits< vg::PhasedGenome::iterator >::value_type()'],['../classvg_1_1SmallBitset.html#a424751e879964b97d81879b1c2ef2e25',1,'vg::SmallBitset::value_type()'],['../classvg_1_1count__back__inserter.html#a18a57c061e584b32ad1cc805c59b8a84',1,'vg::count_back_inserter::value_type()'],['../structvg_1_1VectorView_1_1const__iterator.html#a9dbd79edd9a90a030c98fe15df98749c',1,'vg::VectorView::const_iterator::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#ae6286581a32d15a3a27ea7413e38cf4c',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::value_type()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a4864777b7b0405f28848b8a478867cb3',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::value_type()']]],
+ ['vectorizablehandlegraph_13884',['VectorizableHandleGraph',['../namespacevg.html#a449aa64ac606119e59f71cecb8a3b218',1,'vg']]],
+ ['verbosity_13885',['Verbosity',['../classvg_1_1HaplotypePartitioner.html#a7b5fa99a041f7c61f73644541dd926b1',1,'vg::HaplotypePartitioner::Verbosity()'],['../classvg_1_1Recombinator.html#a097faaea0512d01e5e7732dd1991f129',1,'vg::Recombinator::Verbosity()']]]
];
diff --git a/search/typedefs_13.js b/search/typedefs_13.js
index 110f762837..f51b299e65 100644
--- a/search/typedefs_13.js
+++ b/search/typedefs_13.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['window_5ft_13882',['window_t',['../classvg_1_1StreamIndexBase.html#ad94010282265d6d8743f31ed5b3e98ce',1,'vg::StreamIndexBase']]]
+ ['window_5ft_13886',['window_t',['../classvg_1_1StreamIndexBase.html#ad94010282265d6d8743f31ed5b3e98ce',1,'vg::StreamIndexBase']]]
];
diff --git a/search/typedefs_2.js b/search/typedefs_2.js
index cea9a58e2d..5a46893233 100644
--- a/search/typedefs_2.js
+++ b/search/typedefs_2.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['calltable_13767',['CallTable',['../classvg_1_1NestedFlowCaller.html#a91631dee2c59c209559b94ab7d1d171e',1,'vg::NestedFlowCaller']]],
- ['candidate_5fid_5ft_13768',['candidate_id_t',['../classvg_1_1MultipathMapper.html#a78bdd800abf19efb551d5d20ced71c55',1,'vg::MultipathMapper']]],
- ['chain_13769',['Chain',['../namespacevg.html#aceea01d66677e39af71921f1bb1911f0',1,'vg']]],
- ['chars_5ft_13770',['chars_t',['../classvg_1_1algorithms_1_1GFAParser.html#a807577028c5739ceb08abac94fe28054',1,'vg::algorithms::GFAParser']]],
- ['clock_13771',['clock',['../classvg_1_1Funnel.html#a8173e5288d688fbf38e324eeb1308978',1,'vg::Funnel::clock()'],['../classvg_1_1Watchdog.html#a7ef04f4ac4f47f7bb02f7ac1b17feb09',1,'vg::Watchdog::clock()']]],
- ['cluster_13772',['Cluster',['../classvg_1_1MinimizerMapper.html#a2a6816fe1ed45359ea629804da5dac2e',1,'vg::MinimizerMapper']]],
- ['cluster_5ft_13773',['cluster_t',['../classvg_1_1MEMClusterer.html#a846067e40dbd876a5344a62145c3326b',1,'vg::MEMClusterer']]],
- ['cluster_5ftype_13774',['cluster_type',['../classvg_1_1GaplessExtender.html#a7ac1326772ac23e766774279d39e9c04',1,'vg::GaplessExtender']]],
- ['clustergraph_5ft_13775',['clustergraph_t',['../classvg_1_1MultipathMapper.html#a7fa302a3f9a8b9993775d3789243e450',1,'vg::MultipathMapper']]],
- ['code_5ftype_13776',['code_type',['../classvg_1_1ZipCode.html#a930c205d47f41592d63fd98aefddd336',1,'vg::ZipCode::code_type()'],['../structvg_1_1MIPayload.html#a9601701523086479bbb59d0d304cf71f',1,'vg::MIPayload::code_type()']]],
- ['compact_5fsequence_5ftype_13777',['compact_sequence_type',['../classvg_1_1Haplotypes.html#aa032022df55d45eed0ad1c509a95a5c7',1,'vg::Haplotypes']]],
- ['const_5fiterator_13778',['const_iterator',['../classvg_1_1ShuffledPairs.html#a69e7d8e10d720d7e2076c901e304c5e7',1,'vg::ShuffledPairs']]],
- ['cursor_5ft_13779',['cursor_t',['../classvg_1_1IndexedVG.html#ac7a8a03a2de8d47f5b40952e62a30915',1,'vg::IndexedVG::cursor_t()'],['../classvg_1_1StreamIndex.html#a70010272f4816ddf7809a5f52a973d1c',1,'vg::StreamIndex::cursor_t()'],['../classvg_1_1StreamSorter.html#ac3d9f35b14e13610b61a55b57d2f6332',1,'vg::StreamSorter::cursor_t()'],['../classvg_1_1algorithms_1_1GFAParser.html#a644fa5c973050092141ea7cf407828c1',1,'vg::algorithms::GFAParser::cursor_t()']]]
+ ['calltable_13771',['CallTable',['../classvg_1_1NestedFlowCaller.html#a91631dee2c59c209559b94ab7d1d171e',1,'vg::NestedFlowCaller']]],
+ ['candidate_5fid_5ft_13772',['candidate_id_t',['../classvg_1_1MultipathMapper.html#a78bdd800abf19efb551d5d20ced71c55',1,'vg::MultipathMapper']]],
+ ['chain_13773',['Chain',['../namespacevg.html#aceea01d66677e39af71921f1bb1911f0',1,'vg']]],
+ ['chars_5ft_13774',['chars_t',['../classvg_1_1algorithms_1_1GFAParser.html#a807577028c5739ceb08abac94fe28054',1,'vg::algorithms::GFAParser']]],
+ ['clock_13775',['clock',['../classvg_1_1Funnel.html#a8173e5288d688fbf38e324eeb1308978',1,'vg::Funnel::clock()'],['../classvg_1_1Watchdog.html#a7ef04f4ac4f47f7bb02f7ac1b17feb09',1,'vg::Watchdog::clock()']]],
+ ['cluster_13776',['Cluster',['../classvg_1_1MinimizerMapper.html#a2a6816fe1ed45359ea629804da5dac2e',1,'vg::MinimizerMapper']]],
+ ['cluster_5ft_13777',['cluster_t',['../classvg_1_1MEMClusterer.html#a846067e40dbd876a5344a62145c3326b',1,'vg::MEMClusterer']]],
+ ['cluster_5ftype_13778',['cluster_type',['../classvg_1_1GaplessExtender.html#a7ac1326772ac23e766774279d39e9c04',1,'vg::GaplessExtender']]],
+ ['clustergraph_5ft_13779',['clustergraph_t',['../classvg_1_1MultipathMapper.html#a7fa302a3f9a8b9993775d3789243e450',1,'vg::MultipathMapper']]],
+ ['code_5ftype_13780',['code_type',['../classvg_1_1ZipCode.html#a930c205d47f41592d63fd98aefddd336',1,'vg::ZipCode::code_type()'],['../structvg_1_1MIPayload.html#a9601701523086479bbb59d0d304cf71f',1,'vg::MIPayload::code_type()']]],
+ ['compact_5fsequence_5ftype_13781',['compact_sequence_type',['../classvg_1_1Haplotypes.html#aa032022df55d45eed0ad1c509a95a5c7',1,'vg::Haplotypes']]],
+ ['const_5fiterator_13782',['const_iterator',['../classvg_1_1ShuffledPairs.html#a69e7d8e10d720d7e2076c901e304c5e7',1,'vg::ShuffledPairs']]],
+ ['cursor_5ft_13783',['cursor_t',['../classvg_1_1IndexedVG.html#ac7a8a03a2de8d47f5b40952e62a30915',1,'vg::IndexedVG::cursor_t()'],['../classvg_1_1StreamIndex.html#a70010272f4816ddf7809a5f52a973d1c',1,'vg::StreamIndex::cursor_t()'],['../classvg_1_1StreamSorter.html#ac3d9f35b14e13610b61a55b57d2f6332',1,'vg::StreamSorter::cursor_t()'],['../classvg_1_1algorithms_1_1GFAParser.html#a644fa5c973050092141ea7cf407828c1',1,'vg::algorithms::GFAParser::cursor_t()']]]
];
diff --git a/search/typedefs_3.js b/search/typedefs_3.js
index aa88e0b8b3..4570d5c41c 100644
--- a/search/typedefs_3.js
+++ b/search/typedefs_3.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['decomposition_5fsource_5ft_13780',['decomposition_source_t',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a5e521833234f94ccd3d4874d361a858b',1,'handlegraph::BuildableSnarlDecomposition']]],
- ['deletablehandlegraph_13781',['DeletableHandleGraph',['../namespacevg.html#aa6df851edf21daea75fc6dc1dd81a78f',1,'vg']]],
- ['difference_5ftype_13782',['difference_type',['../classvg_1_1count__back__inserter.html#a5179c0c806e711f2561e389293ada86f',1,'vg::count_back_inserter::difference_type()'],['../structvg_1_1VectorView_1_1const__iterator.html#a1a5f1849c8062c6ebba6a70fe5cbb1cb',1,'vg::VectorView::const_iterator::difference_type()']]],
- ['duration_13783',['duration',['../classvg_1_1Watchdog.html#aba6d996685d0d7939c5ff17176710233',1,'vg::Watchdog']]]
+ ['decomposition_5fsource_5ft_13784',['decomposition_source_t',['../classhandlegraph_1_1BuildableSnarlDecomposition.html#a5e521833234f94ccd3d4874d361a858b',1,'handlegraph::BuildableSnarlDecomposition']]],
+ ['deletablehandlegraph_13785',['DeletableHandleGraph',['../namespacevg.html#aa6df851edf21daea75fc6dc1dd81a78f',1,'vg']]],
+ ['difference_5ftype_13786',['difference_type',['../classvg_1_1count__back__inserter.html#a5179c0c806e711f2561e389293ada86f',1,'vg::count_back_inserter::difference_type()'],['../structvg_1_1VectorView_1_1const__iterator.html#a1a5f1849c8062c6ebba6a70fe5cbb1cb',1,'vg::VectorView::const_iterator::difference_type()']]],
+ ['duration_13787',['duration',['../classvg_1_1Watchdog.html#aba6d996685d0d7939c5ff17176710233',1,'vg::Watchdog']]]
];
diff --git a/search/typedefs_4.js b/search/typedefs_4.js
index 101d627c32..633ebb99d9 100644
--- a/search/typedefs_4.js
+++ b/search/typedefs_4.js
@@ -1,9 +1,9 @@
var searchData=
[
- ['edge_5fref_5ft_13784',['edge_ref_t',['../classvg_1_1DiagramExplainer.html#a2d4b4c635125dbf94228a6bf7d245254',1,'vg::DiagramExplainer']]],
- ['edge_5ft_13785',['edge_t',['../namespacevg.html#a3de8fe5f38b1730a36af4ad9c4258963',1,'vg::edge_t()'],['../namespacehandlegraph.html#a91452647367df9cfc96454c0cd07ce7b',1,'handlegraph::edge_t()'],['../namespacevg_1_1io.html#a51e10b2bc70fa91b79b32c5aadeab4ff',1,'vg::io::edge_t()']]],
- ['edgemapping_13786',['EdgeMapping',['../namespacevg.html#a7a29090bbc6b842c2362f9da44a4a57c',1,'vg']]],
- ['effective_5fposition_5ft_13787',['effective_position_t',['../classvg_1_1Funnel.html#a56cbd7625da0c6a99ce37fac67513c55',1,'vg::Funnel']]],
- ['emitter_5ft_13788',['emitter_t',['../classvg_1_1StreamSorter.html#a6454b204b096a5736ce98310aada955d',1,'vg::StreamSorter']]],
- ['exon_5fnodes_5ft_13789',['exon_nodes_t',['../namespacevg.html#a8ae488d495e344881cbcf599ebdd2355',1,'vg']]]
+ ['edge_5fref_5ft_13788',['edge_ref_t',['../classvg_1_1DiagramExplainer.html#a2d4b4c635125dbf94228a6bf7d245254',1,'vg::DiagramExplainer']]],
+ ['edge_5ft_13789',['edge_t',['../namespacevg.html#a3de8fe5f38b1730a36af4ad9c4258963',1,'vg::edge_t()'],['../namespacehandlegraph.html#a91452647367df9cfc96454c0cd07ce7b',1,'handlegraph::edge_t()'],['../namespacevg_1_1io.html#a51e10b2bc70fa91b79b32c5aadeab4ff',1,'vg::io::edge_t()']]],
+ ['edgemapping_13790',['EdgeMapping',['../namespacevg.html#a7a29090bbc6b842c2362f9da44a4a57c',1,'vg']]],
+ ['effective_5fposition_5ft_13791',['effective_position_t',['../classvg_1_1Funnel.html#a56cbd7625da0c6a99ce37fac67513c55',1,'vg::Funnel']]],
+ ['emitter_5ft_13792',['emitter_t',['../classvg_1_1StreamSorter.html#a6454b204b096a5736ce98310aada955d',1,'vg::StreamSorter']]],
+ ['exon_5fnodes_5ft_13793',['exon_nodes_t',['../namespacevg.html#a8ae488d495e344881cbcf599ebdd2355',1,'vg']]]
];
diff --git a/search/typedefs_5.js b/search/typedefs_5.js
index 05f25d7a2b..4ac9f07fc1 100644
--- a/search/typedefs_5.js
+++ b/search/typedefs_5.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['feature_5ft_13790',['feature_t',['../annotate__main_8cpp.html#a5a0961fa7aa44ef6daf62ffda946003b',1,'annotate_main.cpp']]]
+ ['feature_5ft_13794',['feature_t',['../annotate__main_8cpp.html#a5a0961fa7aa44ef6daf62ffda946003b',1,'annotate_main.cpp']]]
];
diff --git a/search/typedefs_6.js b/search/typedefs_6.js
index b651e79051..85c3b142ff 100644
--- a/search/typedefs_6.js
+++ b/search/typedefs_6.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['gamindex_13791',['GAMIndex',['../namespacevg.html#a9b677be2f409ffcbefd5d9f6149c80c1',1,'vg']]],
- ['gamsorter_13792',['GAMSorter',['../namespacevg.html#a6c00bf57d75db83e41ac19a88882c043',1,'vg']]],
- ['gen_5fflat_5fnode_13793',['gen_flat_node',['../structhaplo_1_1haplo__DP__rectangle.html#a87d1fd7ca4ac40321f912724bf5c3f8c',1,'haplo::haplo_DP_rectangle']]],
- ['gen_5frange_5ft_13794',['gen_range_t',['../structhaplo_1_1haplo__DP__rectangle.html#af3fc7fee833ac23bdbc93f73fb5be9d9',1,'haplo::haplo_DP_rectangle']]],
- ['group_5flistener_5ft_13795',['group_listener_t',['../classvg_1_1io_1_1MessageEmitter.html#a4569ac626dfd036074603cc6f05d55e1',1,'vg::io::MessageEmitter::group_listener_t()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a3fdef59aeb9c688e752463a2257ebbfd',1,'vg::io::ProtobufEmitter::group_listener_t()']]]
+ ['gamindex_13795',['GAMIndex',['../namespacevg.html#a9b677be2f409ffcbefd5d9f6149c80c1',1,'vg']]],
+ ['gamsorter_13796',['GAMSorter',['../namespacevg.html#a6c00bf57d75db83e41ac19a88882c043',1,'vg']]],
+ ['gen_5fflat_5fnode_13797',['gen_flat_node',['../structhaplo_1_1haplo__DP__rectangle.html#a87d1fd7ca4ac40321f912724bf5c3f8c',1,'haplo::haplo_DP_rectangle']]],
+ ['gen_5frange_5ft_13798',['gen_range_t',['../structhaplo_1_1haplo__DP__rectangle.html#af3fc7fee833ac23bdbc93f73fb5be9d9',1,'haplo::haplo_DP_rectangle']]],
+ ['group_5flistener_5ft_13799',['group_listener_t',['../classvg_1_1io_1_1MessageEmitter.html#a4569ac626dfd036074603cc6f05d55e1',1,'vg::io::MessageEmitter::group_listener_t()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a3fdef59aeb9c688e752463a2257ebbfd',1,'vg::io::ProtobufEmitter::group_listener_t()']]]
];
diff --git a/search/typedefs_7.js b/search/typedefs_7.js
index 302c072c5b..b35bffdfa7 100644
--- a/search/typedefs_7.js
+++ b/search/typedefs_7.js
@@ -1,10 +1,10 @@
var searchData=
[
- ['handle2component_13796',['Handle2Component',['../namespacevg.html#a7143bc6d4008d03bc4a0ac4d4ba26948',1,'vg']]],
- ['handle_5ft_13797',['handle_t',['../namespacevg.html#aaed4a2b7bc668cf2e076733ee26e036a',1,'vg::handle_t()'],['../namespacevg_1_1io.html#a3943ae5818e3556e216014f0df531502',1,'vg::io::handle_t()']]],
- ['handlegraph_13798',['HandleGraph',['../namespacevg.html#ad5781c55c25f1446e1fc74c72c051c62',1,'vg::HandleGraph()'],['../namespacevg_1_1io.html#a172e1fe036e09c51c5a60918463de08f',1,'vg::io::HandleGraph()']]],
- ['handleset_13799',['HandleSet',['../namespacevg.html#a0942a662fe36dad76d2d0e310ec66e3f',1,'vg']]],
- ['haplo_5fscore_5ftype_13800',['haplo_score_type',['../namespacehaplo.html#aa35eb194ac0f5a70dae8d2283c170736',1,'haplo']]],
- ['hit_5ft_13801',['hit_t',['../classvg_1_1MEMClusterer.html#a679c48e684ac52020fb363aa946037c7',1,'vg::MEMClusterer']]],
- ['holder_13802',['Holder',['../structvg_1_1subcommand_1_1RangeArgSpec.html#ad4fcbe28c637e8a88821368d02ec7621',1,'vg::subcommand::RangeArgSpec::Holder()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ad6398c9b83de015bcad49cf70c0e572f',1,'vg::subcommand::FlagArgSpec::Holder()']]]
+ ['handle2component_13800',['Handle2Component',['../namespacevg.html#a7143bc6d4008d03bc4a0ac4d4ba26948',1,'vg']]],
+ ['handle_5ft_13801',['handle_t',['../namespacevg.html#aaed4a2b7bc668cf2e076733ee26e036a',1,'vg::handle_t()'],['../namespacevg_1_1io.html#a3943ae5818e3556e216014f0df531502',1,'vg::io::handle_t()']]],
+ ['handlegraph_13802',['HandleGraph',['../namespacevg.html#ad5781c55c25f1446e1fc74c72c051c62',1,'vg::HandleGraph()'],['../namespacevg_1_1io.html#a172e1fe036e09c51c5a60918463de08f',1,'vg::io::HandleGraph()']]],
+ ['handleset_13803',['HandleSet',['../namespacevg.html#a0942a662fe36dad76d2d0e310ec66e3f',1,'vg']]],
+ ['haplo_5fscore_5ftype_13804',['haplo_score_type',['../namespacehaplo.html#aa35eb194ac0f5a70dae8d2283c170736',1,'haplo']]],
+ ['hit_5ft_13805',['hit_t',['../classvg_1_1MEMClusterer.html#a679c48e684ac52020fb363aa946037c7',1,'vg::MEMClusterer']]],
+ ['holder_13806',['Holder',['../structvg_1_1subcommand_1_1RangeArgSpec.html#ad4fcbe28c637e8a88821368d02ec7621',1,'vg::subcommand::RangeArgSpec::Holder()'],['../structvg_1_1subcommand_1_1FlagArgSpec.html#ad6398c9b83de015bcad49cf70c0e572f',1,'vg::subcommand::FlagArgSpec::Holder()']]]
];
diff --git a/search/typedefs_8.js b/search/typedefs_8.js
index 981df8fe0f..86473bb1fd 100644
--- a/search/typedefs_8.js
+++ b/search/typedefs_8.js
@@ -1,10 +1,10 @@
var searchData=
[
- ['id_5ft_13803',['id_t',['../namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821',1,'vg::id_t()'],['../namespacehandlegraph.html#a9d001e7b9d625e6b4ef53430e6a0c180',1,'handlegraph::id_t()']]],
- ['immutablepath_13804',['ImmutablePath',['../classvg_1_1MinimizerMapper.html#af12f40d8ae25f153fba1dc122fda29f0',1,'vg::MinimizerMapper']]],
- ['incrementalsearchstate_13805',['IncrementalSearchState',['../namespacehaplo.html#ae3347fe51140216cb836936c306c97bf',1,'haplo']]],
- ['indexgroup_13806',['IndexGroup',['../namespacevg.html#a96bc10f0ba77bc672e88a9f7d6e126b6',1,'vg']]],
- ['indexname_13807',['IndexName',['../namespacevg.html#a7027e98a84fa4b0fa42f72bf4a1d862f',1,'vg']]],
- ['iterator_13808',['iterator',['../structvg_1_1PathIndex.html#a0a0f36c0f57cc92dfb70f05eb4e5c482',1,'vg::PathIndex']]],
- ['iterator_5fcategory_13809',['iterator_category',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#afe1f2a02d394f83c867bdca78ac9fc50',1,'std::iterator_traits< vg::PhasedGenome::iterator >::iterator_category()'],['../classvg_1_1count__back__inserter.html#a21cffdfe58f87b579e5f71c16390e39d',1,'vg::count_back_inserter::iterator_category()'],['../structvg_1_1VectorView_1_1const__iterator.html#a3e5943959256e2400b3ab9b486cad7a9',1,'vg::VectorView::const_iterator::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#a11520b7b8d397962dd529faebccde56a',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a01b368cc72243f1d414e88999b856b34',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::iterator_category()']]]
+ ['id_5ft_13807',['id_t',['../namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821',1,'vg::id_t()'],['../namespacehandlegraph.html#a9d001e7b9d625e6b4ef53430e6a0c180',1,'handlegraph::id_t()']]],
+ ['immutablepath_13808',['ImmutablePath',['../classvg_1_1MinimizerMapper.html#af12f40d8ae25f153fba1dc122fda29f0',1,'vg::MinimizerMapper']]],
+ ['incrementalsearchstate_13809',['IncrementalSearchState',['../namespacehaplo.html#ae3347fe51140216cb836936c306c97bf',1,'haplo']]],
+ ['indexgroup_13810',['IndexGroup',['../namespacevg.html#a96bc10f0ba77bc672e88a9f7d6e126b6',1,'vg']]],
+ ['indexname_13811',['IndexName',['../namespacevg.html#a7027e98a84fa4b0fa42f72bf4a1d862f',1,'vg']]],
+ ['iterator_13812',['iterator',['../structvg_1_1PathIndex.html#a0a0f36c0f57cc92dfb70f05eb4e5c482',1,'vg::PathIndex']]],
+ ['iterator_5fcategory_13813',['iterator_category',['../structstd_1_1iterator__traits_3_01vg_1_1PhasedGenome_1_1iterator_01_4.html#afe1f2a02d394f83c867bdca78ac9fc50',1,'std::iterator_traits< vg::PhasedGenome::iterator >::iterator_category()'],['../classvg_1_1count__back__inserter.html#a21cffdfe58f87b579e5f71c16390e39d',1,'vg::count_back_inserter::iterator_category()'],['../structvg_1_1VectorView_1_1const__iterator.html#a3e5943959256e2400b3ab9b486cad7a9',1,'vg::VectorView::const_iterator::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1iterator_01_4.html#a11520b7b8d397962dd529faebccde56a',1,'std::iterator_traits< vg::ZipCodeTree::iterator >::iterator_category()'],['../structstd_1_1iterator__traits_3_01vg_1_1ZipCodeTree_1_1reverse__iterator_01_4.html#a01b368cc72243f1d414e88999b856b34',1,'std::iterator_traits< vg::ZipCodeTree::reverse_iterator >::iterator_category()']]]
];
diff --git a/search/typedefs_9.js b/search/typedefs_9.js
index 05d24b3873..2d45a345f8 100644
--- a/search/typedefs_9.js
+++ b/search/typedefs_9.js
@@ -1,5 +1,5 @@
var searchData=
[
- ['key_5ftype_13810',['key_type',['../structvg_1_1WFAPoint.html#a7f118f60c7b8ac46926e6627afaa4d23',1,'vg::WFAPoint']]],
- ['kmer_5ftype_13811',['kmer_type',['../classvg_1_1ParallelKFFReader.html#a2691b5fdcfab5c9b5187fdf3a979e2e1',1,'vg::ParallelKFFReader::kmer_type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a13b4b76384742f4ee127b52faff37aa6',1,'vg::Haplotypes::Subchain::kmer_type()'],['../classvg_1_1HaplotypePartitioner.html#a2780337120cfec8463356829af22aa97',1,'vg::HaplotypePartitioner::kmer_type()']]]
+ ['key_5ftype_13814',['key_type',['../structvg_1_1WFAPoint.html#a7f118f60c7b8ac46926e6627afaa4d23',1,'vg::WFAPoint']]],
+ ['kmer_5ftype_13815',['kmer_type',['../classvg_1_1ParallelKFFReader.html#a2691b5fdcfab5c9b5187fdf3a979e2e1',1,'vg::ParallelKFFReader::kmer_type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a13b4b76384742f4ee127b52faff37aa6',1,'vg::Haplotypes::Subchain::kmer_type()'],['../classvg_1_1HaplotypePartitioner.html#a2780337120cfec8463356829af22aa97',1,'vg::HaplotypePartitioner::kmer_type()']]]
];
diff --git a/search/typedefs_a.js b/search/typedefs_a.js
index 23a287a5c0..b5b5e0355a 100644
--- a/search/typedefs_a.js
+++ b/search/typedefs_a.js
@@ -1,4 +1,4 @@
var searchData=
[
- ['load_5ffunction_5ft_13812',['load_function_t',['../namespacevg_1_1io.html#a645533291ad3ae31bd8db73e51b3ac31',1,'vg::io']]]
+ ['load_5ffunction_5ft_13816',['load_function_t',['../namespacevg_1_1io.html#a645533291ad3ae31bd8db73e51b3ac31',1,'vg::io']]]
];
diff --git a/search/typedefs_b.js b/search/typedefs_b.js
index 2fd558a3b4..b2d426ed2f 100644
--- a/search/typedefs_b.js
+++ b/search/typedefs_b.js
@@ -1,15 +1,15 @@
var searchData=
[
- ['map_5fentry_5ftype_13813',['map_entry_type',['../structvg_1_1WFAPoint.html#ac125c09256ece943d40cf65152a9837a',1,'vg::WFAPoint']]],
- ['mapping_5ftype_13814',['mapping_type',['../structvg_1_1RebuildJob.html#afdbb259fb3fc369a7824f6420b2043c0',1,'vg::RebuildJob']]],
- ['match_5ffanouts_5ft_13815',['match_fanouts_t',['../classvg_1_1MEMClusterer.html#a3127930f2b575bed2937c21382924480',1,'vg::MEMClusterer::match_fanouts_t()'],['../classvg_1_1MultipathMapper.html#a165e5c0531ff4337ce6542da263d3fbd',1,'vg::MultipathMapper::match_fanouts_t()']]],
- ['memcluster_5ft_13816',['memcluster_t',['../classvg_1_1MultipathMapper.html#acae95760b8750cf3b2bb48d00fe499fd',1,'vg::MultipathMapper']]],
- ['message_5fconsumer_5ffunction_5ft_13817',['message_consumer_function_t',['../namespacevg_1_1io.html#a618e8c9e44f63328bb2c0742ab0e69c2',1,'vg::io']]],
- ['message_5flistener_5ft_13818',['message_listener_t',['../classvg_1_1io_1_1ProtobufEmitter.html#a735167dc9e644a83d0e9fd206b241ce1',1,'vg::io::ProtobufEmitter']]],
- ['message_5fsender_5ffunction_5ft_13819',['message_sender_function_t',['../namespacevg_1_1io.html#a26ea41d1ec4cf44b436a345f1eefccf1',1,'vg::io']]],
- ['minimizer_5findex_5ftype_13820',['minimizer_index_type',['../classvg_1_1HaplotypePartitioner.html#a9a059ded0fd7ed983801fa4d16f7cd5d',1,'vg::HaplotypePartitioner']]],
- ['mutablehandlegraph_13821',['MutableHandleGraph',['../namespacevg.html#a293aa7465cc63a2581914d6a85a0e4b8',1,'vg']]],
- ['mutablepathdeletablehandlegraph_13822',['MutablePathDeletableHandleGraph',['../namespacevg.html#a2f0cc7bac7a4f92b2b523357f8940aa5',1,'vg']]],
- ['mutablepathhandlegraph_13823',['MutablePathHandleGraph',['../namespacevg.html#a24350c08e6d69244e6930f41fee00e1f',1,'vg']]],
- ['mutablepathmutablehandlegraph_13824',['MutablePathMutableHandleGraph',['../namespacevg.html#aa2f83c48d4ecdcfd8f2604f10e863aea',1,'vg']]]
+ ['map_5fentry_5ftype_13817',['map_entry_type',['../structvg_1_1WFAPoint.html#ac125c09256ece943d40cf65152a9837a',1,'vg::WFAPoint']]],
+ ['mapping_5ftype_13818',['mapping_type',['../structvg_1_1RebuildJob.html#afdbb259fb3fc369a7824f6420b2043c0',1,'vg::RebuildJob']]],
+ ['match_5ffanouts_5ft_13819',['match_fanouts_t',['../classvg_1_1MEMClusterer.html#a3127930f2b575bed2937c21382924480',1,'vg::MEMClusterer::match_fanouts_t()'],['../classvg_1_1MultipathMapper.html#a165e5c0531ff4337ce6542da263d3fbd',1,'vg::MultipathMapper::match_fanouts_t()']]],
+ ['memcluster_5ft_13820',['memcluster_t',['../classvg_1_1MultipathMapper.html#acae95760b8750cf3b2bb48d00fe499fd',1,'vg::MultipathMapper']]],
+ ['message_5fconsumer_5ffunction_5ft_13821',['message_consumer_function_t',['../namespacevg_1_1io.html#a618e8c9e44f63328bb2c0742ab0e69c2',1,'vg::io']]],
+ ['message_5flistener_5ft_13822',['message_listener_t',['../classvg_1_1io_1_1ProtobufEmitter.html#a735167dc9e644a83d0e9fd206b241ce1',1,'vg::io::ProtobufEmitter']]],
+ ['message_5fsender_5ffunction_5ft_13823',['message_sender_function_t',['../namespacevg_1_1io.html#a26ea41d1ec4cf44b436a345f1eefccf1',1,'vg::io']]],
+ ['minimizer_5findex_5ftype_13824',['minimizer_index_type',['../classvg_1_1HaplotypePartitioner.html#a9a059ded0fd7ed983801fa4d16f7cd5d',1,'vg::HaplotypePartitioner']]],
+ ['mutablehandlegraph_13825',['MutableHandleGraph',['../namespacevg.html#a293aa7465cc63a2581914d6a85a0e4b8',1,'vg']]],
+ ['mutablepathdeletablehandlegraph_13826',['MutablePathDeletableHandleGraph',['../namespacevg.html#a2f0cc7bac7a4f92b2b523357f8940aa5',1,'vg']]],
+ ['mutablepathhandlegraph_13827',['MutablePathHandleGraph',['../namespacevg.html#a24350c08e6d69244e6930f41fee00e1f',1,'vg']]],
+ ['mutablepathmutablehandlegraph_13828',['MutablePathMutableHandleGraph',['../namespacevg.html#aa2f83c48d4ecdcfd8f2604f10e863aea',1,'vg']]]
];
diff --git a/search/typedefs_c.js b/search/typedefs_c.js
index b5dca37b9a..8615e2c8fd 100644
--- a/search/typedefs_c.js
+++ b/search/typedefs_c.js
@@ -1,8 +1,8 @@
var searchData=
[
- ['namednodebacktranslation_13825',['NamedNodeBackTranslation',['../namespacevg.html#a2c7b4f84e5a75aee3d3abf4b65b0000f',1,'vg']]],
- ['net_5fidentifier_5ft_13826',['net_identifier_t',['../namespacevg.html#a064c859d9612d9c2b240b9c0d01f8a85',1,'vg']]],
- ['nid_5ft_13827',['nid_t',['../namespacevg.html#a26f660292f00451f15d1c95d9b8c6ffb',1,'vg::nid_t()'],['../namespacexg.html#a8f8752f074f0e121862f9dd3aabfbb45',1,'xg::nid_t()'],['../namespacehandlegraph.html#a93c2889b752934c4b2488b37cbdd278b',1,'handlegraph::nid_t()'],['../namespacevg_1_1io.html#a43c8209ab6c2c1d48c0ca50c24fd0d13',1,'vg::io::nid_t()']]],
- ['node_13828',['Node',['../structvg_1_1Tree.html#ad5b04c67e4c1390c2ae46d1db40548f7',1,'vg::Tree']]],
- ['nodetype_13829',['nodeType',['../structhaplo_1_1linear__haplo__structure.html#a2eb8780c98a02ad3a070d3d2b027170e',1,'haplo::linear_haplo_structure']]]
+ ['namednodebacktranslation_13829',['NamedNodeBackTranslation',['../namespacevg.html#a2c7b4f84e5a75aee3d3abf4b65b0000f',1,'vg']]],
+ ['net_5fidentifier_5ft_13830',['net_identifier_t',['../namespacevg.html#a064c859d9612d9c2b240b9c0d01f8a85',1,'vg']]],
+ ['nid_5ft_13831',['nid_t',['../namespacevg.html#a26f660292f00451f15d1c95d9b8c6ffb',1,'vg::nid_t()'],['../namespacexg.html#a8f8752f074f0e121862f9dd3aabfbb45',1,'xg::nid_t()'],['../namespacehandlegraph.html#a93c2889b752934c4b2488b37cbdd278b',1,'handlegraph::nid_t()'],['../namespacevg_1_1io.html#a43c8209ab6c2c1d48c0ca50c24fd0d13',1,'vg::io::nid_t()']]],
+ ['node_13832',['Node',['../structvg_1_1Tree.html#ad5b04c67e4c1390c2ae46d1db40548f7',1,'vg::Tree']]],
+ ['nodetype_13833',['nodeType',['../structhaplo_1_1linear__haplo__structure.html#a2eb8780c98a02ad3a070d3d2b027170e',1,'haplo::linear_haplo_structure']]]
];
diff --git a/search/typedefs_d.js b/search/typedefs_d.js
index 5e10dff130..77e9ddd227 100644
--- a/search/typedefs_d.js
+++ b/search/typedefs_d.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['off_5ft_13830',['off_t',['../namespacehandlegraph.html#a0dcae34b861ba40c47d177dc06537bf7',1,'handlegraph']]],
- ['offset_5ft_13831',['offset_t',['../namespacevg.html#afe223f2c7890c76de5e00b43ceb37add',1,'vg::offset_t()'],['../namespacehandlegraph.html#a5aba28c40bd7f181cac4e8d73d6edef8',1,'handlegraph::offset_t()']]],
- ['oriented_5fnode_5frange_5ft_13832',['oriented_node_range_t',['../namespacevg.html#acf54b55d1c1d16a3d64f1bae268a58af',1,'vg::oriented_node_range_t()'],['../namespacehandlegraph.html#aa9a6ea7613d52c42947d4faa2a189bba',1,'handlegraph::oriented_node_range_t()']]]
+ ['off_5ft_13834',['off_t',['../namespacehandlegraph.html#a0dcae34b861ba40c47d177dc06537bf7',1,'handlegraph']]],
+ ['offset_5ft_13835',['offset_t',['../namespacevg.html#afe223f2c7890c76de5e00b43ceb37add',1,'vg::offset_t()'],['../namespacehandlegraph.html#a5aba28c40bd7f181cac4e8d73d6edef8',1,'handlegraph::offset_t()']]],
+ ['oriented_5fnode_5frange_5ft_13836',['oriented_node_range_t',['../namespacevg.html#acf54b55d1c1d16a3d64f1bae268a58af',1,'vg::oriented_node_range_t()'],['../namespacehandlegraph.html#aa9a6ea7613d52c42947d4faa2a189bba',1,'handlegraph::oriented_node_range_t()']]]
];
diff --git a/search/typedefs_e.js b/search/typedefs_e.js
index db84f8dcb7..47fc6dbba7 100644
--- a/search/typedefs_e.js
+++ b/search/typedefs_e.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['param_5ftype_13833',['param_type',['../classvg_1_1discrete__distribution.html#a923a04239b0ceb7026d193aa671100e4',1,'vg::discrete_distribution']]],
- ['pareto_5fpoint_13834',['pareto_point',['../namespacevg.html#a1aa2d026eb3edc0c692e19e5a493feef',1,'vg']]],
- ['path_5fchunk_5ft_13835',['path_chunk_t',['../classvg_1_1Surjector.html#a3ce06e344f93607bd066fd58d33fc7e0',1,'vg::Surjector']]],
- ['path_5fhandle_5ft_13836',['path_handle_t',['../namespacevg.html#aaf7aeec04909c1aac0ad991764d48e24',1,'vg::path_handle_t()'],['../namespacevg_1_1io.html#a5cab7a1a96fc203865d8ca67a372b24f',1,'vg::io::path_handle_t()']]],
- ['path_5foffset_5fcollection_5ft_13837',['path_offset_collection_t',['../namespacevg_1_1algorithms.html#a6474017f8ab54b0c6e20095206a880a8',1,'vg::algorithms']]],
- ['path_5ftype_13838',['path_type',['../classvg_1_1PhaseUnfolder.html#a402b0f84990279594bfbb1cd71ffd8e5',1,'vg::PhaseUnfolder::path_type()'],['../structjob__type.html#a8749aa5a745848ff8d5a6e72bdc002e6',1,'job_type::path_type()']]],
- ['pathhandlegraph_13839',['PathHandleGraph',['../namespacevg.html#abeb2636bd0db3101259ef6803cb4e591',1,'vg']]],
- ['pathinterval_13840',['PathInterval',['../namespacevg.html#ae8f438fe1484a4bcc51d06ad13058c9c',1,'vg']]],
- ['pathmetadata_13841',['PathMetadata',['../namespacevg.html#ab5f7f6692a7600f1fa62428255c5bb61',1,'vg']]],
- ['pathpositionhandlegraph_13842',['PathPositionHandleGraph',['../namespacevg.html#a2481be7fa8c46933b9b99108e4c797b3',1,'vg']]],
- ['pathsense_13843',['PathSense',['../namespacevg.html#a15c1e75e93ab89aacd0eb7e1f0299724',1,'vg']]],
- ['pointer_13844',['pointer',['../classvg_1_1count__back__inserter.html#ab120548e9cd73fcc1ed1f8680b4b5baa',1,'vg::count_back_inserter::pointer()'],['../structvg_1_1VectorView_1_1const__iterator.html#a8b8e23d22e4b85f617c466337d5f0ea2',1,'vg::VectorView::const_iterator::pointer()']]],
- ['pos_5ft_13845',['pos_t',['../namespacevg.html#a8232142f432c4dd8e7cfe96e1f50e039',1,'vg::pos_t()'],['../namespacexg.html#aa22555920305243ff489dc6ed79db5d7',1,'xg::pos_t()'],['../namespacehandlegraph.html#a0abc3c64da852112ad2bc0fc9dd5afce',1,'handlegraph::pos_t()']]]
+ ['param_5ftype_13837',['param_type',['../classvg_1_1discrete__distribution.html#a923a04239b0ceb7026d193aa671100e4',1,'vg::discrete_distribution']]],
+ ['pareto_5fpoint_13838',['pareto_point',['../namespacevg.html#a1aa2d026eb3edc0c692e19e5a493feef',1,'vg']]],
+ ['path_5fchunk_5ft_13839',['path_chunk_t',['../classvg_1_1Surjector.html#a3ce06e344f93607bd066fd58d33fc7e0',1,'vg::Surjector']]],
+ ['path_5fhandle_5ft_13840',['path_handle_t',['../namespacevg.html#aaf7aeec04909c1aac0ad991764d48e24',1,'vg::path_handle_t()'],['../namespacevg_1_1io.html#a5cab7a1a96fc203865d8ca67a372b24f',1,'vg::io::path_handle_t()']]],
+ ['path_5foffset_5fcollection_5ft_13841',['path_offset_collection_t',['../namespacevg_1_1algorithms.html#a6474017f8ab54b0c6e20095206a880a8',1,'vg::algorithms']]],
+ ['path_5ftype_13842',['path_type',['../classvg_1_1PhaseUnfolder.html#a402b0f84990279594bfbb1cd71ffd8e5',1,'vg::PhaseUnfolder::path_type()'],['../structjob__type.html#a8749aa5a745848ff8d5a6e72bdc002e6',1,'job_type::path_type()']]],
+ ['pathhandlegraph_13843',['PathHandleGraph',['../namespacevg.html#abeb2636bd0db3101259ef6803cb4e591',1,'vg']]],
+ ['pathinterval_13844',['PathInterval',['../namespacevg.html#ae8f438fe1484a4bcc51d06ad13058c9c',1,'vg']]],
+ ['pathmetadata_13845',['PathMetadata',['../namespacevg.html#ab5f7f6692a7600f1fa62428255c5bb61',1,'vg']]],
+ ['pathpositionhandlegraph_13846',['PathPositionHandleGraph',['../namespacevg.html#a2481be7fa8c46933b9b99108e4c797b3',1,'vg']]],
+ ['pathsense_13847',['PathSense',['../namespacevg.html#a15c1e75e93ab89aacd0eb7e1f0299724',1,'vg']]],
+ ['pointer_13848',['pointer',['../classvg_1_1count__back__inserter.html#ab120548e9cd73fcc1ed1f8680b4b5baa',1,'vg::count_back_inserter::pointer()'],['../structvg_1_1VectorView_1_1const__iterator.html#a8b8e23d22e4b85f617c466337d5f0ea2',1,'vg::VectorView::const_iterator::pointer()']]],
+ ['pos_5ft_13849',['pos_t',['../namespacevg.html#a8232142f432c4dd8e7cfe96e1f50e039',1,'vg::pos_t()'],['../namespacexg.html#aa22555920305243ff489dc6ed79db5d7',1,'xg::pos_t()'],['../namespacehandlegraph.html#a0abc3c64da852112ad2bc0fc9dd5afce',1,'handlegraph::pos_t()']]]
];
diff --git a/search/typedefs_f.js b/search/typedefs_f.js
index 38a4bcdfe4..c89314c612 100644
--- a/search/typedefs_f.js
+++ b/search/typedefs_f.js
@@ -1,10 +1,10 @@
var searchData=
[
- ['rankedhandlegraph_13846',['RankedHandleGraph',['../namespacevg.html#a215e44b59d26cf0745f02218dfd902a2',1,'vg']]],
- ['real_5ft_13847',['real_t',['../namespacevg.html#a7392de2ef03532b2ec3461ebb178c75a',1,'vg']]],
- ['recipefunc_13848',['RecipeFunc',['../namespacevg.html#a1ff09b399af11722aeee121ae6f4fd9b',1,'vg']]],
- ['recipename_13849',['RecipeName',['../namespacevg.html#a6119d0b9707c042b0c2cde5d77b670cb',1,'vg']]],
- ['reference_13850',['reference',['../classvg_1_1count__back__inserter.html#a84eca4db3ffead0102aa62bd53000631',1,'vg::count_back_inserter::reference()'],['../structvg_1_1VectorView_1_1const__iterator.html#a037cb8cbbd9c2be6c471ee6aa9bfbb1d',1,'vg::VectorView::const_iterator::reference()']]],
- ['referencepathvectorizableoverlayhelper_13851',['ReferencePathVectorizableOverlayHelper',['../call__main_8cpp.html#adc0e01cf2a62b559e7c67d23dfbd757e',1,'call_main.cpp']]],
- ['result_5ftype_13852',['result_type',['../classvg_1_1uniform__real__distribution.html#a45f57ac9dad3e93958eda6a596748faa',1,'vg::uniform_real_distribution::result_type()'],['../classvg_1_1normal__distribution.html#a3cf267467b3608710fc42fc70f5df9ab',1,'vg::normal_distribution::result_type()'],['../classvg_1_1truncated__normal__distribution.html#a4a25c23c8e6024d988a0ac8617415897',1,'vg::truncated_normal_distribution::result_type()'],['../classvg_1_1WideningPRNG.html#a167ab33bf96b19131d4d85738c37e5ce',1,'vg::WideningPRNG::result_type()'],['../classvg_1_1uniform__int__distribution.html#a06f14fe90ff4a3b995f9e2100b11487d',1,'vg::uniform_int_distribution::result_type()'],['../classvg_1_1discrete__distribution.html#a06c8d8862509e0b67c9ed940b7a6c204',1,'vg::discrete_distribution::result_type()']]]
+ ['rankedhandlegraph_13850',['RankedHandleGraph',['../namespacevg.html#a215e44b59d26cf0745f02218dfd902a2',1,'vg']]],
+ ['real_5ft_13851',['real_t',['../namespacevg.html#a7392de2ef03532b2ec3461ebb178c75a',1,'vg']]],
+ ['recipefunc_13852',['RecipeFunc',['../namespacevg.html#a1ff09b399af11722aeee121ae6f4fd9b',1,'vg']]],
+ ['recipename_13853',['RecipeName',['../namespacevg.html#a6119d0b9707c042b0c2cde5d77b670cb',1,'vg']]],
+ ['reference_13854',['reference',['../classvg_1_1count__back__inserter.html#a84eca4db3ffead0102aa62bd53000631',1,'vg::count_back_inserter::reference()'],['../structvg_1_1VectorView_1_1const__iterator.html#a037cb8cbbd9c2be6c471ee6aa9bfbb1d',1,'vg::VectorView::const_iterator::reference()']]],
+ ['referencepathvectorizableoverlayhelper_13855',['ReferencePathVectorizableOverlayHelper',['../call__main_8cpp.html#adc0e01cf2a62b559e7c67d23dfbd757e',1,'call_main.cpp']]],
+ ['result_5ftype_13856',['result_type',['../classvg_1_1uniform__real__distribution.html#a45f57ac9dad3e93958eda6a596748faa',1,'vg::uniform_real_distribution::result_type()'],['../classvg_1_1normal__distribution.html#a3cf267467b3608710fc42fc70f5df9ab',1,'vg::normal_distribution::result_type()'],['../classvg_1_1truncated__normal__distribution.html#a4a25c23c8e6024d988a0ac8617415897',1,'vg::truncated_normal_distribution::result_type()'],['../classvg_1_1WideningPRNG.html#a167ab33bf96b19131d4d85738c37e5ce',1,'vg::WideningPRNG::result_type()'],['../classvg_1_1uniform__int__distribution.html#a06f14fe90ff4a3b995f9e2100b11487d',1,'vg::uniform_int_distribution::result_type()'],['../classvg_1_1discrete__distribution.html#a06c8d8862509e0b67c9ed940b7a6c204',1,'vg::discrete_distribution::result_type()']]]
];
diff --git a/search/variables_0.js b/search/variables_0.js
index 16e69bdff7..a7e9a1d5bc 100644
--- a/search/variables_0.js
+++ b/search/variables_0.js
@@ -1,26 +1,26 @@
var searchData=
[
- ['_5fannotation_11713',['_annotation',['../classvg_1_1multipath__alignment__t.html#a2335046b7a55314644af26787ce17c57',1,'vg::multipath_alignment_t']]],
- ['_5fconnection_11714',['_connection',['../classvg_1_1subpath__t.html#aeff77a67cc1d89cfae7b48f4c51adff8',1,'vg::subpath_t']]],
- ['_5fedit_11715',['_edit',['../classvg_1_1path__mapping__t.html#a034ff317401dd996ee560579944240ba',1,'vg::path_mapping_t']]],
- ['_5ferror_11716',['_error',['../classj2pb__error.html#a6c1faa9c2a04cb41166771a03f8fe757',1,'j2pb_error']]],
- ['_5ffp_11717',['_fp',['../classvg_1_1io_1_1JSONStreamHelper.html#a9a37ea0b07062cb1fcab096188ac5ced',1,'vg::io::JSONStreamHelper']]],
- ['_5ffrom_5flength_11718',['_from_length',['../classvg_1_1edit__t.html#adb931178b1b372b23ca72ff0601b5100',1,'vg::edit_t']]],
- ['_5fgraph_11719',['_graph',['../classvg_1_1Transcriptome.html#a8750ad3aac9bf4dbd1c24eaa331b3bb0',1,'vg::Transcriptome']]],
- ['_5fis_5freverse_11720',['_is_reverse',['../classvg_1_1position__t.html#ad21985ad91af881608d0cac540e7c4cd',1,'vg::position_t']]],
- ['_5fmapping_11721',['_mapping',['../classvg_1_1path__t.html#aa3dab50bcd2afddc385c07fcf9d09f69',1,'vg::path_t']]],
- ['_5fmapping_5fquality_11722',['_mapping_quality',['../classvg_1_1multipath__alignment__t.html#a7e5dcd268edcf1c6476d202d2f9af9df',1,'vg::multipath_alignment_t']]],
- ['_5fnext_11723',['_next',['../classvg_1_1connection__t.html#a27af84e6107ab6468d7f7c18bfef2afd',1,'vg::connection_t::_next()'],['../classvg_1_1subpath__t.html#aec10df49426bea91a1e508b2a487ab4f',1,'vg::subpath_t::_next()']]],
- ['_5fnode_5fid_11724',['_node_id',['../classvg_1_1position__t.html#a38da84360e1d1c58714575b6c5c7081e',1,'vg::position_t']]],
- ['_5foffset_11725',['_offset',['../classvg_1_1position__t.html#a9a84544deb3e4063fcf024c5bf894d16',1,'vg::position_t']]],
- ['_5fpath_11726',['_path',['../classvg_1_1subpath__t.html#ada5bdc5ea2348b439272c166911dd5d3',1,'vg::subpath_t']]],
- ['_5fpaths_11727',['_paths',['../classvg_1_1Paths.html#a5857b70582a67d2819f5e5db23a984cf',1,'vg::Paths']]],
- ['_5fposition_11728',['_position',['../classvg_1_1path__mapping__t.html#a0fbd0d2e397a143b0e85122705a1277c',1,'vg::path_mapping_t']]],
- ['_5fquality_11729',['_quality',['../classvg_1_1multipath__alignment__t.html#a67f71af08e91f177fb0e7760bc7074c0',1,'vg::multipath_alignment_t']]],
- ['_5fscore_11730',['_score',['../classvg_1_1connection__t.html#ab0316cf5e174e217aa3956fd41e528a5',1,'vg::connection_t::_score()'],['../classvg_1_1subpath__t.html#a50fa6724cbbd23bf0ac35161d04258d3',1,'vg::subpath_t::_score()']]],
- ['_5fsequence_11731',['_sequence',['../classvg_1_1multipath__alignment__t.html#ac43812cbd7b12fc8988220d5c1947eb4',1,'vg::multipath_alignment_t::_sequence()'],['../classvg_1_1edit__t.html#a2cdecadad0717701da4cd59a2b2b8648',1,'vg::edit_t::_sequence()']]],
- ['_5fstart_11732',['_start',['../classvg_1_1multipath__alignment__t.html#a79e11ad80725fbe630e9c16f3125156c',1,'vg::multipath_alignment_t']]],
- ['_5fsubpath_11733',['_subpath',['../classvg_1_1multipath__alignment__t.html#a221bf5199424ee06bd499cd727ef32dc',1,'vg::multipath_alignment_t']]],
- ['_5fto_5flength_11734',['_to_length',['../classvg_1_1edit__t.html#a0c97a42b9ba7eb6bc7693e536b352913',1,'vg::edit_t']]],
- ['_5ftranscript_5fpaths_11735',['_transcript_paths',['../classvg_1_1Transcriptome.html#a8c232c3a1a730b3abc0771f0d45cb341',1,'vg::Transcriptome']]]
+ ['_5fannotation_11717',['_annotation',['../classvg_1_1multipath__alignment__t.html#a2335046b7a55314644af26787ce17c57',1,'vg::multipath_alignment_t']]],
+ ['_5fconnection_11718',['_connection',['../classvg_1_1subpath__t.html#aeff77a67cc1d89cfae7b48f4c51adff8',1,'vg::subpath_t']]],
+ ['_5fedit_11719',['_edit',['../classvg_1_1path__mapping__t.html#a034ff317401dd996ee560579944240ba',1,'vg::path_mapping_t']]],
+ ['_5ferror_11720',['_error',['../classj2pb__error.html#a6c1faa9c2a04cb41166771a03f8fe757',1,'j2pb_error']]],
+ ['_5ffp_11721',['_fp',['../classvg_1_1io_1_1JSONStreamHelper.html#a9a37ea0b07062cb1fcab096188ac5ced',1,'vg::io::JSONStreamHelper']]],
+ ['_5ffrom_5flength_11722',['_from_length',['../classvg_1_1edit__t.html#adb931178b1b372b23ca72ff0601b5100',1,'vg::edit_t']]],
+ ['_5fgraph_11723',['_graph',['../classvg_1_1Transcriptome.html#a8750ad3aac9bf4dbd1c24eaa331b3bb0',1,'vg::Transcriptome']]],
+ ['_5fis_5freverse_11724',['_is_reverse',['../classvg_1_1position__t.html#ad21985ad91af881608d0cac540e7c4cd',1,'vg::position_t']]],
+ ['_5fmapping_11725',['_mapping',['../classvg_1_1path__t.html#aa3dab50bcd2afddc385c07fcf9d09f69',1,'vg::path_t']]],
+ ['_5fmapping_5fquality_11726',['_mapping_quality',['../classvg_1_1multipath__alignment__t.html#a7e5dcd268edcf1c6476d202d2f9af9df',1,'vg::multipath_alignment_t']]],
+ ['_5fnext_11727',['_next',['../classvg_1_1connection__t.html#a27af84e6107ab6468d7f7c18bfef2afd',1,'vg::connection_t::_next()'],['../classvg_1_1subpath__t.html#aec10df49426bea91a1e508b2a487ab4f',1,'vg::subpath_t::_next()']]],
+ ['_5fnode_5fid_11728',['_node_id',['../classvg_1_1position__t.html#a38da84360e1d1c58714575b6c5c7081e',1,'vg::position_t']]],
+ ['_5foffset_11729',['_offset',['../classvg_1_1position__t.html#a9a84544deb3e4063fcf024c5bf894d16',1,'vg::position_t']]],
+ ['_5fpath_11730',['_path',['../classvg_1_1subpath__t.html#ada5bdc5ea2348b439272c166911dd5d3',1,'vg::subpath_t']]],
+ ['_5fpaths_11731',['_paths',['../classvg_1_1Paths.html#a5857b70582a67d2819f5e5db23a984cf',1,'vg::Paths']]],
+ ['_5fposition_11732',['_position',['../classvg_1_1path__mapping__t.html#a0fbd0d2e397a143b0e85122705a1277c',1,'vg::path_mapping_t']]],
+ ['_5fquality_11733',['_quality',['../classvg_1_1multipath__alignment__t.html#a67f71af08e91f177fb0e7760bc7074c0',1,'vg::multipath_alignment_t']]],
+ ['_5fscore_11734',['_score',['../classvg_1_1connection__t.html#ab0316cf5e174e217aa3956fd41e528a5',1,'vg::connection_t::_score()'],['../classvg_1_1subpath__t.html#a50fa6724cbbd23bf0ac35161d04258d3',1,'vg::subpath_t::_score()']]],
+ ['_5fsequence_11735',['_sequence',['../classvg_1_1multipath__alignment__t.html#ac43812cbd7b12fc8988220d5c1947eb4',1,'vg::multipath_alignment_t::_sequence()'],['../classvg_1_1edit__t.html#a2cdecadad0717701da4cd59a2b2b8648',1,'vg::edit_t::_sequence()']]],
+ ['_5fstart_11736',['_start',['../classvg_1_1multipath__alignment__t.html#a79e11ad80725fbe630e9c16f3125156c',1,'vg::multipath_alignment_t']]],
+ ['_5fsubpath_11737',['_subpath',['../classvg_1_1multipath__alignment__t.html#a221bf5199424ee06bd499cd727ef32dc',1,'vg::multipath_alignment_t']]],
+ ['_5fto_5flength_11738',['_to_length',['../classvg_1_1edit__t.html#a0c97a42b9ba7eb6bc7693e536b352913',1,'vg::edit_t']]],
+ ['_5ftranscript_5fpaths_11739',['_transcript_paths',['../classvg_1_1Transcriptome.html#a8c232c3a1a730b3abc0771f0d45cb341',1,'vg::Transcriptome']]]
];
diff --git a/search/variables_1.js b/search/variables_1.js
index 43437a2ce7..0e1bf1d83f 100644
--- a/search/variables_1.js
+++ b/search/variables_1.js
@@ -1,69 +1,69 @@
var searchData=
[
- ['absent_5fscore_11736',['ABSENT_SCORE',['../classvg_1_1Recombinator.html#a872b059f8fdd67afccec2767ff6ce058',1,'vg::Recombinator::ABSENT_SCORE()'],['../structvg_1_1Recombinator_1_1Parameters.html#a3c21dd67f19f0646632968d3068a677a',1,'vg::Recombinator::Parameters::absent_score()']]],
- ['accelerator_11737',['accelerator',['../classvg_1_1BaseMapper.html#ad78381b0ec8c523f52df44fa62759ac1',1,'vg::BaseMapper']]],
- ['access_5fmutex_11738',['access_mutex',['../structvg_1_1Watchdog_1_1thread__state__t.html#adcceae4d1421b6f28cf9bcf395f523cb',1,'vg::Watchdog::thread_state_t']]],
- ['active_5ftree_5findex_11739',['active_tree_index',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#afeab653d90d79b0d099abe3f4db157b5',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['adaptive_5fdiff_5fexponent_11740',['adaptive_diff_exponent',['../classvg_1_1BaseMapper.html#a653e029302e4442dbabd06a70ec4bbec',1,'vg::BaseMapper']]],
- ['adaptive_5freseed_5fdiff_11741',['adaptive_reseed_diff',['../classvg_1_1BaseMapper.html#acf7556c347ea7596624700482dc58c8c',1,'vg::BaseMapper']]],
- ['adaptive_5freseed_5flength_5fmemo_11742',['adaptive_reseed_length_memo',['../classvg_1_1BaseMapper.html#a279b5883907a56ada69b41796230b209',1,'vg::BaseMapper']]],
- ['added_5ffwd_11743',['added_fwd',['../classvg_1_1ExtraNodeGraph.html#a0c76a41ba36fe38013e9003c7e98943c',1,'vg::ExtraNodeGraph']]],
- ['added_5fid_11744',['added_id',['../classvg_1_1ExtraNodeGraph.html#ad136e20b9bad7abf259192e456fad6aa',1,'vg::ExtraNodeGraph']]],
- ['added_5frev_11745',['added_rev',['../classvg_1_1ExtraNodeGraph.html#a7a807c52fdab61ca4a68d47046fcb9e0',1,'vg::ExtraNodeGraph']]],
- ['additional_5fitems_11746',['additional_items',['../structvg_1_1MatchPos_1_1PathList.html#af532abe0cbe593054eeabf67a6c08d38',1,'vg::MatchPos::PathList']]],
- ['adjust_5falignments_5ffor_5fbase_5fquality_11747',['adjust_alignments_for_base_quality',['../classvg_1_1AlignerClient.html#a25db3953c246e94a7e08ef59fc31b82f',1,'vg::AlignerClient']]],
- ['adjust_5ffor_5fbase_5fquality_11748',['adjust_for_base_quality',['../classvg_1_1BandedGlobalAligner.html#a00b5ed0e20f4dd989bf5219b0273828e',1,'vg::BandedGlobalAligner']]],
- ['affinity_11749',['affinity',['../structvg_1_1Genotyper_1_1Affinity.html#a77332c5a3e180693907d5b6d28c7ca32',1,'vg::Genotyper::Affinity']]],
- ['agglomerate_5fmultipath_5falns_11750',['agglomerate_multipath_alns',['../classvg_1_1MultipathMapper.html#ac2613ce4eada04721a135673d2d86981',1,'vg::MultipathMapper']]],
- ['agglomeration_5flength_11751',['agglomeration_length',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a285f217813c237807f2bad3488bcc100',1,'vg::MinimizerMapper::Minimizer']]],
- ['agglomeration_5fstart_11752',['agglomeration_start',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a16c1b60d11d598a235b00792df610ed8',1,'vg::MinimizerMapper::Minimizer']]],
- ['alg2name_11753',['alg2name',['../classvg_1_1Genotyper.html#adc250029dd72b833de1042e972b2a8d7',1,'vg::Genotyper']]],
- ['algorithm_5fdefault_11754',['ALGORITHM_DEFAULT',['../convert__main_8cpp.html#a109b73886515e9f635460704fc5739b4',1,'convert_main.cpp']]],
- ['align_5ffrom_5fchains_11755',['align_from_chains',['../classvg_1_1MinimizerMapper.html#a24270c8f6fa529b9aafafed364d757ad',1,'vg::MinimizerMapper']]],
- ['aligner_11756',['aligner',['../classvg_1_1GaplessExtender.html#ac041ad7cec145f55b68442ac58aeaeed',1,'vg::GaplessExtender::aligner()'],['../classvg_1_1WFAExtender.html#a85f8f39bc292b1b5f0737c70c14c7fdd',1,'vg::WFAExtender::aligner()'],['../classvg_1_1VariantAdder.html#a13027b4029d1afe257878e807b56e24f',1,'vg::VariantAdder::aligner()']]],
- ['alignment_11757',['alignment',['../classvg_1_1BandedGlobalAligner.html#ab0cb70d08f759c4f661206b318a96bd7',1,'vg::BandedGlobalAligner::alignment()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a389f62ad0c08ec025e72334c8840da9f',1,'vg::BandedGlobalAligner::BAMatrix::alignment()'],['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#aafbeded7714f362e7a4b7802fa6f77a1',1,'vg::BandedGlobalAligner::BABuilder::alignment()'],['../structvg_1_1read__alignment__index__t.html#a9ebc304a55ae39fbd56b53b3364e9ad4',1,'vg::read_alignment_index_t::alignment()'],['../structvg_1_1alignment__index__t.html#a6cac7b2c530bb8afb75af158064a17e2',1,'vg::alignment_index_t::alignment()']]],
- ['alignment_5femitter_11758',['alignment_emitter',['../classvg_1_1FlowCaller.html#a0b8865c480506d6176f88f4d4e14f84c',1,'vg::FlowCaller::alignment_emitter()'],['../classvg_1_1NestedFlowCaller.html#a79a11b3a8178ad9e8fa4124d13aa18cf',1,'vg::NestedFlowCaller::alignment_emitter()']]],
- ['alignments_11759',['alignments',['../classvg_1_1MSAConverter.html#a47c97fb19598ec7786d2497e4fb86327',1,'vg::MSAConverter']]],
- ['alignments_5fby_5fedge_11760',['alignments_by_edge',['../structvg_1_1AugmentedGraph.html#ab78aba710aba7ff86e2af85b359fa162',1,'vg::AugmentedGraph']]],
- ['alignments_5fby_5fnode_11761',['alignments_by_node',['../structvg_1_1AugmentedGraph.html#a9fed1d73cde7c2a3b0b616ca0b291d37',1,'vg::AugmentedGraph']]],
- ['all_5fnode_5fproblems_11762',['all_node_problems',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a76c3aacc187732929ffaefa1daa62f46',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['all_5fseeds_11763',['all_seeds',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af2e89181e6c935ac190e86b3251bc512',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['all_5fsnarls_11764',['all_snarls',['../classvg_1_1Genotyper.html#ac177e2664adf7be9b92939148ea77c65',1,'vg::Genotyper']]],
- ['allele_11765',['allele',['../structvg_1_1Locus.html#adc1277c0f4db113e9124b115350f284c',1,'vg::Locus::allele()'],['../structvg_1_1Genotype.html#a1703c340c8866d2c62bfb0f602e9f423',1,'vg::Genotype::allele()']]],
- ['allele_5flength_5frange_11766',['allele_length_range',['../classvg_1_1FlowCaller.html#a5b9bcf3a7c3863815ee585846990a853',1,'vg::FlowCaller']]],
- ['allele_5flog_5flikelihood_11767',['allele_log_likelihood',['../structvg_1_1Locus.html#afde669bf5bab01c5cc7a56d97a3aedcc',1,'vg::Locus']]],
- ['alleles_11768',['alleles',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#ad85e96e34ed648807222b3a4ee027732',1,'haplo::linear_haplo_structure::SNVvector::alleles()'],['../structvg_1_1VG_1_1Plan.html#ab142f645d542a8d08ecfb2253d81f8d7',1,'vg::VG::Plan::alleles()']]],
- ['allow_5fduplicates_11769',['allow_duplicates',['../classvg_1_1PathRestrictedTraversalFinder.html#a153de6a0b89875c0cbe4adb2301421f4',1,'vg::PathRestrictedTraversalFinder']]],
- ['allowed_5fvcf_5fnames_11770',['allowed_vcf_names',['../classvg_1_1Constructor.html#a792c656b37e8b8836cd223751749d401',1,'vg::Constructor']]],
- ['allowed_5fvcf_5fregions_11771',['allowed_vcf_regions',['../classvg_1_1Constructor.html#ac152e7a5407ef743f41e301700203129',1,'vg::Constructor']]],
- ['aln_11772',['aln',['../classvg_1_1AlignmentChainModelVertex.html#ab49913fb60fec26e020912069d8c0103',1,'vg::AlignmentChainModelVertex']]],
- ['aln_5femitter_11773',['aln_emitter',['../classvg_1_1ReadFilter.html#a0dd41aa98c633f881001c8924b212b23',1,'vg::ReadFilter']]],
- ['aln_5femitters_11774',['aln_emitters',['../classvg_1_1MultipathAlignmentEmitter.html#aeac99888a4e0e3d3ae79fbd7a166bb93',1,'vg::MultipathAlignmentEmitter']]],
- ['alphabet_11775',['alphabet',['../classvg_1_1NGSSimulator.html#aa970fcca49e375093b8abf6c3b31e2c5',1,'vg::NGSSimulator']]],
- ['alt_5falignments_11776',['alt_alignments',['../classvg_1_1BandedGlobalAligner.html#a72ad87c059fc959b0258feb87c8dd4bd',1,'vg::BandedGlobalAligner']]],
- ['alt_5fanchor_5fmax_5flength_5fdiff_11777',['alt_anchor_max_length_diff',['../classvg_1_1MultipathMapper.html#a229117ffb8dcad25565d8f65e29ba194',1,'vg::MultipathMapper']]],
- ['alt_5fpaths_11778',['alt_paths',['../classvg_1_1Constructor.html#a19deb52667c009bcb73cd27e7ba2a5ac',1,'vg::Constructor']]],
- ['alt_5ftracebacks_11779',['alt_tracebacks',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#af49884645b194e12cea5a5fdf6182b58',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['alts_5fas_5floci_11780',['alts_as_loci',['../classvg_1_1Constructor.html#aedef6d593704f6739abcb116369935f7',1,'vg::Constructor']]],
- ['always_5fcheck_5fpopulation_11781',['always_check_population',['../classvg_1_1MultipathMapper.html#a135abf9221806d613a60edb087509a06',1,'vg::MultipathMapper']]],
- ['always_5frescue_11782',['always_rescue',['../classvg_1_1Mapper.html#aa49ab15f9f924414fca3c56a7d6660c9',1,'vg::Mapper']]],
- ['ambiguous_5fwarned_5fsequences_11783',['ambiguous_warned_sequences',['../classvg_1_1Constructor.html#ab4733354328ad88166206d95680570f1',1,'vg::Constructor']]],
- ['annotate_5fwith_5fall_5fpath_5fscores_11784',['annotate_with_all_path_scores',['../classvg_1_1Surjector.html#a99dc61c54ce73a8db8526b0f935a14c9',1,'vg::Surjector']]],
- ['annotation_11785',['annotation',['../structvg_1_1Alignment.html#af531ff2b8c2b08c78a8b3095fd52c0d8',1,'vg::Alignment::annotation()'],['../structvg_1_1MultipathAlignment.html#acb66af5a0c0197fe49e7dfbac312bd6d',1,'vg::MultipathAlignment::annotation()']]],
- ['annotation_5fpath_5ffilter_11786',['annotation_path_filter',['../classvg_1_1AbstractReadSampler.html#a90a7ee1e2979f2126e700b2a8e847cc4',1,'vg::AbstractReadSampler']]],
- ['annotation_5fto_5fmatch_11787',['annotation_to_match',['../classvg_1_1ReadFilter.html#a44b9ee21da92a8cd89af5b6538ac32a0',1,'vg::ReadFilter']]],
- ['approximate_5fjobs_11788',['approximate_jobs',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a306ad539729c5e6e0649da847666dcc9',1,'vg::HaplotypePartitioner::Parameters::approximate_jobs()'],['../classvg_1_1HaplotypePartitioner.html#a0ef19f69054a8df7277e7afd2a5de83f',1,'vg::HaplotypePartitioner::APPROXIMATE_JOBS()']]],
- ['args_11789',['args',['../structvg_1_1subcommand_1_1OptionGroup.html#a210a76195aa014e3fcfbebdedc3906c3',1,'vg::subcommand::OptionGroup']]],
- ['assembly_5for_5fname_5fmatch_11790',['ASSEMBLY_OR_NAME_MATCH',['../classhandlegraph_1_1PathMetadata.html#a0a7a5d9b16d9874a15cb9e64e9d23627',1,'handlegraph::PathMetadata']]],
- ['assume_5facyclic_11791',['assume_acyclic',['../classvg_1_1BaseMapper.html#a7127a75ac293b9b05093134ee8e51cd2',1,'vg::BaseMapper']]],
- ['atomic_5fheader_11792',['atomic_header',['../classvg_1_1HTSWriter.html#ab8446e15c0caf781e6a9d26cffaf82da',1,'vg::HTSWriter']]],
- ['attributes_11793',['attributes',['../structvg_1_1GFFRecord.html#af888958f0541209b1e6c0f50285d0d92',1,'vg::GFFRecord']]],
- ['aug_11794',['aug',['../classvg_1_1SupportRestrictedTraversalFinder.html#a567e6115385fa235eb1a761c9051dca0',1,'vg::SupportRestrictedTraversalFinder::aug()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#ae15a9cd1b2a92b7375784b7c0be3d9c4',1,'vg::ReadRestrictedTraversalFinder::aug()']]],
- ['augmented_11795',['augmented',['../classvg_1_1NestedTraversalFinder.html#a313111e30533ab2a685d7c9e112a6b22',1,'vg::NestedTraversalFinder']]],
- ['available_5fshort_5foptions_11796',['available_short_options',['../classvg_1_1ConfigurableParser.html#a529443bfe60e0ab272166ccc15991ce2',1,'vg::ConfigurableParser']]],
- ['average_5fnode_5fsupport_5fswitch_5fthreshold_11797',['average_node_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a31d877c8af983f565b507bbfa18c31b4',1,'vg::TraversalSupportFinder']]],
- ['average_5ftraversal_5fsupport_5fswitch_5fthreshold_11798',['average_traversal_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a1d277cd424d213bf0d475fb4c64b26d2',1,'vg::TraversalSupportFinder']]],
- ['avg_5fnode_5flength_11799',['avg_node_length',['../classvg_1_1BaseMapper.html#ad77c0e853fcfc715a15b8852b8b4f388',1,'vg::BaseMapper']]],
- ['avg_5fnode_5fmapq_5fcache_11800',['avg_node_mapq_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a4d51eddbde9c16f01aa0cc31de00ad7d',1,'vg::CachedPackedTraversalSupportFinder']]],
- ['avg_5fnode_5fsupport_5fcache_11801',['avg_node_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#adbdbdebba95326c21ba7c98017820707',1,'vg::CachedPackedTraversalSupportFinder']]]
+ ['absent_5fscore_11740',['ABSENT_SCORE',['../classvg_1_1Recombinator.html#a872b059f8fdd67afccec2767ff6ce058',1,'vg::Recombinator::ABSENT_SCORE()'],['../structvg_1_1Recombinator_1_1Parameters.html#a3c21dd67f19f0646632968d3068a677a',1,'vg::Recombinator::Parameters::absent_score()']]],
+ ['accelerator_11741',['accelerator',['../classvg_1_1BaseMapper.html#ad78381b0ec8c523f52df44fa62759ac1',1,'vg::BaseMapper']]],
+ ['access_5fmutex_11742',['access_mutex',['../structvg_1_1Watchdog_1_1thread__state__t.html#adcceae4d1421b6f28cf9bcf395f523cb',1,'vg::Watchdog::thread_state_t']]],
+ ['active_5ftree_5findex_11743',['active_tree_index',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#afeab653d90d79b0d099abe3f4db157b5',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['adaptive_5fdiff_5fexponent_11744',['adaptive_diff_exponent',['../classvg_1_1BaseMapper.html#a653e029302e4442dbabd06a70ec4bbec',1,'vg::BaseMapper']]],
+ ['adaptive_5freseed_5fdiff_11745',['adaptive_reseed_diff',['../classvg_1_1BaseMapper.html#acf7556c347ea7596624700482dc58c8c',1,'vg::BaseMapper']]],
+ ['adaptive_5freseed_5flength_5fmemo_11746',['adaptive_reseed_length_memo',['../classvg_1_1BaseMapper.html#a279b5883907a56ada69b41796230b209',1,'vg::BaseMapper']]],
+ ['added_5ffwd_11747',['added_fwd',['../classvg_1_1ExtraNodeGraph.html#a0c76a41ba36fe38013e9003c7e98943c',1,'vg::ExtraNodeGraph']]],
+ ['added_5fid_11748',['added_id',['../classvg_1_1ExtraNodeGraph.html#ad136e20b9bad7abf259192e456fad6aa',1,'vg::ExtraNodeGraph']]],
+ ['added_5frev_11749',['added_rev',['../classvg_1_1ExtraNodeGraph.html#a7a807c52fdab61ca4a68d47046fcb9e0',1,'vg::ExtraNodeGraph']]],
+ ['additional_5fitems_11750',['additional_items',['../structvg_1_1MatchPos_1_1PathList.html#af532abe0cbe593054eeabf67a6c08d38',1,'vg::MatchPos::PathList']]],
+ ['adjust_5falignments_5ffor_5fbase_5fquality_11751',['adjust_alignments_for_base_quality',['../classvg_1_1AlignerClient.html#a25db3953c246e94a7e08ef59fc31b82f',1,'vg::AlignerClient']]],
+ ['adjust_5ffor_5fbase_5fquality_11752',['adjust_for_base_quality',['../classvg_1_1BandedGlobalAligner.html#a00b5ed0e20f4dd989bf5219b0273828e',1,'vg::BandedGlobalAligner']]],
+ ['affinity_11753',['affinity',['../structvg_1_1Genotyper_1_1Affinity.html#a77332c5a3e180693907d5b6d28c7ca32',1,'vg::Genotyper::Affinity']]],
+ ['agglomerate_5fmultipath_5falns_11754',['agglomerate_multipath_alns',['../classvg_1_1MultipathMapper.html#ac2613ce4eada04721a135673d2d86981',1,'vg::MultipathMapper']]],
+ ['agglomeration_5flength_11755',['agglomeration_length',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a285f217813c237807f2bad3488bcc100',1,'vg::MinimizerMapper::Minimizer']]],
+ ['agglomeration_5fstart_11756',['agglomeration_start',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a16c1b60d11d598a235b00792df610ed8',1,'vg::MinimizerMapper::Minimizer']]],
+ ['alg2name_11757',['alg2name',['../classvg_1_1Genotyper.html#adc250029dd72b833de1042e972b2a8d7',1,'vg::Genotyper']]],
+ ['algorithm_5fdefault_11758',['ALGORITHM_DEFAULT',['../convert__main_8cpp.html#a109b73886515e9f635460704fc5739b4',1,'convert_main.cpp']]],
+ ['align_5ffrom_5fchains_11759',['align_from_chains',['../classvg_1_1MinimizerMapper.html#a24270c8f6fa529b9aafafed364d757ad',1,'vg::MinimizerMapper']]],
+ ['aligner_11760',['aligner',['../classvg_1_1GaplessExtender.html#ac041ad7cec145f55b68442ac58aeaeed',1,'vg::GaplessExtender::aligner()'],['../classvg_1_1WFAExtender.html#a85f8f39bc292b1b5f0737c70c14c7fdd',1,'vg::WFAExtender::aligner()'],['../classvg_1_1VariantAdder.html#a13027b4029d1afe257878e807b56e24f',1,'vg::VariantAdder::aligner()']]],
+ ['alignment_11761',['alignment',['../classvg_1_1BandedGlobalAligner.html#ab0cb70d08f759c4f661206b318a96bd7',1,'vg::BandedGlobalAligner::alignment()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a389f62ad0c08ec025e72334c8840da9f',1,'vg::BandedGlobalAligner::BAMatrix::alignment()'],['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#aafbeded7714f362e7a4b7802fa6f77a1',1,'vg::BandedGlobalAligner::BABuilder::alignment()'],['../structvg_1_1read__alignment__index__t.html#a9ebc304a55ae39fbd56b53b3364e9ad4',1,'vg::read_alignment_index_t::alignment()'],['../structvg_1_1alignment__index__t.html#a6cac7b2c530bb8afb75af158064a17e2',1,'vg::alignment_index_t::alignment()']]],
+ ['alignment_5femitter_11762',['alignment_emitter',['../classvg_1_1FlowCaller.html#a0b8865c480506d6176f88f4d4e14f84c',1,'vg::FlowCaller::alignment_emitter()'],['../classvg_1_1NestedFlowCaller.html#a79a11b3a8178ad9e8fa4124d13aa18cf',1,'vg::NestedFlowCaller::alignment_emitter()']]],
+ ['alignments_11763',['alignments',['../classvg_1_1MSAConverter.html#a47c97fb19598ec7786d2497e4fb86327',1,'vg::MSAConverter']]],
+ ['alignments_5fby_5fedge_11764',['alignments_by_edge',['../structvg_1_1AugmentedGraph.html#ab78aba710aba7ff86e2af85b359fa162',1,'vg::AugmentedGraph']]],
+ ['alignments_5fby_5fnode_11765',['alignments_by_node',['../structvg_1_1AugmentedGraph.html#a9fed1d73cde7c2a3b0b616ca0b291d37',1,'vg::AugmentedGraph']]],
+ ['all_5fnode_5fproblems_11766',['all_node_problems',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a76c3aacc187732929ffaefa1daa62f46',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['all_5fseeds_11767',['all_seeds',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af2e89181e6c935ac190e86b3251bc512',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['all_5fsnarls_11768',['all_snarls',['../classvg_1_1Genotyper.html#ac177e2664adf7be9b92939148ea77c65',1,'vg::Genotyper']]],
+ ['allele_11769',['allele',['../structvg_1_1Locus.html#adc1277c0f4db113e9124b115350f284c',1,'vg::Locus::allele()'],['../structvg_1_1Genotype.html#a1703c340c8866d2c62bfb0f602e9f423',1,'vg::Genotype::allele()']]],
+ ['allele_5flength_5frange_11770',['allele_length_range',['../classvg_1_1FlowCaller.html#a5b9bcf3a7c3863815ee585846990a853',1,'vg::FlowCaller']]],
+ ['allele_5flog_5flikelihood_11771',['allele_log_likelihood',['../structvg_1_1Locus.html#afde669bf5bab01c5cc7a56d97a3aedcc',1,'vg::Locus']]],
+ ['alleles_11772',['alleles',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#ad85e96e34ed648807222b3a4ee027732',1,'haplo::linear_haplo_structure::SNVvector::alleles()'],['../structvg_1_1VG_1_1Plan.html#ab142f645d542a8d08ecfb2253d81f8d7',1,'vg::VG::Plan::alleles()']]],
+ ['allow_5fduplicates_11773',['allow_duplicates',['../classvg_1_1PathRestrictedTraversalFinder.html#a153de6a0b89875c0cbe4adb2301421f4',1,'vg::PathRestrictedTraversalFinder']]],
+ ['allowed_5fvcf_5fnames_11774',['allowed_vcf_names',['../classvg_1_1Constructor.html#a792c656b37e8b8836cd223751749d401',1,'vg::Constructor']]],
+ ['allowed_5fvcf_5fregions_11775',['allowed_vcf_regions',['../classvg_1_1Constructor.html#ac152e7a5407ef743f41e301700203129',1,'vg::Constructor']]],
+ ['aln_11776',['aln',['../classvg_1_1AlignmentChainModelVertex.html#ab49913fb60fec26e020912069d8c0103',1,'vg::AlignmentChainModelVertex']]],
+ ['aln_5femitter_11777',['aln_emitter',['../classvg_1_1ReadFilter.html#a0dd41aa98c633f881001c8924b212b23',1,'vg::ReadFilter']]],
+ ['aln_5femitters_11778',['aln_emitters',['../classvg_1_1MultipathAlignmentEmitter.html#aeac99888a4e0e3d3ae79fbd7a166bb93',1,'vg::MultipathAlignmentEmitter']]],
+ ['alphabet_11779',['alphabet',['../classvg_1_1NGSSimulator.html#aa970fcca49e375093b8abf6c3b31e2c5',1,'vg::NGSSimulator']]],
+ ['alt_5falignments_11780',['alt_alignments',['../classvg_1_1BandedGlobalAligner.html#a72ad87c059fc959b0258feb87c8dd4bd',1,'vg::BandedGlobalAligner']]],
+ ['alt_5fanchor_5fmax_5flength_5fdiff_11781',['alt_anchor_max_length_diff',['../classvg_1_1MultipathMapper.html#a229117ffb8dcad25565d8f65e29ba194',1,'vg::MultipathMapper']]],
+ ['alt_5fpaths_11782',['alt_paths',['../classvg_1_1Constructor.html#a19deb52667c009bcb73cd27e7ba2a5ac',1,'vg::Constructor']]],
+ ['alt_5ftracebacks_11783',['alt_tracebacks',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#af49884645b194e12cea5a5fdf6182b58',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['alts_5fas_5floci_11784',['alts_as_loci',['../classvg_1_1Constructor.html#aedef6d593704f6739abcb116369935f7',1,'vg::Constructor']]],
+ ['always_5fcheck_5fpopulation_11785',['always_check_population',['../classvg_1_1MultipathMapper.html#a135abf9221806d613a60edb087509a06',1,'vg::MultipathMapper']]],
+ ['always_5frescue_11786',['always_rescue',['../classvg_1_1Mapper.html#aa49ab15f9f924414fca3c56a7d6660c9',1,'vg::Mapper']]],
+ ['ambiguous_5fwarned_5fsequences_11787',['ambiguous_warned_sequences',['../classvg_1_1Constructor.html#ab4733354328ad88166206d95680570f1',1,'vg::Constructor']]],
+ ['annotate_5fwith_5fall_5fpath_5fscores_11788',['annotate_with_all_path_scores',['../classvg_1_1Surjector.html#a99dc61c54ce73a8db8526b0f935a14c9',1,'vg::Surjector']]],
+ ['annotation_11789',['annotation',['../structvg_1_1Alignment.html#af531ff2b8c2b08c78a8b3095fd52c0d8',1,'vg::Alignment::annotation()'],['../structvg_1_1MultipathAlignment.html#acb66af5a0c0197fe49e7dfbac312bd6d',1,'vg::MultipathAlignment::annotation()']]],
+ ['annotation_5fpath_5ffilter_11790',['annotation_path_filter',['../classvg_1_1AbstractReadSampler.html#a90a7ee1e2979f2126e700b2a8e847cc4',1,'vg::AbstractReadSampler']]],
+ ['annotation_5fto_5fmatch_11791',['annotation_to_match',['../classvg_1_1ReadFilter.html#a44b9ee21da92a8cd89af5b6538ac32a0',1,'vg::ReadFilter']]],
+ ['approximate_5fjobs_11792',['approximate_jobs',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a306ad539729c5e6e0649da847666dcc9',1,'vg::HaplotypePartitioner::Parameters::approximate_jobs()'],['../classvg_1_1HaplotypePartitioner.html#a0ef19f69054a8df7277e7afd2a5de83f',1,'vg::HaplotypePartitioner::APPROXIMATE_JOBS()']]],
+ ['args_11793',['args',['../structvg_1_1subcommand_1_1OptionGroup.html#a210a76195aa014e3fcfbebdedc3906c3',1,'vg::subcommand::OptionGroup']]],
+ ['assembly_5for_5fname_5fmatch_11794',['ASSEMBLY_OR_NAME_MATCH',['../classhandlegraph_1_1PathMetadata.html#a0a7a5d9b16d9874a15cb9e64e9d23627',1,'handlegraph::PathMetadata']]],
+ ['assume_5facyclic_11795',['assume_acyclic',['../classvg_1_1BaseMapper.html#a7127a75ac293b9b05093134ee8e51cd2',1,'vg::BaseMapper']]],
+ ['atomic_5fheader_11796',['atomic_header',['../classvg_1_1HTSWriter.html#ab8446e15c0caf781e6a9d26cffaf82da',1,'vg::HTSWriter']]],
+ ['attributes_11797',['attributes',['../structvg_1_1GFFRecord.html#af888958f0541209b1e6c0f50285d0d92',1,'vg::GFFRecord']]],
+ ['aug_11798',['aug',['../classvg_1_1SupportRestrictedTraversalFinder.html#a567e6115385fa235eb1a761c9051dca0',1,'vg::SupportRestrictedTraversalFinder::aug()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#ae15a9cd1b2a92b7375784b7c0be3d9c4',1,'vg::ReadRestrictedTraversalFinder::aug()']]],
+ ['augmented_11799',['augmented',['../classvg_1_1NestedTraversalFinder.html#a313111e30533ab2a685d7c9e112a6b22',1,'vg::NestedTraversalFinder']]],
+ ['available_5fshort_5foptions_11800',['available_short_options',['../classvg_1_1ConfigurableParser.html#a529443bfe60e0ab272166ccc15991ce2',1,'vg::ConfigurableParser']]],
+ ['average_5fnode_5fsupport_5fswitch_5fthreshold_11801',['average_node_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a31d877c8af983f565b507bbfa18c31b4',1,'vg::TraversalSupportFinder']]],
+ ['average_5ftraversal_5fsupport_5fswitch_5fthreshold_11802',['average_traversal_support_switch_threshold',['../classvg_1_1TraversalSupportFinder.html#a1d277cd424d213bf0d475fb4c64b26d2',1,'vg::TraversalSupportFinder']]],
+ ['avg_5fnode_5flength_11803',['avg_node_length',['../classvg_1_1BaseMapper.html#ad77c0e853fcfc715a15b8852b8b4f388',1,'vg::BaseMapper']]],
+ ['avg_5fnode_5fmapq_5fcache_11804',['avg_node_mapq_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a4d51eddbde9c16f01aa0cc31de00ad7d',1,'vg::CachedPackedTraversalSupportFinder']]],
+ ['avg_5fnode_5fsupport_5fcache_11805',['avg_node_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#adbdbdebba95326c21ba7c98017820707',1,'vg::CachedPackedTraversalSupportFinder']]]
];
diff --git a/search/variables_10.js b/search/variables_10.js
index be20f4797c..02490e9d04 100644
--- a/search/variables_10.js
+++ b/search/variables_10.js
@@ -1,170 +1,170 @@
var searchData=
[
- ['p_5fvalue_5fmemo_13063',['p_value_memo',['../classvg_1_1MultipathMapper.html#a076b5202ca84c7836e93d3e8b71775bf',1,'vg::MultipathMapper']]],
- ['pack_5fnames_13064',['pack_names',['../classvg_1_1Viz.html#abb3fd61d416351930f2e7399e6f6001b',1,'vg::Viz']]],
- ['packer_13065',['packer',['../classvg_1_1PackedTraversalSupportFinder.html#ac48b605c781739b3920b8c36fdb6fcf8',1,'vg::PackedTraversalSupportFinder']]],
- ['packs_13066',['packs',['../classvg_1_1Viz.html#a350ea478ececb5f19170b16cf1539726',1,'vg::Viz']]],
- ['pad_5fband_5fconstant_13067',['pad_band_constant',['../namespacevg_1_1algorithms.html#ab48342aedc7d81e2334c52bb320223c2',1,'vg::algorithms']]],
- ['pad_5fband_5fmin_5frandom_5fwalk_13068',['pad_band_min_random_walk',['../namespacevg_1_1algorithms.html#a3363cc23e6c71e1bb5faac975af7920d',1,'vg::algorithms']]],
- ['pad_5fband_5frandom_5fwalk_13069',['pad_band_random_walk',['../namespacevg_1_1algorithms.html#a6a606c26b5751d935c71d7971a92d99b',1,'vg::algorithms']]],
- ['pad_5fcluster_5fscore_5fthreshold_13070',['pad_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a70b206dc58a148a69657303ff292199f',1,'vg::MinimizerMapper']]],
- ['pad_5fsuspicious_5fanchors_5fto_5flength_13071',['pad_suspicious_anchors_to_length',['../classvg_1_1Surjector.html#a7231e0ecf35ed767417fc37184b0a806',1,'vg::Surjector']]],
- ['pad_5fzipcode_5ftree_5fscore_5fthreshold_13072',['pad_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#aafbc5c792144ae26630c312d2475b19a',1,'vg::MinimizerMapper']]],
- ['pair_5frescue_5fhang_5fthreshold_13073',['pair_rescue_hang_threshold',['../classvg_1_1Mapper.html#a92e1f4de4e6ce576e09005713d1c1cd1',1,'vg::Mapper']]],
- ['pair_5frescue_5fretry_5fthreshold_13074',['pair_rescue_retry_threshold',['../classvg_1_1Mapper.html#a36ed72fe5d33907a75992011ff9ae244',1,'vg::Mapper']]],
- ['paired_5fdistance_5fstdevs_13075',['paired_distance_stdevs',['../classvg_1_1MinimizerMapper.html#a94bd867270265d26c4f2abfbd730f316',1,'vg::MinimizerMapper']]],
- ['paired_5fread_5fname_13076',['paired_read_name',['../structvg_1_1MultipathAlignment.html#a0664790bf6bd37af413697cddff370fb',1,'vg::MultipathAlignment']]],
- ['paired_5frescue_5fscore_5flimit_13077',['paired_rescue_score_limit',['../classvg_1_1MinimizerMapper.html#a923b2f2f9aa86e445add3be0d1c4abae',1,'vg::MinimizerMapper']]],
- ['parent_13078',['parent',['../structvg_1_1WFANode.html#a78adf1a04bc5f5907cc3a46445061e62',1,'vg::WFANode::parent()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ae00d40d340f5114917a9f6ca1cec0460',1,'vg::SnarlManager::SnarlRecord::parent()'],['../structvg_1_1TreeNode.html#a4eb11d266cabbae3e6728d2918c80996',1,'vg::TreeNode::parent()'],['../structvg_1_1VectorView_1_1const__iterator.html#a41fafc961da593dbc8591c6288a33fd6',1,'vg::VectorView::const_iterator::parent()'],['../structvg_1_1Snarl.html#a054af14a2fccdda2209ef9a8f19aa032',1,'vg::Snarl::parent()']]],
- ['parent_5fallele_13079',['parent_allele',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2f21b56cc895482f0f8a4829ccfa3463',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5fchain_13080',['parent_chain',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a37d7d2aa3460ba15b3a51ac4eedefd76',1,'vg::SnarlManager::SnarlRecord']]],
- ['parent_5fchain_5findex_13081',['parent_chain_index',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a7f98f1f84ba0d39301f1adc3333e6dfb',1,'vg::SnarlManager::SnarlRecord']]],
- ['parent_5fchains_13082',['parent_chains',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a3f1ca708ff05e4f649b0d9b22dc539fd',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['parent_5fdepth_13083',['parent_depth',['../structvg_1_1MIPayload.html#af3214bd006207b1d4c417c331b905290',1,'vg::MIPayload']]],
- ['parent_5fdirectory_13084',['parent_directory',['../structvg_1_1temp__file_1_1Handler.html#a1a791a5a813c3d0702594f5ad6915eaf',1,'vg::temp_file::Handler::parent_directory()'],['../structxg_1_1temp__file_1_1Handler.html#a16640b9f416a23bd671f56437bd09aa6',1,'xg::temp_file::Handler::parent_directory()']]],
- ['parent_5fgraph_13085',['parent_graph',['../classvg_1_1JoinedSpliceGraph.html#a274429d072e5be5687ac704393b903a4',1,'vg::JoinedSpliceGraph']]],
- ['parent_5fhandle_13086',['parent_handle',['../structvg_1_1MIPayload.html#a92ead268cf5b206f54e4cf0e95937dfc',1,'vg::MIPayload']]],
- ['parent_5fis_5fchain_13087',['parent_is_chain',['../structvg_1_1MIPayload.html#aa5abaa3ea722cf685fe73fe9502e00c1',1,'vg::MIPayload']]],
- ['parent_5fis_5froot_13088',['parent_is_root',['../structvg_1_1MIPayload.html#a36e03b459c31f012a17a78a1ec6f5391',1,'vg::MIPayload']]],
- ['parent_5flen_13089',['parent_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#abe519281b723c59979299b2657439f6e',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5fnet_5fhandle_13090',['parent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af940526569cd8d070de39e8446390e6f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['parent_5fpath_5finterval_13091',['parent_path_interval',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a4aa790baef1ec47d6546e30f60851e9b',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5frecord_5foffset_13092',['parent_record_offset',['../structvg_1_1MIPayload.html#af185811088055cdd4c371f18883087b2',1,'vg::MIPayload']]],
- ['parent_5fref_5flen_13093',['parent_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ac311ca43aecb9c37302835adadce85af',1,'vg::Deconstructor::NestingInfo']]],
- ['parent_5fsnarls_13094',['parent_snarls',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a03f3e53e97f93f2d2b4daf66f99cd763',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['parent_5ftype_13095',['parent_type',['../structvg_1_1MIPayload.html#aa14d5e8cecee30a8e796832d5ead8578',1,'vg::MIPayload']]],
- ['parse_5fonly_13096',['parse_only',['../structGBWTConfig.html#af8fc6affa1925b48a3af6fff48511340',1,'GBWTConfig']]],
- ['partitioner_5fparameters_13097',['partitioner_parameters',['../structHaplotypesConfig.html#a6080d6a6e4ada9573d11d678b6de79d0',1,'HaplotypesConfig']]],
- ['pass_5fnumber_13098',['pass_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#a9354b35a8f08891654da020502248f2e',1,'vg::algorithms::GFAFormatError']]],
- ['passed_5ffilters_13099',['passed_filters',['../structvg_1_1Funnel_1_1Item.html#a566978051c820d69d63e72763dc38b17',1,'vg::Funnel::Item']]],
- ['passed_5fstatistics_13100',['passed_statistics',['../structvg_1_1Funnel_1_1Item.html#a5ae29ab2e549daa3fa20626fd5d4fb59',1,'vg::Funnel::Item']]],
- ['passing_13101',['passing',['../structvg_1_1Funnel_1_1FilterPerformance.html#a9382a4983a52c3849412717c26205bde',1,'vg::Funnel::FilterPerformance']]],
- ['passing_5fcorrect_13102',['passing_correct',['../structvg_1_1Funnel_1_1FilterPerformance.html#a7622d6acfd5d4075e26ad60b911e72c4',1,'vg::Funnel::FilterPerformance']]],
- ['past_5fend_13103',['past_end',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a06f803fd96e9e94610bc8fa8f9db95f3',1,'vg::GraphSynchronizer::Lock']]],
- ['patch_5falignments_13104',['patch_alignments',['../classvg_1_1Mapper.html#a6c33dd8ad7af82e21f0ee6463e9456fc',1,'vg::Mapper']]],
- ['path_13105',['path',['../structvg_1_1MatchPos.html#a6a24cd3b3befa706a8f4f934034843cf',1,'vg::MatchPos::path()'],['../structvg_1_1WFANode.html#ad947775b8a38d6d03e6c40b5a8ee06c2',1,'vg::WFANode::path()'],['../structvg_1_1GaplessExtension.html#a6d46f3e3d3525ea159b11f6e832a37e0',1,'vg::GaplessExtension::path()'],['../structvg_1_1WFAAlignment.html#afd65b83419307e4f56481adef5c96f71',1,'vg::WFAAlignment::path()'],['../classvg_1_1PathNode.html#aa955184b7b22179c0efd1febdfc55b92',1,'vg::PathNode::path()'],['../structvg_1_1RecombinatorHaplotype.html#ae37ea81b1f65f9c24f05620ecc3f2a80',1,'vg::RecombinatorHaplotype::path()'],['../structvg_1_1EditedTranscriptPath.html#a8945ac17c2039bc54e3697553c1563a2',1,'vg::EditedTranscriptPath::path()'],['../structvg_1_1CompletedTranscriptPath.html#ae6ea83076c2772ac2670e0e06587dc04',1,'vg::CompletedTranscriptPath::path()'],['../structvg_1_1algorithms_1_1walk__t.html#aee19ea04353c3d23bef5d5fd3689965c',1,'vg::algorithms::walk_t::path()'],['../classhandlegraph_1_1PathForEachSocket.html#a5bd264139b15b7e56ad5a2f6f691202b',1,'handlegraph::PathForEachSocket::path()'],['../structgafkluge_1_1GafRecord.html#ae9734ca0963cfb21cb966ee915c9224b',1,'gafkluge::GafRecord::path()'],['../structvg_1_1Graph.html#a850007eb60ce0d25a6bd9799050ec790',1,'vg::Graph::path()'],['../structvg_1_1Alignment.html#a4736db5fe121ef57784c18c3c27aea79',1,'vg::Alignment::path()'],['../structvg_1_1Subpath.html#a69056b48fb59ee83a8b0307838987e19',1,'vg::Subpath::path()']]],
- ['path_5fcollapse_5ftype_13106',['path_collapse_type',['../classvg_1_1Transcriptome.html#a539e8602c6f984142ae866af8730fd34',1,'vg::Transcriptome']]],
- ['path_5fcomponent_5findex_13107',['path_component_index',['../classvg_1_1PathOrientedDistanceMeasurer.html#aec1793ac0e2bf87292b90a5a2c8f14d8',1,'vg::PathOrientedDistanceMeasurer::path_component_index()'],['../classvg_1_1MultipathMapper.html#a0c64ee67ef473d5d5336ae6adf0b66e8',1,'vg::MultipathMapper::path_component_index()']]],
- ['path_5fcount_13108',['path_count',['../classxg_1_1XG.html#a1859cb996668f8d86107d4e0117cf97f',1,'xg::XG']]],
- ['path_5fcover_13109',['path_cover',['../structGBWTConfig.html#a857449dfcac12577f54afbd7d8957336',1,'GBWTConfig']]],
- ['path_5fcover_5fdepth_13110',['path_cover_depth',['../structvg_1_1IndexingParameters.html#a1075d3f3c10502dc02deb564d85ff897',1,'vg::IndexingParameters']]],
- ['path_5fend_13111',['path_end',['../structgafkluge_1_1GafRecord.html#ac1a2b5a9c4152dfb188a72571ecf746a',1,'gafkluge::GafRecord']]],
- ['path_5ffinder_13112',['path_finder',['../classvg_1_1VCFTraversalFinder.html#a7f529cb408098ee45d3e4868ed9fe2b8',1,'vg::VCFTraversalFinder']]],
- ['path_5fgraph_13113',['path_graph',['../classvg_1_1MinimizerMapper.html#aa75ca7504db85f1ba5d340b8213036de',1,'vg::MinimizerMapper::path_graph()'],['../classvg_1_1PhaseUnfolder.html#a974791c770e3999168899eb36cbd2f48',1,'vg::PhaseUnfolder::path_graph()'],['../structGraphHandler.html#aeb4deb32f56c35702b331c0f506d3844',1,'GraphHandler::path_graph()']]],
- ['path_5findexes_13114',['path_indexes',['../classvg_1_1LegacyCaller.html#a5de5c60b4da9b71566fc10a76ed0e211',1,'vg::LegacyCaller']]],
- ['path_5fjaccard_5fwindow_13115',['path_jaccard_window',['../classvg_1_1Deconstructor.html#a0cf545ea26ebb9bbebafefe47524f87b',1,'vg::Deconstructor']]],
- ['path_5flength_13116',['path_length',['../structgafkluge_1_1GafRecord.html#ac9b7a4a556d78f32913392b0706e93e0',1,'gafkluge::GafRecord']]],
- ['path_5flisteners_13117',['path_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aa856090842dafbe0dbaf22bed66fd411',1,'vg::algorithms::GFAParser']]],
- ['path_5fmode_13118',['path_mode',['../structGBWTConfig.html#a218c5f96dd7101b89bdf8e64de3b9949',1,'GBWTConfig']]],
- ['path_5fname_13119',['path_name',['../structvg_1_1FeatureSet_1_1Feature.html#a645900ed3044cc3359c18e109f7460a7',1,'vg::FeatureSet::Feature::path_name()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad19c5f9cbb68abb1bcfe6e3a9fd65382',1,'vg::GraphSynchronizer::Lock::path_name()']]],
- ['path_5fname_5fcsa_5fdelim_13120',['path_name_csa_delim',['../classxg_1_1XG.html#a5b2791b586efb23a131c2d5c00d85593',1,'xg::XG']]],
- ['path_5fnames_13121',['path_names',['../classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138',1,'vg::VariantAdder::path_names()'],['../structGBWTConfig.html#a96ccf4e2605d4dad1a32511169f51969',1,'GBWTConfig::path_names()']]],
- ['path_5fnodes_13122',['path_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a76f9356cd0afea7dea3003caea2526eb',1,'vg::MultipathAlignmentGraph']]],
- ['path_5foffset_13123',['path_offset',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a58b1c09d2f45e4942afd52d975c85b9a',1,'vg::GraphSynchronizer::Lock']]],
- ['path_5forder_5fand_5flength_13124',['path_order_and_length',['../classvg_1_1HTSWriter.html#a2b0a5d9268a4b4901a699f82d857d6e2',1,'vg::HTSWriter']]],
- ['path_5foutput_13125',['path_output',['../structGBWTConfig.html#a91e5194d120c0dbae060bdfe5c60667a',1,'GBWTConfig']]],
- ['path_5fposition_5fhandle_5fgraph_13126',['path_position_handle_graph',['../classvg_1_1MCMCCaller.html#a240741cadefa13b2b4d472f0b6e3b8d3',1,'vg::MCMCCaller']]],
- ['path_5fsampler_13127',['path_sampler',['../classvg_1_1Sampler.html#a8125a49b29eecf4d5037067c813b2cd7',1,'vg::Sampler::path_sampler()'],['../classvg_1_1NGSSimulator.html#a6101d443a8c314416fbc23dbfd3d5bde',1,'vg::NGSSimulator::path_sampler()']]],
- ['path_5fstart_13128',['path_start',['../structgafkluge_1_1GafRecord.html#a14ce42efee5a241bebe4debf852afbae',1,'gafkluge::GafRecord']]],
- ['path_5fsubset_13129',['path_subset',['../classvg_1_1PathSubgraphOverlay.html#aef82f75c24c686645b0255685bc4c6f2',1,'vg::PathSubgraphOverlay']]],
- ['path_5fto_5fploidy_13130',['path_to_ploidy',['../classvg_1_1VCFGenotyper.html#a248d8e2819ba7354c39b3d2077061fed',1,'vg::VCFGenotyper']]],
- ['path_5fto_5fsample_5fphase_13131',['path_to_sample_phase',['../classvg_1_1Deconstructor.html#a8a5562db89e9293a88b2f22e476d1d25',1,'vg::Deconstructor']]],
- ['path_5fto_5fvcf_13132',['path_to_vcf',['../classvg_1_1HaplotypeIndexer.html#a5ff016a7fdf425ec4f3d5408d09b951f',1,'vg::HaplotypeIndexer']]],
- ['path_5ftrav_5ffinder_13133',['path_trav_finder',['../classvg_1_1Deconstructor.html#a73c6c008333acfbb0ffd6fde2360518c',1,'vg::Deconstructor']]],
- ['paths_13134',['paths',['../classvg_1_1SurjectingAlignmentEmitter.html#a3193ef16804780255b9d0bbcef8dc6ca',1,'vg::SurjectingAlignmentEmitter::paths()'],['../classvg_1_1PathTraversalFinder.html#a5a931da9269d7834dcc04e5fb578ff45',1,'vg::PathTraversalFinder::paths()'],['../classvg_1_1VG.html#a7c5150aba84e7ed2bde7986462a79989',1,'vg::VG::paths()'],['../structjob__type.html#a1c12e7fbad645aa2081f00b1a49b296f',1,'job_type::paths()'],['../classxg_1_1XG.html#a1b5defef10208838d0d3a48ddeb91f85',1,'xg::XG::paths()']]],
- ['payload_13135',['payload',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a9b29761900b87e78b6c17dbe8e38d4fe',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
- ['payload_5fnode_5flength_13136',['payload_node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ac80389e7a2ddaae480e60b286186e3aa',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
- ['payload_5fprefix_5fsum_13137',['payload_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ab809433b78a00f00ae46e7061972c9a9',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
- ['pbsize_13138',['pbSize',['../classvg_1_1io_1_1fdinbuf.html#a1756a5735e7daf8ea042bc81343f7a0f',1,'vg::io::fdinbuf::pbSize()'],['../classvg_1_1io_1_1streaminbuf.html#a4cdee06174136df70efd572abfced2c8',1,'vg::io::streaminbuf::pbSize()']]],
- ['penalties_13139',['penalties',['../structhaplo_1_1linear__haplo__structure.html#af55d7f33177180d033e8e925cf20e5fd',1,'haplo::linear_haplo_structure']]],
- ['per_5fbase_13140',['per_base',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a8a85161fa2d79301a9ca6489006a4c62',1,'vg::WFAExtender::ErrorModel::Event']]],
- ['perfect_5fpair_5fidentity_5fthreshold_13141',['perfect_pair_identity_threshold',['../classvg_1_1FragmentLengthStatistics.html#a4e65bc3de5657555df556429284f5251',1,'vg::FragmentLengthStatistics']]],
- ['peripheral_5fattachments_13142',['peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa2e7c9a960855fa8758d9dd6da6454ea',1,'vg::GraphSynchronizer::Lock']]],
- ['periphery_13143',['periphery',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad9bebede56cef5ab20d80828e34d8b6a',1,'vg::GraphSynchronizer::Lock']]],
- ['permutation_5fidx_13144',['permutation_idx',['../classvg_1_1ShuffledPairs_1_1iterator.html#a52dd908e59ff6dac90191a40c63537e0',1,'vg::ShuffledPairs::iterator']]],
- ['permuted_13145',['permuted',['../classvg_1_1ShuffledPairs_1_1iterator.html#a19642461808615472b7b544e04c47243',1,'vg::ShuffledPairs::iterator']]],
- ['pessimistic_5fgap_5fmemo_13146',['pessimistic_gap_memo',['../classvg_1_1MultipathMapper.html#a828e72945f3e24243d5802604e027b47',1,'vg::MultipathMapper']]],
- ['pessimistic_5fgap_5fmultiplier_13147',['pessimistic_gap_multiplier',['../classvg_1_1MultipathMapper.html#aef97cb46d48a242a68c6ed590039e832',1,'vg::MultipathMapper']]],
- ['pessimistic_5ftail_5fgap_5fmemo_13148',['pessimistic_tail_gap_memo',['../classvg_1_1MultipathAlignmentGraph.html#af46ba9972db437bf66f787a9bbe6c3cd',1,'vg::MultipathAlignmentGraph']]],
- ['phase_13149',['phase',['../structvg_1_1GFFRecord.html#adf3d82a77a4837edba29935e08cb2a53',1,'vg::GFFRecord']]],
- ['phase_5fblock_5fmatch_13150',['PHASE_BLOCK_MATCH',['../classhandlegraph_1_1PathMetadata.html#a08fb019956ae31b8ea31920c904ea5fc',1,'handlegraph::PathMetadata']]],
- ['phase_5fhomozygous_13151',['phase_homozygous',['../classvg_1_1HaplotypeIndexer.html#a881e755025092748b18f037fb1078e65',1,'vg::HaplotypeIndexer']]],
- ['phase_5fvisits_13152',['phase_visits',['../structvg_1_1VG_1_1Plan.html#ad18d84799bb31227175746bee50f6940',1,'vg::VG::Plan']]],
- ['phred_5fprob_13153',['phred_prob',['../classvg_1_1NGSSimulator.html#ab8ace60ed77440820944dbdaee5bb123',1,'vg::NGSSimulator']]],
- ['pi_5fiv_13154',['pi_iv',['../classxg_1_1XG.html#a31024f79e1a2564e990e1e4445fed0ce',1,'xg::XG']]],
- ['pinned_5ftail_5fsize_13155',['pinned_tail_size',['../classvg_1_1VariantAdder.html#ab5dea4bb3c4143e8fb4e28205a4d2cd6',1,'vg::VariantAdder']]],
- ['plausible_5frescue_5fcluster_5fcoverage_5fdiff_13156',['plausible_rescue_cluster_coverage_diff',['../classvg_1_1MultipathMapper.html#aea5ee453023a73c3d7c02b929d9ef073',1,'vg::MultipathMapper']]],
- ['pn_5fbv_13157',['pn_bv',['../classxg_1_1XG.html#a50b600c6e29135f595459d447fb1e6bb',1,'xg::XG']]],
- ['pn_5fbv_5frank_13158',['pn_bv_rank',['../classxg_1_1XG.html#a9e24932d14efdf5ab53dce331d424093',1,'xg::XG']]],
- ['pn_5fbv_5fselect_13159',['pn_bv_select',['../classxg_1_1XG.html#a541462516fe4a54499c0b42e4cc95a28',1,'xg::XG']]],
- ['pn_5fcsa_13160',['pn_csa',['../classxg_1_1XG.html#a638068e773deaf37cb68bd39eb4599fc',1,'xg::XG']]],
- ['pn_5fiv_13161',['pn_iv',['../classxg_1_1XG.html#aa9d0f9dc89210720c781d43b54f10e4b',1,'xg::XG']]],
- ['pointer_13162',['pointer',['../classvg_1_1SmallBitset.html#a7c4623fa954362f27858d7714acf38cf',1,'vg::SmallBitset']]],
- ['points_13163',['points',['../classvg_1_1algorithms_1_1Anchor.html#a92c0db96b472fce0a3f130cdf281999d',1,'vg::algorithms::Anchor']]],
- ['points_5fper_5fpossible_5fmatch_13164',['points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a4cb0f074432b4ab94eecd529bc18a6c2',1,'vg::MinimizerMapper']]],
- ['polyploid_5fprior_5fsuccess_5flogprob_13165',['polyploid_prior_success_logprob',['../classvg_1_1Genotyper.html#a97aef0fe84f0514e17e2ec8e00162225',1,'vg::Genotyper']]],
- ['population_5fmax_5fpaths_13166',['population_max_paths',['../classvg_1_1MultipathMapper.html#adfb100b024b23e3e94a31ea41d0b1ac8',1,'vg::MultipathMapper']]],
- ['population_5fpaths_5fhard_5fcap_13167',['population_paths_hard_cap',['../classvg_1_1MultipathMapper.html#aa9d339059fb2f60d192935126c82dbed',1,'vg::MultipathMapper']]],
- ['population_5fsize_13168',['population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#adbcb32fa9395d32959b7c0006f25855c',1,'haplo::haploMath::RRMemo']]],
- ['pos_13169',['pos',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#af6b3dfbfadf9eb6f64672bf7a2cfb9f6',1,'vg::SnarlDistanceIndexClusterer::Seed::pos()'],['../structvg_1_1ChainIterator.html#ae99bd64d13edc9f317cfd3bd9e9d3d2e',1,'vg::ChainIterator::pos()'],['../structvg_1_1KmerPosition.html#a31de02880d6006049d740e6216087961',1,'vg::KmerPosition::pos()']]],
- ['pos_5fto_5fedit_5fto_5fdepth_13170',['pos_to_edit_to_depth',['../classvg_1_1Filter.html#a4de4cfcd2bafcc9405c0ffebe84b61dd',1,'vg::Filter']]],
- ['pos_5fto_5fqual_13171',['pos_to_qual',['../classvg_1_1Filter.html#a619f209f11dd2e9b9ce72db535d402fe',1,'vg::Filter']]],
- ['pos_5fto_5ftrans_13172',['pos_to_trans',['../classvg_1_1Translator.html#ae41a08cff51e5f56aff61136b4c520f0',1,'vg::Translator']]],
- ['position_13173',['position',['../structvg_1_1BREAKPOINT.html#a082deeca85819680dc38ceddf6ccbce7',1,'vg::BREAKPOINT::position()'],['../structvg_1_1RecombinatorHaplotype.html#abedb3835774104b4664b62acd3bea6b6',1,'vg::RecombinatorHaplotype::position()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#ae3a3d3091779285687ae5be43ee61652',1,'vg::algorithms::GFAFormatError::position()'],['../structvg_1_1Mapping.html#a2017c8c72a90df9044e14422a0799c86',1,'vg::Mapping::position()'],['../structvg_1_1KmerMatch.html#af0853c79fa538e1d94090514fd217feb',1,'vg::KmerMatch::position()']]],
- ['position_5ffile_13174',['position_file',['../classvg_1_1NGSSimulator.html#a46a332d871425d98495b0b1215ad88e5',1,'vg::NGSSimulator']]],
- ['positions_13175',['positions',['../classvg_1_1MEMChainModel.html#ab273ba5c21fc25422f873dd5d4fd37c3',1,'vg::MEMChainModel::positions()'],['../classvg_1_1AlignmentChainModelVertex.html#a5b770fe52ded0e65dbfe6af4865a7d58',1,'vg::AlignmentChainModelVertex::positions()'],['../classvg_1_1AlignmentChainModel.html#ac37666966f063162a7bbcbb0b285ce6b',1,'vg::AlignmentChainModel::positions()'],['../classvg_1_1MaximalExactMatch.html#afd57ff44231f95d0ea6ef6d4ba24608e',1,'vg::MaximalExactMatch::positions()']]],
- ['possible_5fscores_13176',['possible_scores',['../classvg_1_1WFATree.html#a4646d73afa5c111f920ab006664c4e7b',1,'vg::WFATree']]],
- ['posterior_13177',['posterior',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#aae17dc073a03b6fc72eef3b281608b68',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['precollapse_5forder_5flength_5fhits_13178',['precollapse_order_length_hits',['../classvg_1_1BaseMapper.html#aaf81156cb8c76c2e961b767a782dda59',1,'vg::BaseMapper']]],
- ['prefilter_5fredundant_5fhits_13179',['prefilter_redundant_hits',['../classvg_1_1BaseMapper.html#afa408c8d202885a288f14ff6e2dc60e0',1,'vg::BaseMapper']]],
- ['prefix_13180',['prefix',['../structvg_1_1BitStringTree_1_1TreeNode.html#ae400b0d9c4fecf6b90fd0d708258df1e',1,'vg::BitStringTree::TreeNode']]],
- ['prefix_5flength_13181',['prefix_length',['../structvg_1_1MultipathProblem.html#a5fdfec89c00fe647e234e84fa72879ed',1,'vg::MultipathProblem']]],
- ['prefix_5fscore_13182',['prefix_score',['../structvg_1_1MultipathProblem.html#a5e3610b3438d69baba7e3be6a6cfdcc0',1,'vg::MultipathProblem']]],
- ['prefix_5fsum_13183',['prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ac09ee425b8f2f95a4c8c4f45b39084b9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild::prefix_sum()'],['../structvg_1_1MIPayload.html#af0dcb83df9249928d947e23f368f41a0',1,'vg::MIPayload::prefix_sum()']]],
- ['prefix_5fsum_5for_5fidentifier_13184',['prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#aadf1912938760b4371b385865fa661f9',1,'vg::ZipCode::node_code_t::prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a736b6676259bc262d66d9814fbbb7142',1,'vg::ZipCode::snarl_code_t::prefix_sum_or_identifier()']]],
- ['prefix_5fsum_5fvalue_13185',['prefix_sum_value',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a09ed2f3574eb36ceccf98ded8c99e7f5',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['prefixes_13186',['prefixes',['../classvg_1_1PhaseUnfolder.html#a64f18b1c10e5d2104bd04df2013f5a0f',1,'vg::PhaseUnfolder']]],
- ['present_13187',['present',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a130ad1d08da8cb8ff5be5f254b904369',1,'vg::SnarlDistanceIndexClusterer::Cluster']]],
- ['present_5fdiscount_13188',['PRESENT_DISCOUNT',['../classvg_1_1Recombinator.html#a5c415fe934bb25c07068a2ca0291ea00',1,'vg::Recombinator::PRESENT_DISCOUNT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a5f62e8ec5640f3d4d06bbda709b44bdc',1,'vg::Recombinator::Parameters::present_discount()']]],
- ['preserve_5fsinks_13189',['preserve_sinks',['../classvg_1_1DozeuPinningOverlay.html#a066fa04f3bf59c7302a0e57036154ab7',1,'vg::DozeuPinningOverlay']]],
- ['prev_13190',['prev',['../classvg_1_1MEMChainModelVertex.html#a8b3867d0ba2a4797202be745d92d11de',1,'vg::MEMChainModelVertex::prev()'],['../classvg_1_1AlignmentChainModelVertex.html#a9979808dd8d6ddaf11d83643ab3e9db2',1,'vg::AlignmentChainModelVertex::prev()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#aea823a7f3329d308107c1de1cf20c1a6',1,'vg::PhasedGenome::HaplotypeNode::prev()']]],
- ['prev_5fchar_13191',['prev_char',['../structvg_1_1kmer__t.html#a006cf626b837e21d26b66925103a34c5',1,'vg::kmer_t']]],
- ['prev_5fchars_13192',['prev_chars',['../structvg_1_1KmerPosition.html#a6c6e2b384e3f9292342999e6f49684c3',1,'vg::KmerPosition']]],
- ['prev_5fcost_13193',['prev_cost',['../classvg_1_1MEMChainModelVertex.html#ad8ad4b22339e6ad06c893c78c63cda5a',1,'vg::MEMChainModelVertex::prev_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#a0dcdae4513868599a6bd50e719f9e4f5',1,'vg::AlignmentChainModelVertex::prev_cost()']]],
- ['prev_5fpos_13194',['prev_pos',['../structvg_1_1kmer__t.html#acf511fd3c535a5d9e2109480ed1528e8',1,'vg::kmer_t']]],
- ['prev_5fstage_5fitems_13195',['prev_stage_items',['../structvg_1_1Funnel_1_1Item.html#a9ee7530fac67298fbcdb27f8280b4a14',1,'vg::Funnel::Item']]],
- ['prev_5fsubpath_13196',['prev_subpath',['../structvg_1_1MultipathProblem.html#a51f2e682e6721f35d88cae8d1cf4a59d',1,'vg::MultipathProblem']]],
- ['previous_5findex_13197',['previous_index',['../structhaplo_1_1haplo__DP__rectangle.html#addd510174b8c5f83418aa6c23e278b36',1,'haplo::haplo_DP_rectangle']]],
- ['previous_5fsizes_13198',['previous_sizes',['../structhaplo_1_1haplo__DP__column.html#a2ece2d4c8c54fbd7fc8e898ced985e6a',1,'haplo::haplo_DP_column']]],
- ['previous_5fsum_13199',['previous_sum',['../structhaplo_1_1haplo__DP__column.html#a474364179d091eda8dd0684d4d86afa8',1,'haplo::haplo_DP_column']]],
- ['previous_5ftag_13200',['previous_tag',['../classvg_1_1io_1_1MessageIterator.html#affc663d4448fe1b213d1c2e9ec64b3bb',1,'vg::io::MessageIterator']]],
- ['previous_5fvalues_13201',['previous_values',['../structhaplo_1_1haplo__DP__column.html#a5e1664796c443719bd4e775f503ab8ad',1,'haplo::haplo_DP_column']]],
- ['primary_13202',['primary',['../classvg_1_1MaximalExactMatch.html#a2e34dcded590361daf8ca3a9ed3fb62f',1,'vg::MaximalExactMatch']]],
- ['primitive_5froot_13203',['primitive_root',['../classvg_1_1ShuffledPairs.html#a78c948366b8eec98b8393ae2ac75f86a',1,'vg::ShuffledPairs']]],
- ['print_5fupdates_13204',['print_updates',['../classvg_1_1VariantAdder.html#af52ce72b2446132042df93857eb12b63',1,'vg::VariantAdder']]],
- ['priority_13205',['priority',['../classvg_1_1subcommand_1_1Subcommand.html#a3f995aec9b4e2367530e1a6bcccb2e53',1,'vg::subcommand::Subcommand']]],
- ['prng_13206',['prng',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ac95b66a8f2e2cda6bc2d45691d496f5e',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['prngs_13207',['prngs',['../classvg_1_1NGSSimulator.html#ab5d12a331a39e82fc07202152f254d70',1,'vg::NGSSimulator']]],
- ['prob_5fsampler_13208',['prob_sampler',['../classvg_1_1NGSSimulator.html#a36ca291ed15a9a3942809d21d0574bc1',1,'vg::NGSSimulator']]],
- ['problem_13209',['problem',['../structvg_1_1AlignmentValidity.html#a1ca7f243aa52fe313bdfac808f4eba92',1,'vg::AlignmentValidity']]],
- ['produces_5fone_5fgbwt_13210',['produces_one_gbwt',['../structGBWTConfig.html#ad752e9efebcc424e596e1c328a9eb583',1,'GBWTConfig']]],
- ['progress_13211',['progress',['../classvg_1_1Progressive.html#af78e64e28b252828a0ba86439125fea4',1,'vg::Progressive']]],
- ['progress_5fbars_13212',['progress_bars',['../classvg_1_1VGset.html#acc491d0a5c0a54c6bbd0636fa44431b7',1,'vg::VGset']]],
- ['progress_5fcount_13213',['progress_count',['../classvg_1_1Progressive.html#a71e61fe99d71d23542d2d7387c23fd4d',1,'vg::Progressive']]],
- ['progress_5fmessage_13214',['progress_message',['../classvg_1_1Progressive.html#a4bb04fe23ceb41467dd14cdf8cc01a71',1,'vg::Progressive']]],
- ['progress_5fseen_13215',['progress_seen',['../classvg_1_1Progressive.html#ac6745d7e07b4b271f9510cd40f06d18e',1,'vg::Progressive']]],
- ['projected_5fcount_13216',['projected_count',['../structvg_1_1Funnel_1_1Stage.html#a74c290d50af94a82c196350d3ee7223d',1,'vg::Funnel::Stage']]],
- ['proto_13217',['proto',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a05cf3104e11f544431c6ed6e709d2361',1,'vg::io::VGAlignmentEmitter::proto()'],['../vg_8proto.html#ace9afe7f815b63b3d93844da5eb8fbbc',1,'proto(): vg.proto']]],
- ['protobuf_5fto_5ftag_13218',['protobuf_to_tag',['../structvg_1_1io_1_1Registry_1_1Tables.html#a9959a1192210db895c2d127dc6a197fc',1,'vg::io::Registry::Tables']]],
- ['provided_5fdirectly_13219',['provided_directly',['../classvg_1_1IndexFile.html#a32bf1b5189843cdcc3ba7eb6068dd46f',1,'vg::IndexFile']]],
- ['prune_5fsubpaths_5fmultiplier_13220',['prune_subpaths_multiplier',['../classvg_1_1MultipathMapper.html#aa8409bc363c70b9df0c3590767d25e92',1,'vg::MultipathMapper']]],
- ['prune_5fsuspicious_5fanchors_13221',['prune_suspicious_anchors',['../classvg_1_1Surjector.html#af01db9677cefc7952fee698f8ee2b672',1,'vg::Surjector']]],
- ['prune_5fthread_5fbuffer_5fsize_13222',['PRUNE_THREAD_BUFFER_SIZE',['../namespacevg_1_1algorithms.html#a64f4abe5d8279f14a52b56ffb47fff34',1,'vg::algorithms']]],
- ['pruning_5fmax_5fedge_5fcount_13223',['pruning_max_edge_count',['../structvg_1_1IndexingParameters.html#ad673cb8b7687d3a60aef1036d1b1dae3',1,'vg::IndexingParameters']]],
- ['pruning_5fmax_5fnode_5fdegree_13224',['pruning_max_node_degree',['../structvg_1_1IndexingParameters.html#a8041e911ac757df80b37fbdbc4943f74',1,'vg::IndexingParameters']]],
- ['pruning_5fmax_5fnode_5fdegree_5fdecrease_5ffactor_13225',['pruning_max_node_degree_decrease_factor',['../structvg_1_1IndexingParameters.html#ac3de2fff42441077c37ff61421b6415d',1,'vg::IndexingParameters']]],
- ['pruning_5fmin_5fcomponent_5fsize_13226',['pruning_min_component_size',['../structvg_1_1IndexingParameters.html#a1f955fc9bdfedd418b900163f36a2e15',1,'vg::IndexingParameters']]],
- ['pruning_5fwalk_5flength_13227',['pruning_walk_length',['../structvg_1_1IndexingParameters.html#ac9f7127d0df7aa1c90ced42a01755763',1,'vg::IndexingParameters']]],
- ['pruning_5fwalk_5flength_5fincrease_5ffactor_13228',['pruning_walk_length_increase_factor',['../structvg_1_1IndexingParameters.html#a7c483115dc36e1e7e8b25684f427442c',1,'vg::IndexingParameters']]],
- ['ptr_13229',['ptr',['../structjson__autoptr.html#a8eeb7c64d99d1378d9524ede91d6faa4',1,'json_autoptr']]]
+ ['p_5fvalue_5fmemo_13067',['p_value_memo',['../classvg_1_1MultipathMapper.html#a076b5202ca84c7836e93d3e8b71775bf',1,'vg::MultipathMapper']]],
+ ['pack_5fnames_13068',['pack_names',['../classvg_1_1Viz.html#abb3fd61d416351930f2e7399e6f6001b',1,'vg::Viz']]],
+ ['packer_13069',['packer',['../classvg_1_1PackedTraversalSupportFinder.html#ac48b605c781739b3920b8c36fdb6fcf8',1,'vg::PackedTraversalSupportFinder']]],
+ ['packs_13070',['packs',['../classvg_1_1Viz.html#a350ea478ececb5f19170b16cf1539726',1,'vg::Viz']]],
+ ['pad_5fband_5fconstant_13071',['pad_band_constant',['../namespacevg_1_1algorithms.html#ab48342aedc7d81e2334c52bb320223c2',1,'vg::algorithms']]],
+ ['pad_5fband_5fmin_5frandom_5fwalk_13072',['pad_band_min_random_walk',['../namespacevg_1_1algorithms.html#a3363cc23e6c71e1bb5faac975af7920d',1,'vg::algorithms']]],
+ ['pad_5fband_5frandom_5fwalk_13073',['pad_band_random_walk',['../namespacevg_1_1algorithms.html#a6a606c26b5751d935c71d7971a92d99b',1,'vg::algorithms']]],
+ ['pad_5fcluster_5fscore_5fthreshold_13074',['pad_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a70b206dc58a148a69657303ff292199f',1,'vg::MinimizerMapper']]],
+ ['pad_5fsuspicious_5fanchors_5fto_5flength_13075',['pad_suspicious_anchors_to_length',['../classvg_1_1Surjector.html#a7231e0ecf35ed767417fc37184b0a806',1,'vg::Surjector']]],
+ ['pad_5fzipcode_5ftree_5fscore_5fthreshold_13076',['pad_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#aafbc5c792144ae26630c312d2475b19a',1,'vg::MinimizerMapper']]],
+ ['pair_5frescue_5fhang_5fthreshold_13077',['pair_rescue_hang_threshold',['../classvg_1_1Mapper.html#a92e1f4de4e6ce576e09005713d1c1cd1',1,'vg::Mapper']]],
+ ['pair_5frescue_5fretry_5fthreshold_13078',['pair_rescue_retry_threshold',['../classvg_1_1Mapper.html#a36ed72fe5d33907a75992011ff9ae244',1,'vg::Mapper']]],
+ ['paired_5fdistance_5fstdevs_13079',['paired_distance_stdevs',['../classvg_1_1MinimizerMapper.html#a94bd867270265d26c4f2abfbd730f316',1,'vg::MinimizerMapper']]],
+ ['paired_5fread_5fname_13080',['paired_read_name',['../structvg_1_1MultipathAlignment.html#a0664790bf6bd37af413697cddff370fb',1,'vg::MultipathAlignment']]],
+ ['paired_5frescue_5fscore_5flimit_13081',['paired_rescue_score_limit',['../classvg_1_1MinimizerMapper.html#a923b2f2f9aa86e445add3be0d1c4abae',1,'vg::MinimizerMapper']]],
+ ['parent_13082',['parent',['../structvg_1_1WFANode.html#a78adf1a04bc5f5907cc3a46445061e62',1,'vg::WFANode::parent()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#ae00d40d340f5114917a9f6ca1cec0460',1,'vg::SnarlManager::SnarlRecord::parent()'],['../structvg_1_1TreeNode.html#a4eb11d266cabbae3e6728d2918c80996',1,'vg::TreeNode::parent()'],['../structvg_1_1VectorView_1_1const__iterator.html#a41fafc961da593dbc8591c6288a33fd6',1,'vg::VectorView::const_iterator::parent()'],['../structvg_1_1Snarl.html#a054af14a2fccdda2209ef9a8f19aa032',1,'vg::Snarl::parent()']]],
+ ['parent_5fallele_13083',['parent_allele',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2f21b56cc895482f0f8a4829ccfa3463',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5fchain_13084',['parent_chain',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a37d7d2aa3460ba15b3a51ac4eedefd76',1,'vg::SnarlManager::SnarlRecord']]],
+ ['parent_5fchain_5findex_13085',['parent_chain_index',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a7f98f1f84ba0d39301f1adc3333e6dfb',1,'vg::SnarlManager::SnarlRecord']]],
+ ['parent_5fchains_13086',['parent_chains',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a3f1ca708ff05e4f649b0d9b22dc539fd',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['parent_5fdepth_13087',['parent_depth',['../structvg_1_1MIPayload.html#af3214bd006207b1d4c417c331b905290',1,'vg::MIPayload']]],
+ ['parent_5fdirectory_13088',['parent_directory',['../structvg_1_1temp__file_1_1Handler.html#a1a791a5a813c3d0702594f5ad6915eaf',1,'vg::temp_file::Handler::parent_directory()'],['../structxg_1_1temp__file_1_1Handler.html#a16640b9f416a23bd671f56437bd09aa6',1,'xg::temp_file::Handler::parent_directory()']]],
+ ['parent_5fgraph_13089',['parent_graph',['../classvg_1_1JoinedSpliceGraph.html#a274429d072e5be5687ac704393b903a4',1,'vg::JoinedSpliceGraph']]],
+ ['parent_5fhandle_13090',['parent_handle',['../structvg_1_1MIPayload.html#a92ead268cf5b206f54e4cf0e95937dfc',1,'vg::MIPayload']]],
+ ['parent_5fis_5fchain_13091',['parent_is_chain',['../structvg_1_1MIPayload.html#aa5abaa3ea722cf685fe73fe9502e00c1',1,'vg::MIPayload']]],
+ ['parent_5fis_5froot_13092',['parent_is_root',['../structvg_1_1MIPayload.html#a36e03b459c31f012a17a78a1ec6f5391',1,'vg::MIPayload']]],
+ ['parent_5flen_13093',['parent_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#abe519281b723c59979299b2657439f6e',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5fnet_5fhandle_13094',['parent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af940526569cd8d070de39e8446390e6f',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['parent_5fpath_5finterval_13095',['parent_path_interval',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a4aa790baef1ec47d6546e30f60851e9b',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5frecord_5foffset_13096',['parent_record_offset',['../structvg_1_1MIPayload.html#af185811088055cdd4c371f18883087b2',1,'vg::MIPayload']]],
+ ['parent_5fref_5flen_13097',['parent_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ac311ca43aecb9c37302835adadce85af',1,'vg::Deconstructor::NestingInfo']]],
+ ['parent_5fsnarls_13098',['parent_snarls',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a03f3e53e97f93f2d2b4daf66f99cd763',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['parent_5ftype_13099',['parent_type',['../structvg_1_1MIPayload.html#aa14d5e8cecee30a8e796832d5ead8578',1,'vg::MIPayload']]],
+ ['parse_5fonly_13100',['parse_only',['../structGBWTConfig.html#af8fc6affa1925b48a3af6fff48511340',1,'GBWTConfig']]],
+ ['partitioner_5fparameters_13101',['partitioner_parameters',['../structHaplotypesConfig.html#a6080d6a6e4ada9573d11d678b6de79d0',1,'HaplotypesConfig']]],
+ ['pass_5fnumber_13102',['pass_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#a9354b35a8f08891654da020502248f2e',1,'vg::algorithms::GFAFormatError']]],
+ ['passed_5ffilters_13103',['passed_filters',['../structvg_1_1Funnel_1_1Item.html#a566978051c820d69d63e72763dc38b17',1,'vg::Funnel::Item']]],
+ ['passed_5fstatistics_13104',['passed_statistics',['../structvg_1_1Funnel_1_1Item.html#a5ae29ab2e549daa3fa20626fd5d4fb59',1,'vg::Funnel::Item']]],
+ ['passing_13105',['passing',['../structvg_1_1Funnel_1_1FilterPerformance.html#a9382a4983a52c3849412717c26205bde',1,'vg::Funnel::FilterPerformance']]],
+ ['passing_5fcorrect_13106',['passing_correct',['../structvg_1_1Funnel_1_1FilterPerformance.html#a7622d6acfd5d4075e26ad60b911e72c4',1,'vg::Funnel::FilterPerformance']]],
+ ['past_5fend_13107',['past_end',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a06f803fd96e9e94610bc8fa8f9db95f3',1,'vg::GraphSynchronizer::Lock']]],
+ ['patch_5falignments_13108',['patch_alignments',['../classvg_1_1Mapper.html#a6c33dd8ad7af82e21f0ee6463e9456fc',1,'vg::Mapper']]],
+ ['path_13109',['path',['../structvg_1_1MatchPos.html#a6a24cd3b3befa706a8f4f934034843cf',1,'vg::MatchPos::path()'],['../structvg_1_1WFANode.html#ad947775b8a38d6d03e6c40b5a8ee06c2',1,'vg::WFANode::path()'],['../structvg_1_1GaplessExtension.html#a6d46f3e3d3525ea159b11f6e832a37e0',1,'vg::GaplessExtension::path()'],['../structvg_1_1WFAAlignment.html#afd65b83419307e4f56481adef5c96f71',1,'vg::WFAAlignment::path()'],['../classvg_1_1PathNode.html#aa955184b7b22179c0efd1febdfc55b92',1,'vg::PathNode::path()'],['../structvg_1_1RecombinatorHaplotype.html#ae37ea81b1f65f9c24f05620ecc3f2a80',1,'vg::RecombinatorHaplotype::path()'],['../structvg_1_1EditedTranscriptPath.html#a8945ac17c2039bc54e3697553c1563a2',1,'vg::EditedTranscriptPath::path()'],['../structvg_1_1CompletedTranscriptPath.html#ae6ea83076c2772ac2670e0e06587dc04',1,'vg::CompletedTranscriptPath::path()'],['../structvg_1_1algorithms_1_1walk__t.html#aee19ea04353c3d23bef5d5fd3689965c',1,'vg::algorithms::walk_t::path()'],['../classhandlegraph_1_1PathForEachSocket.html#a5bd264139b15b7e56ad5a2f6f691202b',1,'handlegraph::PathForEachSocket::path()'],['../structgafkluge_1_1GafRecord.html#ae9734ca0963cfb21cb966ee915c9224b',1,'gafkluge::GafRecord::path()'],['../structvg_1_1Graph.html#a850007eb60ce0d25a6bd9799050ec790',1,'vg::Graph::path()'],['../structvg_1_1Alignment.html#a4736db5fe121ef57784c18c3c27aea79',1,'vg::Alignment::path()'],['../structvg_1_1Subpath.html#a69056b48fb59ee83a8b0307838987e19',1,'vg::Subpath::path()']]],
+ ['path_5fcollapse_5ftype_13110',['path_collapse_type',['../classvg_1_1Transcriptome.html#a539e8602c6f984142ae866af8730fd34',1,'vg::Transcriptome']]],
+ ['path_5fcomponent_5findex_13111',['path_component_index',['../classvg_1_1PathOrientedDistanceMeasurer.html#aec1793ac0e2bf87292b90a5a2c8f14d8',1,'vg::PathOrientedDistanceMeasurer::path_component_index()'],['../classvg_1_1MultipathMapper.html#a0c64ee67ef473d5d5336ae6adf0b66e8',1,'vg::MultipathMapper::path_component_index()']]],
+ ['path_5fcount_13112',['path_count',['../classxg_1_1XG.html#a1859cb996668f8d86107d4e0117cf97f',1,'xg::XG']]],
+ ['path_5fcover_13113',['path_cover',['../structGBWTConfig.html#a857449dfcac12577f54afbd7d8957336',1,'GBWTConfig']]],
+ ['path_5fcover_5fdepth_13114',['path_cover_depth',['../structvg_1_1IndexingParameters.html#a1075d3f3c10502dc02deb564d85ff897',1,'vg::IndexingParameters']]],
+ ['path_5fend_13115',['path_end',['../structgafkluge_1_1GafRecord.html#ac1a2b5a9c4152dfb188a72571ecf746a',1,'gafkluge::GafRecord']]],
+ ['path_5ffinder_13116',['path_finder',['../classvg_1_1VCFTraversalFinder.html#a7f529cb408098ee45d3e4868ed9fe2b8',1,'vg::VCFTraversalFinder']]],
+ ['path_5fgraph_13117',['path_graph',['../classvg_1_1MinimizerMapper.html#aa75ca7504db85f1ba5d340b8213036de',1,'vg::MinimizerMapper::path_graph()'],['../classvg_1_1PhaseUnfolder.html#a974791c770e3999168899eb36cbd2f48',1,'vg::PhaseUnfolder::path_graph()'],['../structGraphHandler.html#aeb4deb32f56c35702b331c0f506d3844',1,'GraphHandler::path_graph()']]],
+ ['path_5findexes_13118',['path_indexes',['../classvg_1_1LegacyCaller.html#a5de5c60b4da9b71566fc10a76ed0e211',1,'vg::LegacyCaller']]],
+ ['path_5fjaccard_5fwindow_13119',['path_jaccard_window',['../classvg_1_1Deconstructor.html#a0cf545ea26ebb9bbebafefe47524f87b',1,'vg::Deconstructor']]],
+ ['path_5flength_13120',['path_length',['../structgafkluge_1_1GafRecord.html#ac9b7a4a556d78f32913392b0706e93e0',1,'gafkluge::GafRecord']]],
+ ['path_5flisteners_13121',['path_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aa856090842dafbe0dbaf22bed66fd411',1,'vg::algorithms::GFAParser']]],
+ ['path_5fmode_13122',['path_mode',['../structGBWTConfig.html#a218c5f96dd7101b89bdf8e64de3b9949',1,'GBWTConfig']]],
+ ['path_5fname_13123',['path_name',['../structvg_1_1FeatureSet_1_1Feature.html#a645900ed3044cc3359c18e109f7460a7',1,'vg::FeatureSet::Feature::path_name()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad19c5f9cbb68abb1bcfe6e3a9fd65382',1,'vg::GraphSynchronizer::Lock::path_name()']]],
+ ['path_5fname_5fcsa_5fdelim_13124',['path_name_csa_delim',['../classxg_1_1XG.html#a5b2791b586efb23a131c2d5c00d85593',1,'xg::XG']]],
+ ['path_5fnames_13125',['path_names',['../classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138',1,'vg::VariantAdder::path_names()'],['../structGBWTConfig.html#a96ccf4e2605d4dad1a32511169f51969',1,'GBWTConfig::path_names()']]],
+ ['path_5fnodes_13126',['path_nodes',['../classvg_1_1MultipathAlignmentGraph.html#a76f9356cd0afea7dea3003caea2526eb',1,'vg::MultipathAlignmentGraph']]],
+ ['path_5foffset_13127',['path_offset',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a58b1c09d2f45e4942afd52d975c85b9a',1,'vg::GraphSynchronizer::Lock']]],
+ ['path_5forder_5fand_5flength_13128',['path_order_and_length',['../classvg_1_1HTSWriter.html#a2b0a5d9268a4b4901a699f82d857d6e2',1,'vg::HTSWriter']]],
+ ['path_5foutput_13129',['path_output',['../structGBWTConfig.html#a91e5194d120c0dbae060bdfe5c60667a',1,'GBWTConfig']]],
+ ['path_5fposition_5fhandle_5fgraph_13130',['path_position_handle_graph',['../classvg_1_1MCMCCaller.html#a240741cadefa13b2b4d472f0b6e3b8d3',1,'vg::MCMCCaller']]],
+ ['path_5fsampler_13131',['path_sampler',['../classvg_1_1Sampler.html#a8125a49b29eecf4d5037067c813b2cd7',1,'vg::Sampler::path_sampler()'],['../classvg_1_1NGSSimulator.html#a6101d443a8c314416fbc23dbfd3d5bde',1,'vg::NGSSimulator::path_sampler()']]],
+ ['path_5fstart_13132',['path_start',['../structgafkluge_1_1GafRecord.html#a14ce42efee5a241bebe4debf852afbae',1,'gafkluge::GafRecord']]],
+ ['path_5fsubset_13133',['path_subset',['../classvg_1_1PathSubgraphOverlay.html#aef82f75c24c686645b0255685bc4c6f2',1,'vg::PathSubgraphOverlay']]],
+ ['path_5fto_5fploidy_13134',['path_to_ploidy',['../classvg_1_1VCFGenotyper.html#a248d8e2819ba7354c39b3d2077061fed',1,'vg::VCFGenotyper']]],
+ ['path_5fto_5fsample_5fphase_13135',['path_to_sample_phase',['../classvg_1_1Deconstructor.html#a8a5562db89e9293a88b2f22e476d1d25',1,'vg::Deconstructor']]],
+ ['path_5fto_5fvcf_13136',['path_to_vcf',['../classvg_1_1HaplotypeIndexer.html#a5ff016a7fdf425ec4f3d5408d09b951f',1,'vg::HaplotypeIndexer']]],
+ ['path_5ftrav_5ffinder_13137',['path_trav_finder',['../classvg_1_1Deconstructor.html#a73c6c008333acfbb0ffd6fde2360518c',1,'vg::Deconstructor']]],
+ ['paths_13138',['paths',['../classvg_1_1SurjectingAlignmentEmitter.html#a3193ef16804780255b9d0bbcef8dc6ca',1,'vg::SurjectingAlignmentEmitter::paths()'],['../classvg_1_1PathTraversalFinder.html#a5a931da9269d7834dcc04e5fb578ff45',1,'vg::PathTraversalFinder::paths()'],['../classvg_1_1VG.html#a7c5150aba84e7ed2bde7986462a79989',1,'vg::VG::paths()'],['../structjob__type.html#a1c12e7fbad645aa2081f00b1a49b296f',1,'job_type::paths()'],['../classxg_1_1XG.html#a1b5defef10208838d0d3a48ddeb91f85',1,'xg::XG::paths()']]],
+ ['payload_13139',['payload',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a9b29761900b87e78b6c17dbe8e38d4fe',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
+ ['payload_5fnode_5flength_13140',['payload_node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ac80389e7a2ddaae480e60b286186e3aa',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
+ ['payload_5fprefix_5fsum_13141',['payload_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#ab809433b78a00f00ae46e7061972c9a9',1,'vg::SnarlDistanceIndexClusterer::SeedCache']]],
+ ['pbsize_13142',['pbSize',['../classvg_1_1io_1_1fdinbuf.html#a1756a5735e7daf8ea042bc81343f7a0f',1,'vg::io::fdinbuf::pbSize()'],['../classvg_1_1io_1_1streaminbuf.html#a4cdee06174136df70efd572abfced2c8',1,'vg::io::streaminbuf::pbSize()']]],
+ ['penalties_13143',['penalties',['../structhaplo_1_1linear__haplo__structure.html#af55d7f33177180d033e8e925cf20e5fd',1,'haplo::linear_haplo_structure']]],
+ ['per_5fbase_13144',['per_base',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a8a85161fa2d79301a9ca6489006a4c62',1,'vg::WFAExtender::ErrorModel::Event']]],
+ ['perfect_5fpair_5fidentity_5fthreshold_13145',['perfect_pair_identity_threshold',['../classvg_1_1FragmentLengthStatistics.html#a4e65bc3de5657555df556429284f5251',1,'vg::FragmentLengthStatistics']]],
+ ['peripheral_5fattachments_13146',['peripheral_attachments',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa2e7c9a960855fa8758d9dd6da6454ea',1,'vg::GraphSynchronizer::Lock']]],
+ ['periphery_13147',['periphery',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad9bebede56cef5ab20d80828e34d8b6a',1,'vg::GraphSynchronizer::Lock']]],
+ ['permutation_5fidx_13148',['permutation_idx',['../classvg_1_1ShuffledPairs_1_1iterator.html#a52dd908e59ff6dac90191a40c63537e0',1,'vg::ShuffledPairs::iterator']]],
+ ['permuted_13149',['permuted',['../classvg_1_1ShuffledPairs_1_1iterator.html#a19642461808615472b7b544e04c47243',1,'vg::ShuffledPairs::iterator']]],
+ ['pessimistic_5fgap_5fmemo_13150',['pessimistic_gap_memo',['../classvg_1_1MultipathMapper.html#a828e72945f3e24243d5802604e027b47',1,'vg::MultipathMapper']]],
+ ['pessimistic_5fgap_5fmultiplier_13151',['pessimistic_gap_multiplier',['../classvg_1_1MultipathMapper.html#aef97cb46d48a242a68c6ed590039e832',1,'vg::MultipathMapper']]],
+ ['pessimistic_5ftail_5fgap_5fmemo_13152',['pessimistic_tail_gap_memo',['../classvg_1_1MultipathAlignmentGraph.html#af46ba9972db437bf66f787a9bbe6c3cd',1,'vg::MultipathAlignmentGraph']]],
+ ['phase_13153',['phase',['../structvg_1_1GFFRecord.html#adf3d82a77a4837edba29935e08cb2a53',1,'vg::GFFRecord']]],
+ ['phase_5fblock_5fmatch_13154',['PHASE_BLOCK_MATCH',['../classhandlegraph_1_1PathMetadata.html#a08fb019956ae31b8ea31920c904ea5fc',1,'handlegraph::PathMetadata']]],
+ ['phase_5fhomozygous_13155',['phase_homozygous',['../classvg_1_1HaplotypeIndexer.html#a881e755025092748b18f037fb1078e65',1,'vg::HaplotypeIndexer']]],
+ ['phase_5fvisits_13156',['phase_visits',['../structvg_1_1VG_1_1Plan.html#ad18d84799bb31227175746bee50f6940',1,'vg::VG::Plan']]],
+ ['phred_5fprob_13157',['phred_prob',['../classvg_1_1NGSSimulator.html#ab8ace60ed77440820944dbdaee5bb123',1,'vg::NGSSimulator']]],
+ ['pi_5fiv_13158',['pi_iv',['../classxg_1_1XG.html#a31024f79e1a2564e990e1e4445fed0ce',1,'xg::XG']]],
+ ['pinned_5ftail_5fsize_13159',['pinned_tail_size',['../classvg_1_1VariantAdder.html#ab5dea4bb3c4143e8fb4e28205a4d2cd6',1,'vg::VariantAdder']]],
+ ['plausible_5frescue_5fcluster_5fcoverage_5fdiff_13160',['plausible_rescue_cluster_coverage_diff',['../classvg_1_1MultipathMapper.html#aea5ee453023a73c3d7c02b929d9ef073',1,'vg::MultipathMapper']]],
+ ['pn_5fbv_13161',['pn_bv',['../classxg_1_1XG.html#a50b600c6e29135f595459d447fb1e6bb',1,'xg::XG']]],
+ ['pn_5fbv_5frank_13162',['pn_bv_rank',['../classxg_1_1XG.html#a9e24932d14efdf5ab53dce331d424093',1,'xg::XG']]],
+ ['pn_5fbv_5fselect_13163',['pn_bv_select',['../classxg_1_1XG.html#a541462516fe4a54499c0b42e4cc95a28',1,'xg::XG']]],
+ ['pn_5fcsa_13164',['pn_csa',['../classxg_1_1XG.html#a638068e773deaf37cb68bd39eb4599fc',1,'xg::XG']]],
+ ['pn_5fiv_13165',['pn_iv',['../classxg_1_1XG.html#aa9d0f9dc89210720c781d43b54f10e4b',1,'xg::XG']]],
+ ['pointer_13166',['pointer',['../classvg_1_1SmallBitset.html#a7c4623fa954362f27858d7714acf38cf',1,'vg::SmallBitset']]],
+ ['points_13167',['points',['../classvg_1_1algorithms_1_1Anchor.html#a92c0db96b472fce0a3f130cdf281999d',1,'vg::algorithms::Anchor']]],
+ ['points_5fper_5fpossible_5fmatch_13168',['points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a4cb0f074432b4ab94eecd529bc18a6c2',1,'vg::MinimizerMapper']]],
+ ['polyploid_5fprior_5fsuccess_5flogprob_13169',['polyploid_prior_success_logprob',['../classvg_1_1Genotyper.html#a97aef0fe84f0514e17e2ec8e00162225',1,'vg::Genotyper']]],
+ ['population_5fmax_5fpaths_13170',['population_max_paths',['../classvg_1_1MultipathMapper.html#adfb100b024b23e3e94a31ea41d0b1ac8',1,'vg::MultipathMapper']]],
+ ['population_5fpaths_5fhard_5fcap_13171',['population_paths_hard_cap',['../classvg_1_1MultipathMapper.html#aa9d339059fb2f60d192935126c82dbed',1,'vg::MultipathMapper']]],
+ ['population_5fsize_13172',['population_size',['../structhaplo_1_1haploMath_1_1RRMemo.html#adbcb32fa9395d32959b7c0006f25855c',1,'haplo::haploMath::RRMemo']]],
+ ['pos_13173',['pos',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#af6b3dfbfadf9eb6f64672bf7a2cfb9f6',1,'vg::SnarlDistanceIndexClusterer::Seed::pos()'],['../structvg_1_1ChainIterator.html#ae99bd64d13edc9f317cfd3bd9e9d3d2e',1,'vg::ChainIterator::pos()'],['../structvg_1_1KmerPosition.html#a31de02880d6006049d740e6216087961',1,'vg::KmerPosition::pos()']]],
+ ['pos_5fto_5fedit_5fto_5fdepth_13174',['pos_to_edit_to_depth',['../classvg_1_1Filter.html#a4de4cfcd2bafcc9405c0ffebe84b61dd',1,'vg::Filter']]],
+ ['pos_5fto_5fqual_13175',['pos_to_qual',['../classvg_1_1Filter.html#a619f209f11dd2e9b9ce72db535d402fe',1,'vg::Filter']]],
+ ['pos_5fto_5ftrans_13176',['pos_to_trans',['../classvg_1_1Translator.html#ae41a08cff51e5f56aff61136b4c520f0',1,'vg::Translator']]],
+ ['position_13177',['position',['../structvg_1_1BREAKPOINT.html#a082deeca85819680dc38ceddf6ccbce7',1,'vg::BREAKPOINT::position()'],['../structvg_1_1RecombinatorHaplotype.html#abedb3835774104b4664b62acd3bea6b6',1,'vg::RecombinatorHaplotype::position()'],['../structvg_1_1algorithms_1_1GFAFormatError.html#ae3a3d3091779285687ae5be43ee61652',1,'vg::algorithms::GFAFormatError::position()'],['../structvg_1_1Mapping.html#a2017c8c72a90df9044e14422a0799c86',1,'vg::Mapping::position()'],['../structvg_1_1KmerMatch.html#af0853c79fa538e1d94090514fd217feb',1,'vg::KmerMatch::position()']]],
+ ['position_5ffile_13178',['position_file',['../classvg_1_1NGSSimulator.html#a46a332d871425d98495b0b1215ad88e5',1,'vg::NGSSimulator']]],
+ ['positions_13179',['positions',['../classvg_1_1MEMChainModel.html#ab273ba5c21fc25422f873dd5d4fd37c3',1,'vg::MEMChainModel::positions()'],['../classvg_1_1AlignmentChainModelVertex.html#a5b770fe52ded0e65dbfe6af4865a7d58',1,'vg::AlignmentChainModelVertex::positions()'],['../classvg_1_1AlignmentChainModel.html#ac37666966f063162a7bbcbb0b285ce6b',1,'vg::AlignmentChainModel::positions()'],['../classvg_1_1MaximalExactMatch.html#afd57ff44231f95d0ea6ef6d4ba24608e',1,'vg::MaximalExactMatch::positions()']]],
+ ['possible_5fscores_13180',['possible_scores',['../classvg_1_1WFATree.html#a4646d73afa5c111f920ab006664c4e7b',1,'vg::WFATree']]],
+ ['posterior_13181',['posterior',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#aae17dc073a03b6fc72eef3b281608b68',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['precollapse_5forder_5flength_5fhits_13182',['precollapse_order_length_hits',['../classvg_1_1BaseMapper.html#aaf81156cb8c76c2e961b767a782dda59',1,'vg::BaseMapper']]],
+ ['prefilter_5fredundant_5fhits_13183',['prefilter_redundant_hits',['../classvg_1_1BaseMapper.html#afa408c8d202885a288f14ff6e2dc60e0',1,'vg::BaseMapper']]],
+ ['prefix_13184',['prefix',['../structvg_1_1BitStringTree_1_1TreeNode.html#ae400b0d9c4fecf6b90fd0d708258df1e',1,'vg::BitStringTree::TreeNode']]],
+ ['prefix_5flength_13185',['prefix_length',['../structvg_1_1MultipathProblem.html#a5fdfec89c00fe647e234e84fa72879ed',1,'vg::MultipathProblem']]],
+ ['prefix_5fscore_13186',['prefix_score',['../structvg_1_1MultipathProblem.html#a5e3610b3438d69baba7e3be6a6cfdcc0',1,'vg::MultipathProblem']]],
+ ['prefix_5fsum_13187',['prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ac09ee425b8f2f95a4c8c4f45b39084b9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild::prefix_sum()'],['../structvg_1_1MIPayload.html#af0dcb83df9249928d947e23f368f41a0',1,'vg::MIPayload::prefix_sum()']]],
+ ['prefix_5fsum_5for_5fidentifier_13188',['prefix_sum_or_identifier',['../structvg_1_1ZipCode_1_1node__code__t.html#aadf1912938760b4371b385865fa661f9',1,'vg::ZipCode::node_code_t::prefix_sum_or_identifier()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a736b6676259bc262d66d9814fbbb7142',1,'vg::ZipCode::snarl_code_t::prefix_sum_or_identifier()']]],
+ ['prefix_5fsum_5fvalue_13189',['prefix_sum_value',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a09ed2f3574eb36ceccf98ded8c99e7f5',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['prefixes_13190',['prefixes',['../classvg_1_1PhaseUnfolder.html#a64f18b1c10e5d2104bd04df2013f5a0f',1,'vg::PhaseUnfolder']]],
+ ['present_13191',['present',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a130ad1d08da8cb8ff5be5f254b904369',1,'vg::SnarlDistanceIndexClusterer::Cluster']]],
+ ['present_5fdiscount_13192',['PRESENT_DISCOUNT',['../classvg_1_1Recombinator.html#a5c415fe934bb25c07068a2ca0291ea00',1,'vg::Recombinator::PRESENT_DISCOUNT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a5f62e8ec5640f3d4d06bbda709b44bdc',1,'vg::Recombinator::Parameters::present_discount()']]],
+ ['preserve_5fsinks_13193',['preserve_sinks',['../classvg_1_1DozeuPinningOverlay.html#a066fa04f3bf59c7302a0e57036154ab7',1,'vg::DozeuPinningOverlay']]],
+ ['prev_13194',['prev',['../classvg_1_1MEMChainModelVertex.html#a8b3867d0ba2a4797202be745d92d11de',1,'vg::MEMChainModelVertex::prev()'],['../classvg_1_1AlignmentChainModelVertex.html#a9979808dd8d6ddaf11d83643ab3e9db2',1,'vg::AlignmentChainModelVertex::prev()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#aea823a7f3329d308107c1de1cf20c1a6',1,'vg::PhasedGenome::HaplotypeNode::prev()']]],
+ ['prev_5fchar_13195',['prev_char',['../structvg_1_1kmer__t.html#a006cf626b837e21d26b66925103a34c5',1,'vg::kmer_t']]],
+ ['prev_5fchars_13196',['prev_chars',['../structvg_1_1KmerPosition.html#a6c6e2b384e3f9292342999e6f49684c3',1,'vg::KmerPosition']]],
+ ['prev_5fcost_13197',['prev_cost',['../classvg_1_1MEMChainModelVertex.html#ad8ad4b22339e6ad06c893c78c63cda5a',1,'vg::MEMChainModelVertex::prev_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#a0dcdae4513868599a6bd50e719f9e4f5',1,'vg::AlignmentChainModelVertex::prev_cost()']]],
+ ['prev_5fpos_13198',['prev_pos',['../structvg_1_1kmer__t.html#acf511fd3c535a5d9e2109480ed1528e8',1,'vg::kmer_t']]],
+ ['prev_5fstage_5fitems_13199',['prev_stage_items',['../structvg_1_1Funnel_1_1Item.html#a9ee7530fac67298fbcdb27f8280b4a14',1,'vg::Funnel::Item']]],
+ ['prev_5fsubpath_13200',['prev_subpath',['../structvg_1_1MultipathProblem.html#a51f2e682e6721f35d88cae8d1cf4a59d',1,'vg::MultipathProblem']]],
+ ['previous_5findex_13201',['previous_index',['../structhaplo_1_1haplo__DP__rectangle.html#addd510174b8c5f83418aa6c23e278b36',1,'haplo::haplo_DP_rectangle']]],
+ ['previous_5fsizes_13202',['previous_sizes',['../structhaplo_1_1haplo__DP__column.html#a2ece2d4c8c54fbd7fc8e898ced985e6a',1,'haplo::haplo_DP_column']]],
+ ['previous_5fsum_13203',['previous_sum',['../structhaplo_1_1haplo__DP__column.html#a474364179d091eda8dd0684d4d86afa8',1,'haplo::haplo_DP_column']]],
+ ['previous_5ftag_13204',['previous_tag',['../classvg_1_1io_1_1MessageIterator.html#affc663d4448fe1b213d1c2e9ec64b3bb',1,'vg::io::MessageIterator']]],
+ ['previous_5fvalues_13205',['previous_values',['../structhaplo_1_1haplo__DP__column.html#a5e1664796c443719bd4e775f503ab8ad',1,'haplo::haplo_DP_column']]],
+ ['primary_13206',['primary',['../classvg_1_1MaximalExactMatch.html#a2e34dcded590361daf8ca3a9ed3fb62f',1,'vg::MaximalExactMatch']]],
+ ['primitive_5froot_13207',['primitive_root',['../classvg_1_1ShuffledPairs.html#a78c948366b8eec98b8393ae2ac75f86a',1,'vg::ShuffledPairs']]],
+ ['print_5fupdates_13208',['print_updates',['../classvg_1_1VariantAdder.html#af52ce72b2446132042df93857eb12b63',1,'vg::VariantAdder']]],
+ ['priority_13209',['priority',['../classvg_1_1subcommand_1_1Subcommand.html#a3f995aec9b4e2367530e1a6bcccb2e53',1,'vg::subcommand::Subcommand']]],
+ ['prng_13210',['prng',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#ac95b66a8f2e2cda6bc2d45691d496f5e',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['prngs_13211',['prngs',['../classvg_1_1NGSSimulator.html#ab5d12a331a39e82fc07202152f254d70',1,'vg::NGSSimulator']]],
+ ['prob_5fsampler_13212',['prob_sampler',['../classvg_1_1NGSSimulator.html#a36ca291ed15a9a3942809d21d0574bc1',1,'vg::NGSSimulator']]],
+ ['problem_13213',['problem',['../structvg_1_1AlignmentValidity.html#a1ca7f243aa52fe313bdfac808f4eba92',1,'vg::AlignmentValidity']]],
+ ['produces_5fone_5fgbwt_13214',['produces_one_gbwt',['../structGBWTConfig.html#ad752e9efebcc424e596e1c328a9eb583',1,'GBWTConfig']]],
+ ['progress_13215',['progress',['../classvg_1_1Progressive.html#af78e64e28b252828a0ba86439125fea4',1,'vg::Progressive']]],
+ ['progress_5fbars_13216',['progress_bars',['../classvg_1_1VGset.html#acc491d0a5c0a54c6bbd0636fa44431b7',1,'vg::VGset']]],
+ ['progress_5fcount_13217',['progress_count',['../classvg_1_1Progressive.html#a71e61fe99d71d23542d2d7387c23fd4d',1,'vg::Progressive']]],
+ ['progress_5fmessage_13218',['progress_message',['../classvg_1_1Progressive.html#a4bb04fe23ceb41467dd14cdf8cc01a71',1,'vg::Progressive']]],
+ ['progress_5fseen_13219',['progress_seen',['../classvg_1_1Progressive.html#ac6745d7e07b4b271f9510cd40f06d18e',1,'vg::Progressive']]],
+ ['projected_5fcount_13220',['projected_count',['../structvg_1_1Funnel_1_1Stage.html#a74c290d50af94a82c196350d3ee7223d',1,'vg::Funnel::Stage']]],
+ ['proto_13221',['proto',['../classvg_1_1io_1_1VGAlignmentEmitter.html#a05cf3104e11f544431c6ed6e709d2361',1,'vg::io::VGAlignmentEmitter::proto()'],['../vg_8proto.html#ace9afe7f815b63b3d93844da5eb8fbbc',1,'proto(): vg.proto']]],
+ ['protobuf_5fto_5ftag_13222',['protobuf_to_tag',['../structvg_1_1io_1_1Registry_1_1Tables.html#a9959a1192210db895c2d127dc6a197fc',1,'vg::io::Registry::Tables']]],
+ ['provided_5fdirectly_13223',['provided_directly',['../classvg_1_1IndexFile.html#a32bf1b5189843cdcc3ba7eb6068dd46f',1,'vg::IndexFile']]],
+ ['prune_5fsubpaths_5fmultiplier_13224',['prune_subpaths_multiplier',['../classvg_1_1MultipathMapper.html#aa8409bc363c70b9df0c3590767d25e92',1,'vg::MultipathMapper']]],
+ ['prune_5fsuspicious_5fanchors_13225',['prune_suspicious_anchors',['../classvg_1_1Surjector.html#af01db9677cefc7952fee698f8ee2b672',1,'vg::Surjector']]],
+ ['prune_5fthread_5fbuffer_5fsize_13226',['PRUNE_THREAD_BUFFER_SIZE',['../namespacevg_1_1algorithms.html#a64f4abe5d8279f14a52b56ffb47fff34',1,'vg::algorithms']]],
+ ['pruning_5fmax_5fedge_5fcount_13227',['pruning_max_edge_count',['../structvg_1_1IndexingParameters.html#ad673cb8b7687d3a60aef1036d1b1dae3',1,'vg::IndexingParameters']]],
+ ['pruning_5fmax_5fnode_5fdegree_13228',['pruning_max_node_degree',['../structvg_1_1IndexingParameters.html#a8041e911ac757df80b37fbdbc4943f74',1,'vg::IndexingParameters']]],
+ ['pruning_5fmax_5fnode_5fdegree_5fdecrease_5ffactor_13229',['pruning_max_node_degree_decrease_factor',['../structvg_1_1IndexingParameters.html#ac3de2fff42441077c37ff61421b6415d',1,'vg::IndexingParameters']]],
+ ['pruning_5fmin_5fcomponent_5fsize_13230',['pruning_min_component_size',['../structvg_1_1IndexingParameters.html#a1f955fc9bdfedd418b900163f36a2e15',1,'vg::IndexingParameters']]],
+ ['pruning_5fwalk_5flength_13231',['pruning_walk_length',['../structvg_1_1IndexingParameters.html#ac9f7127d0df7aa1c90ced42a01755763',1,'vg::IndexingParameters']]],
+ ['pruning_5fwalk_5flength_5fincrease_5ffactor_13232',['pruning_walk_length_increase_factor',['../structvg_1_1IndexingParameters.html#a7c483115dc36e1e7e8b25684f427442c',1,'vg::IndexingParameters']]],
+ ['ptr_13233',['ptr',['../structjson__autoptr.html#a8eeb7c64d99d1378d9524ede91d6faa4',1,'json_autoptr']]]
];
diff --git a/search/variables_11.js b/search/variables_11.js
index 38d7dcfc1a..f4bb1d90db 100644
--- a/search/variables_11.js
+++ b/search/variables_11.js
@@ -1,18 +1,18 @@
var searchData=
[
- ['qual_5fadj_5faligner_13230',['qual_adj_aligner',['../classvg_1_1AlignerClient.html#ad808371671d657c01a8c0a57b34a2046',1,'vg::AlignerClient']]],
- ['qual_5fadj_5ffull_5flength_5fbonuses_13231',['qual_adj_full_length_bonuses',['../classvg_1_1QualAdjAligner.html#a1ada9d3482ad01904b72041f7051647f',1,'vg::QualAdjAligner']]],
- ['qual_5foffset_13232',['qual_offset',['../classvg_1_1Filter.html#ac989d47373aa80519790159a8a67cfc8',1,'vg::Filter']]],
- ['qualities_13233',['qualities',['../structvg_1_1BasePileup.html#aad9e72ab33cea5e54f6f3b37724699d9',1,'vg::BasePileup::qualities()'],['../structvg_1_1EdgePileup.html#a0102dbbfce9153e00bae0520dd15d1ec',1,'vg::EdgePileup::qualities()']]],
- ['quality_13234',['quality',['../structvg_1_1Alignment.html#afe4dfd54e11b8139c3ccbb493faf98dc',1,'vg::Alignment::quality()'],['../structvg_1_1MultipathAlignment.html#aa507c2c93acbbcc309d7808ebae603b6',1,'vg::MultipathAlignment::quality()'],['../structvg_1_1Support.html#aef1cd52697f504165b42fb74ab55bfa9',1,'vg::Support::quality()']]],
- ['quality_5faligners_13235',['quality_aligners',['../classvg_1_1Genotyper.html#a2705913bdfb5f6679afb5475a22ecf61',1,'vg::Genotyper']]],
- ['quality_5fcache_13236',['quality_cache',['../classvg_1_1Packer.html#a36c50d1d60cff7036fd853b3c02b450d',1,'vg::Packer']]],
- ['queried_5fcount_13237',['queried_count',['../classvg_1_1MaximalExactMatch.html#a538bd4e79e6c025d41031bcc46b3a516',1,'vg::MaximalExactMatch']]],
- ['query_5fend_13238',['query_end',['../structgafkluge_1_1GafRecord.html#a44e865cbd6ee8693c0ecda102e7271b9',1,'gafkluge::GafRecord']]],
- ['query_5flength_13239',['query_length',['../structgafkluge_1_1GafRecord.html#a63f1b67e656da360cc9260005e8c0ecd',1,'gafkluge::GafRecord']]],
- ['query_5fname_13240',['query_name',['../structgafkluge_1_1GafRecord.html#adb0c145a0585ca84e235acb160506811',1,'gafkluge::GafRecord']]],
- ['query_5foffset_13241',['query_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a97a6361d1ab730d37f88d27b92218d83',1,'vg::DozeuInterface::graph_pos_s']]],
- ['query_5fposition_13242',['query_position',['../structvg_1_1Alignment.html#a17a81788105d3cb6a777ed6a202cd36f',1,'vg::Alignment']]],
- ['query_5fstart_13243',['query_start',['../structgafkluge_1_1GafRecord.html#a7a92ff5f2dcd4035bfcc661f64d863cd',1,'gafkluge::GafRecord']]],
- ['queue_13244',['queue',['../classvg_1_1JobSchedule.html#ad9c195bda4329dcf7f90e1135388a2bd',1,'vg::JobSchedule']]]
+ ['qual_5fadj_5faligner_13234',['qual_adj_aligner',['../classvg_1_1AlignerClient.html#ad808371671d657c01a8c0a57b34a2046',1,'vg::AlignerClient']]],
+ ['qual_5fadj_5ffull_5flength_5fbonuses_13235',['qual_adj_full_length_bonuses',['../classvg_1_1QualAdjAligner.html#a1ada9d3482ad01904b72041f7051647f',1,'vg::QualAdjAligner']]],
+ ['qual_5foffset_13236',['qual_offset',['../classvg_1_1Filter.html#ac989d47373aa80519790159a8a67cfc8',1,'vg::Filter']]],
+ ['qualities_13237',['qualities',['../structvg_1_1BasePileup.html#aad9e72ab33cea5e54f6f3b37724699d9',1,'vg::BasePileup::qualities()'],['../structvg_1_1EdgePileup.html#a0102dbbfce9153e00bae0520dd15d1ec',1,'vg::EdgePileup::qualities()']]],
+ ['quality_13238',['quality',['../structvg_1_1Alignment.html#afe4dfd54e11b8139c3ccbb493faf98dc',1,'vg::Alignment::quality()'],['../structvg_1_1MultipathAlignment.html#aa507c2c93acbbcc309d7808ebae603b6',1,'vg::MultipathAlignment::quality()'],['../structvg_1_1Support.html#aef1cd52697f504165b42fb74ab55bfa9',1,'vg::Support::quality()']]],
+ ['quality_5faligners_13239',['quality_aligners',['../classvg_1_1Genotyper.html#a2705913bdfb5f6679afb5475a22ecf61',1,'vg::Genotyper']]],
+ ['quality_5fcache_13240',['quality_cache',['../classvg_1_1Packer.html#a36c50d1d60cff7036fd853b3c02b450d',1,'vg::Packer']]],
+ ['queried_5fcount_13241',['queried_count',['../classvg_1_1MaximalExactMatch.html#a538bd4e79e6c025d41031bcc46b3a516',1,'vg::MaximalExactMatch']]],
+ ['query_5fend_13242',['query_end',['../structgafkluge_1_1GafRecord.html#a44e865cbd6ee8693c0ecda102e7271b9',1,'gafkluge::GafRecord']]],
+ ['query_5flength_13243',['query_length',['../structgafkluge_1_1GafRecord.html#a63f1b67e656da360cc9260005e8c0ecd',1,'gafkluge::GafRecord']]],
+ ['query_5fname_13244',['query_name',['../structgafkluge_1_1GafRecord.html#adb0c145a0585ca84e235acb160506811',1,'gafkluge::GafRecord']]],
+ ['query_5foffset_13245',['query_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a97a6361d1ab730d37f88d27b92218d83',1,'vg::DozeuInterface::graph_pos_s']]],
+ ['query_5fposition_13246',['query_position',['../structvg_1_1Alignment.html#a17a81788105d3cb6a777ed6a202cd36f',1,'vg::Alignment']]],
+ ['query_5fstart_13247',['query_start',['../structgafkluge_1_1GafRecord.html#a7a92ff5f2dcd4035bfcc661f64d863cd',1,'gafkluge::GafRecord']]],
+ ['queue_13248',['queue',['../classvg_1_1JobSchedule.html#ad9c195bda4329dcf7f90e1135388a2bd',1,'vg::JobSchedule']]]
];
diff --git a/search/variables_12.js b/search/variables_12.js
index e56c6c0bbb..d1578174c8 100644
--- a/search/variables_12.js
+++ b/search/variables_12.js
@@ -1,126 +1,126 @@
var searchData=
[
- ['r_13245',['R',['../structhaplo_1_1haplo__DP__rectangle.html#a93bec5529e8477c30fca8118e3e44f5f',1,'haplo::haplo_DP_rectangle']]],
- ['r_5findex_13246',['r_index',['../classvg_1_1HaplotypePartitioner.html#a1eac0315eb7daaca955438f4c69f0fcb',1,'vg::HaplotypePartitioner']]],
- ['r_5findex_5fname_13247',['r_index_name',['../structGBWTConfig.html#a230387b96ed4b3bee6cfa11c27cccc63',1,'GBWTConfig::r_index_name()'],['../structHaplotypesConfig.html#ac184346f750f8486f7e68f1e20e95d32',1,'HaplotypesConfig::r_index_name()']]],
- ['r_5fiv_13248',['r_iv',['../classxg_1_1XG.html#aa5b5890158459739ca5e986555bcf74e',1,'xg::XG']]],
- ['random_5fengine_13249',['random_engine',['../classvg_1_1MCMCGenotyper.html#a742e3fb0ca54f531f23d1a8f18cb4da5',1,'vg::MCMCGenotyper']]],
- ['range_13250',['range',['../classvg_1_1MaximalExactMatch.html#a8652369dde83e159dd8c5638745a749c',1,'vg::MaximalExactMatch']]],
- ['range_5fend_5fmatch_13251',['RANGE_END_MATCH',['../classhandlegraph_1_1PathMetadata.html#a938d44c0ba47de41907a6987c6487878',1,'handlegraph::PathMetadata']]],
- ['range_5fend_5fseparator_13252',['RANGE_END_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#acf3518dc192f0f1cc87bdfa85665dc91',1,'handlegraph::PathMetadata']]],
- ['range_5fstart_5fmatch_13253',['RANGE_START_MATCH',['../classhandlegraph_1_1PathMetadata.html#a15ce180ff76a984e3408a70ccf13fd62',1,'handlegraph::PathMetadata']]],
- ['range_5fstart_5fseparator_13254',['RANGE_START_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#a3c20334a1732192586b48a7ac51860ee',1,'handlegraph::PathMetadata']]],
- ['range_5ftable_13255',['range_table',['../classvg_1_1MEMAccelerator.html#a950e1c4779d5f0e8c0088f7b16f36770',1,'vg::MEMAccelerator']]],
- ['range_5fterminator_13256',['RANGE_TERMINATOR',['../classhandlegraph_1_1PathMetadata.html#a1b41a72cbd2850c02a01aa7c8a2b516a',1,'handlegraph::PathMetadata']]],
- ['rank_13257',['rank',['../classvg_1_1mapping__t.html#a8f97d898f658a36c3046b8fcc2c846ff',1,'vg::mapping_t::rank()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ab8b58edefb4cb58e014344c6010eec62',1,'vg::PhasedGenome::iterator::rank()'],['../structvg_1_1Mapping.html#a9ad71eb17b88b2cdd00cee8476e6c7b3',1,'vg::Mapping::rank()']]],
- ['reachable_5fwith_5fgap_13258',['reachable_with_gap',['../structvg_1_1WFATree_1_1ScoreProperties.html#aeef86ffa6d221e25dfc15d97436c408c',1,'vg::WFATree::ScoreProperties']]],
- ['read_13259',['read',['../structvg_1_1alignment__index__t.html#aedfedbedee05ac92a82889330b7a7159',1,'vg::alignment_index_t::read()'],['../structhFILE__backend.html#ad710f254730683318f2d62b9c1ef3d60',1,'hFILE_backend::read()']]],
- ['read_5f1_5fadapter_13260',['read_1_adapter',['../classvg_1_1MultipathMapper.html#ac11fe37f1e47b1f3697e1eeeb703a467',1,'vg::MultipathMapper']]],
- ['read_5f1_5fadapter_5flps_13261',['read_1_adapter_lps',['../classvg_1_1MultipathMapper.html#a72cfecb533ba72974ca4fe736f5e4616',1,'vg::MultipathMapper']]],
- ['read_5f2_5fadapter_13262',['read_2_adapter',['../classvg_1_1MultipathMapper.html#a9dda8a58ca0a9a3b5f8cf6bb6b72b907',1,'vg::MultipathMapper']]],
- ['read_5f2_5fadapter_5flps_13263',['read_2_adapter_lps',['../classvg_1_1MultipathMapper.html#ab14d5973d561097ca08d9e989b04265b',1,'vg::MultipathMapper']]],
- ['read_5fbest_5fleft_13264',['read_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6573a9b29b9df17f33cc6ce50889f408',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['read_5fbest_5fright_13265',['read_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a9509065fa738b008fa7e75325a34b9fe',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['read_5fcluster_5fheads_13266',['read_cluster_heads',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3d23f2d455846fcb6d5ea634926f7dce',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['read_5fdistance_5flimit_13267',['read_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a96bda025a3c371cef79b565d66b31a2a',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['read_5fgroup_13268',['read_group',['../classvg_1_1MinimizerMapper.html#aee3e4b7c4e777da6c09f70218481e3d6',1,'vg::MinimizerMapper::read_group()'],['../classvg_1_1MultipathAlignmentEmitter.html#a931f4785a73cfd9069d7447ba63b71ef',1,'vg::MultipathAlignmentEmitter::read_group()'],['../structvg_1_1Alignment.html#a95102c70d75046f86a2f0a829ba1efe0',1,'vg::Alignment::read_group()'],['../structvg_1_1MultipathAlignment.html#abdc748afaea04b662f170156d8c88343',1,'vg::MultipathAlignment::read_group()']]],
- ['read_5finterval_13269',['read_interval',['../structvg_1_1GaplessExtension.html#a32b115618388c2254ef91c06ac0c9840',1,'vg::GaplessExtension']]],
- ['read_5fmapped_13270',['read_mapped',['../structvg_1_1Alignment.html#af2fc72c769b77c355632e6aab7573046',1,'vg::Alignment']]],
- ['read_5fnum_13271',['read_num',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#aeb827f9966141503abe98ebcce7b2db2',1,'vg::SnarlDistanceIndexClusterer::ClusterHead']]],
- ['read_5foffset_13272',['read_offset',['../structMappingRun.html#a730efdfaef634a4173efe0bd9e4e3da1',1,'MappingRun']]],
- ['read_5fon_5freverse_5fstrand_13273',['read_on_reverse_strand',['../structvg_1_1Alignment.html#a10b4d599e1812ee007e348f8ce8bfe49',1,'vg::Alignment']]],
- ['read_5fpaired_13274',['read_paired',['../structvg_1_1Alignment.html#a2bfa3fffb5f4ea6ab3e98a6340ad16bb',1,'vg::Alignment']]],
- ['read_5funion_5ffind_13275',['read_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#afbf1772f189edd4c5f4a8e74914a4d6c',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['reader_13276',['reader',['../classvg_1_1ParallelKFFReader.html#a88e22492b07cf27f746ca0086d48c6dd',1,'vg::ParallelKFFReader::reader()'],['../classvg_1_1WindowedVcfBuffer.html#a064a56b55dbb562f1b52034a54ed3583',1,'vg::WindowedVcfBuffer::reader()']]],
- ['reads_5fby_5fname_13277',['reads_by_name',['../classvg_1_1PathRestrictedTraversalFinder.html#ac08d8f72efc63adb1bf169d9ed7c107e',1,'vg::PathRestrictedTraversalFinder']]],
- ['realign_5findels_13278',['realign_indels',['../classvg_1_1Genotyper.html#a79ac39be882405a426afaeeef65c9660',1,'vg::Genotyper']]],
- ['recipe_5fregistry_13279',['recipe_registry',['../classvg_1_1IndexRegistry.html#a963c33ba471ce5e0c4e5403d4a86e753',1,'vg::IndexRegistry']]],
- ['recoding_13280',['recoding',['../classvg_1_1ParallelKFFReader.html#aaf7eee70fc5bfbb863fc68ee8840a812',1,'vg::ParallelKFFReader']]],
- ['recombination_5fpenalty_13281',['recombination_penalty',['../classvg_1_1BaseMapper.html#af0e6c250a81dc74df57136242174aa54',1,'vg::BaseMapper::recombination_penalty()'],['../classvg_1_1MultipathMapper.html#a26993f76e9bbe5c48e0b436cc9c3fda8',1,'vg::MultipathMapper::recombination_penalty()']]],
- ['recombinator_5fparameters_13282',['recombinator_parameters',['../structHaplotypesConfig.html#a10886974a276f98f45a26c7b2c51c350',1,'HaplotypesConfig']]],
- ['record_5fbases_13283',['record_bases',['../classvg_1_1Packer.html#a7a3debd842c660a3fc4755fc887c74ec',1,'vg::Packer']]],
- ['record_5fedges_13284',['record_edges',['../classvg_1_1Packer.html#ab6fa0636229479a7368286e43f20ffa2',1,'vg::Packer']]],
- ['record_5fedits_13285',['record_edits',['../classvg_1_1Packer.html#a8200ea3c39e408f3394c4a65fe2e3786',1,'vg::Packer']]],
- ['record_5foffset_13286',['record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa4c597fb92b3074c231b3b02f1dd58a4',1,'vg::ZipCode::snarl_code_t']]],
- ['record_5fqualities_13287',['record_qualities',['../classvg_1_1Packer.html#ab29c0bdd5ae1db4a89db3476ba70ef68',1,'vg::Packer']]],
- ['redundant_5fvertexes_13288',['redundant_vertexes',['../classvg_1_1MEMChainModel.html#a6a4132f34b8c9636e02c186ffa75a333',1,'vg::MEMChainModel::redundant_vertexes()'],['../classvg_1_1AlignmentChainModel.html#a2fd794e91dfc7ee2db7fdc9f921c5134',1,'vg::AlignmentChainModel::redundant_vertexes()']]],
- ['reestimation_5ffrequency_13289',['reestimation_frequency',['../classvg_1_1FragmentLengthDistribution.html#a648954fbcb1fd0295fb22a37d79ed3e7',1,'vg::FragmentLengthDistribution']]],
- ['ref_5fbase_13290',['ref_base',['../structvg_1_1BasePileup.html#a8d68d6e5d3ce5d2a9a448f90ed6dfc09',1,'vg::BasePileup']]],
- ['ref_5foffset_13291',['ref_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a0d0812a9f6be0ad3610fb860fb1bc2d2',1,'vg::DozeuInterface::graph_pos_s']]],
- ['ref_5foffsets_13292',['ref_offsets',['../classvg_1_1LegacyCaller.html#a9aa5ae8255c13d5c19a4cae14f998a8e',1,'vg::LegacyCaller::ref_offsets()'],['../classvg_1_1FlowCaller.html#a454f9cba510f7ebf9e8929c53092583a',1,'vg::FlowCaller::ref_offsets()'],['../classvg_1_1NestedFlowCaller.html#a389525ad359e73ad07da1bac80cb3595',1,'vg::NestedFlowCaller::ref_offsets()'],['../classvg_1_1MCMCCaller.html#acccde0cf44eb8781fc43830f0b3736b3',1,'vg::MCMCCaller::ref_offsets()']]],
- ['ref_5fpath_13293',['ref_path',['../structvg_1_1FlowSort_1_1Growth.html#a34ba660c358c1ec59cd7c70e62780a8c',1,'vg::FlowSort::Growth']]],
- ['ref_5fpath_5fhandle_13294',['ref_path_handle',['../structhaplo_1_1linear__haplo__structure.html#a57eb7d1ebc0bc29e9ba3d1c3955650e9',1,'haplo::linear_haplo_structure']]],
- ['ref_5fpath_5fhandles_13295',['ref_path_handles',['../classvg_1_1MultipathMapper.html#a2ee3920a6e8758880172f6fd07c5f7f2',1,'vg::MultipathMapper']]],
- ['ref_5fpath_5finterval_13296',['ref_path_interval',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#afb6f9c3dbe7a55c17d953489de39e656',1,'vg::NestedFlowCaller::CallRecord']]],
- ['ref_5fpath_5flengths_13297',['ref_path_lengths',['../classvg_1_1MCMCCaller.html#a7638f220d989784503287ea538da21f4',1,'vg::MCMCCaller']]],
- ['ref_5fpath_5fname_13298',['ref_path_name',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a69d34c61dd53d99246bebffa0b68def0',1,'vg::NestedFlowCaller::CallRecord']]],
- ['ref_5fpath_5foffsets_13299',['ref_path_offsets',['../classvg_1_1MCMCCaller.html#a614597d6c55c252d2efb88cdd0048eff',1,'vg::MCMCCaller']]],
- ['ref_5fpath_5fset_13300',['ref_path_set',['../classvg_1_1FlowCaller.html#ac85f8948b4a0c6f9bcb66cccf498c372',1,'vg::FlowCaller::ref_path_set()'],['../classvg_1_1NestedFlowCaller.html#a934f25461550667e553a51ed2fee1fb2',1,'vg::NestedFlowCaller::ref_path_set()']]],
- ['ref_5fpaths_13301',['ref_paths',['../classvg_1_1Deconstructor.html#a8da74d6fff7d5af6caed96723d0bccd9',1,'vg::Deconstructor::ref_paths()'],['../classvg_1_1GAFOutputCaller.html#a2675564b819e50ac8a21ca51eb14c99c',1,'vg::GAFOutputCaller::ref_paths()'],['../classvg_1_1LegacyCaller.html#a73beb7401923d192f8542beb938ea33c',1,'vg::LegacyCaller::ref_paths()'],['../classvg_1_1FlowCaller.html#adb1bb384ccb36d214a22cef04919920c',1,'vg::FlowCaller::ref_paths()'],['../classvg_1_1NestedFlowCaller.html#a5206505cf92654951bef22b42d50381e',1,'vg::NestedFlowCaller::ref_paths()'],['../classvg_1_1MCMCCaller.html#a081ed012622de090f1aad2a82526a59e',1,'vg::MCMCCaller::ref_paths()'],['../structvg_1_1Recombinator_1_1Statistics.html#ac3404816da5f78c7712ad69eb8f9594f',1,'vg::Recombinator::Statistics::ref_paths()']]],
- ['ref_5fploidies_13302',['ref_ploidies',['../classvg_1_1LegacyCaller.html#ac82406147f3603e97d22418ee0e7bdc4',1,'vg::LegacyCaller::ref_ploidies()'],['../classvg_1_1FlowCaller.html#a2487ac1acadd5052a3a18204c426591d',1,'vg::FlowCaller::ref_ploidies()'],['../classvg_1_1NestedFlowCaller.html#a021b1013fe64a99b598ffa291a423e5b',1,'vg::NestedFlowCaller::ref_ploidies()']]],
- ['ref_5fpositions_13303',['ref_positions',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a6065969d77968cd3afc31ca7b8b1a9f0',1,'haplo::linear_haplo_structure::SNVvector']]],
- ['ref_5fsample_13304',['ref_sample',['../structHaplotypesConfig.html#a1575fa9f328d1d823e788f422b6bde43',1,'HaplotypesConfig']]],
- ['ref_5fsamples_13305',['ref_samples',['../classvg_1_1Deconstructor.html#a72834c9d1d667e3283e93f60a3f5057b',1,'vg::Deconstructor']]],
- ['ref_5fsteps_13306',['ref_steps',['../structvg_1_1ParentGenotypeInfo.html#a45d8b5d863b3f74e9eb499acef7a2916',1,'vg::ParentGenotypeInfo']]],
- ['ref_5ftrav_5fidx_13307',['ref_trav_idx',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a7a265b17dc3bc9a34603de7e064230f8',1,'vg::NestedFlowCaller::CallRecord']]],
- ['ref_5ftraversal_13308',['ref_traversal',['../structvg_1_1ParentGenotypeInfo.html#a4e02433e8ac8eae0491d4290f5b78515',1,'vg::ParentGenotypeInfo']]],
- ['reference_5fpaths_13309',['reference_paths',['../classvg_1_1PhaseUnfolder.html#a2bfa46441300e0817643b310aced989b',1,'vg::PhaseUnfolder']]],
- ['reflect_13310',['reflect',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa5776efd133ed466cb82ef4f4b161dfd',1,'vg::GraphSynchronizer::Lock']]],
- ['refpos_13311',['refpos',['../structvg_1_1Alignment.html#a584c3aa15a5c1386d14a97c0ce85c0cf',1,'vg::Alignment']]],
- ['regions_13312',['regions',['../structvg_1_1Funnel_1_1PaintableSpace.html#a001cb606b7e4f79f8be9550b17c6f1b4',1,'vg::Funnel::PaintableSpace::regions()'],['../classvg_1_1HaplotypeIndexer.html#a85285e19121d708649f61b5420ab0777',1,'vg::HaplotypeIndexer::regions()']]],
- ['registered_5fsuffixes_13313',['registered_suffixes',['../classvg_1_1IndexRegistry.html#ad3422d12216130fa07d77dcc3e62ae34',1,'vg::IndexRegistry']]],
- ['registry_13314',['registry',['../classvg_1_1IndexingPlan.html#a7a8e639fb6e8225162a5ff532c4b963d',1,'vg::IndexingPlan']]],
- ['regular_5faligner_13315',['regular_aligner',['../classvg_1_1AlignerClient.html#af164f37a5efb0c05b10fea3841b78e83',1,'vg::AlignerClient']]],
- ['regular_5fsnarl_5fis_5freversed_5foffset_13316',['REGULAR_SNARL_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a40ebd5bef9b1916bbe944baaaff0b122',1,'vg::ZipCode']]],
- ['regular_5fsnarl_5fsize_13317',['REGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a14c19ec53976a951ef9a16f9202ac19e',1,'vg::ZipCode']]],
- ['remove_5ffailing_5fedits_13318',['remove_failing_edits',['../classvg_1_1Filter.html#aea2a2fc6de506793111639e609376bf0',1,'vg::Filter']]],
- ['rename_5fvariants_13319',['rename_variants',['../classvg_1_1HaplotypeIndexer.html#a8061130697dc26811303c4b67b081245',1,'vg::HaplotypeIndexer']]],
- ['rend_13320',['rend',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a864f0d7f9c86b6f057e2b2889ef478a2',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['repeat_5fsize_13321',['repeat_size',['../classvg_1_1ReadFilter.html#a95e0303086c9c6dc7a17d452b7d7f928',1,'vg::ReadFilter']]],
- ['report_5fallelic_5fmapq_13322',['report_allelic_mapq',['../classvg_1_1MultipathMapper.html#a6cc2a29a0a539f37606482c57c78b015',1,'vg::MultipathMapper']]],
- ['report_5fgroup_5fmapq_13323',['report_group_mapq',['../classvg_1_1MultipathMapper.html#a42577bd89395f56ea2045c378b745456',1,'vg::MultipathMapper']]],
- ['rescore_13324',['rescore',['../classvg_1_1ReadFilter.html#a7373ef70ee64562dd779628a234c1080',1,'vg::ReadFilter']]],
- ['rescue_5falgorithm_13325',['rescue_algorithm',['../classvg_1_1MinimizerMapper.html#a17f800e4588567e473ea18a55bd186b9',1,'vg::MinimizerMapper']]],
- ['rescue_5fgraph_5fstd_5fdevs_13326',['rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#aab3573cb5d2878a13b0a40d427e8c943',1,'vg::MultipathMapper']]],
- ['rescue_5fonly_5fanchor_5fmax_13327',['rescue_only_anchor_max',['../classvg_1_1MultipathMapper.html#acd7c1016549d1f96af13b9c317f239f3',1,'vg::MultipathMapper']]],
- ['rescue_5fonly_5fmin_13328',['rescue_only_min',['../classvg_1_1MultipathMapper.html#a2ad423f9fc1a81bbe31e9c25992de378',1,'vg::MultipathMapper']]],
- ['rescue_5fseed_5flimit_13329',['rescue_seed_limit',['../classvg_1_1MinimizerMapper.html#a0a0c7111b38792069bb74af9b74b0978',1,'vg::MinimizerMapper']]],
- ['rescue_5fsubgraph_5fstdevs_13330',['rescue_subgraph_stdevs',['../classvg_1_1MinimizerMapper.html#a411fb85396b07aab41fabc8e34b92481',1,'vg::MinimizerMapper']]],
- ['rescued_13331',['RESCUED',['../classvg_1_1MultipathMapper.html#ab559f7eb874ac770dbbda734c5bc395a',1,'vg::MultipathMapper']]],
- ['reserved_13332',['reserved',['../structvg_1_1Alignment.html#a8374111b6348509e8e9ecca0cd1ac046',1,'vg::Alignment']]],
- ['reset_5falong_5fchain_5fparent_13333',['reset_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#a8934c072a3cdbc8652e8f7fa9f9ef553',1,'vg::subcommand::TickChainLink']]],
- ['restrained_5fgraph_5fextraction_13334',['restrained_graph_extraction',['../classvg_1_1MultipathMapper.html#a0ad5a21ab0cf3c77e3905e299b7d26c4',1,'vg::MultipathMapper']]],
- ['retry_5fon_5fns_13335',['retry_on_Ns',['../classvg_1_1NGSSimulator.html#a95f6ffd660c8c041e4d8b1d36a823bdd',1,'vg::NGSSimulator']]],
- ['reverse_13336',['reverse',['../structvg_1_1Support.html#acc2aa2a4b0278503817664600938c8a2',1,'vg::Support']]],
- ['reversing_5fwalk_5flength_13337',['reversing_walk_length',['../classvg_1_1MultipathMapper.html#af87eaae1274e33230fffe9dca05dbbec',1,'vg::MultipathMapper']]],
- ['rgfa_5flisteners_13338',['rgfa_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a3caa995d2ef8a311e87b1202da714b53',1,'vg::algorithms::GFAParser']]],
- ['rho_13339',['rho',['../structhaplo_1_1haploMath_1_1RRMemo.html#a7536987972e5d717ba43a951adcece82',1,'haplo::haploMath::RRMemo']]],
- ['right_13340',['right',['../structvg_1_1Support.html#ab2fd7cba17f56ce67501f47fda6ae153',1,'vg::Support']]],
- ['right_5fends_13341',['right_ends',['../structvg_1_1ConstructedChunk.html#ac20dbdc398181350e73bee0429fe2842',1,'vg::ConstructedChunk']]],
- ['right_5ffull_13342',['right_full',['../structvg_1_1GaplessExtension.html#ae7ca191732330cb5a6db94ee5531f2ed',1,'vg::GaplessExtension']]],
- ['right_5fhandle_5ftrans_13343',['right_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#aceac5a4b442fbce2c7c422acbdbdd097',1,'vg::JoinedSpliceGraph']]],
- ['right_5fmaximal_13344',['right_maximal',['../structvg_1_1GaplessExtension.html#a8e4d53c78f3c355b5b17bf3e959bbd41',1,'vg::GaplessExtension']]],
- ['right_5fsplice_5foffset_13345',['right_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a152eb3987232cdba5fff9dd9a15ed952',1,'vg::JoinedSpliceGraph']]],
- ['right_5fsubgraph_13346',['right_subgraph',['../classvg_1_1JoinedSpliceGraph.html#a42ce6f52135018237e3e29d2a53c4291',1,'vg::JoinedSpliceGraph']]],
- ['right_5ftelomere_5fnode_13347',['right_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a3d771a24b8889ea668939eac31276ea3',1,'vg::PhasedGenome::Haplotype']]],
- ['ring_5fbuffer_5fsize_13348',['RING_BUFFER_SIZE',['../classvg_1_1io_1_1StreamMultiplexer.html#a6e4432baab9571a1783b2a793b29905a',1,'vg::io::StreamMultiplexer']]],
- ['rng_13349',['rng',['../classvg_1_1Colors.html#a79a79da7cbc2bef7eea8c3ff1e229b7c',1,'vg::Colors::rng()'],['../classvg_1_1Pictographs.html#ac7600f845d01a084a15cff9aacc6bc3e',1,'vg::Pictographs::rng()'],['../classvg_1_1Sampler.html#ad26ea071330c6a4b580af84bec064453',1,'vg::Sampler::rng()'],['../classvg_1_1LazyRNG.html#a6aac64a985fa2fc60c2d32079bd26a63',1,'vg::LazyRNG::rng()']]],
- ['robust_5festimation_5ffraction_13350',['robust_estimation_fraction',['../classvg_1_1FragmentLengthDistribution.html#aa5a2f20742b369464d132a751f52aaf3',1,'vg::FragmentLengthDistribution']]],
- ['root_13351',['root',['../classvg_1_1BitStringTree.html#a69741fde7d47ad2f46dd952eb6bd2d66',1,'vg::BitStringTree::root()'],['../structvg_1_1Tree.html#a730cd8796e579d01c66bea46217047d7',1,'vg::Tree::root()']]],
- ['root_5fchain_5fcomponent_5fcount_5foffset_13352',['ROOT_CHAIN_COMPONENT_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a79816fb11ec20354e677a6b1acd17905',1,'vg::ZipCode']]],
- ['root_5fchain_5fsize_13353',['ROOT_CHAIN_SIZE',['../classvg_1_1ZipCode.html#af83f8e5c14d24fd45ad2318e229299d0',1,'vg::ZipCode']]],
- ['root_5fchains_13354',['root_chains',['../classvg_1_1SnarlManager.html#a2d9758d889f875b1260f49985cf3ef35',1,'vg::SnarlManager']]],
- ['root_5fchildren_13355',['root_children',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a8b902ff993db7c62075ce3371622e781',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['root_5fidentifier_5foffset_13356',['ROOT_IDENTIFIER_OFFSET',['../classvg_1_1ZipCode.html#a9320699634e827ab9c91ade7b39220a9',1,'vg::ZipCode']]],
- ['root_5fis_5fchain_5foffset_13357',['ROOT_IS_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a9fcb55636a3bd5e25d6592952880662b',1,'vg::ZipCode']]],
- ['root_5fnode_5flength_5foffset_13358',['ROOT_NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a97232d726929bf2ebb8fb7fdfbde94fd',1,'vg::ZipCode']]],
- ['root_5fnode_5for_5fchain_5fconnectivity_5for_5flength_5foffset_13359',['ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#afa760e19cc391b5de5adba6b4ca3cdb0',1,'vg::ZipCode']]],
- ['root_5fnode_5fsize_13360',['ROOT_NODE_SIZE',['../classvg_1_1ZipCode.html#afa378af1f64a51675d658d2c4ecb5d95',1,'vg::ZipCode']]],
- ['root_5fsnarl_5fsize_13361',['ROOT_SNARL_SIZE',['../classvg_1_1ZipCode.html#aa2cdcd63b1ac93b431e0e4d5d25df346',1,'vg::ZipCode']]],
- ['root_5ftrim_13362',['root_trim',['../classvg_1_1TreeSubgraph.html#a04044896f4bed03dc15a6c0a07df675d',1,'vg::TreeSubgraph']]],
- ['roots_13363',['roots',['../classvg_1_1SnarlManager.html#ab13a661f6abe1feaf2c4ca4471a85a90',1,'vg::SnarlManager']]],
- ['row_5fidx_13364',['row_idx',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2345d3706d3d46b657e205865f4d4122',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['rr_5fmemos_13365',['rr_memos',['../classvg_1_1MultipathMapper.html#a5709f5cdf31de90145a1178fa166be44',1,'vg::MultipathMapper']]],
- ['running_13366',['running',['../structvg_1_1Range.html#abbd18ac55fecb0e698fcabebc7ae48ad',1,'vg::Range']]],
- ['runs_13367',['runs',['../structvg_1_1BenchmarkResult.html#a564ed18fb2f561f09e74a254854e2d88',1,'vg::BenchmarkResult']]]
+ ['r_13249',['R',['../structhaplo_1_1haplo__DP__rectangle.html#a93bec5529e8477c30fca8118e3e44f5f',1,'haplo::haplo_DP_rectangle']]],
+ ['r_5findex_13250',['r_index',['../classvg_1_1HaplotypePartitioner.html#a1eac0315eb7daaca955438f4c69f0fcb',1,'vg::HaplotypePartitioner']]],
+ ['r_5findex_5fname_13251',['r_index_name',['../structGBWTConfig.html#a230387b96ed4b3bee6cfa11c27cccc63',1,'GBWTConfig::r_index_name()'],['../structHaplotypesConfig.html#ac184346f750f8486f7e68f1e20e95d32',1,'HaplotypesConfig::r_index_name()']]],
+ ['r_5fiv_13252',['r_iv',['../classxg_1_1XG.html#aa5b5890158459739ca5e986555bcf74e',1,'xg::XG']]],
+ ['random_5fengine_13253',['random_engine',['../classvg_1_1MCMCGenotyper.html#a742e3fb0ca54f531f23d1a8f18cb4da5',1,'vg::MCMCGenotyper']]],
+ ['range_13254',['range',['../classvg_1_1MaximalExactMatch.html#a8652369dde83e159dd8c5638745a749c',1,'vg::MaximalExactMatch']]],
+ ['range_5fend_5fmatch_13255',['RANGE_END_MATCH',['../classhandlegraph_1_1PathMetadata.html#a938d44c0ba47de41907a6987c6487878',1,'handlegraph::PathMetadata']]],
+ ['range_5fend_5fseparator_13256',['RANGE_END_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#acf3518dc192f0f1cc87bdfa85665dc91',1,'handlegraph::PathMetadata']]],
+ ['range_5fstart_5fmatch_13257',['RANGE_START_MATCH',['../classhandlegraph_1_1PathMetadata.html#a15ce180ff76a984e3408a70ccf13fd62',1,'handlegraph::PathMetadata']]],
+ ['range_5fstart_5fseparator_13258',['RANGE_START_SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#a3c20334a1732192586b48a7ac51860ee',1,'handlegraph::PathMetadata']]],
+ ['range_5ftable_13259',['range_table',['../classvg_1_1MEMAccelerator.html#a950e1c4779d5f0e8c0088f7b16f36770',1,'vg::MEMAccelerator']]],
+ ['range_5fterminator_13260',['RANGE_TERMINATOR',['../classhandlegraph_1_1PathMetadata.html#a1b41a72cbd2850c02a01aa7c8a2b516a',1,'handlegraph::PathMetadata']]],
+ ['rank_13261',['rank',['../classvg_1_1mapping__t.html#a8f97d898f658a36c3046b8fcc2c846ff',1,'vg::mapping_t::rank()'],['../classvg_1_1PhasedGenome_1_1iterator.html#ab8b58edefb4cb58e014344c6010eec62',1,'vg::PhasedGenome::iterator::rank()'],['../structvg_1_1Mapping.html#a9ad71eb17b88b2cdd00cee8476e6c7b3',1,'vg::Mapping::rank()']]],
+ ['reachable_5fwith_5fgap_13262',['reachable_with_gap',['../structvg_1_1WFATree_1_1ScoreProperties.html#aeef86ffa6d221e25dfc15d97436c408c',1,'vg::WFATree::ScoreProperties']]],
+ ['read_13263',['read',['../structvg_1_1alignment__index__t.html#aedfedbedee05ac92a82889330b7a7159',1,'vg::alignment_index_t::read()'],['../structhFILE__backend.html#ad710f254730683318f2d62b9c1ef3d60',1,'hFILE_backend::read()']]],
+ ['read_5f1_5fadapter_13264',['read_1_adapter',['../classvg_1_1MultipathMapper.html#ac11fe37f1e47b1f3697e1eeeb703a467',1,'vg::MultipathMapper']]],
+ ['read_5f1_5fadapter_5flps_13265',['read_1_adapter_lps',['../classvg_1_1MultipathMapper.html#a72cfecb533ba72974ca4fe736f5e4616',1,'vg::MultipathMapper']]],
+ ['read_5f2_5fadapter_13266',['read_2_adapter',['../classvg_1_1MultipathMapper.html#a9dda8a58ca0a9a3b5f8cf6bb6b72b907',1,'vg::MultipathMapper']]],
+ ['read_5f2_5fadapter_5flps_13267',['read_2_adapter_lps',['../classvg_1_1MultipathMapper.html#ab14d5973d561097ca08d9e989b04265b',1,'vg::MultipathMapper']]],
+ ['read_5fbest_5fleft_13268',['read_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6573a9b29b9df17f33cc6ce50889f408',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['read_5fbest_5fright_13269',['read_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a9509065fa738b008fa7e75325a34b9fe',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['read_5fcluster_5fheads_13270',['read_cluster_heads',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3d23f2d455846fcb6d5ea634926f7dce',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['read_5fdistance_5flimit_13271',['read_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a96bda025a3c371cef79b565d66b31a2a',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['read_5fgroup_13272',['read_group',['../classvg_1_1MinimizerMapper.html#aee3e4b7c4e777da6c09f70218481e3d6',1,'vg::MinimizerMapper::read_group()'],['../classvg_1_1MultipathAlignmentEmitter.html#a931f4785a73cfd9069d7447ba63b71ef',1,'vg::MultipathAlignmentEmitter::read_group()'],['../structvg_1_1Alignment.html#a95102c70d75046f86a2f0a829ba1efe0',1,'vg::Alignment::read_group()'],['../structvg_1_1MultipathAlignment.html#abdc748afaea04b662f170156d8c88343',1,'vg::MultipathAlignment::read_group()']]],
+ ['read_5finterval_13273',['read_interval',['../structvg_1_1GaplessExtension.html#a32b115618388c2254ef91c06ac0c9840',1,'vg::GaplessExtension']]],
+ ['read_5fmapped_13274',['read_mapped',['../structvg_1_1Alignment.html#af2fc72c769b77c355632e6aab7573046',1,'vg::Alignment']]],
+ ['read_5fnum_13275',['read_num',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#aeb827f9966141503abe98ebcce7b2db2',1,'vg::SnarlDistanceIndexClusterer::ClusterHead']]],
+ ['read_5foffset_13276',['read_offset',['../structMappingRun.html#a730efdfaef634a4173efe0bd9e4e3da1',1,'MappingRun']]],
+ ['read_5fon_5freverse_5fstrand_13277',['read_on_reverse_strand',['../structvg_1_1Alignment.html#a10b4d599e1812ee007e348f8ce8bfe49',1,'vg::Alignment']]],
+ ['read_5fpaired_13278',['read_paired',['../structvg_1_1Alignment.html#a2bfa3fffb5f4ea6ab3e98a6340ad16bb',1,'vg::Alignment']]],
+ ['read_5funion_5ffind_13279',['read_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#afbf1772f189edd4c5f4a8e74914a4d6c',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['reader_13280',['reader',['../classvg_1_1ParallelKFFReader.html#a88e22492b07cf27f746ca0086d48c6dd',1,'vg::ParallelKFFReader::reader()'],['../classvg_1_1WindowedVcfBuffer.html#a064a56b55dbb562f1b52034a54ed3583',1,'vg::WindowedVcfBuffer::reader()']]],
+ ['reads_5fby_5fname_13281',['reads_by_name',['../classvg_1_1PathRestrictedTraversalFinder.html#ac08d8f72efc63adb1bf169d9ed7c107e',1,'vg::PathRestrictedTraversalFinder']]],
+ ['realign_5findels_13282',['realign_indels',['../classvg_1_1Genotyper.html#a79ac39be882405a426afaeeef65c9660',1,'vg::Genotyper']]],
+ ['recipe_5fregistry_13283',['recipe_registry',['../classvg_1_1IndexRegistry.html#a963c33ba471ce5e0c4e5403d4a86e753',1,'vg::IndexRegistry']]],
+ ['recoding_13284',['recoding',['../classvg_1_1ParallelKFFReader.html#aaf7eee70fc5bfbb863fc68ee8840a812',1,'vg::ParallelKFFReader']]],
+ ['recombination_5fpenalty_13285',['recombination_penalty',['../classvg_1_1BaseMapper.html#af0e6c250a81dc74df57136242174aa54',1,'vg::BaseMapper::recombination_penalty()'],['../classvg_1_1MultipathMapper.html#a26993f76e9bbe5c48e0b436cc9c3fda8',1,'vg::MultipathMapper::recombination_penalty()']]],
+ ['recombinator_5fparameters_13286',['recombinator_parameters',['../structHaplotypesConfig.html#a10886974a276f98f45a26c7b2c51c350',1,'HaplotypesConfig']]],
+ ['record_5fbases_13287',['record_bases',['../classvg_1_1Packer.html#a7a3debd842c660a3fc4755fc887c74ec',1,'vg::Packer']]],
+ ['record_5fedges_13288',['record_edges',['../classvg_1_1Packer.html#ab6fa0636229479a7368286e43f20ffa2',1,'vg::Packer']]],
+ ['record_5fedits_13289',['record_edits',['../classvg_1_1Packer.html#a8200ea3c39e408f3394c4a65fe2e3786',1,'vg::Packer']]],
+ ['record_5foffset_13290',['record_offset',['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa4c597fb92b3074c231b3b02f1dd58a4',1,'vg::ZipCode::snarl_code_t']]],
+ ['record_5fqualities_13291',['record_qualities',['../classvg_1_1Packer.html#ab29c0bdd5ae1db4a89db3476ba70ef68',1,'vg::Packer']]],
+ ['redundant_5fvertexes_13292',['redundant_vertexes',['../classvg_1_1MEMChainModel.html#a6a4132f34b8c9636e02c186ffa75a333',1,'vg::MEMChainModel::redundant_vertexes()'],['../classvg_1_1AlignmentChainModel.html#a2fd794e91dfc7ee2db7fdc9f921c5134',1,'vg::AlignmentChainModel::redundant_vertexes()']]],
+ ['reestimation_5ffrequency_13293',['reestimation_frequency',['../classvg_1_1FragmentLengthDistribution.html#a648954fbcb1fd0295fb22a37d79ed3e7',1,'vg::FragmentLengthDistribution']]],
+ ['ref_5fbase_13294',['ref_base',['../structvg_1_1BasePileup.html#a8d68d6e5d3ce5d2a9a448f90ed6dfc09',1,'vg::BasePileup']]],
+ ['ref_5foffset_13295',['ref_offset',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a0d0812a9f6be0ad3610fb860fb1bc2d2',1,'vg::DozeuInterface::graph_pos_s']]],
+ ['ref_5foffsets_13296',['ref_offsets',['../classvg_1_1LegacyCaller.html#a9aa5ae8255c13d5c19a4cae14f998a8e',1,'vg::LegacyCaller::ref_offsets()'],['../classvg_1_1FlowCaller.html#a454f9cba510f7ebf9e8929c53092583a',1,'vg::FlowCaller::ref_offsets()'],['../classvg_1_1NestedFlowCaller.html#a389525ad359e73ad07da1bac80cb3595',1,'vg::NestedFlowCaller::ref_offsets()'],['../classvg_1_1MCMCCaller.html#acccde0cf44eb8781fc43830f0b3736b3',1,'vg::MCMCCaller::ref_offsets()']]],
+ ['ref_5fpath_13297',['ref_path',['../structvg_1_1FlowSort_1_1Growth.html#a34ba660c358c1ec59cd7c70e62780a8c',1,'vg::FlowSort::Growth']]],
+ ['ref_5fpath_5fhandle_13298',['ref_path_handle',['../structhaplo_1_1linear__haplo__structure.html#a57eb7d1ebc0bc29e9ba3d1c3955650e9',1,'haplo::linear_haplo_structure']]],
+ ['ref_5fpath_5fhandles_13299',['ref_path_handles',['../classvg_1_1MultipathMapper.html#a2ee3920a6e8758880172f6fd07c5f7f2',1,'vg::MultipathMapper']]],
+ ['ref_5fpath_5finterval_13300',['ref_path_interval',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#afb6f9c3dbe7a55c17d953489de39e656',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['ref_5fpath_5flengths_13301',['ref_path_lengths',['../classvg_1_1MCMCCaller.html#a7638f220d989784503287ea538da21f4',1,'vg::MCMCCaller']]],
+ ['ref_5fpath_5fname_13302',['ref_path_name',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a69d34c61dd53d99246bebffa0b68def0',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['ref_5fpath_5foffsets_13303',['ref_path_offsets',['../classvg_1_1MCMCCaller.html#a614597d6c55c252d2efb88cdd0048eff',1,'vg::MCMCCaller']]],
+ ['ref_5fpath_5fset_13304',['ref_path_set',['../classvg_1_1FlowCaller.html#ac85f8948b4a0c6f9bcb66cccf498c372',1,'vg::FlowCaller::ref_path_set()'],['../classvg_1_1NestedFlowCaller.html#a934f25461550667e553a51ed2fee1fb2',1,'vg::NestedFlowCaller::ref_path_set()']]],
+ ['ref_5fpaths_13305',['ref_paths',['../classvg_1_1Deconstructor.html#a8da74d6fff7d5af6caed96723d0bccd9',1,'vg::Deconstructor::ref_paths()'],['../classvg_1_1GAFOutputCaller.html#a2675564b819e50ac8a21ca51eb14c99c',1,'vg::GAFOutputCaller::ref_paths()'],['../classvg_1_1LegacyCaller.html#a73beb7401923d192f8542beb938ea33c',1,'vg::LegacyCaller::ref_paths()'],['../classvg_1_1FlowCaller.html#adb1bb384ccb36d214a22cef04919920c',1,'vg::FlowCaller::ref_paths()'],['../classvg_1_1NestedFlowCaller.html#a5206505cf92654951bef22b42d50381e',1,'vg::NestedFlowCaller::ref_paths()'],['../classvg_1_1MCMCCaller.html#a081ed012622de090f1aad2a82526a59e',1,'vg::MCMCCaller::ref_paths()'],['../structvg_1_1Recombinator_1_1Statistics.html#ac3404816da5f78c7712ad69eb8f9594f',1,'vg::Recombinator::Statistics::ref_paths()']]],
+ ['ref_5fploidies_13306',['ref_ploidies',['../classvg_1_1LegacyCaller.html#ac82406147f3603e97d22418ee0e7bdc4',1,'vg::LegacyCaller::ref_ploidies()'],['../classvg_1_1FlowCaller.html#a2487ac1acadd5052a3a18204c426591d',1,'vg::FlowCaller::ref_ploidies()'],['../classvg_1_1NestedFlowCaller.html#a021b1013fe64a99b598ffa291a423e5b',1,'vg::NestedFlowCaller::ref_ploidies()']]],
+ ['ref_5fpositions_13307',['ref_positions',['../structhaplo_1_1linear__haplo__structure_1_1SNVvector.html#a6065969d77968cd3afc31ca7b8b1a9f0',1,'haplo::linear_haplo_structure::SNVvector']]],
+ ['ref_5fsample_13308',['ref_sample',['../structHaplotypesConfig.html#a1575fa9f328d1d823e788f422b6bde43',1,'HaplotypesConfig']]],
+ ['ref_5fsamples_13309',['ref_samples',['../classvg_1_1Deconstructor.html#a72834c9d1d667e3283e93f60a3f5057b',1,'vg::Deconstructor']]],
+ ['ref_5fsteps_13310',['ref_steps',['../structvg_1_1ParentGenotypeInfo.html#a45d8b5d863b3f74e9eb499acef7a2916',1,'vg::ParentGenotypeInfo']]],
+ ['ref_5ftrav_5fidx_13311',['ref_trav_idx',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a7a265b17dc3bc9a34603de7e064230f8',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['ref_5ftraversal_13312',['ref_traversal',['../structvg_1_1ParentGenotypeInfo.html#a4e02433e8ac8eae0491d4290f5b78515',1,'vg::ParentGenotypeInfo']]],
+ ['reference_5fpaths_13313',['reference_paths',['../classvg_1_1PhaseUnfolder.html#a2bfa46441300e0817643b310aced989b',1,'vg::PhaseUnfolder']]],
+ ['reflect_13314',['reflect',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aa5776efd133ed466cb82ef4f4b161dfd',1,'vg::GraphSynchronizer::Lock']]],
+ ['refpos_13315',['refpos',['../structvg_1_1Alignment.html#a584c3aa15a5c1386d14a97c0ce85c0cf',1,'vg::Alignment']]],
+ ['regions_13316',['regions',['../structvg_1_1Funnel_1_1PaintableSpace.html#a001cb606b7e4f79f8be9550b17c6f1b4',1,'vg::Funnel::PaintableSpace::regions()'],['../classvg_1_1HaplotypeIndexer.html#a85285e19121d708649f61b5420ab0777',1,'vg::HaplotypeIndexer::regions()']]],
+ ['registered_5fsuffixes_13317',['registered_suffixes',['../classvg_1_1IndexRegistry.html#ad3422d12216130fa07d77dcc3e62ae34',1,'vg::IndexRegistry']]],
+ ['registry_13318',['registry',['../classvg_1_1IndexingPlan.html#a7a8e639fb6e8225162a5ff532c4b963d',1,'vg::IndexingPlan']]],
+ ['regular_5faligner_13319',['regular_aligner',['../classvg_1_1AlignerClient.html#af164f37a5efb0c05b10fea3841b78e83',1,'vg::AlignerClient']]],
+ ['regular_5fsnarl_5fis_5freversed_5foffset_13320',['REGULAR_SNARL_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a40ebd5bef9b1916bbe944baaaff0b122',1,'vg::ZipCode']]],
+ ['regular_5fsnarl_5fsize_13321',['REGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a14c19ec53976a951ef9a16f9202ac19e',1,'vg::ZipCode']]],
+ ['remove_5ffailing_5fedits_13322',['remove_failing_edits',['../classvg_1_1Filter.html#aea2a2fc6de506793111639e609376bf0',1,'vg::Filter']]],
+ ['rename_5fvariants_13323',['rename_variants',['../classvg_1_1HaplotypeIndexer.html#a8061130697dc26811303c4b67b081245',1,'vg::HaplotypeIndexer']]],
+ ['rend_13324',['rend',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a864f0d7f9c86b6f057e2b2889ef478a2',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['repeat_5fsize_13325',['repeat_size',['../classvg_1_1ReadFilter.html#a95e0303086c9c6dc7a17d452b7d7f928',1,'vg::ReadFilter']]],
+ ['report_5fallelic_5fmapq_13326',['report_allelic_mapq',['../classvg_1_1MultipathMapper.html#a6cc2a29a0a539f37606482c57c78b015',1,'vg::MultipathMapper']]],
+ ['report_5fgroup_5fmapq_13327',['report_group_mapq',['../classvg_1_1MultipathMapper.html#a42577bd89395f56ea2045c378b745456',1,'vg::MultipathMapper']]],
+ ['rescore_13328',['rescore',['../classvg_1_1ReadFilter.html#a7373ef70ee64562dd779628a234c1080',1,'vg::ReadFilter']]],
+ ['rescue_5falgorithm_13329',['rescue_algorithm',['../classvg_1_1MinimizerMapper.html#a17f800e4588567e473ea18a55bd186b9',1,'vg::MinimizerMapper']]],
+ ['rescue_5fgraph_5fstd_5fdevs_13330',['rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#aab3573cb5d2878a13b0a40d427e8c943',1,'vg::MultipathMapper']]],
+ ['rescue_5fonly_5fanchor_5fmax_13331',['rescue_only_anchor_max',['../classvg_1_1MultipathMapper.html#acd7c1016549d1f96af13b9c317f239f3',1,'vg::MultipathMapper']]],
+ ['rescue_5fonly_5fmin_13332',['rescue_only_min',['../classvg_1_1MultipathMapper.html#a2ad423f9fc1a81bbe31e9c25992de378',1,'vg::MultipathMapper']]],
+ ['rescue_5fseed_5flimit_13333',['rescue_seed_limit',['../classvg_1_1MinimizerMapper.html#a0a0c7111b38792069bb74af9b74b0978',1,'vg::MinimizerMapper']]],
+ ['rescue_5fsubgraph_5fstdevs_13334',['rescue_subgraph_stdevs',['../classvg_1_1MinimizerMapper.html#a411fb85396b07aab41fabc8e34b92481',1,'vg::MinimizerMapper']]],
+ ['rescued_13335',['RESCUED',['../classvg_1_1MultipathMapper.html#ab559f7eb874ac770dbbda734c5bc395a',1,'vg::MultipathMapper']]],
+ ['reserved_13336',['reserved',['../structvg_1_1Alignment.html#a8374111b6348509e8e9ecca0cd1ac046',1,'vg::Alignment']]],
+ ['reset_5falong_5fchain_5fparent_13337',['reset_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#a8934c072a3cdbc8652e8f7fa9f9ef553',1,'vg::subcommand::TickChainLink']]],
+ ['restrained_5fgraph_5fextraction_13338',['restrained_graph_extraction',['../classvg_1_1MultipathMapper.html#a0ad5a21ab0cf3c77e3905e299b7d26c4',1,'vg::MultipathMapper']]],
+ ['retry_5fon_5fns_13339',['retry_on_Ns',['../classvg_1_1NGSSimulator.html#a95f6ffd660c8c041e4d8b1d36a823bdd',1,'vg::NGSSimulator']]],
+ ['reverse_13340',['reverse',['../structvg_1_1Support.html#acc2aa2a4b0278503817664600938c8a2',1,'vg::Support']]],
+ ['reversing_5fwalk_5flength_13341',['reversing_walk_length',['../classvg_1_1MultipathMapper.html#af87eaae1274e33230fffe9dca05dbbec',1,'vg::MultipathMapper']]],
+ ['rgfa_5flisteners_13342',['rgfa_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a3caa995d2ef8a311e87b1202da714b53',1,'vg::algorithms::GFAParser']]],
+ ['rho_13343',['rho',['../structhaplo_1_1haploMath_1_1RRMemo.html#a7536987972e5d717ba43a951adcece82',1,'haplo::haploMath::RRMemo']]],
+ ['right_13344',['right',['../structvg_1_1Support.html#ab2fd7cba17f56ce67501f47fda6ae153',1,'vg::Support']]],
+ ['right_5fends_13345',['right_ends',['../structvg_1_1ConstructedChunk.html#ac20dbdc398181350e73bee0429fe2842',1,'vg::ConstructedChunk']]],
+ ['right_5ffull_13346',['right_full',['../structvg_1_1GaplessExtension.html#ae7ca191732330cb5a6db94ee5531f2ed',1,'vg::GaplessExtension']]],
+ ['right_5fhandle_5ftrans_13347',['right_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#aceac5a4b442fbce2c7c422acbdbdd097',1,'vg::JoinedSpliceGraph']]],
+ ['right_5fmaximal_13348',['right_maximal',['../structvg_1_1GaplessExtension.html#a8e4d53c78f3c355b5b17bf3e959bbd41',1,'vg::GaplessExtension']]],
+ ['right_5fsplice_5foffset_13349',['right_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a152eb3987232cdba5fff9dd9a15ed952',1,'vg::JoinedSpliceGraph']]],
+ ['right_5fsubgraph_13350',['right_subgraph',['../classvg_1_1JoinedSpliceGraph.html#a42ce6f52135018237e3e29d2a53c4291',1,'vg::JoinedSpliceGraph']]],
+ ['right_5ftelomere_5fnode_13351',['right_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a3d771a24b8889ea668939eac31276ea3',1,'vg::PhasedGenome::Haplotype']]],
+ ['ring_5fbuffer_5fsize_13352',['RING_BUFFER_SIZE',['../classvg_1_1io_1_1StreamMultiplexer.html#a6e4432baab9571a1783b2a793b29905a',1,'vg::io::StreamMultiplexer']]],
+ ['rng_13353',['rng',['../classvg_1_1Colors.html#a79a79da7cbc2bef7eea8c3ff1e229b7c',1,'vg::Colors::rng()'],['../classvg_1_1Pictographs.html#ac7600f845d01a084a15cff9aacc6bc3e',1,'vg::Pictographs::rng()'],['../classvg_1_1Sampler.html#ad26ea071330c6a4b580af84bec064453',1,'vg::Sampler::rng()'],['../classvg_1_1LazyRNG.html#a6aac64a985fa2fc60c2d32079bd26a63',1,'vg::LazyRNG::rng()']]],
+ ['robust_5festimation_5ffraction_13354',['robust_estimation_fraction',['../classvg_1_1FragmentLengthDistribution.html#aa5a2f20742b369464d132a751f52aaf3',1,'vg::FragmentLengthDistribution']]],
+ ['root_13355',['root',['../classvg_1_1BitStringTree.html#a69741fde7d47ad2f46dd952eb6bd2d66',1,'vg::BitStringTree::root()'],['../structvg_1_1Tree.html#a730cd8796e579d01c66bea46217047d7',1,'vg::Tree::root()']]],
+ ['root_5fchain_5fcomponent_5fcount_5foffset_13356',['ROOT_CHAIN_COMPONENT_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a79816fb11ec20354e677a6b1acd17905',1,'vg::ZipCode']]],
+ ['root_5fchain_5fsize_13357',['ROOT_CHAIN_SIZE',['../classvg_1_1ZipCode.html#af83f8e5c14d24fd45ad2318e229299d0',1,'vg::ZipCode']]],
+ ['root_5fchains_13358',['root_chains',['../classvg_1_1SnarlManager.html#a2d9758d889f875b1260f49985cf3ef35',1,'vg::SnarlManager']]],
+ ['root_5fchildren_13359',['root_children',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a8b902ff993db7c62075ce3371622e781',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['root_5fidentifier_5foffset_13360',['ROOT_IDENTIFIER_OFFSET',['../classvg_1_1ZipCode.html#a9320699634e827ab9c91ade7b39220a9',1,'vg::ZipCode']]],
+ ['root_5fis_5fchain_5foffset_13361',['ROOT_IS_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a9fcb55636a3bd5e25d6592952880662b',1,'vg::ZipCode']]],
+ ['root_5fnode_5flength_5foffset_13362',['ROOT_NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a97232d726929bf2ebb8fb7fdfbde94fd',1,'vg::ZipCode']]],
+ ['root_5fnode_5for_5fchain_5fconnectivity_5for_5flength_5foffset_13363',['ROOT_NODE_OR_CHAIN_CONNECTIVITY_OR_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#afa760e19cc391b5de5adba6b4ca3cdb0',1,'vg::ZipCode']]],
+ ['root_5fnode_5fsize_13364',['ROOT_NODE_SIZE',['../classvg_1_1ZipCode.html#afa378af1f64a51675d658d2c4ecb5d95',1,'vg::ZipCode']]],
+ ['root_5fsnarl_5fsize_13365',['ROOT_SNARL_SIZE',['../classvg_1_1ZipCode.html#aa2cdcd63b1ac93b431e0e4d5d25df346',1,'vg::ZipCode']]],
+ ['root_5ftrim_13366',['root_trim',['../classvg_1_1TreeSubgraph.html#a04044896f4bed03dc15a6c0a07df675d',1,'vg::TreeSubgraph']]],
+ ['roots_13367',['roots',['../classvg_1_1SnarlManager.html#ab13a661f6abe1feaf2c4ca4471a85a90',1,'vg::SnarlManager']]],
+ ['row_5fidx_13368',['row_idx',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2345d3706d3d46b657e205865f4d4122',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['rr_5fmemos_13369',['rr_memos',['../classvg_1_1MultipathMapper.html#a5709f5cdf31de90145a1178fa166be44',1,'vg::MultipathMapper']]],
+ ['running_13370',['running',['../structvg_1_1Range.html#abbd18ac55fecb0e698fcabebc7ae48ad',1,'vg::Range']]],
+ ['runs_13371',['runs',['../structvg_1_1BenchmarkResult.html#a564ed18fb2f561f09e74a254854e2d88',1,'vg::BenchmarkResult']]]
];
diff --git a/search/variables_13.js b/search/variables_13.js
index 975aff149d..a93bc1770d 100644
--- a/search/variables_13.js
+++ b/search/variables_13.js
@@ -1,196 +1,196 @@
var searchData=
[
- ['s_5fbv_13368',['s_bv',['../classxg_1_1XG.html#ac8f0eaf8d0d58d489a6da321d8303c46',1,'xg::XG']]],
- ['s_5fbv_5frank_13369',['s_bv_rank',['../classxg_1_1XG.html#a14eb778ecdf51cca8ced32eb42112200',1,'xg::XG']]],
- ['s_5fbv_5fselect_13370',['s_bv_select',['../classxg_1_1XG.html#a45b6e0fcf1dd90f451df245f0ffc3e1c',1,'xg::XG']]],
- ['s_5fiv_13371',['s_iv',['../classxg_1_1XG.html#aa8e40fcbfa8174b689067d87acd818be',1,'xg::XG']]],
- ['safe_5fto_5fget_13372',['safe_to_get',['../classvg_1_1VcfBuffer.html#ac280837b05f233e4420c6e8a7bbef32b',1,'vg::VcfBuffer']]],
- ['sam_5ffiles_13373',['sam_files',['../classvg_1_1HTSWriter.html#a57a7f16757fc6ce944636d69c48903cb',1,'vg::HTSWriter']]],
- ['sam_5fheader_13374',['sam_header',['../classvg_1_1HTSWriter.html#a95cd5874834de9191faf18d39fef9534',1,'vg::HTSWriter']]],
- ['sample_5fcounter_13375',['sample_counter',['../classvg_1_1NGSSimulator.html#ab162ca660d69f66c18c41516a1a69d24',1,'vg::NGSSimulator']]],
- ['sample_5finterval_13376',['sample_interval',['../structvg_1_1RebuildParameters.html#aa4adeffb1f91f55c6f1709e6d1c9cfcb',1,'vg::RebuildParameters']]],
- ['sample_5fname_13377',['sample_name',['../classvg_1_1VCFOutputCaller.html#a70e8288543e7facfb79f5211ce33fa7f',1,'vg::VCFOutputCaller::sample_name()'],['../classvg_1_1MCMCCaller.html#a59582bcf7ba0dc3ae52f3f9a7c8eb80c',1,'vg::MCMCCaller::sample_name()'],['../classvg_1_1MinimizerMapper.html#a2f47382b14baf0482c43034e6484d086',1,'vg::MinimizerMapper::sample_name()'],['../classvg_1_1MultipathAlignmentEmitter.html#a6fa324b9dee313b1fceab7bafa62db24',1,'vg::MultipathAlignmentEmitter::sample_name()'],['../structvg_1_1Alignment.html#ad823d9ed3f413faaf35700a41cfab6e7',1,'vg::Alignment::sample_name()'],['../structvg_1_1MultipathAlignment.html#a90d675553385456c66b572a88fa88650',1,'vg::MultipathAlignment::sample_name()']]],
- ['sample_5fnames_13378',['sample_names',['../classvg_1_1Deconstructor.html#a56f3119a427b1076d0d0d5ca7f478832',1,'vg::Deconstructor']]],
- ['sample_5fploidys_13379',['sample_ploidys',['../classvg_1_1Deconstructor.html#a337113fedde38a57458c9329ffd86aac',1,'vg::Deconstructor']]],
- ['sample_5frange_13380',['sample_range',['../classvg_1_1HaplotypeIndexer.html#a53cb273305c8fb1c039581c1a1b3d76e',1,'vg::HaplotypeIndexer']]],
- ['sample_5fto_5fhaplotypes_13381',['sample_to_haplotypes',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a5e006ad54f202447a37975fa4919481c',1,'vg::Deconstructor::NestingInfo']]],
- ['sample_5fto_5fploidy_13382',['sample_to_ploidy',['../structvg_1_1ParentGenotypeInfo.html#a5ac680b0203fe3cccab8959c84f5d556',1,'vg::ParentGenotypeInfo']]],
- ['sample_5funsheared_5fpaths_13383',['sample_unsheared_paths',['../classvg_1_1NGSSimulator.html#af7441bd12030f0e189aca5ba2e0b47ef',1,'vg::NGSSimulator']]],
- ['samplers_13384',['samplers',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a8d2808d7b690045d11af93fd6619fbf7',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['samples_13385',['samples',['../structGBWTConfig.html#ae5a3dac168e1ea3d38ddd13f5097fa40',1,'GBWTConfig']]],
- ['samples_5fin_5fbatch_13386',['samples_in_batch',['../classvg_1_1HaplotypeIndexer.html#a681bcf3fb6014ae885adb3dec25ff2fc',1,'vg::HaplotypeIndexer']]],
- ['save_5fexplanations_13387',['save_explanations',['../classvg_1_1Explainer.html#a3510aece27ab20079a8a3e87fa702596',1,'vg::Explainer']]],
- ['scc_5fcopy_5fcount_13388',['scc_copy_count',['../classvg_1_1DagifiedGraph.html#a780a2eb98c2a1ad1b106283048f95cf0',1,'vg::DagifiedGraph']]],
- ['scc_5fof_5fhandle_13389',['scc_of_handle',['../classvg_1_1DagifiedGraph.html#afc531153860777849e241cd95ac06b03',1,'vg::DagifiedGraph']]],
- ['score_13390',['score',['../classvg_1_1MEMChainModelVertex.html#a10cf4210b2f802b628111fe2cd1f309b',1,'vg::MEMChainModelVertex::score()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aa0f6834e2a0860792afc6a701d3396c3',1,'vg::MEMClusterer::HitNode::score()'],['../structvg_1_1Funnel_1_1Item.html#a91b9d511109c7c561be120d3346ea3df',1,'vg::Funnel::Item::score()'],['../structvg_1_1WFAPoint.html#a6358c051265bfcc41d857f6df091eebb',1,'vg::WFAPoint::score()'],['../structvg_1_1GaplessExtension.html#a0989b2a97d4403b381dbf68768757d32',1,'vg::GaplessExtension::score()'],['../structvg_1_1WFAAlignment.html#a066d6b546e0308e8df7fc74f42d5de67',1,'vg::WFAAlignment::score()'],['../structvg_1_1Genotyper_1_1Affinity.html#aa0fa1b63d720aa196205be34ee80ee07',1,'vg::Genotyper::Affinity::score()'],['../structvg_1_1GFFRecord.html#aabb70a3b691d378e87cb3fc3fef418ac',1,'vg::GFFRecord::score()'],['../classvg_1_1AlignmentChainModelVertex.html#a207cf7885f1eb8d129d9f599791b0dea',1,'vg::AlignmentChainModelVertex::score()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a002868b55e87a630c4e4f1e1ff213008',1,'vg::MinimizerMapper::Minimizer::score()'],['../structvg_1_1Recombinator_1_1Statistics.html#a348046df697bf6a89261ecfcb6ac6765',1,'vg::Recombinator::Statistics::score()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#abe1c7432c38de20678f5a74798d96bd4',1,'vg::SnarlDistanceIndexClusterer::Cluster::score()'],['../classvg_1_1algorithms_1_1TracedScore.html#a6c63f6d5199ec14c3e912e06f74d9974',1,'vg::algorithms::TracedScore::score()'],['../structvg_1_1Alignment.html#a5c57b95a7ea122139a092427b592ebeb',1,'vg::Alignment::score()'],['../structvg_1_1Subpath.html#acffb5adff6c20c194740186323f1f484',1,'vg::Subpath::score()'],['../structvg_1_1Connection.html#a5e880c9306bb072e08ab6315bdbb1c6f',1,'vg::Connection::score()']]],
- ['score_5fbound_13391',['score_bound',['../classvg_1_1WFATree.html#afdb599de97d172e2afde161ea0f8efc9',1,'vg::WFATree']]],
- ['score_5fmatrix_13392',['score_matrix',['../classvg_1_1GSSWAligner.html#a9ad471080a267eb489e31523ef2b5f2b',1,'vg::GSSWAligner']]],
- ['score_5foutput_13393',['score_output',['../structHaplotypesConfig.html#aea2a24fbc9fbe00f814c1b98d8607079',1,'HaplotypesConfig']]],
- ['scores_13394',['scores',['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ab466534da431354516132617d0f14e95',1,'vg::Recombinator::LocalHaplotype']]],
- ['scratch_13395',['scratch',['../structvg_1_1ChainIterator.html#a277447dceb98d18d597a73f2c790e15c',1,'vg::ChainIterator']]],
- ['search_5fthreads_13396',['search_threads',['../structGBWTConfig.html#a1e999f204cdd3655aac4739f12b3265f',1,'GBWTConfig']]],
- ['secondary_5frescue_5fattempts_13397',['secondary_rescue_attempts',['../classvg_1_1MultipathMapper.html#a0203a68c7b346ec30bf2854c78bb3434',1,'vg::MultipathMapper']]],
- ['secondary_5frescue_5fscore_5fdiff_13398',['secondary_rescue_score_diff',['../classvg_1_1MultipathMapper.html#ac5ba763f99c22ff9feccb76333cf1039',1,'vg::MultipathMapper']]],
- ['secondary_5frescue_5fsubopt_5fdiff_13399',['secondary_rescue_subopt_diff',['../classvg_1_1MultipathMapper.html#aee081b4a0ee6adadb2dff205a24a2c7a',1,'vg::MultipathMapper']]],
- ['secondary_5fscore_13400',['secondary_score',['../structvg_1_1Alignment.html#a58502a21a2588a5ac8baaa6e31c81eb4',1,'vg::Alignment']]],
- ['seed_13401',['seed',['../classvg_1_1MCMCGenotyper.html#aa2399e6a45d2595e08053cdb66207b37',1,'vg::MCMCGenotyper::seed()'],['../classvg_1_1NGSSimulator.html#a99ce1e3ba72956bbf9d1cbaa0fd89014',1,'vg::NGSSimulator::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a1430e1d0dccc75ffa1962408e6226a21',1,'vg::SnarlDistanceIndexClusterer::SeedCache::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#aae124944787f51e8d8fc23cb274f0350',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::seed()'],['../classvg_1_1SpliceRegion.html#a10732e3be85dbecaf6d046ba52f9f716',1,'vg::SpliceRegion::seed()'],['../classvg_1_1StreamSorter.html#a8875748639a885dfacf261956a9b3ee4',1,'vg::StreamSorter::seed()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a38ffc441fe03ec44c1c089eba2b76ae2',1,'vg::ZipCodeTree::oriented_seed_t::seed()']]],
- ['seed_5fcount_5fprefix_5fsum_13402',['seed_count_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af787cd3652afaa91cdebf97673456004',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['seed_5findices_13403',['seed_indices',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ad587cbee5a1b577adbc9548a99f857b4',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['seed_5flength_13404',['seed_length',['../classvg_1_1algorithms_1_1Anchor.html#a739e4bcbda94fa20b8d99ad5340b5fc6',1,'vg::algorithms::Anchor']]],
- ['seed_5fsort_5forder_13405',['seed_sort_order',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ae40d481f31fd4ece290a206482ed5a13',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['seeds_13406',['seeds',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a7451a72162f19b00d1bd44fc62be0297',1,'vg::BandedGlobalAligner::BAMatrix::seeds()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a0531ebefe7a686d6624c7b5f60357aeb',1,'vg::SnarlDistanceIndexClusterer::Cluster::seeds()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ac8b2807cb1f656be384407ed36b1c926',1,'vg::ZipCodeForest::forest_growing_state_t::seeds()']]],
- ['seek_13407',['seek',['../structhFILE__backend.html#a93b5b1dcb35560b106e1cccb38476ddb',1,'hFILE_backend']]],
- ['seen_5fread_5fnames_13408',['seen_read_names',['../classvg_1_1ReadFilter.html#a613b00bb83a119d89911ed4315e4e24a',1,'vg::ReadFilter']]],
- ['segment_5fto_5fname_13409',['segment_to_name',['../classvg_1_1FlatFileBackTranslation.html#a09f2373723a0f9901698cf8315a3f813',1,'vg::FlatFileBackTranslation']]],
- ['segment_5ftranslation_13410',['segment_translation',['../structGBWTConfig.html#a8415ef08abc7ef4e9d854dc100d0df15',1,'GBWTConfig']]],
- ['sense_5fto_5fstring_13411',['SENSE_TO_STRING',['../paths__main_8cpp.html#a16ad253f4e8c46b88b363e1ffc613c51',1,'paths_main.cpp']]],
- ['separator_13412',['SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#ac50cb6403ceaabd3f878e2c4f2195f56',1,'handlegraph::PathMetadata']]],
- ['seq_13413',['seq',['../structvg_1_1kmer__t.html#a98b04ac70a36cf6feae80b03b3a32eb2',1,'vg::kmer_t::seq()'],['../structvg_1_1Region.html#a938cc852fd08f11656bdfbd204843017',1,'vg::Region::seq()'],['../structvg_1_1VG_1_1Plan.html#a4bb5a9fa8f5bb32c2e94d3c038f9cf95',1,'vg::VG::Plan::seq()'],['../structvg_1_1algorithms_1_1kmer__t.html#a5c235e7c7f3a819e291956d8e307821a',1,'vg::algorithms::kmer_t::seq()'],['../structvg_1_1algorithms_1_1walk__t.html#a65bec2a64da1b8f7c3820d49b5bef09f',1,'vg::algorithms::walk_t::seq()']]],
- ['seq_5flength_13414',['seq_length',['../classvg_1_1Viz.html#a2f5862e76ca098060b503d03de76c024',1,'vg::Viz::seq_length()'],['../classxg_1_1XG.html#a7eadd7681a21479f7f31c240047cdffe',1,'xg::XG::seq_length()']]],
- ['seq_5foffset_13415',['seq_offset',['../structvg_1_1MatchPos.html#a85fc0d2a7af86db887d649d3c968755e',1,'vg::MatchPos::seq_offset()'],['../structvg_1_1WFAPoint.html#a14ceda5614586a0e3ef44b729ad179c0',1,'vg::WFAPoint::seq_offset()'],['../structvg_1_1WFAAlignment.html#a1fc0e09c8462c5aa10d4f0acbc2a8f2d',1,'vg::WFAAlignment::seq_offset()']]],
- ['sequence_13416',['sequence',['../classvg_1_1ExtraNodeGraph.html#ad485e6609536566720fe5a48f7e2af84',1,'vg::ExtraNodeGraph::sequence()'],['../classvg_1_1WFATree.html#abbd67ff2f910ad5a4c0c1f49b10394a5',1,'vg::WFATree::sequence()'],['../structvg_1_1PathIndex.html#a0b807b5252299d9b0f1c9168079a591f',1,'vg::PathIndex::sequence()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#a2e6f784aa4bde512d84c0f1d3cedd01f',1,'vg::Recombinator::LocalHaplotype::sequence()'],['../structvg_1_1Node.html#a9a0e8995bc48aa5e24977d1bd20e91a3',1,'vg::Node::sequence()'],['../structvg_1_1Edit.html#a4a7726b24b28ed819d37b9c39ae839d1',1,'vg::Edit::sequence()'],['../structvg_1_1Alignment.html#a2ae1f06d48c37997cee72b7cd3210a83',1,'vg::Alignment::sequence()'],['../structvg_1_1MultipathAlignment.html#ae6c263b75effad9b08e514c5852f1221',1,'vg::MultipathAlignment::sequence()'],['../structvg_1_1KmerMatch.html#ab434e30bbaf0fbb10425d5bc35ac50b2',1,'vg::KmerMatch::sequence()']]],
- ['sequence_5fid_13417',['sequence_id',['../structvg_1_1GFFRecord.html#a91b952a4d9d5c4f44e6def80e33073c8',1,'vg::GFFRecord::sequence_id()'],['../structvg_1_1RecombinatorHaplotype.html#a3b372fd165a3e707a50e2a0a1f61cef5',1,'vg::RecombinatorHaplotype::sequence_id()']]],
- ['sequence_5fsource_13418',['sequence_source',['../structGraphHandler.html#a1583ae5e2c88d3099b62255a28978316',1,'GraphHandler']]],
- ['sequences_13419',['sequences',['../structvg_1_1Haplotypes_1_1Subchain.html#aae0d847a9118ccb4ff178c3ac7c759eb',1,'vg::Haplotypes::Subchain']]],
- ['set_5frefpos_13420',['set_refpos',['../classvg_1_1MinimizerMapper.html#a7fe47fe6075b79253609a04601d0995e',1,'vg::MinimizerMapper']]],
- ['sha1_5fvariant_5fname_13421',['sha1_variant_name',['../classvg_1_1Constructor.html#afafc25fc7021c48463894db9abce2f66',1,'vg::Constructor']]],
- ['shift_5fprune_5fdiff_13422',['shift_prune_diff',['../classvg_1_1Surjector.html#a3768ca4fe69ba4c58cdbfe81343c56bd',1,'vg::Surjector']]],
- ['short_5fmem_5ffilter_5ffactor_13423',['short_mem_filter_factor',['../classvg_1_1BaseMapper.html#ac92eb174ad81e8714bf43e4b08aecdb9',1,'vg::BaseMapper']]],
- ['short_5foption_13424',['short_option',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a60f696e33fce1e021b3454176ce0885f',1,'vg::subcommand::BaseArgSpec']]],
- ['short_5foptions_13425',['short_options',['../classvg_1_1ConfigurableParser.html#adfde71f165bbcb110831c12e862aa891',1,'vg::ConfigurableParser']]],
- ['short_5fopts_13426',['short_opts',['../classvg_1_1BaseOption.html#a04134150cfd3143bf1f43f55af5fd3d6',1,'vg::BaseOption']]],
- ['short_5fread_5fminimizer_5fk_13427',['short_read_minimizer_k',['../structvg_1_1IndexingParameters.html#a74ed1f6b8e93329efc15654c9eac5749',1,'vg::IndexingParameters']]],
- ['short_5fread_5fminimizer_5fw_13428',['short_read_minimizer_W',['../structvg_1_1IndexingParameters.html#a882b758e0f629a9cd2e9297b193c42df',1,'vg::IndexingParameters::short_read_minimizer_W()'],['../structvg_1_1IndexingParameters.html#acf0c2287ca7ee00853bd27af02757650',1,'vg::IndexingParameters::short_read_minimizer_w()']]],
- ['show_5fcnv_13429',['show_cnv',['../classvg_1_1Viz.html#ace366df624ca2b225d3c8d20d9cb15db',1,'vg::Viz']]],
- ['show_5fdna_13430',['show_dna',['../classvg_1_1Viz.html#a2b8e6f510bca9925fd39e37feddce251',1,'vg::Viz']]],
- ['show_5fpath_5finfo_13431',['show_path_info',['../classvg_1_1Deconstructor.html#a6d2894dc3b9ea0fea97e2a78e11e2a51',1,'vg::Deconstructor']]],
- ['show_5fpaths_13432',['show_paths',['../classvg_1_1Viz.html#a501ab25fb94a4d3abd508af7bc77aac3',1,'vg::Viz']]],
- ['show_5fprogress_13433',['show_progress',['../structvg_1_1GBWTHandler.html#a7513df04845c0145e6933236346ec8fc',1,'vg::GBWTHandler::show_progress()'],['../structvg_1_1RebuildParameters.html#a4a86fbc222841919a70452f4a6e8c463',1,'vg::RebuildParameters::show_progress()'],['../classvg_1_1Genotyper.html#a72599c00acaed553e0d235e5c73d4b82',1,'vg::Genotyper::show_progress()'],['../classvg_1_1GraphCaller.html#a1179324159b5518ebd0eb7d5fb71edd5',1,'vg::GraphCaller::show_progress()'],['../classvg_1_1Progressive.html#a6653625f496832c4cb8711185d5e04cb',1,'vg::Progressive::show_progress()'],['../classvg_1_1Transcriptome.html#af92e5c3f2b2216b98f30f5518fc3b785',1,'vg::Transcriptome::show_progress()'],['../classvg_1_1VGset.html#aa848e2230f2d5c016c0a816cfa14501e',1,'vg::VGset::show_progress()'],['../structGBWTConfig.html#a075b0013542a10eb0708e94f20cb18a6',1,'GBWTConfig::show_progress()']]],
- ['show_5fwork_13434',['show_work',['../classvg_1_1MinimizerMapper.html#a089bb5c8a56a7614a2f494690f3b5acd',1,'vg::MinimizerMapper']]],
- ['sibling_5findices_5fat_5fdepth_13435',['sibling_indices_at_depth',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a0c95aeef3ec92915788ebf083154e265',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['sigma_13436',['sigma',['../classvg_1_1FragmentLengthDistribution.html#a6462bb11645a893b5dc2de057714d8f6',1,'vg::FragmentLengthDistribution']]],
- ['simplify_5ftopologies_13437',['simplify_topologies',['../classvg_1_1MultipathMapper.html#a5f865a27bd34ffce2e2ea1d05fc02b43',1,'vg::MultipathMapper']]],
- ['simultaneous_5fpair_5falignment_13438',['simultaneous_pair_alignment',['../classvg_1_1Mapper.html#ae83170a63789f8984e82e225486ca5bd',1,'vg::Mapper']]],
- ['since_5flast_5ffragment_5flength_5festimate_13439',['since_last_fragment_length_estimate',['../classvg_1_1FragmentLengthStatistics.html#ae79e46e68a3b9aa6c87863a6354c01a2',1,'vg::FragmentLengthStatistics']]],
- ['sink_5ffwd_13440',['sink_fwd',['../classvg_1_1SourceSinkOverlay.html#a2718021aade5e48683cdc07c5d5b16f7',1,'vg::SourceSinkOverlay']]],
- ['sink_5fid_13441',['sink_id',['../classvg_1_1SourceSinkOverlay.html#a02ca8620a0e90dbf0190fe285d11a687',1,'vg::SourceSinkOverlay']]],
- ['sink_5fnodes_13442',['sink_nodes',['../classvg_1_1BandedGlobalAligner.html#ad3ba4ffebb1e61d6ce59a995eac74f68',1,'vg::BandedGlobalAligner']]],
- ['sink_5frev_13443',['sink_rev',['../classvg_1_1SourceSinkOverlay.html#a4c00143bd29d3f3adbf571f6333ea761',1,'vg::SourceSinkOverlay']]],
- ['site_5fends_13444',['site_ends',['../classvg_1_1PhasedGenome.html#afc338c2bf1776ec1ccb29c8efee6aaa3',1,'vg::PhasedGenome']]],
- ['site_5fmanager_13445',['site_manager',['../classvg_1_1SmallSnarlSimplifier.html#a4991294aedb029a70d1d4f459e009bd3',1,'vg::SmallSnarlSimplifier']]],
- ['site_5fstarts_13446',['site_starts',['../classvg_1_1PhasedGenome.html#accfaae53e12f924b914623734a68102f',1,'vg::PhasedGenome']]],
- ['sites_13447',['sites',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a7fee7818b260154898be386649d3bfe7',1,'vg::PhasedGenome::Haplotype']]],
- ['size_13448',['size',['../classvg_1_1algorithms_1_1Anchor.html#a96921a8307e8e97ba77869b58d6d7292',1,'vg::algorithms::Anchor::size()'],['../structjob__type.html#adbc606f42800cfce3697b017578356b9',1,'job_type::size()']]],
- ['size_5ft_5fis_5fnonzero_13449',['size_t_is_nonzero',['../namespacevg_1_1subcommand.html#a62e7f4f685f1aabc28ff82aa02f00f7f',1,'vg::subcommand']]],
- ['size_5ft_5fis_5fpositive_13450',['size_t_is_positive',['../namespacevg_1_1subcommand.html#ae20ec7174b0b153b2657c4931dcca448',1,'vg::subcommand']]],
- ['skip_5falt_13451',['skip_alt',['../classvg_1_1VCFTraversalFinder.html#acc753182667fd49d9afe5eba697c92da',1,'vg::VCFTraversalFinder']]],
- ['skip_5fstructural_5fduplications_13452',['skip_structural_duplications',['../classvg_1_1VariantAdder.html#a0c90a9845a662358588f517e2cf91501',1,'vg::VariantAdder']]],
- ['skippable_13453',['skippable',['../classvg_1_1algorithms_1_1Anchor.html#ade34685bea83f218a9756478bcca25a0',1,'vg::algorithms::Anchor']]],
- ['snarl_13454',['snarl',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#aee85ad3c21e883f05b67c62fbf05be72',1,'vg::ReplaceSnarlHaplotypeCommand::snarl()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#acad9926afa69d4de3d5424ac1f03582d',1,'vg::SnarlManager::SnarlRecord::snarl()'],['../structvg_1_1Visit.html#a7e671bbc7437a16dd3549a6fc49fd2a9',1,'vg::Visit::snarl()']]],
- ['snarl_5fcaller_13455',['snarl_caller',['../classvg_1_1GraphCaller.html#a4b8c6f32019db8528bb6835fdce12ddb',1,'vg::GraphCaller']]],
- ['snarl_5fchain_5fcomponent_5foffset_13456',['SNARL_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#a807c487a518301d1726f87f7eda443a4',1,'vg::ZipCode']]],
- ['snarl_5fchild_5fcount_5foffset_13457',['SNARL_CHILD_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a37503629f90af0de452b6bc534ad43f5',1,'vg::ZipCode']]],
- ['snarl_5finto_13458',['snarl_into',['../classvg_1_1SnarlManager.html#a0f1d327aa074d59976802999d0d179d1',1,'vg::SnarlManager']]],
- ['snarl_5fis_5fregular_5foffset_13459',['SNARL_IS_REGULAR_OFFSET',['../classvg_1_1ZipCode.html#ad56c1879d223a2151795d2532932d1c8',1,'vg::ZipCode']]],
- ['snarl_5flength_5foffset_13460',['SNARL_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#ade2f247378ce48537e06399e215013d5',1,'vg::ZipCode']]],
- ['snarl_5fmanager_13461',['snarl_manager',['../classvg_1_1GraphCaller.html#a55afa68762956066ccbea2e332342266',1,'vg::GraphCaller::snarl_manager()'],['../classvg_1_1SnarlGraph.html#a292ca2c610a5f06fd06325f193557823',1,'vg::SnarlGraph::snarl_manager()'],['../classvg_1_1Masker.html#a4554deca5d95bdb68843ca7a656170fa',1,'vg::Masker::snarl_manager()'],['../classvg_1_1MCMCCaller.html#a4dad48c8bc658476ff4a6b0ed22817de',1,'vg::MCMCCaller::snarl_manager()'],['../classvg_1_1MultipathMapper.html#a82e1a1af4b8ba0170cf7817cd44f1008',1,'vg::MultipathMapper::snarl_manager()'],['../classvg_1_1NestedTraversalFinder.html#a3b15745919bd3bd7427d487eea14884b',1,'vg::NestedTraversalFinder::snarl_manager()'],['../classvg_1_1PhasedGenome.html#a56494287a449d9b95f24ac7d0e505522',1,'vg::PhasedGenome::snarl_manager()'],['../classvg_1_1RegionExpander.html#ac7c7121e538614d43356e7318769db65',1,'vg::RegionExpander::snarl_manager()'],['../classvg_1_1SupportBasedSnarlCaller.html#a86c40f2d62950d1f484aa6dd84abf60d',1,'vg::SupportBasedSnarlCaller::snarl_manager()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a8e29fb04ba5a9516d74d1da133f06330',1,'vg::ExhaustiveTraversalFinder::snarl_manager()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#a0c4e67f35a6f1e8536a81a781c7cba22',1,'vg::ReadRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a015de241431375a1b43ac32b852246f6',1,'vg::PathRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1RepresentativeTraversalFinder.html#a48de8b31240c6ddda7ff40164ae7708b',1,'vg::RepresentativeTraversalFinder::snarl_manager()'],['../classvg_1_1VCFTraversalFinder.html#ae2fac6aac1b86163b495ef183e3340d9',1,'vg::VCFTraversalFinder::snarl_manager()'],['../classvg_1_1FlowTraversalFinder.html#ab0f619b27f1f2d911e6625ab61ecddeb',1,'vg::FlowTraversalFinder::snarl_manager()'],['../classvg_1_1TraversalSupportFinder.html#adc97ab06de5c4aa553db92bae3879ee5',1,'vg::TraversalSupportFinder::snarl_manager()']]],
- ['snarl_5fnumber_13462',['snarl_number',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#add50ce54457a4031ed0d8fd0b3b34e9f',1,'vg::SnarlManager::SnarlRecord']]],
- ['snarl_5foffset_5fin_5fchain_5foffset_13463',['SNARL_OFFSET_IN_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a65ff5123c5439118b1b390179cffd818',1,'vg::ZipCode']]],
- ['snarl_5frank_5for_5fidentifier_13464',['snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4859d74d9e82058d5e6066dd0e99470e',1,'vg::ZipCode::chain_code_t']]],
- ['snarl_5freference_5flength_5fhistogram_13465',['snarl_reference_length_histogram',['../classvg_1_1Genotyper.html#ac0d4917131823fc2dab43927347d4623',1,'vg::Genotyper']]],
- ['snarl_5ftraversals_13466',['snarl_traversals',['../classvg_1_1Genotyper.html#a7ec1915674299d727c61377e91385974',1,'vg::Genotyper']]],
- ['snarlmanager_13467',['snarlmanager',['../classvg_1_1PathBasedTraversalFinder.html#a905239f50078de78279dd9f0ff82faf3',1,'vg::PathBasedTraversalFinder']]],
- ['snarls_13468',['snarls',['../classvg_1_1SnarlGraph.html#ac9db23e9d10f3c39f25a5397afb9d4fa',1,'vg::SnarlGraph::snarls()'],['../classvg_1_1MCMCGenotyper.html#a23913225e8b2d0d4dfbdb713ccf495c3',1,'vg::MCMCGenotyper::snarls()'],['../classvg_1_1SnarlManager.html#ab56cf756bc65189eeb1d4f1f3f6573b6',1,'vg::SnarlManager::snarls()']]],
- ['soft_5fclip_5flimit_13469',['soft_clip_limit',['../classvg_1_1Filter.html#abe44432fa541eee27db7789cc9db066b',1,'vg::Filter']]],
- ['soft_5fclipped_13470',['soft_clipped',['../structvg_1_1Alignment.html#a6cb12eae3f4fa017bc98b59a91a5414f',1,'vg::Alignment']]],
- ['softclip_5fthreshold_13471',['softclip_threshold',['../classvg_1_1Mapper.html#a4320fc9bb3cda3bd7b25ebc5b8644d80',1,'vg::Mapper']]],
- ['sort_5fby_5fchain_5fscore_13472',['sort_by_chain_score',['../classvg_1_1MinimizerMapper.html#a1006ffeadb8f60e819d8cfbf24e33109',1,'vg::MinimizerMapper']]],
- ['sort_5fvalue_13473',['sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a0c2510fe5ebea3b2a8cc9105e5a9d9fc',1,'vg::ZipCodeForest::sort_value_t']]],
- ['sort_5fvalues_5fby_5fseed_13474',['sort_values_by_seed',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a94161554748068a953a678af49bc31b7',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['source_13475',['source',['../structvg_1_1GFFRecord.html#a5bc594d1d69edca2081740dcc5e27bbf',1,'vg::GFFRecord::source()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a440d7f98f38d52de226e584f88784381',1,'vg::SnarlDistanceIndexClusterer::Seed::source()'],['../classvg_1_1algorithms_1_1TracedScore.html#aefa6367efc91b8d4e0964cd66e4f51d7',1,'vg::algorithms::TracedScore::source()']]],
- ['source_5ffwd_13476',['source_fwd',['../classvg_1_1SourceSinkOverlay.html#ae2d7c52a07eeef273ad95972c158c940',1,'vg::SourceSinkOverlay']]],
- ['source_5fid_13477',['source_id',['../classvg_1_1SourceSinkOverlay.html#a3bc0ab05f0048a8a6b8a31055b3d35c0',1,'vg::SourceSinkOverlay']]],
- ['source_5fnodes_13478',['source_nodes',['../classvg_1_1BandedGlobalAligner.html#a15f4ae7556005bd51512b6be93112291',1,'vg::BandedGlobalAligner']]],
- ['source_5fpaths_13479',['source_paths',['../classvg_1_1Sampler.html#aea2c52dbdae36a6729621fe3279c2d61',1,'vg::Sampler::source_paths()'],['../classvg_1_1NGSSimulator.html#ac377f66a4c6d84f5cb660950d56022ff',1,'vg::NGSSimulator::source_paths()']]],
- ['source_5frev_13480',['source_rev',['../classvg_1_1SourceSinkOverlay.html#a4ad14a56e07ef3fdc3a0346f4f6e0e05',1,'vg::SourceSinkOverlay']]],
- ['space_5fefficient_5fcounting_13481',['space_efficient_counting',['../structvg_1_1IndexingParameters.html#ad22ab98cf3f06bb2c033578dc15ae49e',1,'vg::IndexingParameters']]],
- ['sparse_5fto_5fdense_13482',['sparse_to_dense',['../classvg_1_1SparseUnionFind.html#a4c161121ec4681cee764e1c261af865d',1,'vg::SparseUnionFind']]],
- ['splice_5frescue_5fgraph_5fstd_5fdevs_13483',['splice_rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#a0fcadd278d752aba5c9bb143f5f3a0d6',1,'vg::MultipathMapper']]],
- ['splice_5fstats_13484',['splice_stats',['../classvg_1_1MultipathMapper.html#a64556e12bae6880e876d0d16fe44efb9',1,'vg::MultipathMapper']]],
- ['spliced_5fdefault_5fsubgraph_5flimit_13485',['SPLICED_DEFAULT_SUBGRAPH_LIMIT',['../classvg_1_1Surjector.html#a8af3e56b9463fbbf483e78477f4a7172',1,'vg::Surjector']]],
- ['split_5fread_5flimit_13486',['split_read_limit',['../classvg_1_1Filter.html#a0a0eca1fab7afdaec1d6311116dfe4a4',1,'vg::Filter']]],
- ['split_5fsupports_13487',['split_supports',['../structvg_1_1BREAKPOINT.html#ad93eef0590346c5658ceb194c78204c5',1,'vg::BREAKPOINT']]],
- ['stack_5fdata_13488',['stack_data',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a8c90da41cf4a8c9beb5794ce8bb0bd1c',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['stage_5fname_13489',['stage_name',['../classvg_1_1Funnel.html#a832c7d0be58aa6fa1e8dd8e7780e6850',1,'vg::Funnel']]],
- ['stage_5fstart_5ftime_13490',['stage_start_time',['../classvg_1_1Funnel.html#a74a7f57094e7e1a8040ed9df34932aee',1,'vg::Funnel']]],
- ['stages_13491',['stages',['../classvg_1_1Funnel.html#a48bdc3457d5f66a3f454bcde8d42883e',1,'vg::Funnel']]],
- ['standard_5flibrary_13492',['STANDARD_LIBRARY',['../classvg_1_1Version.html#a679d78a021abc99f587596a38e2fbf84',1,'vg::Version']]],
- ['star_5fallele_13493',['star_allele',['../classvg_1_1Deconstructor.html#a11591e3c8e54882b5c695f691cec6a62',1,'vg::Deconstructor']]],
- ['start_13494',['start',['../structvg_1_1BREAKPOINT.html#a624e7af692ef989d559a3e14e5075d4b',1,'vg::BREAKPOINT::start()'],['../structvg_1_1GFFRecord.html#a1515c4a06b600c34d84b012b0195423a',1,'vg::GFFRecord::start()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#af564269e9eaf8eb68f4c4c3ce1ba3932',1,'vg::GraphSynchronizer::Lock::start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af3baaf52c08ac684ac2571a9f4f56ec0',1,'vg::Haplotypes::Subchain::start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a16932e227f0ac0972fb63bc300a5374d',1,'vg::HaplotypePartitioner::Subchain::start()'],['../structvg_1_1Region.html#a3905a368a833ae5f090f3faafa1b55bc',1,'vg::Region::start()'],['../classvg_1_1NetGraph.html#a2d7b0b659aae1f47312bb76aae43dda0',1,'vg::NetGraph::start()'],['../classvg_1_1algorithms_1_1Anchor.html#a67c31c873448badab1dab33385f290bc',1,'vg::algorithms::Anchor::start()'],['../structMappingRun.html#ae556594581cecb906e1972405df7c460',1,'MappingRun::start()'],['../structReferenceInterval.html#aaeb76d7fd3436409b6bf5500350527dd',1,'ReferenceInterval::start()'],['../structvg_1_1Range.html#a372fbc9ba00e9eb4785fcd049b2451cf',1,'vg::Range::start()'],['../structgafkluge_1_1GafStep.html#abd90c68888f2f19e733a03597e520d2f',1,'gafkluge::GafStep::start()'],['../structvg_1_1MultipathAlignment.html#a8003b8991108e99465d8fd80fc74cc03',1,'vg::MultipathAlignment::start()'],['../structvg_1_1Snarl.html#a2a35b60b251ab2d8429b6afcd387448f',1,'vg::Snarl::start()']]],
- ['start_5fend_5freachable_13495',['start_end_reachable',['../structvg_1_1Snarl.html#acab3c449de2871769eb9a39ba5f9b8f8',1,'vg::Snarl']]],
- ['start_5foffset_13496',['start_offset',['../classvg_1_1algorithms_1_1Anchor.html#af25f1f44ad6e51d8f5d318a9b2d816f9',1,'vg::algorithms::Anchor']]],
- ['start_5fpos_13497',['start_pos',['../classvg_1_1MEMClusterer_1_1HitNode.html#ac1772330432b54080ac41ec1a4302d8d',1,'vg::MEMClusterer::HitNode::start_pos()'],['../classvg_1_1algorithms_1_1Anchor.html#a78487c55bbc790fc1f2a05396ded3530',1,'vg::algorithms::Anchor::start_pos()']]],
- ['start_5fpos_5fsamplers_13498',['start_pos_samplers',['../classvg_1_1NGSSimulator.html#abe06d132967858ffa36a6f5235a506f2',1,'vg::NGSSimulator']]],
- ['start_5fseed_13499',['start_seed',['../classvg_1_1algorithms_1_1Anchor.html#a3eb9aa25a9ead7787d829468c571bdd0',1,'vg::algorithms::Anchor']]],
- ['start_5fself_5freachable_13500',['start_self_reachable',['../structvg_1_1Snarl.html#a9a2de860018e3c8cfd512f6a1904f18c',1,'vg::Snarl']]],
- ['start_5ftime_13501',['start_time',['../classvg_1_1Funnel.html#af72a0ecffb7bd38fcd89ee3c71dd638b',1,'vg::Funnel']]],
- ['start_5fzip_13502',['start_zip',['../classvg_1_1algorithms_1_1Anchor.html#a7cd7ad6f5f36dfb5c760ac995a258d88',1,'vg::algorithms::Anchor']]],
- ['state_13503',['state',['../structvg_1_1WFANode.html#ac59b2dd030133cc65cc0bf47af486ef0',1,'vg::WFANode::state()'],['../structvg_1_1GaplessExtension.html#a1b799cab247ae9b2551e902a9f7f2b25',1,'vg::GaplessExtension::state()'],['../classvg_1_1GenomeState.html#ab0f68d58776dcd18a1ef85409a29e452',1,'vg::GenomeState::state()'],['../structhaplo_1_1haplo__DP__rectangle.html#aff798553a0dfd177413b1649e049e574',1,'haplo::haplo_DP_rectangle::state()'],['../classvg_1_1Watchdog.html#a0cecf66da11a5f71e837a9d1b6f6c291',1,'vg::Watchdog::state()']]],
- ['states_13504',['states',['../classvg_1_1PhaseUnfolder.html#ac7d3333de41989b2ca10db84ddb1d5a8',1,'vg::PhaseUnfolder']]],
- ['stdev_13505',['stdev',['../structvg_1_1SummaryStatistics.html#abea415bc0808b7714dee7cb6556dcf30',1,'vg::SummaryStatistics']]],
- ['step_13506',['step',['../structvg_1_1Range.html#a05a0a35957e0a0e127b9ef55a305df76',1,'vg::Range::step()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a44f22277ea90f802ae502bdb5bf8e478',1,'handlegraph::PathForEachSocket::iterator::step()']]],
- ['steps_13507',['steps',['../classvg_1_1IndexingPlan.html#afe22bdcd727f981fb262b8d29819dee2',1,'vg::IndexingPlan']]],
- ['steps_5fof_5fhandle_5fmemo_13508',['steps_of_handle_memo',['../classvg_1_1MemoizingGraph.html#ac2e7cde55ff928b866d7e26caccdd35e',1,'vg::MemoizingGraph']]],
- ['stop_5fon_5fduplicate_5fpaths_13509',['stop_on_duplicate_paths',['../classvg_1_1algorithms_1_1GFAParser.html#abe8f148f7941fc1fbc449687b9623c21',1,'vg::algorithms::GFAParser']]],
- ['stop_5ftime_13510',['stop_time',['../classvg_1_1Funnel.html#a59b3ea467d461a57b8801c8845b0bdb3',1,'vg::Funnel']]],
- ['stop_5fwatcher_13511',['stop_watcher',['../classvg_1_1Watchdog.html#a2fbb9a2b514a26515e508ee665295449',1,'vg::Watchdog']]],
- ['stored_5fcrash_5fcontext_13512',['stored_crash_context',['../namespacevg.html#aeb1b2d0c77858355b8bfbbe4406f0931',1,'vg']]],
- ['strand_13513',['strand',['../structgafkluge_1_1GafRecord.html#a38f3845982a15cf080267890fe7e0b3b',1,'gafkluge::GafRecord']]],
- ['strand_5fis_5frev_13514',['strand_is_rev',['../structvg_1_1GFFRecord.html#a08edb7d13481c70c0cfbba949e4f81ce',1,'vg::GFFRecord']]],
- ['strand_5fsampler_13515',['strand_sampler',['../classvg_1_1NGSSimulator.html#a71a4b2c30a477a86d4b7c9f5d6ab3a28',1,'vg::NGSSimulator']]],
- ['strict_5fconflict_5fchecking_13516',['strict_conflict_checking',['../classvg_1_1Deconstructor.html#a565e2bb8d83d007a630f8f3db37c8b43',1,'vg::Deconstructor']]],
- ['strip_5fbonuses_13517',['strip_bonuses',['../classvg_1_1BaseMapper.html#a34ab4a12d44f5b17b5b6caa03ea4cd79',1,'vg::BaseMapper']]],
- ['stripped_5fmatch_5falg_5fmax_5flength_13518',['stripped_match_alg_max_length',['../classvg_1_1MultipathMapper.html#aee2a7d30863137faeb2b9925c195262d',1,'vg::MultipathMapper']]],
- ['stripped_5fmatch_5falg_5fstrip_5flength_13519',['stripped_match_alg_strip_length',['../classvg_1_1MultipathMapper.html#a892c094e2a5b4dcce87b47a0ee27bff8',1,'vg::MultipathMapper']]],
- ['stripped_5fmatch_5falg_5ftarget_5fcount_13520',['stripped_match_alg_target_count',['../classvg_1_1MultipathMapper.html#a3a8af36f7fbbe431ea804f83e75a684d',1,'vg::MultipathMapper']]],
- ['sub_5fdurations_13521',['sub_durations',['../structvg_1_1Funnel_1_1Stage.html#af090e9aa3d82046a91766e05cdec814d',1,'vg::Funnel::Stage']]],
- ['sub_5fmem_5fcount_5fthinning_13522',['sub_mem_count_thinning',['../classvg_1_1BaseMapper.html#a8d9a00e1d809346bc62f6f2c1e4fbe32',1,'vg::BaseMapper']]],
- ['sub_5fmem_5fthinning_5fburn_5fin_13523',['sub_mem_thinning_burn_in',['../classvg_1_1BaseMapper.html#a4e17a40bafbd8832d551acb01298403d',1,'vg::BaseMapper']]],
- ['sub_5fpoly_5frate_13524',['sub_poly_rate',['../classvg_1_1NGSSimulator.html#a2078f130a3782a67206ad9c2c20067ea',1,'vg::NGSSimulator']]],
- ['sub_5fscore_13525',['sub_score',['../classvg_1_1ReadFilter.html#a529c0b978b3855bab3dc1074fd18a711',1,'vg::ReadFilter']]],
- ['subchain_5fid_13526',['subchain_id',['../structHaplotypesConfig.html#ae5e75f47f0768d4e5da28a15baaa702e',1,'HaplotypesConfig']]],
- ['subchain_5flength_13527',['SUBCHAIN_LENGTH',['../classvg_1_1HaplotypePartitioner.html#a3343e960c394c9c092d08ff931f37081',1,'vg::HaplotypePartitioner::SUBCHAIN_LENGTH()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#ac912479fc22acc7c9078978e71597ad9',1,'vg::HaplotypePartitioner::Parameters::subchain_length()']]],
- ['subchains_13528',['subchains',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ae31e41720bb3a859e4762aa9e2c5318b',1,'vg::Haplotypes::TopLevelChain::subchains()'],['../structvg_1_1Recombinator_1_1Statistics.html#ab6d38eac9e036f7b2b0f19736529e3a9',1,'vg::Recombinator::Statistics::subchains()']]],
- ['subgraph_13529',['subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aae76f24549ed2f49dc12176f46dfea8d',1,'vg::GraphSynchronizer::Lock::subgraph()'],['../classvg_1_1SpliceRegion.html#aa12379182f8abfc5239c38b433d1b4b8',1,'vg::SpliceRegion::subgraph()']]],
- ['subgraph_5fmin_13530',['subgraph_min',['../structPruningParameters.html#ada52c2750edf0333574238f15adb1c84',1,'PruningParameters']]],
- ['subgraph_5fprune_13531',['subgraph_prune',['../classvg_1_1VariantAdder.html#a39e87cff1b1cf12920a36b78bdcc2ddc',1,'vg::VariantAdder']]],
- ['subgroups_13532',['subgroups',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a17a3b23ed098272dfa4f3a9226ac5bef',1,'vg::subcommand::GroupedOptionGroup']]],
- ['subpath_13533',['subpath',['../structvg_1_1MultipathAlignment.html#aa92c4cbfee9b5e076c41ca466b44617c',1,'vg::MultipathAlignment']]],
- ['subpath_5fhandles_13534',['subpath_handles',['../classvg_1_1SubpathOverlay.html#ab1edd258ddd2cce726bfbc79b32b2476',1,'vg::SubpathOverlay']]],
- ['subpath_5fto_5flength_13535',['subpath_to_length',['../classvg_1_1HTSWriter.html#a24dca4e57dcfb498da8f18946194f600',1,'vg::HTSWriter']]],
- ['subsequences_13536',['subsequences',['../classvg_1_1ReadFilter.html#a98cd220c402ec88c512121825ed690df',1,'vg::ReadFilter']]],
- ['substage_5fname_13537',['substage_name',['../classvg_1_1Funnel.html#a4cfa61145fcd97f5710c3d609e72a997',1,'vg::Funnel']]],
- ['substage_5fstart_5ftime_13538',['substage_start_time',['../classvg_1_1Funnel.html#ae8b9248bf65562b44ac8b65f50619c70',1,'vg::Funnel']]],
- ['suffix_13539',['suffix',['../classvg_1_1IndexFile.html#acc1a7b94cb2a464d4941e7092aa83612',1,'vg::IndexFile']]],
- ['suffixes_13540',['suffixes',['../classvg_1_1PhaseUnfolder.html#a8e235a2b6022ec40a6e66c63c8dd1df0',1,'vg::PhaseUnfolder']]],
- ['suggested_5fedges_13541',['suggested_edges',['../classvg_1_1DiagramExplainer.html#a14bbd52421b049d538e13a357209b9ff',1,'vg::DiagramExplainer']]],
- ['sum_13542',['sum',['../structhaplo_1_1haplo__DP__column.html#aeb237931ba6de582496ded7d42517f3a',1,'haplo::haplo_DP_column']]],
- ['super_13543',['super',['../classvg_1_1PathSubgraph.html#a223501d50e8c102bbd7bf602d19b9400',1,'vg::PathSubgraph::super()'],['../classvg_1_1SubHandleGraph.html#aa17f9e8ba0b1b374b852390a9bf0c56a',1,'vg::SubHandleGraph::super()'],['../classvg_1_1TreeSubgraph.html#a1096d8426347b21730e2d7d81527ffc0',1,'vg::TreeSubgraph::super()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ad63f143f0bebc5d600dca495e9fdff77',1,'handlegraph::algorithms::SubHandleGraph::super()']]],
- ['support_13544',['support',['../structvg_1_1Locus.html#a42e45ba2fa1310b9fba6774b24cdd447',1,'vg::Locus::support()'],['../structvg_1_1LocationSupport.html#a479f1a778e85f8d3747c0b7c44ad5760',1,'vg::LocationSupport::support()']]],
- ['support_5ffinder_13545',['support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a2af17a0bf619778576c49627563994dc',1,'vg::SupportBasedSnarlCaller']]],
- ['suppress_5fcluster_5fmerging_13546',['suppress_cluster_merging',['../classvg_1_1MultipathMapper.html#ad25f17a8c485548abf5f63517937067f',1,'vg::MultipathMapper']]],
- ['suppress_5fmismapping_5fdetection_13547',['suppress_mismapping_detection',['../classvg_1_1MultipathMapper.html#a514a648b0822a7c74e853ab78aed7d95',1,'vg::MultipathMapper']]],
- ['suppress_5fmulticomponent_5fsplitting_13548',['suppress_multicomponent_splitting',['../classvg_1_1MultipathMapper.html#a2dae3baa09f211a0762d121a6c48dc58',1,'vg::MultipathMapper']]],
- ['suppress_5fp_5fvalue_5fmemoization_13549',['suppress_p_value_memoization',['../classvg_1_1MultipathMapper.html#afd6fee3779079af7a2932c7c29098b2d',1,'vg::MultipathMapper']]],
- ['suppress_5ftail_5fanchors_13550',['suppress_tail_anchors',['../classvg_1_1MultipathMapper.html#ad4c0e1fea285f378ef5c7eb23e9baf89',1,'vg::MultipathMapper']]],
- ['surface_13551',['surface',['../classvg_1_1Viz.html#ad93aa239a30c3b7a017348e22f184b85',1,'vg::Viz']]],
- ['surject_5fsubpath_5fglobal_13552',['surject_subpath_global',['../classvg_1_1SurjectingAlignmentEmitter.html#a730237d7e198244c27b29aff8a7d8b7d',1,'vg::SurjectingAlignmentEmitter']]],
- ['surjector_13553',['surjector',['../classvg_1_1SurjectingAlignmentEmitter.html#a7ff6c0ffab9177150fe4941a8ae71c70',1,'vg::SurjectingAlignmentEmitter']]],
- ['sv_5ftype_13554',['SV_TYPE',['../structvg_1_1BREAKPOINT.html#a52c38d41e036406a3c2e79d9f4bbfc50',1,'vg::BREAKPOINT']]],
- ['symbol_5fcount_13555',['symbol_count',['../classvg_1_1Pictographs.html#a38abbb70a4bdb0b40e5beb2b43cee1d5',1,'vg::Pictographs']]],
- ['symbolic_5fallele_5fwarnings_13556',['symbolic_allele_warnings',['../classvg_1_1Constructor.html#a245d775942ede32387b95497803e114c',1,'vg::Constructor']]],
- ['symbols_13557',['symbols',['../classvg_1_1Pictographs.html#a2504adc26acf0c09e9cccb06e80e1d7b',1,'vg::Pictographs']]],
- ['sync_13558',['sync',['../classvg_1_1VariantAdder.html#abc5742437534663752fccb79b5302b42',1,'vg::VariantAdder']]],
- ['synchronizer_13559',['synchronizer',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad2fcccf51dbd2136c680322341847b78',1,'vg::GraphSynchronizer::Lock']]],
- ['syntax_13560',['syntax',['../vg_8proto.html#adbedb258e13546cc707a6ebb073a3d8a',1,'vg.proto']]]
+ ['s_5fbv_13372',['s_bv',['../classxg_1_1XG.html#ac8f0eaf8d0d58d489a6da321d8303c46',1,'xg::XG']]],
+ ['s_5fbv_5frank_13373',['s_bv_rank',['../classxg_1_1XG.html#a14eb778ecdf51cca8ced32eb42112200',1,'xg::XG']]],
+ ['s_5fbv_5fselect_13374',['s_bv_select',['../classxg_1_1XG.html#a45b6e0fcf1dd90f451df245f0ffc3e1c',1,'xg::XG']]],
+ ['s_5fiv_13375',['s_iv',['../classxg_1_1XG.html#aa8e40fcbfa8174b689067d87acd818be',1,'xg::XG']]],
+ ['safe_5fto_5fget_13376',['safe_to_get',['../classvg_1_1VcfBuffer.html#ac280837b05f233e4420c6e8a7bbef32b',1,'vg::VcfBuffer']]],
+ ['sam_5ffiles_13377',['sam_files',['../classvg_1_1HTSWriter.html#a57a7f16757fc6ce944636d69c48903cb',1,'vg::HTSWriter']]],
+ ['sam_5fheader_13378',['sam_header',['../classvg_1_1HTSWriter.html#a95cd5874834de9191faf18d39fef9534',1,'vg::HTSWriter']]],
+ ['sample_5fcounter_13379',['sample_counter',['../classvg_1_1NGSSimulator.html#ab162ca660d69f66c18c41516a1a69d24',1,'vg::NGSSimulator']]],
+ ['sample_5finterval_13380',['sample_interval',['../structvg_1_1RebuildParameters.html#aa4adeffb1f91f55c6f1709e6d1c9cfcb',1,'vg::RebuildParameters']]],
+ ['sample_5fname_13381',['sample_name',['../classvg_1_1VCFOutputCaller.html#a70e8288543e7facfb79f5211ce33fa7f',1,'vg::VCFOutputCaller::sample_name()'],['../classvg_1_1MCMCCaller.html#a59582bcf7ba0dc3ae52f3f9a7c8eb80c',1,'vg::MCMCCaller::sample_name()'],['../classvg_1_1MinimizerMapper.html#a2f47382b14baf0482c43034e6484d086',1,'vg::MinimizerMapper::sample_name()'],['../classvg_1_1MultipathAlignmentEmitter.html#a6fa324b9dee313b1fceab7bafa62db24',1,'vg::MultipathAlignmentEmitter::sample_name()'],['../structvg_1_1Alignment.html#ad823d9ed3f413faaf35700a41cfab6e7',1,'vg::Alignment::sample_name()'],['../structvg_1_1MultipathAlignment.html#a90d675553385456c66b572a88fa88650',1,'vg::MultipathAlignment::sample_name()']]],
+ ['sample_5fnames_13382',['sample_names',['../classvg_1_1Deconstructor.html#a56f3119a427b1076d0d0d5ca7f478832',1,'vg::Deconstructor']]],
+ ['sample_5fploidys_13383',['sample_ploidys',['../classvg_1_1Deconstructor.html#a337113fedde38a57458c9329ffd86aac',1,'vg::Deconstructor']]],
+ ['sample_5frange_13384',['sample_range',['../classvg_1_1HaplotypeIndexer.html#a53cb273305c8fb1c039581c1a1b3d76e',1,'vg::HaplotypeIndexer']]],
+ ['sample_5fto_5fhaplotypes_13385',['sample_to_haplotypes',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a5e006ad54f202447a37975fa4919481c',1,'vg::Deconstructor::NestingInfo']]],
+ ['sample_5fto_5fploidy_13386',['sample_to_ploidy',['../structvg_1_1ParentGenotypeInfo.html#a5ac680b0203fe3cccab8959c84f5d556',1,'vg::ParentGenotypeInfo']]],
+ ['sample_5funsheared_5fpaths_13387',['sample_unsheared_paths',['../classvg_1_1NGSSimulator.html#af7441bd12030f0e189aca5ba2e0b47ef',1,'vg::NGSSimulator']]],
+ ['samplers_13388',['samplers',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a8d2808d7b690045d11af93fd6619fbf7',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['samples_13389',['samples',['../structGBWTConfig.html#ae5a3dac168e1ea3d38ddd13f5097fa40',1,'GBWTConfig']]],
+ ['samples_5fin_5fbatch_13390',['samples_in_batch',['../classvg_1_1HaplotypeIndexer.html#a681bcf3fb6014ae885adb3dec25ff2fc',1,'vg::HaplotypeIndexer']]],
+ ['save_5fexplanations_13391',['save_explanations',['../classvg_1_1Explainer.html#a3510aece27ab20079a8a3e87fa702596',1,'vg::Explainer']]],
+ ['scc_5fcopy_5fcount_13392',['scc_copy_count',['../classvg_1_1DagifiedGraph.html#a780a2eb98c2a1ad1b106283048f95cf0',1,'vg::DagifiedGraph']]],
+ ['scc_5fof_5fhandle_13393',['scc_of_handle',['../classvg_1_1DagifiedGraph.html#afc531153860777849e241cd95ac06b03',1,'vg::DagifiedGraph']]],
+ ['score_13394',['score',['../classvg_1_1MEMChainModelVertex.html#a10cf4210b2f802b628111fe2cd1f309b',1,'vg::MEMChainModelVertex::score()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#aa0f6834e2a0860792afc6a701d3396c3',1,'vg::MEMClusterer::HitNode::score()'],['../structvg_1_1Funnel_1_1Item.html#a91b9d511109c7c561be120d3346ea3df',1,'vg::Funnel::Item::score()'],['../structvg_1_1WFAPoint.html#a6358c051265bfcc41d857f6df091eebb',1,'vg::WFAPoint::score()'],['../structvg_1_1GaplessExtension.html#a0989b2a97d4403b381dbf68768757d32',1,'vg::GaplessExtension::score()'],['../structvg_1_1WFAAlignment.html#a066d6b546e0308e8df7fc74f42d5de67',1,'vg::WFAAlignment::score()'],['../structvg_1_1Genotyper_1_1Affinity.html#aa0fa1b63d720aa196205be34ee80ee07',1,'vg::Genotyper::Affinity::score()'],['../structvg_1_1GFFRecord.html#aabb70a3b691d378e87cb3fc3fef418ac',1,'vg::GFFRecord::score()'],['../classvg_1_1AlignmentChainModelVertex.html#a207cf7885f1eb8d129d9f599791b0dea',1,'vg::AlignmentChainModelVertex::score()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a002868b55e87a630c4e4f1e1ff213008',1,'vg::MinimizerMapper::Minimizer::score()'],['../structvg_1_1Recombinator_1_1Statistics.html#a348046df697bf6a89261ecfcb6ac6765',1,'vg::Recombinator::Statistics::score()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#abe1c7432c38de20678f5a74798d96bd4',1,'vg::SnarlDistanceIndexClusterer::Cluster::score()'],['../classvg_1_1algorithms_1_1TracedScore.html#a6c63f6d5199ec14c3e912e06f74d9974',1,'vg::algorithms::TracedScore::score()'],['../structvg_1_1Alignment.html#a5c57b95a7ea122139a092427b592ebeb',1,'vg::Alignment::score()'],['../structvg_1_1Subpath.html#acffb5adff6c20c194740186323f1f484',1,'vg::Subpath::score()'],['../structvg_1_1Connection.html#a5e880c9306bb072e08ab6315bdbb1c6f',1,'vg::Connection::score()']]],
+ ['score_5fbound_13395',['score_bound',['../classvg_1_1WFATree.html#afdb599de97d172e2afde161ea0f8efc9',1,'vg::WFATree']]],
+ ['score_5fmatrix_13396',['score_matrix',['../classvg_1_1GSSWAligner.html#a9ad471080a267eb489e31523ef2b5f2b',1,'vg::GSSWAligner']]],
+ ['score_5foutput_13397',['score_output',['../structHaplotypesConfig.html#aea2a24fbc9fbe00f814c1b98d8607079',1,'HaplotypesConfig']]],
+ ['scores_13398',['scores',['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ab466534da431354516132617d0f14e95',1,'vg::Recombinator::LocalHaplotype']]],
+ ['scratch_13399',['scratch',['../structvg_1_1ChainIterator.html#a277447dceb98d18d597a73f2c790e15c',1,'vg::ChainIterator']]],
+ ['search_5fthreads_13400',['search_threads',['../structGBWTConfig.html#a1e999f204cdd3655aac4739f12b3265f',1,'GBWTConfig']]],
+ ['secondary_5frescue_5fattempts_13401',['secondary_rescue_attempts',['../classvg_1_1MultipathMapper.html#a0203a68c7b346ec30bf2854c78bb3434',1,'vg::MultipathMapper']]],
+ ['secondary_5frescue_5fscore_5fdiff_13402',['secondary_rescue_score_diff',['../classvg_1_1MultipathMapper.html#ac5ba763f99c22ff9feccb76333cf1039',1,'vg::MultipathMapper']]],
+ ['secondary_5frescue_5fsubopt_5fdiff_13403',['secondary_rescue_subopt_diff',['../classvg_1_1MultipathMapper.html#aee081b4a0ee6adadb2dff205a24a2c7a',1,'vg::MultipathMapper']]],
+ ['secondary_5fscore_13404',['secondary_score',['../structvg_1_1Alignment.html#a58502a21a2588a5ac8baaa6e31c81eb4',1,'vg::Alignment']]],
+ ['seed_13405',['seed',['../classvg_1_1MCMCGenotyper.html#aa2399e6a45d2595e08053cdb66207b37',1,'vg::MCMCGenotyper::seed()'],['../classvg_1_1NGSSimulator.html#a99ce1e3ba72956bbf9d1cbaa0fd89014',1,'vg::NGSSimulator::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a1430e1d0dccc75ffa1962408e6226a21',1,'vg::SnarlDistanceIndexClusterer::SeedCache::seed()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#aae124944787f51e8d8fc23cb274f0350',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::seed()'],['../classvg_1_1SpliceRegion.html#a10732e3be85dbecaf6d046ba52f9f716',1,'vg::SpliceRegion::seed()'],['../classvg_1_1StreamSorter.html#a8875748639a885dfacf261956a9b3ee4',1,'vg::StreamSorter::seed()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a38ffc441fe03ec44c1c089eba2b76ae2',1,'vg::ZipCodeTree::oriented_seed_t::seed()']]],
+ ['seed_5fcount_5fprefix_5fsum_13406',['seed_count_prefix_sum',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af787cd3652afaa91cdebf97673456004',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['seed_5findices_13407',['seed_indices',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ad587cbee5a1b577adbc9548a99f857b4',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['seed_5flength_13408',['seed_length',['../classvg_1_1algorithms_1_1Anchor.html#a739e4bcbda94fa20b8d99ad5340b5fc6',1,'vg::algorithms::Anchor']]],
+ ['seed_5fsort_5forder_13409',['seed_sort_order',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ae40d481f31fd4ece290a206482ed5a13',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['seeds_13410',['seeds',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a7451a72162f19b00d1bd44fc62be0297',1,'vg::BandedGlobalAligner::BAMatrix::seeds()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#a0531ebefe7a686d6624c7b5f60357aeb',1,'vg::SnarlDistanceIndexClusterer::Cluster::seeds()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ac8b2807cb1f656be384407ed36b1c926',1,'vg::ZipCodeForest::forest_growing_state_t::seeds()']]],
+ ['seek_13411',['seek',['../structhFILE__backend.html#a93b5b1dcb35560b106e1cccb38476ddb',1,'hFILE_backend']]],
+ ['seen_5fread_5fnames_13412',['seen_read_names',['../classvg_1_1ReadFilter.html#a613b00bb83a119d89911ed4315e4e24a',1,'vg::ReadFilter']]],
+ ['segment_5fto_5fname_13413',['segment_to_name',['../classvg_1_1FlatFileBackTranslation.html#a09f2373723a0f9901698cf8315a3f813',1,'vg::FlatFileBackTranslation']]],
+ ['segment_5ftranslation_13414',['segment_translation',['../structGBWTConfig.html#a8415ef08abc7ef4e9d854dc100d0df15',1,'GBWTConfig']]],
+ ['sense_5fto_5fstring_13415',['SENSE_TO_STRING',['../paths__main_8cpp.html#a16ad253f4e8c46b88b363e1ffc613c51',1,'paths_main.cpp']]],
+ ['separator_13416',['SEPARATOR',['../classhandlegraph_1_1PathMetadata.html#ac50cb6403ceaabd3f878e2c4f2195f56',1,'handlegraph::PathMetadata']]],
+ ['seq_13417',['seq',['../structvg_1_1kmer__t.html#a98b04ac70a36cf6feae80b03b3a32eb2',1,'vg::kmer_t::seq()'],['../structvg_1_1Region.html#a938cc852fd08f11656bdfbd204843017',1,'vg::Region::seq()'],['../structvg_1_1VG_1_1Plan.html#a4bb5a9fa8f5bb32c2e94d3c038f9cf95',1,'vg::VG::Plan::seq()'],['../structvg_1_1algorithms_1_1kmer__t.html#a5c235e7c7f3a819e291956d8e307821a',1,'vg::algorithms::kmer_t::seq()'],['../structvg_1_1algorithms_1_1walk__t.html#a65bec2a64da1b8f7c3820d49b5bef09f',1,'vg::algorithms::walk_t::seq()']]],
+ ['seq_5flength_13418',['seq_length',['../classvg_1_1Viz.html#a2f5862e76ca098060b503d03de76c024',1,'vg::Viz::seq_length()'],['../classxg_1_1XG.html#a7eadd7681a21479f7f31c240047cdffe',1,'xg::XG::seq_length()']]],
+ ['seq_5foffset_13419',['seq_offset',['../structvg_1_1MatchPos.html#a85fc0d2a7af86db887d649d3c968755e',1,'vg::MatchPos::seq_offset()'],['../structvg_1_1WFAPoint.html#a14ceda5614586a0e3ef44b729ad179c0',1,'vg::WFAPoint::seq_offset()'],['../structvg_1_1WFAAlignment.html#a1fc0e09c8462c5aa10d4f0acbc2a8f2d',1,'vg::WFAAlignment::seq_offset()']]],
+ ['sequence_13420',['sequence',['../classvg_1_1ExtraNodeGraph.html#ad485e6609536566720fe5a48f7e2af84',1,'vg::ExtraNodeGraph::sequence()'],['../classvg_1_1WFATree.html#abbd67ff2f910ad5a4c0c1f49b10394a5',1,'vg::WFATree::sequence()'],['../structvg_1_1PathIndex.html#a0b807b5252299d9b0f1c9168079a591f',1,'vg::PathIndex::sequence()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#a2e6f784aa4bde512d84c0f1d3cedd01f',1,'vg::Recombinator::LocalHaplotype::sequence()'],['../structvg_1_1Node.html#a9a0e8995bc48aa5e24977d1bd20e91a3',1,'vg::Node::sequence()'],['../structvg_1_1Edit.html#a4a7726b24b28ed819d37b9c39ae839d1',1,'vg::Edit::sequence()'],['../structvg_1_1Alignment.html#a2ae1f06d48c37997cee72b7cd3210a83',1,'vg::Alignment::sequence()'],['../structvg_1_1MultipathAlignment.html#ae6c263b75effad9b08e514c5852f1221',1,'vg::MultipathAlignment::sequence()'],['../structvg_1_1KmerMatch.html#ab434e30bbaf0fbb10425d5bc35ac50b2',1,'vg::KmerMatch::sequence()']]],
+ ['sequence_5fid_13421',['sequence_id',['../structvg_1_1GFFRecord.html#a91b952a4d9d5c4f44e6def80e33073c8',1,'vg::GFFRecord::sequence_id()'],['../structvg_1_1RecombinatorHaplotype.html#a3b372fd165a3e707a50e2a0a1f61cef5',1,'vg::RecombinatorHaplotype::sequence_id()']]],
+ ['sequence_5fsource_13422',['sequence_source',['../structGraphHandler.html#a1583ae5e2c88d3099b62255a28978316',1,'GraphHandler']]],
+ ['sequences_13423',['sequences',['../structvg_1_1Haplotypes_1_1Subchain.html#aae0d847a9118ccb4ff178c3ac7c759eb',1,'vg::Haplotypes::Subchain']]],
+ ['set_5frefpos_13424',['set_refpos',['../classvg_1_1MinimizerMapper.html#a7fe47fe6075b79253609a04601d0995e',1,'vg::MinimizerMapper']]],
+ ['sha1_5fvariant_5fname_13425',['sha1_variant_name',['../classvg_1_1Constructor.html#afafc25fc7021c48463894db9abce2f66',1,'vg::Constructor']]],
+ ['shift_5fprune_5fdiff_13426',['shift_prune_diff',['../classvg_1_1Surjector.html#a3768ca4fe69ba4c58cdbfe81343c56bd',1,'vg::Surjector']]],
+ ['short_5fmem_5ffilter_5ffactor_13427',['short_mem_filter_factor',['../classvg_1_1BaseMapper.html#ac92eb174ad81e8714bf43e4b08aecdb9',1,'vg::BaseMapper']]],
+ ['short_5foption_13428',['short_option',['../structvg_1_1subcommand_1_1BaseArgSpec.html#a60f696e33fce1e021b3454176ce0885f',1,'vg::subcommand::BaseArgSpec']]],
+ ['short_5foptions_13429',['short_options',['../classvg_1_1ConfigurableParser.html#adfde71f165bbcb110831c12e862aa891',1,'vg::ConfigurableParser']]],
+ ['short_5fopts_13430',['short_opts',['../classvg_1_1BaseOption.html#a04134150cfd3143bf1f43f55af5fd3d6',1,'vg::BaseOption']]],
+ ['short_5fread_5fminimizer_5fk_13431',['short_read_minimizer_k',['../structvg_1_1IndexingParameters.html#a74ed1f6b8e93329efc15654c9eac5749',1,'vg::IndexingParameters']]],
+ ['short_5fread_5fminimizer_5fw_13432',['short_read_minimizer_W',['../structvg_1_1IndexingParameters.html#a882b758e0f629a9cd2e9297b193c42df',1,'vg::IndexingParameters::short_read_minimizer_W()'],['../structvg_1_1IndexingParameters.html#acf0c2287ca7ee00853bd27af02757650',1,'vg::IndexingParameters::short_read_minimizer_w()']]],
+ ['show_5fcnv_13433',['show_cnv',['../classvg_1_1Viz.html#ace366df624ca2b225d3c8d20d9cb15db',1,'vg::Viz']]],
+ ['show_5fdna_13434',['show_dna',['../classvg_1_1Viz.html#a2b8e6f510bca9925fd39e37feddce251',1,'vg::Viz']]],
+ ['show_5fpath_5finfo_13435',['show_path_info',['../classvg_1_1Deconstructor.html#a6d2894dc3b9ea0fea97e2a78e11e2a51',1,'vg::Deconstructor']]],
+ ['show_5fpaths_13436',['show_paths',['../classvg_1_1Viz.html#a501ab25fb94a4d3abd508af7bc77aac3',1,'vg::Viz']]],
+ ['show_5fprogress_13437',['show_progress',['../structvg_1_1GBWTHandler.html#a7513df04845c0145e6933236346ec8fc',1,'vg::GBWTHandler::show_progress()'],['../structvg_1_1RebuildParameters.html#a4a86fbc222841919a70452f4a6e8c463',1,'vg::RebuildParameters::show_progress()'],['../classvg_1_1Genotyper.html#a72599c00acaed553e0d235e5c73d4b82',1,'vg::Genotyper::show_progress()'],['../classvg_1_1GraphCaller.html#a1179324159b5518ebd0eb7d5fb71edd5',1,'vg::GraphCaller::show_progress()'],['../classvg_1_1Progressive.html#a6653625f496832c4cb8711185d5e04cb',1,'vg::Progressive::show_progress()'],['../classvg_1_1Transcriptome.html#af92e5c3f2b2216b98f30f5518fc3b785',1,'vg::Transcriptome::show_progress()'],['../classvg_1_1VGset.html#aa848e2230f2d5c016c0a816cfa14501e',1,'vg::VGset::show_progress()'],['../structGBWTConfig.html#a075b0013542a10eb0708e94f20cb18a6',1,'GBWTConfig::show_progress()']]],
+ ['show_5fwork_13438',['show_work',['../classvg_1_1MinimizerMapper.html#a089bb5c8a56a7614a2f494690f3b5acd',1,'vg::MinimizerMapper']]],
+ ['sibling_5findices_5fat_5fdepth_13439',['sibling_indices_at_depth',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a0c95aeef3ec92915788ebf083154e265',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['sigma_13440',['sigma',['../classvg_1_1FragmentLengthDistribution.html#a6462bb11645a893b5dc2de057714d8f6',1,'vg::FragmentLengthDistribution']]],
+ ['simplify_5ftopologies_13441',['simplify_topologies',['../classvg_1_1MultipathMapper.html#a5f865a27bd34ffce2e2ea1d05fc02b43',1,'vg::MultipathMapper']]],
+ ['simultaneous_5fpair_5falignment_13442',['simultaneous_pair_alignment',['../classvg_1_1Mapper.html#ae83170a63789f8984e82e225486ca5bd',1,'vg::Mapper']]],
+ ['since_5flast_5ffragment_5flength_5festimate_13443',['since_last_fragment_length_estimate',['../classvg_1_1FragmentLengthStatistics.html#ae79e46e68a3b9aa6c87863a6354c01a2',1,'vg::FragmentLengthStatistics']]],
+ ['sink_5ffwd_13444',['sink_fwd',['../classvg_1_1SourceSinkOverlay.html#a2718021aade5e48683cdc07c5d5b16f7',1,'vg::SourceSinkOverlay']]],
+ ['sink_5fid_13445',['sink_id',['../classvg_1_1SourceSinkOverlay.html#a02ca8620a0e90dbf0190fe285d11a687',1,'vg::SourceSinkOverlay']]],
+ ['sink_5fnodes_13446',['sink_nodes',['../classvg_1_1BandedGlobalAligner.html#ad3ba4ffebb1e61d6ce59a995eac74f68',1,'vg::BandedGlobalAligner']]],
+ ['sink_5frev_13447',['sink_rev',['../classvg_1_1SourceSinkOverlay.html#a4c00143bd29d3f3adbf571f6333ea761',1,'vg::SourceSinkOverlay']]],
+ ['site_5fends_13448',['site_ends',['../classvg_1_1PhasedGenome.html#afc338c2bf1776ec1ccb29c8efee6aaa3',1,'vg::PhasedGenome']]],
+ ['site_5fmanager_13449',['site_manager',['../classvg_1_1SmallSnarlSimplifier.html#a4991294aedb029a70d1d4f459e009bd3',1,'vg::SmallSnarlSimplifier']]],
+ ['site_5fstarts_13450',['site_starts',['../classvg_1_1PhasedGenome.html#accfaae53e12f924b914623734a68102f',1,'vg::PhasedGenome']]],
+ ['sites_13451',['sites',['../classvg_1_1PhasedGenome_1_1Haplotype.html#a7fee7818b260154898be386649d3bfe7',1,'vg::PhasedGenome::Haplotype']]],
+ ['size_13452',['size',['../classvg_1_1algorithms_1_1Anchor.html#a96921a8307e8e97ba77869b58d6d7292',1,'vg::algorithms::Anchor::size()'],['../structjob__type.html#adbc606f42800cfce3697b017578356b9',1,'job_type::size()']]],
+ ['size_5ft_5fis_5fnonzero_13453',['size_t_is_nonzero',['../namespacevg_1_1subcommand.html#a62e7f4f685f1aabc28ff82aa02f00f7f',1,'vg::subcommand']]],
+ ['size_5ft_5fis_5fpositive_13454',['size_t_is_positive',['../namespacevg_1_1subcommand.html#ae20ec7174b0b153b2657c4931dcca448',1,'vg::subcommand']]],
+ ['skip_5falt_13455',['skip_alt',['../classvg_1_1VCFTraversalFinder.html#acc753182667fd49d9afe5eba697c92da',1,'vg::VCFTraversalFinder']]],
+ ['skip_5fstructural_5fduplications_13456',['skip_structural_duplications',['../classvg_1_1VariantAdder.html#a0c90a9845a662358588f517e2cf91501',1,'vg::VariantAdder']]],
+ ['skippable_13457',['skippable',['../classvg_1_1algorithms_1_1Anchor.html#ade34685bea83f218a9756478bcca25a0',1,'vg::algorithms::Anchor']]],
+ ['snarl_13458',['snarl',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#aee85ad3c21e883f05b67c62fbf05be72',1,'vg::ReplaceSnarlHaplotypeCommand::snarl()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#acad9926afa69d4de3d5424ac1f03582d',1,'vg::SnarlManager::SnarlRecord::snarl()'],['../structvg_1_1Visit.html#a7e671bbc7437a16dd3549a6fc49fd2a9',1,'vg::Visit::snarl()']]],
+ ['snarl_5fcaller_13459',['snarl_caller',['../classvg_1_1GraphCaller.html#a4b8c6f32019db8528bb6835fdce12ddb',1,'vg::GraphCaller']]],
+ ['snarl_5fchain_5fcomponent_5foffset_13460',['SNARL_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#a807c487a518301d1726f87f7eda443a4',1,'vg::ZipCode']]],
+ ['snarl_5fchild_5fcount_5foffset_13461',['SNARL_CHILD_COUNT_OFFSET',['../classvg_1_1ZipCode.html#a37503629f90af0de452b6bc534ad43f5',1,'vg::ZipCode']]],
+ ['snarl_5finto_13462',['snarl_into',['../classvg_1_1SnarlManager.html#a0f1d327aa074d59976802999d0d179d1',1,'vg::SnarlManager']]],
+ ['snarl_5fis_5fregular_5foffset_13463',['SNARL_IS_REGULAR_OFFSET',['../classvg_1_1ZipCode.html#ad56c1879d223a2151795d2532932d1c8',1,'vg::ZipCode']]],
+ ['snarl_5flength_5foffset_13464',['SNARL_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#ade2f247378ce48537e06399e215013d5',1,'vg::ZipCode']]],
+ ['snarl_5fmanager_13465',['snarl_manager',['../classvg_1_1GraphCaller.html#a55afa68762956066ccbea2e332342266',1,'vg::GraphCaller::snarl_manager()'],['../classvg_1_1SnarlGraph.html#a292ca2c610a5f06fd06325f193557823',1,'vg::SnarlGraph::snarl_manager()'],['../classvg_1_1Masker.html#a4554deca5d95bdb68843ca7a656170fa',1,'vg::Masker::snarl_manager()'],['../classvg_1_1MCMCCaller.html#a4dad48c8bc658476ff4a6b0ed22817de',1,'vg::MCMCCaller::snarl_manager()'],['../classvg_1_1MultipathMapper.html#a82e1a1af4b8ba0170cf7817cd44f1008',1,'vg::MultipathMapper::snarl_manager()'],['../classvg_1_1NestedTraversalFinder.html#a3b15745919bd3bd7427d487eea14884b',1,'vg::NestedTraversalFinder::snarl_manager()'],['../classvg_1_1PhasedGenome.html#a56494287a449d9b95f24ac7d0e505522',1,'vg::PhasedGenome::snarl_manager()'],['../classvg_1_1RegionExpander.html#ac7c7121e538614d43356e7318769db65',1,'vg::RegionExpander::snarl_manager()'],['../classvg_1_1SupportBasedSnarlCaller.html#a86c40f2d62950d1f484aa6dd84abf60d',1,'vg::SupportBasedSnarlCaller::snarl_manager()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a8e29fb04ba5a9516d74d1da133f06330',1,'vg::ExhaustiveTraversalFinder::snarl_manager()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#a0c4e67f35a6f1e8536a81a781c7cba22',1,'vg::ReadRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a015de241431375a1b43ac32b852246f6',1,'vg::PathRestrictedTraversalFinder::snarl_manager()'],['../classvg_1_1RepresentativeTraversalFinder.html#a48de8b31240c6ddda7ff40164ae7708b',1,'vg::RepresentativeTraversalFinder::snarl_manager()'],['../classvg_1_1VCFTraversalFinder.html#ae2fac6aac1b86163b495ef183e3340d9',1,'vg::VCFTraversalFinder::snarl_manager()'],['../classvg_1_1FlowTraversalFinder.html#ab0f619b27f1f2d911e6625ab61ecddeb',1,'vg::FlowTraversalFinder::snarl_manager()'],['../classvg_1_1TraversalSupportFinder.html#adc97ab06de5c4aa553db92bae3879ee5',1,'vg::TraversalSupportFinder::snarl_manager()']]],
+ ['snarl_5fnumber_13466',['snarl_number',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#add50ce54457a4031ed0d8fd0b3b34e9f',1,'vg::SnarlManager::SnarlRecord']]],
+ ['snarl_5foffset_5fin_5fchain_5foffset_13467',['SNARL_OFFSET_IN_CHAIN_OFFSET',['../classvg_1_1ZipCode.html#a65ff5123c5439118b1b390179cffd818',1,'vg::ZipCode']]],
+ ['snarl_5frank_5for_5fidentifier_13468',['snarl_rank_or_identifier',['../structvg_1_1ZipCode_1_1chain__code__t.html#a4859d74d9e82058d5e6066dd0e99470e',1,'vg::ZipCode::chain_code_t']]],
+ ['snarl_5freference_5flength_5fhistogram_13469',['snarl_reference_length_histogram',['../classvg_1_1Genotyper.html#ac0d4917131823fc2dab43927347d4623',1,'vg::Genotyper']]],
+ ['snarl_5ftraversals_13470',['snarl_traversals',['../classvg_1_1Genotyper.html#a7ec1915674299d727c61377e91385974',1,'vg::Genotyper']]],
+ ['snarlmanager_13471',['snarlmanager',['../classvg_1_1PathBasedTraversalFinder.html#a905239f50078de78279dd9f0ff82faf3',1,'vg::PathBasedTraversalFinder']]],
+ ['snarls_13472',['snarls',['../classvg_1_1SnarlGraph.html#ac9db23e9d10f3c39f25a5397afb9d4fa',1,'vg::SnarlGraph::snarls()'],['../classvg_1_1MCMCGenotyper.html#a23913225e8b2d0d4dfbdb713ccf495c3',1,'vg::MCMCGenotyper::snarls()'],['../classvg_1_1SnarlManager.html#ab56cf756bc65189eeb1d4f1f3f6573b6',1,'vg::SnarlManager::snarls()']]],
+ ['soft_5fclip_5flimit_13473',['soft_clip_limit',['../classvg_1_1Filter.html#abe44432fa541eee27db7789cc9db066b',1,'vg::Filter']]],
+ ['soft_5fclipped_13474',['soft_clipped',['../structvg_1_1Alignment.html#a6cb12eae3f4fa017bc98b59a91a5414f',1,'vg::Alignment']]],
+ ['softclip_5fthreshold_13475',['softclip_threshold',['../classvg_1_1Mapper.html#a4320fc9bb3cda3bd7b25ebc5b8644d80',1,'vg::Mapper']]],
+ ['sort_5fby_5fchain_5fscore_13476',['sort_by_chain_score',['../classvg_1_1MinimizerMapper.html#a1006ffeadb8f60e819d8cfbf24e33109',1,'vg::MinimizerMapper']]],
+ ['sort_5fvalue_13477',['sort_value',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a0c2510fe5ebea3b2a8cc9105e5a9d9fc',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['sort_5fvalues_5fby_5fseed_13478',['sort_values_by_seed',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a94161554748068a953a678af49bc31b7',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['source_13479',['source',['../structvg_1_1GFFRecord.html#a5bc594d1d69edca2081740dcc5e27bbf',1,'vg::GFFRecord::source()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a440d7f98f38d52de226e584f88784381',1,'vg::SnarlDistanceIndexClusterer::Seed::source()'],['../classvg_1_1algorithms_1_1TracedScore.html#aefa6367efc91b8d4e0964cd66e4f51d7',1,'vg::algorithms::TracedScore::source()']]],
+ ['source_5ffwd_13480',['source_fwd',['../classvg_1_1SourceSinkOverlay.html#ae2d7c52a07eeef273ad95972c158c940',1,'vg::SourceSinkOverlay']]],
+ ['source_5fid_13481',['source_id',['../classvg_1_1SourceSinkOverlay.html#a3bc0ab05f0048a8a6b8a31055b3d35c0',1,'vg::SourceSinkOverlay']]],
+ ['source_5fnodes_13482',['source_nodes',['../classvg_1_1BandedGlobalAligner.html#a15f4ae7556005bd51512b6be93112291',1,'vg::BandedGlobalAligner']]],
+ ['source_5fpaths_13483',['source_paths',['../classvg_1_1Sampler.html#aea2c52dbdae36a6729621fe3279c2d61',1,'vg::Sampler::source_paths()'],['../classvg_1_1NGSSimulator.html#ac377f66a4c6d84f5cb660950d56022ff',1,'vg::NGSSimulator::source_paths()']]],
+ ['source_5frev_13484',['source_rev',['../classvg_1_1SourceSinkOverlay.html#a4ad14a56e07ef3fdc3a0346f4f6e0e05',1,'vg::SourceSinkOverlay']]],
+ ['space_5fefficient_5fcounting_13485',['space_efficient_counting',['../structvg_1_1IndexingParameters.html#ad22ab98cf3f06bb2c033578dc15ae49e',1,'vg::IndexingParameters']]],
+ ['sparse_5fto_5fdense_13486',['sparse_to_dense',['../classvg_1_1SparseUnionFind.html#a4c161121ec4681cee764e1c261af865d',1,'vg::SparseUnionFind']]],
+ ['splice_5frescue_5fgraph_5fstd_5fdevs_13487',['splice_rescue_graph_std_devs',['../classvg_1_1MultipathMapper.html#a0fcadd278d752aba5c9bb143f5f3a0d6',1,'vg::MultipathMapper']]],
+ ['splice_5fstats_13488',['splice_stats',['../classvg_1_1MultipathMapper.html#a64556e12bae6880e876d0d16fe44efb9',1,'vg::MultipathMapper']]],
+ ['spliced_5fdefault_5fsubgraph_5flimit_13489',['SPLICED_DEFAULT_SUBGRAPH_LIMIT',['../classvg_1_1Surjector.html#a8af3e56b9463fbbf483e78477f4a7172',1,'vg::Surjector']]],
+ ['split_5fread_5flimit_13490',['split_read_limit',['../classvg_1_1Filter.html#a0a0eca1fab7afdaec1d6311116dfe4a4',1,'vg::Filter']]],
+ ['split_5fsupports_13491',['split_supports',['../structvg_1_1BREAKPOINT.html#ad93eef0590346c5658ceb194c78204c5',1,'vg::BREAKPOINT']]],
+ ['stack_5fdata_13492',['stack_data',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a8c90da41cf4a8c9beb5794ce8bb0bd1c',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['stage_5fname_13493',['stage_name',['../classvg_1_1Funnel.html#a832c7d0be58aa6fa1e8dd8e7780e6850',1,'vg::Funnel']]],
+ ['stage_5fstart_5ftime_13494',['stage_start_time',['../classvg_1_1Funnel.html#a74a7f57094e7e1a8040ed9df34932aee',1,'vg::Funnel']]],
+ ['stages_13495',['stages',['../classvg_1_1Funnel.html#a48bdc3457d5f66a3f454bcde8d42883e',1,'vg::Funnel']]],
+ ['standard_5flibrary_13496',['STANDARD_LIBRARY',['../classvg_1_1Version.html#a679d78a021abc99f587596a38e2fbf84',1,'vg::Version']]],
+ ['star_5fallele_13497',['star_allele',['../classvg_1_1Deconstructor.html#a11591e3c8e54882b5c695f691cec6a62',1,'vg::Deconstructor']]],
+ ['start_13498',['start',['../structvg_1_1BREAKPOINT.html#a624e7af692ef989d559a3e14e5075d4b',1,'vg::BREAKPOINT::start()'],['../structvg_1_1GFFRecord.html#a1515c4a06b600c34d84b012b0195423a',1,'vg::GFFRecord::start()'],['../classvg_1_1GraphSynchronizer_1_1Lock.html#af564269e9eaf8eb68f4c4c3ce1ba3932',1,'vg::GraphSynchronizer::Lock::start()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af3baaf52c08ac684ac2571a9f4f56ec0',1,'vg::Haplotypes::Subchain::start()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a16932e227f0ac0972fb63bc300a5374d',1,'vg::HaplotypePartitioner::Subchain::start()'],['../structvg_1_1Region.html#a3905a368a833ae5f090f3faafa1b55bc',1,'vg::Region::start()'],['../classvg_1_1NetGraph.html#a2d7b0b659aae1f47312bb76aae43dda0',1,'vg::NetGraph::start()'],['../classvg_1_1algorithms_1_1Anchor.html#a67c31c873448badab1dab33385f290bc',1,'vg::algorithms::Anchor::start()'],['../structMappingRun.html#ae556594581cecb906e1972405df7c460',1,'MappingRun::start()'],['../structReferenceInterval.html#aaeb76d7fd3436409b6bf5500350527dd',1,'ReferenceInterval::start()'],['../structvg_1_1Range.html#a372fbc9ba00e9eb4785fcd049b2451cf',1,'vg::Range::start()'],['../structgafkluge_1_1GafStep.html#abd90c68888f2f19e733a03597e520d2f',1,'gafkluge::GafStep::start()'],['../structvg_1_1MultipathAlignment.html#a8003b8991108e99465d8fd80fc74cc03',1,'vg::MultipathAlignment::start()'],['../structvg_1_1Snarl.html#a2a35b60b251ab2d8429b6afcd387448f',1,'vg::Snarl::start()']]],
+ ['start_5fend_5freachable_13499',['start_end_reachable',['../structvg_1_1Snarl.html#acab3c449de2871769eb9a39ba5f9b8f8',1,'vg::Snarl']]],
+ ['start_5foffset_13500',['start_offset',['../classvg_1_1algorithms_1_1Anchor.html#af25f1f44ad6e51d8f5d318a9b2d816f9',1,'vg::algorithms::Anchor']]],
+ ['start_5fpos_13501',['start_pos',['../classvg_1_1MEMClusterer_1_1HitNode.html#ac1772330432b54080ac41ec1a4302d8d',1,'vg::MEMClusterer::HitNode::start_pos()'],['../classvg_1_1algorithms_1_1Anchor.html#a78487c55bbc790fc1f2a05396ded3530',1,'vg::algorithms::Anchor::start_pos()']]],
+ ['start_5fpos_5fsamplers_13502',['start_pos_samplers',['../classvg_1_1NGSSimulator.html#abe06d132967858ffa36a6f5235a506f2',1,'vg::NGSSimulator']]],
+ ['start_5fseed_13503',['start_seed',['../classvg_1_1algorithms_1_1Anchor.html#a3eb9aa25a9ead7787d829468c571bdd0',1,'vg::algorithms::Anchor']]],
+ ['start_5fself_5freachable_13504',['start_self_reachable',['../structvg_1_1Snarl.html#a9a2de860018e3c8cfd512f6a1904f18c',1,'vg::Snarl']]],
+ ['start_5ftime_13505',['start_time',['../classvg_1_1Funnel.html#af72a0ecffb7bd38fcd89ee3c71dd638b',1,'vg::Funnel']]],
+ ['start_5fzip_13506',['start_zip',['../classvg_1_1algorithms_1_1Anchor.html#a7cd7ad6f5f36dfb5c760ac995a258d88',1,'vg::algorithms::Anchor']]],
+ ['state_13507',['state',['../structvg_1_1WFANode.html#ac59b2dd030133cc65cc0bf47af486ef0',1,'vg::WFANode::state()'],['../structvg_1_1GaplessExtension.html#a1b799cab247ae9b2551e902a9f7f2b25',1,'vg::GaplessExtension::state()'],['../classvg_1_1GenomeState.html#ab0f68d58776dcd18a1ef85409a29e452',1,'vg::GenomeState::state()'],['../structhaplo_1_1haplo__DP__rectangle.html#aff798553a0dfd177413b1649e049e574',1,'haplo::haplo_DP_rectangle::state()'],['../classvg_1_1Watchdog.html#a0cecf66da11a5f71e837a9d1b6f6c291',1,'vg::Watchdog::state()']]],
+ ['states_13508',['states',['../classvg_1_1PhaseUnfolder.html#ac7d3333de41989b2ca10db84ddb1d5a8',1,'vg::PhaseUnfolder']]],
+ ['stdev_13509',['stdev',['../structvg_1_1SummaryStatistics.html#abea415bc0808b7714dee7cb6556dcf30',1,'vg::SummaryStatistics']]],
+ ['step_13510',['step',['../structvg_1_1Range.html#a05a0a35957e0a0e127b9ef55a305df76',1,'vg::Range::step()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a44f22277ea90f802ae502bdb5bf8e478',1,'handlegraph::PathForEachSocket::iterator::step()']]],
+ ['steps_13511',['steps',['../classvg_1_1IndexingPlan.html#afe22bdcd727f981fb262b8d29819dee2',1,'vg::IndexingPlan']]],
+ ['steps_5fof_5fhandle_5fmemo_13512',['steps_of_handle_memo',['../classvg_1_1MemoizingGraph.html#ac2e7cde55ff928b866d7e26caccdd35e',1,'vg::MemoizingGraph']]],
+ ['stop_5fon_5fduplicate_5fpaths_13513',['stop_on_duplicate_paths',['../classvg_1_1algorithms_1_1GFAParser.html#abe8f148f7941fc1fbc449687b9623c21',1,'vg::algorithms::GFAParser']]],
+ ['stop_5ftime_13514',['stop_time',['../classvg_1_1Funnel.html#a59b3ea467d461a57b8801c8845b0bdb3',1,'vg::Funnel']]],
+ ['stop_5fwatcher_13515',['stop_watcher',['../classvg_1_1Watchdog.html#a2fbb9a2b514a26515e508ee665295449',1,'vg::Watchdog']]],
+ ['stored_5fcrash_5fcontext_13516',['stored_crash_context',['../namespacevg.html#aeb1b2d0c77858355b8bfbbe4406f0931',1,'vg']]],
+ ['strand_13517',['strand',['../structgafkluge_1_1GafRecord.html#a38f3845982a15cf080267890fe7e0b3b',1,'gafkluge::GafRecord']]],
+ ['strand_5fis_5frev_13518',['strand_is_rev',['../structvg_1_1GFFRecord.html#a08edb7d13481c70c0cfbba949e4f81ce',1,'vg::GFFRecord']]],
+ ['strand_5fsampler_13519',['strand_sampler',['../classvg_1_1NGSSimulator.html#a71a4b2c30a477a86d4b7c9f5d6ab3a28',1,'vg::NGSSimulator']]],
+ ['strict_5fconflict_5fchecking_13520',['strict_conflict_checking',['../classvg_1_1Deconstructor.html#a565e2bb8d83d007a630f8f3db37c8b43',1,'vg::Deconstructor']]],
+ ['strip_5fbonuses_13521',['strip_bonuses',['../classvg_1_1BaseMapper.html#a34ab4a12d44f5b17b5b6caa03ea4cd79',1,'vg::BaseMapper']]],
+ ['stripped_5fmatch_5falg_5fmax_5flength_13522',['stripped_match_alg_max_length',['../classvg_1_1MultipathMapper.html#aee2a7d30863137faeb2b9925c195262d',1,'vg::MultipathMapper']]],
+ ['stripped_5fmatch_5falg_5fstrip_5flength_13523',['stripped_match_alg_strip_length',['../classvg_1_1MultipathMapper.html#a892c094e2a5b4dcce87b47a0ee27bff8',1,'vg::MultipathMapper']]],
+ ['stripped_5fmatch_5falg_5ftarget_5fcount_13524',['stripped_match_alg_target_count',['../classvg_1_1MultipathMapper.html#a3a8af36f7fbbe431ea804f83e75a684d',1,'vg::MultipathMapper']]],
+ ['sub_5fdurations_13525',['sub_durations',['../structvg_1_1Funnel_1_1Stage.html#af090e9aa3d82046a91766e05cdec814d',1,'vg::Funnel::Stage']]],
+ ['sub_5fmem_5fcount_5fthinning_13526',['sub_mem_count_thinning',['../classvg_1_1BaseMapper.html#a8d9a00e1d809346bc62f6f2c1e4fbe32',1,'vg::BaseMapper']]],
+ ['sub_5fmem_5fthinning_5fburn_5fin_13527',['sub_mem_thinning_burn_in',['../classvg_1_1BaseMapper.html#a4e17a40bafbd8832d551acb01298403d',1,'vg::BaseMapper']]],
+ ['sub_5fpoly_5frate_13528',['sub_poly_rate',['../classvg_1_1NGSSimulator.html#a2078f130a3782a67206ad9c2c20067ea',1,'vg::NGSSimulator']]],
+ ['sub_5fscore_13529',['sub_score',['../classvg_1_1ReadFilter.html#a529c0b978b3855bab3dc1074fd18a711',1,'vg::ReadFilter']]],
+ ['subchain_5fid_13530',['subchain_id',['../structHaplotypesConfig.html#ae5e75f47f0768d4e5da28a15baaa702e',1,'HaplotypesConfig']]],
+ ['subchain_5flength_13531',['SUBCHAIN_LENGTH',['../classvg_1_1HaplotypePartitioner.html#a3343e960c394c9c092d08ff931f37081',1,'vg::HaplotypePartitioner::SUBCHAIN_LENGTH()'],['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#ac912479fc22acc7c9078978e71597ad9',1,'vg::HaplotypePartitioner::Parameters::subchain_length()']]],
+ ['subchains_13532',['subchains',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#ae31e41720bb3a859e4762aa9e2c5318b',1,'vg::Haplotypes::TopLevelChain::subchains()'],['../structvg_1_1Recombinator_1_1Statistics.html#ab6d38eac9e036f7b2b0f19736529e3a9',1,'vg::Recombinator::Statistics::subchains()']]],
+ ['subgraph_13533',['subgraph',['../classvg_1_1GraphSynchronizer_1_1Lock.html#aae76f24549ed2f49dc12176f46dfea8d',1,'vg::GraphSynchronizer::Lock::subgraph()'],['../classvg_1_1SpliceRegion.html#aa12379182f8abfc5239c38b433d1b4b8',1,'vg::SpliceRegion::subgraph()']]],
+ ['subgraph_5fmin_13534',['subgraph_min',['../structPruningParameters.html#ada52c2750edf0333574238f15adb1c84',1,'PruningParameters']]],
+ ['subgraph_5fprune_13535',['subgraph_prune',['../classvg_1_1VariantAdder.html#a39e87cff1b1cf12920a36b78bdcc2ddc',1,'vg::VariantAdder']]],
+ ['subgroups_13536',['subgroups',['../structvg_1_1subcommand_1_1GroupedOptionGroup.html#a17a3b23ed098272dfa4f3a9226ac5bef',1,'vg::subcommand::GroupedOptionGroup']]],
+ ['subpath_13537',['subpath',['../structvg_1_1MultipathAlignment.html#aa92c4cbfee9b5e076c41ca466b44617c',1,'vg::MultipathAlignment']]],
+ ['subpath_5fhandles_13538',['subpath_handles',['../classvg_1_1SubpathOverlay.html#ab1edd258ddd2cce726bfbc79b32b2476',1,'vg::SubpathOverlay']]],
+ ['subpath_5fto_5flength_13539',['subpath_to_length',['../classvg_1_1HTSWriter.html#a24dca4e57dcfb498da8f18946194f600',1,'vg::HTSWriter']]],
+ ['subsequences_13540',['subsequences',['../classvg_1_1ReadFilter.html#a98cd220c402ec88c512121825ed690df',1,'vg::ReadFilter']]],
+ ['substage_5fname_13541',['substage_name',['../classvg_1_1Funnel.html#a4cfa61145fcd97f5710c3d609e72a997',1,'vg::Funnel']]],
+ ['substage_5fstart_5ftime_13542',['substage_start_time',['../classvg_1_1Funnel.html#ae8b9248bf65562b44ac8b65f50619c70',1,'vg::Funnel']]],
+ ['suffix_13543',['suffix',['../classvg_1_1IndexFile.html#acc1a7b94cb2a464d4941e7092aa83612',1,'vg::IndexFile']]],
+ ['suffixes_13544',['suffixes',['../classvg_1_1PhaseUnfolder.html#a8e235a2b6022ec40a6e66c63c8dd1df0',1,'vg::PhaseUnfolder']]],
+ ['suggested_5fedges_13545',['suggested_edges',['../classvg_1_1DiagramExplainer.html#a14bbd52421b049d538e13a357209b9ff',1,'vg::DiagramExplainer']]],
+ ['sum_13546',['sum',['../structhaplo_1_1haplo__DP__column.html#aeb237931ba6de582496ded7d42517f3a',1,'haplo::haplo_DP_column']]],
+ ['super_13547',['super',['../classvg_1_1PathSubgraph.html#a223501d50e8c102bbd7bf602d19b9400',1,'vg::PathSubgraph::super()'],['../classvg_1_1SubHandleGraph.html#aa17f9e8ba0b1b374b852390a9bf0c56a',1,'vg::SubHandleGraph::super()'],['../classvg_1_1TreeSubgraph.html#a1096d8426347b21730e2d7d81527ffc0',1,'vg::TreeSubgraph::super()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ad63f143f0bebc5d600dca495e9fdff77',1,'handlegraph::algorithms::SubHandleGraph::super()']]],
+ ['support_13548',['support',['../structvg_1_1Locus.html#a42e45ba2fa1310b9fba6774b24cdd447',1,'vg::Locus::support()'],['../structvg_1_1LocationSupport.html#a479f1a778e85f8d3747c0b7c44ad5760',1,'vg::LocationSupport::support()']]],
+ ['support_5ffinder_13549',['support_finder',['../classvg_1_1SupportBasedSnarlCaller.html#a2af17a0bf619778576c49627563994dc',1,'vg::SupportBasedSnarlCaller']]],
+ ['suppress_5fcluster_5fmerging_13550',['suppress_cluster_merging',['../classvg_1_1MultipathMapper.html#ad25f17a8c485548abf5f63517937067f',1,'vg::MultipathMapper']]],
+ ['suppress_5fmismapping_5fdetection_13551',['suppress_mismapping_detection',['../classvg_1_1MultipathMapper.html#a514a648b0822a7c74e853ab78aed7d95',1,'vg::MultipathMapper']]],
+ ['suppress_5fmulticomponent_5fsplitting_13552',['suppress_multicomponent_splitting',['../classvg_1_1MultipathMapper.html#a2dae3baa09f211a0762d121a6c48dc58',1,'vg::MultipathMapper']]],
+ ['suppress_5fp_5fvalue_5fmemoization_13553',['suppress_p_value_memoization',['../classvg_1_1MultipathMapper.html#afd6fee3779079af7a2932c7c29098b2d',1,'vg::MultipathMapper']]],
+ ['suppress_5ftail_5fanchors_13554',['suppress_tail_anchors',['../classvg_1_1MultipathMapper.html#ad4c0e1fea285f378ef5c7eb23e9baf89',1,'vg::MultipathMapper']]],
+ ['surface_13555',['surface',['../classvg_1_1Viz.html#ad93aa239a30c3b7a017348e22f184b85',1,'vg::Viz']]],
+ ['surject_5fsubpath_5fglobal_13556',['surject_subpath_global',['../classvg_1_1SurjectingAlignmentEmitter.html#a730237d7e198244c27b29aff8a7d8b7d',1,'vg::SurjectingAlignmentEmitter']]],
+ ['surjector_13557',['surjector',['../classvg_1_1SurjectingAlignmentEmitter.html#a7ff6c0ffab9177150fe4941a8ae71c70',1,'vg::SurjectingAlignmentEmitter']]],
+ ['sv_5ftype_13558',['SV_TYPE',['../structvg_1_1BREAKPOINT.html#a52c38d41e036406a3c2e79d9f4bbfc50',1,'vg::BREAKPOINT']]],
+ ['symbol_5fcount_13559',['symbol_count',['../classvg_1_1Pictographs.html#a38abbb70a4bdb0b40e5beb2b43cee1d5',1,'vg::Pictographs']]],
+ ['symbolic_5fallele_5fwarnings_13560',['symbolic_allele_warnings',['../classvg_1_1Constructor.html#a245d775942ede32387b95497803e114c',1,'vg::Constructor']]],
+ ['symbols_13561',['symbols',['../classvg_1_1Pictographs.html#a2504adc26acf0c09e9cccb06e80e1d7b',1,'vg::Pictographs']]],
+ ['sync_13562',['sync',['../classvg_1_1VariantAdder.html#abc5742437534663752fccb79b5302b42',1,'vg::VariantAdder']]],
+ ['synchronizer_13563',['synchronizer',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ad2fcccf51dbd2136c680322341847b78',1,'vg::GraphSynchronizer::Lock']]],
+ ['syntax_13564',['syntax',['../vg_8proto.html#adbedb258e13546cc707a6ebb073a3d8a',1,'vg.proto']]]
];
diff --git a/search/variables_14.js b/search/variables_14.js
index 74148c74f1..ec6f6ba783 100644
--- a/search/variables_14.js
+++ b/search/variables_14.js
@@ -1,92 +1,92 @@
var searchData=
[
- ['tag_13561',['tag',['../structvg_1_1Funnel_1_1Item.html#acba00ec4fad9a9b3f1a0f9c8dcb4484c',1,'vg::Funnel::Item::tag()'],['../structvg_1_1Funnel_1_1Stage.html#a9efc6bb2afa857b7c8d5c055a3adaae6',1,'vg::Funnel::Stage::tag()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a17e22f4ea8e69209b9aff2c00deb9ba4',1,'vg::io::ProtobufEmitter::tag()']]],
- ['tag_5flength_13562',['tag_length',['../structvg_1_1Funnel_1_1Item.html#a965c4d888554644e3cbfc5deae970b92',1,'vg::Funnel::Item']]],
- ['tag_5fspace_13563',['tag_space',['../structvg_1_1Funnel_1_1Stage.html#a582d8a4caf1dbfda777913e2032fa403',1,'vg::Funnel::Stage']]],
- ['tag_5fstart_13564',['tag_start',['../structvg_1_1Funnel_1_1Item.html#a40097e3acf4a20046f5679c5601f823f',1,'vg::Funnel::Item']]],
- ['tag_5fto_5floader_13565',['tag_to_loader',['../structvg_1_1io_1_1Registry_1_1Tables.html#a965e60de0073226a98deef0757d7dfa8',1,'vg::io::Registry::Tables']]],
- ['tag_5fto_5fprotobuf_13566',['tag_to_protobuf',['../structvg_1_1io_1_1Registry_1_1Tables.html#abac3d9be375a86c8f55e5777e97fe323',1,'vg::io::Registry::Tables']]],
- ['tags_13567',['tags',['../structGBWTConfig.html#af72aa6461315f4e981c6308ede36fc64',1,'GBWTConfig']]],
- ['tags_5fto_5fset_13568',['tags_to_set',['../structGBWTConfig.html#abf5b058641892fe0532de896d8a6cdeb',1,'GBWTConfig']]],
- ['tail_5fgap_5fmemo_5fmax_5fsize_13569',['tail_gap_memo_max_size',['../classvg_1_1MultipathAlignmentGraph.html#a12e62ccfd7e7adb135d169f7e2671509',1,'vg::MultipathAlignmentGraph']]],
- ['target_13570',['target',['../classvg_1_1InsufficientInputException.html#aa40303513d2f82efe6690afe9b8a75ce',1,'vg::InsufficientInputException']]],
- ['target_5flength_13571',['TARGET_LENGTH',['../structvg_1_1WFANode.html#a761a104c95d2f39fa286c39c4aeaa6ba',1,'vg::WFANode']]],
- ['target_5fmemory_5fusage_13572',['target_memory_usage',['../classvg_1_1IndexRegistry.html#a6d6ef1d1e1488c9a32feaddca19cdb1a',1,'vg::IndexRegistry']]],
- ['target_5foffset_13573',['target_offset',['../structvg_1_1WFANode.html#ab230231efd27b35e2db2b6055e187f50',1,'vg::WFANode']]],
- ['targets_13574',['targets',['../classvg_1_1IndexingPlan.html#adda5d82310890614f02b317e46e702a1',1,'vg::IndexingPlan']]],
- ['task_5fname_13575',['task_name',['../structvg_1_1Watchdog_1_1thread__state__t.html#a797bf67f4267c5ffeda247c041f7cd14',1,'vg::Watchdog::thread_state_t']]],
- ['telomere_5fpair_13576',['telomere_pair',['../structvg_1_1SwapHaplotypesCommand.html#a6a5922c2e74c8227f07631fd2f8cc5f9',1,'vg::SwapHaplotypesCommand']]],
- ['telomeres_13577',['telomeres',['../classvg_1_1GenomeState.html#a2e1564254538fec6438c931a5263ab8a',1,'vg::GenomeState']]],
- ['test_5fmean_13578',['test_mean',['../structvg_1_1BenchmarkResult.html#a7bd2a14daeee009dd5845ba44454d7b5',1,'vg::BenchmarkResult']]],
- ['test_5fstddev_13579',['test_stddev',['../structvg_1_1BenchmarkResult.html#a54499cba0e5b1927efb68c3cf4adcff3',1,'vg::BenchmarkResult']]],
- ['thin_5falignment_5fcutoff_13580',['thin_alignment_cutoff',['../classvg_1_1VariantAdder.html#a12ef17f5d02d950a436d20e651588a81',1,'vg::VariantAdder']]],
- ['thread_5fbreakpoint_5fcursors_13581',['thread_breakpoint_cursors',['../classvg_1_1io_1_1StreamMultiplexer.html#a836843731535676ddd71a68cd3cd6d7f',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fchunk_5finflation_5ffactor_13582',['thread_chunk_inflation_factor',['../structvg_1_1IndexingParameters.html#a4eb6ab42c2e0c51a9a8891ec24ab9433',1,'vg::IndexingParameters']]],
- ['thread_5fextension_13583',['thread_extension',['../classvg_1_1Mapper.html#ad2f2408aba30a38eda90a10c28cbf410',1,'vg::Mapper']]],
- ['thread_5fmax_5fretained_5fbytes_13584',['THREAD_MAX_RETAINED_BYTES',['../classvg_1_1DozeuInterface.html#a7f00debc965248ba99fc5450ed35e24d',1,'vg::DozeuInterface']]],
- ['thread_5fqueue_5fbyte_5fcounts_13585',['thread_queue_byte_counts',['../classvg_1_1io_1_1StreamMultiplexer.html#a9ec3374dee16f6ee0ce853b04a4d6967',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueue_5fempty_5fslots_13586',['thread_queue_empty_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#a62843d99c1215b3d01109142f2356327',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueue_5ffilled_5fslots_13587',['thread_queue_filled_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#ad34283d480d468d52412bce3daeae5c4',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueue_5fmutexes_13588',['thread_queue_mutexes',['../classvg_1_1io_1_1StreamMultiplexer.html#ae0404331337813a02b7bafd0fb95e10a',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fqueues_13589',['thread_queues',['../classvg_1_1io_1_1StreamMultiplexer.html#aa4bc760981467acc3bff684653ffebd5',1,'vg::io::StreamMultiplexer']]],
- ['thread_5fstreams_13590',['thread_streams',['../classvg_1_1io_1_1StreamMultiplexer.html#a9e75e8ebd9b414f7438dea9b43af3b56',1,'vg::io::StreamMultiplexer']]],
- ['threads_13591',['threads',['../classvg_1_1ReadFilter.html#a41808c4d5db46d1405ac906a01bbf794',1,'vg::ReadFilter::threads()'],['../structHaplotypesConfig.html#a179bec8b7054c7eaa5aaf9e055322d63',1,'HaplotypesConfig::threads()']]],
- ['tick_5falong_5fchain_5fparent_13592',['tick_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#ad9ae4a6d3f61a4d18c56fe85f0259fb8',1,'vg::subcommand::TickChainLink']]],
- ['time_13593',['time',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#a92a84b5696522b5290e1407cd55dff83',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['time_5fused_13594',['time_used',['../structvg_1_1Alignment.html#a0c8b04a220715a894a19dcc70ed581c0',1,'vg::Alignment']]],
- ['timed_5fout_13595',['timed_out',['../structvg_1_1Watchdog_1_1thread__state__t.html#a0a1e9d9760eaa0803da68a1ef3a0cdb0',1,'vg::Watchdog::thread_state_t']]],
- ['timeout_13596',['timeout',['../classvg_1_1Watchdog.html#aff48af7cbc77f123d30fefd9aa005181',1,'vg::Watchdog']]],
- ['tmpfstream_5flocks_13597',['tmpfstream_locks',['../classvg_1_1Packer.html#a0f98b46ac443166dc94b2bd3c6b8d5a9',1,'vg::Packer']]],
- ['tmpfstreams_13598',['tmpfstreams',['../classvg_1_1Packer.html#a12c9d820a3b4ba6fdec28b9f05677f64',1,'vg::Packer']]],
- ['to_13599',['to',['../classvg_1_1WFATree.html#abb28a51f09daa96b500ce7a030876f0e',1,'vg::WFATree::to()'],['../structvg_1_1RecombinatorFragment.html#a73179f74032a4ca87c8e4c4a35b78a7c',1,'vg::RecombinatorFragment::to()'],['../structvg_1_1Edge.html#affb3decf0a8b18ad319405c303cdf6a5',1,'vg::Edge::to()'],['../structvg_1_1Alignment.html#a9db86772c1bd48808c0588f96f3c0865',1,'vg::Alignment::to()'],['../structvg_1_1Translation.html#a25a5dc4de6c11119522e319af3639e30',1,'vg::Translation::to()']]],
- ['to_5fcorrect_13600',['to_correct',['../structvg_1_1Alignment.html#a8957ee4a5a3ef66c93f6b6b685774df2',1,'vg::Alignment']]],
- ['to_5fend_13601',['to_end',['../structvg_1_1Edge.html#af1538e8b7416c9af6aae7b3d587182dd',1,'vg::Edge']]],
- ['to_5fidx_13602',['to_idx',['../classvg_1_1MEMClusterer_1_1HitEdge.html#a94b63347e0a6a9907b5573fae257aace',1,'vg::MEMClusterer::HitEdge']]],
- ['to_5flength_13603',['to_length',['../structvg_1_1Edit.html#a4f9854d5ba5503280306f1a06bfb3c89',1,'vg::Edit']]],
- ['to_5fmatrix_13604',['to_matrix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a6d6778356b79ef4f4831acafc090f566',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['to_5fnode_5fid_13605',['to_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a3ebf9c322668234f32083e3f9d42b38f',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['to_5fremove_13606',['to_remove',['../structGBWTConfig.html#aa7b2d855903feadc683c6f1379374dbe',1,'GBWTConfig']]],
- ['to_5fswap_13607',['to_swap',['../structvg_1_1SwapHaplotypesCommand.html#a89b3e32d9f79d7e50bce707c47a18962',1,'vg::SwapHaplotypesCommand']]],
- ['top_13608',['top',['../structhaplo_1_1int__itvl__t.html#a28cb4dd08f57cf179227ae76784bdbde',1,'haplo::int_itvl_t']]],
- ['top_5fborder_13609',['top_border',['../classvg_1_1Viz.html#a9e044e100116d5fe502953643f07d2d2',1,'vg::Viz']]],
- ['top_5fdiag_13610',['top_diag',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a76c5471f0be987920ff0076101367fbc',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['top_5fk_13611',['top_k',['../classvg_1_1PoissonSupportSnarlCaller.html#a4610e26e36319f7b2620566c7b655c63',1,'vg::PoissonSupportSnarlCaller']]],
- ['top_5flevel_5fchains_13612',['top_level_chains',['../structvg_1_1Haplotypes_1_1Header.html#a8223ce0e3fe99009151debc39caf9c0b',1,'vg::Haplotypes::Header']]],
- ['top_5fm_13613',['top_m',['../classvg_1_1PoissonSupportSnarlCaller.html#af61d6e6931ba127537e41cfdbf258d38',1,'vg::PoissonSupportSnarlCaller']]],
- ['top_5ftracebacks_13614',['top_tracebacks',['../classvg_1_1MultipathMapper.html#a122b1eaa39c84e9b18a971ebe6566030',1,'vg::MultipathMapper']]],
- ['topological_5forder_13615',['topological_order',['../classvg_1_1BandedGlobalAligner.html#a45b4ad348f9232013df241afece68afc',1,'vg::BandedGlobalAligner']]],
- ['total_5fbits_13616',['TOTAL_BITS',['../classvg_1_1BitString.html#a881dbf42b0dc52a67f0c1edfa4e971f8',1,'vg::BitString']]],
- ['total_5fkmers_13617',['total_kmers',['../structvg_1_1Haplotypes_1_1Header.html#a491f20acd55ad36b6b9b3c24f5b6a39e',1,'vg::Haplotypes::Header']]],
- ['total_5fseq_5flength_13618',['total_seq_length',['../classvg_1_1BaseMapper.html#a45439a16e3d38573e5cc59cb95462878',1,'vg::BaseMapper::total_seq_length()'],['../classvg_1_1Sampler.html#a1e14636749c41aa2d525177bf1a68cf5',1,'vg::Sampler::total_seq_length()'],['../classvg_1_1NGSSimulator.html#ac83d417596d2d157ddc5903d41be1fef',1,'vg::NGSSimulator::total_seq_length()']]],
- ['total_5fsize_13619',['total_size',['../structvg_1_1RebuildJob.html#aefe022edfe253c6c08690bd0e41dbaa1',1,'vg::RebuildJob']]],
- ['total_5fsubchains_13620',['total_subchains',['../structvg_1_1Haplotypes_1_1Header.html#a64217b5f412fcf46e65dee628abec4dc',1,'vg::Haplotypes::Header']]],
- ['track_5fcomponents_13621',['track_components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6bc63fbe77aee54235636bbc228a9e96',1,'vg::MEMClusterer::HitGraph']]],
- ['track_5fcorrectness_13622',['track_correctness',['../classvg_1_1MinimizerMapper.html#a7896c6cccfa011c4fbad1b916d30052e',1,'vg::MinimizerMapper']]],
- ['track_5fposition_13623',['track_position',['../classvg_1_1MinimizerMapper.html#a35a153c8cd62696021e17fe9d970b2b3',1,'vg::MinimizerMapper']]],
- ['track_5fprovenance_13624',['track_provenance',['../classvg_1_1MinimizerMapper.html#aeabec85347521c1f42ef51e0453c4e5f',1,'vg::MinimizerMapper']]],
- ['transcript_5fnames_13625',['transcript_names',['../structvg_1_1TranscriptPath.html#a325799db73bd6e750d5f4ee45014861c',1,'vg::TranscriptPath']]],
- ['transcript_5ftag_13626',['transcript_tag',['../classvg_1_1Transcriptome.html#a56a00bd350c02600e5474fc89791d5bd',1,'vg::Transcriptome']]],
- ['transition_5fdistrs_5f1_13627',['transition_distrs_1',['../classvg_1_1NGSSimulator.html#a571f3ff879e38077e8d7dad879157d55',1,'vg::NGSSimulator']]],
- ['transition_5fdistrs_5f2_13628',['transition_distrs_2',['../classvg_1_1NGSSimulator.html#ad3d0c480b5ecd2fa7c5209d86b41911d',1,'vg::NGSSimulator']]],
- ['transition_5ftable_13629',['transition_table',['../classvg_1_1DinucleotideMachine.html#a6a81eedb016f3d90fa5b0e2757537531',1,'vg::DinucleotideMachine']]],
- ['translate_5fthrough_13630',['translate_through',['../classvg_1_1io_1_1GafAlignmentEmitter.html#a2e7cff4276d5f1cd7857f91d8970be0e',1,'vg::io::GafAlignmentEmitter']]],
- ['translation_13631',['translation',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a7bbe9fc362769137eb5446c5ba9d4e49',1,'vg::BackTranslatingAlignmentEmitter::translation()'],['../classvg_1_1VCFOutputCaller.html#a212346d7a629ae3280ce3eb39606237b',1,'vg::VCFOutputCaller::translation()']]],
- ['translations_13632',['translations',['../classvg_1_1Translator.html#aba17cd4fd008c2dbee1da376db1807be',1,'vg::Translator']]],
- ['translator_13633',['translator',['../structvg_1_1AugmentedGraph.html#a3ac035d37452eb611b943cfa4754d6c6',1,'vg::AugmentedGraph::translator()'],['../classvg_1_1Genotyper.html#ad14928554aace83524e80d8c109e17b2',1,'vg::Genotyper::translator()']]],
- ['trav_13634',['trav',['../classvg_1_1MCMCCaller.html#a44187bff29621c4b3ff13560ea748223',1,'vg::MCMCCaller']]],
- ['trav_5fpadding_13635',['trav_padding',['../classvg_1_1GAFOutputCaller.html#a1ef9a3f2df7cfbd1a35e3ee8f56f4657',1,'vg::GAFOutputCaller']]],
- ['traversal_13636',['traversal',['../classvg_1_1mapping__t.html#a9ef6e5278c0ac9ce077ea2c8e0902674',1,'vg::mapping_t']]],
- ['traversal_5falg_13637',['traversal_alg',['../classvg_1_1Genotyper.html#a5b040c1636f479b52dbdb641e82f74dd',1,'vg::Genotyper']]],
- ['traversal_5ffinder_13638',['traversal_finder',['../classvg_1_1VCFGenotyper.html#afa0dd907b77ec7bd5d33f972c06ab131',1,'vg::VCFGenotyper::traversal_finder()'],['../classvg_1_1LegacyCaller.html#ada2c8e9befb0cbe8043779758468664a',1,'vg::LegacyCaller::traversal_finder()'],['../classvg_1_1FlowCaller.html#ad55a5eccba503ff1543b553ce5cd813f',1,'vg::FlowCaller::traversal_finder()'],['../classvg_1_1NestedFlowCaller.html#aaf2b6c922dfa6c16913325243496a126',1,'vg::NestedFlowCaller::traversal_finder()'],['../classvg_1_1SmallSnarlSimplifier.html#aaf858ca21b486fe45acbf92a4cbea5ba',1,'vg::SmallSnarlSimplifier::traversal_finder()']]],
- ['traversals_5fonly_13639',['traversals_only',['../classvg_1_1VCFGenotyper.html#a61906c71880dba31065f8cf04b95b60d',1,'vg::VCFGenotyper::traversals_only()'],['../classvg_1_1FlowCaller.html#ad20a95ea02344c6b21a4912381e7b984',1,'vg::FlowCaller::traversals_only()'],['../classvg_1_1NestedFlowCaller.html#a5012c7a944e3c3d57148ff11d0a7a174',1,'vg::NestedFlowCaller::traversals_only()']]],
- ['travs_13640',['travs',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a1ee05f25a4d87f1d40abfdea92d9d942',1,'vg::NestedFlowCaller::CallRecord']]],
- ['tree_13641',['tree',['../classvg_1_1TreeSubgraph.html#a91ef2cd31f18ada628b0990faae105a1',1,'vg::TreeSubgraph']]],
- ['trees_13642',['trees',['../classvg_1_1ZipCodeForest.html#af85d4ca7594aee84b37f7864e24e5ce6',1,'vg::ZipCodeForest']]],
- ['trim_5findels_13643',['trim_indels',['../classvg_1_1Constructor.html#a130c318e05428ee7973135ac5ea26b50',1,'vg::Constructor']]],
- ['truncation_5fmultiplicity_5fmq_5flimit_13644',['truncation_multiplicity_mq_limit',['../classvg_1_1MultipathMapper.html#a2f61a2ded5875ca3e7bf656d2198522a',1,'vg::MultipathMapper']]],
- ['tumor_5fsupports_13645',['tumor_supports',['../structvg_1_1BREAKPOINT.html#a66f75cad38b9fa5a3aab6b09b7a4ef8a',1,'vg::BREAKPOINT']]],
- ['tvs_13646',['tvs',['../classvg_1_1TVSClusterer.html#ad59ad1a2a88d40a980a7b7fb2cc18a0d',1,'vg::TVSClusterer']]],
- ['type_13647',['type',['../structvg_1_1GFFRecord.html#a0cc4e99f9e73fafafa9be311151ef0d7',1,'vg::GFFRecord::type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a2710528f0d6c0e15f824b38963a9ffe6',1,'vg::Haplotypes::Subchain::type()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a22b9b6cfc7735eedf7a813234b606761',1,'vg::HaplotypePartitioner::Subchain::type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ad39deee97644fc66b6c0a2514db7622a',1,'vg::ZipCodeTree::tree_item_t::type()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af21cc2ebf18d65a28c08ef24db23eee1',1,'vg::ZipCodeForest::child_info_t::type()'],['../structReferenceInterval.html#af544c6bc00b6fc4653ba71e869bbc4a5',1,'ReferenceInterval::type()'],['../structvg_1_1Snarl.html#a9490890cd7fff85dc32a25cb58d471f6',1,'vg::Snarl::type()']]],
- ['type_5fto_5fbare_5floaders_13648',['type_to_bare_loaders',['../structvg_1_1io_1_1Registry_1_1Tables.html#a6330f82f362346c61bdb1607773e812a',1,'vg::io::Registry::Tables']]],
- ['type_5fto_5fsaver_13649',['type_to_saver',['../structvg_1_1io_1_1Registry_1_1Tables.html#af3921832709101fdc87cfca00da3f2bf',1,'vg::io::Registry::Tables']]]
+ ['tag_13565',['tag',['../structvg_1_1Funnel_1_1Item.html#acba00ec4fad9a9b3f1a0f9c8dcb4484c',1,'vg::Funnel::Item::tag()'],['../structvg_1_1Funnel_1_1Stage.html#a9efc6bb2afa857b7c8d5c055a3adaae6',1,'vg::Funnel::Stage::tag()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a17e22f4ea8e69209b9aff2c00deb9ba4',1,'vg::io::ProtobufEmitter::tag()']]],
+ ['tag_5flength_13566',['tag_length',['../structvg_1_1Funnel_1_1Item.html#a965c4d888554644e3cbfc5deae970b92',1,'vg::Funnel::Item']]],
+ ['tag_5fspace_13567',['tag_space',['../structvg_1_1Funnel_1_1Stage.html#a582d8a4caf1dbfda777913e2032fa403',1,'vg::Funnel::Stage']]],
+ ['tag_5fstart_13568',['tag_start',['../structvg_1_1Funnel_1_1Item.html#a40097e3acf4a20046f5679c5601f823f',1,'vg::Funnel::Item']]],
+ ['tag_5fto_5floader_13569',['tag_to_loader',['../structvg_1_1io_1_1Registry_1_1Tables.html#a965e60de0073226a98deef0757d7dfa8',1,'vg::io::Registry::Tables']]],
+ ['tag_5fto_5fprotobuf_13570',['tag_to_protobuf',['../structvg_1_1io_1_1Registry_1_1Tables.html#abac3d9be375a86c8f55e5777e97fe323',1,'vg::io::Registry::Tables']]],
+ ['tags_13571',['tags',['../structGBWTConfig.html#af72aa6461315f4e981c6308ede36fc64',1,'GBWTConfig']]],
+ ['tags_5fto_5fset_13572',['tags_to_set',['../structGBWTConfig.html#abf5b058641892fe0532de896d8a6cdeb',1,'GBWTConfig']]],
+ ['tail_5fgap_5fmemo_5fmax_5fsize_13573',['tail_gap_memo_max_size',['../classvg_1_1MultipathAlignmentGraph.html#a12e62ccfd7e7adb135d169f7e2671509',1,'vg::MultipathAlignmentGraph']]],
+ ['target_13574',['target',['../classvg_1_1InsufficientInputException.html#aa40303513d2f82efe6690afe9b8a75ce',1,'vg::InsufficientInputException']]],
+ ['target_5flength_13575',['TARGET_LENGTH',['../structvg_1_1WFANode.html#a761a104c95d2f39fa286c39c4aeaa6ba',1,'vg::WFANode']]],
+ ['target_5fmemory_5fusage_13576',['target_memory_usage',['../classvg_1_1IndexRegistry.html#a6d6ef1d1e1488c9a32feaddca19cdb1a',1,'vg::IndexRegistry']]],
+ ['target_5foffset_13577',['target_offset',['../structvg_1_1WFANode.html#ab230231efd27b35e2db2b6055e187f50',1,'vg::WFANode']]],
+ ['targets_13578',['targets',['../classvg_1_1IndexingPlan.html#adda5d82310890614f02b317e46e702a1',1,'vg::IndexingPlan']]],
+ ['task_5fname_13579',['task_name',['../structvg_1_1Watchdog_1_1thread__state__t.html#a797bf67f4267c5ffeda247c041f7cd14',1,'vg::Watchdog::thread_state_t']]],
+ ['telomere_5fpair_13580',['telomere_pair',['../structvg_1_1SwapHaplotypesCommand.html#a6a5922c2e74c8227f07631fd2f8cc5f9',1,'vg::SwapHaplotypesCommand']]],
+ ['telomeres_13581',['telomeres',['../classvg_1_1GenomeState.html#a2e1564254538fec6438c931a5263ab8a',1,'vg::GenomeState']]],
+ ['test_5fmean_13582',['test_mean',['../structvg_1_1BenchmarkResult.html#a7bd2a14daeee009dd5845ba44454d7b5',1,'vg::BenchmarkResult']]],
+ ['test_5fstddev_13583',['test_stddev',['../structvg_1_1BenchmarkResult.html#a54499cba0e5b1927efb68c3cf4adcff3',1,'vg::BenchmarkResult']]],
+ ['thin_5falignment_5fcutoff_13584',['thin_alignment_cutoff',['../classvg_1_1VariantAdder.html#a12ef17f5d02d950a436d20e651588a81',1,'vg::VariantAdder']]],
+ ['thread_5fbreakpoint_5fcursors_13585',['thread_breakpoint_cursors',['../classvg_1_1io_1_1StreamMultiplexer.html#a836843731535676ddd71a68cd3cd6d7f',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fchunk_5finflation_5ffactor_13586',['thread_chunk_inflation_factor',['../structvg_1_1IndexingParameters.html#a4eb6ab42c2e0c51a9a8891ec24ab9433',1,'vg::IndexingParameters']]],
+ ['thread_5fextension_13587',['thread_extension',['../classvg_1_1Mapper.html#ad2f2408aba30a38eda90a10c28cbf410',1,'vg::Mapper']]],
+ ['thread_5fmax_5fretained_5fbytes_13588',['THREAD_MAX_RETAINED_BYTES',['../classvg_1_1DozeuInterface.html#a7f00debc965248ba99fc5450ed35e24d',1,'vg::DozeuInterface']]],
+ ['thread_5fqueue_5fbyte_5fcounts_13589',['thread_queue_byte_counts',['../classvg_1_1io_1_1StreamMultiplexer.html#a9ec3374dee16f6ee0ce853b04a4d6967',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueue_5fempty_5fslots_13590',['thread_queue_empty_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#a62843d99c1215b3d01109142f2356327',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueue_5ffilled_5fslots_13591',['thread_queue_filled_slots',['../classvg_1_1io_1_1StreamMultiplexer.html#ad34283d480d468d52412bce3daeae5c4',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueue_5fmutexes_13592',['thread_queue_mutexes',['../classvg_1_1io_1_1StreamMultiplexer.html#ae0404331337813a02b7bafd0fb95e10a',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fqueues_13593',['thread_queues',['../classvg_1_1io_1_1StreamMultiplexer.html#aa4bc760981467acc3bff684653ffebd5',1,'vg::io::StreamMultiplexer']]],
+ ['thread_5fstreams_13594',['thread_streams',['../classvg_1_1io_1_1StreamMultiplexer.html#a9e75e8ebd9b414f7438dea9b43af3b56',1,'vg::io::StreamMultiplexer']]],
+ ['threads_13595',['threads',['../classvg_1_1ReadFilter.html#a41808c4d5db46d1405ac906a01bbf794',1,'vg::ReadFilter::threads()'],['../structHaplotypesConfig.html#a179bec8b7054c7eaa5aaf9e055322d63',1,'HaplotypesConfig::threads()']]],
+ ['tick_5falong_5fchain_5fparent_13596',['tick_along_chain_parent',['../structvg_1_1subcommand_1_1TickChainLink.html#ad9ae4a6d3f61a4d18c56fe85f0259fb8',1,'vg::subcommand::TickChainLink']]],
+ ['time_13597',['time',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#a92a84b5696522b5290e1407cd55dff83',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['time_5fused_13598',['time_used',['../structvg_1_1Alignment.html#a0c8b04a220715a894a19dcc70ed581c0',1,'vg::Alignment']]],
+ ['timed_5fout_13599',['timed_out',['../structvg_1_1Watchdog_1_1thread__state__t.html#a0a1e9d9760eaa0803da68a1ef3a0cdb0',1,'vg::Watchdog::thread_state_t']]],
+ ['timeout_13600',['timeout',['../classvg_1_1Watchdog.html#aff48af7cbc77f123d30fefd9aa005181',1,'vg::Watchdog']]],
+ ['tmpfstream_5flocks_13601',['tmpfstream_locks',['../classvg_1_1Packer.html#a0f98b46ac443166dc94b2bd3c6b8d5a9',1,'vg::Packer']]],
+ ['tmpfstreams_13602',['tmpfstreams',['../classvg_1_1Packer.html#a12c9d820a3b4ba6fdec28b9f05677f64',1,'vg::Packer']]],
+ ['to_13603',['to',['../classvg_1_1WFATree.html#abb28a51f09daa96b500ce7a030876f0e',1,'vg::WFATree::to()'],['../structvg_1_1RecombinatorFragment.html#a73179f74032a4ca87c8e4c4a35b78a7c',1,'vg::RecombinatorFragment::to()'],['../structvg_1_1Edge.html#affb3decf0a8b18ad319405c303cdf6a5',1,'vg::Edge::to()'],['../structvg_1_1Alignment.html#a9db86772c1bd48808c0588f96f3c0865',1,'vg::Alignment::to()'],['../structvg_1_1Translation.html#a25a5dc4de6c11119522e319af3639e30',1,'vg::Translation::to()']]],
+ ['to_5fcorrect_13604',['to_correct',['../structvg_1_1Alignment.html#a8957ee4a5a3ef66c93f6b6b685774df2',1,'vg::Alignment']]],
+ ['to_5fend_13605',['to_end',['../structvg_1_1Edge.html#af1538e8b7416c9af6aae7b3d587182dd',1,'vg::Edge']]],
+ ['to_5fidx_13606',['to_idx',['../classvg_1_1MEMClusterer_1_1HitEdge.html#a94b63347e0a6a9907b5573fae257aace',1,'vg::MEMClusterer::HitEdge']]],
+ ['to_5flength_13607',['to_length',['../structvg_1_1Edit.html#a4f9854d5ba5503280306f1a06bfb3c89',1,'vg::Edit']]],
+ ['to_5fmatrix_13608',['to_matrix',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a6d6778356b79ef4f4831acafc090f566',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['to_5fnode_5fid_13609',['to_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a3ebf9c322668234f32083e3f9d42b38f',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['to_5fremove_13610',['to_remove',['../structGBWTConfig.html#aa7b2d855903feadc683c6f1379374dbe',1,'GBWTConfig']]],
+ ['to_5fswap_13611',['to_swap',['../structvg_1_1SwapHaplotypesCommand.html#a89b3e32d9f79d7e50bce707c47a18962',1,'vg::SwapHaplotypesCommand']]],
+ ['top_13612',['top',['../structhaplo_1_1int__itvl__t.html#a28cb4dd08f57cf179227ae76784bdbde',1,'haplo::int_itvl_t']]],
+ ['top_5fborder_13613',['top_border',['../classvg_1_1Viz.html#a9e044e100116d5fe502953643f07d2d2',1,'vg::Viz']]],
+ ['top_5fdiag_13614',['top_diag',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a76c5471f0be987920ff0076101367fbc',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['top_5fk_13615',['top_k',['../classvg_1_1PoissonSupportSnarlCaller.html#a4610e26e36319f7b2620566c7b655c63',1,'vg::PoissonSupportSnarlCaller']]],
+ ['top_5flevel_5fchains_13616',['top_level_chains',['../structvg_1_1Haplotypes_1_1Header.html#a8223ce0e3fe99009151debc39caf9c0b',1,'vg::Haplotypes::Header']]],
+ ['top_5fm_13617',['top_m',['../classvg_1_1PoissonSupportSnarlCaller.html#af61d6e6931ba127537e41cfdbf258d38',1,'vg::PoissonSupportSnarlCaller']]],
+ ['top_5ftracebacks_13618',['top_tracebacks',['../classvg_1_1MultipathMapper.html#a122b1eaa39c84e9b18a971ebe6566030',1,'vg::MultipathMapper']]],
+ ['topological_5forder_13619',['topological_order',['../classvg_1_1BandedGlobalAligner.html#a45b4ad348f9232013df241afece68afc',1,'vg::BandedGlobalAligner']]],
+ ['total_5fbits_13620',['TOTAL_BITS',['../classvg_1_1BitString.html#a881dbf42b0dc52a67f0c1edfa4e971f8',1,'vg::BitString']]],
+ ['total_5fkmers_13621',['total_kmers',['../structvg_1_1Haplotypes_1_1Header.html#a491f20acd55ad36b6b9b3c24f5b6a39e',1,'vg::Haplotypes::Header']]],
+ ['total_5fseq_5flength_13622',['total_seq_length',['../classvg_1_1BaseMapper.html#a45439a16e3d38573e5cc59cb95462878',1,'vg::BaseMapper::total_seq_length()'],['../classvg_1_1Sampler.html#a1e14636749c41aa2d525177bf1a68cf5',1,'vg::Sampler::total_seq_length()'],['../classvg_1_1NGSSimulator.html#ac83d417596d2d157ddc5903d41be1fef',1,'vg::NGSSimulator::total_seq_length()']]],
+ ['total_5fsize_13623',['total_size',['../structvg_1_1RebuildJob.html#aefe022edfe253c6c08690bd0e41dbaa1',1,'vg::RebuildJob']]],
+ ['total_5fsubchains_13624',['total_subchains',['../structvg_1_1Haplotypes_1_1Header.html#a64217b5f412fcf46e65dee628abec4dc',1,'vg::Haplotypes::Header']]],
+ ['track_5fcomponents_13625',['track_components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#a6bc63fbe77aee54235636bbc228a9e96',1,'vg::MEMClusterer::HitGraph']]],
+ ['track_5fcorrectness_13626',['track_correctness',['../classvg_1_1MinimizerMapper.html#a7896c6cccfa011c4fbad1b916d30052e',1,'vg::MinimizerMapper']]],
+ ['track_5fposition_13627',['track_position',['../classvg_1_1MinimizerMapper.html#a35a153c8cd62696021e17fe9d970b2b3',1,'vg::MinimizerMapper']]],
+ ['track_5fprovenance_13628',['track_provenance',['../classvg_1_1MinimizerMapper.html#aeabec85347521c1f42ef51e0453c4e5f',1,'vg::MinimizerMapper']]],
+ ['transcript_5fnames_13629',['transcript_names',['../structvg_1_1TranscriptPath.html#a325799db73bd6e750d5f4ee45014861c',1,'vg::TranscriptPath']]],
+ ['transcript_5ftag_13630',['transcript_tag',['../classvg_1_1Transcriptome.html#a56a00bd350c02600e5474fc89791d5bd',1,'vg::Transcriptome']]],
+ ['transition_5fdistrs_5f1_13631',['transition_distrs_1',['../classvg_1_1NGSSimulator.html#a571f3ff879e38077e8d7dad879157d55',1,'vg::NGSSimulator']]],
+ ['transition_5fdistrs_5f2_13632',['transition_distrs_2',['../classvg_1_1NGSSimulator.html#ad3d0c480b5ecd2fa7c5209d86b41911d',1,'vg::NGSSimulator']]],
+ ['transition_5ftable_13633',['transition_table',['../classvg_1_1DinucleotideMachine.html#a6a81eedb016f3d90fa5b0e2757537531',1,'vg::DinucleotideMachine']]],
+ ['translate_5fthrough_13634',['translate_through',['../classvg_1_1io_1_1GafAlignmentEmitter.html#a2e7cff4276d5f1cd7857f91d8970be0e',1,'vg::io::GafAlignmentEmitter']]],
+ ['translation_13635',['translation',['../classvg_1_1BackTranslatingAlignmentEmitter.html#a7bbe9fc362769137eb5446c5ba9d4e49',1,'vg::BackTranslatingAlignmentEmitter::translation()'],['../classvg_1_1VCFOutputCaller.html#a212346d7a629ae3280ce3eb39606237b',1,'vg::VCFOutputCaller::translation()']]],
+ ['translations_13636',['translations',['../classvg_1_1Translator.html#aba17cd4fd008c2dbee1da376db1807be',1,'vg::Translator']]],
+ ['translator_13637',['translator',['../structvg_1_1AugmentedGraph.html#a3ac035d37452eb611b943cfa4754d6c6',1,'vg::AugmentedGraph::translator()'],['../classvg_1_1Genotyper.html#ad14928554aace83524e80d8c109e17b2',1,'vg::Genotyper::translator()']]],
+ ['trav_13638',['trav',['../classvg_1_1MCMCCaller.html#a44187bff29621c4b3ff13560ea748223',1,'vg::MCMCCaller']]],
+ ['trav_5fpadding_13639',['trav_padding',['../classvg_1_1GAFOutputCaller.html#a1ef9a3f2df7cfbd1a35e3ee8f56f4657',1,'vg::GAFOutputCaller']]],
+ ['traversal_13640',['traversal',['../classvg_1_1mapping__t.html#a9ef6e5278c0ac9ce077ea2c8e0902674',1,'vg::mapping_t']]],
+ ['traversal_5falg_13641',['traversal_alg',['../classvg_1_1Genotyper.html#a5b040c1636f479b52dbdb641e82f74dd',1,'vg::Genotyper']]],
+ ['traversal_5ffinder_13642',['traversal_finder',['../classvg_1_1VCFGenotyper.html#afa0dd907b77ec7bd5d33f972c06ab131',1,'vg::VCFGenotyper::traversal_finder()'],['../classvg_1_1LegacyCaller.html#ada2c8e9befb0cbe8043779758468664a',1,'vg::LegacyCaller::traversal_finder()'],['../classvg_1_1FlowCaller.html#ad55a5eccba503ff1543b553ce5cd813f',1,'vg::FlowCaller::traversal_finder()'],['../classvg_1_1NestedFlowCaller.html#aaf2b6c922dfa6c16913325243496a126',1,'vg::NestedFlowCaller::traversal_finder()'],['../classvg_1_1SmallSnarlSimplifier.html#aaf858ca21b486fe45acbf92a4cbea5ba',1,'vg::SmallSnarlSimplifier::traversal_finder()']]],
+ ['traversals_5fonly_13643',['traversals_only',['../classvg_1_1VCFGenotyper.html#a61906c71880dba31065f8cf04b95b60d',1,'vg::VCFGenotyper::traversals_only()'],['../classvg_1_1FlowCaller.html#ad20a95ea02344c6b21a4912381e7b984',1,'vg::FlowCaller::traversals_only()'],['../classvg_1_1NestedFlowCaller.html#a5012c7a944e3c3d57148ff11d0a7a174',1,'vg::NestedFlowCaller::traversals_only()']]],
+ ['travs_13644',['travs',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#a1ee05f25a4d87f1d40abfdea92d9d942',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['tree_13645',['tree',['../classvg_1_1TreeSubgraph.html#a91ef2cd31f18ada628b0990faae105a1',1,'vg::TreeSubgraph']]],
+ ['trees_13646',['trees',['../classvg_1_1ZipCodeForest.html#af85d4ca7594aee84b37f7864e24e5ce6',1,'vg::ZipCodeForest']]],
+ ['trim_5findels_13647',['trim_indels',['../classvg_1_1Constructor.html#a130c318e05428ee7973135ac5ea26b50',1,'vg::Constructor']]],
+ ['truncation_5fmultiplicity_5fmq_5flimit_13648',['truncation_multiplicity_mq_limit',['../classvg_1_1MultipathMapper.html#a2f61a2ded5875ca3e7bf656d2198522a',1,'vg::MultipathMapper']]],
+ ['tumor_5fsupports_13649',['tumor_supports',['../structvg_1_1BREAKPOINT.html#a66f75cad38b9fa5a3aab6b09b7a4ef8a',1,'vg::BREAKPOINT']]],
+ ['tvs_13650',['tvs',['../classvg_1_1TVSClusterer.html#ad59ad1a2a88d40a980a7b7fb2cc18a0d',1,'vg::TVSClusterer']]],
+ ['type_13651',['type',['../structvg_1_1GFFRecord.html#a0cc4e99f9e73fafafa9be311151ef0d7',1,'vg::GFFRecord::type()'],['../structvg_1_1Haplotypes_1_1Subchain.html#a2710528f0d6c0e15f824b38963a9ffe6',1,'vg::Haplotypes::Subchain::type()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a22b9b6cfc7735eedf7a813234b606761',1,'vg::HaplotypePartitioner::Subchain::type()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ad39deee97644fc66b6c0a2514db7622a',1,'vg::ZipCodeTree::tree_item_t::type()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af21cc2ebf18d65a28c08ef24db23eee1',1,'vg::ZipCodeForest::child_info_t::type()'],['../structReferenceInterval.html#af544c6bc00b6fc4653ba71e869bbc4a5',1,'ReferenceInterval::type()'],['../structvg_1_1Snarl.html#a9490890cd7fff85dc32a25cb58d471f6',1,'vg::Snarl::type()']]],
+ ['type_5fto_5fbare_5floaders_13652',['type_to_bare_loaders',['../structvg_1_1io_1_1Registry_1_1Tables.html#a6330f82f362346c61bdb1607773e812a',1,'vg::io::Registry::Tables']]],
+ ['type_5fto_5fsaver_13653',['type_to_saver',['../structvg_1_1io_1_1Registry_1_1Tables.html#af3921832709101fdc87cfca00da3f2bf',1,'vg::io::Registry::Tables']]]
];
diff --git a/search/variables_15.js b/search/variables_15.js
index d0c13ce30f..81e0f636c1 100644
--- a/search/variables_15.js
+++ b/search/variables_15.js
@@ -1,35 +1,35 @@
var searchData=
[
- ['uf_13650',['uf',['../classvg_1_1ContractingGraph.html#a0397c367ca4856e715fe3400b351d715',1,'vg::ContractingGraph']]],
- ['unaligned_5fbands_13651',['unaligned_bands',['../classvg_1_1AlignmentChainModel.html#a86bcd77b21cc9b8b9c2b9f100fb9ce71',1,'vg::AlignmentChainModel']]],
- ['unaltered_5fmotif_5fdata_13652',['unaltered_motif_data',['../classvg_1_1SpliceStats.html#a8958ca644d2a270c59a67d2038ce85eb',1,'vg::SpliceStats']]],
- ['unary_5fboundaries_13653',['unary_boundaries',['../classvg_1_1NetGraph.html#ae573871a7c3cd0be507222751f870f72',1,'vg::NetGraph']]],
- ['uncanonicalizable_5fsv_5fwarned_13654',['uncanonicalizable_sv_warned',['../classvg_1_1Constructor.html#ac7747658550e74b383a491a06e04ea99',1,'vg::Constructor']]],
- ['uncompressed_5fout_13655',['uncompressed_out',['../classvg_1_1io_1_1MessageEmitter.html#a19f6d714ad67ec55346998140ce79258',1,'vg::io::MessageEmitter']]],
- ['uncompressed_5fout_5fostream_13656',['uncompressed_out_ostream',['../classvg_1_1io_1_1MessageEmitter.html#aeb08e36bd3266eabc11d2d27e6336812',1,'vg::io::MessageEmitter']]],
- ['uncompressed_5fout_5fwritten_13657',['uncompressed_out_written',['../classvg_1_1io_1_1MessageEmitter.html#ae75aa23f1b6b85340f7bc586282e7c55',1,'vg::io::MessageEmitter']]],
- ['unfold_5fmax_5flength_13658',['unfold_max_length',['../classvg_1_1Genotyper.html#ab3e4270419b361c9455125ca305709e2',1,'vg::Genotyper']]],
- ['union_5ffind_13659',['union_find',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a6bcd65e92edd9e1bf925a9e4a8c7cc01',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
- ['uniqueness_13660',['uniqueness',['../structvg_1_1Alignment.html#a2d744ce39b375cdeb8adfc3721a18eb0',1,'vg::Alignment']]],
- ['universe_5fsize_13661',['universe_size',['../classvg_1_1SmallBitset.html#aa8dbf9601e90ce99f26895d8a4d79de0',1,'vg::SmallBitset']]],
- ['unpaired_5fpenalty_13662',['unpaired_penalty',['../classvg_1_1BaseMapper.html#ad20ea9a68bcaca157350595f03b4601c',1,'vg::BaseMapper']]],
- ['unstranded_13663',['unstranded',['../classvg_1_1OrientedDistanceClusterer.html#a34e43333ce3f5294f28b3cadc18c54ac',1,'vg::OrientedDistanceClusterer']]],
- ['untangle_5fallele_5ftraversals_13664',['untangle_allele_traversals',['../classvg_1_1Deconstructor.html#a3be6aea7084e6875585939a3cd40476e',1,'vg::Deconstructor']]],
- ['upper_5fbound_13665',['upper_bound',['../structvg_1_1BREAKPOINT.html#add7be6a634fda8c98ff9627ecd454683',1,'vg::BREAKPOINT']]],
- ['upper_5fbound_5fheuristic_13666',['upper_bound_heuristic',['../classvg_1_1TargetValueSearch.html#ac3930066893407bf6fd3e57a717bba0c',1,'vg::TargetValueSearch']]],
- ['usable_5fbits_13667',['USABLE_BITS',['../structvg_1_1varint__vector__t.html#a86e608e634d04476754226a796122066',1,'vg::varint_vector_t']]],
- ['use_5fapprox_5fsub_5fmem_5fcount_13668',['use_approx_sub_mem_count',['../classvg_1_1BaseMapper.html#abf1a0a71b2bcc7763690fed623383fb3',1,'vg::BaseMapper']]],
- ['use_5favg_13669',['use_avg',['../classvg_1_1Filter.html#a271fe98c839b17295ecef0dc54cb7d7e',1,'vg::Filter']]],
- ['use_5fbounded_5fsyncmers_13670',['use_bounded_syncmers',['../structvg_1_1IndexingParameters.html#ae034b19e5a2e71bccc1bf35addbe0b45',1,'vg::IndexingParameters']]],
- ['use_5fcluster_5fmq_13671',['use_cluster_mq',['../classvg_1_1Mapper.html#a2c4c837c39fa708de934f5c24c3c371e',1,'vg::Mapper']]],
- ['use_5fexplored_5fcap_13672',['use_explored_cap',['../classvg_1_1MinimizerMapper.html#a84b734b0d1be3a5015eb92f8c331b6f3',1,'vg::MinimizerMapper']]],
- ['use_5ffanout_5fmatch_5falg_13673',['use_fanout_match_alg',['../classvg_1_1MultipathMapper.html#ac02b5155c59ad4603f0cc633b2dfad8a',1,'vg::MultipathMapper']]],
- ['use_5fgreedy_5fmem_5frestarts_13674',['use_greedy_mem_restarts',['../classvg_1_1BaseMapper.html#ad95c004337db9d7de612c3cffe4f90f8',1,'vg::BaseMapper']]],
- ['use_5finternal_5fconnectivity_13675',['use_internal_connectivity',['../classvg_1_1NetGraph.html#a57dedbbe009595f748dc3c4deae2dc72',1,'vg::NetGraph']]],
- ['use_5fmapq_13676',['use_mapq',['../classvg_1_1Genotyper.html#a5991ce66cc2a9ea45bd27d288dd7d9b8',1,'vg::Genotyper::use_mapq()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a0588ea9ea69bf3c4c3f9108549e6102b',1,'vg::PoissonSupportSnarlCaller::use_mapq()']]],
- ['use_5fmin_5fdist_5fclusterer_13677',['use_min_dist_clusterer',['../classvg_1_1MultipathMapper.html#aed5898444e134f0fb95ae527d215e88f',1,'vg::MultipathMapper']]],
- ['use_5fpessimistic_5ftail_5falignment_13678',['use_pessimistic_tail_alignment',['../classvg_1_1MultipathMapper.html#a552098fc2ac26aa17929d31f7a0f1ecd',1,'vg::MultipathMapper']]],
- ['use_5fpopulation_5fmapqs_13679',['use_population_mapqs',['../classvg_1_1MultipathMapper.html#aaaecbb0881e444042662a72907442fc1',1,'vg::MultipathMapper']]],
- ['use_5fstripped_5fmatch_5falg_13680',['use_stripped_match_alg',['../classvg_1_1MultipathMapper.html#ac9ea306291983b4c10ff1ec97b6d1adc',1,'vg::MultipathMapper']]],
- ['use_5ftvs_5fclusterer_13681',['use_tvs_clusterer',['../classvg_1_1MultipathMapper.html#afaa33d747ce1393304aa96bc5245a4f8',1,'vg::MultipathMapper']]]
+ ['uf_13654',['uf',['../classvg_1_1ContractingGraph.html#a0397c367ca4856e715fe3400b351d715',1,'vg::ContractingGraph']]],
+ ['unaligned_5fbands_13655',['unaligned_bands',['../classvg_1_1AlignmentChainModel.html#a86bcd77b21cc9b8b9c2b9f100fb9ce71',1,'vg::AlignmentChainModel']]],
+ ['unaltered_5fmotif_5fdata_13656',['unaltered_motif_data',['../classvg_1_1SpliceStats.html#a8958ca644d2a270c59a67d2038ce85eb',1,'vg::SpliceStats']]],
+ ['unary_5fboundaries_13657',['unary_boundaries',['../classvg_1_1NetGraph.html#ae573871a7c3cd0be507222751f870f72',1,'vg::NetGraph']]],
+ ['uncanonicalizable_5fsv_5fwarned_13658',['uncanonicalizable_sv_warned',['../classvg_1_1Constructor.html#ac7747658550e74b383a491a06e04ea99',1,'vg::Constructor']]],
+ ['uncompressed_5fout_13659',['uncompressed_out',['../classvg_1_1io_1_1MessageEmitter.html#a19f6d714ad67ec55346998140ce79258',1,'vg::io::MessageEmitter']]],
+ ['uncompressed_5fout_5fostream_13660',['uncompressed_out_ostream',['../classvg_1_1io_1_1MessageEmitter.html#aeb08e36bd3266eabc11d2d27e6336812',1,'vg::io::MessageEmitter']]],
+ ['uncompressed_5fout_5fwritten_13661',['uncompressed_out_written',['../classvg_1_1io_1_1MessageEmitter.html#ae75aa23f1b6b85340f7bc586282e7c55',1,'vg::io::MessageEmitter']]],
+ ['unfold_5fmax_5flength_13662',['unfold_max_length',['../classvg_1_1Genotyper.html#ab3e4270419b361c9455125ca305709e2',1,'vg::Genotyper']]],
+ ['union_5ffind_13663',['union_find',['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a6bcd65e92edd9e1bf925a9e4a8c7cc01',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph']]],
+ ['uniqueness_13664',['uniqueness',['../structvg_1_1Alignment.html#a2d744ce39b375cdeb8adfc3721a18eb0',1,'vg::Alignment']]],
+ ['universe_5fsize_13665',['universe_size',['../classvg_1_1SmallBitset.html#aa8dbf9601e90ce99f26895d8a4d79de0',1,'vg::SmallBitset']]],
+ ['unpaired_5fpenalty_13666',['unpaired_penalty',['../classvg_1_1BaseMapper.html#ad20ea9a68bcaca157350595f03b4601c',1,'vg::BaseMapper']]],
+ ['unstranded_13667',['unstranded',['../classvg_1_1OrientedDistanceClusterer.html#a34e43333ce3f5294f28b3cadc18c54ac',1,'vg::OrientedDistanceClusterer']]],
+ ['untangle_5fallele_5ftraversals_13668',['untangle_allele_traversals',['../classvg_1_1Deconstructor.html#a3be6aea7084e6875585939a3cd40476e',1,'vg::Deconstructor']]],
+ ['upper_5fbound_13669',['upper_bound',['../structvg_1_1BREAKPOINT.html#add7be6a634fda8c98ff9627ecd454683',1,'vg::BREAKPOINT']]],
+ ['upper_5fbound_5fheuristic_13670',['upper_bound_heuristic',['../classvg_1_1TargetValueSearch.html#ac3930066893407bf6fd3e57a717bba0c',1,'vg::TargetValueSearch']]],
+ ['usable_5fbits_13671',['USABLE_BITS',['../structvg_1_1varint__vector__t.html#a86e608e634d04476754226a796122066',1,'vg::varint_vector_t']]],
+ ['use_5fapprox_5fsub_5fmem_5fcount_13672',['use_approx_sub_mem_count',['../classvg_1_1BaseMapper.html#abf1a0a71b2bcc7763690fed623383fb3',1,'vg::BaseMapper']]],
+ ['use_5favg_13673',['use_avg',['../classvg_1_1Filter.html#a271fe98c839b17295ecef0dc54cb7d7e',1,'vg::Filter']]],
+ ['use_5fbounded_5fsyncmers_13674',['use_bounded_syncmers',['../structvg_1_1IndexingParameters.html#ae034b19e5a2e71bccc1bf35addbe0b45',1,'vg::IndexingParameters']]],
+ ['use_5fcluster_5fmq_13675',['use_cluster_mq',['../classvg_1_1Mapper.html#a2c4c837c39fa708de934f5c24c3c371e',1,'vg::Mapper']]],
+ ['use_5fexplored_5fcap_13676',['use_explored_cap',['../classvg_1_1MinimizerMapper.html#a84b734b0d1be3a5015eb92f8c331b6f3',1,'vg::MinimizerMapper']]],
+ ['use_5ffanout_5fmatch_5falg_13677',['use_fanout_match_alg',['../classvg_1_1MultipathMapper.html#ac02b5155c59ad4603f0cc633b2dfad8a',1,'vg::MultipathMapper']]],
+ ['use_5fgreedy_5fmem_5frestarts_13678',['use_greedy_mem_restarts',['../classvg_1_1BaseMapper.html#ad95c004337db9d7de612c3cffe4f90f8',1,'vg::BaseMapper']]],
+ ['use_5finternal_5fconnectivity_13679',['use_internal_connectivity',['../classvg_1_1NetGraph.html#a57dedbbe009595f748dc3c4deae2dc72',1,'vg::NetGraph']]],
+ ['use_5fmapq_13680',['use_mapq',['../classvg_1_1Genotyper.html#a5991ce66cc2a9ea45bd27d288dd7d9b8',1,'vg::Genotyper::use_mapq()'],['../classvg_1_1PoissonSupportSnarlCaller.html#a0588ea9ea69bf3c4c3f9108549e6102b',1,'vg::PoissonSupportSnarlCaller::use_mapq()']]],
+ ['use_5fmin_5fdist_5fclusterer_13681',['use_min_dist_clusterer',['../classvg_1_1MultipathMapper.html#aed5898444e134f0fb95ae527d215e88f',1,'vg::MultipathMapper']]],
+ ['use_5fpessimistic_5ftail_5falignment_13682',['use_pessimistic_tail_alignment',['../classvg_1_1MultipathMapper.html#a552098fc2ac26aa17929d31f7a0f1ecd',1,'vg::MultipathMapper']]],
+ ['use_5fpopulation_5fmapqs_13683',['use_population_mapqs',['../classvg_1_1MultipathMapper.html#aaaecbb0881e444042662a72907442fc1',1,'vg::MultipathMapper']]],
+ ['use_5fstripped_5fmatch_5falg_13684',['use_stripped_match_alg',['../classvg_1_1MultipathMapper.html#ac9ea306291983b4c10ff1ec97b6d1adc',1,'vg::MultipathMapper']]],
+ ['use_5ftvs_5fclusterer_13685',['use_tvs_clusterer',['../classvg_1_1MultipathMapper.html#afaa33d747ce1393304aa96bc5245a4f8',1,'vg::MultipathMapper']]]
];
diff --git a/search/variables_16.js b/search/variables_16.js
index 8990e1942a..2942b93c75 100644
--- a/search/variables_16.js
+++ b/search/variables_16.js
@@ -1,30 +1,30 @@
var searchData=
[
- ['v_13682',['v',['../structvg_1_1TreeNode.html#aa4855443d5325cd35ff3d1d5a6855190',1,'vg::TreeNode']]],
- ['validate_13683',['validate',['../structHaplotypesConfig.html#a6eeffe1089fb8292af1674eacc00e8a4',1,'HaplotypesConfig']]],
- ['validator_13684',['validator',['../structvg_1_1subcommand_1_1ArgSpec.html#a542e2d18276cafc5c6219a47be001197',1,'vg::subcommand::ArgSpec']]],
- ['value_13685',['value',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#abaad50c48424395686b10a95dfc16ab7',1,'vg::MinimizerMapper::Minimizer::value()'],['../classvg_1_1BaseOption.html#aa74c66fcf0f363ce08bb6e5060fd42e5',1,'vg::BaseOption::value()'],['../classvg_1_1SmallBitset.html#a486a8a8a5a30fab268ae96a9cf464fdd',1,'vg::SmallBitset::value()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#af141b75a2e3f2014b3289b3cffe99c44',1,'vg::ZipCodeTree::tree_item_t::value()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#a5d3fb39613dc2935ea316d87d2244f7b',1,'vg::ZipCodeForest::child_info_t::value()'],['../structvg_1_1subcommand_1_1Valuation.html#a88e369b92873968c8d7b68cc78ce1b1d',1,'vg::subcommand::Valuation::value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a518e378dc3759f070912c8cf42ae83cd',1,'vg::subcommand::ValueArgSpec::value()'],['../classvg_1_1io_1_1MessageIterator.html#a698864a67e1e721c06a97875f6cbcbde',1,'vg::io::MessageIterator::value()'],['../classvg_1_1io_1_1ProtobufIterator.html#aa66494ab08ee29d36b1aa04f0213f566',1,'vg::io::ProtobufIterator::value()']]],
- ['value_5fat_13686',['value_at',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a2146c37988fd520600d806d1606f0f3f',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['value_5fbits_13687',['VALUE_BITS',['../classvg_1_1SmallBitset.html#a1570694b6aa163d390bc65f3ad2e015d',1,'vg::SmallBitset']]],
- ['value_5fmask_13688',['VALUE_MASK',['../classvg_1_1SmallBitset.html#a0d940c085d362391f5bc531bd948623a',1,'vg::SmallBitset']]],
- ['value_5fset_13689',['value_set',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a215243ebe6068e28cb2ad00472a9a4d9',1,'vg::subcommand::ValueArgSpec']]],
- ['value_5fshift_13690',['VALUE_SHIFT',['../classvg_1_1SmallBitset.html#ad5a1d72bf8ad3ce5c8341da2fa78eafb',1,'vg::SmallBitset']]],
- ['values_13691',['values',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a341b8cdfa0d90adaea6f9c52196b5de6',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t']]],
- ['var_13692',['var',['../namespacevg.html#afe7fae89b379b5411189ac0ac74b2dd4',1,'vg']]],
- ['variant_5falts_13693',['variant_alts',['../structvg_1_1VG_1_1Plan.html#ad2b28e3a651018396d6c0a1b3377e161',1,'vg::VG::Plan']]],
- ['variant_5frange_13694',['variant_range',['../classvg_1_1VariantAdder.html#aa23751086259b5976ffe78169a6000b9',1,'vg::VariantAdder']]],
- ['variant_5fsource_13695',['variant_source',['../classvg_1_1RareVariantSimplifier.html#afd96f926d4135c8c1ae967ad22aad03a',1,'vg::RareVariantSimplifier']]],
- ['variant_5fto_5ftraversal_13696',['variant_to_traversal',['../classvg_1_1VG.html#ac697184acf2edadca58ddc776f9f4e7e',1,'vg::VG']]],
- ['variants_5fafter_13697',['variants_after',['../classvg_1_1WindowedVcfBuffer.html#a8c0bf4d78e07bcc7ec8f58287452ad9e',1,'vg::WindowedVcfBuffer']]],
- ['variants_5fbefore_13698',['variants_before',['../classvg_1_1WindowedVcfBuffer.html#a24156cab3205fcb845418259a91ada3a',1,'vg::WindowedVcfBuffer']]],
- ['vars_5fper_5fchunk_13699',['vars_per_chunk',['../classvg_1_1Constructor.html#a7cc8ae0e38492082ba8e886ea174944f',1,'vg::Constructor']]],
- ['vcf_5finput_13700',['vcf_input',['../structHaplotypesConfig.html#a8d58855b93c6c570420598f99f2d8ea2',1,'HaplotypesConfig']]],
- ['vcf_5fto_5ffasta_5frenames_13701',['vcf_to_fasta_renames',['../classvg_1_1NameMapper.html#afd130381fc9ad1a930932e672fda80d1',1,'vg::NameMapper']]],
- ['verbose_13702',['verbose',['../classvg_1_1NestedTraversalFinder.html#a67980934b7315e90dcd63fa046b465b7',1,'vg::NestedTraversalFinder::verbose()'],['../classvg_1_1ReadFilter.html#aa207b19d222c64919714bae506b726a6',1,'vg::ReadFilter::verbose()'],['../classvg_1_1RepresentativeTraversalFinder.html#a6af3519805d1115b006ad8b3bf2d3a3e',1,'vg::RepresentativeTraversalFinder::verbose()'],['../classvg_1_1io_1_1MessageIterator.html#af3f1540514c644f1d01212d515f603e6',1,'vg::io::MessageIterator::verbose()']]],
- ['verbosity_13703',['verbosity',['../structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579',1,'vg::IndexingParameters::verbosity()'],['../classvg_1_1HaplotypePartitioner.html#ac5d1210d753c0fe6ed936f18f02e2cd2',1,'vg::HaplotypePartitioner::verbosity()'],['../classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12',1,'vg::Recombinator::verbosity()'],['../structHaplotypesConfig.html#ad04e07b242265b989bc2b93479676b84',1,'HaplotypesConfig::verbosity()']]],
- ['version_13704',['version',['../structvg_1_1Haplotypes_1_1Header.html#ac2e1810f289c24ac4c2f74d8df9df5ec',1,'vg::Haplotypes::Header::version()'],['../classvg_1_1ZipCodeCollection.html#ad97d400ad51f2d7d1a880d81bbf8993d',1,'vg::ZipCodeCollection::version()'],['../structvg_1_1Haplotypes_1_1Header.html#a68bfc0fe68e8fc1b42ad078eaa234777',1,'vg::Haplotypes::Header::VERSION()'],['../classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222',1,'vg::Version::VERSION()']]],
- ['vg_13705',['vg',['../classvg_1_1FlowSort.html#abd481c5b9e6c9c5aeaf846652dd3c76f',1,'vg::FlowSort']]],
- ['vg_5ffilename_13706',['vg_filename',['../classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0',1,'vg::IndexedVG']]],
- ['visit_13707',['visit',['../structvg_1_1SnarlTraversal.html#aff14559c1e4fb55bdf87320f3a4ee636',1,'vg::SnarlTraversal']]],
- ['visited_13708',['visited',['../classvg_1_1HandleGraphNodeSet.html#a6a1318a8e451562f282bf960032634f4',1,'vg::HandleGraphNodeSet']]]
+ ['v_13686',['v',['../structvg_1_1TreeNode.html#aa4855443d5325cd35ff3d1d5a6855190',1,'vg::TreeNode']]],
+ ['validate_13687',['validate',['../structHaplotypesConfig.html#a6eeffe1089fb8292af1674eacc00e8a4',1,'HaplotypesConfig']]],
+ ['validator_13688',['validator',['../structvg_1_1subcommand_1_1ArgSpec.html#a542e2d18276cafc5c6219a47be001197',1,'vg::subcommand::ArgSpec']]],
+ ['value_13689',['value',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#abaad50c48424395686b10a95dfc16ab7',1,'vg::MinimizerMapper::Minimizer::value()'],['../classvg_1_1BaseOption.html#aa74c66fcf0f363ce08bb6e5060fd42e5',1,'vg::BaseOption::value()'],['../classvg_1_1SmallBitset.html#a486a8a8a5a30fab268ae96a9cf464fdd',1,'vg::SmallBitset::value()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#af141b75a2e3f2014b3289b3cffe99c44',1,'vg::ZipCodeTree::tree_item_t::value()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#a5d3fb39613dc2935ea316d87d2244f7b',1,'vg::ZipCodeForest::child_info_t::value()'],['../structvg_1_1subcommand_1_1Valuation.html#a88e369b92873968c8d7b68cc78ce1b1d',1,'vg::subcommand::Valuation::value()'],['../structvg_1_1subcommand_1_1ValueArgSpec.html#a518e378dc3759f070912c8cf42ae83cd',1,'vg::subcommand::ValueArgSpec::value()'],['../classvg_1_1io_1_1MessageIterator.html#a698864a67e1e721c06a97875f6cbcbde',1,'vg::io::MessageIterator::value()'],['../classvg_1_1io_1_1ProtobufIterator.html#aa66494ab08ee29d36b1aa04f0213f566',1,'vg::io::ProtobufIterator::value()']]],
+ ['value_5fat_13690',['value_at',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a2146c37988fd520600d806d1606f0f3f',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['value_5fbits_13691',['VALUE_BITS',['../classvg_1_1SmallBitset.html#a1570694b6aa163d390bc65f3ad2e015d',1,'vg::SmallBitset']]],
+ ['value_5fmask_13692',['VALUE_MASK',['../classvg_1_1SmallBitset.html#a0d940c085d362391f5bc531bd948623a',1,'vg::SmallBitset']]],
+ ['value_5fset_13693',['value_set',['../structvg_1_1subcommand_1_1ValueArgSpec.html#a215243ebe6068e28cb2ad00472a9a4d9',1,'vg::subcommand::ValueArgSpec']]],
+ ['value_5fshift_13694',['VALUE_SHIFT',['../classvg_1_1SmallBitset.html#ad5a1d72bf8ad3ce5c8341da2fa78eafb',1,'vg::SmallBitset']]],
+ ['values_13695',['values',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__collection__t.html#a341b8cdfa0d90adaea6f9c52196b5de6',1,'vg::MinimizerMapper::aligner_stats_t::stat_collection_t']]],
+ ['var_13696',['var',['../namespacevg.html#afe7fae89b379b5411189ac0ac74b2dd4',1,'vg']]],
+ ['variant_5falts_13697',['variant_alts',['../structvg_1_1VG_1_1Plan.html#ad2b28e3a651018396d6c0a1b3377e161',1,'vg::VG::Plan']]],
+ ['variant_5frange_13698',['variant_range',['../classvg_1_1VariantAdder.html#aa23751086259b5976ffe78169a6000b9',1,'vg::VariantAdder']]],
+ ['variant_5fsource_13699',['variant_source',['../classvg_1_1RareVariantSimplifier.html#afd96f926d4135c8c1ae967ad22aad03a',1,'vg::RareVariantSimplifier']]],
+ ['variant_5fto_5ftraversal_13700',['variant_to_traversal',['../classvg_1_1VG.html#ac697184acf2edadca58ddc776f9f4e7e',1,'vg::VG']]],
+ ['variants_5fafter_13701',['variants_after',['../classvg_1_1WindowedVcfBuffer.html#a8c0bf4d78e07bcc7ec8f58287452ad9e',1,'vg::WindowedVcfBuffer']]],
+ ['variants_5fbefore_13702',['variants_before',['../classvg_1_1WindowedVcfBuffer.html#a24156cab3205fcb845418259a91ada3a',1,'vg::WindowedVcfBuffer']]],
+ ['vars_5fper_5fchunk_13703',['vars_per_chunk',['../classvg_1_1Constructor.html#a7cc8ae0e38492082ba8e886ea174944f',1,'vg::Constructor']]],
+ ['vcf_5finput_13704',['vcf_input',['../structHaplotypesConfig.html#a8d58855b93c6c570420598f99f2d8ea2',1,'HaplotypesConfig']]],
+ ['vcf_5fto_5ffasta_5frenames_13705',['vcf_to_fasta_renames',['../classvg_1_1NameMapper.html#afd130381fc9ad1a930932e672fda80d1',1,'vg::NameMapper']]],
+ ['verbose_13706',['verbose',['../classvg_1_1NestedTraversalFinder.html#a67980934b7315e90dcd63fa046b465b7',1,'vg::NestedTraversalFinder::verbose()'],['../classvg_1_1ReadFilter.html#aa207b19d222c64919714bae506b726a6',1,'vg::ReadFilter::verbose()'],['../classvg_1_1RepresentativeTraversalFinder.html#a6af3519805d1115b006ad8b3bf2d3a3e',1,'vg::RepresentativeTraversalFinder::verbose()'],['../classvg_1_1io_1_1MessageIterator.html#af3f1540514c644f1d01212d515f603e6',1,'vg::io::MessageIterator::verbose()']]],
+ ['verbosity_13707',['verbosity',['../structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579',1,'vg::IndexingParameters::verbosity()'],['../classvg_1_1HaplotypePartitioner.html#ac5d1210d753c0fe6ed936f18f02e2cd2',1,'vg::HaplotypePartitioner::verbosity()'],['../classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12',1,'vg::Recombinator::verbosity()'],['../structHaplotypesConfig.html#ad04e07b242265b989bc2b93479676b84',1,'HaplotypesConfig::verbosity()']]],
+ ['version_13708',['version',['../structvg_1_1Haplotypes_1_1Header.html#ac2e1810f289c24ac4c2f74d8df9df5ec',1,'vg::Haplotypes::Header::version()'],['../classvg_1_1ZipCodeCollection.html#ad97d400ad51f2d7d1a880d81bbf8993d',1,'vg::ZipCodeCollection::version()'],['../structvg_1_1Haplotypes_1_1Header.html#a68bfc0fe68e8fc1b42ad078eaa234777',1,'vg::Haplotypes::Header::VERSION()'],['../classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222',1,'vg::Version::VERSION()']]],
+ ['vg_13709',['vg',['../classvg_1_1FlowSort.html#abd481c5b9e6c9c5aeaf846652dd3c76f',1,'vg::FlowSort']]],
+ ['vg_5ffilename_13710',['vg_filename',['../classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0',1,'vg::IndexedVG']]],
+ ['visit_13711',['visit',['../structvg_1_1SnarlTraversal.html#aff14559c1e4fb55bdf87320f3a4ee636',1,'vg::SnarlTraversal']]],
+ ['visited_13712',['visited',['../classvg_1_1HandleGraphNodeSet.html#a6a1318a8e451562f282bf960032634f4',1,'vg::HandleGraphNodeSet']]]
];
diff --git a/search/variables_17.js b/search/variables_17.js
index fedb263cd6..020df4a67f 100644
--- a/search/variables_17.js
+++ b/search/variables_17.js
@@ -1,43 +1,43 @@
var searchData=
[
- ['w_13709',['w',['../structHaplotypesConfig.html#afc08b5bf2dd526161ebb29c1ea37d1b4',1,'HaplotypesConfig']]],
- ['wabbit_5fmap_13710',['wabbit_map',['../classVectorizer.html#abc8fdb5dcd0ccc39c2b042633ef6820e',1,'Vectorizer']]],
- ['wait_5ffor_5fregion_13711',['wait_for_region',['../classvg_1_1GraphSynchronizer.html#a7f9e68c4e2172bc4a5c7040272a59d38',1,'vg::GraphSynchronizer']]],
- ['walk_5flisteners_13712',['walk_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a349711aec5bbd3063812eae72727c170',1,'vg::algorithms::GFAParser']]],
- ['warn_5fon_5fambiguous_13713',['warn_on_ambiguous',['../classvg_1_1Constructor.html#a24e663d6eee52a9f723faf398cf720fa',1,'vg::Constructor']]],
- ['warn_5fon_5flowercase_13714',['warn_on_lowercase',['../classvg_1_1Constructor.html#a9da8d803e6e0c0be942ca2ecc35e9267',1,'vg::Constructor']]],
- ['warn_5fon_5fmissing_5fvariants_13715',['warn_on_missing_variants',['../classvg_1_1HaplotypeIndexer.html#afb3592792a7d781cb6e88fe7949b7bfe',1,'vg::HaplotypeIndexer']]],
- ['warn_5fon_5fscore_5ffail_13716',['warn_on_score_fail',['../namespacehaplo.html#ab22b0954ba9062360178078ce504f1c2',1,'haplo']]],
- ['warned_5fabout_5fbad_5fdistribution_13717',['warned_about_bad_distribution',['../classvg_1_1MinimizerMapper.html#a3915618267605133f2e9144c693e68e5',1,'vg::MinimizerMapper']]],
- ['warned_5fabout_5fchunking_13718',['warned_about_chunking',['../classvg_1_1Mapper.html#a45dffe2dc008aebd254388281034d27f',1,'vg::Mapper']]],
- ['warned_5fabout_5frescue_5fsize_13719',['warned_about_rescue_size',['../classvg_1_1MinimizerMapper.html#a70bd402b25f6008362e82858be9fe9bc',1,'vg::MinimizerMapper']]],
- ['warned_5fabout_5frewrites_13720',['warned_about_rewrites',['../classvg_1_1VG.html#a8f0519dc706937b8b593f803f3d8eac4',1,'vg::VG']]],
- ['warned_5fabout_5fsubgraph_5fsize_13721',['warned_about_subgraph_size',['../classvg_1_1Surjector.html#affb3a5676516b7042d5c2d08734ea3c8',1,'vg::Surjector']]],
- ['warned_5fabout_5ftail_5fsize_13722',['warned_about_tail_size',['../classvg_1_1MinimizerMapper.html#a0b74ef2cf6f1fd04290172a91623584a',1,'vg::MinimizerMapper']]],
- ['watchdog_5ftimeout_13723',['watchdog_timeout',['../structGiraffeMainOptions.html#a51b24824ec0a06a5b080f8578090fa56',1,'GiraffeMainOptions']]],
- ['watcher_13724',['watcher',['../classvg_1_1Watchdog.html#a39ef2d296adea6283596aadd48457e02',1,'vg::Watchdog']]],
- ['wavefronts_13725',['wavefronts',['../structvg_1_1WFANode.html#a6b8938c80565dd8c9219945b2a5be194',1,'vg::WFANode']]],
- ['weight_13726',['weight',['../classvg_1_1MEMChainModelVertex.html#ad73c85aeb85dde48dd3201260720956b',1,'vg::MEMChainModelVertex::weight()'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a5e9984583bd37a31e8b172fea582e6fd',1,'vg::MEMClusterer::HitEdge::weight()'],['../classvg_1_1AlignmentChainModelVertex.html#a874c1b3121234990ab1c1519921b9c6c',1,'vg::AlignmentChainModelVertex::weight()'],['../structvg_1_1algorithms_1_1Edge.html#a25cfc0a5279fb8d40cc7527099449dc1',1,'vg::algorithms::Edge::weight()'],['../structvg_1_1algorithms_1_1Node.html#a38e105d20eb7efa802dd6b07824cd620',1,'vg::algorithms::Node::weight()']]],
- ['wfa_5fdistance_13727',['wfa_distance',['../classvg_1_1MinimizerMapper.html#adde3e90703e3137d7cb8a0e0c217686b',1,'vg::MinimizerMapper']]],
- ['wfa_5fdistance_5fper_5fbase_13728',['wfa_distance_per_base',['../classvg_1_1MinimizerMapper.html#ae77b975a0ba7e7bddf4d01e92074c1de',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fdistance_13729',['wfa_max_distance',['../classvg_1_1MinimizerMapper.html#a99da16075a34ebad4a01fe94f5d7d4cf',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fmax_5fmismatches_13730',['wfa_max_max_mismatches',['../classvg_1_1MinimizerMapper.html#a65d94bb81e375a2affda69e92e131908',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fmismatches_13731',['wfa_max_mismatches',['../classvg_1_1MinimizerMapper.html#a16b9080b48c374fd3a8d927368379bba',1,'vg::MinimizerMapper']]],
- ['wfa_5fmax_5fmismatches_5fper_5fbase_13732',['wfa_max_mismatches_per_base',['../classvg_1_1MinimizerMapper.html#af1800dc292b642aa366730c8f6034475',1,'vg::MinimizerMapper']]],
- ['wfa_5fmiddle_13733',['wfa_middle',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a18a47b29e26174cc24a57f71ec8f5f9c',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
- ['wfa_5ftail_13734',['wfa_tail',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#aaf4d71d87fb51ba736806a35cb6f1bc0',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
- ['whitespace_13735',['whitespace',['../namespacevg.html#a466eef41b2208daa1c649e71022cdc44',1,'vg']]],
- ['whole_5falignment_5fcutoff_13736',['whole_alignment_cutoff',['../classvg_1_1VariantAdder.html#ab40df39042e4ce4fee3eeea919be1c96',1,'vg::VariantAdder']]],
- ['whole_5fgraph_5flock_13737',['whole_graph_lock',['../classvg_1_1GraphSynchronizer.html#aa1a7be56b29656fa604b44b37e134c80',1,'vg::GraphSynchronizer']]],
- ['window_5flength_13738',['window_length',['../classvg_1_1Filter.html#ad719ad4c073cbe1298c9911e1c1cb329',1,'vg::Filter']]],
- ['window_5fshift_13739',['WINDOW_SHIFT',['../classvg_1_1StreamIndexBase.html#a1f8223f4ff9ca3d9892d13d2708aff73',1,'vg::StreamIndexBase']]],
- ['window_5fsize_13740',['window_size',['../classvg_1_1WindowedVcfBuffer.html#a898deb05050ba62533e294b7cf959fe3',1,'vg::WindowedVcfBuffer']]],
- ['window_5fto_5fstart_13741',['window_to_start',['../classvg_1_1StreamIndexBase.html#a47fab2baab7953595105558d0fcba4e2',1,'vg::StreamIndexBase']]],
- ['work_5fdir_13742',['work_dir',['../classvg_1_1IndexRegistry.html#ab2e9084645b146ff321f70a231161d66',1,'vg::IndexRegistry']]],
- ['wrapped_5fostream_13743',['wrapped_ostream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a14d9a1a0917016a7af46f2960608d302',1,'vg::io::BlockedGzipOutputStream']]],
- ['write_13744',['write',['../structhFILE__backend.html#ada22f61f6280c429aca37d82ef4c31a4',1,'hFILE_backend']]],
- ['write_5foutput_13745',['write_output',['../classvg_1_1ReadFilter.html#a249032f1613c12263e7c14d83b4e527e',1,'vg::ReadFilter']]],
- ['write_5ftsv_13746',['write_tsv',['../classvg_1_1ReadFilter.html#a9979d9966e9ea82a9cd160dbf38d4b7c',1,'vg::ReadFilter']]],
- ['writer_5fstop_13747',['writer_stop',['../classvg_1_1io_1_1StreamMultiplexer.html#ae51a3ffdfe9ec988bf732e4904dcbf60',1,'vg::io::StreamMultiplexer']]],
- ['writer_5fthread_13748',['writer_thread',['../classvg_1_1io_1_1StreamMultiplexer.html#a56a9d39b8ccdd13f07e835ad7a967a60',1,'vg::io::StreamMultiplexer']]]
+ ['w_13713',['w',['../structHaplotypesConfig.html#afc08b5bf2dd526161ebb29c1ea37d1b4',1,'HaplotypesConfig']]],
+ ['wabbit_5fmap_13714',['wabbit_map',['../classVectorizer.html#abc8fdb5dcd0ccc39c2b042633ef6820e',1,'Vectorizer']]],
+ ['wait_5ffor_5fregion_13715',['wait_for_region',['../classvg_1_1GraphSynchronizer.html#a7f9e68c4e2172bc4a5c7040272a59d38',1,'vg::GraphSynchronizer']]],
+ ['walk_5flisteners_13716',['walk_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#a349711aec5bbd3063812eae72727c170',1,'vg::algorithms::GFAParser']]],
+ ['warn_5fon_5fambiguous_13717',['warn_on_ambiguous',['../classvg_1_1Constructor.html#a24e663d6eee52a9f723faf398cf720fa',1,'vg::Constructor']]],
+ ['warn_5fon_5flowercase_13718',['warn_on_lowercase',['../classvg_1_1Constructor.html#a9da8d803e6e0c0be942ca2ecc35e9267',1,'vg::Constructor']]],
+ ['warn_5fon_5fmissing_5fvariants_13719',['warn_on_missing_variants',['../classvg_1_1HaplotypeIndexer.html#afb3592792a7d781cb6e88fe7949b7bfe',1,'vg::HaplotypeIndexer']]],
+ ['warn_5fon_5fscore_5ffail_13720',['warn_on_score_fail',['../namespacehaplo.html#ab22b0954ba9062360178078ce504f1c2',1,'haplo']]],
+ ['warned_5fabout_5fbad_5fdistribution_13721',['warned_about_bad_distribution',['../classvg_1_1MinimizerMapper.html#a3915618267605133f2e9144c693e68e5',1,'vg::MinimizerMapper']]],
+ ['warned_5fabout_5fchunking_13722',['warned_about_chunking',['../classvg_1_1Mapper.html#a45dffe2dc008aebd254388281034d27f',1,'vg::Mapper']]],
+ ['warned_5fabout_5frescue_5fsize_13723',['warned_about_rescue_size',['../classvg_1_1MinimizerMapper.html#a70bd402b25f6008362e82858be9fe9bc',1,'vg::MinimizerMapper']]],
+ ['warned_5fabout_5frewrites_13724',['warned_about_rewrites',['../classvg_1_1VG.html#a8f0519dc706937b8b593f803f3d8eac4',1,'vg::VG']]],
+ ['warned_5fabout_5fsubgraph_5fsize_13725',['warned_about_subgraph_size',['../classvg_1_1Surjector.html#affb3a5676516b7042d5c2d08734ea3c8',1,'vg::Surjector']]],
+ ['warned_5fabout_5ftail_5fsize_13726',['warned_about_tail_size',['../classvg_1_1MinimizerMapper.html#a0b74ef2cf6f1fd04290172a91623584a',1,'vg::MinimizerMapper']]],
+ ['watchdog_5ftimeout_13727',['watchdog_timeout',['../structGiraffeMainOptions.html#a51b24824ec0a06a5b080f8578090fa56',1,'GiraffeMainOptions']]],
+ ['watcher_13728',['watcher',['../classvg_1_1Watchdog.html#a39ef2d296adea6283596aadd48457e02',1,'vg::Watchdog']]],
+ ['wavefronts_13729',['wavefronts',['../structvg_1_1WFANode.html#a6b8938c80565dd8c9219945b2a5be194',1,'vg::WFANode']]],
+ ['weight_13730',['weight',['../classvg_1_1MEMChainModelVertex.html#ad73c85aeb85dde48dd3201260720956b',1,'vg::MEMChainModelVertex::weight()'],['../classvg_1_1MEMClusterer_1_1HitEdge.html#a5e9984583bd37a31e8b172fea582e6fd',1,'vg::MEMClusterer::HitEdge::weight()'],['../classvg_1_1AlignmentChainModelVertex.html#a874c1b3121234990ab1c1519921b9c6c',1,'vg::AlignmentChainModelVertex::weight()'],['../structvg_1_1algorithms_1_1Edge.html#a25cfc0a5279fb8d40cc7527099449dc1',1,'vg::algorithms::Edge::weight()'],['../structvg_1_1algorithms_1_1Node.html#a38e105d20eb7efa802dd6b07824cd620',1,'vg::algorithms::Node::weight()']]],
+ ['wfa_5fdistance_13731',['wfa_distance',['../classvg_1_1MinimizerMapper.html#adde3e90703e3137d7cb8a0e0c217686b',1,'vg::MinimizerMapper']]],
+ ['wfa_5fdistance_5fper_5fbase_13732',['wfa_distance_per_base',['../classvg_1_1MinimizerMapper.html#ae77b975a0ba7e7bddf4d01e92074c1de',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fdistance_13733',['wfa_max_distance',['../classvg_1_1MinimizerMapper.html#a99da16075a34ebad4a01fe94f5d7d4cf',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fmax_5fmismatches_13734',['wfa_max_max_mismatches',['../classvg_1_1MinimizerMapper.html#a65d94bb81e375a2affda69e92e131908',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fmismatches_13735',['wfa_max_mismatches',['../classvg_1_1MinimizerMapper.html#a16b9080b48c374fd3a8d927368379bba',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmax_5fmismatches_5fper_5fbase_13736',['wfa_max_mismatches_per_base',['../classvg_1_1MinimizerMapper.html#af1800dc292b642aa366730c8f6034475',1,'vg::MinimizerMapper']]],
+ ['wfa_5fmiddle_13737',['wfa_middle',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a18a47b29e26174cc24a57f71ec8f5f9c',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
+ ['wfa_5ftail_13738',['wfa_tail',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#aaf4d71d87fb51ba736806a35cb6f1bc0',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
+ ['whitespace_13739',['whitespace',['../namespacevg.html#a466eef41b2208daa1c649e71022cdc44',1,'vg']]],
+ ['whole_5falignment_5fcutoff_13740',['whole_alignment_cutoff',['../classvg_1_1VariantAdder.html#ab40df39042e4ce4fee3eeea919be1c96',1,'vg::VariantAdder']]],
+ ['whole_5fgraph_5flock_13741',['whole_graph_lock',['../classvg_1_1GraphSynchronizer.html#aa1a7be56b29656fa604b44b37e134c80',1,'vg::GraphSynchronizer']]],
+ ['window_5flength_13742',['window_length',['../classvg_1_1Filter.html#ad719ad4c073cbe1298c9911e1c1cb329',1,'vg::Filter']]],
+ ['window_5fshift_13743',['WINDOW_SHIFT',['../classvg_1_1StreamIndexBase.html#a1f8223f4ff9ca3d9892d13d2708aff73',1,'vg::StreamIndexBase']]],
+ ['window_5fsize_13744',['window_size',['../classvg_1_1WindowedVcfBuffer.html#a898deb05050ba62533e294b7cf959fe3',1,'vg::WindowedVcfBuffer']]],
+ ['window_5fto_5fstart_13745',['window_to_start',['../classvg_1_1StreamIndexBase.html#a47fab2baab7953595105558d0fcba4e2',1,'vg::StreamIndexBase']]],
+ ['work_5fdir_13746',['work_dir',['../classvg_1_1IndexRegistry.html#ab2e9084645b146ff321f70a231161d66',1,'vg::IndexRegistry']]],
+ ['wrapped_5fostream_13747',['wrapped_ostream',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a14d9a1a0917016a7af46f2960608d302',1,'vg::io::BlockedGzipOutputStream']]],
+ ['write_13748',['write',['../structhFILE__backend.html#ada22f61f6280c429aca37d82ef4c31a4',1,'hFILE_backend']]],
+ ['write_5foutput_13749',['write_output',['../classvg_1_1ReadFilter.html#a249032f1613c12263e7c14d83b4e527e',1,'vg::ReadFilter']]],
+ ['write_5ftsv_13750',['write_tsv',['../classvg_1_1ReadFilter.html#a9979d9966e9ea82a9cd160dbf38d4b7c',1,'vg::ReadFilter']]],
+ ['writer_5fstop_13751',['writer_stop',['../classvg_1_1io_1_1StreamMultiplexer.html#ae51a3ffdfe9ec988bf732e4904dcbf60',1,'vg::io::StreamMultiplexer']]],
+ ['writer_5fthread_13752',['writer_thread',['../classvg_1_1io_1_1StreamMultiplexer.html#a56a9d39b8ccdd13f07e835ad7a967a60',1,'vg::io::StreamMultiplexer']]]
];
diff --git a/search/variables_18.js b/search/variables_18.js
index 3e88d72db8..b19dba9e13 100644
--- a/search/variables_18.js
+++ b/search/variables_18.js
@@ -1,6 +1,6 @@
var searchData=
[
- ['xdrops_13749',['xdrops',['../classvg_1_1Aligner.html#a6379438f31b8f9f5900acb7ba00596f8',1,'vg::Aligner::xdrops()'],['../classvg_1_1QualAdjAligner.html#a996c23b1f8d703c099a376c0bc610a97',1,'vg::QualAdjAligner::xdrops()']]],
- ['xgidx_13750',['xgidx',['../classvg_1_1Viz.html#a1c854dabf978e525e6fab1223927ab2c',1,'vg::Viz']]],
- ['xindex_13751',['xindex',['../classvg_1_1BaseMapper.html#a0afffd854c5bcf69e8bd1125de4c7267',1,'vg::BaseMapper']]]
+ ['xdrops_13753',['xdrops',['../classvg_1_1Aligner.html#a6379438f31b8f9f5900acb7ba00596f8',1,'vg::Aligner::xdrops()'],['../classvg_1_1QualAdjAligner.html#a996c23b1f8d703c099a376c0bc610a97',1,'vg::QualAdjAligner::xdrops()']]],
+ ['xgidx_13754',['xgidx',['../classvg_1_1Viz.html#a1c854dabf978e525e6fab1223927ab2c',1,'vg::Viz']]],
+ ['xindex_13755',['xindex',['../classvg_1_1BaseMapper.html#a0afffd854c5bcf69e8bd1125de4c7267',1,'vg::BaseMapper']]]
];
diff --git a/search/variables_19.js b/search/variables_19.js
index 28b48717a8..aecd7379ee 100644
--- a/search/variables_19.js
+++ b/search/variables_19.js
@@ -1,11 +1,11 @@
var searchData=
[
- ['zip_5fcode_5ftree_13752',['zip_code_tree',['../classvg_1_1ZipCodeTree.html#ad2ffc1171ce7791a9c047612efddeeaa',1,'vg::ZipCodeTree']]],
- ['zip_5fforest_13753',['zip_forest',['../classvg_1_1MinimizerMapper.html#a5e9775389a175cbe4141678d5a4613dd',1,'vg::MinimizerMapper']]],
- ['zipcode_13754',['zipcode',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a97855edffa7660f988e3f4b7dad3fc9f',1,'vg::SnarlDistanceIndexClusterer::Seed::zipcode()'],['../classvg_1_1ZipCode.html#a4d8456b4edb18c6c6d812b05b5e4783e',1,'vg::ZipCode::zipcode()']]],
- ['zipcode_5fdepth_13755',['zipcode_depth',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d982a3ef3c1a8ec4c0759a6638e00a9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['zipcode_5ftree_5fcoverage_5fthreshold_13756',['zipcode_tree_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a3af651e9d670f2688887a78128db39f5',1,'vg::MinimizerMapper']]],
- ['zipcode_5ftree_5fscale_13757',['zipcode_tree_scale',['../classvg_1_1MinimizerMapper.html#ab88fdcdafabde8c33f21c176f544ab01',1,'vg::MinimizerMapper']]],
- ['zipcode_5ftree_5fscore_5fthreshold_13758',['zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a98bd33607a6fe87a99e24e6ea4388c01',1,'vg::MinimizerMapper']]],
- ['zipcodes_13759',['zipcodes',['../classvg_1_1MinimizerMapper.html#adc4e2829dcbe163a606e567373aa10f4',1,'vg::MinimizerMapper::zipcodes()'],['../classvg_1_1ZipCodeCollection.html#a73068c82a1be054f59074d37b63fe74d',1,'vg::ZipCodeCollection::zipcodes()']]]
+ ['zip_5fcode_5ftree_13756',['zip_code_tree',['../classvg_1_1ZipCodeTree.html#ad2ffc1171ce7791a9c047612efddeeaa',1,'vg::ZipCodeTree']]],
+ ['zip_5fforest_13757',['zip_forest',['../classvg_1_1MinimizerMapper.html#a5e9775389a175cbe4141678d5a4613dd',1,'vg::MinimizerMapper']]],
+ ['zipcode_13758',['zipcode',['../structvg_1_1SnarlDistanceIndexClusterer_1_1Seed.html#a97855edffa7660f988e3f4b7dad3fc9f',1,'vg::SnarlDistanceIndexClusterer::Seed::zipcode()'],['../classvg_1_1ZipCode.html#a4d8456b4edb18c6c6d812b05b5e4783e',1,'vg::ZipCode::zipcode()']]],
+ ['zipcode_5fdepth_13759',['zipcode_depth',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d982a3ef3c1a8ec4c0759a6638e00a9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['zipcode_5ftree_5fcoverage_5fthreshold_13760',['zipcode_tree_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a3af651e9d670f2688887a78128db39f5',1,'vg::MinimizerMapper']]],
+ ['zipcode_5ftree_5fscale_13761',['zipcode_tree_scale',['../classvg_1_1MinimizerMapper.html#ab88fdcdafabde8c33f21c176f544ab01',1,'vg::MinimizerMapper']]],
+ ['zipcode_5ftree_5fscore_5fthreshold_13762',['zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a98bd33607a6fe87a99e24e6ea4388c01',1,'vg::MinimizerMapper']]],
+ ['zipcodes_13763',['zipcodes',['../classvg_1_1MinimizerMapper.html#adc4e2829dcbe163a606e567373aa10f4',1,'vg::MinimizerMapper::zipcodes()'],['../classvg_1_1ZipCodeCollection.html#a73068c82a1be054f59074d37b63fe74d',1,'vg::ZipCodeCollection::zipcodes()']]]
];
diff --git a/search/variables_2.js b/search/variables_2.js
index f7250ba93e..c7db813b57 100644
--- a/search/variables_2.js
+++ b/search/variables_2.js
@@ -1,63 +1,63 @@
var searchData=
[
- ['backbone_11802',['backbone',['../structvg_1_1FlowSort_1_1Growth.html#a5ccf8c38e2125849aa7ca9881fd382a2',1,'vg::FlowSort::Growth']]],
- ['backed_5fup_11803',['backed_up',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a29a0e513c0dbdb75df3eccd7171f7126',1,'vg::io::BlockedGzipOutputStream']]],
- ['background_5fsampler_11804',['background_sampler',['../classvg_1_1NGSSimulator.html#af563bf84d1cde24a88de7c99c80bb554',1,'vg::NGSSimulator']]],
- ['backing_11805',['backing',['../classvg_1_1BackTranslatingAlignmentEmitter.html#aa2fa599b551d4fd3f919b52551b054a4',1,'vg::BackTranslatingAlignmentEmitter::backing()'],['../classvg_1_1ExtraNodeGraph.html#aa446c8a449571a12838c7854f6cd6e62',1,'vg::ExtraNodeGraph::backing()'],['../classvg_1_1SourceSinkOverlay.html#a7b24e9281e335eff4f843d8bcc404338',1,'vg::SourceSinkOverlay::backing()'],['../classvg_1_1SurjectingAlignmentEmitter.html#af0f444c46830595ef5e59b3a5a3ecf7f',1,'vg::SurjectingAlignmentEmitter::backing()']]],
- ['backing_5ffiles_11806',['backing_files',['../classvg_1_1HTSWriter.html#ad6b1fd5c6e6dc4f91601f115bd1e7410',1,'vg::HTSWriter']]],
- ['backing_5fgraph_11807',['backing_graph',['../classvg_1_1GenomeState.html#a6f80e8bfc104b6cdd893e5c4f531b7a5',1,'vg::GenomeState::backing_graph()'],['../classvg_1_1SnarlGraph.html#a0fb6ae55337eee52df735c639d95e0ee',1,'vg::SnarlGraph::backing_graph()'],['../classvg_1_1SubgraphOverlay.html#ad8dfd04e7366558348cbdfc8d2dcbe82',1,'vg::SubgraphOverlay::backing_graph()'],['../classvg_1_1SubpathOverlay.html#a488214ff530eb17181d5d874669f1fe8',1,'vg::SubpathOverlay::backing_graph()']]],
- ['backing_5fheads_11808',['backing_heads',['../classvg_1_1SourceSinkOverlay.html#a140bd95f83c688d57ee20d94f9d87632',1,'vg::SourceSinkOverlay']]],
- ['backing_5fpath_5fgraph_11809',['backing_path_graph',['../classvg_1_1PathSubgraphOverlay.html#aee64c898292ae80a20c103ff694044cc',1,'vg::PathSubgraphOverlay']]],
- ['backing_5fstream_11810',['backing_stream',['../classvg_1_1io_1_1StreamMultiplexer.html#a465b3bcbc4159b7cf997d35e972d6a03',1,'vg::io::StreamMultiplexer']]],
- ['backing_5ftails_11811',['backing_tails',['../classvg_1_1SourceSinkOverlay.html#ac110058d99ca5f758bbd5313475d4de0',1,'vg::SourceSinkOverlay']]],
- ['backward_11812',['backward',['../classvg_1_1NodeTraversal.html#a72105a87488c202b0326f4a5db46694c',1,'vg::NodeTraversal::backward()'],['../structvg_1_1KmerMatch.html#a412c20eb11307d010d98aac09f561865',1,'vg::KmerMatch::backward()'],['../structvg_1_1Visit.html#ae6f7470943b579f982246c3c581b6f21',1,'vg::Visit::backward()']]],
- ['bad_5fedit_5findex_11813',['bad_edit_index',['../structvg_1_1AlignmentValidity.html#a119694f70fdc07a8a330b28344d03085',1,'vg::AlignmentValidity']]],
- ['bad_5fmapping_5findex_11814',['bad_mapping_index',['../structvg_1_1AlignmentValidity.html#afbddd888c109262d0d44a1aeb0189a38',1,'vg::AlignmentValidity']]],
- ['bad_5fread_5fposition_11815',['bad_read_position',['../structvg_1_1AlignmentValidity.html#a0e6ae39178e6b06f429d262b1dd3cafe',1,'vg::AlignmentValidity']]],
- ['bad_5fsubchains_11816',['bad_subchains',['../structvg_1_1Recombinator_1_1Statistics.html#a9f62fa5f4471a9038be1f8f985bc23c6',1,'vg::Recombinator::Statistics']]],
- ['badness_5fthreshold_11817',['BADNESS_THRESHOLD',['../classvg_1_1Recombinator.html#ab0972e74057cd602cca62399879bf234',1,'vg::Recombinator::BADNESS_THRESHOLD()'],['../structvg_1_1Recombinator_1_1Parameters.html#ab5a37f5b72d89f7b60c4b62c53678a27',1,'vg::Recombinator::Parameters::badness_threshold()']]],
- ['bam_5fdna_5flookup_11818',['BAM_DNA_LOOKUP',['../namespacevg.html#ade7204b42260155b9a98a6d18c24a0b7',1,'vg']]],
- ['band_5fbegin_11819',['band_begin',['../classvg_1_1AlignmentChainModelVertex.html#a80e1c7143112904a01ece86659f4eefc',1,'vg::AlignmentChainModelVertex']]],
- ['band_5fidx_11820',['band_idx',['../classvg_1_1AlignmentChainModelVertex.html#a8205d0551dd9afb41286cbd0c495de5f',1,'vg::AlignmentChainModelVertex']]],
- ['band_5fmultimaps_11821',['band_multimaps',['../classvg_1_1Mapper.html#a14c43941838d031dd02e6917a82c7206',1,'vg::Mapper']]],
- ['banded_5fmatrices_11822',['banded_matrices',['../classvg_1_1BandedGlobalAligner.html#ab61c92f8ff975ce22553b7118267b9c7',1,'vg::BandedGlobalAligner']]],
- ['base_11823',['base',['../classvg_1_1WideningPRNG.html#a9b5354cb704288d9e1e1f32420fdc38a',1,'vg::WideningPRNG::base()'],['../structvg_1_1io_1_1hFILE__cppstream.html#a5be044ba653125da78a8cba8b8a47354',1,'vg::io::hFILE_cppstream::base()']]],
- ['base_5fgraph_11824',['base_graph',['../structvg_1_1AugmentedGraph.html#a0022757311c1ac569ebfa42e651637af',1,'vg::AugmentedGraph']]],
- ['base_5flocks_11825',['base_locks',['../classvg_1_1Packer.html#a737fd5df5675c766e4b7873ca0570e28',1,'vg::Packer']]],
- ['base_5fpileup_11826',['base_pileup',['../structvg_1_1NodePileup.html#a7ce88a430f079f1d72f96659edeb02de',1,'vg::NodePileup']]],
- ['baseline_5ferror_5flarge_11827',['baseline_error_large',['../classvg_1_1PoissonSupportSnarlCaller.html#a9164191ad441f1323f4b6cd406bc4030',1,'vg::PoissonSupportSnarlCaller']]],
- ['baseline_5ferror_5fsmall_11828',['baseline_error_small',['../classvg_1_1PoissonSupportSnarlCaller.html#a68e6d4d6785bdb4eca4f57504b7dcd21',1,'vg::PoissonSupportSnarlCaller']]],
- ['bases_11829',['bases',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#ac93c990d7797a13e58adfea3ef77c2c4',1,'vg::MinimizerMapper::aligner_stats_t::bases()'],['../structvg_1_1BasePileup.html#ab1ca874f6f9ee568866822a408300ba8',1,'vg::BasePileup::bases()']]],
- ['bases_5fper_5fchunk_11830',['bases_per_chunk',['../classvg_1_1Constructor.html#ae525487466a66456d7169cc5047abf90',1,'vg::Constructor']]],
- ['batch_5ffile_5fprefix_11831',['batch_file_prefix',['../classvg_1_1HaplotypeIndexer.html#aa818eebd7cffc81773e8bea65bd398cb',1,'vg::HaplotypeIndexer']]],
- ['batch_5fsize_11832',['batch_size',['../structvg_1_1RebuildParameters.html#a09072f32de9f3ee479f3d7d35f9aa851',1,'vg::RebuildParameters::batch_size()'],['../classvg_1_1ReadFilter.html#a89cd59970cfca5bf91f828f84035e39a',1,'vg::ReadFilter::batch_size()'],['../structGiraffeMainOptions.html#ad3fd6a5c42e1889a384cf319294d0d80',1,'GiraffeMainOptions::batch_size()']]],
- ['begin_11833',['begin',['../structvg_1_1kmer__t.html#ace8cd88692b6bb3c25a2989a4c505d1a',1,'vg::kmer_t::begin()'],['../classvg_1_1MaximalExactMatch.html#a894b11889ee0ef652acbfb84527e5225',1,'vg::MaximalExactMatch::begin()'],['../classvg_1_1PathNode.html#a4b103c45ebef87573a2b0288a2fc483c',1,'vg::PathNode::begin()'],['../structvg_1_1algorithms_1_1kmer__t.html#a7623139debae3d31f6246cfb4f4c0346',1,'vg::algorithms::kmer_t::begin()'],['../structvg_1_1algorithms_1_1walk__t.html#a3d07d5849d404936cf9dd87bb5071d4c',1,'vg::algorithms::walk_t::begin()']]],
- ['bga_5fmiddle_11834',['bga_middle',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a23f42993536a3162f0dec0ecfb826f80',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
- ['bgzf_5ffooter_5flength_11835',['BGZF_FOOTER_LENGTH',['../classvg_1_1HTSWriter.html#a00ebb72aacf4587e3d95a3a359da3323',1,'vg::HTSWriter']]],
- ['bgzip_5fin_11836',['bgzip_in',['../classvg_1_1io_1_1MessageIterator.html#a7102e7dfdf1fbcfcd0b037eb39b8d21f',1,'vg::io::MessageIterator']]],
- ['bgzip_5fout_11837',['bgzip_out',['../classvg_1_1io_1_1MessageEmitter.html#a591f1c1d3271301d0df6999cf15eb801',1,'vg::io::MessageEmitter']]],
- ['bidirectional_5fhaplo_5ftx_5fgbwt_11838',['bidirectional_haplo_tx_gbwt',['../structvg_1_1IndexingParameters.html#a68d4ceb62ffb8768c1b2334475843333',1,'vg::IndexingParameters']]],
- ['bin_5fsize_11839',['bin_size',['../classvg_1_1Packer.html#a528fbf835285899061cd6947e163976d',1,'vg::Packer']]],
- ['bin_5fto_5franges_11840',['bin_to_ranges',['../classvg_1_1StreamIndexBase.html#a4801a54e202c9214718c71db7cea12a9',1,'vg::StreamIndexBase']]],
- ['bins_5fby_5fid_5fprefix_11841',['bins_by_id_prefix',['../classvg_1_1StreamIndexBase.html#a19b9a91061212bfd558a384fa19d4854',1,'vg::StreamIndexBase']]],
- ['bit_5flength_11842',['bit_length',['../classvg_1_1BitString.html#afa7b98ed5fc1b88e1a0fa99fd23ab991',1,'vg::BitString']]],
- ['bits_11843',['bits',['../classvg_1_1BitString.html#a42e6375ac0a96473ebe1884625732419',1,'vg::BitString']]],
- ['block_5flength_11844',['block_length',['../structgafkluge_1_1GafRecord.html#a7db887c2322105fed3d1a6cf5251a4b8',1,'gafkluge::GafRecord']]],
- ['border_11845',['border',['../classvg_1_1PhaseUnfolder.html#a29ec1d4e6557b27c4f92c0280c80b90a',1,'vg::PhaseUnfolder']]],
- ['border_5foffsets_11846',['border_offsets',['../structvg_1_1Exon.html#a8795bd3f2b1e61bb0566258c071668b7',1,'vg::Exon']]],
- ['border_5fsteps_11847',['border_steps',['../structvg_1_1Exon.html#a5bf97d169b75ac1c1d3ef1dd216da4a6',1,'vg::Exon']]],
- ['bottom_11848',['bottom',['../structhaplo_1_1int__itvl__t.html#a9124b7f6c7e637788d1a72b54ac1b7dc',1,'haplo::int_itvl_t']]],
- ['bottom_5fdiag_11849',['bottom_diag',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a9814adda35066d761c279d543a2493a2',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['buf_11850',['buf',['../classvg_1_1io_1_1fdostream.html#a29e1c13616b7f681cc118a0f87cf41f3',1,'vg::io::fdostream::buf()'],['../classvg_1_1io_1_1fdistream.html#ac2350f53e295903da182147ae46bc5f9',1,'vg::io::fdistream::buf()'],['../classvg_1_1io_1_1streamistream.html#ac4e5618c21e53b709bb7a8c2fe60edde',1,'vg::io::streamistream::buf()']]],
- ['buffer_11851',['buffer',['../classvg_1_1ParallelKFFReader.html#a168bab05d98310420ce3fe904ef4d7fc',1,'vg::ParallelKFFReader::buffer()'],['../classvg_1_1VcfBuffer.html#a92c8a919554e2a7dd2ca34fae94948fc',1,'vg::VcfBuffer::buffer()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aab5cfa13ff5e0449e105a0d9117aa38f',1,'vg::io::BlockedGzipOutputStream::buffer()'],['../classvg_1_1io_1_1fdinbuf.html#a1d32c47153a2a414ab06c867f0e05dfb',1,'vg::io::fdinbuf::buffer()'],['../classvg_1_1io_1_1streaminbuf.html#a183f94182736936b75529e14fad0f395',1,'vg::io::streaminbuf::buffer()']]],
- ['buffer_5fsize_11852',['buffer_size',['../classvg_1_1ReadFilter.html#a2d00933de6bd943fed0a4ec48112f39e',1,'vg::ReadFilter::buffer_size()'],['../structvg_1_1Recombinator_1_1Parameters.html#af3236201a75f6aab642971e426299d8f',1,'vg::Recombinator::Parameters::buffer_size()']]],
- ['bufsize_11853',['bufSize',['../classvg_1_1io_1_1fdinbuf.html#ae20c45d02cdacbc8a27b61ac41eb8f6f',1,'vg::io::fdinbuf::bufSize()'],['../classvg_1_1io_1_1streaminbuf.html#a633a4a419dad259a742de7e50f0568f1',1,'vg::io::streaminbuf::bufSize()']]],
- ['build_11854',['build',['../structGBWTConfig.html#a42e99c87bd24d0ac5c3fc7ba0ab55408',1,'GBWTConfig']]],
- ['build_5fhost_11855',['BUILD_HOST',['../classvg_1_1Version.html#a6e1e33f37aa4d73f0a9038e03bbbaec7',1,'vg::Version']]],
- ['build_5fjobs_11856',['build_jobs',['../structGBWTConfig.html#a8a68b2e91d01ea3d3ea71bc2f8a5898b',1,'GBWTConfig']]],
- ['build_5fuser_11857',['BUILD_USER',['../classvg_1_1Version.html#a0ed0401bd4a0b5d42c2c40048f67f66c',1,'vg::Version']]],
- ['burn_5fin_11858',['burn_in',['../classvg_1_1MCMCGenotyper.html#a90b861c9698794a805c9276064f9551c',1,'vg::MCMCGenotyper']]],
- ['by_5fid_11859',['by_id',['../structvg_1_1PathIndex.html#a3f5697a5db586a467dc4923e2cccbfe1',1,'vg::PathIndex']]],
- ['by_5fstart_11860',['by_start',['../structvg_1_1PathIndex.html#a55cb6181f7b4b80016aaf2fefbb402c2',1,'vg::PathIndex']]],
- ['byte_5fcount_11861',['byte_count',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aca10a84d86b0e9db6ef5727f9e454add',1,'vg::io::BlockedGzipInputStream::byte_count()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a745da931cd84709a1a8b8f64e357d2fb',1,'vg::io::BlockedGzipOutputStream::byte_count()']]]
+ ['backbone_11806',['backbone',['../structvg_1_1FlowSort_1_1Growth.html#a5ccf8c38e2125849aa7ca9881fd382a2',1,'vg::FlowSort::Growth']]],
+ ['backed_5fup_11807',['backed_up',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a29a0e513c0dbdb75df3eccd7171f7126',1,'vg::io::BlockedGzipOutputStream']]],
+ ['background_5fsampler_11808',['background_sampler',['../classvg_1_1NGSSimulator.html#af563bf84d1cde24a88de7c99c80bb554',1,'vg::NGSSimulator']]],
+ ['backing_11809',['backing',['../classvg_1_1BackTranslatingAlignmentEmitter.html#aa2fa599b551d4fd3f919b52551b054a4',1,'vg::BackTranslatingAlignmentEmitter::backing()'],['../classvg_1_1ExtraNodeGraph.html#aa446c8a449571a12838c7854f6cd6e62',1,'vg::ExtraNodeGraph::backing()'],['../classvg_1_1SourceSinkOverlay.html#a7b24e9281e335eff4f843d8bcc404338',1,'vg::SourceSinkOverlay::backing()'],['../classvg_1_1SurjectingAlignmentEmitter.html#af0f444c46830595ef5e59b3a5a3ecf7f',1,'vg::SurjectingAlignmentEmitter::backing()']]],
+ ['backing_5ffiles_11810',['backing_files',['../classvg_1_1HTSWriter.html#ad6b1fd5c6e6dc4f91601f115bd1e7410',1,'vg::HTSWriter']]],
+ ['backing_5fgraph_11811',['backing_graph',['../classvg_1_1GenomeState.html#a6f80e8bfc104b6cdd893e5c4f531b7a5',1,'vg::GenomeState::backing_graph()'],['../classvg_1_1SnarlGraph.html#a0fb6ae55337eee52df735c639d95e0ee',1,'vg::SnarlGraph::backing_graph()'],['../classvg_1_1SubgraphOverlay.html#ad8dfd04e7366558348cbdfc8d2dcbe82',1,'vg::SubgraphOverlay::backing_graph()'],['../classvg_1_1SubpathOverlay.html#a488214ff530eb17181d5d874669f1fe8',1,'vg::SubpathOverlay::backing_graph()']]],
+ ['backing_5fheads_11812',['backing_heads',['../classvg_1_1SourceSinkOverlay.html#a140bd95f83c688d57ee20d94f9d87632',1,'vg::SourceSinkOverlay']]],
+ ['backing_5fpath_5fgraph_11813',['backing_path_graph',['../classvg_1_1PathSubgraphOverlay.html#aee64c898292ae80a20c103ff694044cc',1,'vg::PathSubgraphOverlay']]],
+ ['backing_5fstream_11814',['backing_stream',['../classvg_1_1io_1_1StreamMultiplexer.html#a465b3bcbc4159b7cf997d35e972d6a03',1,'vg::io::StreamMultiplexer']]],
+ ['backing_5ftails_11815',['backing_tails',['../classvg_1_1SourceSinkOverlay.html#ac110058d99ca5f758bbd5313475d4de0',1,'vg::SourceSinkOverlay']]],
+ ['backward_11816',['backward',['../classvg_1_1NodeTraversal.html#a72105a87488c202b0326f4a5db46694c',1,'vg::NodeTraversal::backward()'],['../structvg_1_1KmerMatch.html#a412c20eb11307d010d98aac09f561865',1,'vg::KmerMatch::backward()'],['../structvg_1_1Visit.html#ae6f7470943b579f982246c3c581b6f21',1,'vg::Visit::backward()']]],
+ ['bad_5fedit_5findex_11817',['bad_edit_index',['../structvg_1_1AlignmentValidity.html#a119694f70fdc07a8a330b28344d03085',1,'vg::AlignmentValidity']]],
+ ['bad_5fmapping_5findex_11818',['bad_mapping_index',['../structvg_1_1AlignmentValidity.html#afbddd888c109262d0d44a1aeb0189a38',1,'vg::AlignmentValidity']]],
+ ['bad_5fread_5fposition_11819',['bad_read_position',['../structvg_1_1AlignmentValidity.html#a0e6ae39178e6b06f429d262b1dd3cafe',1,'vg::AlignmentValidity']]],
+ ['bad_5fsubchains_11820',['bad_subchains',['../structvg_1_1Recombinator_1_1Statistics.html#a9f62fa5f4471a9038be1f8f985bc23c6',1,'vg::Recombinator::Statistics']]],
+ ['badness_5fthreshold_11821',['BADNESS_THRESHOLD',['../classvg_1_1Recombinator.html#ab0972e74057cd602cca62399879bf234',1,'vg::Recombinator::BADNESS_THRESHOLD()'],['../structvg_1_1Recombinator_1_1Parameters.html#ab5a37f5b72d89f7b60c4b62c53678a27',1,'vg::Recombinator::Parameters::badness_threshold()']]],
+ ['bam_5fdna_5flookup_11822',['BAM_DNA_LOOKUP',['../namespacevg.html#ade7204b42260155b9a98a6d18c24a0b7',1,'vg']]],
+ ['band_5fbegin_11823',['band_begin',['../classvg_1_1AlignmentChainModelVertex.html#a80e1c7143112904a01ece86659f4eefc',1,'vg::AlignmentChainModelVertex']]],
+ ['band_5fidx_11824',['band_idx',['../classvg_1_1AlignmentChainModelVertex.html#a8205d0551dd9afb41286cbd0c495de5f',1,'vg::AlignmentChainModelVertex']]],
+ ['band_5fmultimaps_11825',['band_multimaps',['../classvg_1_1Mapper.html#a14c43941838d031dd02e6917a82c7206',1,'vg::Mapper']]],
+ ['banded_5fmatrices_11826',['banded_matrices',['../classvg_1_1BandedGlobalAligner.html#ab61c92f8ff975ce22553b7118267b9c7',1,'vg::BandedGlobalAligner']]],
+ ['base_11827',['base',['../classvg_1_1WideningPRNG.html#a9b5354cb704288d9e1e1f32420fdc38a',1,'vg::WideningPRNG::base()'],['../structvg_1_1io_1_1hFILE__cppstream.html#a5be044ba653125da78a8cba8b8a47354',1,'vg::io::hFILE_cppstream::base()']]],
+ ['base_5fgraph_11828',['base_graph',['../structvg_1_1AugmentedGraph.html#a0022757311c1ac569ebfa42e651637af',1,'vg::AugmentedGraph']]],
+ ['base_5flocks_11829',['base_locks',['../classvg_1_1Packer.html#a737fd5df5675c766e4b7873ca0570e28',1,'vg::Packer']]],
+ ['base_5fpileup_11830',['base_pileup',['../structvg_1_1NodePileup.html#a7ce88a430f079f1d72f96659edeb02de',1,'vg::NodePileup']]],
+ ['baseline_5ferror_5flarge_11831',['baseline_error_large',['../classvg_1_1PoissonSupportSnarlCaller.html#a9164191ad441f1323f4b6cd406bc4030',1,'vg::PoissonSupportSnarlCaller']]],
+ ['baseline_5ferror_5fsmall_11832',['baseline_error_small',['../classvg_1_1PoissonSupportSnarlCaller.html#a68e6d4d6785bdb4eca4f57504b7dcd21',1,'vg::PoissonSupportSnarlCaller']]],
+ ['bases_11833',['bases',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#ac93c990d7797a13e58adfea3ef77c2c4',1,'vg::MinimizerMapper::aligner_stats_t::bases()'],['../structvg_1_1BasePileup.html#ab1ca874f6f9ee568866822a408300ba8',1,'vg::BasePileup::bases()']]],
+ ['bases_5fper_5fchunk_11834',['bases_per_chunk',['../classvg_1_1Constructor.html#ae525487466a66456d7169cc5047abf90',1,'vg::Constructor']]],
+ ['batch_5ffile_5fprefix_11835',['batch_file_prefix',['../classvg_1_1HaplotypeIndexer.html#aa818eebd7cffc81773e8bea65bd398cb',1,'vg::HaplotypeIndexer']]],
+ ['batch_5fsize_11836',['batch_size',['../structvg_1_1RebuildParameters.html#a09072f32de9f3ee479f3d7d35f9aa851',1,'vg::RebuildParameters::batch_size()'],['../classvg_1_1ReadFilter.html#a89cd59970cfca5bf91f828f84035e39a',1,'vg::ReadFilter::batch_size()'],['../structGiraffeMainOptions.html#ad3fd6a5c42e1889a384cf319294d0d80',1,'GiraffeMainOptions::batch_size()']]],
+ ['begin_11837',['begin',['../structvg_1_1kmer__t.html#ace8cd88692b6bb3c25a2989a4c505d1a',1,'vg::kmer_t::begin()'],['../classvg_1_1MaximalExactMatch.html#a894b11889ee0ef652acbfb84527e5225',1,'vg::MaximalExactMatch::begin()'],['../classvg_1_1PathNode.html#a4b103c45ebef87573a2b0288a2fc483c',1,'vg::PathNode::begin()'],['../structvg_1_1algorithms_1_1kmer__t.html#a7623139debae3d31f6246cfb4f4c0346',1,'vg::algorithms::kmer_t::begin()'],['../structvg_1_1algorithms_1_1walk__t.html#a3d07d5849d404936cf9dd87bb5071d4c',1,'vg::algorithms::walk_t::begin()']]],
+ ['bga_5fmiddle_11838',['bga_middle',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a23f42993536a3162f0dec0ecfb826f80',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
+ ['bgzf_5ffooter_5flength_11839',['BGZF_FOOTER_LENGTH',['../classvg_1_1HTSWriter.html#a00ebb72aacf4587e3d95a3a359da3323',1,'vg::HTSWriter']]],
+ ['bgzip_5fin_11840',['bgzip_in',['../classvg_1_1io_1_1MessageIterator.html#a7102e7dfdf1fbcfcd0b037eb39b8d21f',1,'vg::io::MessageIterator']]],
+ ['bgzip_5fout_11841',['bgzip_out',['../classvg_1_1io_1_1MessageEmitter.html#a591f1c1d3271301d0df6999cf15eb801',1,'vg::io::MessageEmitter']]],
+ ['bidirectional_5fhaplo_5ftx_5fgbwt_11842',['bidirectional_haplo_tx_gbwt',['../structvg_1_1IndexingParameters.html#a68d4ceb62ffb8768c1b2334475843333',1,'vg::IndexingParameters']]],
+ ['bin_5fsize_11843',['bin_size',['../classvg_1_1Packer.html#a528fbf835285899061cd6947e163976d',1,'vg::Packer']]],
+ ['bin_5fto_5franges_11844',['bin_to_ranges',['../classvg_1_1StreamIndexBase.html#a4801a54e202c9214718c71db7cea12a9',1,'vg::StreamIndexBase']]],
+ ['bins_5fby_5fid_5fprefix_11845',['bins_by_id_prefix',['../classvg_1_1StreamIndexBase.html#a19b9a91061212bfd558a384fa19d4854',1,'vg::StreamIndexBase']]],
+ ['bit_5flength_11846',['bit_length',['../classvg_1_1BitString.html#afa7b98ed5fc1b88e1a0fa99fd23ab991',1,'vg::BitString']]],
+ ['bits_11847',['bits',['../classvg_1_1BitString.html#a42e6375ac0a96473ebe1884625732419',1,'vg::BitString']]],
+ ['block_5flength_11848',['block_length',['../structgafkluge_1_1GafRecord.html#a7db887c2322105fed3d1a6cf5251a4b8',1,'gafkluge::GafRecord']]],
+ ['border_11849',['border',['../classvg_1_1PhaseUnfolder.html#a29ec1d4e6557b27c4f92c0280c80b90a',1,'vg::PhaseUnfolder']]],
+ ['border_5foffsets_11850',['border_offsets',['../structvg_1_1Exon.html#a8795bd3f2b1e61bb0566258c071668b7',1,'vg::Exon']]],
+ ['border_5fsteps_11851',['border_steps',['../structvg_1_1Exon.html#a5bf97d169b75ac1c1d3ef1dd216da4a6',1,'vg::Exon']]],
+ ['bottom_11852',['bottom',['../structhaplo_1_1int__itvl__t.html#a9124b7f6c7e637788d1a72b54ac1b7dc',1,'haplo::int_itvl_t']]],
+ ['bottom_5fdiag_11853',['bottom_diag',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a9814adda35066d761c279d543a2493a2',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['buf_11854',['buf',['../classvg_1_1io_1_1fdostream.html#a29e1c13616b7f681cc118a0f87cf41f3',1,'vg::io::fdostream::buf()'],['../classvg_1_1io_1_1fdistream.html#ac2350f53e295903da182147ae46bc5f9',1,'vg::io::fdistream::buf()'],['../classvg_1_1io_1_1streamistream.html#ac4e5618c21e53b709bb7a8c2fe60edde',1,'vg::io::streamistream::buf()']]],
+ ['buffer_11855',['buffer',['../classvg_1_1ParallelKFFReader.html#a168bab05d98310420ce3fe904ef4d7fc',1,'vg::ParallelKFFReader::buffer()'],['../classvg_1_1VcfBuffer.html#a92c8a919554e2a7dd2ca34fae94948fc',1,'vg::VcfBuffer::buffer()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#aab5cfa13ff5e0449e105a0d9117aa38f',1,'vg::io::BlockedGzipOutputStream::buffer()'],['../classvg_1_1io_1_1fdinbuf.html#a1d32c47153a2a414ab06c867f0e05dfb',1,'vg::io::fdinbuf::buffer()'],['../classvg_1_1io_1_1streaminbuf.html#a183f94182736936b75529e14fad0f395',1,'vg::io::streaminbuf::buffer()']]],
+ ['buffer_5fsize_11856',['buffer_size',['../classvg_1_1ReadFilter.html#a2d00933de6bd943fed0a4ec48112f39e',1,'vg::ReadFilter::buffer_size()'],['../structvg_1_1Recombinator_1_1Parameters.html#af3236201a75f6aab642971e426299d8f',1,'vg::Recombinator::Parameters::buffer_size()']]],
+ ['bufsize_11857',['bufSize',['../classvg_1_1io_1_1fdinbuf.html#ae20c45d02cdacbc8a27b61ac41eb8f6f',1,'vg::io::fdinbuf::bufSize()'],['../classvg_1_1io_1_1streaminbuf.html#a633a4a419dad259a742de7e50f0568f1',1,'vg::io::streaminbuf::bufSize()']]],
+ ['build_11858',['build',['../structGBWTConfig.html#a42e99c87bd24d0ac5c3fc7ba0ab55408',1,'GBWTConfig']]],
+ ['build_5fhost_11859',['BUILD_HOST',['../classvg_1_1Version.html#a6e1e33f37aa4d73f0a9038e03bbbaec7',1,'vg::Version']]],
+ ['build_5fjobs_11860',['build_jobs',['../structGBWTConfig.html#a8a68b2e91d01ea3d3ea71bc2f8a5898b',1,'GBWTConfig']]],
+ ['build_5fuser_11861',['BUILD_USER',['../classvg_1_1Version.html#a0ed0401bd4a0b5d42c2c40048f67f66c',1,'vg::Version']]],
+ ['burn_5fin_11862',['burn_in',['../classvg_1_1MCMCGenotyper.html#a90b861c9698794a805c9276064f9551c',1,'vg::MCMCGenotyper']]],
+ ['by_5fid_11863',['by_id',['../structvg_1_1PathIndex.html#a3f5697a5db586a467dc4923e2cccbfe1',1,'vg::PathIndex']]],
+ ['by_5fstart_11864',['by_start',['../structvg_1_1PathIndex.html#a55cb6181f7b4b80016aaf2fefbb402c2',1,'vg::PathIndex']]],
+ ['byte_5fcount_11865',['byte_count',['../classvg_1_1io_1_1BlockedGzipInputStream.html#aca10a84d86b0e9db6ef5727f9e454add',1,'vg::io::BlockedGzipInputStream::byte_count()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a745da931cd84709a1a8b8f64e357d2fb',1,'vg::io::BlockedGzipOutputStream::byte_count()']]]
];
diff --git a/search/variables_3.js b/search/variables_3.js
index 65eff651f8..601bfcc815 100644
--- a/search/variables_3.js
+++ b/search/variables_3.js
@@ -1,110 +1,110 @@
var searchData=
[
- ['cache_5fmutex_11862',['cache_mutex',['../classvg_1_1IndexedVG.html#aa347c0557a522623570dd02e7dee39e0',1,'vg::IndexedVG']]],
- ['cached_5ffragment_5fdirection_11863',['cached_fragment_direction',['../classvg_1_1FragmentLengthStatistics.html#a98af439ae4d8612054a965bd7b9a5420',1,'vg::FragmentLengthStatistics']]],
- ['cached_5ffragment_5flength_5fmean_11864',['cached_fragment_length_mean',['../classvg_1_1FragmentLengthStatistics.html#a837fe6834481ce1b4981c8838a88c9c2',1,'vg::FragmentLengthStatistics']]],
- ['cached_5ffragment_5flength_5fstdev_11865',['cached_fragment_length_stdev',['../classvg_1_1FragmentLengthStatistics.html#ab1e6c7664c21e3ab33a68fd3e37e48d0',1,'vg::FragmentLengthStatistics']]],
- ['cached_5ffragment_5forientation_5fsame_11866',['cached_fragment_orientation_same',['../classvg_1_1FragmentLengthStatistics.html#ac7d06aa4fc1cc543f395ac2f7edaf583',1,'vg::FragmentLengthStatistics']]],
- ['cached_5fgenotypes_11867',['cached_genotypes',['../classvg_1_1WindowedVcfBuffer.html#a3ad6b744291240805d0a810a9399c1fc',1,'vg::WindowedVcfBuffer']]],
- ['candidate_5fnode_11868',['candidate_node',['../classvg_1_1WFATree.html#a6b2349b00204c39b5495f7e5163c51f3',1,'vg::WFATree']]],
- ['candidate_5fpoint_11869',['candidate_point',['../classvg_1_1WFATree.html#aa76e2e4ad1b023beda464e4e74312df5',1,'vg::WFATree']]],
- ['candidates_5fper_5fwindow_11870',['candidates_per_window',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ab1badd75611d7d30cfcc7d387aa2986a',1,'vg::MinimizerMapper::Minimizer']]],
- ['category_11871',['category',['../classvg_1_1subcommand_1_1Subcommand.html#a6042accceefeb06bb5c072932f4b7ac7',1,'vg::subcommand::Subcommand']]],
- ['chain_5fcomponent_11872',['chain_component',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#a03483f9fdf052ee593d00ec7c81a112e',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild::chain_component()'],['../structvg_1_1ZipCode_1_1node__code__t.html#a1ee3a4ce4e384773a2e60529d0ffa164',1,'vg::ZipCode::node_code_t::chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#abc0c1e1fe5087a0d66770e9c50307087',1,'vg::ZipCode::snarl_code_t::chain_component()'],['../structvg_1_1MIPayload.html#a1626a24c1382d7ea6d3adac18e5b99da',1,'vg::MIPayload::chain_component()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#ac8523531191e2bcc417241927652a796',1,'vg::ZipCodeForest::child_info_t::chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a1cfde618c8d709150e74189e0cba5a27',1,'vg::ZipCodeForest::sort_value_t::chain_component()']]],
- ['chain_5fcomponent_5fcount_5foffset_11873',['CHAIN_COMPONENT_COUNT_OFFSET',['../classvg_1_1ZipCode.html#ab40504f6209a6f30cb7e378fbf33f0de',1,'vg::ZipCode']]],
- ['chain_5fcomponent_5fend_11874',['chain_component_end',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#abaf783676e94e3827f49b82101aa0fdb',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['chain_5fcomponent_5fstart_11875',['chain_component_start',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#aabdc7d7fb2de98df48fcf1c8757c1de3',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['chain_5fdeletions_11876',['chain_deletions',['../classvg_1_1Constructor.html#a57a532cd2bab1d857bee058633ffa525',1,'vg::Constructor']]],
- ['chain_5fend_11877',['chain_end',['../structvg_1_1ChainIterator.html#a84b0d882b4586bd543ec841c6b3dfdc9',1,'vg::ChainIterator']]],
- ['chain_5fend_5frewrites_11878',['chain_end_rewrites',['../classvg_1_1NetGraph.html#a68b5171889d2b1ec26040f5e38fae86e',1,'vg::NetGraph']]],
- ['chain_5fends_5fby_5fstart_11879',['chain_ends_by_start',['../classvg_1_1NetGraph.html#a76c5bb7e62e87ab890cf7568c8ab74b6',1,'vg::NetGraph']]],
- ['chain_5fid_11880',['chain_id',['../structHaplotypesConfig.html#a75b5eb4fa333aa23bc509da04d7fa8c4',1,'HaplotypesConfig']]],
- ['chain_5flength_5foffset_11881',['CHAIN_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a757ad6220e506eab844abfb8cba7708d',1,'vg::ZipCode']]],
- ['chain_5forder_11882',['chain_order',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a8f666fce1536ead5badef1f8d4bf933d',1,'vg::ZipCodeForest::sort_value_t']]],
- ['chain_5frank_5fin_5fsnarl_5foffset_11883',['CHAIN_RANK_IN_SNARL_OFFSET',['../classvg_1_1ZipCode.html#a2743aa5e6e6311cca7ecae55060fcca0',1,'vg::ZipCode']]],
- ['chain_5fscore_5fthreshold_11884',['chain_score_threshold',['../classvg_1_1MinimizerMapper.html#a012d6c74e5b277ee2e6367cf23bfd080',1,'vg::MinimizerMapper']]],
- ['chain_5fsize_11885',['CHAIN_SIZE',['../classvg_1_1ZipCode.html#afd9eacafb083235372fdaf423d80f0ab',1,'vg::ZipCode']]],
- ['chain_5fstart_11886',['chain_start',['../structvg_1_1ChainIterator.html#a61e019f94f481b190d14bebe51264c09',1,'vg::ChainIterator']]],
- ['chains_11887',['chains',['../classvg_1_1Haplotypes.html#aabf788ef8783a229fa095209bf61d7eb',1,'vg::Haplotypes::chains()'],['../structvg_1_1Recombinator_1_1Statistics.html#aaa836bc7ed5921c15348a6de2eb7d70c',1,'vg::Recombinator::Statistics::chains()']]],
- ['char_5fcount_11888',['char_count',['../classvg_1_1Pictographs.html#ad19f958ce6ab190b47a0c2761923d013',1,'vg::Pictographs']]],
- ['chars_11889',['chars',['../classvg_1_1Pictographs.html#a322a2d02ca384f0c182944bf8eebcb09',1,'vg::Pictographs']]],
- ['checkin_5fhigh_5fwater_5fkb_11890',['checkin_high_water_kb',['../structvg_1_1Watchdog_1_1thread__state__t.html#a5f8bf15e6a488344b99f4bad238ac8c3',1,'vg::Watchdog::thread_state_t']]],
- ['child_5fchains_11891',['child_chains',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a4d3d44b4a07fd7598a414eae1f5a2d33',1,'vg::SnarlManager::SnarlRecord']]],
- ['child_5fcount_11892',['child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a4e3ac789e40b6f4121617e005714a79c',1,'vg::ZipCode::snarl_code_t']]],
- ['child_5fsnarls_11893',['child_snarls',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a9d15f088f3408149667a770a317be38b',1,'vg::Deconstructor::NestingInfo']]],
- ['child_5fsupport_5fmap_11894',['child_support_map',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#a74cf9ff59f390e4f99f035a88a1955a7',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
- ['children_11895',['children',['../structvg_1_1WFANode.html#a3526a0ecf760bf0026933381d155d03e',1,'vg::WFANode::children()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af8ca30771e80ac1edcd8faf25c062ccb',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::children()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a0bfacb041ef897faedba2cf2585c9fb0',1,'vg::SnarlManager::SnarlRecord::children()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#aec0e7ef56323148869869a0b02560aa5',1,'vg::BitStringTree::TreeNode::children()'],['../classvg_1_1TreeSubgraph.html#a77f31b395c329f4c42d585208e8f9683',1,'vg::TreeSubgraph::children()'],['../structvg_1_1TreeNode.html#a5a5645da982fa8a9acb280ef031960d2',1,'vg::TreeNode::children()']]],
- ['choose_5fband_5fpadding_11896',['choose_band_padding',['../classvg_1_1MinimizerMapper.html#acf23e356fb872617417ff73d54f6f141',1,'vg::MinimizerMapper::choose_band_padding()'],['../classvg_1_1MultipathMapper.html#ad22aedacbf14468b19d459ca6f54abb8',1,'vg::MultipathMapper::choose_band_padding()'],['../classvg_1_1Surjector.html#affc7c08128f0896d0f45637f569d4fd7',1,'vg::Surjector::choose_band_padding()']]],
- ['chrom_11897',['chrom',['../structvg_1_1Transcript.html#aa2556a6a9f2d167e0dee96f4539a1546',1,'vg::Transcript']]],
- ['chrom_5flength_11898',['chrom_length',['../structvg_1_1Transcript.html#ab05bde98d9d530da82b09c58bba3a99b',1,'vg::Transcript']]],
- ['circular_11899',['circular',['../classvg_1_1Paths.html#ad8af70b16e2280fba6e46418842229fa',1,'vg::Paths']]],
- ['close_11900',['close',['../structhFILE__backend.html#a590725a4192591efd3349067808cde27',1,'hFILE_backend']]],
- ['cluster_5fcoverage_5fthreshold_11901',['cluster_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a4aa953562a49de5befd8c80ee5e84a22',1,'vg::MinimizerMapper']]],
- ['cluster_5fnum_11902',['cluster_num',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#aa8519f410a3b43ce925c5fc921baa9f2',1,'vg::SnarlDistanceIndexClusterer::ClusterHead']]],
- ['cluster_5fscore_5fthreshold_11903',['cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a10276fc66be2c41c2ebebd78e1f643de',1,'vg::MinimizerMapper']]],
- ['cluster_5fthreshold_11904',['cluster_threshold',['../classvg_1_1Deconstructor.html#aa017394121b89e9cc01409fbf4590284',1,'vg::Deconstructor']]],
- ['clusterer_11905',['clusterer',['../classvg_1_1MinimizerMapper.html#a1d3d028f723db14f5b41bf892e991c6d',1,'vg::MinimizerMapper']]],
- ['code_5ftype_11906',['code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a719ada0df51daf0a56ec5bfc4dea9e79',1,'vg::ZipCode::snarl_code_t::code_type()'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ad6d61cbfe143a02c7ddfaf0ff5247328',1,'vg::ZipCodeForest::interval_state_t::code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aedfc6150b51e00a2825e71fc5198362e',1,'vg::ZipCodeForest::sort_value_t::code_type()']]],
- ['codenames_11907',['codenames',['../classvg_1_1Version.html#afa3c976df333371eaad42c698bf4a5a9',1,'vg::Version']]],
- ['codes_5fby_5foption_11908',['codes_by_option',['../classvg_1_1ConfigurableParser.html#aea0db01f1fd00b96a309053cb66881c4',1,'vg::ConfigurableParser']]],
- ['cohort_11909',['cohort',['../structhaplo_1_1linear__haplo__structure.html#ae0e8f21ee11e664612aefb8f0f678c40',1,'haplo::linear_haplo_structure']]],
- ['col_5fidx_11910',['col_idx',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#aac3083f9fb9e9521011f7a637753c302',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['colors_11911',['colors',['../classvg_1_1Colors.html#a20b7cf0022c8e1340b82176e5715cd2f',1,'vg::Colors']]],
- ['column_5fnumber_11912',['column_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#af7c4a1117dd302f20b96d796d289e35c',1,'vg::algorithms::GFAFormatError']]],
- ['column_5fof_11913',['column_of',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#af6f26344b2eec01c2f3847dfbbad5b3d',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['compiler_11914',['COMPILER',['../classvg_1_1Version.html#a20177da26bdbb15b48bae0c20b02b273',1,'vg::Version']]],
- ['complement_11915',['complement',['../classvg_1_1ReverseGraph.html#af2508e0ccbc9186701840c7630b7c505',1,'vg::ReverseGraph::complement()'],['../structvg_1_1ChainIterator.html#a6699e092f944e1c311b4bbdf2e2cbe38',1,'vg::ChainIterator::complement()']]],
- ['complement_5ffilter_11916',['complement_filter',['../classvg_1_1ReadFilter.html#ab7e72e4f3440fdc2a846de1e81fe2230',1,'vg::ReadFilter']]],
- ['component_5fmin_5fdist_11917',['component_min_dist',['../classvg_1_1MultipathMapper.html#a0e4207de854cc470b9bd734b459e1b9c',1,'vg::MultipathMapper']]],
- ['component_5fparams_11918',['component_params',['../classvg_1_1SpliceStats.html#a047fa558519f40fb6414f4f2499be210',1,'vg::SpliceStats']]],
- ['component_5fpath_5fset_5fof_5fpath_11919',['component_path_set_of_path',['../classvg_1_1PathComponentIndex.html#acfecfcd0941270d0811524d8b029dc53',1,'vg::PathComponentIndex']]],
- ['component_5fpath_5fsets_11920',['component_path_sets',['../classvg_1_1PathComponentIndex.html#ac569cc4c6e7d19c65b82db1fe781cbb8',1,'vg::PathComponentIndex']]],
- ['components_11921',['components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab0952f2992c99f031ac813bfa563bf34',1,'vg::MEMClusterer::HitGraph']]],
- ['compressed_11922',['compressed',['../structvg_1_1GBWTHandler.html#ab411b9b6da9c6f80918cc64718761490',1,'vg::GBWTHandler']]],
- ['cond_5fdistrs_11923',['cond_distrs',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a8bef106a51ae52b02b3cf9ea9179dc69',1,'vg::NGSSimulator::MarkovDistribution']]],
- ['configurables_11924',['configurables',['../classvg_1_1ConfigurableParser.html#a022f098012e68510e490a407261bf01e',1,'vg::ConfigurableParser']]],
- ['connection_11925',['connection',['../structvg_1_1Subpath.html#a45ec767985d769bc4998fa7d705e90f9',1,'vg::Subpath']]],
- ['connections_11926',['connections',['../structvg_1_1Recombinator_1_1Statistics.html#aa7af651546e773183d3b4e182f97645d',1,'vg::Recombinator::Statistics']]],
- ['connectivity_11927',['connectivity',['../classvg_1_1NetGraph.html#aa1014dccd8e1bfa54a434a6caf0c4d40',1,'vg::NetGraph::connectivity()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#aa0fbdc9240295e4abbc909b68a6e591a',1,'vg::ZipCode::chain_code_t::connectivity()']]],
- ['consistent_11928',['consistent',['../structvg_1_1Genotyper_1_1Affinity.html#af58e963c9680682966f810d4f922cb5f',1,'vg::Genotyper::Affinity']]],
- ['construction_5fjobs_11929',['construction_jobs',['../structvg_1_1Haplotypes_1_1Header.html#a3e2571325f5aaeabced578bc43c8533c',1,'vg::Haplotypes::Header']]],
- ['containing_5fnet_5fhandle_11930',['containing_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a8416c3bb55a8a3e699348067738c900b',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['content_11931',['content',['../structvg_1_1BitStringTree_1_1TreeNode.html#a654e2ccb451511ff925aa9d66e290fbe',1,'vg::BitStringTree::TreeNode']]],
- ['contents_11932',['contents',['../classvg_1_1SubHandleGraph.html#a6d06eff177c6d87feadd561675c11b73',1,'vg::SubHandleGraph::contents()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a6e710dba31d9417bb75647b7f25fbab0',1,'handlegraph::algorithms::SubHandleGraph::contents()']]],
- ['context_5fbases_11933',['context_bases',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ae4a5790fef0070239e02d0f14bab68c3',1,'vg::GraphSynchronizer::Lock']]],
- ['context_5flength_11934',['context_length',['../structGBWTConfig.html#acc79271b2d7fe244bb008277aa3564ec',1,'GBWTConfig']]],
- ['contig_11935',['contig',['../structvg_1_1BREAKPOINT.html#a8daffa4f64b5d59660eb3b3b00de7d0a',1,'vg::BREAKPOINT']]],
- ['contig_5fname_11936',['contig_name',['../structvg_1_1RecombinatorHaplotype.html#ab812d5260c6b86e1568c4d25bfdbe488',1,'vg::RecombinatorHaplotype::contig_name()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a9478eb5ec8559cfcfcb57677e718e256',1,'vg::Haplotypes::TopLevelChain::contig_name()']]],
- ['contig_5fprefix_11937',['contig_prefix',['../structHaplotypesConfig.html#aafaf3f6a87d34073bd46ea058b1f9e73',1,'HaplotypesConfig']]],
- ['contigs_11938',['contigs',['../structGBWTConfig.html#a72eddaf43b65805e38fc978933fd8b2d',1,'GBWTConfig']]],
- ['control_5fmean_11939',['control_mean',['../structvg_1_1BenchmarkResult.html#a54072b6e4cb8401a4784e9e20b3ca6de',1,'vg::BenchmarkResult']]],
- ['control_5fstddev_11940',['control_stddev',['../structvg_1_1BenchmarkResult.html#ac6db5580a02c1860981365245812304e',1,'vg::BenchmarkResult']]],
- ['coordinates_11941',['coordinates',['../structvg_1_1Exon.html#a845cd3e89b345eeeba6177c6cdbf202a',1,'vg::Exon']]],
- ['copy_5fid_11942',['copy_id',['../structvg_1_1TranscriptPath.html#af8b88c3ff6130af4aaa1674d30cbc89d',1,'vg::TranscriptPath']]],
- ['correct_11943',['correct',['../structvg_1_1Alignment.html#a07751b50cfb9c985fccc2c701bfc55fc',1,'vg::Alignment']]],
- ['correctly_5fmapped_11944',['correctly_mapped',['../structvg_1_1Alignment.html#a9ec303e39d844ec1e6289ddfbcdd7911',1,'vg::Alignment']]],
- ['count_11945',['count',['../classvg_1_1count__back__inserter.html#aab6ae0ee48226650d3e5833c4bdd787a',1,'vg::count_back_inserter']]],
- ['count_5fof_5fmax_11946',['count_of_max',['../structvg_1_1SummaryStatistics.html#a3245d457bac967cb81a89a1351016b9b',1,'vg::SummaryStatistics']]],
- ['count_5fpaths_11947',['count_paths',['../structGBWTConfig.html#a9a0bd4ea251be07cbe2336a93981b614',1,'GBWTConfig']]],
- ['counts_11948',['counts',['../structvg_1_1Counts.html#ada1e3e24df7c078970806cb6da1fce51',1,'vg::Counts']]],
- ['cov_5fbin_5fsize_11949',['cov_bin_size',['../classvg_1_1Packer.html#a63fd3c0a6d18bbb64f18e3afbecd552c',1,'vg::Packer']]],
- ['coverage_11950',['COVERAGE',['../classvg_1_1Recombinator.html#a567c0ae71f8bae880186eb4758dc2cd1',1,'vg::Recombinator::COVERAGE()'],['../structvg_1_1Recombinator_1_1Parameters.html#a53570bd1e3ae8fc31135027b77784d18',1,'vg::Recombinator::Parameters::coverage()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#add34ea5cbb2c555485c0b9be5d22b668',1,'vg::SnarlDistanceIndexClusterer::Cluster::coverage()']]],
- ['coverage_5fciv_11951',['coverage_civ',['../classvg_1_1Packer.html#adc0b40cfa531d0edbc50c9ed7bfcf84e',1,'vg::Packer']]],
- ['coverage_5fdynamic_11952',['coverage_dynamic',['../classvg_1_1Packer.html#a6d48a90c1ed0484bc7992ee798003a0b',1,'vg::Packer']]],
- ['cr_11953',['cr',['../classvg_1_1Viz.html#a1c514ef7170a0f6a195aeed7b2cd0b20',1,'vg::Viz']]],
- ['crossing_5fedges_11954',['crossing_edges',['../classvg_1_1PhaseUnfolder.html#a326b5a34e3c5255b95fbad3eb536fa48',1,'vg::PhaseUnfolder']]],
- ['cumulative_5fseq_5flen_11955',['cumulative_seq_len',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a60ef2a91471d83aaaa6d52cb13b800e8',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['curr_11956',['curr',['../structvg_1_1kmer__t.html#a9b8741fa3ec61bc5f1e03bbf86455be6',1,'vg::kmer_t::curr()'],['../structvg_1_1PathBranch.html#a14bc112cacb6ea533eef7f69d2abb4c5',1,'vg::PathBranch::curr()'],['../structvg_1_1algorithms_1_1kmer__t.html#a461e739df40ec66bba376bfd913bcc10',1,'vg::algorithms::kmer_t::curr()'],['../structvg_1_1algorithms_1_1walk__t.html#a0940baf10cc23ee2c424ccf2b2cd61d4',1,'vg::algorithms::walk_t::curr()']]],
- ['curr_5fdeflxn_11957',['curr_deflxn',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#ad6fb487aa27ac7baca766a597243fe99',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['curr_5ftraceback_11958',['curr_traceback',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9e2f8458aa7f547adda7154ef90a1c5c',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['current_11959',['current',['../structvg_1_1IncrementIter.html#a63f121c026a4681a4bf61ad56198542b',1,'vg::IncrementIter::current()'],['../classvg_1_1WindowedVcfBuffer.html#a9e4eeb593eee805717734190d9940f79',1,'vg::WindowedVcfBuffer::current()']]],
- ['current_5fchains_11960',['current_chains',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af221d0d08c843344be01e68bd1c0464e',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['current_5fid_11961',['current_id',['../classvg_1_1VG.html#a68f4b0cfbadab3cebace110733565d38',1,'vg::VG']]],
- ['current_5fnode_5fid_11962',['current_node_id',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#afbd1560242a69c0b36dbe0f6ffb81684',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['current_5fnode_5fsequence_11963',['current_node_sequence',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a47a70166200af736bc64f4cc7adbfdad',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['current_5fstate_11964',['current_state',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ab50fbed67d1840cdf36756e1b9d7f67f',1,'vg::ZipCodeTree::reverse_iterator']]],
- ['current_5fversion_11965',['CURRENT_VERSION',['../classxg_1_1XG.html#a4d1d5b61619c685244aeaaa4830cb285',1,'xg::XG']]],
- ['cursor_5fpool_11966',['cursor_pool',['../classvg_1_1IndexedVG.html#a62d27a5ec1f917733604d724ab413f7f',1,'vg::IndexedVG']]],
- ['cursor_5fpool_5fmutex_11967',['cursor_pool_mutex',['../classvg_1_1IndexedVG.html#a0e1a3526d6d76ea816b5cc579ae39227',1,'vg::IndexedVG']]],
- ['cursor_5fstreams_11968',['cursor_streams',['../classvg_1_1IndexedVG.html#a73bae46f21d980ec8b4f198396c8060a',1,'vg::IndexedVG']]]
+ ['cache_5fmutex_11866',['cache_mutex',['../classvg_1_1IndexedVG.html#aa347c0557a522623570dd02e7dee39e0',1,'vg::IndexedVG']]],
+ ['cached_5ffragment_5fdirection_11867',['cached_fragment_direction',['../classvg_1_1FragmentLengthStatistics.html#a98af439ae4d8612054a965bd7b9a5420',1,'vg::FragmentLengthStatistics']]],
+ ['cached_5ffragment_5flength_5fmean_11868',['cached_fragment_length_mean',['../classvg_1_1FragmentLengthStatistics.html#a837fe6834481ce1b4981c8838a88c9c2',1,'vg::FragmentLengthStatistics']]],
+ ['cached_5ffragment_5flength_5fstdev_11869',['cached_fragment_length_stdev',['../classvg_1_1FragmentLengthStatistics.html#ab1e6c7664c21e3ab33a68fd3e37e48d0',1,'vg::FragmentLengthStatistics']]],
+ ['cached_5ffragment_5forientation_5fsame_11870',['cached_fragment_orientation_same',['../classvg_1_1FragmentLengthStatistics.html#ac7d06aa4fc1cc543f395ac2f7edaf583',1,'vg::FragmentLengthStatistics']]],
+ ['cached_5fgenotypes_11871',['cached_genotypes',['../classvg_1_1WindowedVcfBuffer.html#a3ad6b744291240805d0a810a9399c1fc',1,'vg::WindowedVcfBuffer']]],
+ ['candidate_5fnode_11872',['candidate_node',['../classvg_1_1WFATree.html#a6b2349b00204c39b5495f7e5163c51f3',1,'vg::WFATree']]],
+ ['candidate_5fpoint_11873',['candidate_point',['../classvg_1_1WFATree.html#aa76e2e4ad1b023beda464e4e74312df5',1,'vg::WFATree']]],
+ ['candidates_5fper_5fwindow_11874',['candidates_per_window',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ab1badd75611d7d30cfcc7d387aa2986a',1,'vg::MinimizerMapper::Minimizer']]],
+ ['category_11875',['category',['../classvg_1_1subcommand_1_1Subcommand.html#a6042accceefeb06bb5c072932f4b7ac7',1,'vg::subcommand::Subcommand']]],
+ ['chain_5fcomponent_11876',['chain_component',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#a03483f9fdf052ee593d00ec7c81a112e',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild::chain_component()'],['../structvg_1_1ZipCode_1_1node__code__t.html#a1ee3a4ce4e384773a2e60529d0ffa164',1,'vg::ZipCode::node_code_t::chain_component()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#abc0c1e1fe5087a0d66770e9c50307087',1,'vg::ZipCode::snarl_code_t::chain_component()'],['../structvg_1_1MIPayload.html#a1626a24c1382d7ea6d3adac18e5b99da',1,'vg::MIPayload::chain_component()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#ac8523531191e2bcc417241927652a796',1,'vg::ZipCodeForest::child_info_t::chain_component()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a1cfde618c8d709150e74189e0cba5a27',1,'vg::ZipCodeForest::sort_value_t::chain_component()']]],
+ ['chain_5fcomponent_5fcount_5foffset_11877',['CHAIN_COMPONENT_COUNT_OFFSET',['../classvg_1_1ZipCode.html#ab40504f6209a6f30cb7e378fbf33f0de',1,'vg::ZipCode']]],
+ ['chain_5fcomponent_5fend_11878',['chain_component_end',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#abaf783676e94e3827f49b82101aa0fdb',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['chain_5fcomponent_5fstart_11879',['chain_component_start',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#aabdc7d7fb2de98df48fcf1c8757c1de3',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['chain_5fdeletions_11880',['chain_deletions',['../classvg_1_1Constructor.html#a57a532cd2bab1d857bee058633ffa525',1,'vg::Constructor']]],
+ ['chain_5fend_11881',['chain_end',['../structvg_1_1ChainIterator.html#a84b0d882b4586bd543ec841c6b3dfdc9',1,'vg::ChainIterator']]],
+ ['chain_5fend_5frewrites_11882',['chain_end_rewrites',['../classvg_1_1NetGraph.html#a68b5171889d2b1ec26040f5e38fae86e',1,'vg::NetGraph']]],
+ ['chain_5fends_5fby_5fstart_11883',['chain_ends_by_start',['../classvg_1_1NetGraph.html#a76c5bb7e62e87ab890cf7568c8ab74b6',1,'vg::NetGraph']]],
+ ['chain_5fid_11884',['chain_id',['../structHaplotypesConfig.html#a75b5eb4fa333aa23bc509da04d7fa8c4',1,'HaplotypesConfig']]],
+ ['chain_5flength_5foffset_11885',['CHAIN_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a757ad6220e506eab844abfb8cba7708d',1,'vg::ZipCode']]],
+ ['chain_5forder_11886',['chain_order',['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#a8f666fce1536ead5badef1f8d4bf933d',1,'vg::ZipCodeForest::sort_value_t']]],
+ ['chain_5frank_5fin_5fsnarl_5foffset_11887',['CHAIN_RANK_IN_SNARL_OFFSET',['../classvg_1_1ZipCode.html#a2743aa5e6e6311cca7ecae55060fcca0',1,'vg::ZipCode']]],
+ ['chain_5fscore_5fthreshold_11888',['chain_score_threshold',['../classvg_1_1MinimizerMapper.html#a012d6c74e5b277ee2e6367cf23bfd080',1,'vg::MinimizerMapper']]],
+ ['chain_5fsize_11889',['CHAIN_SIZE',['../classvg_1_1ZipCode.html#afd9eacafb083235372fdaf423d80f0ab',1,'vg::ZipCode']]],
+ ['chain_5fstart_11890',['chain_start',['../structvg_1_1ChainIterator.html#a61e019f94f481b190d14bebe51264c09',1,'vg::ChainIterator']]],
+ ['chains_11891',['chains',['../classvg_1_1Haplotypes.html#aabf788ef8783a229fa095209bf61d7eb',1,'vg::Haplotypes::chains()'],['../structvg_1_1Recombinator_1_1Statistics.html#aaa836bc7ed5921c15348a6de2eb7d70c',1,'vg::Recombinator::Statistics::chains()']]],
+ ['char_5fcount_11892',['char_count',['../classvg_1_1Pictographs.html#ad19f958ce6ab190b47a0c2761923d013',1,'vg::Pictographs']]],
+ ['chars_11893',['chars',['../classvg_1_1Pictographs.html#a322a2d02ca384f0c182944bf8eebcb09',1,'vg::Pictographs']]],
+ ['checkin_5fhigh_5fwater_5fkb_11894',['checkin_high_water_kb',['../structvg_1_1Watchdog_1_1thread__state__t.html#a5f8bf15e6a488344b99f4bad238ac8c3',1,'vg::Watchdog::thread_state_t']]],
+ ['child_5fchains_11895',['child_chains',['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a4d3d44b4a07fd7598a414eae1f5a2d33',1,'vg::SnarlManager::SnarlRecord']]],
+ ['child_5fcount_11896',['child_count',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a4e3ac789e40b6f4121617e005714a79c',1,'vg::ZipCode::snarl_code_t']]],
+ ['child_5fsnarls_11897',['child_snarls',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a9d15f088f3408149667a770a317be38b',1,'vg::Deconstructor::NestingInfo']]],
+ ['child_5fsupport_5fmap_11898',['child_support_map',['../classvg_1_1NestedCachedPackedTraversalSupportFinder.html#a74cf9ff59f390e4f99f035a88a1955a7',1,'vg::NestedCachedPackedTraversalSupportFinder']]],
+ ['children_11899',['children',['../structvg_1_1WFANode.html#a3526a0ecf760bf0026933381d155d03e',1,'vg::WFANode::children()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af8ca30771e80ac1edcd8faf25c062ccb',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::children()'],['../structvg_1_1SnarlManager_1_1SnarlRecord.html#a0bfacb041ef897faedba2cf2585c9fb0',1,'vg::SnarlManager::SnarlRecord::children()'],['../structvg_1_1BitStringTree_1_1TreeNode.html#aec0e7ef56323148869869a0b02560aa5',1,'vg::BitStringTree::TreeNode::children()'],['../classvg_1_1TreeSubgraph.html#a77f31b395c329f4c42d585208e8f9683',1,'vg::TreeSubgraph::children()'],['../structvg_1_1TreeNode.html#a5a5645da982fa8a9acb280ef031960d2',1,'vg::TreeNode::children()']]],
+ ['choose_5fband_5fpadding_11900',['choose_band_padding',['../classvg_1_1MinimizerMapper.html#acf23e356fb872617417ff73d54f6f141',1,'vg::MinimizerMapper::choose_band_padding()'],['../classvg_1_1MultipathMapper.html#ad22aedacbf14468b19d459ca6f54abb8',1,'vg::MultipathMapper::choose_band_padding()'],['../classvg_1_1Surjector.html#affc7c08128f0896d0f45637f569d4fd7',1,'vg::Surjector::choose_band_padding()']]],
+ ['chrom_11901',['chrom',['../structvg_1_1Transcript.html#aa2556a6a9f2d167e0dee96f4539a1546',1,'vg::Transcript']]],
+ ['chrom_5flength_11902',['chrom_length',['../structvg_1_1Transcript.html#ab05bde98d9d530da82b09c58bba3a99b',1,'vg::Transcript']]],
+ ['circular_11903',['circular',['../classvg_1_1Paths.html#ad8af70b16e2280fba6e46418842229fa',1,'vg::Paths']]],
+ ['close_11904',['close',['../structhFILE__backend.html#a590725a4192591efd3349067808cde27',1,'hFILE_backend']]],
+ ['cluster_5fcoverage_5fthreshold_11905',['cluster_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a4aa953562a49de5befd8c80ee5e84a22',1,'vg::MinimizerMapper']]],
+ ['cluster_5fnum_11906',['cluster_num',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#aa8519f410a3b43ce925c5fc921baa9f2',1,'vg::SnarlDistanceIndexClusterer::ClusterHead']]],
+ ['cluster_5fscore_5fthreshold_11907',['cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a10276fc66be2c41c2ebebd78e1f643de',1,'vg::MinimizerMapper']]],
+ ['cluster_5fthreshold_11908',['cluster_threshold',['../classvg_1_1Deconstructor.html#aa017394121b89e9cc01409fbf4590284',1,'vg::Deconstructor']]],
+ ['clusterer_11909',['clusterer',['../classvg_1_1MinimizerMapper.html#a1d3d028f723db14f5b41bf892e991c6d',1,'vg::MinimizerMapper']]],
+ ['code_5ftype_11910',['code_type',['../structvg_1_1ZipCode_1_1snarl__code__t.html#a719ada0df51daf0a56ec5bfc4dea9e79',1,'vg::ZipCode::snarl_code_t::code_type()'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ad6d61cbfe143a02c7ddfaf0ff5247328',1,'vg::ZipCodeForest::interval_state_t::code_type()'],['../structvg_1_1ZipCodeForest_1_1sort__value__t.html#aedfc6150b51e00a2825e71fc5198362e',1,'vg::ZipCodeForest::sort_value_t::code_type()']]],
+ ['codenames_11911',['codenames',['../classvg_1_1Version.html#afa3c976df333371eaad42c698bf4a5a9',1,'vg::Version']]],
+ ['codes_5fby_5foption_11912',['codes_by_option',['../classvg_1_1ConfigurableParser.html#aea0db01f1fd00b96a309053cb66881c4',1,'vg::ConfigurableParser']]],
+ ['cohort_11913',['cohort',['../structhaplo_1_1linear__haplo__structure.html#ae0e8f21ee11e664612aefb8f0f678c40',1,'haplo::linear_haplo_structure']]],
+ ['col_5fidx_11914',['col_idx',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#aac3083f9fb9e9521011f7a637753c302',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['colors_11915',['colors',['../classvg_1_1Colors.html#a20b7cf0022c8e1340b82176e5715cd2f',1,'vg::Colors']]],
+ ['column_5fnumber_11916',['column_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#af7c4a1117dd302f20b96d796d289e35c',1,'vg::algorithms::GFAFormatError']]],
+ ['column_5fof_11917',['column_of',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#af6f26344b2eec01c2f3847dfbbad5b3d',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['compiler_11918',['COMPILER',['../classvg_1_1Version.html#a20177da26bdbb15b48bae0c20b02b273',1,'vg::Version']]],
+ ['complement_11919',['complement',['../classvg_1_1ReverseGraph.html#af2508e0ccbc9186701840c7630b7c505',1,'vg::ReverseGraph::complement()'],['../structvg_1_1ChainIterator.html#a6699e092f944e1c311b4bbdf2e2cbe38',1,'vg::ChainIterator::complement()']]],
+ ['complement_5ffilter_11920',['complement_filter',['../classvg_1_1ReadFilter.html#ab7e72e4f3440fdc2a846de1e81fe2230',1,'vg::ReadFilter']]],
+ ['component_5fmin_5fdist_11921',['component_min_dist',['../classvg_1_1MultipathMapper.html#a0e4207de854cc470b9bd734b459e1b9c',1,'vg::MultipathMapper']]],
+ ['component_5fparams_11922',['component_params',['../classvg_1_1SpliceStats.html#a047fa558519f40fb6414f4f2499be210',1,'vg::SpliceStats']]],
+ ['component_5fpath_5fset_5fof_5fpath_11923',['component_path_set_of_path',['../classvg_1_1PathComponentIndex.html#acfecfcd0941270d0811524d8b029dc53',1,'vg::PathComponentIndex']]],
+ ['component_5fpath_5fsets_11924',['component_path_sets',['../classvg_1_1PathComponentIndex.html#ac569cc4c6e7d19c65b82db1fe781cbb8',1,'vg::PathComponentIndex']]],
+ ['components_11925',['components',['../classvg_1_1MEMClusterer_1_1HitGraph.html#ab0952f2992c99f031ac813bfa563bf34',1,'vg::MEMClusterer::HitGraph']]],
+ ['compressed_11926',['compressed',['../structvg_1_1GBWTHandler.html#ab411b9b6da9c6f80918cc64718761490',1,'vg::GBWTHandler']]],
+ ['cond_5fdistrs_11927',['cond_distrs',['../classvg_1_1NGSSimulator_1_1MarkovDistribution.html#a8bef106a51ae52b02b3cf9ea9179dc69',1,'vg::NGSSimulator::MarkovDistribution']]],
+ ['configurables_11928',['configurables',['../classvg_1_1ConfigurableParser.html#a022f098012e68510e490a407261bf01e',1,'vg::ConfigurableParser']]],
+ ['connection_11929',['connection',['../structvg_1_1Subpath.html#a45ec767985d769bc4998fa7d705e90f9',1,'vg::Subpath']]],
+ ['connections_11930',['connections',['../structvg_1_1Recombinator_1_1Statistics.html#aa7af651546e773183d3b4e182f97645d',1,'vg::Recombinator::Statistics']]],
+ ['connectivity_11931',['connectivity',['../classvg_1_1NetGraph.html#aa1014dccd8e1bfa54a434a6caf0c4d40',1,'vg::NetGraph::connectivity()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#aa0fbdc9240295e4abbc909b68a6e591a',1,'vg::ZipCode::chain_code_t::connectivity()']]],
+ ['consistent_11932',['consistent',['../structvg_1_1Genotyper_1_1Affinity.html#af58e963c9680682966f810d4f922cb5f',1,'vg::Genotyper::Affinity']]],
+ ['construction_5fjobs_11933',['construction_jobs',['../structvg_1_1Haplotypes_1_1Header.html#a3e2571325f5aaeabced578bc43c8533c',1,'vg::Haplotypes::Header']]],
+ ['containing_5fnet_5fhandle_11934',['containing_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a8416c3bb55a8a3e699348067738c900b',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['content_11935',['content',['../structvg_1_1BitStringTree_1_1TreeNode.html#a654e2ccb451511ff925aa9d66e290fbe',1,'vg::BitStringTree::TreeNode']]],
+ ['contents_11936',['contents',['../classvg_1_1SubHandleGraph.html#a6d06eff177c6d87feadd561675c11b73',1,'vg::SubHandleGraph::contents()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#a6e710dba31d9417bb75647b7f25fbab0',1,'handlegraph::algorithms::SubHandleGraph::contents()']]],
+ ['context_5fbases_11937',['context_bases',['../classvg_1_1GraphSynchronizer_1_1Lock.html#ae4a5790fef0070239e02d0f14bab68c3',1,'vg::GraphSynchronizer::Lock']]],
+ ['context_5flength_11938',['context_length',['../structGBWTConfig.html#acc79271b2d7fe244bb008277aa3564ec',1,'GBWTConfig']]],
+ ['contig_11939',['contig',['../structvg_1_1BREAKPOINT.html#a8daffa4f64b5d59660eb3b3b00de7d0a',1,'vg::BREAKPOINT']]],
+ ['contig_5fname_11940',['contig_name',['../structvg_1_1RecombinatorHaplotype.html#ab812d5260c6b86e1568c4d25bfdbe488',1,'vg::RecombinatorHaplotype::contig_name()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a9478eb5ec8559cfcfcb57677e718e256',1,'vg::Haplotypes::TopLevelChain::contig_name()']]],
+ ['contig_5fprefix_11941',['contig_prefix',['../structHaplotypesConfig.html#aafaf3f6a87d34073bd46ea058b1f9e73',1,'HaplotypesConfig']]],
+ ['contigs_11942',['contigs',['../structGBWTConfig.html#a72eddaf43b65805e38fc978933fd8b2d',1,'GBWTConfig']]],
+ ['control_5fmean_11943',['control_mean',['../structvg_1_1BenchmarkResult.html#a54072b6e4cb8401a4784e9e20b3ca6de',1,'vg::BenchmarkResult']]],
+ ['control_5fstddev_11944',['control_stddev',['../structvg_1_1BenchmarkResult.html#ac6db5580a02c1860981365245812304e',1,'vg::BenchmarkResult']]],
+ ['coordinates_11945',['coordinates',['../structvg_1_1Exon.html#a845cd3e89b345eeeba6177c6cdbf202a',1,'vg::Exon']]],
+ ['copy_5fid_11946',['copy_id',['../structvg_1_1TranscriptPath.html#af8b88c3ff6130af4aaa1674d30cbc89d',1,'vg::TranscriptPath']]],
+ ['correct_11947',['correct',['../structvg_1_1Alignment.html#a07751b50cfb9c985fccc2c701bfc55fc',1,'vg::Alignment']]],
+ ['correctly_5fmapped_11948',['correctly_mapped',['../structvg_1_1Alignment.html#a9ec303e39d844ec1e6289ddfbcdd7911',1,'vg::Alignment']]],
+ ['count_11949',['count',['../classvg_1_1count__back__inserter.html#aab6ae0ee48226650d3e5833c4bdd787a',1,'vg::count_back_inserter']]],
+ ['count_5fof_5fmax_11950',['count_of_max',['../structvg_1_1SummaryStatistics.html#a3245d457bac967cb81a89a1351016b9b',1,'vg::SummaryStatistics']]],
+ ['count_5fpaths_11951',['count_paths',['../structGBWTConfig.html#a9a0bd4ea251be07cbe2336a93981b614',1,'GBWTConfig']]],
+ ['counts_11952',['counts',['../structvg_1_1Counts.html#ada1e3e24df7c078970806cb6da1fce51',1,'vg::Counts']]],
+ ['cov_5fbin_5fsize_11953',['cov_bin_size',['../classvg_1_1Packer.html#a63fd3c0a6d18bbb64f18e3afbecd552c',1,'vg::Packer']]],
+ ['coverage_11954',['COVERAGE',['../classvg_1_1Recombinator.html#a567c0ae71f8bae880186eb4758dc2cd1',1,'vg::Recombinator::COVERAGE()'],['../structvg_1_1Recombinator_1_1Parameters.html#a53570bd1e3ae8fc31135027b77784d18',1,'vg::Recombinator::Parameters::coverage()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#add34ea5cbb2c555485c0b9be5d22b668',1,'vg::SnarlDistanceIndexClusterer::Cluster::coverage()']]],
+ ['coverage_5fciv_11955',['coverage_civ',['../classvg_1_1Packer.html#adc0b40cfa531d0edbc50c9ed7bfcf84e',1,'vg::Packer']]],
+ ['coverage_5fdynamic_11956',['coverage_dynamic',['../classvg_1_1Packer.html#a6d48a90c1ed0484bc7992ee798003a0b',1,'vg::Packer']]],
+ ['cr_11957',['cr',['../classvg_1_1Viz.html#a1c514ef7170a0f6a195aeed7b2cd0b20',1,'vg::Viz']]],
+ ['crossing_5fedges_11958',['crossing_edges',['../classvg_1_1PhaseUnfolder.html#a326b5a34e3c5255b95fbad3eb536fa48',1,'vg::PhaseUnfolder']]],
+ ['cumulative_5fseq_5flen_11959',['cumulative_seq_len',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a60ef2a91471d83aaaa6d52cb13b800e8',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['curr_11960',['curr',['../structvg_1_1kmer__t.html#a9b8741fa3ec61bc5f1e03bbf86455be6',1,'vg::kmer_t::curr()'],['../structvg_1_1PathBranch.html#a14bc112cacb6ea533eef7f69d2abb4c5',1,'vg::PathBranch::curr()'],['../structvg_1_1algorithms_1_1kmer__t.html#a461e739df40ec66bba376bfd913bcc10',1,'vg::algorithms::kmer_t::curr()'],['../structvg_1_1algorithms_1_1walk__t.html#a0940baf10cc23ee2c424ccf2b2cd61d4',1,'vg::algorithms::walk_t::curr()']]],
+ ['curr_5fdeflxn_11961',['curr_deflxn',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#ad6fb487aa27ac7baca766a597243fe99',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['curr_5ftraceback_11962',['curr_traceback',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9e2f8458aa7f547adda7154ef90a1c5c',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['current_11963',['current',['../structvg_1_1IncrementIter.html#a63f121c026a4681a4bf61ad56198542b',1,'vg::IncrementIter::current()'],['../classvg_1_1WindowedVcfBuffer.html#a9e4eeb593eee805717734190d9940f79',1,'vg::WindowedVcfBuffer::current()']]],
+ ['current_5fchains_11964',['current_chains',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#af221d0d08c843344be01e68bd1c0464e',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['current_5fid_11965',['current_id',['../classvg_1_1VG.html#a68f4b0cfbadab3cebace110733565d38',1,'vg::VG']]],
+ ['current_5fnode_5fid_11966',['current_node_id',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#afbd1560242a69c0b36dbe0f6ffb81684',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['current_5fnode_5fsequence_11967',['current_node_sequence',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a47a70166200af736bc64f4cc7adbfdad',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['current_5fstate_11968',['current_state',['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#ab50fbed67d1840cdf36756e1b9d7f67f',1,'vg::ZipCodeTree::reverse_iterator']]],
+ ['current_5fversion_11969',['CURRENT_VERSION',['../classxg_1_1XG.html#a4d1d5b61619c685244aeaaa4830cb285',1,'xg::XG']]],
+ ['cursor_5fpool_11970',['cursor_pool',['../classvg_1_1IndexedVG.html#a62d27a5ec1f917733604d724ab413f7f',1,'vg::IndexedVG']]],
+ ['cursor_5fpool_5fmutex_11971',['cursor_pool_mutex',['../classvg_1_1IndexedVG.html#a0e1a3526d6d76ea816b5cc579ae39227',1,'vg::IndexedVG']]],
+ ['cursor_5fstreams_11972',['cursor_streams',['../classvg_1_1IndexedVG.html#a73bae46f21d980ec8b4f198396c8060a',1,'vg::IndexedVG']]]
];
diff --git a/search/variables_4.js b/search/variables_4.js
index c60fee0e26..4a1a6965b5 100644
--- a/search/variables_4.js
+++ b/search/variables_4.js
@@ -1,176 +1,176 @@
var searchData=
[
- ['dagify_5fsteps_11969',['dagify_steps',['../classvg_1_1Genotyper.html#a384f22f52c2a1f78b7ca613468e2e186',1,'vg::Genotyper']]],
- ['data_11970',['data',['../structvg_1_1kff__recoding__t.html#a4ee9792be54b558f2d20f4caeb08ca66',1,'vg::kff_recoding_t::data()'],['../classvg_1_1SmallBitset.html#a071d06af5d058cbe3753b40ae29efd1a',1,'vg::SmallBitset::data()'],['../structvg_1_1varint__vector__t.html#ac8b714c4409d76b3d436d25884eb53b3',1,'vg::varint_vector_t::data()'],['../structhandlegraph_1_1handle__t.html#a83dd8888c344b33ba7e3ebf8c0b578a9',1,'handlegraph::handle_t::data()'],['../structhandlegraph_1_1path__handle__t.html#a887f73bef5f50884ab956f6cb7b544c0',1,'handlegraph::path_handle_t::data()'],['../structhandlegraph_1_1step__handle__t.html#ad62b1978c001199b0077ea154c350dfe',1,'handlegraph::step_handle_t::data()'],['../structhandlegraph_1_1net__handle__t.html#a1f37223d796f8f9a85fa8228d88ff760',1,'handlegraph::net_handle_t::data()']]],
- ['data_5fbytes_11971',['data_bytes',['../classvg_1_1ParallelKFFReader.html#a3045db32747d9ae74db589dbfd3ed011',1,'vg::ParallelKFFReader']]],
- ['data_5fwidth_11972',['data_width',['../classvg_1_1Packer.html#a2ebdd5cb535ee0264886e084dbdd00f4',1,'vg::Packer']]],
- ['dead_5fend_11973',['dead_end',['../structvg_1_1WFANode.html#a209c5a0d9b49196134038a4cd79ed0d1',1,'vg::WFANode']]],
- ['debug_11974',['debug',['../classvg_1_1BaseMapper.html#a5ce344e730fbb7cdc6b6d57b4ca76cf2',1,'vg::BaseMapper']]],
- ['decoder_11975',['decoder',['../classvg_1_1ZipCode.html#aca73fa641d8bb6c33cb98dc1873cb263',1,'vg::ZipCode']]],
- ['default_5falign_5ffrom_5fchains_11976',['default_align_from_chains',['../classvg_1_1MinimizerMapper.html#afcd2b69495a1a199acf78d2c7a5b9cc6',1,'vg::MinimizerMapper']]],
- ['default_5fbatch_5fsize_11977',['default_batch_size',['../structGiraffeMainOptions.html#abf990cc986a8d914022dff4bba5ae632',1,'GiraffeMainOptions']]],
- ['default_5fchain_5fscore_5fthreshold_11978',['default_chain_score_threshold',['../classvg_1_1MinimizerMapper.html#a0b244b594d69d2d7c8fecf4e81c14d68',1,'vg::MinimizerMapper']]],
- ['default_5fcluster_5fcoverage_5fthreshold_11979',['default_cluster_coverage_threshold',['../classvg_1_1MinimizerMapper.html#aeb9d4054c5b90f3af8404b841a71d634',1,'vg::MinimizerMapper']]],
- ['default_5fcluster_5fscore_5fthreshold_11980',['default_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a6dc3278193f869e9e05da6db101c509c',1,'vg::MinimizerMapper']]],
- ['default_5fdistance_5flimit_11981',['default_distance_limit',['../classvg_1_1MinimizerMapper.html#a65b0d0ad12d3891423022138797fbb8c',1,'vg::MinimizerMapper']]],
- ['default_5fdo_5fdp_11982',['default_do_dp',['../classvg_1_1MinimizerMapper.html#a70503b3c1d0be5ec64f82ce6e18bf3b5',1,'vg::MinimizerMapper']]],
- ['default_5ferror_5fmodel_11983',['default_error_model',['../classvg_1_1WFAExtender.html#af4e721ca734a32164df1e6ff9cce233c',1,'vg::WFAExtender']]],
- ['default_5fexclude_5foverlapping_5fmin_11984',['default_exclude_overlapping_min',['../classvg_1_1MinimizerMapper.html#a2828121ea966812ed56cac02ab5eb779',1,'vg::MinimizerMapper']]],
- ['default_5fextension_5fscore_5fthreshold_11985',['default_extension_score_threshold',['../classvg_1_1MinimizerMapper.html#a19ffcd52d8076fbee5e0ae8c6cb645a8',1,'vg::MinimizerMapper']]],
- ['default_5fextension_5fset_5fmin_5fscore_11986',['default_extension_set_min_score',['../classvg_1_1MinimizerMapper.html#ad25575d1e55539f50a77a959adac5697',1,'vg::MinimizerMapper']]],
- ['default_5fextension_5fset_5fscore_5fthreshold_11987',['default_extension_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a83ad907b2bb4955d69984b067c6701db',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fgap_5fscale_11988',['default_fragment_gap_scale',['../classvg_1_1MinimizerMapper.html#ae03d9220adb714b422a782c26b35c86c',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fmax_5findel_5fbases_11989',['default_fragment_max_indel_bases',['../classvg_1_1MinimizerMapper.html#a0fde24a54cd539268f195f730425bc05',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fmax_5findel_5fbases_5fper_5fbase_11990',['default_fragment_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a4d3b8401a10bb332a34ec92b658139af',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fmax_5flookback_5fbases_11991',['default_fragment_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#a65e69109575da406b2b020e629f95c89',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fmax_5flookback_5fbases_5fper_5fbase_11992',['default_fragment_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#ad3219ef35a8b2a3f879dd40279e0170a',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fmax_5fmin_5fscore_11993',['default_fragment_max_min_score',['../classvg_1_1MinimizerMapper.html#a13904c0a444d50cf1a4bbcd5b34e9c0d',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fmin_5fscore_11994',['default_fragment_min_score',['../classvg_1_1MinimizerMapper.html#a02028299d3998732a8d2df5c6617af60',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fpoints_5fper_5fpossible_5fmatch_11995',['default_fragment_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a184bc5e3d7cd0637a0611f48e32b241b',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fscore_5ffraction_11996',['default_fragment_score_fraction',['../classvg_1_1MinimizerMapper.html#aef5088c7916a178a0287f9b5e3176d49',1,'vg::MinimizerMapper']]],
- ['default_5ffragment_5fset_5fscore_5fthreshold_11997',['default_fragment_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a1085d1335cebc9bb11ac31cbd45058a1',1,'vg::MinimizerMapper']]],
- ['default_5fgap_5fscale_11998',['default_gap_scale',['../classvg_1_1MinimizerMapper.html#a2739e3b492d0978a4c17c761a0946bcd',1,'vg::MinimizerMapper']]],
- ['default_5fgapless_5fextension_5flimit_11999',['default_gapless_extension_limit',['../classvg_1_1MinimizerMapper.html#a988cc9dff2f312de4bdfce08887cd896',1,'vg::MinimizerMapper']]],
- ['default_5fhard_5fhit_5fcap_12000',['default_hard_hit_cap',['../classvg_1_1MinimizerMapper.html#adaea07e204eca95eeac41c22013725d6',1,'vg::MinimizerMapper']]],
- ['default_5fhit_5fcap_12001',['default_hit_cap',['../classvg_1_1MinimizerMapper.html#aa09637c461eee0cec06bd75475102147',1,'vg::MinimizerMapper']]],
- ['default_5fitem_5fbonus_12002',['default_item_bonus',['../classvg_1_1MinimizerMapper.html#a47b33ac9dea218de205fdf4d5c3d53de',1,'vg::MinimizerMapper']]],
- ['default_5fitem_5fscale_12003',['default_item_scale',['../classvg_1_1MinimizerMapper.html#a95fe7acf05497e31363fe201f9dc22b4',1,'vg::MinimizerMapper']]],
- ['default_5fiterations_12004',['DEFAULT_ITERATIONS',['../minimizer__main_8cpp.html#a62c07e69eba05821e728bdf3389a500d',1,'minimizer_main.cpp']]],
- ['default_5fk_12005',['DEFAULT_K',['../structvg_1_1Haplotypes_1_1Header.html#a85d1a35162f23b04d49e1533e12e4a7c',1,'vg::Haplotypes::Header']]],
- ['default_5flog_5freads_12006',['default_log_reads',['../structGiraffeMainOptions.html#aa6a8ecfcb8fc48b9378c1c8608901f20',1,'GiraffeMainOptions']]],
- ['default_5fmapq_5fscore_5fscale_12007',['default_mapq_score_scale',['../classvg_1_1MinimizerMapper.html#a950b83222eb55cd956eb604006d5a3d6',1,'vg::MinimizerMapper']]],
- ['default_5fmapq_5fscore_5fwindow_12008',['default_mapq_score_window',['../classvg_1_1MinimizerMapper.html#a0ffc9c3cb0e41b00ef47dc0a9039e445',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5falignments_12009',['default_max_alignments',['../classvg_1_1MinimizerMapper.html#a0630ced82cb222e941d227b87c3242cc',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fchain_5fconnection_12010',['default_max_chain_connection',['../classvg_1_1MinimizerMapper.html#a03af3423a0607432df929adb6e34dc00',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fchaining_5fproblems_12011',['default_max_chaining_problems',['../classvg_1_1MinimizerMapper.html#a2046e2c404be2f31d1a60e80cf8bfca8',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fchains_5fper_5ftree_12012',['default_max_chains_per_tree',['../classvg_1_1MinimizerMapper.html#a8fd75b16ce33d33287c898cb7056e3d5',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fdirect_5fto_5fchain_12013',['default_max_direct_to_chain',['../classvg_1_1MinimizerMapper.html#a46015a99b97b88cf6a5721933135d449',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fdozeu_5fcells_12014',['default_max_dozeu_cells',['../classvg_1_1MinimizerMapper.html#af849d482a02c0e58a7f80ebb60d8c58b',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fdp_5fcells_12015',['default_max_dp_cells',['../classvg_1_1MinimizerMapper.html#a245ad5daaf4a2d92300dc1703709997b',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fextension_5fmismatches_12016',['default_max_extension_mismatches',['../classvg_1_1MinimizerMapper.html#a9dbe25a46a44ab36757a010e08b4527b',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fextensions_12017',['default_max_extensions',['../classvg_1_1MinimizerMapper.html#adcebeb61c302cf85887e35947d778b82',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5ffragment_5flength_12018',['default_max_fragment_length',['../classvg_1_1MinimizerMapper.html#aef322db760a61242dbb35055171269c8',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5ffragments_12019',['default_max_fragments',['../classvg_1_1MinimizerMapper.html#ac1b0554a6a6f531e00215880027aef19',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5findel_5fbases_12020',['default_max_indel_bases',['../classvg_1_1MinimizerMapper.html#a941e35e0ce18efa4de95f7773810df4c',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5findel_5fbases_5fper_5fbase_12021',['default_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a9b891451941f27e9a03628869da2f795',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5flocal_5fextensions_12022',['default_max_local_extensions',['../classvg_1_1MinimizerMapper.html#a02cb88ed7a5912500972581c1a94a953',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5flookback_5fbases_12023',['default_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#a43fd52a005cf7ce74ab3ccc3a0818130',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5flookback_5fbases_5fper_5fbase_12024',['default_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a077f290854fc4522a2874bb24db0bc5f',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fmiddle_5fdp_5flength_12025',['default_max_middle_dp_length',['../classvg_1_1MinimizerMapper.html#a9693b4420ce66b5d2b9a11d7fcbcf8ed',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fmiddle_5fgap_12026',['default_max_middle_gap',['../classvg_1_1MinimizerMapper.html#aeb435adbfa094f550ffde3994b7935bb',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fmin_5fchain_5fscore_12027',['default_max_min_chain_score',['../classvg_1_1MinimizerMapper.html#addec6b6b7907c12c4001dcecb656a6a1',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fmultimaps_12028',['default_max_multimaps',['../classvg_1_1MinimizerMapper.html#acef30cb743117b4bab6062caabaa4bcc',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5frescue_5fattempts_12029',['default_max_rescue_attempts',['../classvg_1_1MinimizerMapper.html#aeeccbf0f4919ea1bfa9ddc223a2c0668',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fskipped_5fbases_12030',['default_max_skipped_bases',['../classvg_1_1MinimizerMapper.html#aef0223d05eb9dad4dcd8f6c3600dcd47',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fslide_12031',['DEFAULT_MAX_SLIDE',['../classvg_1_1Surjector.html#a3484c973d05e38e523cc45c85ee4d9f3',1,'vg::Surjector']]],
- ['default_5fmax_5ftail_5fdp_5flength_12032',['default_max_tail_dp_length',['../classvg_1_1MinimizerMapper.html#a21cf128cd5f45135a8b9861d55eb7f7f',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5ftail_5fgap_12033',['default_max_tail_gap',['../classvg_1_1MinimizerMapper.html#a24d37bb5c13e910d0f74fa5f818b2db5',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5ftail_5flength_12034',['default_max_tail_length',['../classvg_1_1MinimizerMapper.html#ae60300bb4ed2185de21379fe5735f3a2',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5fthreads_12035',['DEFAULT_MAX_THREADS',['../namespacehaplotypes__defaults.html#a5767132ecebb35fbe62b9dc8e55d66a9',1,'haplotypes_defaults::DEFAULT_MAX_THREADS()'],['../minimizer__main_8cpp.html#a5b3b08bd8224196307cb86df71ff927d',1,'DEFAULT_MAX_THREADS(): minimizer_main.cpp']]],
- ['default_5fmax_5fto_5ffragment_12036',['default_max_to_fragment',['../classvg_1_1MinimizerMapper.html#a872367a94f5b074e81db6af4d0d33130',1,'vg::MinimizerMapper']]],
- ['default_5fmax_5funique_5fmin_12037',['default_max_unique_min',['../classvg_1_1MinimizerMapper.html#a76c18cd5496e664b660c17f892fd0a9d',1,'vg::MinimizerMapper']]],
- ['default_5fmin_5fchain_5fscore_5fper_5fbase_12038',['default_min_chain_score_per_base',['../classvg_1_1MinimizerMapper.html#a98337be6c0a1ca4eac0c131448492115',1,'vg::MinimizerMapper']]],
- ['default_5fmin_5fchaining_5fproblems_12039',['default_min_chaining_problems',['../classvg_1_1MinimizerMapper.html#a79a21722c70fb0d54fd4fb66f09b7085',1,'vg::MinimizerMapper']]],
- ['default_5fmin_5fchains_12040',['default_min_chains',['../classvg_1_1MinimizerMapper.html#a14ee8de796304cc5c30fe5f2485c97aa',1,'vg::MinimizerMapper']]],
- ['default_5fmin_5fextension_5fsets_12041',['default_min_extension_sets',['../classvg_1_1MinimizerMapper.html#af55ebc7ba993565e61c16f8133e2b618',1,'vg::MinimizerMapper']]],
- ['default_5fmin_5fextensions_12042',['default_min_extensions',['../classvg_1_1MinimizerMapper.html#a6c64b28b199566f3684d272c57097962',1,'vg::MinimizerMapper']]],
- ['default_5fmin_5fto_5ffragment_12043',['default_min_to_fragment',['../classvg_1_1MinimizerMapper.html#a4d0a26197071962f77dc4ce29608c1a5',1,'vg::MinimizerMapper']]],
- ['default_5fmin_5funique_5fnode_5ffraction_12044',['default_min_unique_node_fraction',['../classvg_1_1MinimizerMapper.html#ab3835a6952cc643f0b29dbe10ffdbc9e',1,'vg::MinimizerMapper']]],
- ['default_5fminimizer_5fcoverage_5fflank_12045',['default_minimizer_coverage_flank',['../classvg_1_1MinimizerMapper.html#a53a4e8bca5b336db81534e731e7501c1',1,'vg::MinimizerMapper']]],
- ['default_5fminimizer_5fdownsampling_5fmax_5fwindow_5flength_12046',['default_minimizer_downsampling_max_window_length',['../classvg_1_1MinimizerMapper.html#a7ba0c8275fc70249b743b8a327c16dbd',1,'vg::MinimizerMapper']]],
- ['default_5fminimizer_5fdownsampling_5fwindow_5fcount_12047',['default_minimizer_downsampling_window_count',['../classvg_1_1MinimizerMapper.html#aedf57a0048ea44081f2f75d844a210d6',1,'vg::MinimizerMapper']]],
- ['default_5fminimizer_5fscore_5ffraction_12048',['default_minimizer_score_fraction',['../classvg_1_1MinimizerMapper.html#aecd1b06ba8d1d6325d21827422777ecd',1,'vg::MinimizerMapper']]],
- ['default_5fnum_5fbp_5fper_5fmin_12049',['default_num_bp_per_min',['../classvg_1_1MinimizerMapper.html#a270d4aa37a8c19a9953af4185fe2dc81',1,'vg::MinimizerMapper']]],
- ['default_5fpad_5fcluster_5fscore_5fthreshold_12050',['default_pad_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a76b49c1bb20fe42732db8fc6e111bd73',1,'vg::MinimizerMapper']]],
- ['default_5fpad_5fzipcode_5ftree_5fscore_5fthreshold_12051',['default_pad_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a737e7ee21406911540ae4bd78fb13e56',1,'vg::MinimizerMapper']]],
- ['default_5fpaired_5fdistance_5fstdevs_12052',['default_paired_distance_stdevs',['../classvg_1_1MinimizerMapper.html#a075eb4ce854be73a0764fc1149721346',1,'vg::MinimizerMapper']]],
- ['default_5fpaired_5frescue_5fscore_5flimit_12053',['default_paired_rescue_score_limit',['../classvg_1_1MinimizerMapper.html#a82a26ad5a15d724ffb19dee9e105f35e',1,'vg::MinimizerMapper']]],
- ['default_5fparallel_5fbatchsize_12054',['DEFAULT_PARALLEL_BATCHSIZE',['../namespacevg_1_1io.html#aba1d6c41cb6ff7b47e64b6b584af0363',1,'vg::io']]],
- ['default_5fpath_5fweight_12055',['DEFAULT_PATH_WEIGHT',['../classvg_1_1FlowSort.html#a68d8af802f0e2a61c81bf0ae4ebfc301',1,'vg::FlowSort']]],
- ['default_5fpoints_5fper_5fpossible_5fmatch_12056',['default_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a01cea9c6a1146b7643f7814e899dba1a',1,'vg::MinimizerMapper']]],
- ['default_5frescue_5fseed_5flimit_12057',['default_rescue_seed_limit',['../classvg_1_1MinimizerMapper.html#aba9daaa16afb07adba5aadd1a16bef28',1,'vg::MinimizerMapper']]],
- ['default_5frescue_5fsubgraph_5fstdevs_12058',['default_rescue_subgraph_stdevs',['../classvg_1_1MinimizerMapper.html#abba75ee681b890855b6d6152581100e9',1,'vg::MinimizerMapper']]],
- ['default_5fsequence_5fquality_12059',['default_sequence_quality',['../classvg_1_1Genotyper.html#a3c40092b41694cacc7e531bf7f9fb8aa',1,'vg::Genotyper']]],
- ['default_5fset_5frefpos_12060',['default_set_refpos',['../classvg_1_1MinimizerMapper.html#a130e242a6647d32605daa663b0d96998',1,'vg::MinimizerMapper']]],
- ['default_5fshow_5fwork_12061',['default_show_work',['../classvg_1_1MinimizerMapper.html#a5b420aef79b283dfe483246b135aa2e1',1,'vg::MinimizerMapper']]],
- ['default_5fsort_5fby_5fchain_5fscore_12062',['default_sort_by_chain_score',['../classvg_1_1MinimizerMapper.html#a660c0927845a795613529acf90fceefe',1,'vg::MinimizerMapper']]],
- ['default_5fsubgraph_5flimit_12063',['DEFAULT_SUBGRAPH_LIMIT',['../classvg_1_1Surjector.html#ac78645d41b2dfd88bece81c86a5b7090',1,'vg::Surjector']]],
- ['default_5fthreshold_12064',['DEFAULT_THRESHOLD',['../minimizer__main_8cpp.html#a777231a8126ad759ff713c50090c6bfb',1,'minimizer_main.cpp']]],
- ['default_5ftrack_5fcorrectness_12065',['default_track_correctness',['../classvg_1_1MinimizerMapper.html#afcc3e652ef8dd9d78edb5ac14a0fd602',1,'vg::MinimizerMapper']]],
- ['default_5ftrack_5fposition_12066',['default_track_position',['../classvg_1_1MinimizerMapper.html#a3357a4536f0714508781c4ef201d002c',1,'vg::MinimizerMapper']]],
- ['default_5ftrack_5fprovenance_12067',['default_track_provenance',['../classvg_1_1MinimizerMapper.html#a0fb3483a8d2c18fa30688532eb70f117',1,'vg::MinimizerMapper']]],
- ['default_5fuse_5fexplored_5fcap_12068',['default_use_explored_cap',['../classvg_1_1MinimizerMapper.html#adc6c21f5f381f4a6ea7e7e777dc64f21',1,'vg::MinimizerMapper']]],
- ['default_5fvalue_12069',['default_value',['../classvg_1_1BaseOption.html#ade40b0f856c10a12e3fc7847f4a33b7a',1,'vg::BaseOption::default_value()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a05bdfbeff1f2b1a8d68a4bf9dd6d0d53',1,'vg::subcommand::ArgSpec::default_value()']]],
- ['default_5fwatchdog_5ftimeout_12070',['default_watchdog_timeout',['../structGiraffeMainOptions.html#a8e3b0f47ff4f761544f077f2d591096e',1,'GiraffeMainOptions']]],
- ['default_5fwfa_5fdistance_12071',['default_wfa_distance',['../classvg_1_1MinimizerMapper.html#a2b1eabff9087e4acd64cc0e1d49130ee',1,'vg::MinimizerMapper']]],
- ['default_5fwfa_5fdistance_5fper_5fbase_12072',['default_wfa_distance_per_base',['../classvg_1_1MinimizerMapper.html#ac88d6ddb37fc3e7c5fb2eba6c1f5e107',1,'vg::MinimizerMapper']]],
- ['default_5fwfa_5fmax_5fdistance_12073',['default_wfa_max_distance',['../classvg_1_1MinimizerMapper.html#a51aa239042c3adaff5ac10c6c4486cc5',1,'vg::MinimizerMapper']]],
- ['default_5fwfa_5fmax_5fmax_5fmismatches_12074',['default_wfa_max_max_mismatches',['../classvg_1_1MinimizerMapper.html#a8a532cd9bd5ce16848673592a9fb18ec',1,'vg::MinimizerMapper']]],
- ['default_5fwfa_5fmax_5fmismatches_12075',['default_wfa_max_mismatches',['../classvg_1_1MinimizerMapper.html#a1d0c74a11cc55135d11b08c8fbc96ca2',1,'vg::MinimizerMapper']]],
- ['default_5fwfa_5fmax_5fmismatches_5fper_5fbase_12076',['default_wfa_max_mismatches_per_base',['../classvg_1_1MinimizerMapper.html#a0ddeeb08b47f9d091dbee44fee6711d5',1,'vg::MinimizerMapper']]],
- ['default_5fzipcode_5ftree_5fcoverage_5fthreshold_12077',['default_zipcode_tree_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a36ba9324ef7edf8b9625697570d7d971',1,'vg::MinimizerMapper']]],
- ['default_5fzipcode_5ftree_5fscale_12078',['default_zipcode_tree_scale',['../classvg_1_1MinimizerMapper.html#a82714c6b597295d464e8e0000d849184',1,'vg::MinimizerMapper']]],
- ['default_5fzipcode_5ftree_5fscore_5fthreshold_12079',['default_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a4ea6f674bb701f8f07e4e31b79fb79d1',1,'vg::MinimizerMapper']]],
- ['defaultcompresslevel_12080',['DEFAULTCOMPRESSLEVEL',['../namespacezstdutil.html#a449e02cc311816ade9a49c134e38adc8',1,'zstdutil']]],
- ['defining_5fpath_12081',['defining_path',['../classvg_1_1PathSubgraph.html#a907a18a155eace47d2f8a1f9bacf4894',1,'vg::PathSubgraph']]],
- ['defray_5fcount_12082',['defray_count',['../classvg_1_1ReadFilter.html#aef4ec3c75ed003564641757d0d78b6ea',1,'vg::ReadFilter']]],
- ['defray_5flength_12083',['defray_length',['../classvg_1_1ReadFilter.html#ab1a4ac583b2b783404b20e985c4a5f5e',1,'vg::ReadFilter']]],
- ['deleted_5fprior_5flogprob_12084',['deleted_prior_logprob',['../classvg_1_1Genotyper.html#a853fb8840552901b359153ec80aa81e1',1,'vg::Genotyper']]],
- ['deletion_5faligner_12085',['deletion_aligner',['../classvg_1_1GSSWAligner.html#a7bd8654938361b8edf947fb888dcd6d8',1,'vg::GSSWAligner']]],
- ['deletions_12086',['DELETIONS',['../structvg_1_1WFANode.html#acf73ec9a87e0d2e04b2ae4d0e13158e6',1,'vg::WFANode::DELETIONS()'],['../structvg_1_1DeleteHaplotypeCommand.html#a33e4ac2752620369abb200e585e667a4',1,'vg::DeleteHaplotypeCommand::deletions()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a3371d6a46feb1f9d218a577156aef698',1,'vg::ReplaceLocalHaplotypeCommand::deletions()']]],
- ['delim1_12087',['delim1',['../classvg_1_1Packer.html#acffc9465bdaa0bb770372edf788aad48',1,'vg::Packer']]],
- ['delim2_12088',['delim2',['../classvg_1_1Packer.html#a0d1336853823c62812b2009e80085800',1,'vg::Packer']]],
- ['dense_5fto_5fsparse_12089',['dense_to_sparse',['../classvg_1_1SparseUnionFind.html#a9b682c8492591af4002cae1830ebd243',1,'vg::SparseUnionFind']]],
- ['depth_12090',['depth',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a7c0e5760255d3f47d6fbce1da89d32db',1,'vg::ZipCodeForest::interval_state_t']]],
- ['depth_5ferr_12091',['depth_err',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#ac8c734835666c796508c7714c332c467',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['depth_5findex_12092',['depth_index',['../classvg_1_1PoissonSupportSnarlCaller.html#adebf4d923f033aa67032c4340d9ebb1e',1,'vg::PoissonSupportSnarlCaller']]],
- ['depth_5fpadding_5ffactor_12093',['depth_padding_factor',['../classvg_1_1PoissonSupportSnarlCaller.html#a53eec737bc91a46f91161c18ddc26cd7',1,'vg::PoissonSupportSnarlCaller']]],
- ['description_12094',['description',['../classvg_1_1BaseOption.html#a4468cf61e5b31a06929303e91f096f6d',1,'vg::BaseOption::description()'],['../classvg_1_1subcommand_1_1Subcommand.html#ab74ec1dfb7410088f2a0fa0d368a34f9',1,'vg::subcommand::Subcommand::description()']]],
- ['dest_12095',['dest',['../structvg_1_1subcommand_1_1ArgSpec.html#a817d3125f130981b273565c384291fc9',1,'vg::subcommand::ArgSpec']]],
- ['diagonal_12096',['diagonal',['../structvg_1_1WFAPoint.html#ad95025eb9daeb494c52fabdf713ec1d0',1,'vg::WFAPoint']]],
- ['dinuc_5fmachine_12097',['dinuc_machine',['../classvg_1_1MultipathMapper.html#a4000f9a9d804ef14a51bb48c22029089',1,'vg::MultipathMapper']]],
- ['diploid_5fprior_5flogprob_12098',['diploid_prior_logprob',['../classvg_1_1Genotyper.html#ac748204c3fb19573569172ee57b1d082',1,'vg::Genotyper']]],
- ['diploid_5fsampling_12099',['diploid_sampling',['../structvg_1_1Recombinator_1_1Parameters.html#a8aa7a7fe3df17bdbed79475f26d2d884',1,'vg::Recombinator::Parameters']]],
- ['directed_5facyclic_5fnet_5fgraph_12100',['directed_acyclic_net_graph',['../structvg_1_1Snarl.html#a6cbd6de509a74e1ac363eb14c679b4de',1,'vg::Snarl']]],
- ['dirnames_12101',['dirnames',['../structvg_1_1temp__file_1_1Handler.html#a3b0eaa40b8b866abc58f94ca6b38f425',1,'vg::temp_file::Handler']]],
- ['discard_5foverlaps_12102',['discard_overlaps',['../classvg_1_1HaplotypeIndexer.html#a9991b56b5003075a5a072e06e669a3c1',1,'vg::HaplotypeIndexer']]],
- ['discordant_5finsert_5fsize_12103',['discordant_insert_size',['../structvg_1_1Alignment.html#a5cf554f770c01df31d8b4046b3ed5f50',1,'vg::Alignment']]],
- ['distance_12104',['distance',['../classvg_1_1MEMClusterer_1_1HitEdge.html#a9792b646c0a3905c5b111d3a61d336f2',1,'vg::MEMClusterer::HitEdge::distance()'],['../structvg_1_1WFAExtender_1_1ErrorModel.html#a700d6dd2d1d47e2aa9c24c474a023a06',1,'vg::WFAExtender::ErrorModel::distance()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#a12043bbec5e8e59b9eb0ff5afc0d2d0d',1,'vg::ZipCodeTree::seed_result_t::distance()']]],
- ['distance_5fend_5fleft_12105',['distance_end_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a5baab4c86f719c18e9c20224bb10a69a',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_end_left()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#acd2b78cff4271a4ae10fe0d9d5618c5c',1,'vg::ZipCode::snarl_code_t::distance_end_left()']]],
- ['distance_5fend_5fright_12106',['distance_end_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a06be78a0dab9e6283c66daf6da692ea8',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_end_right()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa720e8028e5d3c9ffef77220f08a3df8',1,'vg::ZipCode::snarl_code_t::distance_end_right()']]],
- ['distance_5findex_12107',['distance_index',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a7dd96ca42452dc97acf3063f37435f54',1,'vg::SnarlOrientedDistanceMeasurer::distance_index()'],['../classvg_1_1SnarlMinDistance.html#a950b6521bc5cd59d9f0fc77fd3536f3c',1,'vg::SnarlMinDistance::distance_index()'],['../classvg_1_1TipAnchoredMaxDistance.html#aebb225450c55b6e08eee6d17c9a5f9cd',1,'vg::TipAnchoredMaxDistance::distance_index()'],['../classvg_1_1MinDistanceClusterer.html#a2984cbfe6a052ea92f02ce4cfa16c7cf',1,'vg::MinDistanceClusterer::distance_index()'],['../classvg_1_1MinimizerMapper.html#aac910751d5f0072fa0fbc799bedf1d37',1,'vg::MinimizerMapper::distance_index()'],['../classvg_1_1MultipathMapper.html#a25c0af4ac91144555a4aebccd6fcb38a',1,'vg::MultipathMapper::distance_index()'],['../classvg_1_1HaplotypePartitioner.html#a1fbaa44f3948a107163ddef5026b593e',1,'vg::HaplotypePartitioner::distance_index()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#aa3ee07e1c0cbacde2d5d524d65a03204',1,'vg::SnarlDistanceIndexClusterer::distance_index()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a97a144ab519382e88430c4a8b24bb8a8',1,'vg::ZipCodeForest::forest_growing_state_t::distance_index()']]],
- ['distance_5fleft_12108',['distance_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#abdf47604f137abb50e7c94eae524a7a7',1,'vg::SnarlDistanceIndexClusterer::SeedCache::distance_left()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a4fb89d65780b1ed5106b392825b41654',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::distance_left()']]],
- ['distance_5flimit_12109',['distance_limit',['../classvg_1_1MinimizerMapper.html#a2fa22653d0c63a1d7bf41946f6f62a55',1,'vg::MinimizerMapper::distance_limit()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a5b19e98cc2c6be5427e011dd577aa9b0',1,'vg::ZipCodeTree::reverse_iterator::distance_limit()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a55c12dad8377ccb6c4289a38c98d175a',1,'vg::ZipCodeForest::forest_growing_state_t::distance_limit()']]],
- ['distance_5fmeasurer_12110',['distance_measurer',['../classvg_1_1OrientedDistanceClusterer.html#a73c5578cbd124a60d54b49474937b78b',1,'vg::OrientedDistanceClusterer']]],
- ['distance_5fname_12111',['distance_name',['../structHaplotypesConfig.html#a7c90afeb06a1a670d1c562e282289fe1',1,'HaplotypesConfig']]],
- ['distance_5fright_12112',['distance_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a13406bb1b2145f75987bf84f23bc5717',1,'vg::SnarlDistanceIndexClusterer::SeedCache::distance_right()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a7e393752378e18d98e0990244e35aefc',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::distance_right()']]],
- ['distance_5fstart_5fleft_12113',['distance_start_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a703f0b7ef0e56b44ab6fa13c4458fbb2',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_start_left()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa072d11c220e73b6db0c36d18b47ef5d',1,'vg::ZipCode::snarl_code_t::distance_start_left()']]],
- ['distance_5fstart_5fright_12114',['distance_start_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a40a9152941e9e3dab83127a6cb78e0e7',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_start_right()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#acbb68d2ef2a7862066db2906924624f3',1,'vg::ZipCode::snarl_code_t::distance_start_right()']]],
- ['distances_12115',['distances',['../structvg_1_1ZipCodeForest_1_1child__info__t.html#aa54c4d24186e3d1a855537d6ea12d3ad',1,'vg::ZipCodeForest::child_info_t']]],
- ['do_5fdp_12116',['do_dp',['../classvg_1_1MinimizerMapper.html#a80efe32334434e2121f45d9683e2b53b',1,'vg::MinimizerMapper']]],
- ['do_5fremap_12117',['do_remap',['../classvg_1_1Filter.html#a7c02ec9d43e85148a82acf980728e9ac',1,'vg::Filter']]],
- ['do_5fspliced_5falignment_12118',['do_spliced_alignment',['../classvg_1_1MultipathMapper.html#a450de2dc7f618164fec361a296be0df3',1,'vg::MultipathMapper']]],
- ['do_5fsvs_12119',['do_svs',['../classvg_1_1Constructor.html#a2e48ae756193c44a889202591a562d18',1,'vg::Constructor']]],
- ['dominated_5fpath_5fchunk_5fdiff_12120',['dominated_path_chunk_diff',['../classvg_1_1Surjector.html#ace7092128b309c97f00fc688d3311c14',1,'vg::Surjector']]],
- ['double_5fis_5ffraction_12121',['double_is_fraction',['../namespacevg_1_1subcommand.html#a6f44735d61e600db634ef1968f64c7c5',1,'vg::subcommand']]],
- ['double_5fis_5fnonnegative_12122',['double_is_nonnegative',['../namespacevg_1_1subcommand.html#a7e565a520f46689e6fe5d38887c7f135',1,'vg::subcommand']]],
- ['double_5fis_5fpositive_12123',['double_is_positive',['../namespacevg_1_1subcommand.html#a750f1011d067a25d64e3157e7435b78f',1,'vg::subcommand']]],
- ['doubling_5fsteps_12124',['doubling_steps',['../classvg_1_1VariantAdder.html#a07970f9f50038e088ef054cde57755af',1,'vg::VariantAdder']]],
- ['downsample_5fcontext_5flength_12125',['downsample_context_length',['../structvg_1_1IndexingParameters.html#ac805da027e770df83d21c5c86f922165',1,'vg::IndexingParameters']]],
- ['downsample_5fcoverage_12126',['downsample_coverage',['../classvg_1_1Surjector.html#a9f599519246cb13464ffe2bbde8bccbe',1,'vg::Surjector']]],
- ['downsample_5fprobability_12127',['downsample_probability',['../classvg_1_1ReadFilter.html#a44099974ab2ac2d374e4530b064e1908',1,'vg::ReadFilter']]],
- ['downsample_5fseed_5fmask_12128',['downsample_seed_mask',['../classvg_1_1ReadFilter.html#a881165b11e7539bc03e331f16b1a5f0a',1,'vg::ReadFilter']]],
- ['downsample_5fthreshold_12129',['downsample_threshold',['../structvg_1_1IndexingParameters.html#aafe781017908d4c15538093514c53e61',1,'vg::IndexingParameters']]],
- ['dozeu_5ftail_12130',['dozeu_tail',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a7a193ad86c14a5cca14d982f16c0f252',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
- ['dp_5fcolumn_12131',['DP_column',['../structhaplo_1_1haplo__DP.html#aac064205c5153507bc6e25e465873ade',1,'haplo::haplo_DP']]],
- ['dp_5fscore_12132',['dp_score',['../classvg_1_1MEMClusterer_1_1HitNode.html#a7db6db0a42c9f87de4bf20c94abca967',1,'vg::MEMClusterer::HitNode']]],
- ['drop_5fchain_12133',['drop_chain',['../classvg_1_1Mapper.html#a838f9ae9f5f33ba048cf036788dece6a',1,'vg::Mapper']]],
- ['drop_5fhairpin_5fpaths_12134',['drop_hairpin_paths',['../classvg_1_1SmallSnarlSimplifier.html#a929e965d0e8441162fa2fe94c29760de',1,'vg::SmallSnarlSimplifier']]],
- ['drop_5fsplit_12135',['drop_split',['../classvg_1_1ReadFilter.html#a52316fdf4e8b2ee3741bfbc4a89727a7',1,'vg::ReadFilter']]],
- ['dry_5frun_12136',['dry_run',['../structvg_1_1RebuildParameters.html#af83ad08bd1ac55470c1ecbb2862d6b68',1,'vg::RebuildParameters']]],
- ['duplicated_5fhandles_12137',['duplicated_handles',['../classvg_1_1DozeuPinningOverlay.html#a253129512ddaf2db6fa4c81b5f9a5b92',1,'vg::DozeuPinningOverlay']]],
- ['duration_12138',['duration',['../structvg_1_1Funnel_1_1Stage.html#a30cb16fa4dcf3f41ef0af169f9900e86',1,'vg::Funnel::Stage']]],
- ['dynamic_12139',['dynamic',['../structvg_1_1GBWTHandler.html#a1fddb1a69a6f6ec6c28016ca13c35894',1,'vg::GBWTHandler']]],
- ['dynamic_5fmax_5falt_5falns_12140',['dynamic_max_alt_alns',['../classvg_1_1MultipathMapper.html#a0b5bddc4e714e176cfe9c1a9680fa60a',1,'vg::MultipathMapper']]],
- ['dz_12141',['dz',['../classvg_1_1DozeuInterface.html#a7df127f3d122bd29a38453a08c5c22b8',1,'vg::DozeuInterface']]]
+ ['dagify_5fsteps_11973',['dagify_steps',['../classvg_1_1Genotyper.html#a384f22f52c2a1f78b7ca613468e2e186',1,'vg::Genotyper']]],
+ ['data_11974',['data',['../structvg_1_1kff__recoding__t.html#a4ee9792be54b558f2d20f4caeb08ca66',1,'vg::kff_recoding_t::data()'],['../classvg_1_1SmallBitset.html#a071d06af5d058cbe3753b40ae29efd1a',1,'vg::SmallBitset::data()'],['../structvg_1_1varint__vector__t.html#ac8b714c4409d76b3d436d25884eb53b3',1,'vg::varint_vector_t::data()'],['../structhandlegraph_1_1handle__t.html#a83dd8888c344b33ba7e3ebf8c0b578a9',1,'handlegraph::handle_t::data()'],['../structhandlegraph_1_1path__handle__t.html#a887f73bef5f50884ab956f6cb7b544c0',1,'handlegraph::path_handle_t::data()'],['../structhandlegraph_1_1step__handle__t.html#ad62b1978c001199b0077ea154c350dfe',1,'handlegraph::step_handle_t::data()'],['../structhandlegraph_1_1net__handle__t.html#a1f37223d796f8f9a85fa8228d88ff760',1,'handlegraph::net_handle_t::data()']]],
+ ['data_5fbytes_11975',['data_bytes',['../classvg_1_1ParallelKFFReader.html#a3045db32747d9ae74db589dbfd3ed011',1,'vg::ParallelKFFReader']]],
+ ['data_5fwidth_11976',['data_width',['../classvg_1_1Packer.html#a2ebdd5cb535ee0264886e084dbdd00f4',1,'vg::Packer']]],
+ ['dead_5fend_11977',['dead_end',['../structvg_1_1WFANode.html#a209c5a0d9b49196134038a4cd79ed0d1',1,'vg::WFANode']]],
+ ['debug_11978',['debug',['../classvg_1_1BaseMapper.html#a5ce344e730fbb7cdc6b6d57b4ca76cf2',1,'vg::BaseMapper']]],
+ ['decoder_11979',['decoder',['../classvg_1_1ZipCode.html#aca73fa641d8bb6c33cb98dc1873cb263',1,'vg::ZipCode']]],
+ ['default_5falign_5ffrom_5fchains_11980',['default_align_from_chains',['../classvg_1_1MinimizerMapper.html#afcd2b69495a1a199acf78d2c7a5b9cc6',1,'vg::MinimizerMapper']]],
+ ['default_5fbatch_5fsize_11981',['default_batch_size',['../structGiraffeMainOptions.html#abf990cc986a8d914022dff4bba5ae632',1,'GiraffeMainOptions']]],
+ ['default_5fchain_5fscore_5fthreshold_11982',['default_chain_score_threshold',['../classvg_1_1MinimizerMapper.html#a0b244b594d69d2d7c8fecf4e81c14d68',1,'vg::MinimizerMapper']]],
+ ['default_5fcluster_5fcoverage_5fthreshold_11983',['default_cluster_coverage_threshold',['../classvg_1_1MinimizerMapper.html#aeb9d4054c5b90f3af8404b841a71d634',1,'vg::MinimizerMapper']]],
+ ['default_5fcluster_5fscore_5fthreshold_11984',['default_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a6dc3278193f869e9e05da6db101c509c',1,'vg::MinimizerMapper']]],
+ ['default_5fdistance_5flimit_11985',['default_distance_limit',['../classvg_1_1MinimizerMapper.html#a65b0d0ad12d3891423022138797fbb8c',1,'vg::MinimizerMapper']]],
+ ['default_5fdo_5fdp_11986',['default_do_dp',['../classvg_1_1MinimizerMapper.html#a70503b3c1d0be5ec64f82ce6e18bf3b5',1,'vg::MinimizerMapper']]],
+ ['default_5ferror_5fmodel_11987',['default_error_model',['../classvg_1_1WFAExtender.html#af4e721ca734a32164df1e6ff9cce233c',1,'vg::WFAExtender']]],
+ ['default_5fexclude_5foverlapping_5fmin_11988',['default_exclude_overlapping_min',['../classvg_1_1MinimizerMapper.html#a2828121ea966812ed56cac02ab5eb779',1,'vg::MinimizerMapper']]],
+ ['default_5fextension_5fscore_5fthreshold_11989',['default_extension_score_threshold',['../classvg_1_1MinimizerMapper.html#a19ffcd52d8076fbee5e0ae8c6cb645a8',1,'vg::MinimizerMapper']]],
+ ['default_5fextension_5fset_5fmin_5fscore_11990',['default_extension_set_min_score',['../classvg_1_1MinimizerMapper.html#ad25575d1e55539f50a77a959adac5697',1,'vg::MinimizerMapper']]],
+ ['default_5fextension_5fset_5fscore_5fthreshold_11991',['default_extension_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a83ad907b2bb4955d69984b067c6701db',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fgap_5fscale_11992',['default_fragment_gap_scale',['../classvg_1_1MinimizerMapper.html#ae03d9220adb714b422a782c26b35c86c',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fmax_5findel_5fbases_11993',['default_fragment_max_indel_bases',['../classvg_1_1MinimizerMapper.html#a0fde24a54cd539268f195f730425bc05',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fmax_5findel_5fbases_5fper_5fbase_11994',['default_fragment_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a4d3b8401a10bb332a34ec92b658139af',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fmax_5flookback_5fbases_11995',['default_fragment_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#a65e69109575da406b2b020e629f95c89',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fmax_5flookback_5fbases_5fper_5fbase_11996',['default_fragment_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#ad3219ef35a8b2a3f879dd40279e0170a',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fmax_5fmin_5fscore_11997',['default_fragment_max_min_score',['../classvg_1_1MinimizerMapper.html#a13904c0a444d50cf1a4bbcd5b34e9c0d',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fmin_5fscore_11998',['default_fragment_min_score',['../classvg_1_1MinimizerMapper.html#a02028299d3998732a8d2df5c6617af60',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fpoints_5fper_5fpossible_5fmatch_11999',['default_fragment_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a184bc5e3d7cd0637a0611f48e32b241b',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fscore_5ffraction_12000',['default_fragment_score_fraction',['../classvg_1_1MinimizerMapper.html#aef5088c7916a178a0287f9b5e3176d49',1,'vg::MinimizerMapper']]],
+ ['default_5ffragment_5fset_5fscore_5fthreshold_12001',['default_fragment_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a1085d1335cebc9bb11ac31cbd45058a1',1,'vg::MinimizerMapper']]],
+ ['default_5fgap_5fscale_12002',['default_gap_scale',['../classvg_1_1MinimizerMapper.html#a2739e3b492d0978a4c17c761a0946bcd',1,'vg::MinimizerMapper']]],
+ ['default_5fgapless_5fextension_5flimit_12003',['default_gapless_extension_limit',['../classvg_1_1MinimizerMapper.html#a988cc9dff2f312de4bdfce08887cd896',1,'vg::MinimizerMapper']]],
+ ['default_5fhard_5fhit_5fcap_12004',['default_hard_hit_cap',['../classvg_1_1MinimizerMapper.html#adaea07e204eca95eeac41c22013725d6',1,'vg::MinimizerMapper']]],
+ ['default_5fhit_5fcap_12005',['default_hit_cap',['../classvg_1_1MinimizerMapper.html#aa09637c461eee0cec06bd75475102147',1,'vg::MinimizerMapper']]],
+ ['default_5fitem_5fbonus_12006',['default_item_bonus',['../classvg_1_1MinimizerMapper.html#a47b33ac9dea218de205fdf4d5c3d53de',1,'vg::MinimizerMapper']]],
+ ['default_5fitem_5fscale_12007',['default_item_scale',['../classvg_1_1MinimizerMapper.html#a95fe7acf05497e31363fe201f9dc22b4',1,'vg::MinimizerMapper']]],
+ ['default_5fiterations_12008',['DEFAULT_ITERATIONS',['../minimizer__main_8cpp.html#a62c07e69eba05821e728bdf3389a500d',1,'minimizer_main.cpp']]],
+ ['default_5fk_12009',['DEFAULT_K',['../structvg_1_1Haplotypes_1_1Header.html#a85d1a35162f23b04d49e1533e12e4a7c',1,'vg::Haplotypes::Header']]],
+ ['default_5flog_5freads_12010',['default_log_reads',['../structGiraffeMainOptions.html#aa6a8ecfcb8fc48b9378c1c8608901f20',1,'GiraffeMainOptions']]],
+ ['default_5fmapq_5fscore_5fscale_12011',['default_mapq_score_scale',['../classvg_1_1MinimizerMapper.html#a950b83222eb55cd956eb604006d5a3d6',1,'vg::MinimizerMapper']]],
+ ['default_5fmapq_5fscore_5fwindow_12012',['default_mapq_score_window',['../classvg_1_1MinimizerMapper.html#a0ffc9c3cb0e41b00ef47dc0a9039e445',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5falignments_12013',['default_max_alignments',['../classvg_1_1MinimizerMapper.html#a0630ced82cb222e941d227b87c3242cc',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fchain_5fconnection_12014',['default_max_chain_connection',['../classvg_1_1MinimizerMapper.html#a03af3423a0607432df929adb6e34dc00',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fchaining_5fproblems_12015',['default_max_chaining_problems',['../classvg_1_1MinimizerMapper.html#a2046e2c404be2f31d1a60e80cf8bfca8',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fchains_5fper_5ftree_12016',['default_max_chains_per_tree',['../classvg_1_1MinimizerMapper.html#a8fd75b16ce33d33287c898cb7056e3d5',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fdirect_5fto_5fchain_12017',['default_max_direct_to_chain',['../classvg_1_1MinimizerMapper.html#a46015a99b97b88cf6a5721933135d449',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fdozeu_5fcells_12018',['default_max_dozeu_cells',['../classvg_1_1MinimizerMapper.html#af849d482a02c0e58a7f80ebb60d8c58b',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fdp_5fcells_12019',['default_max_dp_cells',['../classvg_1_1MinimizerMapper.html#a245ad5daaf4a2d92300dc1703709997b',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fextension_5fmismatches_12020',['default_max_extension_mismatches',['../classvg_1_1MinimizerMapper.html#a9dbe25a46a44ab36757a010e08b4527b',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fextensions_12021',['default_max_extensions',['../classvg_1_1MinimizerMapper.html#adcebeb61c302cf85887e35947d778b82',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5ffragment_5flength_12022',['default_max_fragment_length',['../classvg_1_1MinimizerMapper.html#aef322db760a61242dbb35055171269c8',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5ffragments_12023',['default_max_fragments',['../classvg_1_1MinimizerMapper.html#ac1b0554a6a6f531e00215880027aef19',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5findel_5fbases_12024',['default_max_indel_bases',['../classvg_1_1MinimizerMapper.html#a941e35e0ce18efa4de95f7773810df4c',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5findel_5fbases_5fper_5fbase_12025',['default_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a9b891451941f27e9a03628869da2f795',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5flocal_5fextensions_12026',['default_max_local_extensions',['../classvg_1_1MinimizerMapper.html#a02cb88ed7a5912500972581c1a94a953',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5flookback_5fbases_12027',['default_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#a43fd52a005cf7ce74ab3ccc3a0818130',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5flookback_5fbases_5fper_5fbase_12028',['default_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a077f290854fc4522a2874bb24db0bc5f',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fmiddle_5fdp_5flength_12029',['default_max_middle_dp_length',['../classvg_1_1MinimizerMapper.html#a9693b4420ce66b5d2b9a11d7fcbcf8ed',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fmiddle_5fgap_12030',['default_max_middle_gap',['../classvg_1_1MinimizerMapper.html#aeb435adbfa094f550ffde3994b7935bb',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fmin_5fchain_5fscore_12031',['default_max_min_chain_score',['../classvg_1_1MinimizerMapper.html#addec6b6b7907c12c4001dcecb656a6a1',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fmultimaps_12032',['default_max_multimaps',['../classvg_1_1MinimizerMapper.html#acef30cb743117b4bab6062caabaa4bcc',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5frescue_5fattempts_12033',['default_max_rescue_attempts',['../classvg_1_1MinimizerMapper.html#aeeccbf0f4919ea1bfa9ddc223a2c0668',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fskipped_5fbases_12034',['default_max_skipped_bases',['../classvg_1_1MinimizerMapper.html#aef0223d05eb9dad4dcd8f6c3600dcd47',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fslide_12035',['DEFAULT_MAX_SLIDE',['../classvg_1_1Surjector.html#a3484c973d05e38e523cc45c85ee4d9f3',1,'vg::Surjector']]],
+ ['default_5fmax_5ftail_5fdp_5flength_12036',['default_max_tail_dp_length',['../classvg_1_1MinimizerMapper.html#a21cf128cd5f45135a8b9861d55eb7f7f',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5ftail_5fgap_12037',['default_max_tail_gap',['../classvg_1_1MinimizerMapper.html#a24d37bb5c13e910d0f74fa5f818b2db5',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5ftail_5flength_12038',['default_max_tail_length',['../classvg_1_1MinimizerMapper.html#ae60300bb4ed2185de21379fe5735f3a2',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5fthreads_12039',['DEFAULT_MAX_THREADS',['../namespacehaplotypes__defaults.html#a5767132ecebb35fbe62b9dc8e55d66a9',1,'haplotypes_defaults::DEFAULT_MAX_THREADS()'],['../minimizer__main_8cpp.html#a5b3b08bd8224196307cb86df71ff927d',1,'DEFAULT_MAX_THREADS(): minimizer_main.cpp']]],
+ ['default_5fmax_5fto_5ffragment_12040',['default_max_to_fragment',['../classvg_1_1MinimizerMapper.html#a872367a94f5b074e81db6af4d0d33130',1,'vg::MinimizerMapper']]],
+ ['default_5fmax_5funique_5fmin_12041',['default_max_unique_min',['../classvg_1_1MinimizerMapper.html#a76c18cd5496e664b660c17f892fd0a9d',1,'vg::MinimizerMapper']]],
+ ['default_5fmin_5fchain_5fscore_5fper_5fbase_12042',['default_min_chain_score_per_base',['../classvg_1_1MinimizerMapper.html#a98337be6c0a1ca4eac0c131448492115',1,'vg::MinimizerMapper']]],
+ ['default_5fmin_5fchaining_5fproblems_12043',['default_min_chaining_problems',['../classvg_1_1MinimizerMapper.html#a79a21722c70fb0d54fd4fb66f09b7085',1,'vg::MinimizerMapper']]],
+ ['default_5fmin_5fchains_12044',['default_min_chains',['../classvg_1_1MinimizerMapper.html#a14ee8de796304cc5c30fe5f2485c97aa',1,'vg::MinimizerMapper']]],
+ ['default_5fmin_5fextension_5fsets_12045',['default_min_extension_sets',['../classvg_1_1MinimizerMapper.html#af55ebc7ba993565e61c16f8133e2b618',1,'vg::MinimizerMapper']]],
+ ['default_5fmin_5fextensions_12046',['default_min_extensions',['../classvg_1_1MinimizerMapper.html#a6c64b28b199566f3684d272c57097962',1,'vg::MinimizerMapper']]],
+ ['default_5fmin_5fto_5ffragment_12047',['default_min_to_fragment',['../classvg_1_1MinimizerMapper.html#a4d0a26197071962f77dc4ce29608c1a5',1,'vg::MinimizerMapper']]],
+ ['default_5fmin_5funique_5fnode_5ffraction_12048',['default_min_unique_node_fraction',['../classvg_1_1MinimizerMapper.html#ab3835a6952cc643f0b29dbe10ffdbc9e',1,'vg::MinimizerMapper']]],
+ ['default_5fminimizer_5fcoverage_5fflank_12049',['default_minimizer_coverage_flank',['../classvg_1_1MinimizerMapper.html#a53a4e8bca5b336db81534e731e7501c1',1,'vg::MinimizerMapper']]],
+ ['default_5fminimizer_5fdownsampling_5fmax_5fwindow_5flength_12050',['default_minimizer_downsampling_max_window_length',['../classvg_1_1MinimizerMapper.html#a7ba0c8275fc70249b743b8a327c16dbd',1,'vg::MinimizerMapper']]],
+ ['default_5fminimizer_5fdownsampling_5fwindow_5fcount_12051',['default_minimizer_downsampling_window_count',['../classvg_1_1MinimizerMapper.html#aedf57a0048ea44081f2f75d844a210d6',1,'vg::MinimizerMapper']]],
+ ['default_5fminimizer_5fscore_5ffraction_12052',['default_minimizer_score_fraction',['../classvg_1_1MinimizerMapper.html#aecd1b06ba8d1d6325d21827422777ecd',1,'vg::MinimizerMapper']]],
+ ['default_5fnum_5fbp_5fper_5fmin_12053',['default_num_bp_per_min',['../classvg_1_1MinimizerMapper.html#a270d4aa37a8c19a9953af4185fe2dc81',1,'vg::MinimizerMapper']]],
+ ['default_5fpad_5fcluster_5fscore_5fthreshold_12054',['default_pad_cluster_score_threshold',['../classvg_1_1MinimizerMapper.html#a76b49c1bb20fe42732db8fc6e111bd73',1,'vg::MinimizerMapper']]],
+ ['default_5fpad_5fzipcode_5ftree_5fscore_5fthreshold_12055',['default_pad_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a737e7ee21406911540ae4bd78fb13e56',1,'vg::MinimizerMapper']]],
+ ['default_5fpaired_5fdistance_5fstdevs_12056',['default_paired_distance_stdevs',['../classvg_1_1MinimizerMapper.html#a075eb4ce854be73a0764fc1149721346',1,'vg::MinimizerMapper']]],
+ ['default_5fpaired_5frescue_5fscore_5flimit_12057',['default_paired_rescue_score_limit',['../classvg_1_1MinimizerMapper.html#a82a26ad5a15d724ffb19dee9e105f35e',1,'vg::MinimizerMapper']]],
+ ['default_5fparallel_5fbatchsize_12058',['DEFAULT_PARALLEL_BATCHSIZE',['../namespacevg_1_1io.html#aba1d6c41cb6ff7b47e64b6b584af0363',1,'vg::io']]],
+ ['default_5fpath_5fweight_12059',['DEFAULT_PATH_WEIGHT',['../classvg_1_1FlowSort.html#a68d8af802f0e2a61c81bf0ae4ebfc301',1,'vg::FlowSort']]],
+ ['default_5fpoints_5fper_5fpossible_5fmatch_12060',['default_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a01cea9c6a1146b7643f7814e899dba1a',1,'vg::MinimizerMapper']]],
+ ['default_5frescue_5fseed_5flimit_12061',['default_rescue_seed_limit',['../classvg_1_1MinimizerMapper.html#aba9daaa16afb07adba5aadd1a16bef28',1,'vg::MinimizerMapper']]],
+ ['default_5frescue_5fsubgraph_5fstdevs_12062',['default_rescue_subgraph_stdevs',['../classvg_1_1MinimizerMapper.html#abba75ee681b890855b6d6152581100e9',1,'vg::MinimizerMapper']]],
+ ['default_5fsequence_5fquality_12063',['default_sequence_quality',['../classvg_1_1Genotyper.html#a3c40092b41694cacc7e531bf7f9fb8aa',1,'vg::Genotyper']]],
+ ['default_5fset_5frefpos_12064',['default_set_refpos',['../classvg_1_1MinimizerMapper.html#a130e242a6647d32605daa663b0d96998',1,'vg::MinimizerMapper']]],
+ ['default_5fshow_5fwork_12065',['default_show_work',['../classvg_1_1MinimizerMapper.html#a5b420aef79b283dfe483246b135aa2e1',1,'vg::MinimizerMapper']]],
+ ['default_5fsort_5fby_5fchain_5fscore_12066',['default_sort_by_chain_score',['../classvg_1_1MinimizerMapper.html#a660c0927845a795613529acf90fceefe',1,'vg::MinimizerMapper']]],
+ ['default_5fsubgraph_5flimit_12067',['DEFAULT_SUBGRAPH_LIMIT',['../classvg_1_1Surjector.html#ac78645d41b2dfd88bece81c86a5b7090',1,'vg::Surjector']]],
+ ['default_5fthreshold_12068',['DEFAULT_THRESHOLD',['../minimizer__main_8cpp.html#a777231a8126ad759ff713c50090c6bfb',1,'minimizer_main.cpp']]],
+ ['default_5ftrack_5fcorrectness_12069',['default_track_correctness',['../classvg_1_1MinimizerMapper.html#afcc3e652ef8dd9d78edb5ac14a0fd602',1,'vg::MinimizerMapper']]],
+ ['default_5ftrack_5fposition_12070',['default_track_position',['../classvg_1_1MinimizerMapper.html#a3357a4536f0714508781c4ef201d002c',1,'vg::MinimizerMapper']]],
+ ['default_5ftrack_5fprovenance_12071',['default_track_provenance',['../classvg_1_1MinimizerMapper.html#a0fb3483a8d2c18fa30688532eb70f117',1,'vg::MinimizerMapper']]],
+ ['default_5fuse_5fexplored_5fcap_12072',['default_use_explored_cap',['../classvg_1_1MinimizerMapper.html#adc6c21f5f381f4a6ea7e7e777dc64f21',1,'vg::MinimizerMapper']]],
+ ['default_5fvalue_12073',['default_value',['../classvg_1_1BaseOption.html#ade40b0f856c10a12e3fc7847f4a33b7a',1,'vg::BaseOption::default_value()'],['../structvg_1_1subcommand_1_1ArgSpec.html#a05bdfbeff1f2b1a8d68a4bf9dd6d0d53',1,'vg::subcommand::ArgSpec::default_value()']]],
+ ['default_5fwatchdog_5ftimeout_12074',['default_watchdog_timeout',['../structGiraffeMainOptions.html#a8e3b0f47ff4f761544f077f2d591096e',1,'GiraffeMainOptions']]],
+ ['default_5fwfa_5fdistance_12075',['default_wfa_distance',['../classvg_1_1MinimizerMapper.html#a2b1eabff9087e4acd64cc0e1d49130ee',1,'vg::MinimizerMapper']]],
+ ['default_5fwfa_5fdistance_5fper_5fbase_12076',['default_wfa_distance_per_base',['../classvg_1_1MinimizerMapper.html#ac88d6ddb37fc3e7c5fb2eba6c1f5e107',1,'vg::MinimizerMapper']]],
+ ['default_5fwfa_5fmax_5fdistance_12077',['default_wfa_max_distance',['../classvg_1_1MinimizerMapper.html#a51aa239042c3adaff5ac10c6c4486cc5',1,'vg::MinimizerMapper']]],
+ ['default_5fwfa_5fmax_5fmax_5fmismatches_12078',['default_wfa_max_max_mismatches',['../classvg_1_1MinimizerMapper.html#a8a532cd9bd5ce16848673592a9fb18ec',1,'vg::MinimizerMapper']]],
+ ['default_5fwfa_5fmax_5fmismatches_12079',['default_wfa_max_mismatches',['../classvg_1_1MinimizerMapper.html#a1d0c74a11cc55135d11b08c8fbc96ca2',1,'vg::MinimizerMapper']]],
+ ['default_5fwfa_5fmax_5fmismatches_5fper_5fbase_12080',['default_wfa_max_mismatches_per_base',['../classvg_1_1MinimizerMapper.html#a0ddeeb08b47f9d091dbee44fee6711d5',1,'vg::MinimizerMapper']]],
+ ['default_5fzipcode_5ftree_5fcoverage_5fthreshold_12081',['default_zipcode_tree_coverage_threshold',['../classvg_1_1MinimizerMapper.html#a36ba9324ef7edf8b9625697570d7d971',1,'vg::MinimizerMapper']]],
+ ['default_5fzipcode_5ftree_5fscale_12082',['default_zipcode_tree_scale',['../classvg_1_1MinimizerMapper.html#a82714c6b597295d464e8e0000d849184',1,'vg::MinimizerMapper']]],
+ ['default_5fzipcode_5ftree_5fscore_5fthreshold_12083',['default_zipcode_tree_score_threshold',['../classvg_1_1MinimizerMapper.html#a4ea6f674bb701f8f07e4e31b79fb79d1',1,'vg::MinimizerMapper']]],
+ ['defaultcompresslevel_12084',['DEFAULTCOMPRESSLEVEL',['../namespacezstdutil.html#a449e02cc311816ade9a49c134e38adc8',1,'zstdutil']]],
+ ['defining_5fpath_12085',['defining_path',['../classvg_1_1PathSubgraph.html#a907a18a155eace47d2f8a1f9bacf4894',1,'vg::PathSubgraph']]],
+ ['defray_5fcount_12086',['defray_count',['../classvg_1_1ReadFilter.html#aef4ec3c75ed003564641757d0d78b6ea',1,'vg::ReadFilter']]],
+ ['defray_5flength_12087',['defray_length',['../classvg_1_1ReadFilter.html#ab1a4ac583b2b783404b20e985c4a5f5e',1,'vg::ReadFilter']]],
+ ['deleted_5fprior_5flogprob_12088',['deleted_prior_logprob',['../classvg_1_1Genotyper.html#a853fb8840552901b359153ec80aa81e1',1,'vg::Genotyper']]],
+ ['deletion_5faligner_12089',['deletion_aligner',['../classvg_1_1GSSWAligner.html#a7bd8654938361b8edf947fb888dcd6d8',1,'vg::GSSWAligner']]],
+ ['deletions_12090',['DELETIONS',['../structvg_1_1WFANode.html#acf73ec9a87e0d2e04b2ae4d0e13158e6',1,'vg::WFANode::DELETIONS()'],['../structvg_1_1DeleteHaplotypeCommand.html#a33e4ac2752620369abb200e585e667a4',1,'vg::DeleteHaplotypeCommand::deletions()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a3371d6a46feb1f9d218a577156aef698',1,'vg::ReplaceLocalHaplotypeCommand::deletions()']]],
+ ['delim1_12091',['delim1',['../classvg_1_1Packer.html#acffc9465bdaa0bb770372edf788aad48',1,'vg::Packer']]],
+ ['delim2_12092',['delim2',['../classvg_1_1Packer.html#a0d1336853823c62812b2009e80085800',1,'vg::Packer']]],
+ ['dense_5fto_5fsparse_12093',['dense_to_sparse',['../classvg_1_1SparseUnionFind.html#a9b682c8492591af4002cae1830ebd243',1,'vg::SparseUnionFind']]],
+ ['depth_12094',['depth',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a7c0e5760255d3f47d6fbce1da89d32db',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['depth_5ferr_12095',['depth_err',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#ac8c734835666c796508c7714c332c467',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['depth_5findex_12096',['depth_index',['../classvg_1_1PoissonSupportSnarlCaller.html#adebf4d923f033aa67032c4340d9ebb1e',1,'vg::PoissonSupportSnarlCaller']]],
+ ['depth_5fpadding_5ffactor_12097',['depth_padding_factor',['../classvg_1_1PoissonSupportSnarlCaller.html#a53eec737bc91a46f91161c18ddc26cd7',1,'vg::PoissonSupportSnarlCaller']]],
+ ['description_12098',['description',['../classvg_1_1BaseOption.html#a4468cf61e5b31a06929303e91f096f6d',1,'vg::BaseOption::description()'],['../classvg_1_1subcommand_1_1Subcommand.html#ab74ec1dfb7410088f2a0fa0d368a34f9',1,'vg::subcommand::Subcommand::description()']]],
+ ['dest_12099',['dest',['../structvg_1_1subcommand_1_1ArgSpec.html#a817d3125f130981b273565c384291fc9',1,'vg::subcommand::ArgSpec']]],
+ ['diagonal_12100',['diagonal',['../structvg_1_1WFAPoint.html#ad95025eb9daeb494c52fabdf713ec1d0',1,'vg::WFAPoint']]],
+ ['dinuc_5fmachine_12101',['dinuc_machine',['../classvg_1_1MultipathMapper.html#a4000f9a9d804ef14a51bb48c22029089',1,'vg::MultipathMapper']]],
+ ['diploid_5fprior_5flogprob_12102',['diploid_prior_logprob',['../classvg_1_1Genotyper.html#ac748204c3fb19573569172ee57b1d082',1,'vg::Genotyper']]],
+ ['diploid_5fsampling_12103',['diploid_sampling',['../structvg_1_1Recombinator_1_1Parameters.html#a8aa7a7fe3df17bdbed79475f26d2d884',1,'vg::Recombinator::Parameters']]],
+ ['directed_5facyclic_5fnet_5fgraph_12104',['directed_acyclic_net_graph',['../structvg_1_1Snarl.html#a6cbd6de509a74e1ac363eb14c679b4de',1,'vg::Snarl']]],
+ ['dirnames_12105',['dirnames',['../structvg_1_1temp__file_1_1Handler.html#a3b0eaa40b8b866abc58f94ca6b38f425',1,'vg::temp_file::Handler']]],
+ ['discard_5foverlaps_12106',['discard_overlaps',['../classvg_1_1HaplotypeIndexer.html#a9991b56b5003075a5a072e06e669a3c1',1,'vg::HaplotypeIndexer']]],
+ ['discordant_5finsert_5fsize_12107',['discordant_insert_size',['../structvg_1_1Alignment.html#a5cf554f770c01df31d8b4046b3ed5f50',1,'vg::Alignment']]],
+ ['distance_12108',['distance',['../classvg_1_1MEMClusterer_1_1HitEdge.html#a9792b646c0a3905c5b111d3a61d336f2',1,'vg::MEMClusterer::HitEdge::distance()'],['../structvg_1_1WFAExtender_1_1ErrorModel.html#a700d6dd2d1d47e2aa9c24c474a023a06',1,'vg::WFAExtender::ErrorModel::distance()'],['../structvg_1_1ZipCodeTree_1_1seed__result__t.html#a12043bbec5e8e59b9eb0ff5afc0d2d0d',1,'vg::ZipCodeTree::seed_result_t::distance()']]],
+ ['distance_5fend_5fleft_12109',['distance_end_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a5baab4c86f719c18e9c20224bb10a69a',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_end_left()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#acd2b78cff4271a4ae10fe0d9d5618c5c',1,'vg::ZipCode::snarl_code_t::distance_end_left()']]],
+ ['distance_5fend_5fright_12110',['distance_end_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a06be78a0dab9e6283c66daf6da692ea8',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_end_right()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa720e8028e5d3c9ffef77220f08a3df8',1,'vg::ZipCode::snarl_code_t::distance_end_right()']]],
+ ['distance_5findex_12111',['distance_index',['../classvg_1_1SnarlOrientedDistanceMeasurer.html#a7dd96ca42452dc97acf3063f37435f54',1,'vg::SnarlOrientedDistanceMeasurer::distance_index()'],['../classvg_1_1SnarlMinDistance.html#a950b6521bc5cd59d9f0fc77fd3536f3c',1,'vg::SnarlMinDistance::distance_index()'],['../classvg_1_1TipAnchoredMaxDistance.html#aebb225450c55b6e08eee6d17c9a5f9cd',1,'vg::TipAnchoredMaxDistance::distance_index()'],['../classvg_1_1MinDistanceClusterer.html#a2984cbfe6a052ea92f02ce4cfa16c7cf',1,'vg::MinDistanceClusterer::distance_index()'],['../classvg_1_1MinimizerMapper.html#aac910751d5f0072fa0fbc799bedf1d37',1,'vg::MinimizerMapper::distance_index()'],['../classvg_1_1MultipathMapper.html#a25c0af4ac91144555a4aebccd6fcb38a',1,'vg::MultipathMapper::distance_index()'],['../classvg_1_1HaplotypePartitioner.html#a1fbaa44f3948a107163ddef5026b593e',1,'vg::HaplotypePartitioner::distance_index()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#aa3ee07e1c0cbacde2d5d524d65a03204',1,'vg::SnarlDistanceIndexClusterer::distance_index()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a97a144ab519382e88430c4a8b24bb8a8',1,'vg::ZipCodeForest::forest_growing_state_t::distance_index()']]],
+ ['distance_5fleft_12112',['distance_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#abdf47604f137abb50e7c94eae524a7a7',1,'vg::SnarlDistanceIndexClusterer::SeedCache::distance_left()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a4fb89d65780b1ed5106b392825b41654',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::distance_left()']]],
+ ['distance_5flimit_12113',['distance_limit',['../classvg_1_1MinimizerMapper.html#a2fa22653d0c63a1d7bf41946f6f62a55',1,'vg::MinimizerMapper::distance_limit()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a5b19e98cc2c6be5427e011dd577aa9b0',1,'vg::ZipCodeTree::reverse_iterator::distance_limit()'],['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a55c12dad8377ccb6c4289a38c98d175a',1,'vg::ZipCodeForest::forest_growing_state_t::distance_limit()']]],
+ ['distance_5fmeasurer_12114',['distance_measurer',['../classvg_1_1OrientedDistanceClusterer.html#a73c5578cbd124a60d54b49474937b78b',1,'vg::OrientedDistanceClusterer']]],
+ ['distance_5fname_12115',['distance_name',['../structHaplotypesConfig.html#a7c90afeb06a1a670d1c562e282289fe1',1,'HaplotypesConfig']]],
+ ['distance_5fright_12116',['distance_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SeedCache.html#a13406bb1b2145f75987bf84f23bc5717',1,'vg::SnarlDistanceIndexClusterer::SeedCache::distance_right()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusterHead.html#a7e393752378e18d98e0990244e35aefc',1,'vg::SnarlDistanceIndexClusterer::ClusterHead::distance_right()']]],
+ ['distance_5fstart_5fleft_12117',['distance_start_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a703f0b7ef0e56b44ab6fa13c4458fbb2',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_start_left()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#aa072d11c220e73b6db0c36d18b47ef5d',1,'vg::ZipCode::snarl_code_t::distance_start_left()']]],
+ ['distance_5fstart_5fright_12118',['distance_start_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a40a9152941e9e3dab83127a6cb78e0e7',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_start_right()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#acbb68d2ef2a7862066db2906924624f3',1,'vg::ZipCode::snarl_code_t::distance_start_right()']]],
+ ['distances_12119',['distances',['../structvg_1_1ZipCodeForest_1_1child__info__t.html#aa54c4d24186e3d1a855537d6ea12d3ad',1,'vg::ZipCodeForest::child_info_t']]],
+ ['do_5fdp_12120',['do_dp',['../classvg_1_1MinimizerMapper.html#a80efe32334434e2121f45d9683e2b53b',1,'vg::MinimizerMapper']]],
+ ['do_5fremap_12121',['do_remap',['../classvg_1_1Filter.html#a7c02ec9d43e85148a82acf980728e9ac',1,'vg::Filter']]],
+ ['do_5fspliced_5falignment_12122',['do_spliced_alignment',['../classvg_1_1MultipathMapper.html#a450de2dc7f618164fec361a296be0df3',1,'vg::MultipathMapper']]],
+ ['do_5fsvs_12123',['do_svs',['../classvg_1_1Constructor.html#a2e48ae756193c44a889202591a562d18',1,'vg::Constructor']]],
+ ['dominated_5fpath_5fchunk_5fdiff_12124',['dominated_path_chunk_diff',['../classvg_1_1Surjector.html#ace7092128b309c97f00fc688d3311c14',1,'vg::Surjector']]],
+ ['double_5fis_5ffraction_12125',['double_is_fraction',['../namespacevg_1_1subcommand.html#a6f44735d61e600db634ef1968f64c7c5',1,'vg::subcommand']]],
+ ['double_5fis_5fnonnegative_12126',['double_is_nonnegative',['../namespacevg_1_1subcommand.html#a7e565a520f46689e6fe5d38887c7f135',1,'vg::subcommand']]],
+ ['double_5fis_5fpositive_12127',['double_is_positive',['../namespacevg_1_1subcommand.html#a750f1011d067a25d64e3157e7435b78f',1,'vg::subcommand']]],
+ ['doubling_5fsteps_12128',['doubling_steps',['../classvg_1_1VariantAdder.html#a07970f9f50038e088ef054cde57755af',1,'vg::VariantAdder']]],
+ ['downsample_5fcontext_5flength_12129',['downsample_context_length',['../structvg_1_1IndexingParameters.html#ac805da027e770df83d21c5c86f922165',1,'vg::IndexingParameters']]],
+ ['downsample_5fcoverage_12130',['downsample_coverage',['../classvg_1_1Surjector.html#a9f599519246cb13464ffe2bbde8bccbe',1,'vg::Surjector']]],
+ ['downsample_5fprobability_12131',['downsample_probability',['../classvg_1_1ReadFilter.html#a44099974ab2ac2d374e4530b064e1908',1,'vg::ReadFilter']]],
+ ['downsample_5fseed_5fmask_12132',['downsample_seed_mask',['../classvg_1_1ReadFilter.html#a881165b11e7539bc03e331f16b1a5f0a',1,'vg::ReadFilter']]],
+ ['downsample_5fthreshold_12133',['downsample_threshold',['../structvg_1_1IndexingParameters.html#aafe781017908d4c15538093514c53e61',1,'vg::IndexingParameters']]],
+ ['dozeu_5ftail_12134',['dozeu_tail',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t_1_1stat__set__t.html#a7a193ad86c14a5cca14d982f16c0f252',1,'vg::MinimizerMapper::aligner_stats_t::stat_set_t']]],
+ ['dp_5fcolumn_12135',['DP_column',['../structhaplo_1_1haplo__DP.html#aac064205c5153507bc6e25e465873ade',1,'haplo::haplo_DP']]],
+ ['dp_5fscore_12136',['dp_score',['../classvg_1_1MEMClusterer_1_1HitNode.html#a7db6db0a42c9f87de4bf20c94abca967',1,'vg::MEMClusterer::HitNode']]],
+ ['drop_5fchain_12137',['drop_chain',['../classvg_1_1Mapper.html#a838f9ae9f5f33ba048cf036788dece6a',1,'vg::Mapper']]],
+ ['drop_5fhairpin_5fpaths_12138',['drop_hairpin_paths',['../classvg_1_1SmallSnarlSimplifier.html#a929e965d0e8441162fa2fe94c29760de',1,'vg::SmallSnarlSimplifier']]],
+ ['drop_5fsplit_12139',['drop_split',['../classvg_1_1ReadFilter.html#a52316fdf4e8b2ee3741bfbc4a89727a7',1,'vg::ReadFilter']]],
+ ['dry_5frun_12140',['dry_run',['../structvg_1_1RebuildParameters.html#af83ad08bd1ac55470c1ecbb2862d6b68',1,'vg::RebuildParameters']]],
+ ['duplicated_5fhandles_12141',['duplicated_handles',['../classvg_1_1DozeuPinningOverlay.html#a253129512ddaf2db6fa4c81b5f9a5b92',1,'vg::DozeuPinningOverlay']]],
+ ['duration_12142',['duration',['../structvg_1_1Funnel_1_1Stage.html#a30cb16fa4dcf3f41ef0af169f9900e86',1,'vg::Funnel::Stage']]],
+ ['dynamic_12143',['dynamic',['../structvg_1_1GBWTHandler.html#a1fddb1a69a6f6ec6c28016ca13c35894',1,'vg::GBWTHandler']]],
+ ['dynamic_5fmax_5falt_5falns_12144',['dynamic_max_alt_alns',['../classvg_1_1MultipathMapper.html#a0b5bddc4e714e176cfe9c1a9680fa60a',1,'vg::MultipathMapper']]],
+ ['dz_12145',['dz',['../classvg_1_1DozeuInterface.html#a7df127f3d122bd29a38453a08c5c22b8',1,'vg::DozeuInterface']]]
];
diff --git a/search/variables_5.js b/search/variables_5.js
index e9c4aac62c..2557d5ebdc 100644
--- a/search/variables_5.js
+++ b/search/variables_5.js
@@ -1,81 +1,81 @@
var searchData=
[
- ['earlier_5fstage_5fitems_12142',['earlier_stage_items',['../structvg_1_1Funnel_1_1Item.html#a0e3bcc678e4f1d348d87941074869007',1,'vg::Funnel::Item']]],
- ['early_5fstop_5fnumber_12143',['early_stop_number',['../classvg_1_1ComponentMinDistanceClusterer.html#a9fe2885de251320cc9c1deeffa8372ec',1,'vg::ComponentMinDistanceClusterer']]],
- ['eat_5ftrivial_5fchildren_12144',['eat_trivial_children',['../classvg_1_1RepresentativeTraversalFinder.html#a7399762276304b196332d0660c169605',1,'vg::RepresentativeTraversalFinder']]],
- ['edge_12145',['edge',['../structvg_1_1Graph.html#ae581df485daa482523eb1a7954ac9561',1,'vg::Graph::edge()'],['../structvg_1_1EdgePileup.html#a61793befcf507143604cf6e0af1cab6a',1,'vg::EdgePileup::edge()']]],
- ['edge_5fby_5fsides_12146',['edge_by_sides',['../classvg_1_1VG.html#ab754d45647580a21216bd010b72c6815',1,'vg::VG']]],
- ['edge_5fcache_12147',['edge_cache',['../classvg_1_1Sampler.html#afb7efec11ad329ffaeaf4e5519b797a6',1,'vg::Sampler']]],
- ['edge_5fcount_12148',['edge_count',['../classxg_1_1XG.html#aa017ea1f9125608d81a752abafd188dd',1,'xg::XG']]],
- ['edge_5fcov_5fbin_5fsize_12149',['edge_cov_bin_size',['../classvg_1_1Packer.html#a7d637f7488a749a1f05342e2b532ef71',1,'vg::Packer']]],
- ['edge_5fcoverage_5fciv_12150',['edge_coverage_civ',['../classvg_1_1Packer.html#a11f2e82fc82448717a4e7ad63b777f27',1,'vg::Packer']]],
- ['edge_5fcoverage_5fdynamic_12151',['edge_coverage_dynamic',['../classvg_1_1Packer.html#a5338d62c679b5173b571e2dd54e2c566',1,'vg::Packer']]],
- ['edge_5findex_12152',['edge_index',['../classvg_1_1VG.html#a2e2c02a8216f0bb9b3a78e985845ea1b',1,'vg::VG']]],
- ['edge_5flisteners_12153',['edge_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#ab784883f08cbef73ec9e735c0459414d',1,'vg::algorithms::GFAParser']]],
- ['edge_5flocks_12154',['edge_locks',['../classvg_1_1Packer.html#a5ae954ebc4876bebfd5ed564856d5399',1,'vg::Packer']]],
- ['edge_5fmax_12155',['edge_max',['../classvg_1_1VariantAdder.html#aa17185d06cdf8969bf249fb316dbf07d',1,'vg::VariantAdder::edge_max()'],['../structPruningParameters.html#a3dbdbc8714fab9d6f2bcb282d9fa7c59',1,'PruningParameters::edge_max()']]],
- ['edge_5fpileups_12156',['edge_pileups',['../structvg_1_1Pileup.html#af21485035738e0f7c01912f4416138b7',1,'vg::Pileup']]],
- ['edge_5fsupport_5fcache_12157',['edge_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a522597cae1d53338cc7cce4d8f2220af',1,'vg::CachedPackedTraversalSupportFinder']]],
- ['edge_5fsupports_12158',['edge_supports',['../structvg_1_1SupportAugmentedGraph.html#a8ad39feeefa25e87a09571524f0467ef',1,'vg::SupportAugmentedGraph']]],
- ['edge_5fweight_12159',['edge_weight',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a0a343b1685fe587b3ddd3e68a8c1e456',1,'vg::FlowSort::WeightedGraph']]],
- ['edge_5fweight_5fcallback_12160',['edge_weight_callback',['../classvg_1_1FlowTraversalFinder.html#ab47146aa9a038f781c2931b7bacb76a6',1,'vg::FlowTraversalFinder']]],
- ['edges_12161',['edges',['../classvg_1_1DiagramExplainer.html#ae31406383532a45ab3664f06735c9136',1,'vg::DiagramExplainer::edges()'],['../classvg_1_1PathNode.html#a6cb73afb96a71fde67792e70c3a6eed1',1,'vg::PathNode::edges()'],['../structvg_1_1algorithms_1_1Node.html#a0bbc2e49725fa2baa9a7aa3d6f5cbc13',1,'vg::algorithms::Node::edges()']]],
- ['edges_5ffrom_12162',['edges_from',['../classvg_1_1MEMClusterer_1_1HitNode.html#a08f1cb5b86c27e7b763d16bcaeff2555',1,'vg::MEMClusterer::HitNode']]],
- ['edges_5fin_5fnodes_12163',['edges_in_nodes',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a66f3b9dc262d89dfedae8189e8869d9e',1,'vg::FlowSort::WeightedGraph']]],
- ['edges_5fon_5fend_12164',['edges_on_end',['../classvg_1_1VG.html#a678bafc48a8e02155efc591991201122',1,'vg::VG']]],
- ['edges_5fon_5fstart_12165',['edges_on_start',['../classvg_1_1VG.html#a00590435d38e7ddf8a77b731d8a1a755',1,'vg::VG']]],
- ['edges_5fout_5fnodes_12166',['edges_out_nodes',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a72ef824e7b4558654602d87b00ef7b64',1,'vg::FlowSort::WeightedGraph']]],
- ['edges_5fto_12167',['edges_to',['../classvg_1_1MEMClusterer_1_1HitNode.html#a9c63a5662cc86132572113bbcebb05a8',1,'vg::MEMClusterer::HitNode']]],
- ['edit_12168',['edit',['../structvg_1_1Mapping.html#a657c55428cdcb049036edde19e0dbc2c',1,'vg::Mapping']]],
- ['edit_5fcount_12169',['edit_count',['../classvg_1_1Packer.html#a9b05681219f9fc45a6f65b5e59c8224e',1,'vg::Packer']]],
- ['edit_5fcsas_12170',['edit_csas',['../classvg_1_1Packer.html#ae988670f49b31afbd2bf3397eadd5ba8',1,'vg::Packer']]],
- ['edit_5flength_12171',['edit_length',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a119b871b6c0f65afac16120b33f8778e',1,'vg::BandedGlobalAligner::BABuilder::edit_length()'],['../classvg_1_1Packer.html#ac995b84ca9cb65010b04ac600514ca34',1,'vg::Packer::edit_length()']]],
- ['edit_5fread_5fend_5fidx_12172',['edit_read_end_idx',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a23e8527fcdc9cd46287a12ed651ebf1f',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['edit_5ftmpfile_5fnames_12173',['edit_tmpfile_names',['../classvg_1_1Packer.html#ad4ccd5a38811117a363b9f69f7c45832',1,'vg::Packer']]],
- ['edits_12174',['edits',['../structvg_1_1WFAAlignment.html#aff6c4f80af4102e6d3d9b7784ae898e3',1,'vg::WFAAlignment']]],
- ['effective_5fposition_12175',['effective_position',['../structvg_1_1Funnel_1_1Item.html#ae58d707f16725f62a5ddadd7d065f95b',1,'vg::Funnel::Item']]],
- ['embedded_5falignments_12176',['embedded_alignments',['../structvg_1_1AugmentedGraph.html#acde3270a37d6e01cfbf34ac3853e50b9',1,'vg::AugmentedGraph']]],
- ['embedded_5fpath_5fnames_12177',['embedded_path_names',['../structvg_1_1TranscriptPath.html#a2a7bd811b7e8523c287c3f5de96339c9',1,'vg::TranscriptPath']]],
- ['emit_5fto_12178',['emit_to',['../namespacevg_1_1io.html#a4547db1ae9c6b6b3cf0ba9f4aed17e14',1,'vg::io']]],
- ['emitter_12179',['emitter',['../classvg_1_1GAFOutputCaller.html#a57c3b9e5bbe695c83c523e59865dee86',1,'vg::GAFOutputCaller']]],
- ['empty_5fedge_5fends_12180',['empty_edge_ends',['../classvg_1_1VG.html#a7d18d29606bbdb7875f7d8a8042dd29a',1,'vg::VG']]],
- ['empty_5ffull_5fpaths_12181',['empty_full_paths',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a23e1eb082e5f26d87c43dfa1b7ec133d',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['empty_5fids_12182',['empty_ids',['../classvg_1_1VG.html#a071f0034788bdcd778d5d0c76ba4f6b6',1,'vg::VG']]],
- ['empty_5fscore_12183',['empty_score',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a615b7711ad30debfdeee5441eae251e5',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
- ['enabled_12184',['enabled',['../classvg_1_1Explainer.html#aab4405f76ac87a52ec7acd6e833a11c7',1,'vg::Explainer']]],
- ['encoding_12185',['encoding',['../classvg_1_1ParallelKFFReader.html#ae239a972872083d7585b58fba2773b00',1,'vg::ParallelKFFReader']]],
- ['end_12186',['end',['../structvg_1_1GFFRecord.html#a16b3feda67511be06c247abb7fdaadff',1,'vg::GFFRecord::end()'],['../structvg_1_1kmer__t.html#a0bd5e9d1a1806df8a601686c300adf63',1,'vg::kmer_t::end()'],['../classvg_1_1MaximalExactMatch.html#aa9b666f4e8b24ccbcfb6b6520ca3d9aa',1,'vg::MaximalExactMatch::end()'],['../classvg_1_1PathNode.html#ad05607b13e239822f7ddc3522d807d27',1,'vg::PathNode::end()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af4d6a1ceb7bfeca4656781b8e2a1ece8',1,'vg::Haplotypes::Subchain::end()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a8854a555b9cdb1168df34f0d4fa529ff',1,'vg::HaplotypePartitioner::Subchain::end()'],['../structvg_1_1Region.html#af0af8f5918029a238aea4efe9258c2f5',1,'vg::Region::end()'],['../classvg_1_1NetGraph.html#ae4610aa5b5468087cb80bcd7d3062475',1,'vg::NetGraph::end()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aa392ebaad77834fab7b6a5fafd891abe',1,'vg::ZipCodeTree::iterator::end()'],['../structvg_1_1algorithms_1_1kmer__t.html#a0f16e45a7dbcae72b66342a752a6b4f9',1,'vg::algorithms::kmer_t::end()'],['../structvg_1_1algorithms_1_1walk__t.html#aa9f43084546a1cb2504850e5be168ae1',1,'vg::algorithms::walk_t::end()'],['../structReferenceInterval.html#a8f400dd758acd1f6ebff643d6b822ce7',1,'ReferenceInterval::end()'],['../structvg_1_1Range.html#a5cdb02cc75f84b274ffbe6b50a148025',1,'vg::Range::end()'],['../structgafkluge_1_1GafStep.html#a40e160ff2811ac460c4e33b5e2ac974f',1,'gafkluge::GafStep::end()'],['../structvg_1_1Snarl.html#a9cfca2c378ed8f699c6d5e4a752242e4',1,'vg::Snarl::end()']]],
- ['end_5ffile_12187',['end_file',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ad31df557e0da72dbd81c865855454e25',1,'vg::io::BlockedGzipOutputStream']]],
- ['end_5foffset_12188',['end_offset',['../classvg_1_1algorithms_1_1Anchor.html#ab6c13fc2cdf7820ec92036d406dde823',1,'vg::algorithms::Anchor']]],
- ['end_5fpos_12189',['end_pos',['../classvg_1_1algorithms_1_1Anchor.html#abecd5e7de3a068e14f96fe05adaf4e29',1,'vg::algorithms::Anchor']]],
- ['end_5fseed_12190',['end_seed',['../classvg_1_1algorithms_1_1Anchor.html#a097a5d87932312ecf7e73a05d6a4dd54',1,'vg::algorithms::Anchor']]],
- ['end_5fself_5freachable_12191',['end_self_reachable',['../structvg_1_1Snarl.html#a18c06a3bd33bd3385147838d4c7b867c',1,'vg::Snarl']]],
- ['end_5fzip_12192',['end_zip',['../classvg_1_1algorithms_1_1Anchor.html#aabad16a036718cc6ddf080d871cdc9bc',1,'vg::algorithms::Anchor']]],
- ['endpoints_12193',['endpoints',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a2b1f1d67a76ef6de89f8f30bd794f603',1,'vg::GraphSynchronizer::Lock']]],
- ['entries_12194',['entries',['../structhaplo_1_1haplo__DP__column.html#aa46ab429b8d5eba3919e2c1cbf2e9a4e',1,'haplo::haplo_DP_column::entries()'],['../structvg_1_1subcommand_1_1Preset.html#ac689c36f8bc510aafb17f89b59c309c2',1,'vg::subcommand::Preset::entries()']]],
- ['error_5fmodel_12195',['error_model',['../classvg_1_1WFAExtender.html#a1378f212c728e87b7ba1231b1b2a2d2d',1,'vg::WFAExtender']]],
- ['error_5fon_5fmissing_5fpath_12196',['error_on_missing_path',['../classvg_1_1Transcriptome.html#a9c23e99ed885b6c5856f5a6baf1d7f95',1,'vg::Transcriptome']]],
- ['exact_5fname_12197',['exact_name',['../classvg_1_1ReadFilter.html#a3165602af2a80ad642c9f900f9bf723e',1,'vg::ReadFilter']]],
- ['exclude_5foverlapping_5fmin_12198',['exclude_overlapping_min',['../classvg_1_1MinimizerMapper.html#aca75c152e0c37e2ed5592400d3eb5fa7',1,'vg::MinimizerMapper']]],
- ['exclude_5funaligned_12199',['exclude_unaligned',['../classvg_1_1BaseMapper.html#ac71be220eec4224b249a6536db70bbe5',1,'vg::BaseMapper']]],
- ['excluded_5ffeatures_12200',['excluded_features',['../classvg_1_1ReadFilter.html#a621533fd4d338b7b5cee85df4a64c8ef',1,'vg::ReadFilter']]],
- ['excluded_5frefpos_5fcontigs_12201',['excluded_refpos_contigs',['../classvg_1_1ReadFilter.html#a019f6eab0ba08ab063f2f9b1226a0cf0',1,'vg::ReadFilter']]],
- ['excluded_5fsamples_12202',['excluded_samples',['../classvg_1_1HaplotypeIndexer.html#a116eb86acabeb52c7da7a1688686c034',1,'vg::HaplotypeIndexer']]],
- ['exec_12203',['exec',['../structvg_1_1IndexRecipe.html#a948544cdea8166535520fee48304b5ee',1,'vg::IndexRecipe']]],
- ['exons_12204',['exons',['../structvg_1_1Transcript.html#afc456b6b43f918028aee362aaa016209',1,'vg::Transcript']]],
- ['exp_5frho_12205',['exp_rho',['../structhaplo_1_1haploMath_1_1RRMemo.html#a7979b3ef938f0a887ea1b5511d33e9f6',1,'haplo::haploMath::RRMemo']]],
- ['expected_5fdepth_12206',['expected_depth',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a33a46269b733b08e64c4ccc021b342b6',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['expected_5fseparation_12207',['expected_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a2691d4683754ab1487bd76dd2e4aa720',1,'vg::GreedyMinDistanceClusterer']]],
- ['explanation_5fnumber_12208',['explanation_number',['../classvg_1_1Explainer.html#ad93fa7fe7f64d180b6c606ffba47ba11',1,'vg::Explainer']]],
- ['extender_12209',['extender',['../classvg_1_1MinimizerMapper.html#a30d6a39763a954968818b76b0463aa89',1,'vg::MinimizerMapper']]],
- ['extension_5fscore_5fthreshold_12210',['extension_score_threshold',['../classvg_1_1MinimizerMapper.html#adeff081b3c6a83ddfa7f620245b61fd0',1,'vg::MinimizerMapper']]],
- ['extension_5fset_5fmin_5fscore_12211',['extension_set_min_score',['../classvg_1_1MinimizerMapper.html#aceeb71c78d5d236c86272ee14592cd10',1,'vg::MinimizerMapper']]],
- ['extension_5fset_5fscore_5fthreshold_12212',['extension_set_score_threshold',['../classvg_1_1MinimizerMapper.html#ac47b8ebb0479d86727c97e37e7f103ee',1,'vg::MinimizerMapper']]],
- ['external_5fid_5fmap_12213',['external_id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a2047be69a33b61966ddd33570c96a632',1,'vg::algorithms::GFAParser']]],
- ['extra_5fdata_12214',['extra_data',['../structvg_1_1FeatureSet_1_1Feature.html#ad95acb3def1e4c9b5fa2a590b77e4993',1,'vg::FeatureSet::Feature']]],
- ['extra_5ffragments_12215',['extra_fragments',['../structvg_1_1Recombinator_1_1Statistics.html#afe44ec6921b89debb44dcc5b07ce7caf',1,'vg::Recombinator::Statistics::extra_fragments()'],['../structvg_1_1Recombinator_1_1Parameters.html#a23a4c5772ec0d526b632b280e91e48ca',1,'vg::Recombinator::Parameters::extra_fragments()']]],
- ['extra_5fmultimaps_12216',['extra_multimaps',['../classvg_1_1Mapper.html#afe9cdcfbff73199e755c5bead44c9674',1,'vg::Mapper']]],
- ['extra_5fsnarls_12217',['extra_snarls',['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a24af34e8be6cb50546e914cb088977a1',1,'vg::HaplotypePartitioner::Subchain']]],
- ['extract_5fleft_12218',['extract_left',['../classvg_1_1IncrementalSubgraph.html#a8b93ae511b47d189bdcf996d88f04f9d',1,'vg::IncrementalSubgraph']]],
- ['extracted_12219',['extracted',['../classvg_1_1IncrementalSubgraph.html#a07d9afa325ba5788ae4ad9cb4539d644',1,'vg::IncrementalSubgraph']]]
+ ['earlier_5fstage_5fitems_12146',['earlier_stage_items',['../structvg_1_1Funnel_1_1Item.html#a0e3bcc678e4f1d348d87941074869007',1,'vg::Funnel::Item']]],
+ ['early_5fstop_5fnumber_12147',['early_stop_number',['../classvg_1_1ComponentMinDistanceClusterer.html#a9fe2885de251320cc9c1deeffa8372ec',1,'vg::ComponentMinDistanceClusterer']]],
+ ['eat_5ftrivial_5fchildren_12148',['eat_trivial_children',['../classvg_1_1RepresentativeTraversalFinder.html#a7399762276304b196332d0660c169605',1,'vg::RepresentativeTraversalFinder']]],
+ ['edge_12149',['edge',['../structvg_1_1Graph.html#ae581df485daa482523eb1a7954ac9561',1,'vg::Graph::edge()'],['../structvg_1_1EdgePileup.html#a61793befcf507143604cf6e0af1cab6a',1,'vg::EdgePileup::edge()']]],
+ ['edge_5fby_5fsides_12150',['edge_by_sides',['../classvg_1_1VG.html#ab754d45647580a21216bd010b72c6815',1,'vg::VG']]],
+ ['edge_5fcache_12151',['edge_cache',['../classvg_1_1Sampler.html#afb7efec11ad329ffaeaf4e5519b797a6',1,'vg::Sampler']]],
+ ['edge_5fcount_12152',['edge_count',['../classxg_1_1XG.html#aa017ea1f9125608d81a752abafd188dd',1,'xg::XG']]],
+ ['edge_5fcov_5fbin_5fsize_12153',['edge_cov_bin_size',['../classvg_1_1Packer.html#a7d637f7488a749a1f05342e2b532ef71',1,'vg::Packer']]],
+ ['edge_5fcoverage_5fciv_12154',['edge_coverage_civ',['../classvg_1_1Packer.html#a11f2e82fc82448717a4e7ad63b777f27',1,'vg::Packer']]],
+ ['edge_5fcoverage_5fdynamic_12155',['edge_coverage_dynamic',['../classvg_1_1Packer.html#a5338d62c679b5173b571e2dd54e2c566',1,'vg::Packer']]],
+ ['edge_5findex_12156',['edge_index',['../classvg_1_1VG.html#a2e2c02a8216f0bb9b3a78e985845ea1b',1,'vg::VG']]],
+ ['edge_5flisteners_12157',['edge_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#ab784883f08cbef73ec9e735c0459414d',1,'vg::algorithms::GFAParser']]],
+ ['edge_5flocks_12158',['edge_locks',['../classvg_1_1Packer.html#a5ae954ebc4876bebfd5ed564856d5399',1,'vg::Packer']]],
+ ['edge_5fmax_12159',['edge_max',['../classvg_1_1VariantAdder.html#aa17185d06cdf8969bf249fb316dbf07d',1,'vg::VariantAdder::edge_max()'],['../structPruningParameters.html#a3dbdbc8714fab9d6f2bcb282d9fa7c59',1,'PruningParameters::edge_max()']]],
+ ['edge_5fpileups_12160',['edge_pileups',['../structvg_1_1Pileup.html#af21485035738e0f7c01912f4416138b7',1,'vg::Pileup']]],
+ ['edge_5fsupport_5fcache_12161',['edge_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a522597cae1d53338cc7cce4d8f2220af',1,'vg::CachedPackedTraversalSupportFinder']]],
+ ['edge_5fsupports_12162',['edge_supports',['../structvg_1_1SupportAugmentedGraph.html#a8ad39feeefa25e87a09571524f0467ef',1,'vg::SupportAugmentedGraph']]],
+ ['edge_5fweight_12163',['edge_weight',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a0a343b1685fe587b3ddd3e68a8c1e456',1,'vg::FlowSort::WeightedGraph']]],
+ ['edge_5fweight_5fcallback_12164',['edge_weight_callback',['../classvg_1_1FlowTraversalFinder.html#ab47146aa9a038f781c2931b7bacb76a6',1,'vg::FlowTraversalFinder']]],
+ ['edges_12165',['edges',['../classvg_1_1DiagramExplainer.html#ae31406383532a45ab3664f06735c9136',1,'vg::DiagramExplainer::edges()'],['../classvg_1_1PathNode.html#a6cb73afb96a71fde67792e70c3a6eed1',1,'vg::PathNode::edges()'],['../structvg_1_1algorithms_1_1Node.html#a0bbc2e49725fa2baa9a7aa3d6f5cbc13',1,'vg::algorithms::Node::edges()']]],
+ ['edges_5ffrom_12166',['edges_from',['../classvg_1_1MEMClusterer_1_1HitNode.html#a08f1cb5b86c27e7b763d16bcaeff2555',1,'vg::MEMClusterer::HitNode']]],
+ ['edges_5fin_5fnodes_12167',['edges_in_nodes',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a66f3b9dc262d89dfedae8189e8869d9e',1,'vg::FlowSort::WeightedGraph']]],
+ ['edges_5fon_5fend_12168',['edges_on_end',['../classvg_1_1VG.html#a678bafc48a8e02155efc591991201122',1,'vg::VG']]],
+ ['edges_5fon_5fstart_12169',['edges_on_start',['../classvg_1_1VG.html#a00590435d38e7ddf8a77b731d8a1a755',1,'vg::VG']]],
+ ['edges_5fout_5fnodes_12170',['edges_out_nodes',['../structvg_1_1FlowSort_1_1WeightedGraph.html#a72ef824e7b4558654602d87b00ef7b64',1,'vg::FlowSort::WeightedGraph']]],
+ ['edges_5fto_12171',['edges_to',['../classvg_1_1MEMClusterer_1_1HitNode.html#a9c63a5662cc86132572113bbcebb05a8',1,'vg::MEMClusterer::HitNode']]],
+ ['edit_12172',['edit',['../structvg_1_1Mapping.html#a657c55428cdcb049036edde19e0dbc2c',1,'vg::Mapping']]],
+ ['edit_5fcount_12173',['edit_count',['../classvg_1_1Packer.html#a9b05681219f9fc45a6f65b5e59c8224e',1,'vg::Packer']]],
+ ['edit_5fcsas_12174',['edit_csas',['../classvg_1_1Packer.html#ae988670f49b31afbd2bf3397eadd5ba8',1,'vg::Packer']]],
+ ['edit_5flength_12175',['edit_length',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a119b871b6c0f65afac16120b33f8778e',1,'vg::BandedGlobalAligner::BABuilder::edit_length()'],['../classvg_1_1Packer.html#ac995b84ca9cb65010b04ac600514ca34',1,'vg::Packer::edit_length()']]],
+ ['edit_5fread_5fend_5fidx_12176',['edit_read_end_idx',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a23e8527fcdc9cd46287a12ed651ebf1f',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['edit_5ftmpfile_5fnames_12177',['edit_tmpfile_names',['../classvg_1_1Packer.html#ad4ccd5a38811117a363b9f69f7c45832',1,'vg::Packer']]],
+ ['edits_12178',['edits',['../structvg_1_1WFAAlignment.html#aff6c4f80af4102e6d3d9b7784ae898e3',1,'vg::WFAAlignment']]],
+ ['effective_5fposition_12179',['effective_position',['../structvg_1_1Funnel_1_1Item.html#ae58d707f16725f62a5ddadd7d065f95b',1,'vg::Funnel::Item']]],
+ ['embedded_5falignments_12180',['embedded_alignments',['../structvg_1_1AugmentedGraph.html#acde3270a37d6e01cfbf34ac3853e50b9',1,'vg::AugmentedGraph']]],
+ ['embedded_5fpath_5fnames_12181',['embedded_path_names',['../structvg_1_1TranscriptPath.html#a2a7bd811b7e8523c287c3f5de96339c9',1,'vg::TranscriptPath']]],
+ ['emit_5fto_12182',['emit_to',['../namespacevg_1_1io.html#a4547db1ae9c6b6b3cf0ba9f4aed17e14',1,'vg::io']]],
+ ['emitter_12183',['emitter',['../classvg_1_1GAFOutputCaller.html#a57c3b9e5bbe695c83c523e59865dee86',1,'vg::GAFOutputCaller']]],
+ ['empty_5fedge_5fends_12184',['empty_edge_ends',['../classvg_1_1VG.html#a7d18d29606bbdb7875f7d8a8042dd29a',1,'vg::VG']]],
+ ['empty_5ffull_5fpaths_12185',['empty_full_paths',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a23e1eb082e5f26d87c43dfa1b7ec133d',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['empty_5fids_12186',['empty_ids',['../classvg_1_1VG.html#a071f0034788bdcd778d5d0c76ba4f6b6',1,'vg::VG']]],
+ ['empty_5fscore_12187',['empty_score',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a615b7711ad30debfdeee5441eae251e5',1,'vg::BandedGlobalAligner::AltTracebackStack']]],
+ ['enabled_12188',['enabled',['../classvg_1_1Explainer.html#aab4405f76ac87a52ec7acd6e833a11c7',1,'vg::Explainer']]],
+ ['encoding_12189',['encoding',['../classvg_1_1ParallelKFFReader.html#ae239a972872083d7585b58fba2773b00',1,'vg::ParallelKFFReader']]],
+ ['end_12190',['end',['../structvg_1_1GFFRecord.html#a16b3feda67511be06c247abb7fdaadff',1,'vg::GFFRecord::end()'],['../structvg_1_1kmer__t.html#a0bd5e9d1a1806df8a601686c300adf63',1,'vg::kmer_t::end()'],['../classvg_1_1MaximalExactMatch.html#aa9b666f4e8b24ccbcfb6b6520ca3d9aa',1,'vg::MaximalExactMatch::end()'],['../classvg_1_1PathNode.html#ad05607b13e239822f7ddc3522d807d27',1,'vg::PathNode::end()'],['../structvg_1_1Haplotypes_1_1Subchain.html#af4d6a1ceb7bfeca4656781b8e2a1ece8',1,'vg::Haplotypes::Subchain::end()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a8854a555b9cdb1168df34f0d4fa529ff',1,'vg::HaplotypePartitioner::Subchain::end()'],['../structvg_1_1Region.html#af0af8f5918029a238aea4efe9258c2f5',1,'vg::Region::end()'],['../classvg_1_1NetGraph.html#ae4610aa5b5468087cb80bcd7d3062475',1,'vg::NetGraph::end()'],['../classvg_1_1ZipCodeTree_1_1iterator.html#aa392ebaad77834fab7b6a5fafd891abe',1,'vg::ZipCodeTree::iterator::end()'],['../structvg_1_1algorithms_1_1kmer__t.html#a0f16e45a7dbcae72b66342a752a6b4f9',1,'vg::algorithms::kmer_t::end()'],['../structvg_1_1algorithms_1_1walk__t.html#aa9f43084546a1cb2504850e5be168ae1',1,'vg::algorithms::walk_t::end()'],['../structReferenceInterval.html#a8f400dd758acd1f6ebff643d6b822ce7',1,'ReferenceInterval::end()'],['../structvg_1_1Range.html#a5cdb02cc75f84b274ffbe6b50a148025',1,'vg::Range::end()'],['../structgafkluge_1_1GafStep.html#a40e160ff2811ac460c4e33b5e2ac974f',1,'gafkluge::GafStep::end()'],['../structvg_1_1Snarl.html#a9cfca2c378ed8f699c6d5e4a752242e4',1,'vg::Snarl::end()']]],
+ ['end_5ffile_12191',['end_file',['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ad31df557e0da72dbd81c865855454e25',1,'vg::io::BlockedGzipOutputStream']]],
+ ['end_5foffset_12192',['end_offset',['../classvg_1_1algorithms_1_1Anchor.html#ab6c13fc2cdf7820ec92036d406dde823',1,'vg::algorithms::Anchor']]],
+ ['end_5fpos_12193',['end_pos',['../classvg_1_1algorithms_1_1Anchor.html#abecd5e7de3a068e14f96fe05adaf4e29',1,'vg::algorithms::Anchor']]],
+ ['end_5fseed_12194',['end_seed',['../classvg_1_1algorithms_1_1Anchor.html#a097a5d87932312ecf7e73a05d6a4dd54',1,'vg::algorithms::Anchor']]],
+ ['end_5fself_5freachable_12195',['end_self_reachable',['../structvg_1_1Snarl.html#a18c06a3bd33bd3385147838d4c7b867c',1,'vg::Snarl']]],
+ ['end_5fzip_12196',['end_zip',['../classvg_1_1algorithms_1_1Anchor.html#aabad16a036718cc6ddf080d871cdc9bc',1,'vg::algorithms::Anchor']]],
+ ['endpoints_12197',['endpoints',['../classvg_1_1GraphSynchronizer_1_1Lock.html#a2b1f1d67a76ef6de89f8f30bd794f603',1,'vg::GraphSynchronizer::Lock']]],
+ ['entries_12198',['entries',['../structhaplo_1_1haplo__DP__column.html#aa46ab429b8d5eba3919e2c1cbf2e9a4e',1,'haplo::haplo_DP_column::entries()'],['../structvg_1_1subcommand_1_1Preset.html#ac689c36f8bc510aafb17f89b59c309c2',1,'vg::subcommand::Preset::entries()']]],
+ ['error_5fmodel_12199',['error_model',['../classvg_1_1WFAExtender.html#a1378f212c728e87b7ba1231b1b2a2d2d',1,'vg::WFAExtender']]],
+ ['error_5fon_5fmissing_5fpath_12200',['error_on_missing_path',['../classvg_1_1Transcriptome.html#a9c23e99ed885b6c5856f5a6baf1d7f95',1,'vg::Transcriptome']]],
+ ['exact_5fname_12201',['exact_name',['../classvg_1_1ReadFilter.html#a3165602af2a80ad642c9f900f9bf723e',1,'vg::ReadFilter']]],
+ ['exclude_5foverlapping_5fmin_12202',['exclude_overlapping_min',['../classvg_1_1MinimizerMapper.html#aca75c152e0c37e2ed5592400d3eb5fa7',1,'vg::MinimizerMapper']]],
+ ['exclude_5funaligned_12203',['exclude_unaligned',['../classvg_1_1BaseMapper.html#ac71be220eec4224b249a6536db70bbe5',1,'vg::BaseMapper']]],
+ ['excluded_5ffeatures_12204',['excluded_features',['../classvg_1_1ReadFilter.html#a621533fd4d338b7b5cee85df4a64c8ef',1,'vg::ReadFilter']]],
+ ['excluded_5frefpos_5fcontigs_12205',['excluded_refpos_contigs',['../classvg_1_1ReadFilter.html#a019f6eab0ba08ab063f2f9b1226a0cf0',1,'vg::ReadFilter']]],
+ ['excluded_5fsamples_12206',['excluded_samples',['../classvg_1_1HaplotypeIndexer.html#a116eb86acabeb52c7da7a1688686c034',1,'vg::HaplotypeIndexer']]],
+ ['exec_12207',['exec',['../structvg_1_1IndexRecipe.html#a948544cdea8166535520fee48304b5ee',1,'vg::IndexRecipe']]],
+ ['exons_12208',['exons',['../structvg_1_1Transcript.html#afc456b6b43f918028aee362aaa016209',1,'vg::Transcript']]],
+ ['exp_5frho_12209',['exp_rho',['../structhaplo_1_1haploMath_1_1RRMemo.html#a7979b3ef938f0a887ea1b5511d33e9f6',1,'haplo::haploMath::RRMemo']]],
+ ['expected_5fdepth_12210',['expected_depth',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a33a46269b733b08e64c4ccc021b342b6',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['expected_5fseparation_12211',['expected_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a2691d4683754ab1487bd76dd2e4aa720',1,'vg::GreedyMinDistanceClusterer']]],
+ ['explanation_5fnumber_12212',['explanation_number',['../classvg_1_1Explainer.html#ad93fa7fe7f64d180b6c606ffba47ba11',1,'vg::Explainer']]],
+ ['extender_12213',['extender',['../classvg_1_1MinimizerMapper.html#a30d6a39763a954968818b76b0463aa89',1,'vg::MinimizerMapper']]],
+ ['extension_5fscore_5fthreshold_12214',['extension_score_threshold',['../classvg_1_1MinimizerMapper.html#adeff081b3c6a83ddfa7f620245b61fd0',1,'vg::MinimizerMapper']]],
+ ['extension_5fset_5fmin_5fscore_12215',['extension_set_min_score',['../classvg_1_1MinimizerMapper.html#aceeb71c78d5d236c86272ee14592cd10',1,'vg::MinimizerMapper']]],
+ ['extension_5fset_5fscore_5fthreshold_12216',['extension_set_score_threshold',['../classvg_1_1MinimizerMapper.html#ac47b8ebb0479d86727c97e37e7f103ee',1,'vg::MinimizerMapper']]],
+ ['external_5fid_5fmap_12217',['external_id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a2047be69a33b61966ddd33570c96a632',1,'vg::algorithms::GFAParser']]],
+ ['extra_5fdata_12218',['extra_data',['../structvg_1_1FeatureSet_1_1Feature.html#ad95acb3def1e4c9b5fa2a590b77e4993',1,'vg::FeatureSet::Feature']]],
+ ['extra_5ffragments_12219',['extra_fragments',['../structvg_1_1Recombinator_1_1Statistics.html#afe44ec6921b89debb44dcc5b07ce7caf',1,'vg::Recombinator::Statistics::extra_fragments()'],['../structvg_1_1Recombinator_1_1Parameters.html#a23a4c5772ec0d526b632b280e91e48ca',1,'vg::Recombinator::Parameters::extra_fragments()']]],
+ ['extra_5fmultimaps_12220',['extra_multimaps',['../classvg_1_1Mapper.html#afe9cdcfbff73199e755c5bead44c9674',1,'vg::Mapper']]],
+ ['extra_5fsnarls_12221',['extra_snarls',['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#a24af34e8be6cb50546e914cb088977a1',1,'vg::HaplotypePartitioner::Subchain']]],
+ ['extract_5fleft_12222',['extract_left',['../classvg_1_1IncrementalSubgraph.html#a8b93ae511b47d189bdcf996d88f04f9d',1,'vg::IncrementalSubgraph']]],
+ ['extracted_12223',['extracted',['../classvg_1_1IncrementalSubgraph.html#a07d9afa325ba5788ae4ad9cb4539d644',1,'vg::IncrementalSubgraph']]]
];
diff --git a/search/variables_6.js b/search/variables_6.js
index 6934232284..6978ad5517 100644
--- a/search/variables_6.js
+++ b/search/variables_6.js
@@ -1,88 +1,88 @@
var searchData=
[
- ['failed_5ffilter_12220',['failed_filter',['../structvg_1_1Funnel_1_1Item.html#ac661e647007faace0ce5949268f0969d',1,'vg::Funnel::Item']]],
- ['failed_5fstatistic_12221',['failed_statistic',['../structvg_1_1Funnel_1_1Item.html#a88e8b76d62aac942c29cfbefe38ec5ca',1,'vg::Funnel::Item']]],
- ['failing_12222',['failing',['../structvg_1_1Funnel_1_1FilterPerformance.html#aad9ef34a13eb3d6d7e5bf5ad42beb166',1,'vg::Funnel::FilterPerformance']]],
- ['failing_5fcorrect_12223',['failing_correct',['../structvg_1_1Funnel_1_1FilterPerformance.html#a898f945e74a3583f316aa523920dc019',1,'vg::Funnel::FilterPerformance']]],
- ['fallbacks_12224',['fallbacks',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#a05ade9374ee7ffa5c34d3ed6ed8c5da6',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['fanout_5flength_5fthreshold_12225',['fanout_length_threshold',['../classvg_1_1BaseMapper.html#acd8be356ec0cdddaba2597913e75e2ef',1,'vg::BaseMapper']]],
- ['fast_5freseed_12226',['fast_reseed',['../classvg_1_1BaseMapper.html#a85f811924225d6de6f0a26b168ed1df3',1,'vg::BaseMapper']]],
- ['fast_5freseed_5flength_5fdiff_12227',['fast_reseed_length_diff',['../classvg_1_1BaseMapper.html#a74ce7cb0903b14c4b4132f504dcdc412',1,'vg::BaseMapper']]],
- ['fasta_5fto_5fvcf_5frenames_12228',['fasta_to_vcf_renames',['../classvg_1_1NameMapper.html#ad908156325375d8008c9ac68790b71e8',1,'vg::NameMapper']]],
- ['fd_12229',['fd',['../classvg_1_1io_1_1fdoutbuf.html#a24cff1494bb89ccb0375e895a4519e19',1,'vg::io::fdoutbuf::fd()'],['../classvg_1_1io_1_1fdinbuf.html#a6ca34c4abbb45cb5ecb87960fdd3a5f1',1,'vg::io::fdinbuf::fd()']]],
- ['feature_5fname_12230',['feature_name',['../structvg_1_1FeatureSet_1_1Feature.html#a0a95f9497d07cd5fed761983787884c6',1,'vg::FeatureSet::Feature']]],
- ['feature_5ftype_12231',['feature_type',['../classvg_1_1Transcriptome.html#ab06c748015ef113e0c3357c2b99e88cb',1,'vg::Transcriptome']]],
- ['features_12232',['features',['../classvg_1_1FeatureSet.html#a43f00a84d400bf90ee2cb26d1bf561d7',1,'vg::FeatureSet::features()'],['../classvg_1_1SmallSnarlSimplifier.html#af9de906fc14f2cf280aaad638acaa526',1,'vg::SmallSnarlSimplifier::features()']]],
- ['file_12233',['file',['../classvg_1_1VcfBuffer.html#a6d744dafd27fb2fdea09d106b1553a55',1,'vg::VcfBuffer']]],
- ['file_5fi_12234',['file_i',['../structGafFile.html#a681e364f129e72d2a27585e5cd54a327',1,'GafFile']]],
- ['file_5fname_12235',['file_name',['../structvg_1_1algorithms_1_1GFAFormatError.html#a7690e2726357a7663055f6f99e7448f4',1,'vg::algorithms::GFAFormatError']]],
- ['filename_12236',['filename',['../structvg_1_1GBWTHandler.html#a551e856227d00e32f1c66691d44ec502',1,'vg::GBWTHandler::filename()'],['../structjob__type.html#a9453f5bf04ab3780dcb2fa1c8264eb65',1,'job_type::filename()']]],
- ['filenames_12237',['filenames',['../classvg_1_1IndexFile.html#ac839a4016a34b52e297f8159d0de9e76',1,'vg::IndexFile::filenames()'],['../structvg_1_1temp__file_1_1Handler.html#a31034b76a60ff07d49afc2979084ed13',1,'vg::temp_file::Handler::filenames()'],['../classvg_1_1VGset.html#a49cf0bee988a30fb024218dd4f4eed56',1,'vg::VGset::filenames()'],['../structxg_1_1temp__file_1_1Handler.html#ad61c52d26a2feddf0770d74d4ff65754',1,'xg::temp_file::Handler::filenames()']]],
- ['filter_5fmatches_12238',['filter_matches',['../classvg_1_1Filter.html#ab1a5ffa8d8e0205909a9ed33e1ff26f5',1,'vg::Filter']]],
- ['filter_5fon_5fall_12239',['filter_on_all',['../classvg_1_1ReadFilter.html#a0789571cd8039786e8eb53e5e6f53cee',1,'vg::ReadFilter']]],
- ['filter_5fshort_5fmems_12240',['filter_short_mems',['../classvg_1_1BaseMapper.html#a883a1d2afe593993dc7e5f0268a3caa6',1,'vg::BaseMapper']]],
- ['finished_5fdecoding_12241',['finished_decoding',['../classvg_1_1ZipCode.html#a5baffcb4fe80bf3c0968b18217e14ea5',1,'vg::ZipCode']]],
- ['first_12242',['first',['../structvg_1_1FeatureSet_1_1Feature.html#ade37c17b95cc0314dc381e93b04ff7b4',1,'vg::FeatureSet::Feature']]],
- ['fixed_5ffragment_5fmodel_12243',['fixed_fragment_model',['../classvg_1_1FragmentLengthStatistics.html#a8c3c6bfb99c7cef159520adb58be271d',1,'vg::FragmentLengthStatistics']]],
- ['flank_5frange_12244',['flank_range',['../classvg_1_1VariantAdder.html#a1761b88c30f6fc8e9e40a99d6f66d9dd',1,'vg::VariantAdder']]],
- ['flat_12245',['flat',['../classvg_1_1Constructor.html#a2def54af1f72ad07cf84ff26fbbcc398',1,'vg::Constructor']]],
- ['flat_5fnode_12246',['flat_node',['../structhaplo_1_1haplo__DP__rectangle.html#a5c211ab946bf46fc45b1815482fd790a',1,'haplo::haplo_DP_rectangle']]],
- ['flush_12247',['flush',['../structhFILE__backend.html#a3f28679664f8e8fd71f8bdb16962e6b2',1,'hFILE_backend']]],
- ['force_5fhaplotype_5fcount_12248',['force_haplotype_count',['../classvg_1_1MultipathMapper.html#a4c89cc1e5c4696682c6bc9282de4b034',1,'vg::MultipathMapper']]],
- ['force_5fphasing_12249',['force_phasing',['../classvg_1_1HaplotypeIndexer.html#acb44a055288c0a9debed5662e461959e',1,'vg::HaplotypeIndexer']]],
- ['force_5funequal_12250',['force_unequal',['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac1dcdb35b0b8fc51f2aee4abea3ce242',1,'handlegraph::PathForEachSocket::iterator']]],
- ['forks_12251',['forks',['../structvg_1_1algorithms_1_1kmer__t.html#ac3f2de8e523f01cdca5d05ffd5a91a4d',1,'vg::algorithms::kmer_t::forks()'],['../structvg_1_1algorithms_1_1walk__t.html#a10f5d30f390ed54e49b4785d3edf7f98',1,'vg::algorithms::walk_t::forks()']]],
- ['format_12252',['FORMAT',['../classhandlegraph_1_1PathMetadata.html#a366a9d88528dcb5a25a44c6984bcaa66',1,'handlegraph::PathMetadata::FORMAT()'],['../classvg_1_1HTSWriter.html#a4c549b347cd3dba4710e1a195445a8b0',1,'vg::HTSWriter::format()'],['../classvg_1_1MultipathAlignmentEmitter.html#acfd964033f896160e64be1710025466c',1,'vg::MultipathAlignmentEmitter::format()']]],
- ['forward_12253',['forward',['../structvg_1_1Support.html#afe50d5886e57f3ff8594bddb90dfc8fa',1,'vg::Support']]],
- ['forward_5fgraph_12254',['forward_graph',['../classvg_1_1ReverseGraph.html#ab5cdf413526444fe31d07e3dce91d0f8',1,'vg::ReverseGraph']]],
- ['forward_5fmultiplier_12255',['forward_multiplier',['../classvg_1_1GreedyMinDistanceClusterer.html#a4423fb0153d3e55694c29fea2d5388af',1,'vg::GreedyMinDistanceClusterer']]],
- ['forward_5fonly_12256',['forward_only',['../classvg_1_1Sampler.html#a5d105468c850a483ff1b7696b1da7507',1,'vg::Sampler']]],
- ['frac_5fscore_12257',['frac_score',['../classvg_1_1ReadFilter.html#a28e3876fb7401ecf89e9cd75fee37d59',1,'vg::ReadFilter']]],
- ['frag_5fstats_12258',['frag_stats',['../classvg_1_1Mapper.html#a2574eba87f3d7e8e93bf3fee99dacf27',1,'vg::Mapper']]],
- ['fragl_5fsupports_12259',['fragl_supports',['../structvg_1_1BREAKPOINT.html#a282d8840a4a956ce5d76ca1638871df7',1,'vg::BREAKPOINT']]],
- ['fragment_12260',['fragment',['../classvg_1_1MaximalExactMatch.html#aba77f1e25d2845c54f13e2ebc774b0b3',1,'vg::MaximalExactMatch::fragment()'],['../structvg_1_1read__alignment__index__t.html#a068797505b4341843ff1c4899c2c3b23',1,'vg::read_alignment_index_t::fragment()'],['../structvg_1_1alignment__index__t.html#a07b79acb488a39171e138d5593f57d47',1,'vg::alignment_index_t::fragment()'],['../structvg_1_1RecombinatorHaplotype.html#aae088d4a961f202b8cd949e6a6cc7951',1,'vg::RecombinatorHaplotype::fragment()'],['../structvg_1_1RecombinatorFragment.html#a86e6dbf48a53af506e480847a759a8a4',1,'vg::RecombinatorFragment::fragment()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#adabededd78dcfa907533bf94555dd502',1,'vg::SnarlDistanceIndexClusterer::Cluster::fragment()'],['../structvg_1_1Alignment.html#a600fa84d6905316c0964dd035ac48687',1,'vg::Alignment::fragment()']]],
- ['fragment_5fbest_5fleft_12261',['fragment_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af38c9c2b9aaa74591a9724e2d4ec5bd9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['fragment_5fbest_5fright_12262',['fragment_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ac6a766cba9f06e06845ef0d6ba7fb9dc',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['fragment_5fdirections_12263',['fragment_directions',['../classvg_1_1FragmentLengthStatistics.html#a04cfcfa9321c794d2b29c9e88e30cc22',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fdistance_5flimit_12264',['fragment_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a2a5781315318cd19e0ae59cbb9195754',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['fragment_5fgap_5fscale_12265',['fragment_gap_scale',['../classvg_1_1MinimizerMapper.html#ab8cec4d830d940527099df5cc9ff4b74',1,'vg::MinimizerMapper']]],
- ['fragment_5flength_5fcache_5fsize_12266',['fragment_length_cache_size',['../classvg_1_1FragmentLengthStatistics.html#a8616a97cafb7618fed2b27c08e91afee',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5flength_5fdistr_12267',['fragment_length_distr',['../classvg_1_1PairedEndMapper.html#a9d232033ef120e15c47d13fab2750bc1',1,'vg::PairedEndMapper::fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#ab019d5888d75bbe36d8eb444d148ac50',1,'vg::MinimizerMapper::fragment_length_distr()']]],
- ['fragment_5flength_5fdistribution_12268',['fragment_length_distribution',['../structvg_1_1Alignment.html#ab13fb82c1707e0c6934d5c5ffd4c3ffa',1,'vg::Alignment']]],
- ['fragment_5flength_5fwarning_5ffactor_12269',['fragment_length_warning_factor',['../classvg_1_1MultipathMapper.html#af0e2a57df540a8eafefc7eec55908b24',1,'vg::MultipathMapper']]],
- ['fragment_5flengths_12270',['fragment_lengths',['../classvg_1_1FragmentLengthStatistics.html#a7640ef7754d2b2b92fc65744e9b25eda',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fmax_12271',['fragment_max',['../classvg_1_1FragmentLengthStatistics.html#a79552864430d5905bc58a388dbc423ef',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fmax_5findel_5fbases_12272',['fragment_max_indel_bases',['../classvg_1_1MinimizerMapper.html#ab1d94c16cfd9cbbdfbc8d8650c07df37',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5findel_5fbases_5fper_5fbase_12273',['fragment_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a464e344d9bd2b5d3cc9b5b5d3a0efd30',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5flookback_5fbases_12274',['fragment_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ac0c7392b8a860133dc2b97a0361e2342',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5flookback_5fbases_5fper_5fbase_12275',['fragment_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a40b63e97284b2f5c18e76df3ed7c2146',1,'vg::MinimizerMapper']]],
- ['fragment_5fmax_5fmin_5fscore_12276',['fragment_max_min_score',['../classvg_1_1MinimizerMapper.html#a62cd471d896d263d9b6d4cceece17d22',1,'vg::MinimizerMapper']]],
- ['fragment_5fmean_12277',['fragment_mean',['../classvg_1_1NGSSimulator.html#a2a96486c1fa9a2c4ebf4167139898afc',1,'vg::NGSSimulator']]],
- ['fragment_5fmin_5fscore_12278',['fragment_min_score',['../classvg_1_1MinimizerMapper.html#a7d0ae5e86deecd194163f939142c38e9',1,'vg::MinimizerMapper']]],
- ['fragment_5fmodel_5fupdate_5finterval_12279',['fragment_model_update_interval',['../classvg_1_1FragmentLengthStatistics.html#a37b3e1be0011fae099dd9aef7653c2b6',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fnext_12280',['fragment_next',['../structvg_1_1Alignment.html#a79ace3e74254f2a6e1ed5bdf09eb226f',1,'vg::Alignment']]],
- ['fragment_5forientations_12281',['fragment_orientations',['../classvg_1_1FragmentLengthStatistics.html#a56a5a981f87edb64149c2b5e5d54df78',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fpoints_5fper_5fpossible_5fmatch_12282',['fragment_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a3b6dbf3556520243639b058698727908',1,'vg::MinimizerMapper']]],
- ['fragment_5fprev_12283',['fragment_prev',['../structvg_1_1Alignment.html#a82a59f4fec8b7fcd069563d99fa04228',1,'vg::Alignment']]],
- ['fragment_5fscore_12284',['fragment_score',['../structvg_1_1Alignment.html#a2a105371920e65f6764f8b723ae6648d',1,'vg::Alignment']]],
- ['fragment_5fscore_5ffraction_12285',['fragment_score_fraction',['../classvg_1_1MinimizerMapper.html#af04f1529476f620ef8c21c15cf44092b',1,'vg::MinimizerMapper']]],
- ['fragment_5fsd_12286',['fragment_sd',['../classvg_1_1NGSSimulator.html#a62d1cb98ae226228eaa9fabc05cf6f47',1,'vg::NGSSimulator']]],
- ['fragment_5fset_5fscore_5fthreshold_12287',['fragment_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a2e064f8ef605db553d7d27d3e05f8a78',1,'vg::MinimizerMapper']]],
- ['fragment_5fsigma_12288',['fragment_sigma',['../classvg_1_1FragmentLengthStatistics.html#aef6f205fdda8e179ef3355218c9c32c1',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5fsize_12289',['fragment_size',['../classvg_1_1FragmentLengthStatistics.html#ad703c2e5fc7b03154ec6861a2be1e98b',1,'vg::FragmentLengthStatistics']]],
- ['fragment_5funion_5ffind_12290',['fragment_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a335bcb97a05564c08d4ed9a5f2f25c20',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['fragments_12291',['fragments',['../structvg_1_1Recombinator_1_1Statistics.html#a8d8a6052fd27254595e54301be1a6f32',1,'vg::Recombinator::Statistics']]],
- ['frequency_12292',['frequency',['../classvg_1_1MCMCGenotyper.html#a4f8407692d3a6657442269ab9356952c',1,'vg::MCMCGenotyper']]],
- ['from_12293',['from',['../classvg_1_1WFATree.html#a0892abaa48691fcd665163851857a6ba',1,'vg::WFATree::from()'],['../structvg_1_1RecombinatorFragment.html#abb2373fe6dc187291239d57ceff36042',1,'vg::RecombinatorFragment::from()'],['../structvg_1_1Edge.html#a3dfaeceda2846f9b2562d5e6acafd468',1,'vg::Edge::from()'],['../structvg_1_1Translation.html#af19bb0bf7b6d241f3e61f27b83199a1f',1,'vg::Translation::from()']]],
- ['from_5flength_12294',['from_length',['../structvg_1_1Edit.html#ae9694807752cc5cd06519f498cfba06c',1,'vg::Edit']]],
- ['from_5fnode_5fid_12295',['from_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2084bf098f9ffe829a0de4ca12ae0f3e',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
- ['from_5fstart_12296',['from_start',['../structvg_1_1Edge.html#aadc916440008619a27cdd0c388e8ba86',1,'vg::Edge']]],
- ['frontier_12297',['frontier',['../classvg_1_1IncrementalSubgraph.html#acfc80beeefec7f96a686a85db694985a',1,'vg::IncrementalSubgraph']]],
- ['frontier_5fcopy_5flimit_12298',['frontier_copy_limit',['../classvg_1_1IncrementalSubgraph.html#af136b632b259faac2edc944a06b97011',1,'vg::IncrementalSubgraph']]],
- ['frontier_5fcount_12299',['frontier_count',['../classvg_1_1IncrementalSubgraph.html#aa5becc3ca659a557a83bff4de8643ff4',1,'vg::IncrementalSubgraph']]],
- ['frontier_5findex_12300',['frontier_index',['../classvg_1_1IncrementalSubgraph.html#a877311143c9e9791fa85b29ae7a1351c',1,'vg::IncrementalSubgraph']]],
- ['full_5fhaplotypes_12301',['full_haplotypes',['../structvg_1_1Recombinator_1_1Statistics.html#a5ae651194a7e9670ae435f46cedf00f3',1,'vg::Recombinator::Statistics']]],
- ['full_5flength_5fbonus_12302',['full_length_bonus',['../classvg_1_1GSSWAligner.html#a24ee1a1d5b84c90c7fc77a4b7d8660bd',1,'vg::GSSWAligner::full_length_bonus()'],['../structScoringOptions.html#a86fa76ce2c5e6a086ea66dd60a8e9701',1,'ScoringOptions::full_length_bonus()']]],
- ['fulltrace_12303',['fullTrace',['../namespacevg.html#abd1798abb6fcee86ab5b0539fb764eb2',1,'vg']]],
- ['funnel_5fname_12304',['funnel_name',['../classvg_1_1Funnel.html#aae00e188df16e84d5ecdb12e6ce5d51e',1,'vg::Funnel']]]
+ ['failed_5ffilter_12224',['failed_filter',['../structvg_1_1Funnel_1_1Item.html#ac661e647007faace0ce5949268f0969d',1,'vg::Funnel::Item']]],
+ ['failed_5fstatistic_12225',['failed_statistic',['../structvg_1_1Funnel_1_1Item.html#a88e8b76d62aac942c29cfbefe38ec5ca',1,'vg::Funnel::Item']]],
+ ['failing_12226',['failing',['../structvg_1_1Funnel_1_1FilterPerformance.html#aad9ef34a13eb3d6d7e5bf5ad42beb166',1,'vg::Funnel::FilterPerformance']]],
+ ['failing_5fcorrect_12227',['failing_correct',['../structvg_1_1Funnel_1_1FilterPerformance.html#a898f945e74a3583f316aa523920dc019',1,'vg::Funnel::FilterPerformance']]],
+ ['fallbacks_12228',['fallbacks',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#a05ade9374ee7ffa5c34d3ed6ed8c5da6',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['fanout_5flength_5fthreshold_12229',['fanout_length_threshold',['../classvg_1_1BaseMapper.html#acd8be356ec0cdddaba2597913e75e2ef',1,'vg::BaseMapper']]],
+ ['fast_5freseed_12230',['fast_reseed',['../classvg_1_1BaseMapper.html#a85f811924225d6de6f0a26b168ed1df3',1,'vg::BaseMapper']]],
+ ['fast_5freseed_5flength_5fdiff_12231',['fast_reseed_length_diff',['../classvg_1_1BaseMapper.html#a74ce7cb0903b14c4b4132f504dcdc412',1,'vg::BaseMapper']]],
+ ['fasta_5fto_5fvcf_5frenames_12232',['fasta_to_vcf_renames',['../classvg_1_1NameMapper.html#ad908156325375d8008c9ac68790b71e8',1,'vg::NameMapper']]],
+ ['fd_12233',['fd',['../classvg_1_1io_1_1fdoutbuf.html#a24cff1494bb89ccb0375e895a4519e19',1,'vg::io::fdoutbuf::fd()'],['../classvg_1_1io_1_1fdinbuf.html#a6ca34c4abbb45cb5ecb87960fdd3a5f1',1,'vg::io::fdinbuf::fd()']]],
+ ['feature_5fname_12234',['feature_name',['../structvg_1_1FeatureSet_1_1Feature.html#a0a95f9497d07cd5fed761983787884c6',1,'vg::FeatureSet::Feature']]],
+ ['feature_5ftype_12235',['feature_type',['../classvg_1_1Transcriptome.html#ab06c748015ef113e0c3357c2b99e88cb',1,'vg::Transcriptome']]],
+ ['features_12236',['features',['../classvg_1_1FeatureSet.html#a43f00a84d400bf90ee2cb26d1bf561d7',1,'vg::FeatureSet::features()'],['../classvg_1_1SmallSnarlSimplifier.html#af9de906fc14f2cf280aaad638acaa526',1,'vg::SmallSnarlSimplifier::features()']]],
+ ['file_12237',['file',['../classvg_1_1VcfBuffer.html#a6d744dafd27fb2fdea09d106b1553a55',1,'vg::VcfBuffer']]],
+ ['file_5fi_12238',['file_i',['../structGafFile.html#a681e364f129e72d2a27585e5cd54a327',1,'GafFile']]],
+ ['file_5fname_12239',['file_name',['../structvg_1_1algorithms_1_1GFAFormatError.html#a7690e2726357a7663055f6f99e7448f4',1,'vg::algorithms::GFAFormatError']]],
+ ['filename_12240',['filename',['../structvg_1_1GBWTHandler.html#a551e856227d00e32f1c66691d44ec502',1,'vg::GBWTHandler::filename()'],['../structjob__type.html#a9453f5bf04ab3780dcb2fa1c8264eb65',1,'job_type::filename()']]],
+ ['filenames_12241',['filenames',['../classvg_1_1IndexFile.html#ac839a4016a34b52e297f8159d0de9e76',1,'vg::IndexFile::filenames()'],['../structvg_1_1temp__file_1_1Handler.html#a31034b76a60ff07d49afc2979084ed13',1,'vg::temp_file::Handler::filenames()'],['../classvg_1_1VGset.html#a49cf0bee988a30fb024218dd4f4eed56',1,'vg::VGset::filenames()'],['../structxg_1_1temp__file_1_1Handler.html#ad61c52d26a2feddf0770d74d4ff65754',1,'xg::temp_file::Handler::filenames()']]],
+ ['filter_5fmatches_12242',['filter_matches',['../classvg_1_1Filter.html#ab1a5ffa8d8e0205909a9ed33e1ff26f5',1,'vg::Filter']]],
+ ['filter_5fon_5fall_12243',['filter_on_all',['../classvg_1_1ReadFilter.html#a0789571cd8039786e8eb53e5e6f53cee',1,'vg::ReadFilter']]],
+ ['filter_5fshort_5fmems_12244',['filter_short_mems',['../classvg_1_1BaseMapper.html#a883a1d2afe593993dc7e5f0268a3caa6',1,'vg::BaseMapper']]],
+ ['finished_5fdecoding_12245',['finished_decoding',['../classvg_1_1ZipCode.html#a5baffcb4fe80bf3c0968b18217e14ea5',1,'vg::ZipCode']]],
+ ['first_12246',['first',['../structvg_1_1FeatureSet_1_1Feature.html#ade37c17b95cc0314dc381e93b04ff7b4',1,'vg::FeatureSet::Feature']]],
+ ['fixed_5ffragment_5fmodel_12247',['fixed_fragment_model',['../classvg_1_1FragmentLengthStatistics.html#a8c3c6bfb99c7cef159520adb58be271d',1,'vg::FragmentLengthStatistics']]],
+ ['flank_5frange_12248',['flank_range',['../classvg_1_1VariantAdder.html#a1761b88c30f6fc8e9e40a99d6f66d9dd',1,'vg::VariantAdder']]],
+ ['flat_12249',['flat',['../classvg_1_1Constructor.html#a2def54af1f72ad07cf84ff26fbbcc398',1,'vg::Constructor']]],
+ ['flat_5fnode_12250',['flat_node',['../structhaplo_1_1haplo__DP__rectangle.html#a5c211ab946bf46fc45b1815482fd790a',1,'haplo::haplo_DP_rectangle']]],
+ ['flush_12251',['flush',['../structhFILE__backend.html#a3f28679664f8e8fd71f8bdb16962e6b2',1,'hFILE_backend']]],
+ ['force_5fhaplotype_5fcount_12252',['force_haplotype_count',['../classvg_1_1MultipathMapper.html#a4c89cc1e5c4696682c6bc9282de4b034',1,'vg::MultipathMapper']]],
+ ['force_5fphasing_12253',['force_phasing',['../classvg_1_1HaplotypeIndexer.html#acb44a055288c0a9debed5662e461959e',1,'vg::HaplotypeIndexer']]],
+ ['force_5funequal_12254',['force_unequal',['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#ac1dcdb35b0b8fc51f2aee4abea3ce242',1,'handlegraph::PathForEachSocket::iterator']]],
+ ['forks_12255',['forks',['../structvg_1_1algorithms_1_1kmer__t.html#ac3f2de8e523f01cdca5d05ffd5a91a4d',1,'vg::algorithms::kmer_t::forks()'],['../structvg_1_1algorithms_1_1walk__t.html#a10f5d30f390ed54e49b4785d3edf7f98',1,'vg::algorithms::walk_t::forks()']]],
+ ['format_12256',['FORMAT',['../classhandlegraph_1_1PathMetadata.html#a366a9d88528dcb5a25a44c6984bcaa66',1,'handlegraph::PathMetadata::FORMAT()'],['../classvg_1_1HTSWriter.html#a4c549b347cd3dba4710e1a195445a8b0',1,'vg::HTSWriter::format()'],['../classvg_1_1MultipathAlignmentEmitter.html#acfd964033f896160e64be1710025466c',1,'vg::MultipathAlignmentEmitter::format()']]],
+ ['forward_12257',['forward',['../structvg_1_1Support.html#afe50d5886e57f3ff8594bddb90dfc8fa',1,'vg::Support']]],
+ ['forward_5fgraph_12258',['forward_graph',['../classvg_1_1ReverseGraph.html#ab5cdf413526444fe31d07e3dce91d0f8',1,'vg::ReverseGraph']]],
+ ['forward_5fmultiplier_12259',['forward_multiplier',['../classvg_1_1GreedyMinDistanceClusterer.html#a4423fb0153d3e55694c29fea2d5388af',1,'vg::GreedyMinDistanceClusterer']]],
+ ['forward_5fonly_12260',['forward_only',['../classvg_1_1Sampler.html#a5d105468c850a483ff1b7696b1da7507',1,'vg::Sampler']]],
+ ['frac_5fscore_12261',['frac_score',['../classvg_1_1ReadFilter.html#a28e3876fb7401ecf89e9cd75fee37d59',1,'vg::ReadFilter']]],
+ ['frag_5fstats_12262',['frag_stats',['../classvg_1_1Mapper.html#a2574eba87f3d7e8e93bf3fee99dacf27',1,'vg::Mapper']]],
+ ['fragl_5fsupports_12263',['fragl_supports',['../structvg_1_1BREAKPOINT.html#a282d8840a4a956ce5d76ca1638871df7',1,'vg::BREAKPOINT']]],
+ ['fragment_12264',['fragment',['../classvg_1_1MaximalExactMatch.html#aba77f1e25d2845c54f13e2ebc774b0b3',1,'vg::MaximalExactMatch::fragment()'],['../structvg_1_1read__alignment__index__t.html#a068797505b4341843ff1c4899c2c3b23',1,'vg::read_alignment_index_t::fragment()'],['../structvg_1_1alignment__index__t.html#a07b79acb488a39171e138d5593f57d47',1,'vg::alignment_index_t::fragment()'],['../structvg_1_1RecombinatorHaplotype.html#aae088d4a961f202b8cd949e6a6cc7951',1,'vg::RecombinatorHaplotype::fragment()'],['../structvg_1_1RecombinatorFragment.html#a86e6dbf48a53af506e480847a759a8a4',1,'vg::RecombinatorFragment::fragment()'],['../structvg_1_1SnarlDistanceIndexClusterer_1_1Cluster.html#adabededd78dcfa907533bf94555dd502',1,'vg::SnarlDistanceIndexClusterer::Cluster::fragment()'],['../structvg_1_1Alignment.html#a600fa84d6905316c0964dd035ac48687',1,'vg::Alignment::fragment()']]],
+ ['fragment_5fbest_5fleft_12265',['fragment_best_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af38c9c2b9aaa74591a9724e2d4ec5bd9',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['fragment_5fbest_5fright_12266',['fragment_best_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ac6a766cba9f06e06845ef0d6ba7fb9dc',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['fragment_5fdirections_12267',['fragment_directions',['../classvg_1_1FragmentLengthStatistics.html#a04cfcfa9321c794d2b29c9e88e30cc22',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fdistance_5flimit_12268',['fragment_distance_limit',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a2a5781315318cd19e0ae59cbb9195754',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['fragment_5fgap_5fscale_12269',['fragment_gap_scale',['../classvg_1_1MinimizerMapper.html#ab8cec4d830d940527099df5cc9ff4b74',1,'vg::MinimizerMapper']]],
+ ['fragment_5flength_5fcache_5fsize_12270',['fragment_length_cache_size',['../classvg_1_1FragmentLengthStatistics.html#a8616a97cafb7618fed2b27c08e91afee',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5flength_5fdistr_12271',['fragment_length_distr',['../classvg_1_1PairedEndMapper.html#a9d232033ef120e15c47d13fab2750bc1',1,'vg::PairedEndMapper::fragment_length_distr()'],['../classvg_1_1MinimizerMapper.html#ab019d5888d75bbe36d8eb444d148ac50',1,'vg::MinimizerMapper::fragment_length_distr()']]],
+ ['fragment_5flength_5fdistribution_12272',['fragment_length_distribution',['../structvg_1_1Alignment.html#ab13fb82c1707e0c6934d5c5ffd4c3ffa',1,'vg::Alignment']]],
+ ['fragment_5flength_5fwarning_5ffactor_12273',['fragment_length_warning_factor',['../classvg_1_1MultipathMapper.html#af0e2a57df540a8eafefc7eec55908b24',1,'vg::MultipathMapper']]],
+ ['fragment_5flengths_12274',['fragment_lengths',['../classvg_1_1FragmentLengthStatistics.html#a7640ef7754d2b2b92fc65744e9b25eda',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fmax_12275',['fragment_max',['../classvg_1_1FragmentLengthStatistics.html#a79552864430d5905bc58a388dbc423ef',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fmax_5findel_5fbases_12276',['fragment_max_indel_bases',['../classvg_1_1MinimizerMapper.html#ab1d94c16cfd9cbbdfbc8d8650c07df37',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5findel_5fbases_5fper_5fbase_12277',['fragment_max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a464e344d9bd2b5d3cc9b5b5d3a0efd30',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5flookback_5fbases_12278',['fragment_max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ac0c7392b8a860133dc2b97a0361e2342',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5flookback_5fbases_5fper_5fbase_12279',['fragment_max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a40b63e97284b2f5c18e76df3ed7c2146',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmax_5fmin_5fscore_12280',['fragment_max_min_score',['../classvg_1_1MinimizerMapper.html#a62cd471d896d263d9b6d4cceece17d22',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmean_12281',['fragment_mean',['../classvg_1_1NGSSimulator.html#a2a96486c1fa9a2c4ebf4167139898afc',1,'vg::NGSSimulator']]],
+ ['fragment_5fmin_5fscore_12282',['fragment_min_score',['../classvg_1_1MinimizerMapper.html#a7d0ae5e86deecd194163f939142c38e9',1,'vg::MinimizerMapper']]],
+ ['fragment_5fmodel_5fupdate_5finterval_12283',['fragment_model_update_interval',['../classvg_1_1FragmentLengthStatistics.html#a37b3e1be0011fae099dd9aef7653c2b6',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fnext_12284',['fragment_next',['../structvg_1_1Alignment.html#a79ace3e74254f2a6e1ed5bdf09eb226f',1,'vg::Alignment']]],
+ ['fragment_5forientations_12285',['fragment_orientations',['../classvg_1_1FragmentLengthStatistics.html#a56a5a981f87edb64149c2b5e5d54df78',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fpoints_5fper_5fpossible_5fmatch_12286',['fragment_points_per_possible_match',['../classvg_1_1MinimizerMapper.html#a3b6dbf3556520243639b058698727908',1,'vg::MinimizerMapper']]],
+ ['fragment_5fprev_12287',['fragment_prev',['../structvg_1_1Alignment.html#a82a59f4fec8b7fcd069563d99fa04228',1,'vg::Alignment']]],
+ ['fragment_5fscore_12288',['fragment_score',['../structvg_1_1Alignment.html#a2a105371920e65f6764f8b723ae6648d',1,'vg::Alignment']]],
+ ['fragment_5fscore_5ffraction_12289',['fragment_score_fraction',['../classvg_1_1MinimizerMapper.html#af04f1529476f620ef8c21c15cf44092b',1,'vg::MinimizerMapper']]],
+ ['fragment_5fsd_12290',['fragment_sd',['../classvg_1_1NGSSimulator.html#a62d1cb98ae226228eaa9fabc05cf6f47',1,'vg::NGSSimulator']]],
+ ['fragment_5fset_5fscore_5fthreshold_12291',['fragment_set_score_threshold',['../classvg_1_1MinimizerMapper.html#a2e064f8ef605db553d7d27d3e05f8a78',1,'vg::MinimizerMapper']]],
+ ['fragment_5fsigma_12292',['fragment_sigma',['../classvg_1_1FragmentLengthStatistics.html#aef6f205fdda8e179ef3355218c9c32c1',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5fsize_12293',['fragment_size',['../classvg_1_1FragmentLengthStatistics.html#ad703c2e5fc7b03154ec6861a2be1e98b',1,'vg::FragmentLengthStatistics']]],
+ ['fragment_5funion_5ffind_12294',['fragment_union_find',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#a335bcb97a05564c08d4ed9a5f2f25c20',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['fragments_12295',['fragments',['../structvg_1_1Recombinator_1_1Statistics.html#a8d8a6052fd27254595e54301be1a6f32',1,'vg::Recombinator::Statistics']]],
+ ['frequency_12296',['frequency',['../classvg_1_1MCMCGenotyper.html#a4f8407692d3a6657442269ab9356952c',1,'vg::MCMCGenotyper']]],
+ ['from_12297',['from',['../classvg_1_1WFATree.html#a0892abaa48691fcd665163851857a6ba',1,'vg::WFATree::from()'],['../structvg_1_1RecombinatorFragment.html#abb2373fe6dc187291239d57ceff36042',1,'vg::RecombinatorFragment::from()'],['../structvg_1_1Edge.html#a3dfaeceda2846f9b2562d5e6acafd468',1,'vg::Edge::from()'],['../structvg_1_1Translation.html#af19bb0bf7b6d241f3e61f27b83199a1f',1,'vg::Translation::from()']]],
+ ['from_5flength_12298',['from_length',['../structvg_1_1Edit.html#ae9694807752cc5cd06519f498cfba06c',1,'vg::Edit']]],
+ ['from_5fnode_5fid_12299',['from_node_id',['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack_1_1Deflection.html#a2084bf098f9ffe829a0de4ca12ae0f3e',1,'vg::BandedGlobalAligner::AltTracebackStack::Deflection']]],
+ ['from_5fstart_12300',['from_start',['../structvg_1_1Edge.html#aadc916440008619a27cdd0c388e8ba86',1,'vg::Edge']]],
+ ['frontier_12301',['frontier',['../classvg_1_1IncrementalSubgraph.html#acfc80beeefec7f96a686a85db694985a',1,'vg::IncrementalSubgraph']]],
+ ['frontier_5fcopy_5flimit_12302',['frontier_copy_limit',['../classvg_1_1IncrementalSubgraph.html#af136b632b259faac2edc944a06b97011',1,'vg::IncrementalSubgraph']]],
+ ['frontier_5fcount_12303',['frontier_count',['../classvg_1_1IncrementalSubgraph.html#aa5becc3ca659a557a83bff4de8643ff4',1,'vg::IncrementalSubgraph']]],
+ ['frontier_5findex_12304',['frontier_index',['../classvg_1_1IncrementalSubgraph.html#a877311143c9e9791fa85b29ae7a1351c',1,'vg::IncrementalSubgraph']]],
+ ['full_5fhaplotypes_12305',['full_haplotypes',['../structvg_1_1Recombinator_1_1Statistics.html#a5ae651194a7e9670ae435f46cedf00f3',1,'vg::Recombinator::Statistics']]],
+ ['full_5flength_5fbonus_12306',['full_length_bonus',['../classvg_1_1GSSWAligner.html#a24ee1a1d5b84c90c7fc77a4b7d8660bd',1,'vg::GSSWAligner::full_length_bonus()'],['../structScoringOptions.html#a86fa76ce2c5e6a086ea66dd60a8e9701',1,'ScoringOptions::full_length_bonus()']]],
+ ['fulltrace_12307',['fullTrace',['../namespacevg.html#abd1798abb6fcee86ab5b0539fb764eb2',1,'vg']]],
+ ['funnel_5fname_12308',['funnel_name',['../classvg_1_1Funnel.html#aae00e188df16e84d5ecdb12e6ce5d51e',1,'vg::Funnel']]]
];
diff --git a/search/variables_7.js b/search/variables_7.js
index 11d91d7980..b5ebcc5bf7 100644
--- a/search/variables_7.js
+++ b/search/variables_7.js
@@ -1,86 +1,86 @@
var searchData=
[
- ['g_5fbv_12305',['g_bv',['../classxg_1_1XG.html#a7fcb333bb6acf85ce76d81de9735b88a',1,'xg::XG']]],
- ['g_5fbv_5frank_12306',['g_bv_rank',['../classxg_1_1XG.html#abbbc82ab0fe4b0d8abe7e5890a89b952',1,'xg::XG']]],
- ['g_5fbv_5fselect_12307',['g_bv_select',['../classxg_1_1XG.html#a9eb31aaf28e0ab90154233692bdc0c05',1,'xg::XG']]],
- ['g_5fiv_12308',['g_iv',['../classxg_1_1XG.html#a7b4b76e9a150ca86d54cee59a3825f4d',1,'xg::XG']]],
- ['g_5fnode_5fheader_5flength_12309',['G_NODE_HEADER_LENGTH',['../classxg_1_1XG.html#a8a1f38f3430d796f7b2ae452fd80ebbf',1,'xg::XG']]],
- ['g_5fnode_5fid_5foffset_12310',['G_NODE_ID_OFFSET',['../classxg_1_1XG.html#a841f4db9d178690c836a21b6adc9fafe',1,'xg::XG']]],
- ['g_5fnode_5fleft_5fcount_5foffset_12311',['G_NODE_LEFT_COUNT_OFFSET',['../classxg_1_1XG.html#a9028d42350d55a928483b76579549145',1,'xg::XG']]],
- ['g_5fnode_5flength_5foffset_12312',['G_NODE_LENGTH_OFFSET',['../classxg_1_1XG.html#aaf4de09d0f39174f42c793492976acc9',1,'xg::XG']]],
- ['g_5fnode_5fright_5fcount_5foffset_12313',['G_NODE_RIGHT_COUNT_OFFSET',['../classxg_1_1XG.html#ad4aacfc7ad17ddc586566f8d2a5e92e5',1,'xg::XG']]],
- ['g_5fnode_5fseq_5fstart_5foffset_12314',['G_NODE_SEQ_START_OFFSET',['../classxg_1_1XG.html#a19673db503954e65456196d791f7db04',1,'xg::XG']]],
- ['gaf_12315',['gaf',['../structGafFile.html#a9dcebeb1a298c34516bdd969dc439560',1,'GafFile']]],
- ['gaf_5foutput_12316',['gaf_output',['../classvg_1_1VCFGenotyper.html#ae00bbce9945411dbab0d14e7cdb4b8c2',1,'vg::VCFGenotyper::gaf_output()'],['../classvg_1_1FlowCaller.html#a93037892a9148b952b186852f77f0fa8',1,'vg::FlowCaller::gaf_output()'],['../classvg_1_1NestedFlowCaller.html#a9114ad05033bc7d50becae55041dfae0',1,'vg::NestedFlowCaller::gaf_output()']]],
- ['gaf_5fsample_5fname_12317',['gaf_sample_name',['../classvg_1_1GAFOutputCaller.html#a23554330b3cf641645fe7b3070c6d203',1,'vg::GAFOutputCaller']]],
- ['gam_5fformat_12318',['gam_format',['../structGBWTConfig.html#a1fcbf295cfa998c40744359748fda6c7',1,'GBWTConfig']]],
- ['gap_5fdistance_5flimit_12319',['gap_distance_limit',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ad9d07441a40519ff349163eb7d87c916',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['gap_5fextend_12320',['gap_extend',['../classvg_1_1WFATree.html#abe47c55fbdfa81f6b0df6ffdb4c3591e',1,'vg::WFATree::gap_extend()'],['../structScoringOptions.html#a8ae3e44719121535cd43560dddc267aa',1,'ScoringOptions::gap_extend()']]],
- ['gap_5fextension_12321',['gap_extension',['../classvg_1_1GSSWAligner.html#afd2379af50d751eee892a10529d64ffb',1,'vg::GSSWAligner::gap_extension()'],['../classvg_1_1DeletionAligner.html#a5fdfc2ac3a633a6e3cd61c2e3beeae97',1,'vg::DeletionAligner::gap_extension()'],['../classvg_1_1SSWAligner.html#a2248e3e561aab8d3b1036d51850b3c2f',1,'vg::SSWAligner::gap_extension()']]],
- ['gap_5flength_12322',['gap_length',['../structvg_1_1WFAExtender_1_1ErrorModel.html#a9cf62e400ef2e4efb434e8e5a452e7e8',1,'vg::WFAExtender::ErrorModel']]],
- ['gap_5fmemo_5fmax_5fsize_12323',['gap_memo_max_size',['../classvg_1_1MultipathMapper.html#a864cc168b7061cf1885ef61785e474d3',1,'vg::MultipathMapper']]],
- ['gap_5fopen_12324',['gap_open',['../classvg_1_1GSSWAligner.html#aa5c0a63b73ad2ff8ec8f05062c768c22',1,'vg::GSSWAligner::gap_open()'],['../classvg_1_1DeletionAligner.html#a7791fe71828711b3208db54db784cf1d',1,'vg::DeletionAligner::gap_open()'],['../classvg_1_1WFATree.html#aec0c57320c07468df3201a106f7e6aa0',1,'vg::WFATree::gap_open()'],['../classvg_1_1SSWAligner.html#a15398a23880418599e81370d485fec0f',1,'vg::SSWAligner::gap_open()'],['../structScoringOptions.html#ab399d0cf09e907906b42d500a54194bc',1,'ScoringOptions::gap_open()']]],
- ['gap_5fscale_12325',['gap_scale',['../classvg_1_1MinimizerMapper.html#a5e6e66b39ed25c3d81f82546231d790a',1,'vg::MinimizerMapper']]],
- ['gapless_5fextension_5flimit_12326',['gapless_extension_limit',['../classvg_1_1MinimizerMapper.html#af0eb242f1ec9aaaa52e7d03446d09cbf',1,'vg::MinimizerMapper']]],
- ['gaps_12327',['gaps',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ac60921b93f505b6731badc2aef7f64f5',1,'vg::WFAExtender::ErrorModel']]],
- ['gbwt_12328',['gbwt',['../classvg_1_1Deconstructor.html#a52b3fcd3d7357f5dd3624d9caa56539f',1,'vg::Deconstructor::gbwt()'],['../classvg_1_1GBWTTraversalFinder.html#a7827a0ee00890a2d8cf1716017e39db7',1,'vg::GBWTTraversalFinder::gbwt()']]],
- ['gbwt_5fbuffer_5fsize_12329',['gbwt_buffer_size',['../classvg_1_1HaplotypeIndexer.html#abc8d5ce81546e16ffb7bf652c098bb11',1,'vg::HaplotypeIndexer']]],
- ['gbwt_5fgraph_12330',['gbwt_graph',['../classvg_1_1MinimizerMapper.html#abb94c27ed347a36fb38f91cf23a582fb',1,'vg::MinimizerMapper::gbwt_graph()'],['../structGraphHandler.html#ad86c0372b075e6e0c5bfbf61801b3222',1,'GraphHandler::gbwt_graph()']]],
- ['gbwt_5findex_12331',['gbwt_index',['../classvg_1_1PhaseUnfolder.html#abe0ad79b8b65bea2a4f871913c83ee65',1,'vg::PhaseUnfolder']]],
- ['gbwt_5finsert_5fbatch_5fsize_12332',['gbwt_insert_batch_size',['../structvg_1_1IndexingParameters.html#ab408ae73a85875de5dfe376e340f8840',1,'vg::IndexingParameters']]],
- ['gbwt_5finsert_5fbatch_5fsize_5fincrease_5ffactor_12333',['gbwt_insert_batch_size_increase_factor',['../structvg_1_1IndexingParameters.html#a721125abeca5c4755e875f2e3d8c1d2f',1,'vg::IndexingParameters']]],
- ['gbwt_5fname_12334',['gbwt_name',['../structGBWTConfig.html#a5fe3f0a41311811ddf16bcd7dbab4f91',1,'GBWTConfig']]],
- ['gbwt_5foutput_12335',['gbwt_output',['../structGBWTConfig.html#a8d9b4d70bb33f75cb147ee91b75c89af',1,'GBWTConfig']]],
- ['gbwt_5freference_5fsamples_12336',['gbwt_reference_samples',['../classvg_1_1Deconstructor.html#a8f81a59e45aad56aa6edc19756a9eb14',1,'vg::Deconstructor']]],
- ['gbwt_5fsample_5fto_5fphase_5frange_12337',['gbwt_sample_to_phase_range',['../classvg_1_1Deconstructor.html#a5f58aa9a4d3f29e330a9c9e1c9541884',1,'vg::Deconstructor']]],
- ['gbwt_5fsampling_5finterval_12338',['gbwt_sampling_interval',['../structvg_1_1IndexingParameters.html#abd33e81c954cb14ed31455a3950abe64',1,'vg::IndexingParameters']]],
- ['gbwt_5ftrav_5ffinder_12339',['gbwt_trav_finder',['../classvg_1_1Deconstructor.html#a41a7ff33e08c5eee5d2d7088dbc238f4',1,'vg::Deconstructor']]],
- ['gbwtgraph_5fname_12340',['gbwtgraph_name',['../structGBWTConfig.html#ac8e90b7bda206414a7055a98f5b55e85',1,'GBWTConfig']]],
- ['gbz_12341',['gbz',['../classvg_1_1GBZGraph.html#ac56a91ab9fe591aa7781cd751fe94ed4',1,'vg::GBZGraph::gbz()'],['../classvg_1_1HaplotypePartitioner.html#a533f084057db81844dd0c02f36fb5498',1,'vg::HaplotypePartitioner::gbz()'],['../classvg_1_1Recombinator.html#a977b21bbcc9ea6520dbc97a5014488e6',1,'vg::Recombinator::gbz()']]],
- ['gbz_5fformat_12342',['gbz_format',['../structGBWTConfig.html#a14fe1675f26aa9b74381640c4cffdd47',1,'GBWTConfig']]],
- ['gbz_5foutput_12343',['gbz_output',['../structHaplotypesConfig.html#af71ee285e699443b559375aeac054eb8',1,'HaplotypesConfig']]],
- ['gc_5fcontent_5festimate_12344',['gc_content_estimate',['../classvg_1_1AlignerClient.html#a65428f092aaa5d894b709e247cf0121a',1,'vg::AlignerClient']]],
- ['gcsa_12345',['gcsa',['../classvg_1_1BaseMapper.html#aa41db0eca93c379087c90b602a6ce751',1,'vg::BaseMapper']]],
- ['gcsa_5fdoubling_5fsteps_12346',['gcsa_doubling_steps',['../structvg_1_1IndexingParameters.html#ab480b0e1f6dca30213719734b78904e5',1,'vg::IndexingParameters']]],
- ['gcsa_5find_12347',['gcsa_ind',['../classvg_1_1Filter.html#ae98fe5c85ea704f1ef262b5556bbbbbb',1,'vg::Filter']]],
- ['gcsa_5finitial_5fkmer_5flength_12348',['gcsa_initial_kmer_length',['../structvg_1_1IndexingParameters.html#a890a5822bd592090eaf5b529816ecb32',1,'vg::IndexingParameters']]],
- ['gcsa_5fsize_5flimit_12349',['gcsa_size_limit',['../structvg_1_1IndexingParameters.html#a144f6b2b03ccc7ecf4b7d3a504aed1b7',1,'vg::IndexingParameters']]],
- ['generalizations_12350',['generalizations',['../classvg_1_1IndexRegistry.html#a665cc9431438ef50124b29e518465a05',1,'vg::IndexRegistry']]],
- ['genome_12351',['genome',['../classvg_1_1MCMCCaller.html#ad4278b11272792c879ab3463b513ae1e',1,'vg::MCMCCaller']]],
- ['genotype_12352',['genotype',['../structvg_1_1Locus.html#a144d9dc0f9d61910db33decca23e4755',1,'vg::Locus']]],
- ['genotype_5fby_5fploidy_12353',['genotype_by_ploidy',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#af331caba29195578f8a48ed527232ed1',1,'vg::NestedFlowCaller::CallRecord']]],
- ['genotype_5fsnarls_12354',['genotype_snarls',['../classvg_1_1FlowCaller.html#ae47f36ad1ec53a2381f970d159acbd64',1,'vg::FlowCaller::genotype_snarls()'],['../classvg_1_1NestedFlowCaller.html#a4c00174974936972c989b905a921b154',1,'vg::NestedFlowCaller::genotype_snarls()']]],
- ['get_5fedge_5fsupport_12355',['get_edge_support',['../classvg_1_1RepresentativeTraversalFinder.html#a452fdd307124349d6b65aa434bab48c7',1,'vg::RepresentativeTraversalFinder']]],
- ['get_5fhandle_5fmemo_12356',['get_handle_memo',['../classvg_1_1MemoizingGraph.html#a522abfb6d16b8e96a77ff6f114275cf8',1,'vg::MemoizingGraph']]],
- ['get_5findex_12357',['get_index',['../classvg_1_1RepresentativeTraversalFinder.html#a3e15061afb4437ec04334ed77732fa81',1,'vg::RepresentativeTraversalFinder']]],
- ['get_5fnode_5fsupport_12358',['get_node_support',['../classvg_1_1RepresentativeTraversalFinder.html#a40f64596e2e8bb4b78120f351fa3bf79',1,'vg::RepresentativeTraversalFinder']]],
- ['get_5frescue_5fgraph_5ffrom_5fpaths_12359',['get_rescue_graph_from_paths',['../classvg_1_1MultipathMapper.html#a655c6fb1dc987ac5f430007594d7bb42',1,'vg::MultipathMapper']]],
- ['get_5fseed_12360',['get_seed',['../classvg_1_1LazyRNG.html#ac3c6839c2730166a6cb8a10facf8a0c7',1,'vg::LazyRNG']]],
- ['gfa_5fid_5fspace_12361',['gfa_id_space',['../classvg_1_1GFAHandleGraph.html#a74dbb782d6ffa6301fc97f7e540ebe40',1,'vg::GFAHandleGraph']]],
- ['gfa_5fparameters_12362',['gfa_parameters',['../structGBWTConfig.html#a07b86c3ec44037b22504eb86d9ebd78d',1,'GBWTConfig']]],
- ['gff_5ffeature_5fname_12363',['gff_feature_name',['../structvg_1_1IndexingParameters.html#aaeec45d17c4d60468c14debb7fb46709',1,'vg::IndexingParameters']]],
- ['gff_5ftranscript_5ftag_12364',['gff_transcript_tag',['../structvg_1_1IndexingParameters.html#aa795ef116d75fdbf71092b831fce2c21',1,'vg::IndexingParameters']]],
- ['giraffe_5fgbwt_5fdownsample_12365',['giraffe_gbwt_downsample',['../structvg_1_1IndexingParameters.html#a915eada866d050e347f4b3c00ef5dab9',1,'vg::IndexingParameters']]],
- ['globals_12366',['globals',['../classvg_1_1DiagramExplainer.html#ac7ea94549f8c5ecddece74889a88ea88',1,'vg::DiagramExplainer']]],
- ['go_5fleft_12367',['go_left',['../structvg_1_1ChainIterator.html#a785251461ea63262f67548eeadea7684',1,'vg::ChainIterator']]],
- ['gq_12368',['gq',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a021adf386d5306f56c3a330412c13000',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['grandparent_5fnet_5fhandle_12369',['grandparent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6ca403df1dfe6e9554571dba400448f8',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['graph_12370',['graph',['../classvg_1_1BandedGlobalAligner.html#af5168385acfc1ca71f0757269452e5a7',1,'vg::BandedGlobalAligner::graph()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9d4f47628b410f5639f985dae1b1b5e0',1,'vg::BandedGlobalAligner::AltTracebackStack::graph()'],['../classvg_1_1CactusSnarlFinder.html#abb2127506508ae3515f901375b205e2d',1,'vg::CactusSnarlFinder::graph()'],['../classvg_1_1PathChunker.html#afbe0c85ff99dd1134fefcf439b212d4f',1,'vg::PathChunker::graph()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a528e7742b43628c6c93c6542810ffdfd',1,'vg::PathOrientedDistanceMeasurer::graph()'],['../structvg_1_1ConstructedChunk.html#a27e2145253b94e1edecf0f456a12268b',1,'vg::ConstructedChunk::graph()'],['../classvg_1_1ContractingGraph.html#ab79d18f0c2f96761ebdad601ec4ec3d4',1,'vg::ContractingGraph::graph()'],['../classvg_1_1DagifiedGraph.html#a5b2dd0d18c17b2e10aa1b6b6280018ee',1,'vg::DagifiedGraph::graph()'],['../classvg_1_1Deconstructor.html#a74cd5fde9496dcc1865ed74fda2c4ae4',1,'vg::Deconstructor::graph()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a50561ac0fc9bcfd983a71c9fec2b6d2e',1,'vg::DozeuInterface::OrderedGraph::graph()'],['../classvg_1_1DozeuPinningOverlay.html#aff912b269bf3e749ef52c0d86fe12fcf',1,'vg::DozeuPinningOverlay::graph()'],['../classvg_1_1WFATree.html#a313dc78cf7698c0b50b3fb2b0ec28a81',1,'vg::WFATree::graph()'],['../classvg_1_1GaplessExtender.html#a8780650e736d01abf2dd910a3dd235c3',1,'vg::GaplessExtender::graph()'],['../classvg_1_1WFAExtender.html#a7362ec7bfdf80dc2fc343e483bdf0e5d',1,'vg::WFAExtender::graph()'],['../classvg_1_1SnarlState.html#a62e2fb69d55ee9cf1e2653dc4c9c8ead',1,'vg::SnarlState::graph()'],['../structvg_1_1AugmentedGraph.html#afb05832f68a8db43e7a8c510397b8ce3',1,'vg::AugmentedGraph::graph()'],['../classvg_1_1VCFGenotyper.html#ab76cadfc9e7398a693e7a0cb656dc37a',1,'vg::VCFGenotyper::graph()'],['../classvg_1_1LegacyCaller.html#a5065baf9582814e816349b53bc54a4e9',1,'vg::LegacyCaller::graph()'],['../classvg_1_1FlowCaller.html#a5193a03f37a60ed6bdf91157bf02c6dc',1,'vg::FlowCaller::graph()'],['../classvg_1_1NestedFlowCaller.html#af2cc9a536a0a2ca0fd857793f0985d68',1,'vg::NestedFlowCaller::graph()'],['../classvg_1_1GraphSynchronizer.html#ab0856b30a01193d100f9e470ea61a67c',1,'vg::GraphSynchronizer::graph()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a99d071619c6462165528d8428d4bb7fa',1,'haplo::hDP_gbwt_graph_accessor::graph()'],['../structhaplo_1_1linear__haplo__structure.html#acb5692ebbb1a6f91db791d01bb2ab294',1,'haplo::linear_haplo_structure::graph()'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#adf4336380ac7e4944628281010e7057a',1,'vg::SplicedHTSAlignmentEmitter::graph()'],['../classvg_1_1IdentityOverlay.html#aa5f51840702ebb847bc1193bea756960',1,'vg::IdentityOverlay::graph()'],['../classvg_1_1IncrementalSubgraph.html#a45a1fbda6452cbdade4d40bc4dab539c',1,'vg::IncrementalSubgraph::graph()'],['../classvg_1_1AliasGraph.html#a85dd8f136025b7325d9fa19058d2bb4f',1,'vg::AliasGraph::graph()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a932e7e9593e73f7a76a8f1756f4fb1f8',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::graph()'],['../classvg_1_1HandleGraphNodeSet.html#a1d0f4da0abcf0379dfe1672cce88a055',1,'vg::HandleGraphNodeSet::graph()'],['../classvg_1_1Masker.html#a58ab29d84eb1ad7d8d8884927850d674',1,'vg::Masker::graph()'],['../classvg_1_1MCMCGenotyper.html#a63ef4fabc83c478b9ac7933ba16c5adc',1,'vg::MCMCGenotyper::graph()'],['../classvg_1_1MemoizingGraph.html#ae619ad2dfa33c00eced07b7a987e9796',1,'vg::MemoizingGraph::graph()'],['../classvg_1_1MultipathAlignmentEmitter.html#aaaf74750129abc432b73f66d226d35c6',1,'vg::MultipathAlignmentEmitter::graph()'],['../classvg_1_1NullMaskingGraph.html#a691c9aa63e3e20dbba329691b482f311',1,'vg::NullMaskingGraph::graph()'],['../classvg_1_1Packer.html#a52ac5f2ff5549fe1b296efc53204e94f',1,'vg::Packer::graph()'],['../classvg_1_1RareVariantSimplifier.html#ace754988b74595f36762993abead625f',1,'vg::RareVariantSimplifier::graph()'],['../classvg_1_1ReadFilter.html#a73ca67996129403044a23de9544e88fd',1,'vg::ReadFilter::graph()'],['../classvg_1_1RegionExpander.html#af23424b8d8c2f809311afb6b3dceca08',1,'vg::RegionExpander::graph()'],['../classvg_1_1AbstractReadSampler.html#a07bbefa0c0af8f9c4cb5b2c45bcdae53',1,'vg::AbstractReadSampler::graph()'],['../classvg_1_1SmallSnarlSimplifier.html#a54a08fa74dda470c28e2850ded312175',1,'vg::SmallSnarlSimplifier::graph()'],['../classvg_1_1SupportBasedSnarlCaller.html#ab0f5bd05d950be25e87a9f5fbc345a5c',1,'vg::SupportBasedSnarlCaller::graph()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a49cfcfdb9e2c378e973dd8a883e154df',1,'vg::SnarlDistanceIndexClusterer::graph()'],['../classvg_1_1HandleGraphSnarlFinder.html#a377e8778235836602280747eb5813f58',1,'vg::HandleGraphSnarlFinder::graph()'],['../classvg_1_1NetGraph.html#acbae58f3fb38de99ea4a0f0b16ede465',1,'vg::NetGraph::graph()'],['../classvg_1_1StrandSplitGraph.html#a61683c11a40d1881132614159ffc0543',1,'vg::StrandSplitGraph::graph()'],['../classvg_1_1Surjector.html#a118010284d37b604a7bcd7eb8dd13537',1,'vg::Surjector::graph()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a66b0e7a1ac972af0e4d381e4202e1f5e',1,'vg::ExhaustiveTraversalFinder::graph()'],['../classvg_1_1PathRestrictedTraversalFinder.html#aef70365b3b1ee2afb3ac622748923a90',1,'vg::PathRestrictedTraversalFinder::graph()'],['../classvg_1_1PathBasedTraversalFinder.html#a16635d1b5be7de4078a9c2369a1b8073',1,'vg::PathBasedTraversalFinder::graph()'],['../classvg_1_1PathTraversalFinder.html#a7ae6d1d377192e4fab7a9074b83bddbd',1,'vg::PathTraversalFinder::graph()'],['../classvg_1_1TrivialTraversalFinder.html#aeb55a5539b54fd0bf8b4e59db2d4ffca',1,'vg::TrivialTraversalFinder::graph()'],['../classvg_1_1RepresentativeTraversalFinder.html#a66eedfed30f7b436c4eef2b339e356ba',1,'vg::RepresentativeTraversalFinder::graph()'],['../classvg_1_1VCFTraversalFinder.html#ac8e35bbc2e0c34475f13f8d6989fa5b6',1,'vg::VCFTraversalFinder::graph()'],['../classvg_1_1FlowTraversalFinder.html#ad092938a00c2c7c2b046d88fe47c73a8',1,'vg::FlowTraversalFinder::graph()'],['../classvg_1_1GBWTTraversalFinder.html#a1279ffc672ec8ee2fc6e6f1825462e15',1,'vg::GBWTTraversalFinder::graph()'],['../classvg_1_1TraversalSupportFinder.html#a388ac720c48b44f21da264209a25a3b3',1,'vg::TraversalSupportFinder::graph()'],['../classvg_1_1VariantAdder.html#a149b01f65cc10625177011221dfef354',1,'vg::VariantAdder::graph()'],['../classvg_1_1VG.html#a4772c77ed932bfed4d21e247918381a4',1,'vg::VG::graph()'],['../structvg_1_1VG_1_1Plan.html#a06f927768c287c88f81d9761d61da231',1,'vg::VG::Plan::graph()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a0a6667c750efa2c5264c6ffe1c5727aa',1,'handlegraph::PathForEachSocket::iterator::graph()'],['../classhandlegraph_1_1PathForEachSocket.html#a0bdd335f78e28a6a26ab2605c06fa601',1,'handlegraph::PathForEachSocket::graph()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a956c6bef21a026c7426da0650a2927b8',1,'vg::io::GafAlignmentEmitter::graph()']]],
- ['graph_5fname_12371',['graph_name',['../structGBWTConfig.html#adb800365228cdbb56b99c207e6a342ea',1,'GBWTConfig::graph_name()'],['../structHaplotypesConfig.html#a232a96ba620bbe67e61468c7841bec9d',1,'HaplotypesConfig::graph_name()']]],
- ['graph_5foutput_12372',['graph_output',['../structGBWTConfig.html#adb60e4d83216b0c6b9a4ffd821a54ffb',1,'GBWTConfig']]],
- ['greedy_5fmin_5fdist_12373',['greedy_min_dist',['../classvg_1_1MultipathMapper.html#a97d02064d377122ed8cef9e53340ba90',1,'vg::MultipathMapper']]],
- ['greedy_5fpieces_12374',['greedy_pieces',['../classvg_1_1Constructor.html#ac4dce51a25e5f773a0c53e8cd9f07628',1,'vg::Constructor']]],
- ['greedy_5frestart_5fassume_5fsubstitution_12375',['greedy_restart_assume_substitution',['../classvg_1_1BaseMapper.html#a5a3324ff0b1faccb4e976e0d1a369712',1,'vg::BaseMapper']]],
- ['greedy_5frestart_5fmax_5fcount_12376',['greedy_restart_max_count',['../classvg_1_1BaseMapper.html#a5d9a1c8549138e423e1a95a40590fee6',1,'vg::BaseMapper']]],
- ['greedy_5frestart_5fmax_5flcp_12377',['greedy_restart_max_lcp',['../classvg_1_1BaseMapper.html#a4cad1e0b9a03002f35eee233cc34ac54',1,'vg::BaseMapper']]],
- ['greedy_5frestart_5fmin_5flength_12378',['greedy_restart_min_length',['../classvg_1_1BaseMapper.html#abe669bcb3e32a8afb3e71443bbe5076a',1,'vg::BaseMapper']]],
- ['group_12379',['group',['../classvg_1_1io_1_1MessageEmitter.html#adb0173ebe6170c259448c8dd1d4c0dde',1,'vg::io::MessageEmitter']]],
- ['group_5fcache_12380',['group_cache',['../classvg_1_1IndexedVG.html#a0024489b3eb887d90d18af839722ce66',1,'vg::IndexedVG']]],
- ['group_5fcount_12381',['group_count',['../classvg_1_1io_1_1MessageIterator.html#a34611c431fac53c556d57036cee7e4fe',1,'vg::io::MessageIterator']]],
- ['group_5fhandlers_12382',['group_handlers',['../classvg_1_1io_1_1MessageEmitter.html#a8e586d31762cb47872de4b4723e01696',1,'vg::io::MessageEmitter::group_handlers()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a176d09f4d40ef21965c7a66abc546dbd',1,'vg::io::ProtobufEmitter::group_handlers()']]],
- ['group_5fidx_12383',['group_idx',['../classvg_1_1io_1_1MessageIterator.html#ab2a47479856b6bb8d6fe3c943519d83d',1,'vg::io::MessageIterator']]],
- ['group_5fsize_12384',['group_size',['../structvg_1_1Funnel_1_1Item.html#a23706e46f9ebd56acbea3c612358bb79',1,'vg::Funnel::Item']]],
- ['group_5ftag_12385',['group_tag',['../classvg_1_1io_1_1MessageEmitter.html#ad240e5c3ae379aa3257c498dd4c4e1bf',1,'vg::io::MessageEmitter']]],
- ['group_5fvo_12386',['group_vo',['../classvg_1_1io_1_1MessageIterator.html#ae569fd7dc6129edc5e5dac52b1a67f84',1,'vg::io::MessageIterator']]],
- ['gz_5fsuffix_12387',['GZ_SUFFIX',['../rna__main_8cpp.html#a79e5666abc1e2270209776bd472798e7',1,'rna_main.cpp']]]
+ ['g_5fbv_12309',['g_bv',['../classxg_1_1XG.html#a7fcb333bb6acf85ce76d81de9735b88a',1,'xg::XG']]],
+ ['g_5fbv_5frank_12310',['g_bv_rank',['../classxg_1_1XG.html#abbbc82ab0fe4b0d8abe7e5890a89b952',1,'xg::XG']]],
+ ['g_5fbv_5fselect_12311',['g_bv_select',['../classxg_1_1XG.html#a9eb31aaf28e0ab90154233692bdc0c05',1,'xg::XG']]],
+ ['g_5fiv_12312',['g_iv',['../classxg_1_1XG.html#a7b4b76e9a150ca86d54cee59a3825f4d',1,'xg::XG']]],
+ ['g_5fnode_5fheader_5flength_12313',['G_NODE_HEADER_LENGTH',['../classxg_1_1XG.html#a8a1f38f3430d796f7b2ae452fd80ebbf',1,'xg::XG']]],
+ ['g_5fnode_5fid_5foffset_12314',['G_NODE_ID_OFFSET',['../classxg_1_1XG.html#a841f4db9d178690c836a21b6adc9fafe',1,'xg::XG']]],
+ ['g_5fnode_5fleft_5fcount_5foffset_12315',['G_NODE_LEFT_COUNT_OFFSET',['../classxg_1_1XG.html#a9028d42350d55a928483b76579549145',1,'xg::XG']]],
+ ['g_5fnode_5flength_5foffset_12316',['G_NODE_LENGTH_OFFSET',['../classxg_1_1XG.html#aaf4de09d0f39174f42c793492976acc9',1,'xg::XG']]],
+ ['g_5fnode_5fright_5fcount_5foffset_12317',['G_NODE_RIGHT_COUNT_OFFSET',['../classxg_1_1XG.html#ad4aacfc7ad17ddc586566f8d2a5e92e5',1,'xg::XG']]],
+ ['g_5fnode_5fseq_5fstart_5foffset_12318',['G_NODE_SEQ_START_OFFSET',['../classxg_1_1XG.html#a19673db503954e65456196d791f7db04',1,'xg::XG']]],
+ ['gaf_12319',['gaf',['../structGafFile.html#a9dcebeb1a298c34516bdd969dc439560',1,'GafFile']]],
+ ['gaf_5foutput_12320',['gaf_output',['../classvg_1_1VCFGenotyper.html#ae00bbce9945411dbab0d14e7cdb4b8c2',1,'vg::VCFGenotyper::gaf_output()'],['../classvg_1_1FlowCaller.html#a93037892a9148b952b186852f77f0fa8',1,'vg::FlowCaller::gaf_output()'],['../classvg_1_1NestedFlowCaller.html#a9114ad05033bc7d50becae55041dfae0',1,'vg::NestedFlowCaller::gaf_output()']]],
+ ['gaf_5fsample_5fname_12321',['gaf_sample_name',['../classvg_1_1GAFOutputCaller.html#a23554330b3cf641645fe7b3070c6d203',1,'vg::GAFOutputCaller']]],
+ ['gam_5fformat_12322',['gam_format',['../structGBWTConfig.html#a1fcbf295cfa998c40744359748fda6c7',1,'GBWTConfig']]],
+ ['gap_5fdistance_5flimit_12323',['gap_distance_limit',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#ad9d07441a40519ff349163eb7d87c916',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['gap_5fextend_12324',['gap_extend',['../classvg_1_1WFATree.html#abe47c55fbdfa81f6b0df6ffdb4c3591e',1,'vg::WFATree::gap_extend()'],['../structScoringOptions.html#a8ae3e44719121535cd43560dddc267aa',1,'ScoringOptions::gap_extend()']]],
+ ['gap_5fextension_12325',['gap_extension',['../classvg_1_1GSSWAligner.html#afd2379af50d751eee892a10529d64ffb',1,'vg::GSSWAligner::gap_extension()'],['../classvg_1_1DeletionAligner.html#a5fdfc2ac3a633a6e3cd61c2e3beeae97',1,'vg::DeletionAligner::gap_extension()'],['../classvg_1_1SSWAligner.html#a2248e3e561aab8d3b1036d51850b3c2f',1,'vg::SSWAligner::gap_extension()']]],
+ ['gap_5flength_12326',['gap_length',['../structvg_1_1WFAExtender_1_1ErrorModel.html#a9cf62e400ef2e4efb434e8e5a452e7e8',1,'vg::WFAExtender::ErrorModel']]],
+ ['gap_5fmemo_5fmax_5fsize_12327',['gap_memo_max_size',['../classvg_1_1MultipathMapper.html#a864cc168b7061cf1885ef61785e474d3',1,'vg::MultipathMapper']]],
+ ['gap_5fopen_12328',['gap_open',['../classvg_1_1GSSWAligner.html#aa5c0a63b73ad2ff8ec8f05062c768c22',1,'vg::GSSWAligner::gap_open()'],['../classvg_1_1DeletionAligner.html#a7791fe71828711b3208db54db784cf1d',1,'vg::DeletionAligner::gap_open()'],['../classvg_1_1WFATree.html#aec0c57320c07468df3201a106f7e6aa0',1,'vg::WFATree::gap_open()'],['../classvg_1_1SSWAligner.html#a15398a23880418599e81370d485fec0f',1,'vg::SSWAligner::gap_open()'],['../structScoringOptions.html#ab399d0cf09e907906b42d500a54194bc',1,'ScoringOptions::gap_open()']]],
+ ['gap_5fscale_12329',['gap_scale',['../classvg_1_1MinimizerMapper.html#a5e6e66b39ed25c3d81f82546231d790a',1,'vg::MinimizerMapper']]],
+ ['gapless_5fextension_5flimit_12330',['gapless_extension_limit',['../classvg_1_1MinimizerMapper.html#af0eb242f1ec9aaaa52e7d03446d09cbf',1,'vg::MinimizerMapper']]],
+ ['gaps_12331',['gaps',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ac60921b93f505b6731badc2aef7f64f5',1,'vg::WFAExtender::ErrorModel']]],
+ ['gbwt_12332',['gbwt',['../classvg_1_1Deconstructor.html#a52b3fcd3d7357f5dd3624d9caa56539f',1,'vg::Deconstructor::gbwt()'],['../classvg_1_1GBWTTraversalFinder.html#a7827a0ee00890a2d8cf1716017e39db7',1,'vg::GBWTTraversalFinder::gbwt()']]],
+ ['gbwt_5fbuffer_5fsize_12333',['gbwt_buffer_size',['../classvg_1_1HaplotypeIndexer.html#abc8d5ce81546e16ffb7bf652c098bb11',1,'vg::HaplotypeIndexer']]],
+ ['gbwt_5fgraph_12334',['gbwt_graph',['../classvg_1_1MinimizerMapper.html#abb94c27ed347a36fb38f91cf23a582fb',1,'vg::MinimizerMapper::gbwt_graph()'],['../structGraphHandler.html#ad86c0372b075e6e0c5bfbf61801b3222',1,'GraphHandler::gbwt_graph()']]],
+ ['gbwt_5findex_12335',['gbwt_index',['../classvg_1_1PhaseUnfolder.html#abe0ad79b8b65bea2a4f871913c83ee65',1,'vg::PhaseUnfolder']]],
+ ['gbwt_5finsert_5fbatch_5fsize_12336',['gbwt_insert_batch_size',['../structvg_1_1IndexingParameters.html#ab408ae73a85875de5dfe376e340f8840',1,'vg::IndexingParameters']]],
+ ['gbwt_5finsert_5fbatch_5fsize_5fincrease_5ffactor_12337',['gbwt_insert_batch_size_increase_factor',['../structvg_1_1IndexingParameters.html#a721125abeca5c4755e875f2e3d8c1d2f',1,'vg::IndexingParameters']]],
+ ['gbwt_5fname_12338',['gbwt_name',['../structGBWTConfig.html#a5fe3f0a41311811ddf16bcd7dbab4f91',1,'GBWTConfig']]],
+ ['gbwt_5foutput_12339',['gbwt_output',['../structGBWTConfig.html#a8d9b4d70bb33f75cb147ee91b75c89af',1,'GBWTConfig']]],
+ ['gbwt_5freference_5fsamples_12340',['gbwt_reference_samples',['../classvg_1_1Deconstructor.html#a8f81a59e45aad56aa6edc19756a9eb14',1,'vg::Deconstructor']]],
+ ['gbwt_5fsample_5fto_5fphase_5frange_12341',['gbwt_sample_to_phase_range',['../classvg_1_1Deconstructor.html#a5f58aa9a4d3f29e330a9c9e1c9541884',1,'vg::Deconstructor']]],
+ ['gbwt_5fsampling_5finterval_12342',['gbwt_sampling_interval',['../structvg_1_1IndexingParameters.html#abd33e81c954cb14ed31455a3950abe64',1,'vg::IndexingParameters']]],
+ ['gbwt_5ftrav_5ffinder_12343',['gbwt_trav_finder',['../classvg_1_1Deconstructor.html#a41a7ff33e08c5eee5d2d7088dbc238f4',1,'vg::Deconstructor']]],
+ ['gbwtgraph_5fname_12344',['gbwtgraph_name',['../structGBWTConfig.html#ac8e90b7bda206414a7055a98f5b55e85',1,'GBWTConfig']]],
+ ['gbz_12345',['gbz',['../classvg_1_1GBZGraph.html#ac56a91ab9fe591aa7781cd751fe94ed4',1,'vg::GBZGraph::gbz()'],['../classvg_1_1HaplotypePartitioner.html#a533f084057db81844dd0c02f36fb5498',1,'vg::HaplotypePartitioner::gbz()'],['../classvg_1_1Recombinator.html#a977b21bbcc9ea6520dbc97a5014488e6',1,'vg::Recombinator::gbz()']]],
+ ['gbz_5fformat_12346',['gbz_format',['../structGBWTConfig.html#a14fe1675f26aa9b74381640c4cffdd47',1,'GBWTConfig']]],
+ ['gbz_5foutput_12347',['gbz_output',['../structHaplotypesConfig.html#af71ee285e699443b559375aeac054eb8',1,'HaplotypesConfig']]],
+ ['gc_5fcontent_5festimate_12348',['gc_content_estimate',['../classvg_1_1AlignerClient.html#a65428f092aaa5d894b709e247cf0121a',1,'vg::AlignerClient']]],
+ ['gcsa_12349',['gcsa',['../classvg_1_1BaseMapper.html#aa41db0eca93c379087c90b602a6ce751',1,'vg::BaseMapper']]],
+ ['gcsa_5fdoubling_5fsteps_12350',['gcsa_doubling_steps',['../structvg_1_1IndexingParameters.html#ab480b0e1f6dca30213719734b78904e5',1,'vg::IndexingParameters']]],
+ ['gcsa_5find_12351',['gcsa_ind',['../classvg_1_1Filter.html#ae98fe5c85ea704f1ef262b5556bbbbbb',1,'vg::Filter']]],
+ ['gcsa_5finitial_5fkmer_5flength_12352',['gcsa_initial_kmer_length',['../structvg_1_1IndexingParameters.html#a890a5822bd592090eaf5b529816ecb32',1,'vg::IndexingParameters']]],
+ ['gcsa_5fsize_5flimit_12353',['gcsa_size_limit',['../structvg_1_1IndexingParameters.html#a144f6b2b03ccc7ecf4b7d3a504aed1b7',1,'vg::IndexingParameters']]],
+ ['generalizations_12354',['generalizations',['../classvg_1_1IndexRegistry.html#a665cc9431438ef50124b29e518465a05',1,'vg::IndexRegistry']]],
+ ['genome_12355',['genome',['../classvg_1_1MCMCCaller.html#ad4278b11272792c879ab3463b513ae1e',1,'vg::MCMCCaller']]],
+ ['genotype_12356',['genotype',['../structvg_1_1Locus.html#a144d9dc0f9d61910db33decca23e4755',1,'vg::Locus']]],
+ ['genotype_5fby_5fploidy_12357',['genotype_by_ploidy',['../structvg_1_1NestedFlowCaller_1_1CallRecord.html#af331caba29195578f8a48ed527232ed1',1,'vg::NestedFlowCaller::CallRecord']]],
+ ['genotype_5fsnarls_12358',['genotype_snarls',['../classvg_1_1FlowCaller.html#ae47f36ad1ec53a2381f970d159acbd64',1,'vg::FlowCaller::genotype_snarls()'],['../classvg_1_1NestedFlowCaller.html#a4c00174974936972c989b905a921b154',1,'vg::NestedFlowCaller::genotype_snarls()']]],
+ ['get_5fedge_5fsupport_12359',['get_edge_support',['../classvg_1_1RepresentativeTraversalFinder.html#a452fdd307124349d6b65aa434bab48c7',1,'vg::RepresentativeTraversalFinder']]],
+ ['get_5fhandle_5fmemo_12360',['get_handle_memo',['../classvg_1_1MemoizingGraph.html#a522abfb6d16b8e96a77ff6f114275cf8',1,'vg::MemoizingGraph']]],
+ ['get_5findex_12361',['get_index',['../classvg_1_1RepresentativeTraversalFinder.html#a3e15061afb4437ec04334ed77732fa81',1,'vg::RepresentativeTraversalFinder']]],
+ ['get_5fnode_5fsupport_12362',['get_node_support',['../classvg_1_1RepresentativeTraversalFinder.html#a40f64596e2e8bb4b78120f351fa3bf79',1,'vg::RepresentativeTraversalFinder']]],
+ ['get_5frescue_5fgraph_5ffrom_5fpaths_12363',['get_rescue_graph_from_paths',['../classvg_1_1MultipathMapper.html#a655c6fb1dc987ac5f430007594d7bb42',1,'vg::MultipathMapper']]],
+ ['get_5fseed_12364',['get_seed',['../classvg_1_1LazyRNG.html#ac3c6839c2730166a6cb8a10facf8a0c7',1,'vg::LazyRNG']]],
+ ['gfa_5fid_5fspace_12365',['gfa_id_space',['../classvg_1_1GFAHandleGraph.html#a74dbb782d6ffa6301fc97f7e540ebe40',1,'vg::GFAHandleGraph']]],
+ ['gfa_5fparameters_12366',['gfa_parameters',['../structGBWTConfig.html#a07b86c3ec44037b22504eb86d9ebd78d',1,'GBWTConfig']]],
+ ['gff_5ffeature_5fname_12367',['gff_feature_name',['../structvg_1_1IndexingParameters.html#aaeec45d17c4d60468c14debb7fb46709',1,'vg::IndexingParameters']]],
+ ['gff_5ftranscript_5ftag_12368',['gff_transcript_tag',['../structvg_1_1IndexingParameters.html#aa795ef116d75fdbf71092b831fce2c21',1,'vg::IndexingParameters']]],
+ ['giraffe_5fgbwt_5fdownsample_12369',['giraffe_gbwt_downsample',['../structvg_1_1IndexingParameters.html#a915eada866d050e347f4b3c00ef5dab9',1,'vg::IndexingParameters']]],
+ ['globals_12370',['globals',['../classvg_1_1DiagramExplainer.html#ac7ea94549f8c5ecddece74889a88ea88',1,'vg::DiagramExplainer']]],
+ ['go_5fleft_12371',['go_left',['../structvg_1_1ChainIterator.html#a785251461ea63262f67548eeadea7684',1,'vg::ChainIterator']]],
+ ['gq_12372',['gq',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a021adf386d5306f56c3a330412c13000',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['grandparent_5fnet_5fhandle_12373',['grandparent_net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a6ca403df1dfe6e9554571dba400448f8',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['graph_12374',['graph',['../classvg_1_1BandedGlobalAligner.html#af5168385acfc1ca71f0757269452e5a7',1,'vg::BandedGlobalAligner::graph()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9d4f47628b410f5639f985dae1b1b5e0',1,'vg::BandedGlobalAligner::AltTracebackStack::graph()'],['../classvg_1_1CactusSnarlFinder.html#abb2127506508ae3515f901375b205e2d',1,'vg::CactusSnarlFinder::graph()'],['../classvg_1_1PathChunker.html#afbe0c85ff99dd1134fefcf439b212d4f',1,'vg::PathChunker::graph()'],['../classvg_1_1PathOrientedDistanceMeasurer.html#a528e7742b43628c6c93c6542810ffdfd',1,'vg::PathOrientedDistanceMeasurer::graph()'],['../structvg_1_1ConstructedChunk.html#a27e2145253b94e1edecf0f456a12268b',1,'vg::ConstructedChunk::graph()'],['../classvg_1_1ContractingGraph.html#ab79d18f0c2f96761ebdad601ec4ec3d4',1,'vg::ContractingGraph::graph()'],['../classvg_1_1DagifiedGraph.html#a5b2dd0d18c17b2e10aa1b6b6280018ee',1,'vg::DagifiedGraph::graph()'],['../classvg_1_1Deconstructor.html#a74cd5fde9496dcc1865ed74fda2c4ae4',1,'vg::Deconstructor::graph()'],['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a50561ac0fc9bcfd983a71c9fec2b6d2e',1,'vg::DozeuInterface::OrderedGraph::graph()'],['../classvg_1_1DozeuPinningOverlay.html#aff912b269bf3e749ef52c0d86fe12fcf',1,'vg::DozeuPinningOverlay::graph()'],['../classvg_1_1WFATree.html#a313dc78cf7698c0b50b3fb2b0ec28a81',1,'vg::WFATree::graph()'],['../classvg_1_1GaplessExtender.html#a8780650e736d01abf2dd910a3dd235c3',1,'vg::GaplessExtender::graph()'],['../classvg_1_1WFAExtender.html#a7362ec7bfdf80dc2fc343e483bdf0e5d',1,'vg::WFAExtender::graph()'],['../classvg_1_1SnarlState.html#a62e2fb69d55ee9cf1e2653dc4c9c8ead',1,'vg::SnarlState::graph()'],['../structvg_1_1AugmentedGraph.html#afb05832f68a8db43e7a8c510397b8ce3',1,'vg::AugmentedGraph::graph()'],['../classvg_1_1VCFGenotyper.html#ab76cadfc9e7398a693e7a0cb656dc37a',1,'vg::VCFGenotyper::graph()'],['../classvg_1_1LegacyCaller.html#a5065baf9582814e816349b53bc54a4e9',1,'vg::LegacyCaller::graph()'],['../classvg_1_1FlowCaller.html#a5193a03f37a60ed6bdf91157bf02c6dc',1,'vg::FlowCaller::graph()'],['../classvg_1_1NestedFlowCaller.html#af2cc9a536a0a2ca0fd857793f0985d68',1,'vg::NestedFlowCaller::graph()'],['../classvg_1_1GraphSynchronizer.html#ab0856b30a01193d100f9e470ea61a67c',1,'vg::GraphSynchronizer::graph()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a99d071619c6462165528d8428d4bb7fa',1,'haplo::hDP_gbwt_graph_accessor::graph()'],['../structhaplo_1_1linear__haplo__structure.html#acb5692ebbb1a6f91db791d01bb2ab294',1,'haplo::linear_haplo_structure::graph()'],['../classvg_1_1SplicedHTSAlignmentEmitter.html#adf4336380ac7e4944628281010e7057a',1,'vg::SplicedHTSAlignmentEmitter::graph()'],['../classvg_1_1IdentityOverlay.html#aa5f51840702ebb847bc1193bea756960',1,'vg::IdentityOverlay::graph()'],['../classvg_1_1IncrementalSubgraph.html#a45a1fbda6452cbdade4d40bc4dab539c',1,'vg::IncrementalSubgraph::graph()'],['../classvg_1_1AliasGraph.html#a85dd8f136025b7325d9fa19058d2bb4f',1,'vg::AliasGraph::graph()'],['../classvg_1_1IntegratedSnarlFinder_1_1MergedAdjacencyGraph.html#a932e7e9593e73f7a76a8f1756f4fb1f8',1,'vg::IntegratedSnarlFinder::MergedAdjacencyGraph::graph()'],['../classvg_1_1HandleGraphNodeSet.html#a1d0f4da0abcf0379dfe1672cce88a055',1,'vg::HandleGraphNodeSet::graph()'],['../classvg_1_1Masker.html#a58ab29d84eb1ad7d8d8884927850d674',1,'vg::Masker::graph()'],['../classvg_1_1MCMCGenotyper.html#a63ef4fabc83c478b9ac7933ba16c5adc',1,'vg::MCMCGenotyper::graph()'],['../classvg_1_1MemoizingGraph.html#ae619ad2dfa33c00eced07b7a987e9796',1,'vg::MemoizingGraph::graph()'],['../classvg_1_1MultipathAlignmentEmitter.html#aaaf74750129abc432b73f66d226d35c6',1,'vg::MultipathAlignmentEmitter::graph()'],['../classvg_1_1NullMaskingGraph.html#a691c9aa63e3e20dbba329691b482f311',1,'vg::NullMaskingGraph::graph()'],['../classvg_1_1Packer.html#a52ac5f2ff5549fe1b296efc53204e94f',1,'vg::Packer::graph()'],['../classvg_1_1RareVariantSimplifier.html#ace754988b74595f36762993abead625f',1,'vg::RareVariantSimplifier::graph()'],['../classvg_1_1ReadFilter.html#a73ca67996129403044a23de9544e88fd',1,'vg::ReadFilter::graph()'],['../classvg_1_1RegionExpander.html#af23424b8d8c2f809311afb6b3dceca08',1,'vg::RegionExpander::graph()'],['../classvg_1_1AbstractReadSampler.html#a07bbefa0c0af8f9c4cb5b2c45bcdae53',1,'vg::AbstractReadSampler::graph()'],['../classvg_1_1SmallSnarlSimplifier.html#a54a08fa74dda470c28e2850ded312175',1,'vg::SmallSnarlSimplifier::graph()'],['../classvg_1_1SupportBasedSnarlCaller.html#ab0f5bd05d950be25e87a9f5fbc345a5c',1,'vg::SupportBasedSnarlCaller::graph()'],['../classvg_1_1SnarlDistanceIndexClusterer.html#a49cfcfdb9e2c378e973dd8a883e154df',1,'vg::SnarlDistanceIndexClusterer::graph()'],['../classvg_1_1HandleGraphSnarlFinder.html#a377e8778235836602280747eb5813f58',1,'vg::HandleGraphSnarlFinder::graph()'],['../classvg_1_1NetGraph.html#acbae58f3fb38de99ea4a0f0b16ede465',1,'vg::NetGraph::graph()'],['../classvg_1_1StrandSplitGraph.html#a61683c11a40d1881132614159ffc0543',1,'vg::StrandSplitGraph::graph()'],['../classvg_1_1Surjector.html#a118010284d37b604a7bcd7eb8dd13537',1,'vg::Surjector::graph()'],['../classvg_1_1ExhaustiveTraversalFinder.html#a66b0e7a1ac972af0e4d381e4202e1f5e',1,'vg::ExhaustiveTraversalFinder::graph()'],['../classvg_1_1PathRestrictedTraversalFinder.html#aef70365b3b1ee2afb3ac622748923a90',1,'vg::PathRestrictedTraversalFinder::graph()'],['../classvg_1_1PathBasedTraversalFinder.html#a16635d1b5be7de4078a9c2369a1b8073',1,'vg::PathBasedTraversalFinder::graph()'],['../classvg_1_1PathTraversalFinder.html#a7ae6d1d377192e4fab7a9074b83bddbd',1,'vg::PathTraversalFinder::graph()'],['../classvg_1_1TrivialTraversalFinder.html#aeb55a5539b54fd0bf8b4e59db2d4ffca',1,'vg::TrivialTraversalFinder::graph()'],['../classvg_1_1RepresentativeTraversalFinder.html#a66eedfed30f7b436c4eef2b339e356ba',1,'vg::RepresentativeTraversalFinder::graph()'],['../classvg_1_1VCFTraversalFinder.html#ac8e35bbc2e0c34475f13f8d6989fa5b6',1,'vg::VCFTraversalFinder::graph()'],['../classvg_1_1FlowTraversalFinder.html#ad092938a00c2c7c2b046d88fe47c73a8',1,'vg::FlowTraversalFinder::graph()'],['../classvg_1_1GBWTTraversalFinder.html#a1279ffc672ec8ee2fc6e6f1825462e15',1,'vg::GBWTTraversalFinder::graph()'],['../classvg_1_1TraversalSupportFinder.html#a388ac720c48b44f21da264209a25a3b3',1,'vg::TraversalSupportFinder::graph()'],['../classvg_1_1VariantAdder.html#a149b01f65cc10625177011221dfef354',1,'vg::VariantAdder::graph()'],['../classvg_1_1VG.html#a4772c77ed932bfed4d21e247918381a4',1,'vg::VG::graph()'],['../structvg_1_1VG_1_1Plan.html#a06f927768c287c88f81d9761d61da231',1,'vg::VG::Plan::graph()'],['../classhandlegraph_1_1PathForEachSocket_1_1iterator.html#a0a6667c750efa2c5264c6ffe1c5727aa',1,'handlegraph::PathForEachSocket::iterator::graph()'],['../classhandlegraph_1_1PathForEachSocket.html#a0bdd335f78e28a6a26ab2605c06fa601',1,'handlegraph::PathForEachSocket::graph()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a956c6bef21a026c7426da0650a2927b8',1,'vg::io::GafAlignmentEmitter::graph()']]],
+ ['graph_5fname_12375',['graph_name',['../structGBWTConfig.html#adb800365228cdbb56b99c207e6a342ea',1,'GBWTConfig::graph_name()'],['../structHaplotypesConfig.html#a232a96ba620bbe67e61468c7841bec9d',1,'HaplotypesConfig::graph_name()']]],
+ ['graph_5foutput_12376',['graph_output',['../structGBWTConfig.html#adb60e4d83216b0c6b9a4ffd821a54ffb',1,'GBWTConfig']]],
+ ['greedy_5fmin_5fdist_12377',['greedy_min_dist',['../classvg_1_1MultipathMapper.html#a97d02064d377122ed8cef9e53340ba90',1,'vg::MultipathMapper']]],
+ ['greedy_5fpieces_12378',['greedy_pieces',['../classvg_1_1Constructor.html#ac4dce51a25e5f773a0c53e8cd9f07628',1,'vg::Constructor']]],
+ ['greedy_5frestart_5fassume_5fsubstitution_12379',['greedy_restart_assume_substitution',['../classvg_1_1BaseMapper.html#a5a3324ff0b1faccb4e976e0d1a369712',1,'vg::BaseMapper']]],
+ ['greedy_5frestart_5fmax_5fcount_12380',['greedy_restart_max_count',['../classvg_1_1BaseMapper.html#a5d9a1c8549138e423e1a95a40590fee6',1,'vg::BaseMapper']]],
+ ['greedy_5frestart_5fmax_5flcp_12381',['greedy_restart_max_lcp',['../classvg_1_1BaseMapper.html#a4cad1e0b9a03002f35eee233cc34ac54',1,'vg::BaseMapper']]],
+ ['greedy_5frestart_5fmin_5flength_12382',['greedy_restart_min_length',['../classvg_1_1BaseMapper.html#abe669bcb3e32a8afb3e71443bbe5076a',1,'vg::BaseMapper']]],
+ ['group_12383',['group',['../classvg_1_1io_1_1MessageEmitter.html#adb0173ebe6170c259448c8dd1d4c0dde',1,'vg::io::MessageEmitter']]],
+ ['group_5fcache_12384',['group_cache',['../classvg_1_1IndexedVG.html#a0024489b3eb887d90d18af839722ce66',1,'vg::IndexedVG']]],
+ ['group_5fcount_12385',['group_count',['../classvg_1_1io_1_1MessageIterator.html#a34611c431fac53c556d57036cee7e4fe',1,'vg::io::MessageIterator']]],
+ ['group_5fhandlers_12386',['group_handlers',['../classvg_1_1io_1_1MessageEmitter.html#a8e586d31762cb47872de4b4723e01696',1,'vg::io::MessageEmitter::group_handlers()'],['../classvg_1_1io_1_1ProtobufEmitter.html#a176d09f4d40ef21965c7a66abc546dbd',1,'vg::io::ProtobufEmitter::group_handlers()']]],
+ ['group_5fidx_12387',['group_idx',['../classvg_1_1io_1_1MessageIterator.html#ab2a47479856b6bb8d6fe3c943519d83d',1,'vg::io::MessageIterator']]],
+ ['group_5fsize_12388',['group_size',['../structvg_1_1Funnel_1_1Item.html#a23706e46f9ebd56acbea3c612358bb79',1,'vg::Funnel::Item']]],
+ ['group_5ftag_12389',['group_tag',['../classvg_1_1io_1_1MessageEmitter.html#ad240e5c3ae379aa3257c498dd4c4e1bf',1,'vg::io::MessageEmitter']]],
+ ['group_5fvo_12390',['group_vo',['../classvg_1_1io_1_1MessageIterator.html#ae569fd7dc6129edc5e5dac52b1a67f84',1,'vg::io::MessageIterator']]],
+ ['gz_5fsuffix_12391',['GZ_SUFFIX',['../rna__main_8cpp.html#a79e5666abc1e2270209776bd472798e7',1,'rna_main.cpp']]]
];
diff --git a/search/variables_8.js b/search/variables_8.js
index 557ea58de7..8bc3249091 100644
--- a/search/variables_8.js
+++ b/search/variables_8.js
@@ -1,53 +1,53 @@
var searchData=
[
- ['handle_12388',['handle',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a2d575dc899c6ef50c6ffe7c374573fb9',1,'vg::io::BlockedGzipInputStream::handle()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a726e457d2e98e4ca6ffa742a4378949f',1,'vg::io::BlockedGzipOutputStream::handle()']]],
- ['handle_5fbase_5foption_12389',['handle_base_option',['../classvg_1_1ConfigurableParser.html#a0c39f36cf64d91a336afaac0604ff9f0',1,'vg::ConfigurableParser']]],
- ['handle_5fgraph_12390',['handle_graph',['../classvg_1_1TargetValueSearch.html#a99dd4b74b5894a228a6d31174ca322de',1,'vg::TargetValueSearch::handle_graph()'],['../classvg_1_1MinDistanceClusterer.html#a6bc0aa3fb6df2824a2fe88f941312f09',1,'vg::MinDistanceClusterer::handle_graph()']]],
- ['handle_5fidxs_12391',['handle_idxs',['../classvg_1_1JoinedSpliceGraph.html#af3e4ce836a5ba9b208bde5bfe245a97e',1,'vg::JoinedSpliceGraph']]],
- ['handle_5fval_5frange_12392',['handle_val_range',['../classvg_1_1DagifiedGraph.html#a3cbeb57dc989a7f0963553041c156252',1,'vg::DagifiedGraph::handle_val_range()'],['../classvg_1_1DozeuPinningOverlay.html#a55cd7c6586c7da513046ed232fe95440',1,'vg::DozeuPinningOverlay::handle_val_range()']]],
- ['handles_12393',['handles',['../classxg_1_1XGPath.html#a2363dd10eb299ca6cc52655e517ad9e1',1,'xg::XGPath']]],
- ['haplo_5fnode_12394',['haplo_node',['../classvg_1_1PhasedGenome_1_1iterator.html#a1ae0c6a2bdb23511f58dc2986b36117e',1,'vg::PhasedGenome::iterator']]],
- ['haplo_5fscore_5fprovider_12395',['haplo_score_provider',['../classvg_1_1BaseMapper.html#af69ce88df203124121b71bdfdc6f3694',1,'vg::BaseMapper']]],
- ['haploid_5fprior_5flogprob_12396',['haploid_prior_logprob',['../classvg_1_1Genotyper.html#a76e36b8cc1f5a8a5522c5ae3f57b5464',1,'vg::Genotyper']]],
- ['haploid_5fscoring_12397',['haploid_scoring',['../structvg_1_1Recombinator_1_1Parameters.html#a500ad8a5fa909da483c0d84121b80dbd',1,'vg::Recombinator::Parameters']]],
- ['haplotype_12398',['haplotype',['../structvg_1_1AppendHaplotypeCommand.html#a5dcde06b8eb329a38ae49f612218ad90',1,'vg::AppendHaplotypeCommand::haplotype()'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a096fd6e4d5329e8242d4d1a69e95314b',1,'vg::ReplaceSnarlHaplotypeCommand::haplotype()'],['../structvg_1_1RecombinatorFragment.html#a566d752b9670dbf52d1e3998758c1754',1,'vg::RecombinatorFragment::haplotype()']]],
- ['haplotype_5fconsistency_5fexponent_12399',['haplotype_consistency_exponent',['../classvg_1_1BaseMapper.html#a33465e76a17e2580a6e095f3373239c5',1,'vg::BaseMapper']]],
- ['haplotype_5fgbwt_5fids_12400',['haplotype_gbwt_ids',['../structvg_1_1TranscriptPath.html#aafc713083bff5a107e2eb70e4d131541',1,'vg::TranscriptPath']]],
- ['haplotype_5findexer_12401',['haplotype_indexer',['../structGBWTConfig.html#a29a942d7e187971aa7821a5aacb65acd',1,'GBWTConfig']]],
- ['haplotype_5finput_12402',['haplotype_input',['../structHaplotypesConfig.html#a9bca6d317d27daae42a19413e3e336b2',1,'HaplotypesConfig']]],
- ['haplotype_5fmatch_12403',['HAPLOTYPE_MATCH',['../classhandlegraph_1_1PathMetadata.html#a3f78e2ed41434be9b84823f5724734e9',1,'handlegraph::PathMetadata']]],
- ['haplotype_5fnumber_12404',['haplotype_number',['../classvg_1_1PhasedGenome_1_1iterator.html#a3d0bbf671bf2801e44d23fea4da0e397',1,'vg::PhasedGenome::iterator']]],
- ['haplotype_5foutput_12405',['haplotype_output',['../structHaplotypesConfig.html#a75dc83e4850abb0e9d8542285a844574',1,'HaplotypesConfig']]],
- ['haplotypes_12406',['haplotypes',['../classvg_1_1SnarlState.html#a98f04166481311709d9a8d3b05b0245e',1,'vg::SnarlState::haplotypes()'],['../classvg_1_1PhasedGenome.html#aa7b2bebc28cc37da09216fca8361c75c',1,'vg::PhasedGenome::haplotypes()'],['../structvg_1_1Recombinator_1_1Statistics.html#a1541408a463fbbcea0e4a3ac08bac9df',1,'vg::Recombinator::Statistics::haplotypes()'],['../classvg_1_1Recombinator.html#a536bca6a31d76be8d90571b24b8ff0e8',1,'vg::Recombinator::haplotypes()'],['../structGBWTConfig.html#a1b5f59745e1b75e70af68ef9e8cd0378',1,'GBWTConfig::haplotypes()']]],
- ['hard_5fhit_5fcap_12407',['hard_hit_cap',['../classvg_1_1MinimizerMapper.html#aaf577b72776f431ec4dc5faac505322e',1,'vg::MinimizerMapper']]],
- ['hard_5fhit_5fmax_12408',['hard_hit_max',['../classvg_1_1BaseMapper.html#a4e6260be560a0bf2a10cfb409e611e65',1,'vg::BaseMapper']]],
- ['has_5fbuffer_12409',['has_buffer',['../classvg_1_1VcfBuffer.html#a13f0fa2e0b50cd133c117bd1f34715c3',1,'vg::VcfBuffer']]],
- ['has_5fchain_5fvalues_12410',['has_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab62e9f2483533263e5df33fd9c5ad882',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['has_5fcontent_12411',['has_content',['../structvg_1_1BitStringTree_1_1TreeNode.html#ac222ba76d226ad0f457be10e8c8a8b30',1,'vg::BitStringTree::TreeNode']]],
- ['has_5fgrandparent_5fhandle_12412',['has_grandparent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d823f95b1440029399ae07f5d5ce0ec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['has_5fparent_5fhandle_12413',['has_parent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a67fd7b54bbaafc48baee628bc60efad2',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['has_5fposition_12414',['has_position',['../structvg_1_1algorithms_1_1GFAFormatError.html#adb7cfa3f30ee5710575bee189251b473',1,'vg::algorithms::GFAFormatError']]],
- ['has_5freachability_5fedges_12415',['has_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#a77a113d4c5b6b5ca1d7748c1b812e8d3',1,'vg::MultipathAlignmentGraph']]],
- ['has_5fref_12416',['has_ref',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a27de160925943418d3af61d2e3c753dc',1,'vg::Deconstructor::NestingInfo']]],
- ['has_5fsupports_12417',['has_supports',['../classvg_1_1RepresentativeTraversalFinder.html#a7010e7fc85d3b2454bc5e09a504aee23',1,'vg::RepresentativeTraversalFinder']]],
- ['hash_5ftable_5fmax_5fwidth_12418',['HASH_TABLE_MAX_WIDTH',['../minimizer__main_8cpp.html#a6eb56e166572ca736f815a988e170c68',1,'minimizer_main.cpp']]],
- ['hash_5ftable_5fmin_5fwidth_12419',['HASH_TABLE_MIN_WIDTH',['../minimizer__main_8cpp.html#ab0b28c6a5c118414fc8ca717901f2054',1,'minimizer_main.cpp']]],
- ['head_5ftail_5fnodes_12420',['head_tail_nodes',['../classvg_1_1Paths.html#a3fd42adbd3d58aee08370f043dc1643d',1,'vg::Paths']]],
- ['header_12421',['header',['../classvg_1_1Haplotypes.html#ac2671cb0e5d0cdf19a8aa849ec9a2577',1,'vg::Haplotypes']]],
- ['header_5flisteners_12422',['header_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aeedc94c6fcd57b9da7e627c2136eab45',1,'vg::algorithms::GFAParser']]],
- ['header_5fmutex_12423',['header_mutex',['../classvg_1_1HTSWriter.html#af9d539c1312350395949b75010134032',1,'vg::HTSWriter']]],
- ['heading_12424',['heading',['../structvg_1_1subcommand_1_1OptionGroup.html#a93bdf7b70e92b0a05ec270a4fa1495df',1,'vg::subcommand::OptionGroup']]],
- ['help_12425',['help',['../structvg_1_1subcommand_1_1BaseArgSpec.html#abf8444c205dd6aa3c900d111ffdccac0',1,'vg::subcommand::BaseArgSpec']]],
- ['here_12426',['here',['../structvg_1_1Range.html#a518913f6703568c7e704a2723d81e483',1,'vg::Range']]],
- ['het_5fadjustment_12427',['HET_ADJUSTMENT',['../classvg_1_1Recombinator.html#acfb904a0f73882a7d9140efe4e78108e',1,'vg::Recombinator::HET_ADJUSTMENT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a652df2520fd051ebb03fd8494a6e0b11',1,'vg::Recombinator::Parameters::het_adjustment()']]],
- ['het_5fprior_5flogprob_12428',['het_prior_logprob',['../classvg_1_1Genotyper.html#a21799af8d6da86a3bbcfffb1060d27cf',1,'vg::Genotyper']]],
- ['heterozygous_5fprior_5fln_12429',['heterozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ac5782c89f874dd212631d6451ef4b842',1,'vg::FixedGenotypePriorCalculator']]],
- ['hint_5fpaths_12430',['hint_paths',['../classvg_1_1CactusSnarlFinder.html#a380a95f5119b76793da6ba19320a1750',1,'vg::CactusSnarlFinder']]],
- ['hit_5fcap_12431',['hit_cap',['../classvg_1_1MinimizerMapper.html#a1097206776713f059fca80f221b8478c',1,'vg::MinimizerMapper']]],
- ['hit_5fmax_12432',['hit_max',['../classvg_1_1BaseMapper.html#a29b8cec81cc68e9d90405c42fbc8ef64',1,'vg::BaseMapper']]],
- ['hits_12433',['hits',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aa60067efaa8910104760c8d910471a29',1,'vg::MinimizerMapper::Minimizer']]],
- ['homozygous_5fprior_5fln_12434',['homozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ade32a0216586eb9467d476e2880c188b',1,'vg::FixedGenotypePriorCalculator']]],
- ['hts_5fmode_12435',['hts_mode',['../classvg_1_1HTSWriter.html#ab2151e3837dd1503111bf7d1daa1fa56',1,'vg::HTSWriter']]],
- ['htslib_5fheaders_12436',['HTSLIB_HEADERS',['../classvg_1_1Version.html#a73127428a2f929f7e52e2a1e811cf688',1,'vg::Version']]],
- ['htslib_5flibrary_12437',['HTSLIB_LIBRARY',['../classvg_1_1Version.html#a75639877908fb90dcd272674544f3c4e',1,'vg::Version']]]
+ ['handle_12392',['handle',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a2d575dc899c6ef50c6ffe7c374573fb9',1,'vg::io::BlockedGzipInputStream::handle()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#a726e457d2e98e4ca6ffa742a4378949f',1,'vg::io::BlockedGzipOutputStream::handle()']]],
+ ['handle_5fbase_5foption_12393',['handle_base_option',['../classvg_1_1ConfigurableParser.html#a0c39f36cf64d91a336afaac0604ff9f0',1,'vg::ConfigurableParser']]],
+ ['handle_5fgraph_12394',['handle_graph',['../classvg_1_1TargetValueSearch.html#a99dd4b74b5894a228a6d31174ca322de',1,'vg::TargetValueSearch::handle_graph()'],['../classvg_1_1MinDistanceClusterer.html#a6bc0aa3fb6df2824a2fe88f941312f09',1,'vg::MinDistanceClusterer::handle_graph()']]],
+ ['handle_5fidxs_12395',['handle_idxs',['../classvg_1_1JoinedSpliceGraph.html#af3e4ce836a5ba9b208bde5bfe245a97e',1,'vg::JoinedSpliceGraph']]],
+ ['handle_5fval_5frange_12396',['handle_val_range',['../classvg_1_1DagifiedGraph.html#a3cbeb57dc989a7f0963553041c156252',1,'vg::DagifiedGraph::handle_val_range()'],['../classvg_1_1DozeuPinningOverlay.html#a55cd7c6586c7da513046ed232fe95440',1,'vg::DozeuPinningOverlay::handle_val_range()']]],
+ ['handles_12397',['handles',['../classxg_1_1XGPath.html#a2363dd10eb299ca6cc52655e517ad9e1',1,'xg::XGPath']]],
+ ['haplo_5fnode_12398',['haplo_node',['../classvg_1_1PhasedGenome_1_1iterator.html#a1ae0c6a2bdb23511f58dc2986b36117e',1,'vg::PhasedGenome::iterator']]],
+ ['haplo_5fscore_5fprovider_12399',['haplo_score_provider',['../classvg_1_1BaseMapper.html#af69ce88df203124121b71bdfdc6f3694',1,'vg::BaseMapper']]],
+ ['haploid_5fprior_5flogprob_12400',['haploid_prior_logprob',['../classvg_1_1Genotyper.html#a76e36b8cc1f5a8a5522c5ae3f57b5464',1,'vg::Genotyper']]],
+ ['haploid_5fscoring_12401',['haploid_scoring',['../structvg_1_1Recombinator_1_1Parameters.html#a500ad8a5fa909da483c0d84121b80dbd',1,'vg::Recombinator::Parameters']]],
+ ['haplotype_12402',['haplotype',['../structvg_1_1AppendHaplotypeCommand.html#a5dcde06b8eb329a38ae49f612218ad90',1,'vg::AppendHaplotypeCommand::haplotype()'],['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a096fd6e4d5329e8242d4d1a69e95314b',1,'vg::ReplaceSnarlHaplotypeCommand::haplotype()'],['../structvg_1_1RecombinatorFragment.html#a566d752b9670dbf52d1e3998758c1754',1,'vg::RecombinatorFragment::haplotype()']]],
+ ['haplotype_5fconsistency_5fexponent_12403',['haplotype_consistency_exponent',['../classvg_1_1BaseMapper.html#a33465e76a17e2580a6e095f3373239c5',1,'vg::BaseMapper']]],
+ ['haplotype_5fgbwt_5fids_12404',['haplotype_gbwt_ids',['../structvg_1_1TranscriptPath.html#aafc713083bff5a107e2eb70e4d131541',1,'vg::TranscriptPath']]],
+ ['haplotype_5findexer_12405',['haplotype_indexer',['../structGBWTConfig.html#a29a942d7e187971aa7821a5aacb65acd',1,'GBWTConfig']]],
+ ['haplotype_5finput_12406',['haplotype_input',['../structHaplotypesConfig.html#a9bca6d317d27daae42a19413e3e336b2',1,'HaplotypesConfig']]],
+ ['haplotype_5fmatch_12407',['HAPLOTYPE_MATCH',['../classhandlegraph_1_1PathMetadata.html#a3f78e2ed41434be9b84823f5724734e9',1,'handlegraph::PathMetadata']]],
+ ['haplotype_5fnumber_12408',['haplotype_number',['../classvg_1_1PhasedGenome_1_1iterator.html#a3d0bbf671bf2801e44d23fea4da0e397',1,'vg::PhasedGenome::iterator']]],
+ ['haplotype_5foutput_12409',['haplotype_output',['../structHaplotypesConfig.html#a75dc83e4850abb0e9d8542285a844574',1,'HaplotypesConfig']]],
+ ['haplotypes_12410',['haplotypes',['../classvg_1_1SnarlState.html#a98f04166481311709d9a8d3b05b0245e',1,'vg::SnarlState::haplotypes()'],['../classvg_1_1PhasedGenome.html#aa7b2bebc28cc37da09216fca8361c75c',1,'vg::PhasedGenome::haplotypes()'],['../structvg_1_1Recombinator_1_1Statistics.html#a1541408a463fbbcea0e4a3ac08bac9df',1,'vg::Recombinator::Statistics::haplotypes()'],['../classvg_1_1Recombinator.html#a536bca6a31d76be8d90571b24b8ff0e8',1,'vg::Recombinator::haplotypes()'],['../structGBWTConfig.html#a1b5f59745e1b75e70af68ef9e8cd0378',1,'GBWTConfig::haplotypes()']]],
+ ['hard_5fhit_5fcap_12411',['hard_hit_cap',['../classvg_1_1MinimizerMapper.html#aaf577b72776f431ec4dc5faac505322e',1,'vg::MinimizerMapper']]],
+ ['hard_5fhit_5fmax_12412',['hard_hit_max',['../classvg_1_1BaseMapper.html#a4e6260be560a0bf2a10cfb409e611e65',1,'vg::BaseMapper']]],
+ ['has_5fbuffer_12413',['has_buffer',['../classvg_1_1VcfBuffer.html#a13f0fa2e0b50cd133c117bd1f34715c3',1,'vg::VcfBuffer']]],
+ ['has_5fchain_5fvalues_12414',['has_chain_values',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab62e9f2483533263e5df33fd9c5ad882',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['has_5fcontent_12415',['has_content',['../structvg_1_1BitStringTree_1_1TreeNode.html#ac222ba76d226ad0f457be10e8c8a8b30',1,'vg::BitStringTree::TreeNode']]],
+ ['has_5fgrandparent_5fhandle_12416',['has_grandparent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d823f95b1440029399ae07f5d5ce0ec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['has_5fparent_5fhandle_12417',['has_parent_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a67fd7b54bbaafc48baee628bc60efad2',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['has_5fposition_12418',['has_position',['../structvg_1_1algorithms_1_1GFAFormatError.html#adb7cfa3f30ee5710575bee189251b473',1,'vg::algorithms::GFAFormatError']]],
+ ['has_5freachability_5fedges_12419',['has_reachability_edges',['../classvg_1_1MultipathAlignmentGraph.html#a77a113d4c5b6b5ca1d7748c1b812e8d3',1,'vg::MultipathAlignmentGraph']]],
+ ['has_5fref_12420',['has_ref',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a27de160925943418d3af61d2e3c753dc',1,'vg::Deconstructor::NestingInfo']]],
+ ['has_5fsupports_12421',['has_supports',['../classvg_1_1RepresentativeTraversalFinder.html#a7010e7fc85d3b2454bc5e09a504aee23',1,'vg::RepresentativeTraversalFinder']]],
+ ['hash_5ftable_5fmax_5fwidth_12422',['HASH_TABLE_MAX_WIDTH',['../minimizer__main_8cpp.html#a6eb56e166572ca736f815a988e170c68',1,'minimizer_main.cpp']]],
+ ['hash_5ftable_5fmin_5fwidth_12423',['HASH_TABLE_MIN_WIDTH',['../minimizer__main_8cpp.html#ab0b28c6a5c118414fc8ca717901f2054',1,'minimizer_main.cpp']]],
+ ['head_5ftail_5fnodes_12424',['head_tail_nodes',['../classvg_1_1Paths.html#a3fd42adbd3d58aee08370f043dc1643d',1,'vg::Paths']]],
+ ['header_12425',['header',['../classvg_1_1Haplotypes.html#ac2671cb0e5d0cdf19a8aa849ec9a2577',1,'vg::Haplotypes']]],
+ ['header_5flisteners_12426',['header_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#aeedc94c6fcd57b9da7e627c2136eab45',1,'vg::algorithms::GFAParser']]],
+ ['header_5fmutex_12427',['header_mutex',['../classvg_1_1HTSWriter.html#af9d539c1312350395949b75010134032',1,'vg::HTSWriter']]],
+ ['heading_12428',['heading',['../structvg_1_1subcommand_1_1OptionGroup.html#a93bdf7b70e92b0a05ec270a4fa1495df',1,'vg::subcommand::OptionGroup']]],
+ ['help_12429',['help',['../structvg_1_1subcommand_1_1BaseArgSpec.html#abf8444c205dd6aa3c900d111ffdccac0',1,'vg::subcommand::BaseArgSpec']]],
+ ['here_12430',['here',['../structvg_1_1Range.html#a518913f6703568c7e704a2723d81e483',1,'vg::Range']]],
+ ['het_5fadjustment_12431',['HET_ADJUSTMENT',['../classvg_1_1Recombinator.html#acfb904a0f73882a7d9140efe4e78108e',1,'vg::Recombinator::HET_ADJUSTMENT()'],['../structvg_1_1Recombinator_1_1Parameters.html#a652df2520fd051ebb03fd8494a6e0b11',1,'vg::Recombinator::Parameters::het_adjustment()']]],
+ ['het_5fprior_5flogprob_12432',['het_prior_logprob',['../classvg_1_1Genotyper.html#a21799af8d6da86a3bbcfffb1060d27cf',1,'vg::Genotyper']]],
+ ['heterozygous_5fprior_5fln_12433',['heterozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ac5782c89f874dd212631d6451ef4b842',1,'vg::FixedGenotypePriorCalculator']]],
+ ['hint_5fpaths_12434',['hint_paths',['../classvg_1_1CactusSnarlFinder.html#a380a95f5119b76793da6ba19320a1750',1,'vg::CactusSnarlFinder']]],
+ ['hit_5fcap_12435',['hit_cap',['../classvg_1_1MinimizerMapper.html#a1097206776713f059fca80f221b8478c',1,'vg::MinimizerMapper']]],
+ ['hit_5fmax_12436',['hit_max',['../classvg_1_1BaseMapper.html#a29b8cec81cc68e9d90405c42fbc8ef64',1,'vg::BaseMapper']]],
+ ['hits_12437',['hits',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#aa60067efaa8910104760c8d910471a29',1,'vg::MinimizerMapper::Minimizer']]],
+ ['homozygous_5fprior_5fln_12438',['homozygous_prior_ln',['../classvg_1_1FixedGenotypePriorCalculator.html#ade32a0216586eb9467d476e2880c188b',1,'vg::FixedGenotypePriorCalculator']]],
+ ['hts_5fmode_12439',['hts_mode',['../classvg_1_1HTSWriter.html#ab2151e3837dd1503111bf7d1daa1fa56',1,'vg::HTSWriter']]],
+ ['htslib_5fheaders_12440',['HTSLIB_HEADERS',['../classvg_1_1Version.html#a73127428a2f929f7e52e2a1e811cf688',1,'vg::Version']]],
+ ['htslib_5flibrary_12441',['HTSLIB_LIBRARY',['../classvg_1_1Version.html#a75639877908fb90dcd272674544f3c4e',1,'vg::Version']]]
];
diff --git a/search/variables_9.js b/search/variables_9.js
index 7cb7ad9207..ecf21a548a 100644
--- a/search/variables_9.js
+++ b/search/variables_9.js
@@ -1,100 +1,100 @@
var searchData=
[
- ['id_12438',['id',['../structvg_1_1RecombinatorHaplotype.html#a6b099beac53df44fd9ec1d2c88aa8303',1,'vg::RecombinatorHaplotype::id()'],['../structReferenceInterval.html#a197a86ed0f4a316bd59ea19ba28bee0a',1,'ReferenceInterval::id()'],['../structvg_1_1Node.html#af886497fd0ba196f651b5d8f9678b52d',1,'vg::Node::id()']]],
- ['id_5finterval_12439',['id_interval',['../classvg_1_1HaplotypeIndexer.html#af71885cc768549e78097e76e77e90ea8',1,'vg::HaplotypeIndexer']]],
- ['id_5frank_5fmap_12440',['id_rank_map',['../classvg_1_1Viz.html#a5caef0a1bce287d9a5012d36fc1de043',1,'vg::Viz']]],
- ['id_5fto_5fedge_5findices_12441',['id_to_edge_indices',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75ad6266609d35ec42e64abb2a29c7c8',1,'vg::IndexedVG::CacheEntry']]],
- ['id_5fto_5findex_12442',['id_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a1bef2cbc66c4d3d005cab5f79d5cf76e',1,'vg::subcommand::OptionGroup']]],
- ['id_5fto_5fname_12443',['id_to_name',['../classvg_1_1Paths.html#a75a67b0c836eb9a21ae0eee3a213d62c',1,'vg::Paths::id_to_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a0ef46eac291cd354dc89e90d31e87777',1,'vg::algorithms::GFAIDMapInfo::id_to_name()']]],
- ['id_5fto_5fnode_5findex_12444',['id_to_node_index',['../structvg_1_1IndexedVG_1_1CacheEntry.html#aa83d17938b7e420d9c592707721eed35',1,'vg::IndexedVG::CacheEntry']]],
- ['id_5fto_5frank_12445',['id_to_rank',['../classVectorizer.html#aae03497d2de713a68c6d453d32f9cf4a',1,'Vectorizer']]],
- ['identifier_12446',['identifier',['../classvg_1_1IndexFile.html#a0b5a76c50d22d7325f10fa7b881338b9',1,'vg::IndexFile']]],
- ['identity_12447',['identity',['../structvg_1_1Alignment.html#a06341663199b9893a9f2b288a768cfe3',1,'vg::Alignment']]],
- ['identity_5fweight_12448',['identity_weight',['../classvg_1_1Mapper.html#aabc9f9048a56b9b52fdf8d5271f7f60d',1,'vg::Mapper']]],
- ['ignore_5fmissing_5fcontigs_12449',['ignore_missing_contigs',['../classvg_1_1VariantAdder.html#a7a8bd35e29cbd240fd0f2a7156630943',1,'vg::VariantAdder']]],
- ['image_5fheight_12450',['image_height',['../classvg_1_1Viz.html#ab34e44856e2c4d64ddf4d11aac46e5f6',1,'vg::Viz']]],
- ['image_5fwidth_12451',['image_width',['../classvg_1_1Viz.html#a5dfce1ae146aff9f2aead08e304833bd',1,'vg::Viz']]],
- ['imperfect_5fpairs_5fto_5fretry_12452',['imperfect_pairs_to_retry',['../classvg_1_1Mapper.html#a05444e0f52bddbe50304289a34d0b551',1,'vg::Mapper']]],
- ['in_12453',['in',['../classvg_1_1GFFReader.html#a349dc0d2a38d966c4c4c265ac056346f',1,'vg::GFFReader']]],
- ['in_5ffrom_12454',['in_from',['../classvg_1_1ExtraNodeGraph.html#a4b2d9d6b68d55c26d367ad717b13da15',1,'vg::ExtraNodeGraph']]],
- ['in_5fuse_12455',['in_use',['../structvg_1_1GBWTHandler.html#a1fb3dbca40a78ec37d8e04eef008bd70',1,'vg::GBWTHandler::in_use()'],['../structGraphHandler.html#a44741d974047430e73a3589c74659939',1,'GraphHandler::in_use()']]],
- ['include_5fchildren_12456',['include_children',['../classvg_1_1SparseUnionFind.html#acf3b218b8e2fee9fa73df6d4071eb0da',1,'vg::SparseUnionFind']]],
- ['include_5fendpoints_12457',['include_endpoints',['../classvg_1_1VCFTraversalFinder.html#a27189437955d4b5f8b8ca92433c8fac2',1,'vg::VCFTraversalFinder']]],
- ['include_5ffull_5flength_5fbonuses_12458',['include_full_length_bonuses',['../classvg_1_1Mapper.html#a9472c75cceb3382b70bbd27bfbc4a894',1,'vg::Mapper']]],
- ['include_5fnamed_5fpaths_12459',['include_named_paths',['../structGBWTConfig.html#aedd88b893790abdf53541629fdfdbcd0',1,'GBWTConfig']]],
- ['include_5fnested_12460',['include_nested',['../classvg_1_1VCFOutputCaller.html#afb5fc9a52eb170a49d6f77aad30e13f7',1,'vg::VCFOutputCaller']]],
- ['include_5freference_12461',['include_reference',['../structvg_1_1Recombinator_1_1Parameters.html#a0f3128635c9d1c82a996e4ae060b0072',1,'vg::Recombinator::Parameters']]],
- ['include_5freversing_5ftraversals_12462',['include_reversing_traversals',['../classvg_1_1ExhaustiveTraversalFinder.html#a1904edecc299fc004b02ce44ea9301f8',1,'vg::ExhaustiveTraversalFinder']]],
- ['indel_5ferror_5fprop_12463',['indel_error_prop',['../classvg_1_1NGSSimulator.html#ae16494345e539020ebd09b0998500559',1,'vg::NGSSimulator']]],
- ['indel_5fpoly_5frate_12464',['indel_poly_rate',['../classvg_1_1NGSSimulator.html#af84310145f8991c92d48684a0664ba8e',1,'vg::NGSSimulator']]],
- ['index_12465',['index',['../structhaplo_1_1linear__haplo__structure.html#a79e51544898895192d319f95e95cf2f1',1,'haplo::linear_haplo_structure::index()'],['../classhaplo_1_1GBWTScoreProvider.html#ae24f0ba2be7fdc64cb0d0a33123e41ad',1,'haplo::GBWTScoreProvider::index()'],['../classhaplo_1_1LinearScoreProvider.html#a1ceb289752fb8e83c13e52e82bea393b',1,'haplo::LinearScoreProvider::index()'],['../classvg_1_1IndexedVG.html#a4f618ecb46d596aa053450a4de13e990',1,'vg::IndexedVG::index()']]],
- ['index_5fof_12466',['index_of',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a622e1fefb7e7aa8977623b183ea9b457',1,'vg::DozeuInterface::OrderedGraph']]],
- ['index_5fregistry_12467',['index_registry',['../classvg_1_1IndexRegistry.html#a866b81f28ca2fba68aff7de143f35b9b',1,'vg::IndexRegistry']]],
- ['indexes_12468',['indexes',['../classvg_1_1GraphSynchronizer.html#a1127fed39b1d4775bf03ada4f87b23b4',1,'vg::GraphSynchronizer::indexes()'],['../classvg_1_1RewindPlanException.html#abf38371b59f5d1ebc55806967bc3b12b',1,'vg::RewindPlanException::indexes()'],['../structvg_1_1VectorView.html#a54433c9bb742729c00a4d48adaa88015',1,'vg::VectorView::indexes()']]],
- ['inline_5fitems_12469',['inline_items',['../structvg_1_1MatchPos_1_1PathList.html#abffe04434a41c9f8dfcb85ef8d3d26f9',1,'vg::MatchPos::PathList']]],
- ['inner_5fvalue_12470',['inner_value',['../structhaplo_1_1haplo__DP__rectangle.html#a68817623682eb451f4a5a42a8ae8ef8a',1,'haplo::haplo_DP_rectangle']]],
- ['input_12471',['input',['../structvg_1_1io_1_1hFILE__cppstream.html#a301bcdddd00f4d40033b4ca94691f9a6',1,'vg::io::hFILE_cppstream']]],
- ['input_5fdefault_12472',['INPUT_DEFAULT',['../convert__main_8cpp.html#a9427417f4ca764d74efec8fcaf9e2ca8',1,'convert_main.cpp']]],
- ['input_5ffilenames_12473',['input_filenames',['../structGBWTConfig.html#a106dff4206c7414bf053f9c2405a0739',1,'GBWTConfig']]],
- ['input_5fin_5fprogress_12474',['input_in_progress',['../classvg_1_1Funnel.html#a755941e4c7988487e539256c16b507bb',1,'vg::Funnel']]],
- ['input_5fvcf_12475',['input_vcf',['../classvg_1_1VCFGenotyper.html#a3fea7ea6e20998a5de5e95776e7f67bb',1,'vg::VCFGenotyper']]],
- ['inputs_12476',['inputs',['../structvg_1_1IndexRecipe.html#aa23088153a85cc207ab3901afcd1ff5b',1,'vg::IndexRecipe::inputs()'],['../classvg_1_1InsufficientInputException.html#a8798c889fb558ee1c9042e10e7f136e2',1,'vg::InsufficientInputException::inputs()']]],
- ['inputs_5fas_5fjobs_12477',['inputs_as_jobs',['../structGBWTConfig.html#ac12bbd2e3c10bdaf3ee07de4191c88d6',1,'GBWTConfig']]],
- ['insert_5fcol_12478',['insert_col',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a9a17e99af8ce2b7992fddef79c4e8b18',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['insert_5fmean_12479',['insert_mean',['../classvg_1_1Filter.html#ab8a36803dfa97e61678756f7b7a3a31c',1,'vg::Filter']]],
- ['insert_5frow_12480',['insert_row',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ade4c512c3713ac162359ed6d9207537d',1,'vg::BandedGlobalAligner::BAMatrix']]],
- ['insert_5fsd_12481',['insert_sd',['../classvg_1_1Filter.html#ac302d7b67d23285ad615d864197a9e1b',1,'vg::Filter']]],
- ['insertion_5fbias_5flarge_12482',['insertion_bias_large',['../classvg_1_1PoissonSupportSnarlCaller.html#a82d1c5780e74107618f3e50d7085f38e',1,'vg::PoissonSupportSnarlCaller']]],
- ['insertion_5fbias_5fsmall_12483',['insertion_bias_small',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a5120550fa398555a1a414717469664',1,'vg::PoissonSupportSnarlCaller']]],
- ['insertion_5fthreshold_12484',['insertion_threshold',['../classvg_1_1PoissonSupportSnarlCaller.html#a7787ef040764a33043fdbf3ba2f80509',1,'vg::PoissonSupportSnarlCaller']]],
- ['insertions_12485',['INSERTIONS',['../structvg_1_1WFANode.html#a99807b74ee148f30fae2549a8aa54339',1,'vg::WFANode::INSERTIONS()'],['../structvg_1_1InsertHaplotypeCommand.html#a5dfd52deff7c8c3fc76fa7b4dee45032',1,'vg::InsertHaplotypeCommand::insertions()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a44ad82bbfa6098c648bc1a6fcd61d102',1,'vg::ReplaceLocalHaplotypeCommand::insertions()']]],
- ['int_5fis_5finc_12486',['int_is_inc',['../structhaplo_1_1haplo__DP__rectangle.html#a45856786beeaa7213275fcaf3eaa6878',1,'haplo::haplo_DP_rectangle']]],
- ['int_5fis_5fnonnegative_12487',['int_is_nonnegative',['../namespacevg_1_1subcommand.html#aafa3ba89747f1886e118e7d6421078e3',1,'vg::subcommand']]],
- ['interleaved_12488',['interleaved',['../classvg_1_1ReadFilter.html#a3d7c97fa34473eb5b1e3bce2dd64d6eb',1,'vg::ReadFilter']]],
- ['internal_5fid_5fmap_12489',['internal_id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a5bdb46afdb654469e3dc42fdfbe048ab',1,'vg::algorithms::GFAParser']]],
- ['internal_5fscore_12490',['internal_score',['../structvg_1_1GaplessExtension.html#a0045e76ebc1c911201d6744d6c20e50a',1,'vg::GaplessExtension']]],
- ['interval_5fend_12491',['interval_end',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#af58f43315b7386134bf8a034c0c39694',1,'vg::ZipCodeForest::interval_state_t']]],
- ['interval_5fstart_12492',['interval_start',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a7a2843b5a5a25b77f55ddb80998028bd',1,'vg::ZipCodeForest::interval_state_t']]],
- ['intervals_5fto_5fprocess_12493',['intervals_to_process',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#aafe37939d028547b7ae3ee68fda10ed1',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['inverse_12494',['inverse',['../classvg_1_1Filter.html#a05e7274611008cdd5b89d1fa81605882',1,'vg::Filter::inverse()'],['../classvg_1_1VectorViewInverse.html#a54a9cc36f21c2562f2f0836e5a040773',1,'vg::VectorViewInverse::inverse()']]],
- ['invocations_12495',['invocations',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af75c21b33a10d3ddc7f36f7567cc1aae',1,'vg::MinimizerMapper::aligner_stats_t']]],
- ['irregular_5fsnarl_5fdistance_5fleft_5fend_5foffset_12496',['IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET',['../classvg_1_1ZipCode.html#a0c43ecf172f0ddde09366b3facdad4f9',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fdistance_5fleft_5fstart_5foffset_12497',['IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET',['../classvg_1_1ZipCode.html#a81836246de1e66c3febd653cd0525988',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fdistance_5fright_5fend_5foffset_12498',['IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET',['../classvg_1_1ZipCode.html#a2cccc444095b38bd7e73ff6e55f930be',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fdistance_5fright_5fstart_5foffset_12499',['IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET',['../classvg_1_1ZipCode.html#acdcb0967e1dd6d01833a7fc66f6ef64b',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5frecord_5foffset_12500',['IRREGULAR_SNARL_RECORD_OFFSET',['../classvg_1_1ZipCode.html#a8f5228bda68297b861a839396970f5bc',1,'vg::ZipCode']]],
- ['irregular_5fsnarl_5fsize_12501',['IRREGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a8ec98e693ea6d5c1972479f9066ef405',1,'vg::ZipCode']]],
- ['is_5falt_12502',['is_alt',['../classvg_1_1Paths.html#a3e8fd05a0a584cbae2f2919b5ab98e4d',1,'vg::Paths']]],
- ['is_5fchain_12503',['is_chain',['../structvg_1_1ZipCode_1_1decoder__t.html#abcbad7044eb813105e2cadefbf5a05ff',1,'vg::ZipCode::decoder_t']]],
- ['is_5fchecked_5fin_12504',['is_checked_in',['../structvg_1_1Watchdog_1_1thread__state__t.html#aae7887d9b7548a028a6b7271aabd44eb',1,'vg::Watchdog::thread_state_t']]],
- ['is_5fcircular_12505',['is_circular',['../classxg_1_1XGPath.html#a4cc65b6cfdbd12f6220dde5a716fd345',1,'xg::XGPath::is_circular()'],['../structvg_1_1Path.html#ad04d3a1745f479f32b4a4358bec17c8f',1,'vg::Path::is_circular()']]],
- ['is_5fcompacted_12506',['is_compacted',['../classvg_1_1Packer.html#aa7f90bbde45e8487029a424392b653ad',1,'vg::Packer']]],
- ['is_5fend_12507',['is_end',['../structvg_1_1CactusSide.html#a960c0e9a2c2dc004aac017030f6ad805',1,'vg::CactusSide::is_end()'],['../classvg_1_1NodeSide.html#a1493cac020ed0c9b1cbd37e2a99eb9b5',1,'vg::NodeSide::is_end()']]],
- ['is_5ffixed_12508',['is_fixed',['../classvg_1_1FragmentLengthDistribution.html#adcfca733e40d173dcbaf2e8c617c74ec',1,'vg::FragmentLengthDistribution']]],
- ['is_5fhaplotype_12509',['is_haplotype',['../structvg_1_1TranscriptPath.html#ac4cca688d7aa76da99a285b769b2cab8',1,'vg::TranscriptPath']]],
- ['is_5finterval_12510',['is_interval',['../structgafkluge_1_1GafStep.html#a681b0a984c816cf87468a4143b740a90',1,'gafkluge::GafStep']]],
- ['is_5flooping_5fchain_12511',['is_looping_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#afbb04850e68908d3802cb5164563577b',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['is_5fordered_12512',['is_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a313e2b7266bdfbe3ee864d80a5e7b67c',1,'vg::ZipCodeForest::interval_state_t']]],
- ['is_5fphased_12513',['is_phased',['../structvg_1_1Genotype.html#a7aceacf9d5e3def3d6e675ef34906aab',1,'vg::Genotype']]],
- ['is_5freference_12514',['is_reference',['../structvg_1_1TranscriptPath.html#a61efb7a65128254f6039323ca0507e95',1,'vg::TranscriptPath']]],
- ['is_5frend_12515',['is_rend',['../structvg_1_1ChainIterator.html#adb9db0a0ea4cac8bca359c97d293aaa9',1,'vg::ChainIterator']]],
- ['is_5frepetitive_12516',['is_repetitive',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a4ad3bbc4813727c0af8fa25f18d02512',1,'vg::MinimizerMapper::Minimizer']]],
- ['is_5freverse_12517',['is_reverse',['../structvg_1_1Genotyper_1_1Affinity.html#ae1707128484386f3a20eb8c6a8f9ec95',1,'vg::Genotyper::Affinity::is_reverse()'],['../structvg_1_1Transcript.html#ab7c8b040643b29e7213839f95390625f',1,'vg::Transcript::is_reverse()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a54539368bfd495fe1ab7cbcd60f6d528',1,'vg::ZipCodeTree::oriented_seed_t::is_reverse()'],['../structgafkluge_1_1GafStep.html#a18b7374dcc0b3a2386dd6090fbb7d8fe',1,'gafkluge::GafStep::is_reverse()'],['../structvg_1_1Position.html#aeb715b329bd7371ca380a2f2abdcbd13',1,'vg::Position::is_reverse()']]],
- ['is_5freverse_5fordered_12518',['is_reverse_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae6d743daadce96f680039a166503bee9',1,'vg::ZipCodeForest::interval_state_t']]],
- ['is_5freversed_12519',['is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a781979f7c9ed42859087a19c07be8898',1,'vg::ZipCode::node_code_t::is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8c08c6dddaf7f3d1e75964c6bf701c3d',1,'vg::ZipCode::snarl_code_t::is_reversed()'],['../structvg_1_1MIPayload.html#a391d9d5e1cd44eccb39a6a31f56a6890',1,'vg::MIPayload::is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ab491085e63a9027e460098d5bc3f98ca',1,'vg::ZipCodeTree::tree_item_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af4a9de3c328470293caa0d958094201e',1,'vg::ZipCodeForest::child_info_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae0f46b456027c5360dad34c0480c8ebb',1,'vg::ZipCodeForest::interval_state_t::is_reversed()']]],
- ['is_5freversed_5fin_5fparent_12520',['is_reversed_in_parent',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a81a6e5692e0b2100e9204bdb48454dd6',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['is_5fsecondary_12521',['is_secondary',['../structvg_1_1Alignment.html#a59a4b8c7367fb468e46bcf6ae292888f',1,'vg::Alignment']]],
- ['is_5fseed_12522',['is_seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab29219e6df18063f714a379f5d769cf7',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['is_5fstable_12523',['is_stable',['../structgafkluge_1_1GafStep.html#ad41f5cafc50a114daeec6b0cf08101eb',1,'gafkluge::GafStep']]],
- ['is_5ftrivial_5fchain_12524',['is_trivial_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a8e92509271514f3510eabdfbe7da9e1d',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::is_trivial_chain()'],['../structvg_1_1MIPayload.html#a9a1ab910b382a0ec41e12036f9b8ae04',1,'vg::MIPayload::is_trivial_chain()']]],
- ['is_5fvg_12525',['is_vg',['../classvg_1_1LegacyCaller.html#a80d266e926310b4def5ac48e3211029f',1,'vg::LegacyCaller']]],
- ['isforward_12526',['isForward',['../structvg_1_1BREAKPOINT.html#a3179531d48993e05d802907b730e1631',1,'vg::BREAKPOINT']]],
- ['issue_5furl_12527',['ISSUE_URL',['../namespacevg.html#ae77436235694e5e661c74799ab326d0b',1,'vg']]],
- ['it_12528',['it',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1bc7243523f7c66a5d86bbe6b28176af',1,'vg::ZipCodeTree::iterator::it()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3ab48e9f50bb0651c4eef055721366ea',1,'vg::ZipCodeTree::reverse_iterator::it()']]],
- ['item_5fbonus_12529',['item_bonus',['../classvg_1_1MinimizerMapper.html#a7646fc428d4eb41fb022dd9c61afa687',1,'vg::MinimizerMapper']]],
- ['item_5fcount_12530',['item_count',['../structvg_1_1MatchPos_1_1PathList.html#ad3ebb006eb120b2934d64cece179d0e8',1,'vg::MatchPos::PathList']]],
- ['item_5fscale_12531',['item_scale',['../classvg_1_1MinimizerMapper.html#af637ac92b12ecfebb815cedb5d56f58e',1,'vg::MinimizerMapper']]],
- ['item_5fvo_12532',['item_vo',['../classvg_1_1io_1_1MessageIterator.html#a1f58abce5de3c8f71a82e689c0170c49',1,'vg::io::MessageIterator']]],
- ['items_12533',['items',['../structvg_1_1Funnel_1_1Stage.html#a787bab13fd8bd1bccb1ac8e7821688c6',1,'vg::Funnel::Stage::items()'],['../structvg_1_1VectorView.html#a1d1194d5eac47211eda065d3dc6312ef',1,'vg::VectorView::items()']]],
- ['iteratee_12534',['iteratee',['../classvg_1_1ShuffledPairs_1_1iterator.html#a09d41523db4b9b9c6cebb02ecf7bfa3c',1,'vg::ShuffledPairs::iterator']]]
+ ['id_12442',['id',['../structvg_1_1RecombinatorHaplotype.html#a6b099beac53df44fd9ec1d2c88aa8303',1,'vg::RecombinatorHaplotype::id()'],['../structReferenceInterval.html#a197a86ed0f4a316bd59ea19ba28bee0a',1,'ReferenceInterval::id()'],['../structvg_1_1Node.html#af886497fd0ba196f651b5d8f9678b52d',1,'vg::Node::id()']]],
+ ['id_5finterval_12443',['id_interval',['../classvg_1_1HaplotypeIndexer.html#af71885cc768549e78097e76e77e90ea8',1,'vg::HaplotypeIndexer']]],
+ ['id_5frank_5fmap_12444',['id_rank_map',['../classvg_1_1Viz.html#a5caef0a1bce287d9a5012d36fc1de043',1,'vg::Viz']]],
+ ['id_5fto_5fedge_5findices_12445',['id_to_edge_indices',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a75ad6266609d35ec42e64abb2a29c7c8',1,'vg::IndexedVG::CacheEntry']]],
+ ['id_5fto_5findex_12446',['id_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a1bef2cbc66c4d3d005cab5f79d5cf76e',1,'vg::subcommand::OptionGroup']]],
+ ['id_5fto_5fname_12447',['id_to_name',['../classvg_1_1Paths.html#a75a67b0c836eb9a21ae0eee3a213d62c',1,'vg::Paths::id_to_name()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a0ef46eac291cd354dc89e90d31e87777',1,'vg::algorithms::GFAIDMapInfo::id_to_name()']]],
+ ['id_5fto_5fnode_5findex_12448',['id_to_node_index',['../structvg_1_1IndexedVG_1_1CacheEntry.html#aa83d17938b7e420d9c592707721eed35',1,'vg::IndexedVG::CacheEntry']]],
+ ['id_5fto_5frank_12449',['id_to_rank',['../classVectorizer.html#aae03497d2de713a68c6d453d32f9cf4a',1,'Vectorizer']]],
+ ['identifier_12450',['identifier',['../classvg_1_1IndexFile.html#a0b5a76c50d22d7325f10fa7b881338b9',1,'vg::IndexFile']]],
+ ['identity_12451',['identity',['../structvg_1_1Alignment.html#a06341663199b9893a9f2b288a768cfe3',1,'vg::Alignment']]],
+ ['identity_5fweight_12452',['identity_weight',['../classvg_1_1Mapper.html#aabc9f9048a56b9b52fdf8d5271f7f60d',1,'vg::Mapper']]],
+ ['ignore_5fmissing_5fcontigs_12453',['ignore_missing_contigs',['../classvg_1_1VariantAdder.html#a7a8bd35e29cbd240fd0f2a7156630943',1,'vg::VariantAdder']]],
+ ['image_5fheight_12454',['image_height',['../classvg_1_1Viz.html#ab34e44856e2c4d64ddf4d11aac46e5f6',1,'vg::Viz']]],
+ ['image_5fwidth_12455',['image_width',['../classvg_1_1Viz.html#a5dfce1ae146aff9f2aead08e304833bd',1,'vg::Viz']]],
+ ['imperfect_5fpairs_5fto_5fretry_12456',['imperfect_pairs_to_retry',['../classvg_1_1Mapper.html#a05444e0f52bddbe50304289a34d0b551',1,'vg::Mapper']]],
+ ['in_12457',['in',['../classvg_1_1GFFReader.html#a349dc0d2a38d966c4c4c265ac056346f',1,'vg::GFFReader']]],
+ ['in_5ffrom_12458',['in_from',['../classvg_1_1ExtraNodeGraph.html#a4b2d9d6b68d55c26d367ad717b13da15',1,'vg::ExtraNodeGraph']]],
+ ['in_5fuse_12459',['in_use',['../structvg_1_1GBWTHandler.html#a1fb3dbca40a78ec37d8e04eef008bd70',1,'vg::GBWTHandler::in_use()'],['../structGraphHandler.html#a44741d974047430e73a3589c74659939',1,'GraphHandler::in_use()']]],
+ ['include_5fchildren_12460',['include_children',['../classvg_1_1SparseUnionFind.html#acf3b218b8e2fee9fa73df6d4071eb0da',1,'vg::SparseUnionFind']]],
+ ['include_5fendpoints_12461',['include_endpoints',['../classvg_1_1VCFTraversalFinder.html#a27189437955d4b5f8b8ca92433c8fac2',1,'vg::VCFTraversalFinder']]],
+ ['include_5ffull_5flength_5fbonuses_12462',['include_full_length_bonuses',['../classvg_1_1Mapper.html#a9472c75cceb3382b70bbd27bfbc4a894',1,'vg::Mapper']]],
+ ['include_5fnamed_5fpaths_12463',['include_named_paths',['../structGBWTConfig.html#aedd88b893790abdf53541629fdfdbcd0',1,'GBWTConfig']]],
+ ['include_5fnested_12464',['include_nested',['../classvg_1_1VCFOutputCaller.html#afb5fc9a52eb170a49d6f77aad30e13f7',1,'vg::VCFOutputCaller']]],
+ ['include_5freference_12465',['include_reference',['../structvg_1_1Recombinator_1_1Parameters.html#a0f3128635c9d1c82a996e4ae060b0072',1,'vg::Recombinator::Parameters']]],
+ ['include_5freversing_5ftraversals_12466',['include_reversing_traversals',['../classvg_1_1ExhaustiveTraversalFinder.html#a1904edecc299fc004b02ce44ea9301f8',1,'vg::ExhaustiveTraversalFinder']]],
+ ['indel_5ferror_5fprop_12467',['indel_error_prop',['../classvg_1_1NGSSimulator.html#ae16494345e539020ebd09b0998500559',1,'vg::NGSSimulator']]],
+ ['indel_5fpoly_5frate_12468',['indel_poly_rate',['../classvg_1_1NGSSimulator.html#af84310145f8991c92d48684a0664ba8e',1,'vg::NGSSimulator']]],
+ ['index_12469',['index',['../structhaplo_1_1linear__haplo__structure.html#a79e51544898895192d319f95e95cf2f1',1,'haplo::linear_haplo_structure::index()'],['../classhaplo_1_1GBWTScoreProvider.html#ae24f0ba2be7fdc64cb0d0a33123e41ad',1,'haplo::GBWTScoreProvider::index()'],['../classhaplo_1_1LinearScoreProvider.html#a1ceb289752fb8e83c13e52e82bea393b',1,'haplo::LinearScoreProvider::index()'],['../classvg_1_1IndexedVG.html#a4f618ecb46d596aa053450a4de13e990',1,'vg::IndexedVG::index()']]],
+ ['index_5fof_12470',['index_of',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#a622e1fefb7e7aa8977623b183ea9b457',1,'vg::DozeuInterface::OrderedGraph']]],
+ ['index_5fregistry_12471',['index_registry',['../classvg_1_1IndexRegistry.html#a866b81f28ca2fba68aff7de143f35b9b',1,'vg::IndexRegistry']]],
+ ['indexes_12472',['indexes',['../classvg_1_1GraphSynchronizer.html#a1127fed39b1d4775bf03ada4f87b23b4',1,'vg::GraphSynchronizer::indexes()'],['../classvg_1_1RewindPlanException.html#abf38371b59f5d1ebc55806967bc3b12b',1,'vg::RewindPlanException::indexes()'],['../structvg_1_1VectorView.html#a54433c9bb742729c00a4d48adaa88015',1,'vg::VectorView::indexes()']]],
+ ['inline_5fitems_12473',['inline_items',['../structvg_1_1MatchPos_1_1PathList.html#abffe04434a41c9f8dfcb85ef8d3d26f9',1,'vg::MatchPos::PathList']]],
+ ['inner_5fvalue_12474',['inner_value',['../structhaplo_1_1haplo__DP__rectangle.html#a68817623682eb451f4a5a42a8ae8ef8a',1,'haplo::haplo_DP_rectangle']]],
+ ['input_12475',['input',['../structvg_1_1io_1_1hFILE__cppstream.html#a301bcdddd00f4d40033b4ca94691f9a6',1,'vg::io::hFILE_cppstream']]],
+ ['input_5fdefault_12476',['INPUT_DEFAULT',['../convert__main_8cpp.html#a9427417f4ca764d74efec8fcaf9e2ca8',1,'convert_main.cpp']]],
+ ['input_5ffilenames_12477',['input_filenames',['../structGBWTConfig.html#a106dff4206c7414bf053f9c2405a0739',1,'GBWTConfig']]],
+ ['input_5fin_5fprogress_12478',['input_in_progress',['../classvg_1_1Funnel.html#a755941e4c7988487e539256c16b507bb',1,'vg::Funnel']]],
+ ['input_5fvcf_12479',['input_vcf',['../classvg_1_1VCFGenotyper.html#a3fea7ea6e20998a5de5e95776e7f67bb',1,'vg::VCFGenotyper']]],
+ ['inputs_12480',['inputs',['../structvg_1_1IndexRecipe.html#aa23088153a85cc207ab3901afcd1ff5b',1,'vg::IndexRecipe::inputs()'],['../classvg_1_1InsufficientInputException.html#a8798c889fb558ee1c9042e10e7f136e2',1,'vg::InsufficientInputException::inputs()']]],
+ ['inputs_5fas_5fjobs_12481',['inputs_as_jobs',['../structGBWTConfig.html#ac12bbd2e3c10bdaf3ee07de4191c88d6',1,'GBWTConfig']]],
+ ['insert_5fcol_12482',['insert_col',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a9a17e99af8ce2b7992fddef79c4e8b18',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['insert_5fmean_12483',['insert_mean',['../classvg_1_1Filter.html#ab8a36803dfa97e61678756f7b7a3a31c',1,'vg::Filter']]],
+ ['insert_5frow_12484',['insert_row',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ade4c512c3713ac162359ed6d9207537d',1,'vg::BandedGlobalAligner::BAMatrix']]],
+ ['insert_5fsd_12485',['insert_sd',['../classvg_1_1Filter.html#ac302d7b67d23285ad615d864197a9e1b',1,'vg::Filter']]],
+ ['insertion_5fbias_5flarge_12486',['insertion_bias_large',['../classvg_1_1PoissonSupportSnarlCaller.html#a82d1c5780e74107618f3e50d7085f38e',1,'vg::PoissonSupportSnarlCaller']]],
+ ['insertion_5fbias_5fsmall_12487',['insertion_bias_small',['../classvg_1_1PoissonSupportSnarlCaller.html#a4a5120550fa398555a1a414717469664',1,'vg::PoissonSupportSnarlCaller']]],
+ ['insertion_5fthreshold_12488',['insertion_threshold',['../classvg_1_1PoissonSupportSnarlCaller.html#a7787ef040764a33043fdbf3ba2f80509',1,'vg::PoissonSupportSnarlCaller']]],
+ ['insertions_12489',['INSERTIONS',['../structvg_1_1WFANode.html#a99807b74ee148f30fae2549a8aa54339',1,'vg::WFANode::INSERTIONS()'],['../structvg_1_1InsertHaplotypeCommand.html#a5dfd52deff7c8c3fc76fa7b4dee45032',1,'vg::InsertHaplotypeCommand::insertions()'],['../structvg_1_1ReplaceLocalHaplotypeCommand.html#a44ad82bbfa6098c648bc1a6fcd61d102',1,'vg::ReplaceLocalHaplotypeCommand::insertions()']]],
+ ['int_5fis_5finc_12490',['int_is_inc',['../structhaplo_1_1haplo__DP__rectangle.html#a45856786beeaa7213275fcaf3eaa6878',1,'haplo::haplo_DP_rectangle']]],
+ ['int_5fis_5fnonnegative_12491',['int_is_nonnegative',['../namespacevg_1_1subcommand.html#aafa3ba89747f1886e118e7d6421078e3',1,'vg::subcommand']]],
+ ['interleaved_12492',['interleaved',['../classvg_1_1ReadFilter.html#a3d7c97fa34473eb5b1e3bce2dd64d6eb',1,'vg::ReadFilter']]],
+ ['internal_5fid_5fmap_12493',['internal_id_map',['../classvg_1_1algorithms_1_1GFAParser.html#a5bdb46afdb654469e3dc42fdfbe048ab',1,'vg::algorithms::GFAParser']]],
+ ['internal_5fscore_12494',['internal_score',['../structvg_1_1GaplessExtension.html#a0045e76ebc1c911201d6744d6c20e50a',1,'vg::GaplessExtension']]],
+ ['interval_5fend_12495',['interval_end',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#af58f43315b7386134bf8a034c0c39694',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['interval_5fstart_12496',['interval_start',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a7a2843b5a5a25b77f55ddb80998028bd',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['intervals_5fto_5fprocess_12497',['intervals_to_process',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#aafe37939d028547b7ae3ee68fda10ed1',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['inverse_12498',['inverse',['../classvg_1_1Filter.html#a05e7274611008cdd5b89d1fa81605882',1,'vg::Filter::inverse()'],['../classvg_1_1VectorViewInverse.html#a54a9cc36f21c2562f2f0836e5a040773',1,'vg::VectorViewInverse::inverse()']]],
+ ['invocations_12499',['invocations',['../structvg_1_1MinimizerMapper_1_1aligner__stats__t.html#af75c21b33a10d3ddc7f36f7567cc1aae',1,'vg::MinimizerMapper::aligner_stats_t']]],
+ ['irregular_5fsnarl_5fdistance_5fleft_5fend_5foffset_12500',['IRREGULAR_SNARL_DISTANCE_LEFT_END_OFFSET',['../classvg_1_1ZipCode.html#a0c43ecf172f0ddde09366b3facdad4f9',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fdistance_5fleft_5fstart_5foffset_12501',['IRREGULAR_SNARL_DISTANCE_LEFT_START_OFFSET',['../classvg_1_1ZipCode.html#a81836246de1e66c3febd653cd0525988',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fdistance_5fright_5fend_5foffset_12502',['IRREGULAR_SNARL_DISTANCE_RIGHT_END_OFFSET',['../classvg_1_1ZipCode.html#a2cccc444095b38bd7e73ff6e55f930be',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fdistance_5fright_5fstart_5foffset_12503',['IRREGULAR_SNARL_DISTANCE_RIGHT_START_OFFSET',['../classvg_1_1ZipCode.html#acdcb0967e1dd6d01833a7fc66f6ef64b',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5frecord_5foffset_12504',['IRREGULAR_SNARL_RECORD_OFFSET',['../classvg_1_1ZipCode.html#a8f5228bda68297b861a839396970f5bc',1,'vg::ZipCode']]],
+ ['irregular_5fsnarl_5fsize_12505',['IRREGULAR_SNARL_SIZE',['../classvg_1_1ZipCode.html#a8ec98e693ea6d5c1972479f9066ef405',1,'vg::ZipCode']]],
+ ['is_5falt_12506',['is_alt',['../classvg_1_1Paths.html#a3e8fd05a0a584cbae2f2919b5ab98e4d',1,'vg::Paths']]],
+ ['is_5fchain_12507',['is_chain',['../structvg_1_1ZipCode_1_1decoder__t.html#abcbad7044eb813105e2cadefbf5a05ff',1,'vg::ZipCode::decoder_t']]],
+ ['is_5fchecked_5fin_12508',['is_checked_in',['../structvg_1_1Watchdog_1_1thread__state__t.html#aae7887d9b7548a028a6b7271aabd44eb',1,'vg::Watchdog::thread_state_t']]],
+ ['is_5fcircular_12509',['is_circular',['../classxg_1_1XGPath.html#a4cc65b6cfdbd12f6220dde5a716fd345',1,'xg::XGPath::is_circular()'],['../structvg_1_1Path.html#ad04d3a1745f479f32b4a4358bec17c8f',1,'vg::Path::is_circular()']]],
+ ['is_5fcompacted_12510',['is_compacted',['../classvg_1_1Packer.html#aa7f90bbde45e8487029a424392b653ad',1,'vg::Packer']]],
+ ['is_5fend_12511',['is_end',['../structvg_1_1CactusSide.html#a960c0e9a2c2dc004aac017030f6ad805',1,'vg::CactusSide::is_end()'],['../classvg_1_1NodeSide.html#a1493cac020ed0c9b1cbd37e2a99eb9b5',1,'vg::NodeSide::is_end()']]],
+ ['is_5ffixed_12512',['is_fixed',['../classvg_1_1FragmentLengthDistribution.html#adcfca733e40d173dcbaf2e8c617c74ec',1,'vg::FragmentLengthDistribution']]],
+ ['is_5fhaplotype_12513',['is_haplotype',['../structvg_1_1TranscriptPath.html#ac4cca688d7aa76da99a285b769b2cab8',1,'vg::TranscriptPath']]],
+ ['is_5finterval_12514',['is_interval',['../structgafkluge_1_1GafStep.html#a681b0a984c816cf87468a4143b740a90',1,'gafkluge::GafStep']]],
+ ['is_5flooping_5fchain_12515',['is_looping_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#afbb04850e68908d3802cb5164563577b',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['is_5fordered_12516',['is_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#a313e2b7266bdfbe3ee864d80a5e7b67c',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['is_5fphased_12517',['is_phased',['../structvg_1_1Genotype.html#a7aceacf9d5e3def3d6e675ef34906aab',1,'vg::Genotype']]],
+ ['is_5freference_12518',['is_reference',['../structvg_1_1TranscriptPath.html#a61efb7a65128254f6039323ca0507e95',1,'vg::TranscriptPath']]],
+ ['is_5frend_12519',['is_rend',['../structvg_1_1ChainIterator.html#adb9db0a0ea4cac8bca359c97d293aaa9',1,'vg::ChainIterator']]],
+ ['is_5frepetitive_12520',['is_repetitive',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#a4ad3bbc4813727c0af8fa25f18d02512',1,'vg::MinimizerMapper::Minimizer']]],
+ ['is_5freverse_12521',['is_reverse',['../structvg_1_1Genotyper_1_1Affinity.html#ae1707128484386f3a20eb8c6a8f9ec95',1,'vg::Genotyper::Affinity::is_reverse()'],['../structvg_1_1Transcript.html#ab7c8b040643b29e7213839f95390625f',1,'vg::Transcript::is_reverse()'],['../structvg_1_1ZipCodeTree_1_1oriented__seed__t.html#a54539368bfd495fe1ab7cbcd60f6d528',1,'vg::ZipCodeTree::oriented_seed_t::is_reverse()'],['../structgafkluge_1_1GafStep.html#a18b7374dcc0b3a2386dd6090fbb7d8fe',1,'gafkluge::GafStep::is_reverse()'],['../structvg_1_1Position.html#aeb715b329bd7371ca380a2f2abdcbd13',1,'vg::Position::is_reverse()']]],
+ ['is_5freverse_5fordered_12522',['is_reverse_ordered',['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae6d743daadce96f680039a166503bee9',1,'vg::ZipCodeForest::interval_state_t']]],
+ ['is_5freversed_12523',['is_reversed',['../structvg_1_1ZipCode_1_1node__code__t.html#a781979f7c9ed42859087a19c07be8898',1,'vg::ZipCode::node_code_t::is_reversed()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#a8c08c6dddaf7f3d1e75964c6bf701c3d',1,'vg::ZipCode::snarl_code_t::is_reversed()'],['../structvg_1_1MIPayload.html#a391d9d5e1cd44eccb39a6a31f56a6890',1,'vg::MIPayload::is_reversed()'],['../structvg_1_1ZipCodeTree_1_1tree__item__t.html#ab491085e63a9027e460098d5bc3f98ca',1,'vg::ZipCodeTree::tree_item_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1child__info__t.html#af4a9de3c328470293caa0d958094201e',1,'vg::ZipCodeForest::child_info_t::is_reversed()'],['../structvg_1_1ZipCodeForest_1_1interval__state__t.html#ae0f46b456027c5360dad34c0480c8ebb',1,'vg::ZipCodeForest::interval_state_t::is_reversed()']]],
+ ['is_5freversed_5fin_5fparent_12524',['is_reversed_in_parent',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a81a6e5692e0b2100e9204bdb48454dd6',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['is_5fsecondary_12525',['is_secondary',['../structvg_1_1Alignment.html#a59a4b8c7367fb468e46bcf6ae292888f',1,'vg::Alignment']]],
+ ['is_5fseed_12526',['is_seed',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#ab29219e6df18063f714a379f5d769cf7',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['is_5fstable_12527',['is_stable',['../structgafkluge_1_1GafStep.html#ad41f5cafc50a114daeec6b0cf08101eb',1,'gafkluge::GafStep']]],
+ ['is_5ftrivial_5fchain_12528',['is_trivial_chain',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a8e92509271514f3510eabdfbe7da9e1d',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::is_trivial_chain()'],['../structvg_1_1MIPayload.html#a9a1ab910b382a0ec41e12036f9b8ae04',1,'vg::MIPayload::is_trivial_chain()']]],
+ ['is_5fvg_12529',['is_vg',['../classvg_1_1LegacyCaller.html#a80d266e926310b4def5ac48e3211029f',1,'vg::LegacyCaller']]],
+ ['isforward_12530',['isForward',['../structvg_1_1BREAKPOINT.html#a3179531d48993e05d802907b730e1631',1,'vg::BREAKPOINT']]],
+ ['issue_5furl_12531',['ISSUE_URL',['../namespacevg.html#ae77436235694e5e661c74799ab326d0b',1,'vg']]],
+ ['it_12532',['it',['../classvg_1_1ZipCodeTree_1_1iterator.html#a1bc7243523f7c66a5d86bbe6b28176af',1,'vg::ZipCodeTree::iterator::it()'],['../classvg_1_1ZipCodeTree_1_1reverse__iterator.html#a3ab48e9f50bb0651c4eef055721366ea',1,'vg::ZipCodeTree::reverse_iterator::it()']]],
+ ['item_5fbonus_12533',['item_bonus',['../classvg_1_1MinimizerMapper.html#a7646fc428d4eb41fb022dd9c61afa687',1,'vg::MinimizerMapper']]],
+ ['item_5fcount_12534',['item_count',['../structvg_1_1MatchPos_1_1PathList.html#ad3ebb006eb120b2934d64cece179d0e8',1,'vg::MatchPos::PathList']]],
+ ['item_5fscale_12535',['item_scale',['../classvg_1_1MinimizerMapper.html#af637ac92b12ecfebb815cedb5d56f58e',1,'vg::MinimizerMapper']]],
+ ['item_5fvo_12536',['item_vo',['../classvg_1_1io_1_1MessageIterator.html#a1f58abce5de3c8f71a82e689c0170c49',1,'vg::io::MessageIterator']]],
+ ['items_12537',['items',['../structvg_1_1Funnel_1_1Stage.html#a787bab13fd8bd1bccb1ac8e7821688c6',1,'vg::Funnel::Stage::items()'],['../structvg_1_1VectorView.html#a1d1194d5eac47211eda065d3dc6312ef',1,'vg::VectorView::items()']]],
+ ['iteratee_12538',['iteratee',['../classvg_1_1ShuffledPairs_1_1iterator.html#a09d41523db4b9b9c6cebb02ecf7bfa3c',1,'vg::ShuffledPairs::iterator']]]
];
diff --git a/search/variables_a.js b/search/variables_a.js
index 6fbea2e177..1ab16ab37a 100644
--- a/search/variables_a.js
+++ b/search/variables_a.js
@@ -1,7 +1,7 @@
var searchData=
[
- ['job_5ffunc_12535',['job_func',['../classvg_1_1JobSchedule.html#a801f56bdc606a6ef0c3c26ac2a27ec24',1,'vg::JobSchedule']]],
- ['job_5fid_12536',['job_id',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a0f28a2f70f5f09a423d0f97a8e4343c4',1,'vg::Haplotypes::TopLevelChain']]],
- ['jobs_5ffor_5fcached_5fpaths_12537',['jobs_for_cached_paths',['../classvg_1_1Haplotypes.html#a5974594af8a92b2e030163a5359a7265',1,'vg::Haplotypes']]],
- ['joint_5finitial_5fdistr_12538',['joint_initial_distr',['../classvg_1_1NGSSimulator.html#a147d596d664076c94b468230d78290c4',1,'vg::NGSSimulator']]]
+ ['job_5ffunc_12539',['job_func',['../classvg_1_1JobSchedule.html#a801f56bdc606a6ef0c3c26ac2a27ec24',1,'vg::JobSchedule']]],
+ ['job_5fid_12540',['job_id',['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a0f28a2f70f5f09a423d0f97a8e4343c4',1,'vg::Haplotypes::TopLevelChain']]],
+ ['jobs_5ffor_5fcached_5fpaths_12541',['jobs_for_cached_paths',['../classvg_1_1Haplotypes.html#a5974594af8a92b2e030163a5359a7265',1,'vg::Haplotypes']]],
+ ['joint_5finitial_5fdistr_12542',['joint_initial_distr',['../classvg_1_1NGSSimulator.html#a147d596d664076c94b468230d78290c4',1,'vg::NGSSimulator']]]
];
diff --git a/search/variables_b.js b/search/variables_b.js
index 5281952641..49ea336a09 100644
--- a/search/variables_b.js
+++ b/search/variables_b.js
@@ -1,16 +1,16 @@
var searchData=
[
- ['k_12539',['k',['../classvg_1_1ParallelKFFReader.html#a8060dbef6faaf286f33f3af5be8d32c6',1,'vg::ParallelKFFReader::k()'],['../classvg_1_1MEMAccelerator.html#ab01dc4463ca21d56a9059e38f7e6a2fe',1,'vg::MEMAccelerator::k()'],['../structvg_1_1Haplotypes_1_1Header.html#ab0357bc5db25d4ff1590fc540f4f1ffe',1,'vg::Haplotypes::Header::k()'],['../structHaplotypesConfig.html#aaa9163a17295c26ec249d47205be0177',1,'HaplotypesConfig::k()'],['../classvg_1_1FlowTraversalFinder.html#a6f3d138926abc87592571c2182faf31e',1,'vg::FlowTraversalFinder::K()']]],
- ['keep_5fconflicted_5fgenotypes_12540',['keep_conflicted_genotypes',['../classvg_1_1Deconstructor.html#af67896b3d980c332c69159fecafb2ae2',1,'vg::Deconstructor']]],
- ['keep_5fintermediates_12541',['keep_intermediates',['../classvg_1_1IndexRegistry.html#a1b0ad4bff3fc2a7d514c6e1b46d3ca23',1,'vg::IndexRegistry']]],
- ['kff_5fblock_5fsize_12542',['KFF_BLOCK_SIZE',['../classvg_1_1Recombinator.html#aae3d85fd81e178aedb975015652a6cc4',1,'vg::Recombinator']]],
- ['kmer_12543',['kmer',['../structvg_1_1KmerPosition.html#a79c4fa6766d55a1fea8fdc00adab02b3',1,'vg::KmerPosition']]],
- ['kmer_5fcounts_12544',['kmer_counts',['../structvg_1_1Haplotypes_1_1Subchain.html#a68ff855e7047ec8154df21ad2a817c10',1,'vg::Haplotypes::Subchain']]],
- ['kmer_5finput_12545',['kmer_input',['../structHaplotypesConfig.html#adfb31d19cd310ad8ec89e29fe0dd5e28',1,'HaplotypesConfig']]],
- ['kmer_5flength_12546',['kmer_length',['../structPruningParameters.html#ae3cd0ffe16bbdd3d2d5092ef57f4219a',1,'PruningParameters']]],
- ['kmer_5foutput_12547',['kmer_output',['../structHaplotypesConfig.html#ac2857225a416e464c728691eb28d8a2e',1,'HaplotypesConfig']]],
- ['kmer_5fsize_12548',['kmer_size',['../classvg_1_1VariantAdder.html#acda70938d1a3eb2eb5da18dd2805ae26',1,'vg::VariantAdder']]],
- ['kmers_12549',['kmers',['../structvg_1_1Haplotypes_1_1Subchain.html#a57018e7275a6afc9ba8548391b670c3a',1,'vg::Haplotypes::Subchain::kmers()'],['../structvg_1_1Recombinator_1_1Statistics.html#a5a5878a01bd909e752eb99795da76a1f',1,'vg::Recombinator::Statistics::kmers()']]],
- ['kmers_5fpresent_12550',['kmers_present',['../structvg_1_1Haplotypes_1_1Subchain.html#ae50f824b6f2d2e9a33b16613c01a7096',1,'vg::Haplotypes::Subchain']]],
- ['know_5foffset_12551',['know_offset',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a62a78fd952dc7239a74fd042eae0e562',1,'vg::io::BlockedGzipInputStream::know_offset()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae88df3ee23df1392e53453f82b1859e2',1,'vg::io::BlockedGzipOutputStream::know_offset()']]]
+ ['k_12543',['k',['../classvg_1_1ParallelKFFReader.html#a8060dbef6faaf286f33f3af5be8d32c6',1,'vg::ParallelKFFReader::k()'],['../classvg_1_1MEMAccelerator.html#ab01dc4463ca21d56a9059e38f7e6a2fe',1,'vg::MEMAccelerator::k()'],['../structvg_1_1Haplotypes_1_1Header.html#ab0357bc5db25d4ff1590fc540f4f1ffe',1,'vg::Haplotypes::Header::k()'],['../structHaplotypesConfig.html#aaa9163a17295c26ec249d47205be0177',1,'HaplotypesConfig::k()'],['../classvg_1_1FlowTraversalFinder.html#a6f3d138926abc87592571c2182faf31e',1,'vg::FlowTraversalFinder::K()']]],
+ ['keep_5fconflicted_5fgenotypes_12544',['keep_conflicted_genotypes',['../classvg_1_1Deconstructor.html#af67896b3d980c332c69159fecafb2ae2',1,'vg::Deconstructor']]],
+ ['keep_5fintermediates_12545',['keep_intermediates',['../classvg_1_1IndexRegistry.html#a1b0ad4bff3fc2a7d514c6e1b46d3ca23',1,'vg::IndexRegistry']]],
+ ['kff_5fblock_5fsize_12546',['KFF_BLOCK_SIZE',['../classvg_1_1Recombinator.html#aae3d85fd81e178aedb975015652a6cc4',1,'vg::Recombinator']]],
+ ['kmer_12547',['kmer',['../structvg_1_1KmerPosition.html#a79c4fa6766d55a1fea8fdc00adab02b3',1,'vg::KmerPosition']]],
+ ['kmer_5fcounts_12548',['kmer_counts',['../structvg_1_1Haplotypes_1_1Subchain.html#a68ff855e7047ec8154df21ad2a817c10',1,'vg::Haplotypes::Subchain']]],
+ ['kmer_5finput_12549',['kmer_input',['../structHaplotypesConfig.html#adfb31d19cd310ad8ec89e29fe0dd5e28',1,'HaplotypesConfig']]],
+ ['kmer_5flength_12550',['kmer_length',['../structPruningParameters.html#ae3cd0ffe16bbdd3d2d5092ef57f4219a',1,'PruningParameters']]],
+ ['kmer_5foutput_12551',['kmer_output',['../structHaplotypesConfig.html#ac2857225a416e464c728691eb28d8a2e',1,'HaplotypesConfig']]],
+ ['kmer_5fsize_12552',['kmer_size',['../classvg_1_1VariantAdder.html#acda70938d1a3eb2eb5da18dd2805ae26',1,'vg::VariantAdder']]],
+ ['kmers_12553',['kmers',['../structvg_1_1Haplotypes_1_1Subchain.html#a57018e7275a6afc9ba8548391b670c3a',1,'vg::Haplotypes::Subchain::kmers()'],['../structvg_1_1Recombinator_1_1Statistics.html#a5a5878a01bd909e752eb99795da76a1f',1,'vg::Recombinator::Statistics::kmers()']]],
+ ['kmers_5fpresent_12554',['kmers_present',['../structvg_1_1Haplotypes_1_1Subchain.html#ae50f824b6f2d2e9a33b16613c01a7096',1,'vg::Haplotypes::Subchain']]],
+ ['know_5foffset_12555',['know_offset',['../classvg_1_1io_1_1BlockedGzipInputStream.html#a62a78fd952dc7239a74fd042eae0e562',1,'vg::io::BlockedGzipInputStream::know_offset()'],['../classvg_1_1io_1_1BlockedGzipOutputStream.html#ae88df3ee23df1392e53453f82b1859e2',1,'vg::io::BlockedGzipOutputStream::know_offset()']]]
];
diff --git a/search/variables_c.js b/search/variables_c.js
index c2d403c322..9c77a46ae1 100644
--- a/search/variables_c.js
+++ b/search/variables_c.js
@@ -1,64 +1,64 @@
var searchData=
[
- ['lane_12552',['lane',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a197d4920d6cbdfabac08f0de992a425a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
- ['large_5falignment_5fband_5fpadding_12553',['large_alignment_band_padding',['../classvg_1_1VariantAdder.html#aefe81cd7c81a7f3ba54c73e25c24ba3f',1,'vg::VariantAdder']]],
- ['larger_5fprime_12554',['larger_prime',['../classvg_1_1ShuffledPairs.html#a20b31eca7b0fc0185246c560fd8e266d',1,'vg::ShuffledPairs']]],
- ['last_12555',['last',['../structvg_1_1FeatureSet_1_1Feature.html#a9fb23b0b9affcc51a2610bb287b2082b',1,'vg::FeatureSet::Feature']]],
- ['last_5fcheckin_12556',['last_checkin',['../structvg_1_1Watchdog_1_1thread__state__t.html#ad54ba05d09be7a40b4e9504b8d020ea6',1,'vg::Watchdog::thread_state_t']]],
- ['last_5fcomponent_12557',['last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac65c35c84d5c173dc46077e3f0a831e5',1,'vg::ZipCode::chain_code_t']]],
- ['last_5fgroup_5fmin_5fid_12558',['last_group_min_id',['../classvg_1_1StreamIndexBase.html#aef3a7bd46aeb49185a8cd6a9a261e883',1,'vg::StreamIndexBase']]],
- ['last_5fnode_5flength_12559',['last_node_length',['../structvg_1_1PathIndex.html#ac64a3532df12093eeccf3201184ea4d9',1,'vg::PathIndex']]],
- ['last_5fprogress_12560',['last_progress',['../classvg_1_1Progressive.html#a4984481e2b887e5fb78ea40728f1b97f',1,'vg::Progressive']]],
- ['layout_5forder_12561',['layout_order',['../classvg_1_1DagifiedGraph.html#a50789da1e0a8c4ede5e2c1b73c7980a0',1,'vg::DagifiedGraph']]],
- ['lcp_12562',['lcp',['../classvg_1_1BaseMapper.html#a4046b98185c00ff397089435d5b2b8d8',1,'vg::BaseMapper']]],
- ['lcp_5find_12563',['lcp_ind',['../classvg_1_1Filter.html#ab65e7196a6b891a266d16838e5d870d4',1,'vg::Filter']]],
- ['left_12564',['left',['../structvg_1_1Support.html#a31d59f62a09c71915856740c5450ecf5',1,'vg::Support']]],
- ['left_5fborder_12565',['left_border',['../classvg_1_1Viz.html#a4c472c524f9bdfc37d9073f9257ca529',1,'vg::Viz']]],
- ['left_5fends_12566',['left_ends',['../structvg_1_1ConstructedChunk.html#a0d6c6d4304190097a7a832d11a31bf3d',1,'vg::ConstructedChunk']]],
- ['left_5ffull_12567',['left_full',['../structvg_1_1GaplessExtension.html#a6b4301b3f1f75362d7904402fadde5a6',1,'vg::GaplessExtension']]],
- ['left_5fhandle_5ftrans_12568',['left_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#a03cd96a5b62b5a1450587032017a18bf',1,'vg::JoinedSpliceGraph']]],
- ['left_5fmaximal_12569',['left_maximal',['../structvg_1_1GaplessExtension.html#a3b8b053fc8800c5453b002cbc2aad173',1,'vg::GaplessExtension']]],
- ['left_5fsplice_5foffset_12570',['left_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a7b502013abbbbad97b3edbaa24023612',1,'vg::JoinedSpliceGraph']]],
- ['left_5fsubgraph_12571',['left_subgraph',['../classvg_1_1JoinedSpliceGraph.html#ac59cd1a60d45bb3bad8241cadc53c56e',1,'vg::JoinedSpliceGraph']]],
- ['left_5ftelomere_5fnode_12572',['left_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#ac4abe06cebb2edac649930a7597cc126',1,'vg::PhasedGenome::Haplotype']]],
- ['len_12573',['len',['../structvg_1_1SeqComplexity.html#abafe41d418fc2e9c14681e87f994dc0c',1,'vg::SeqComplexity']]],
- ['length_12574',['length',['../structvg_1_1WFAAlignment.html#a742372d503ae6c788b263ec474507b68',1,'vg::WFAAlignment::length()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac06d9b8444018d7490500c9dfa97a03b',1,'haplo::hDP_gbwt_graph_accessor::length()'],['../structhaplo_1_1haplo__DP__column.html#a43833a8ca83be7d6c2daa13b7707f32f',1,'haplo::haplo_DP_column::length()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#afd3e1c8befad3a1911504cfbd3f54ccd',1,'vg::MinimizerMapper::Minimizer::length()'],['../classvg_1_1mapping__t.html#ac2e746a37c551e0ecc8a4549135b8440',1,'vg::mapping_t::length()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#af210cde60043f4b87fa1bbd51487695d',1,'vg::HaplotypePartitioner::Subchain::length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#af7223d49a43bb2863961ab3e4113d2e2',1,'vg::ZipCode::node_code_t::length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a794a822da9c5425158d1ed42da500c03',1,'vg::ZipCode::chain_code_t::length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab0d97bad1f0171c35e784ff6d0c79c2c',1,'vg::ZipCode::snarl_code_t::length()'],['../structvg_1_1algorithms_1_1walk__t.html#a4be6edd3b92c2b9670ea09ec82aa3846',1,'vg::algorithms::walk_t::length()'],['../structMappingRun.html#af5b291d6db781206833956c21d74c94f',1,'MappingRun::length()'],['../structvg_1_1Path.html#ac512f92c7b82e38265062cd3fdc90acf',1,'vg::Path::length()']]],
- ['lengths_12575',['lengths',['../classvg_1_1FragmentLengthDistribution.html#a368340de267064b485b898da2331dc97',1,'vg::FragmentLengthDistribution']]],
- ['likelihood_12576',['likelihood',['../structvg_1_1Genotype.html#afac9953bdbfbc0e3991e1b8a6e7e8c36',1,'vg::Genotype']]],
- ['likelihood_5fln_12577',['likelihood_ln',['../structvg_1_1Genotyper_1_1Affinity.html#ad1c0431bc83746580740d35e43fd2a46',1,'vg::Genotyper::Affinity']]],
- ['line_5fnumber_12578',['line_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#aa460a34b2f085a161a113d4b83cbd1b4',1,'vg::algorithms::GFAFormatError']]],
- ['linear_5fstructure_12579',['linear_structure',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a236e15ad7f30e98b2f6b1e9720b5d922',1,'vg::HaplotypePartitioner::Parameters']]],
- ['list_5fnames_12580',['list_names',['../structGBWTConfig.html#ac775ff572f553bd1dae5a7ee81c14078',1,'GBWTConfig']]],
- ['locked_5fnodes_12581',['locked_nodes',['../classvg_1_1GraphSynchronizer_1_1Lock.html#acfb5bf6caa6040ec1028250324296355',1,'vg::GraphSynchronizer::Lock::locked_nodes()'],['../classvg_1_1GraphSynchronizer.html#a275e3112ec47229a197e3ecc118771c4',1,'vg::GraphSynchronizer::locked_nodes()']]],
- ['locus_12582',['locus',['../structvg_1_1Alignment.html#afe47b70cd7b78e97a9cf18e9c60ef4f0',1,'vg::Alignment']]],
- ['locus_5fmatch_5fany_12583',['LOCUS_MATCH_ANY',['../classhandlegraph_1_1PathMetadata.html#a613e59743ad6e1df8e9682fdf087e715',1,'handlegraph::PathMetadata']]],
- ['locus_5fmatch_5fnumerical_5fwithout_5fhaplotype_12584',['LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#ab26b62f4dc1863aeae2798e008b38c80',1,'handlegraph::PathMetadata']]],
- ['log_5fbase_12585',['log_base',['../classvg_1_1GSSWAligner.html#a5a1a7e6edc3764ff32f7815999d6345f',1,'vg::GSSWAligner::log_base()'],['../classvg_1_1SpliceStats.html#ae01c237b5e011851147a342b8e7aa3ad',1,'vg::SpliceStats::log_base()']]],
- ['log_5fcontinue_5fprobability_12586',['log_continue_probability',['../structhaplo_1_1haploMath_1_1RRMemo.html#afd6af2944e0a42df7f251fe008ba3e90',1,'haplo::haploMath::RRMemo']]],
- ['log_5flikelihood_12587',['log_likelihood',['../structvg_1_1Genotype.html#ad14f6fc449e1086ccd2de2bc4ad419a4',1,'vg::Genotype']]],
- ['log_5flikelihood_5fapprox_5ffactor_12588',['log_likelihood_approx_factor',['../classvg_1_1MultipathMapper.html#a28e3e0b047b5d3c195431982f76084c1',1,'vg::MultipathMapper']]],
- ['log_5fposterior_12589',['log_posterior',['../structvg_1_1Genotype.html#a743da1ba7239bddcd6316a60f66bd307',1,'vg::Genotype']]],
- ['log_5fprior_12590',['log_prior',['../structvg_1_1Genotype.html#a94b836b6384c02e11478b2ec18ab0ad7',1,'vg::Genotype']]],
- ['log_5freads_12591',['log_reads',['../structGiraffeMainOptions.html#a2b54df0c377a105e57c67c93b1b98ce9',1,'GiraffeMainOptions']]],
- ['logs_5fbases_12592',['logS_bases',['../structhaplo_1_1haploMath_1_1RRMemo.html#a00657f76fd1b56312b031ef79728c9c7',1,'haplo::haploMath::RRMemo']]],
- ['logt_5fbase_12593',['logT_base',['../structhaplo_1_1haploMath_1_1RRMemo.html#a8e9b242f45b301e58dbe4e67f6added1',1,'haplo::haploMath::RRMemo']]],
- ['long_5flimit_12594',['LONG_LIMIT',['../classvg_1_1MinimizerMapper.html#a1d68225843da9cfb161b838be3017e58',1,'vg::MinimizerMapper']]],
- ['long_5fopt_12595',['long_opt',['../classvg_1_1BaseOption.html#a580b1cd4960ac113db781935d89cb7b1',1,'vg::BaseOption']]],
- ['long_5foptions_12596',['long_options',['../classvg_1_1ConfigurableParser.html#a25d7c47bbc3c439235fb751722d027c8',1,'vg::ConfigurableParser']]],
- ['long_5foptions_5fused_12597',['long_options_used',['../classvg_1_1ConfigurableParser.html#a60395eaf832c2acfa46fe0763749614f',1,'vg::ConfigurableParser']]],
- ['long_5fread_5fminimizer_5fk_12598',['long_read_minimizer_k',['../structvg_1_1IndexingParameters.html#ac8e9a153245b64380d773561d8534c51',1,'vg::IndexingParameters']]],
- ['long_5fread_5fminimizer_5fw_12599',['long_read_minimizer_w',['../structvg_1_1IndexingParameters.html#a7cf3ea634d6c4b3f45bf2d11867ab70c',1,'vg::IndexingParameters::long_read_minimizer_w()'],['../structvg_1_1IndexingParameters.html#aca76950e194d8a550b71ffcee55aa8df',1,'vg::IndexingParameters::long_read_minimizer_W()']]],
- ['long_5fref_5fcontig_12600',['long_ref_contig',['../classvg_1_1Deconstructor.html#a6341c9416e41420f60f9faf7ea942d07',1,'vg::Deconstructor']]],
- ['loop_5fleft_12601',['loop_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3374b357e0bc3bc98bd131d7dc0a3209',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['loop_5fright_12602',['loop_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae793bc31b5603ef670a83187fde8616c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
- ['low_5fcomplexity_5fp_5fvalue_12603',['low_complexity_p_value',['../classvg_1_1Surjector.html#a1df336db06fea7951c960f71265d513d',1,'vg::Surjector']]],
- ['lower_5fbound_12604',['lower_bound',['../structvg_1_1BREAKPOINT.html#a1b854b285738913830671a54ce0857f5',1,'vg::BREAKPOINT']]],
- ['lower_5fbound_5fheuristic_12605',['lower_bound_heuristic',['../classvg_1_1TargetValueSearch.html#a93c1f2cb35452719dc87fb4ec8cf714e',1,'vg::TargetValueSearch']]],
- ['lowercase_5fwarned_5falt_12606',['lowercase_warned_alt',['../classvg_1_1Constructor.html#af296f5e32632a4fee39ac4bc11589c09',1,'vg::Constructor']]],
- ['lowercase_5fwarned_5fsequences_12607',['lowercase_warned_sequences',['../classvg_1_1Constructor.html#a4a5f08f7d9c8e7bc821a7618e019289d',1,'vg::Constructor']]],
- ['lru_5fcache_5fsize_12608',['lru_cache_size',['../classvg_1_1Packer.html#a32572a24fe3c3b372e1ff24ec9720da0',1,'vg::Packer']]],
- ['lv0_5falt_5flen_12609',['lv0_alt_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a64a400033d2ff787c487d78feee21a7d',1,'vg::Deconstructor::NestingInfo']]],
- ['lv0_5fref_5flen_12610',['lv0_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ab628cbae94feb0e11bd46e09fc1900f4',1,'vg::Deconstructor::NestingInfo']]],
- ['lv0_5fref_5fname_12611',['lv0_ref_name',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2eda67779fb6821700d9c89d8b9671f7',1,'vg::Deconstructor::NestingInfo']]],
- ['lv0_5fref_5fstart_12612',['lv0_ref_start',['../structvg_1_1Deconstructor_1_1NestingInfo.html#af6bb1c0f6383981be4bfea3ce0fe565f',1,'vg::Deconstructor::NestingInfo']]]
+ ['lane_12556',['lane',['../structvg_1_1ReplaceSnarlHaplotypeCommand.html#a197d4920d6cbdfabac08f0de992a425a',1,'vg::ReplaceSnarlHaplotypeCommand']]],
+ ['large_5falignment_5fband_5fpadding_12557',['large_alignment_band_padding',['../classvg_1_1VariantAdder.html#aefe81cd7c81a7f3ba54c73e25c24ba3f',1,'vg::VariantAdder']]],
+ ['larger_5fprime_12558',['larger_prime',['../classvg_1_1ShuffledPairs.html#a20b31eca7b0fc0185246c560fd8e266d',1,'vg::ShuffledPairs']]],
+ ['last_12559',['last',['../structvg_1_1FeatureSet_1_1Feature.html#a9fb23b0b9affcc51a2610bb287b2082b',1,'vg::FeatureSet::Feature']]],
+ ['last_5fcheckin_12560',['last_checkin',['../structvg_1_1Watchdog_1_1thread__state__t.html#ad54ba05d09be7a40b4e9504b8d020ea6',1,'vg::Watchdog::thread_state_t']]],
+ ['last_5fcomponent_12561',['last_component',['../structvg_1_1ZipCode_1_1chain__code__t.html#ac65c35c84d5c173dc46077e3f0a831e5',1,'vg::ZipCode::chain_code_t']]],
+ ['last_5fgroup_5fmin_5fid_12562',['last_group_min_id',['../classvg_1_1StreamIndexBase.html#aef3a7bd46aeb49185a8cd6a9a261e883',1,'vg::StreamIndexBase']]],
+ ['last_5fnode_5flength_12563',['last_node_length',['../structvg_1_1PathIndex.html#ac64a3532df12093eeccf3201184ea4d9',1,'vg::PathIndex']]],
+ ['last_5fprogress_12564',['last_progress',['../classvg_1_1Progressive.html#a4984481e2b887e5fb78ea40728f1b97f',1,'vg::Progressive']]],
+ ['layout_5forder_12565',['layout_order',['../classvg_1_1DagifiedGraph.html#a50789da1e0a8c4ede5e2c1b73c7980a0',1,'vg::DagifiedGraph']]],
+ ['lcp_12566',['lcp',['../classvg_1_1BaseMapper.html#a4046b98185c00ff397089435d5b2b8d8',1,'vg::BaseMapper']]],
+ ['lcp_5find_12567',['lcp_ind',['../classvg_1_1Filter.html#ab65e7196a6b891a266d16838e5d870d4',1,'vg::Filter']]],
+ ['left_12568',['left',['../structvg_1_1Support.html#a31d59f62a09c71915856740c5450ecf5',1,'vg::Support']]],
+ ['left_5fborder_12569',['left_border',['../classvg_1_1Viz.html#a4c472c524f9bdfc37d9073f9257ca529',1,'vg::Viz']]],
+ ['left_5fends_12570',['left_ends',['../structvg_1_1ConstructedChunk.html#a0d6c6d4304190097a7a832d11a31bf3d',1,'vg::ConstructedChunk']]],
+ ['left_5ffull_12571',['left_full',['../structvg_1_1GaplessExtension.html#a6b4301b3f1f75362d7904402fadde5a6',1,'vg::GaplessExtension']]],
+ ['left_5fhandle_5ftrans_12572',['left_handle_trans',['../classvg_1_1JoinedSpliceGraph.html#a03cd96a5b62b5a1450587032017a18bf',1,'vg::JoinedSpliceGraph']]],
+ ['left_5fmaximal_12573',['left_maximal',['../structvg_1_1GaplessExtension.html#a3b8b053fc8800c5453b002cbc2aad173',1,'vg::GaplessExtension']]],
+ ['left_5fsplice_5foffset_12574',['left_splice_offset',['../classvg_1_1JoinedSpliceGraph.html#a7b502013abbbbad97b3edbaa24023612',1,'vg::JoinedSpliceGraph']]],
+ ['left_5fsubgraph_12575',['left_subgraph',['../classvg_1_1JoinedSpliceGraph.html#ac59cd1a60d45bb3bad8241cadc53c56e',1,'vg::JoinedSpliceGraph']]],
+ ['left_5ftelomere_5fnode_12576',['left_telomere_node',['../classvg_1_1PhasedGenome_1_1Haplotype.html#ac4abe06cebb2edac649930a7597cc126',1,'vg::PhasedGenome::Haplotype']]],
+ ['len_12577',['len',['../structvg_1_1SeqComplexity.html#abafe41d418fc2e9c14681e87f994dc0c',1,'vg::SeqComplexity']]],
+ ['length_12578',['length',['../structvg_1_1WFAAlignment.html#a742372d503ae6c788b263ec474507b68',1,'vg::WFAAlignment::length()'],['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac06d9b8444018d7490500c9dfa97a03b',1,'haplo::hDP_gbwt_graph_accessor::length()'],['../structhaplo_1_1haplo__DP__column.html#a43833a8ca83be7d6c2daa13b7707f32f',1,'haplo::haplo_DP_column::length()'],['../structvg_1_1MinimizerMapper_1_1Minimizer.html#afd3e1c8befad3a1911504cfbd3f54ccd',1,'vg::MinimizerMapper::Minimizer::length()'],['../classvg_1_1mapping__t.html#ac2e746a37c551e0ecc8a4549135b8440',1,'vg::mapping_t::length()'],['../structvg_1_1HaplotypePartitioner_1_1Subchain.html#af210cde60043f4b87fa1bbd51487695d',1,'vg::HaplotypePartitioner::Subchain::length()'],['../structvg_1_1ZipCode_1_1node__code__t.html#af7223d49a43bb2863961ab3e4113d2e2',1,'vg::ZipCode::node_code_t::length()'],['../structvg_1_1ZipCode_1_1chain__code__t.html#a794a822da9c5425158d1ed42da500c03',1,'vg::ZipCode::chain_code_t::length()'],['../structvg_1_1ZipCode_1_1snarl__code__t.html#ab0d97bad1f0171c35e784ff6d0c79c2c',1,'vg::ZipCode::snarl_code_t::length()'],['../structvg_1_1algorithms_1_1walk__t.html#a4be6edd3b92c2b9670ea09ec82aa3846',1,'vg::algorithms::walk_t::length()'],['../structMappingRun.html#af5b291d6db781206833956c21d74c94f',1,'MappingRun::length()'],['../structvg_1_1Path.html#ac512f92c7b82e38265062cd3fdc90acf',1,'vg::Path::length()']]],
+ ['lengths_12579',['lengths',['../classvg_1_1FragmentLengthDistribution.html#a368340de267064b485b898da2331dc97',1,'vg::FragmentLengthDistribution']]],
+ ['likelihood_12580',['likelihood',['../structvg_1_1Genotype.html#afac9953bdbfbc0e3991e1b8a6e7e8c36',1,'vg::Genotype']]],
+ ['likelihood_5fln_12581',['likelihood_ln',['../structvg_1_1Genotyper_1_1Affinity.html#ad1c0431bc83746580740d35e43fd2a46',1,'vg::Genotyper::Affinity']]],
+ ['line_5fnumber_12582',['line_number',['../structvg_1_1algorithms_1_1GFAFormatError.html#aa460a34b2f085a161a113d4b83cbd1b4',1,'vg::algorithms::GFAFormatError']]],
+ ['linear_5fstructure_12583',['linear_structure',['../structvg_1_1HaplotypePartitioner_1_1Parameters.html#a236e15ad7f30e98b2f6b1e9720b5d922',1,'vg::HaplotypePartitioner::Parameters']]],
+ ['list_5fnames_12584',['list_names',['../structGBWTConfig.html#ac775ff572f553bd1dae5a7ee81c14078',1,'GBWTConfig']]],
+ ['locked_5fnodes_12585',['locked_nodes',['../classvg_1_1GraphSynchronizer_1_1Lock.html#acfb5bf6caa6040ec1028250324296355',1,'vg::GraphSynchronizer::Lock::locked_nodes()'],['../classvg_1_1GraphSynchronizer.html#a275e3112ec47229a197e3ecc118771c4',1,'vg::GraphSynchronizer::locked_nodes()']]],
+ ['locus_12586',['locus',['../structvg_1_1Alignment.html#afe47b70cd7b78e97a9cf18e9c60ef4f0',1,'vg::Alignment']]],
+ ['locus_5fmatch_5fany_12587',['LOCUS_MATCH_ANY',['../classhandlegraph_1_1PathMetadata.html#a613e59743ad6e1df8e9682fdf087e715',1,'handlegraph::PathMetadata']]],
+ ['locus_5fmatch_5fnumerical_5fwithout_5fhaplotype_12588',['LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#ab26b62f4dc1863aeae2798e008b38c80',1,'handlegraph::PathMetadata']]],
+ ['log_5fbase_12589',['log_base',['../classvg_1_1GSSWAligner.html#a5a1a7e6edc3764ff32f7815999d6345f',1,'vg::GSSWAligner::log_base()'],['../classvg_1_1SpliceStats.html#ae01c237b5e011851147a342b8e7aa3ad',1,'vg::SpliceStats::log_base()']]],
+ ['log_5fcontinue_5fprobability_12590',['log_continue_probability',['../structhaplo_1_1haploMath_1_1RRMemo.html#afd6af2944e0a42df7f251fe008ba3e90',1,'haplo::haploMath::RRMemo']]],
+ ['log_5flikelihood_12591',['log_likelihood',['../structvg_1_1Genotype.html#ad14f6fc449e1086ccd2de2bc4ad419a4',1,'vg::Genotype']]],
+ ['log_5flikelihood_5fapprox_5ffactor_12592',['log_likelihood_approx_factor',['../classvg_1_1MultipathMapper.html#a28e3e0b047b5d3c195431982f76084c1',1,'vg::MultipathMapper']]],
+ ['log_5fposterior_12593',['log_posterior',['../structvg_1_1Genotype.html#a743da1ba7239bddcd6316a60f66bd307',1,'vg::Genotype']]],
+ ['log_5fprior_12594',['log_prior',['../structvg_1_1Genotype.html#a94b836b6384c02e11478b2ec18ab0ad7',1,'vg::Genotype']]],
+ ['log_5freads_12595',['log_reads',['../structGiraffeMainOptions.html#a2b54df0c377a105e57c67c93b1b98ce9',1,'GiraffeMainOptions']]],
+ ['logs_5fbases_12596',['logS_bases',['../structhaplo_1_1haploMath_1_1RRMemo.html#a00657f76fd1b56312b031ef79728c9c7',1,'haplo::haploMath::RRMemo']]],
+ ['logt_5fbase_12597',['logT_base',['../structhaplo_1_1haploMath_1_1RRMemo.html#a8e9b242f45b301e58dbe4e67f6added1',1,'haplo::haploMath::RRMemo']]],
+ ['long_5flimit_12598',['LONG_LIMIT',['../classvg_1_1MinimizerMapper.html#a1d68225843da9cfb161b838be3017e58',1,'vg::MinimizerMapper']]],
+ ['long_5fopt_12599',['long_opt',['../classvg_1_1BaseOption.html#a580b1cd4960ac113db781935d89cb7b1',1,'vg::BaseOption']]],
+ ['long_5foptions_12600',['long_options',['../classvg_1_1ConfigurableParser.html#a25d7c47bbc3c439235fb751722d027c8',1,'vg::ConfigurableParser']]],
+ ['long_5foptions_5fused_12601',['long_options_used',['../classvg_1_1ConfigurableParser.html#a60395eaf832c2acfa46fe0763749614f',1,'vg::ConfigurableParser']]],
+ ['long_5fread_5fminimizer_5fk_12602',['long_read_minimizer_k',['../structvg_1_1IndexingParameters.html#ac8e9a153245b64380d773561d8534c51',1,'vg::IndexingParameters']]],
+ ['long_5fread_5fminimizer_5fw_12603',['long_read_minimizer_w',['../structvg_1_1IndexingParameters.html#a7cf3ea634d6c4b3f45bf2d11867ab70c',1,'vg::IndexingParameters::long_read_minimizer_w()'],['../structvg_1_1IndexingParameters.html#aca76950e194d8a550b71ffcee55aa8df',1,'vg::IndexingParameters::long_read_minimizer_W()']]],
+ ['long_5fref_5fcontig_12604',['long_ref_contig',['../classvg_1_1Deconstructor.html#a6341c9416e41420f60f9faf7ea942d07',1,'vg::Deconstructor']]],
+ ['loop_5fleft_12605',['loop_left',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a3374b357e0bc3bc98bd131d7dc0a3209',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['loop_5fright_12606',['loop_right',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#ae793bc31b5603ef670a83187fde8616c',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem']]],
+ ['low_5fcomplexity_5fp_5fvalue_12607',['low_complexity_p_value',['../classvg_1_1Surjector.html#a1df336db06fea7951c960f71265d513d',1,'vg::Surjector']]],
+ ['lower_5fbound_12608',['lower_bound',['../structvg_1_1BREAKPOINT.html#a1b854b285738913830671a54ce0857f5',1,'vg::BREAKPOINT']]],
+ ['lower_5fbound_5fheuristic_12609',['lower_bound_heuristic',['../classvg_1_1TargetValueSearch.html#a93c1f2cb35452719dc87fb4ec8cf714e',1,'vg::TargetValueSearch']]],
+ ['lowercase_5fwarned_5falt_12610',['lowercase_warned_alt',['../classvg_1_1Constructor.html#af296f5e32632a4fee39ac4bc11589c09',1,'vg::Constructor']]],
+ ['lowercase_5fwarned_5fsequences_12611',['lowercase_warned_sequences',['../classvg_1_1Constructor.html#a4a5f08f7d9c8e7bc821a7618e019289d',1,'vg::Constructor']]],
+ ['lru_5fcache_5fsize_12612',['lru_cache_size',['../classvg_1_1Packer.html#a32572a24fe3c3b372e1ff24ec9720da0',1,'vg::Packer']]],
+ ['lv0_5falt_5flen_12613',['lv0_alt_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a64a400033d2ff787c487d78feee21a7d',1,'vg::Deconstructor::NestingInfo']]],
+ ['lv0_5fref_5flen_12614',['lv0_ref_len',['../structvg_1_1Deconstructor_1_1NestingInfo.html#ab628cbae94feb0e11bd46e09fc1900f4',1,'vg::Deconstructor::NestingInfo']]],
+ ['lv0_5fref_5fname_12615',['lv0_ref_name',['../structvg_1_1Deconstructor_1_1NestingInfo.html#a2eda67779fb6821700d9c89d8b9671f7',1,'vg::Deconstructor::NestingInfo']]],
+ ['lv0_5fref_5fstart_12616',['lv0_ref_start',['../structvg_1_1Deconstructor_1_1NestingInfo.html#af6bb1c0f6383981be4bfea3ce0fe565f',1,'vg::Deconstructor::NestingInfo']]]
];
diff --git a/search/variables_d.js b/search/variables_d.js
index e893184fb8..4fd25b516e 100644
--- a/search/variables_d.js
+++ b/search/variables_d.js
@@ -1,284 +1,284 @@
var searchData=
[
- ['m_5fa_12613',['m_a',['../classvg_1_1uniform__real__distribution.html#a7504f90f6d4dea77942a9ca0c0cc3f57',1,'vg::uniform_real_distribution::m_a()'],['../classvg_1_1uniform__int__distribution.html#a2d084a9d58cbc2f4a202d7ba640207ac',1,'vg::uniform_int_distribution::m_a()']]],
- ['m_5falpha_12614',['m_alpha',['../classvg_1_1truncated__normal__distribution.html#a103e91e1a5b135b61ef12bb1396b073d',1,'vg::truncated_normal_distribution']]],
- ['m_5fb_12615',['m_b',['../classvg_1_1uniform__real__distribution.html#a736effb600abacbb4ad5dbd9960449b7',1,'vg::uniform_real_distribution::m_b()'],['../classvg_1_1uniform__int__distribution.html#a8fcf808d445c2826852f79c4bac7f594',1,'vg::uniform_int_distribution::m_b()']]],
- ['m_5fbeta_12616',['m_beta',['../classvg_1_1truncated__normal__distribution.html#ab4ba11d217ace97234dbc707180a388a',1,'vg::truncated_normal_distribution']]],
- ['m_5fdistu1_12617',['m_distU1',['../classvg_1_1normal__distribution.html#a88845be3c45acd203b683f83a658b3bd',1,'vg::normal_distribution::m_distU1()'],['../classvg_1_1truncated__normal__distribution.html#a0020a9172587312e5342375bb0730ec5',1,'vg::truncated_normal_distribution::m_distU1()']]],
- ['m_5fmean_12618',['m_mean',['../classvg_1_1normal__distribution.html#ac215210d6799c86403804a8700f8870f',1,'vg::normal_distribution']]],
- ['m_5fmu_12619',['m_mu',['../classvg_1_1truncated__normal__distribution.html#a16eb85a95c575485c51f3915c27fb206',1,'vg::truncated_normal_distribution']]],
- ['m_5fsigma_12620',['m_sigma',['../classvg_1_1truncated__normal__distribution.html#acc168175a443e25b3b7a49ddbd2d0d65',1,'vg::truncated_normal_distribution']]],
- ['m_5fstddev_12621',['m_stddev',['../classvg_1_1normal__distribution.html#a4940854c4f61e99e8c62acb754619bed',1,'vg::normal_distribution']]],
- ['m_5fsums_12622',['m_sums',['../classvg_1_1discrete__distribution.html#a175dbe373664d84a0a354f1d2febb1b1',1,'vg::discrete_distribution']]],
- ['m_5fweights_12623',['m_weights',['../classvg_1_1discrete__distribution.html#aae17bac88e7ee1c979e4c44287f9a2fe',1,'vg::discrete_distribution']]],
- ['magic_5fbytes_12624',['MAGIC_BYTES',['../classvg_1_1StreamIndexBase.html#a9bbb2b0134f0e831fc2ec5db056b7397',1,'vg::StreamIndexBase']]],
- ['magic_5fnumber_12625',['MAGIC_NUMBER',['../structvg_1_1Haplotypes_1_1Header.html#a08c60e1b376c1a451b42810f5131758b',1,'vg::Haplotypes::Header::MAGIC_NUMBER()'],['../structvg_1_1Haplotypes_1_1Header.html#ae84cdbdc1d89ebf53496eed304acafd3',1,'vg::Haplotypes::Header::magic_number()'],['../classvg_1_1ZipCodeCollection.html#a27434270b2b8b6e6a66f783efb8150c2',1,'vg::ZipCodeCollection::magic_number()']]],
- ['main_5ffunction_12626',['main_function',['../classvg_1_1subcommand_1_1Subcommand.html#a8c500a86e1c9c51cea715508a19c75fa',1,'vg::subcommand::Subcommand']]],
- ['manager_12627',['manager',['../classvg_1_1GenomeState.html#a6c9277391547084f77ff1dbfbe481310',1,'vg::GenomeState']]],
- ['many_5flimit_12628',['MANY_LIMIT',['../classvg_1_1MinimizerMapper.html#aecc1f538f9a05a7f3fd29b5a425ec522',1,'vg::MinimizerMapper']]],
- ['map_5forder_5fto_5foriginal_12629',['map_order_to_original',['../classvg_1_1WindowedVcfBuffer.html#ab62203851ffc243bd9183f9174739bbd',1,'vg::WindowedVcfBuffer']]],
- ['mapper_5falignment_5fcutoff_12630',['mapper_alignment_cutoff',['../classvg_1_1VariantAdder.html#aa4281d59699cd880523cb47a146e5462',1,'vg::VariantAdder']]],
- ['mapping_12631',['mapping',['../classvg_1_1PhaseUnfolder.html#ae30c8d79f4461cae38e4ec2268a22022',1,'vg::PhaseUnfolder::mapping()'],['../structvg_1_1Path.html#a5d91e68bc4c6f7a5915cb4a42cc21caf',1,'vg::Path::mapping()']]],
- ['mapping_5fedits_12632',['mapping_edits',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a9eb8dcec1e61b69092af38a89e82917a',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['mapping_5fitr_12633',['mapping_itr',['../classvg_1_1Paths.html#ae2bd0d7232fb84776841ac7c4bfea0d2',1,'vg::Paths']]],
- ['mapping_5fpositions_12634',['mapping_positions',['../structvg_1_1PathIndex.html#acc0b1da5ad0b4f428ceb623a4d3f806f',1,'vg::PathIndex']]],
- ['mapping_5fquality_12635',['mapping_quality',['../structvg_1_1Alignment.html#a78851a70cc8a3e8f3e71409693130230',1,'vg::Alignment::mapping_quality()'],['../structvg_1_1MultipathAlignment.html#add653bff58eeb96872463fdc21b3dfd5',1,'vg::MultipathAlignment::mapping_quality()']]],
- ['mapping_5fquality_5fmethod_12636',['mapping_quality_method',['../classvg_1_1BaseMapper.html#a0b1fe81d11d92332f613d8a29dcadb37',1,'vg::BaseMapper']]],
- ['mappings_12637',['mappings',['../structvg_1_1RebuildJob.html#a82f413afdbd0c9f3c697ab84774542bf',1,'vg::RebuildJob']]],
- ['mappings_5fby_5frank_12638',['mappings_by_rank',['../classvg_1_1Paths.html#a27d349c3f4795f1389d3824e1c1e3e8f',1,'vg::Paths']]],
- ['mapq_12639',['mapq',['../structgafkluge_1_1GafRecord.html#a09ffb165e71177223d73e2fea5ed1399',1,'gafkluge::GafRecord']]],
- ['mapq_5fscaling_5ffactor_12640',['mapq_scaling_factor',['../classvg_1_1MultipathMapper.html#aadbb94f74824864d7bed5c63cb85687e',1,'vg::MultipathMapper']]],
- ['mapq_5fscore_5fscale_12641',['mapq_score_scale',['../classvg_1_1MinimizerMapper.html#a0e13799b9b7e3f64d06d10bde825924c',1,'vg::MinimizerMapper']]],
- ['mapq_5fscore_5fwindow_12642',['mapq_score_window',['../classvg_1_1MinimizerMapper.html#ace4a8ce19de89dd8f42f807b71c66dd3',1,'vg::MinimizerMapper']]],
- ['margin_5fafter_12643',['margin_after',['../classvg_1_1algorithms_1_1Anchor.html#ade738d4df1585fa0dc6fc935da262ee0',1,'vg::algorithms::Anchor']]],
- ['margin_5fbefore_12644',['margin_before',['../classvg_1_1algorithms_1_1Anchor.html#a545c9c26a24e8d37459944c5632c79e2',1,'vg::algorithms::Anchor']]],
- ['mask_12645',['mask',['../classvg_1_1ReadMasker.html#ad6d292712ead5b6f89940f020fd8fcc2',1,'vg::ReadMasker::mask()'],['../classvg_1_1GaplessExtender.html#a9824f8144fd4f3515c7333fbeb6e2afd',1,'vg::GaplessExtender::mask()'],['../classvg_1_1WFAExtender.html#a1af2acef8bd391f46798288e9322019b',1,'vg::WFAExtender::mask()']]],
- ['match_12646',['match',['../classvg_1_1GSSWAligner.html#a7323efd4ef078ab5866b8c2b9fea87a8',1,'vg::GSSWAligner::match()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a4fdc2b0adb79d04c4e928a61e891aa84',1,'vg::BandedGlobalAligner::BAMatrix::match()'],['../classvg_1_1SSWAligner.html#a8ec16a3583a2d8347ee9eaf1853b8cc8',1,'vg::SSWAligner::match()'],['../structScoringOptions.html#a3a450e63987f79011a51819efd5420a4',1,'ScoringOptions::match()']]],
- ['match_5fcount_12647',['match_count',['../classvg_1_1MaximalExactMatch.html#ab7a9c66468635a1498efdeb394c1fad6',1,'vg::MaximalExactMatch']]],
- ['matches_12648',['MATCHES',['../structvg_1_1WFANode.html#a0188bfd686597181c42f2384c21e9e19',1,'vg::WFANode::MATCHES()'],['../structvg_1_1SeqComplexity.html#a03e3682e2a96bbf0595d38694d3818ad',1,'vg::SeqComplexity::matches()'],['../structgafkluge_1_1GafRecord.html#a0cac64f74ee1a099fafc4148d08a630c',1,'gafkluge::GafRecord::matches()']]],
- ['matching_12649',['matching',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a6bb2874bc8c41f0606f8f142a465e469',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['mate_5fmapped_5fto_5fdisjoint_5fsubgraph_12650',['mate_mapped_to_disjoint_subgraph',['../structvg_1_1Alignment.html#a95ed4d8c7a57e34a96871b74ff851821',1,'vg::Alignment']]],
- ['mate_5fon_5freverse_5fstrand_12651',['mate_on_reverse_strand',['../structvg_1_1Alignment.html#aef312ed490cb8adf8b89eb36b46ee7d6',1,'vg::Alignment']]],
- ['mate_5frescues_12652',['mate_rescues',['../classvg_1_1Mapper.html#a56cec2a0bdc2a2398bd494cf0acb80a2',1,'vg::Mapper']]],
- ['mate_5funmapped_12653',['mate_unmapped',['../structvg_1_1Alignment.html#a061bf4ec65ccf7ff88e73e9e4ff268b7',1,'vg::Alignment']]],
- ['mates_12654',['mates',['../structvg_1_1BREAKPOINT.html#a7469d5658b49020a71529d1704b962f9',1,'vg::BREAKPOINT']]],
- ['matrix_5fstate_12655',['matrix_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a5b8b44e10a1bc42b694728459e4b4271',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['max_12656',['max',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a45c40bccc3fd5b000987f633c8ec8df4',1,'vg::WFAExtender::ErrorModel::Event']]],
- ['max_5falignment_5fgap_12657',['max_alignment_gap',['../classvg_1_1MultipathMapper.html#aaf8af884f81cfd5ed869f26a8b8403d4',1,'vg::MultipathMapper']]],
- ['max_5falignments_12658',['max_alignments',['../classvg_1_1MinimizerMapper.html#a6062b78a7f795cb2a585eb6695bde675',1,'vg::MinimizerMapper']]],
- ['max_5falt_5fmappings_12659',['max_alt_mappings',['../classvg_1_1MultipathMapper.html#a87223306ba0d983104e48d4ded4e685d',1,'vg::MultipathMapper']]],
- ['max_5fanchors_12660',['max_anchors',['../classvg_1_1Surjector.html#a5a735901a421d305e6cbf13a016fdc9d',1,'vg::Surjector']]],
- ['max_5fattempts_12661',['max_attempts',['../classvg_1_1Mapper.html#ac9973fcf3d75d4396f6b6bdec58156a6',1,'vg::Mapper']]],
- ['max_5fband_5fcells_12662',['max_band_cells',['../classvg_1_1Surjector.html#a0e22a6f6da976c0b505caa6c1ad10ed8',1,'vg::Surjector']]],
- ['max_5fband_5fjump_12663',['max_band_jump',['../classvg_1_1Mapper.html#a916fd22fce2ebf7953863590c45f5150',1,'vg::Mapper']]],
- ['max_5fbranch_5ftrim_5flength_12664',['max_branch_trim_length',['../classvg_1_1MultipathMapper.html#a9e260c61a4b39d27286957c4f012a26a',1,'vg::MultipathMapper']]],
- ['max_5fbubble_5fpaths_12665',['max_bubble_paths',['../classvg_1_1LegacyCaller.html#a807ba6e24d16bac14c24fdc973cb837b',1,'vg::LegacyCaller::max_bubble_paths()'],['../classvg_1_1RepresentativeTraversalFinder.html#ad2de8e0f74e29d2338d0e9f99a764e23',1,'vg::RepresentativeTraversalFinder::max_bubble_paths()']]],
- ['max_5fbuf_5fsize_12666',['max_buf_size',['../classvg_1_1StreamSorter.html#a192491eeef2fa2c99522f2ad23f12035',1,'vg::StreamSorter']]],
- ['max_5fchain_5fconnection_12667',['max_chain_connection',['../classvg_1_1MinimizerMapper.html#a4d54618686eb23ac6a4a2c3579f3fec9',1,'vg::MinimizerMapper']]],
- ['max_5fchaining_5fproblems_12668',['max_chaining_problems',['../classvg_1_1MinimizerMapper.html#a034098134b882ab3e4c8dc0542763f97',1,'vg::MinimizerMapper']]],
- ['max_5fchains_5fper_5ftree_12669',['max_chains_per_tree',['../classvg_1_1MinimizerMapper.html#ada8578ed33c349fa8f9e5ff7562ac71f',1,'vg::MinimizerMapper']]],
- ['max_5fcluster_5fmapping_5fquality_12670',['max_cluster_mapping_quality',['../classvg_1_1Mapper.html#a92ea8476aae3d65f0b46f6c7353c21be',1,'vg::Mapper']]],
- ['max_5fcontext_5fradius_12671',['max_context_radius',['../classvg_1_1VariantAdder.html#a943bba24f9a1a7197744e74ee5465e5d',1,'vg::VariantAdder']]],
- ['max_5fdagify_5fduplications_12672',['max_dagify_duplications',['../classvg_1_1MultipathMapper.html#a10c136d72e6f32ff28cd608efc1f31db',1,'vg::MultipathMapper']]],
- ['max_5fdegree_12673',['max_degree',['../structPruningParameters.html#a58d4dca5e0623280f669e386a5eadd2f',1,'PruningParameters']]],
- ['max_5fdeletion_5fscan_5fnodes_12674',['max_deletion_scan_nodes',['../classvg_1_1VCFTraversalFinder.html#a3e61ffdb1cf6733311b444df38928137',1,'vg::VCFTraversalFinder']]],
- ['max_5fdepth_12675',['max_depth',['../classvg_1_1RepresentativeTraversalFinder.html#a79339337af609bc33f77cf4696962492',1,'vg::RepresentativeTraversalFinder']]],
- ['max_5fdiagonal_12676',['max_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#abde71e96e8aac83b5233fa782b514290',1,'vg::WFATree::ScoreProperties']]],
- ['max_5fdirect_5fto_5fchain_12677',['max_direct_to_chain',['../classvg_1_1MinimizerMapper.html#adfe5996aca0f60eace262a8c06f76f30',1,'vg::MinimizerMapper']]],
- ['max_5fdisplayed_5fsuggestions_5fper_5fcategory_12678',['MAX_DISPLAYED_SUGGESTIONS_PER_CATEGORY',['../classvg_1_1DiagramExplainer.html#abb72da5ad3b5613b80c4a39c7e4b8f18',1,'vg::DiagramExplainer']]],
- ['max_5fdistance_12679',['max_distance',['../classvg_1_1WFATree.html#a761ae97d39a69d470cae27ef7cfb28a9',1,'vg::WFATree::max_distance()'],['../classvg_1_1IncrementalSubgraph.html#a06d0598eae084de70fa40ed859ce9704',1,'vg::IncrementalSubgraph::max_distance()']]],
- ['max_5fdozeu_5fcells_12680',['max_dozeu_cells',['../classvg_1_1MinimizerMapper.html#aa462df061307b0b35996a6ecd33091f7',1,'vg::MinimizerMapper']]],
- ['max_5fdp_5fcells_12681',['max_dp_cells',['../classvg_1_1MinimizerMapper.html#af673f62cfdb402e93acaf2eb81680772',1,'vg::MinimizerMapper']]],
- ['max_5fexpected_5fdist_5fapprox_5ferror_12682',['max_expected_dist_approx_error',['../classvg_1_1OrientedDistanceClusterer.html#a74174c834516a6b4116ff6b9972ae10c',1,'vg::OrientedDistanceClusterer::max_expected_dist_approx_error()'],['../classvg_1_1MultipathMapper.html#a23d02e5f180a337a4b9eff178fc0b65d',1,'vg::MultipathMapper::max_expected_dist_approx_error()']]],
- ['max_5fexponential_5frate_5fintercept_12683',['max_exponential_rate_intercept',['../classvg_1_1MultipathMapper.html#a3b9f8d9eb806a7dd7e05a0b1c4851bc8',1,'vg::MultipathMapper']]],
- ['max_5fexponential_5frate_5fslope_12684',['max_exponential_rate_slope',['../classvg_1_1MultipathMapper.html#a0c2252c568582797db9b65756694eaff',1,'vg::MultipathMapper']]],
- ['max_5fexponential_5fshape_5fintercept_12685',['max_exponential_shape_intercept',['../classvg_1_1MultipathMapper.html#a2e7f7551674fa412abd1333c0baf6672',1,'vg::MultipathMapper']]],
- ['max_5fexponential_5fshape_5fslope_12686',['max_exponential_shape_slope',['../classvg_1_1MultipathMapper.html#a8ea8f5c8ad1906ccf0b878a6821a16e2',1,'vg::MultipathMapper']]],
- ['max_5fextension_5fmismatches_12687',['max_extension_mismatches',['../classvg_1_1MinimizerMapper.html#a30fd35c63e316b4a1fcdeca3752ea667',1,'vg::MinimizerMapper']]],
- ['max_5fextensions_12688',['max_extensions',['../classvg_1_1MinimizerMapper.html#a5d03747a37700e9a3f73c308709f70d1',1,'vg::MinimizerMapper']]],
- ['max_5ffan_5fin_12689',['max_fan_in',['../classvg_1_1StreamSorter.html#a673ce446e1ba8b9917f9475b9003364d',1,'vg::StreamSorter']]],
- ['max_5ffanout_5fbase_5fquality_12690',['max_fanout_base_quality',['../classvg_1_1MultipathMapper.html#a63f9b0403dceed8c8055ce5c423dd8fe',1,'vg::MultipathMapper']]],
- ['max_5ffans_5fout_12691',['max_fans_out',['../classvg_1_1MultipathMapper.html#a46f2835eebe0c9ab495e697c975534b6',1,'vg::MultipathMapper']]],
- ['max_5ffragment_5flength_12692',['max_fragment_length',['../classvg_1_1MinimizerMapper.html#a4575d140e45d04d3d36e6a99bf7b0241',1,'vg::MinimizerMapper']]],
- ['max_5ffragments_12693',['max_fragments',['../classvg_1_1MinimizerMapper.html#a50848190e760fb1f3c45fd785f57c8a3',1,'vg::MinimizerMapper']]],
- ['max_5fgap_12694',['max_gap',['../classvg_1_1MEMClusterer.html#a9b8459888ec7b51e739c3be04825b4fd',1,'vg::MEMClusterer']]],
- ['max_5fgroup_5fsize_12695',['max_group_size',['../classvg_1_1io_1_1MessageEmitter.html#a4bcef07ec2af1cb44f4cd3abfe58f29c',1,'vg::io::MessageEmitter']]],
- ['max_5fhandle_12696',['max_handle',['../classvg_1_1DozeuPinningOverlay.html#a63162330a1caec7a81abf6b5f747da32',1,'vg::DozeuPinningOverlay']]],
- ['max_5fhandle_5fmemo_5fsize_12697',['max_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a478ef9dbdebaccadc78679868baa350d',1,'vg::MemoizingGraph']]],
- ['max_5fhet_5fbias_12698',['max_het_bias',['../classvg_1_1Genotyper.html#a96285d96b960d50199ad3167c20ddf91',1,'vg::Genotyper::max_het_bias()'],['../classvg_1_1RatioSupportSnarlCaller.html#a78f0c7800c9c27021c66d68cbd0335b7',1,'vg::RatioSupportSnarlCaller::max_het_bias()']]],
- ['max_5fid_12699',['max_id',['../structvg_1_1ConstructedChunk.html#aca49ac5cc43f6390443ab02496fdfd74',1,'vg::ConstructedChunk::max_id()'],['../classvg_1_1Constructor.html#a8466741ece82babe9e892a50bd06a1d9',1,'vg::Constructor::max_id()'],['../classvg_1_1DagifiedGraph.html#a154919be0eb8719eb2fa0181584a9c66',1,'vg::DagifiedGraph::max_id()'],['../classvg_1_1SubHandleGraph.html#ad0090894570f0c53d4c3011472a01d37',1,'vg::SubHandleGraph::max_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a90afa5abb895d5bb6800cd99759de14a',1,'vg::algorithms::GFAIDMapInfo::max_id()'],['../classxg_1_1XG.html#a2cf5a51e7056900fd3872792ef5fa2a5',1,'xg::XG::max_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade12e1983845ebfbf47782b8867c708c',1,'handlegraph::algorithms::SubHandleGraph::max_id()']]],
- ['max_5findel_5fbases_12700',['max_indel_bases',['../classvg_1_1MinimizerMapper.html#a05b1280ff66b9ad01015c490f35fc005',1,'vg::MinimizerMapper']]],
- ['max_5findel_5fbases_5fper_5fbase_12701',['max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a82da9f52e8af8e9dde669c903d441adc',1,'vg::MinimizerMapper']]],
- ['max_5findel_5fhet_5fbias_12702',['max_indel_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a9298ec62feb5ab8f593fdf2c6cd2b620',1,'vg::RatioSupportSnarlCaller']]],
- ['max_5finput_5fversion_12703',['MAX_INPUT_VERSION',['../classvg_1_1StreamIndexBase.html#aa497c1ad37621af86f5f40d45e0f30b2',1,'vg::StreamIndexBase']]],
- ['max_5fintron_5flength_12704',['max_intron_length',['../classvg_1_1MultipathMapper.html#a51be0d0325abe9a3afa023477d9c2ab0',1,'vg::MultipathMapper']]],
- ['max_5fiterations_12705',['max_iterations',['../classvg_1_1SmallSnarlSimplifier.html#a212bd3bc07ab19cb42edef936ee62f7a',1,'vg::SmallSnarlSimplifier::max_iterations()'],['../minimizer__main_8cpp.html#a932fcab549241f3cf9efead93803fabc',1,'MAX_ITERATIONS(): minimizer_main.cpp']]],
- ['max_5fkmers_5fper_5fblock_12706',['max_kmers_per_block',['../classvg_1_1ParallelKFFReader.html#a0179377c78c5e599f903b70c954ffd12',1,'vg::ParallelKFFReader']]],
- ['max_5flength_12707',['max_length',['../classvg_1_1ReadFilter.html#a2afae0acb031354f67f95f20dda1c4b8',1,'vg::ReadFilter']]],
- ['max_5flocal_5fextensions_12708',['max_local_extensions',['../classvg_1_1MinimizerMapper.html#a4e6142c1ccdde28230769e5a8b629d9f',1,'vg::MinimizerMapper']]],
- ['max_5flookback_5fbases_12709',['max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ae94869146878dba80c980d4e35830abe',1,'vg::MinimizerMapper']]],
- ['max_5flookback_5fbases_5fper_5fbase_12710',['max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a48ec2ca2886d6f069546d6a424becb61',1,'vg::MinimizerMapper']]],
- ['max_5flow_5fcomplexity_5fanchor_5fprune_12711',['max_low_complexity_anchor_prune',['../classvg_1_1Surjector.html#a0f304005022b214c309ff60a1f186b1f',1,'vg::Surjector']]],
- ['max_5flow_5fcomplexity_5fanchor_5ftrim_12712',['max_low_complexity_anchor_trim',['../classvg_1_1Surjector.html#a9c0cf333d85aef40eda8354075dfa01e',1,'vg::Surjector']]],
- ['max_5fma_5fbias_12713',['max_ma_bias',['../classvg_1_1RatioSupportSnarlCaller.html#ac6d48f0372786d80db440fa67523af9e',1,'vg::RatioSupportSnarlCaller']]],
- ['max_5fmapping_5fp_5fvalue_12714',['max_mapping_p_value',['../classvg_1_1MultipathMapper.html#aa7656b2372ae8450e48a9db512ce309d',1,'vg::MultipathMapper']]],
- ['max_5fmapping_5fquality_12715',['max_mapping_quality',['../classvg_1_1BaseMapper.html#a467884235c316072a1ed7136faa14be3',1,'vg::BaseMapper']]],
- ['max_5fmemory_5fproportion_12716',['max_memory_proportion',['../structvg_1_1IndexingParameters.html#a28aa7110447f9ba3a74e1e3326959751',1,'vg::IndexingParameters']]],
- ['max_5fmessage_5fsize_12717',['MAX_MESSAGE_SIZE',['../classvg_1_1io_1_1MessageEmitter.html#a67ece9e5b7c411ccb40169b650e1f5ae',1,'vg::io::MessageEmitter::MAX_MESSAGE_SIZE()'],['../classvg_1_1io_1_1MessageIterator.html#a5b2b881e4032fb2ecfa8da35ad13e602',1,'vg::io::MessageIterator::MAX_MESSAGE_SIZE()']]],
- ['max_5fmiddle_5fdp_5flength_12718',['max_middle_dp_length',['../classvg_1_1MinimizerMapper.html#aa8bdbd3ae354863aaa50bcd0fdfb340f',1,'vg::MinimizerMapper']]],
- ['max_5fmiddle_5fgap_12719',['max_middle_gap',['../classvg_1_1MinimizerMapper.html#a9e0bcb7de51be992126d051cf343a9c5',1,'vg::MinimizerMapper']]],
- ['max_5fmin_5fchain_5fscore_12720',['max_min_chain_score',['../classvg_1_1MinimizerMapper.html#a5dc73dddd111a8a64b5285a2e75e3ba5',1,'vg::MinimizerMapper']]],
- ['max_5fmismatches_12721',['MAX_MISMATCHES',['../classvg_1_1GaplessExtender.html#aaa77a2fc74630664d12527818826e28b',1,'vg::GaplessExtender']]],
- ['max_5fmissing_5fvariant_5fwarnings_12722',['max_missing_variant_warnings',['../classvg_1_1HaplotypeIndexer.html#a512203218e3b78afa0fc5c0e594e6516',1,'vg::HaplotypeIndexer']]],
- ['max_5fmotif_5fpairs_12723',['max_motif_pairs',['../classvg_1_1MultipathMapper.html#a7427a85cc5f4ff850524ecf929ca72c8',1,'vg::MultipathMapper']]],
- ['max_5fmulti_5falns_12724',['max_multi_alns',['../classvg_1_1BandedGlobalAligner.html#a7191ef47a3e2a5232e5ba74283c646b6',1,'vg::BandedGlobalAligner::max_multi_alns()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9114c48d4516fb6115fe47e910624377',1,'vg::BandedGlobalAligner::AltTracebackStack::max_multi_alns()']]],
- ['max_5fmultimaps_12725',['max_multimaps',['../classvg_1_1Mapper.html#a462268836d2c5f5f4acde6ca9060e593',1,'vg::Mapper::max_multimaps()'],['../classvg_1_1MinimizerMapper.html#aede601962425752ec75ea1d890505357',1,'vg::MinimizerMapper::max_multimaps()']]],
- ['max_5fnode_12726',['max_node',['../classvg_1_1SubgraphOverlay.html#a6eb5155328921c3a0ec46e62c7edfdca',1,'vg::SubgraphOverlay']]],
- ['max_5fnode_5fsize_12727',['max_node_size',['../classvg_1_1Constructor.html#a6ca9a0b7785c1c9c6e859cc75ea2a2f4',1,'vg::Constructor::max_node_size()'],['../structvg_1_1IndexingParameters.html#a6b392a212907d34c6f586cb7cefeac1f',1,'vg::IndexingParameters::max_node_size()'],['../classvg_1_1VariantAdder.html#a3e1dae34969d5779d09819de627a6bd5',1,'vg::VariantAdder::max_node_size()']]],
- ['max_5fnum_5fnodes_12728',['max_num_nodes',['../classvg_1_1IncrementalSubgraph.html#a37038271292f8c25f63b9d3e8400d13e',1,'vg::IncrementalSubgraph']]],
- ['max_5foverhang_12729',['max_overhang',['../classvg_1_1ReadFilter.html#a54c30818834f623c78a2cb0a0e9b4a91',1,'vg::ReadFilter']]],
- ['max_5fp_5fvalue_5fmemo_5fsize_12730',['max_p_value_memo_size',['../classvg_1_1MultipathMapper.html#ada39acac8f403bf92632024be4e448e1',1,'vg::MultipathMapper']]],
- ['max_5fparsed_5fvariant_5fsize_12731',['max_parsed_variant_size',['../classvg_1_1Constructor.html#a2725e8e6876deb0ca0ccf597955163c2',1,'vg::Constructor']]],
- ['max_5fpath_5fid_12732',['max_path_id',['../classvg_1_1Paths.html#ac5e9e182ecf09166f516c6fbf9923a29',1,'vg::Paths']]],
- ['max_5fpath_5flength_12733',['max_path_length',['../classvg_1_1Filter.html#a77225b4859a55b509396332e96c81c0e',1,'vg::Filter']]],
- ['max_5fpath_5fsearch_5fsteps_12734',['max_path_search_steps',['../classvg_1_1Genotyper.html#a500af110546f9572fe40d5ef098552d9',1,'vg::Genotyper::max_path_search_steps()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa61be13e0e070bd8af8fe890b47dfde5',1,'vg::ReadRestrictedTraversalFinder::max_path_search_steps()'],['../classvg_1_1PathRestrictedTraversalFinder.html#af24fb970905bbb3d2e04631fd3d0918b',1,'vg::PathRestrictedTraversalFinder::max_path_search_steps()']]],
- ['max_5fprune_5fiterations_12735',['max_prune_iterations',['../classvg_1_1VCFTraversalFinder.html#a667a1499ac092df03deaa7ec0813d6df',1,'vg::VCFTraversalFinder']]],
- ['max_5freads_12736',['max_reads',['../classvg_1_1ReadFilter.html#a1a4d052b3060e2b8a434310ce6dc14f5',1,'vg::ReadFilter']]],
- ['max_5freads_5fused_12737',['max_reads_used',['../classvg_1_1ReadFilter.html#a06835480f40ef09dd073cc14a469f760',1,'vg::ReadFilter']]],
- ['max_5fref_5fhet_5fbias_12738',['max_ref_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a6012c94aabfcffde89851c587ed34f9e',1,'vg::RatioSupportSnarlCaller']]],
- ['max_5frescue_5fattempts_12739',['max_rescue_attempts',['../classvg_1_1MinimizerMapper.html#a0985bcf3a1ed28098bf0271b251dd6e2',1,'vg::MinimizerMapper::max_rescue_attempts()'],['../classvg_1_1MultipathMapper.html#a87f585b42e49cd2e642ab092e54a309a',1,'vg::MultipathMapper::max_rescue_attempts()']]],
- ['max_5frescue_5fp_5fvalue_12740',['max_rescue_p_value',['../classvg_1_1MultipathMapper.html#afe5cb57d342ca46e5ee2e132d1d238d3',1,'vg::MultipathMapper']]],
- ['max_5frgfa_5frank_12741',['max_rgfa_rank',['../classvg_1_1algorithms_1_1GFAParser.html#ae5841a4a832376b2894cbbb956c89569',1,'vg::algorithms::GFAParser']]],
- ['max_5fsearch_5fdepth_12742',['max_search_depth',['../classvg_1_1LegacyCaller.html#a321503fbe153735736a542d4ad5d9235',1,'vg::LegacyCaller']]],
- ['max_5fsearch_5fwidth_12743',['max_search_width',['../classvg_1_1LegacyCaller.html#a01572bf56d35cc89232fac3dce35c891',1,'vg::LegacyCaller']]],
- ['max_5fseparation_12744',['max_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a1094dccc104bf859b2bdb8b5fac6bec6',1,'vg::GreedyMinDistanceClusterer']]],
- ['max_5fsingle_5fend_5fmappings_5ffor_5frescue_12745',['max_single_end_mappings_for_rescue',['../classvg_1_1MultipathMapper.html#a1dc8310407eabb6cbe419d5765364df7',1,'vg::MultipathMapper']]],
- ['max_5fskipped_5fbases_12746',['max_skipped_bases',['../classvg_1_1MinimizerMapper.html#ad72974afc9d7fadd23716fba49b7e82f',1,'vg::MinimizerMapper']]],
- ['max_5fslide_12747',['max_slide',['../classvg_1_1Surjector.html#a0e40286284b27ccef7fbcc028fc40142',1,'vg::Surjector']]],
- ['max_5fsnarl_5fcut_5fsize_12748',['max_snarl_cut_size',['../classvg_1_1MultipathMapper.html#a507872f1a20d6b0e34b6f9b8dac2639f',1,'vg::MultipathMapper']]],
- ['max_5fsnarl_5fedges_12749',['max_snarl_edges',['../classvg_1_1FlowCaller.html#a07f59c5945984d13f67ec660923c0f81',1,'vg::FlowCaller']]],
- ['max_5fsnarl_5fshallow_5fsize_12750',['max_snarl_shallow_size',['../classvg_1_1NestedFlowCaller.html#ab5e10be4ba6c1d33235e5844cfb8b8c0',1,'vg::NestedFlowCaller']]],
- ['max_5fsoftclip_5fiterations_12751',['max_softclip_iterations',['../classvg_1_1Mapper.html#a145a97f0859865815bba2562024078e9',1,'vg::Mapper']]],
- ['max_5fsoftclip_5foverlap_12752',['max_softclip_overlap',['../classvg_1_1MultipathMapper.html#afcacb8b30589b82487cca2a1755320f3',1,'vg::MultipathMapper']]],
- ['max_5fsplice_5foverhang_12753',['max_splice_overhang',['../classvg_1_1MultipathMapper.html#a8c71d1bf28c8567e878c5cd004b94e8b',1,'vg::MultipathMapper']]],
- ['max_5fsplice_5fref_5fsearch_5flength_12754',['max_splice_ref_search_length',['../classvg_1_1MultipathMapper.html#a4f4bca24b9dbe1a7a40499a30e91c4f6',1,'vg::MultipathMapper']]],
- ['max_5fsteps_5fof_5fhandle_5fmemo_5fsize_12755',['max_steps_of_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a55aadb2458a395d6fd47f9a9c5ddf415',1,'vg::MemoizingGraph']]],
- ['max_5fsub_5fmem_5frecursion_5fdepth_12756',['max_sub_mem_recursion_depth',['../classvg_1_1BaseMapper.html#ac12496865e23fd68ba1f579dcb050037',1,'vg::BaseMapper']]],
- ['max_5fsubgraph_5fbases_5fper_5fread_5fbase_12757',['max_subgraph_bases_per_read_base',['../classvg_1_1Surjector.html#a14e20f641f120ca8fa5206ace84be331',1,'vg::Surjector']]],
- ['max_5fsuboptimal_5fpath_5fscore_5fratio_12758',['max_suboptimal_path_score_ratio',['../classvg_1_1MultipathMapper.html#ac117889984b58f3c0fd3d389a8ee7f26',1,'vg::MultipathMapper']]],
- ['max_5ftag_5flength_12759',['MAX_TAG_LENGTH',['../classvg_1_1io_1_1Registry.html#a8791c3355999775f973ab74fa4111fa2',1,'vg::io::Registry']]],
- ['max_5ftail_5fanchor_5fprune_12760',['max_tail_anchor_prune',['../classvg_1_1Surjector.html#a59034e11562bb0969c25defd215f166b',1,'vg::Surjector']]],
- ['max_5ftail_5fdp_5flength_12761',['max_tail_dp_length',['../classvg_1_1MinimizerMapper.html#ab333ad05b05cdcd8d59bd0c6b2733e04',1,'vg::MinimizerMapper']]],
- ['max_5ftail_5fgap_12762',['max_tail_gap',['../classvg_1_1MinimizerMapper.html#a25dccb476876cf2797743ec916c3d661',1,'vg::MinimizerMapper']]],
- ['max_5ftail_5flength_12763',['max_tail_length',['../classvg_1_1MinimizerMapper.html#ad041c860d77e6ad2bd025bd2da337d7a',1,'vg::MinimizerMapper::max_tail_length()'],['../classvg_1_1Surjector.html#a185cc3fad9b021b08f03880ae0119db6',1,'vg::Surjector::max_tail_length()']]],
- ['max_5ftail_5fmerge_5fsupress_5flength_12764',['max_tail_merge_supress_length',['../classvg_1_1MultipathMapper.html#a8de58bf1942c4aa16b762554268d3e3d',1,'vg::MultipathMapper']]],
- ['max_5ftarget_5ffactor_12765',['max_target_factor',['../classvg_1_1Mapper.html#a5ecf825b76d29c8b8242d8167fae6cc4',1,'vg::Mapper']]],
- ['max_5fto_5ffragment_12766',['max_to_fragment',['../classvg_1_1MinimizerMapper.html#ab6b8884b622acf26ceeae7ea1f2204d6',1,'vg::MinimizerMapper']]],
- ['max_5ftrav_5fsize_12767',['max_trav_size',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a4842f02f38903b12e0c7de54bf0482e3',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
- ['max_5ftraversal_5fcutoff_12768',['max_traversal_cutoff',['../classvg_1_1VCFTraversalFinder.html#a2ece2a9a96c909c7859bd88d54daa559',1,'vg::VCFTraversalFinder']]],
- ['max_5ftraversal_5flength_12769',['max_traversal_length',['../classvg_1_1FlowTraversalFinder.html#a1dbaa147e49e103151629a210977c58b',1,'vg::FlowTraversalFinder']]],
- ['max_5ftries_12770',['max_tries',['../classvg_1_1AbstractReadSampler.html#a68421d544f78d22ed080321929c9fd01',1,'vg::AbstractReadSampler']]],
- ['max_5funcalled_5falleles_12771',['max_uncalled_alleles',['../classvg_1_1VCFOutputCaller.html#acf04132e0a3cf52b5ba58a88f0b2d3d4',1,'vg::VCFOutputCaller']]],
- ['max_5funique_5fmin_12772',['max_unique_min',['../classvg_1_1MinimizerMapper.html#a8862622f6f711cc6a797b26990c9f195',1,'vg::MinimizerMapper']]],
- ['max_5fvalue_12773',['max_value',['../structvg_1_1SummaryStatistics.html#ad86748ae17ecc7acce49364a9fa93a74',1,'vg::SummaryStatistics::max_value()'],['../structvg_1_1varint__vector__t.html#a92149196c806e2230f53f2d62e9bf8b3',1,'vg::varint_vector_t::MAX_VALUE()']]],
- ['max_5fvcf_5fline_5flength_12774',['max_vcf_line_length',['../classvg_1_1VCFOutputCaller.html#a549336b5a84bfdef74b8ae8116b1b151',1,'vg::VCFOutputCaller']]],
- ['max_5fwalk_12775',['max_walk',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6d8dc74ae9eaaabf35ba1c89cfae8a11',1,'vg::PathOrientedDistanceMeasurer']]],
- ['max_5fwidth_12776',['max_width',['../classvg_1_1RepresentativeTraversalFinder.html#aac2939337439d7566246889b3a4655c6',1,'vg::RepresentativeTraversalFinder']]],
- ['max_5fxdrop_5fgap_5flength_12777',['max_xdrop_gap_length',['../classvg_1_1Mapper.html#a2754b67772ef25cb66d06b66b8caeb55',1,'vg::Mapper']]],
- ['maximum_5fquality_12778',['maximum_quality',['../classvg_1_1Packer.html#a0de02be2009ac1d477d5cc8fefccab1c',1,'vg::Packer']]],
- ['maximum_5fsample_5fsize_12779',['maximum_sample_size',['../classvg_1_1FragmentLengthDistribution.html#a82ad9fe36dc81ea108a530b7f9792b78',1,'vg::FragmentLengthDistribution']]],
- ['maybe_5fmq_5fthreshold_12780',['maybe_mq_threshold',['../classvg_1_1Mapper.html#a26d2d7d3964d9210c963b325c64678b0',1,'vg::Mapper']]],
- ['mean_12781',['mean',['../structvg_1_1SummaryStatistics.html#a275cb7138ffd1285cbdad3ae7017cbe8',1,'vg::SummaryStatistics']]],
- ['median_12782',['median',['../structvg_1_1SummaryStatistics.html#ae98f01cfb86f82f0e9185c63fb57445f',1,'vg::SummaryStatistics']]],
- ['mem_12783',['mem',['../classvg_1_1MEMChainModelVertex.html#acd9990963345deb38096763554ae4b3d',1,'vg::MEMChainModelVertex::mem()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#a9f3480f5d231cf8d4325ae558a379f10',1,'vg::MEMClusterer::HitNode::mem()']]],
- ['mem_5fcoverage_5fmin_5fratio_12784',['mem_coverage_min_ratio',['../classvg_1_1MultipathMapper.html#ae977e7bbf30ca7634e7422aa76c16e71',1,'vg::MultipathMapper']]],
- ['mem_5freseed_5flength_12785',['mem_reseed_length',['../classvg_1_1BaseMapper.html#abaea877646c1be5aea6200201d28c4cf',1,'vg::BaseMapper']]],
- ['memo_12786',['memo',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a382739dd7136e759c6a01725ddebd301',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['memory_5fhigh_5fwater_5fkb_12787',['memory_high_water_kb',['../classvg_1_1Watchdog.html#aa759f3d73ebe15aeb95a13a8c86a0b59',1,'vg::Watchdog']]],
- ['merge_12788',['merge',['../structGBWTConfig.html#a850f9f30af38996cc64f1fabb20a6458',1,'GBWTConfig']]],
- ['merge_5fparameters_12789',['merge_parameters',['../structGBWTConfig.html#a77aea6d71d3a6904f01eeccf1f950318',1,'GBWTConfig']]],
- ['merged_5fgroup_12790',['merged_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#acd6301aa5e085df9fa56ba8b102cdde6',1,'vg::IndexedVG::CacheEntry']]],
- ['message_12791',['message',['../structvg_1_1AlignmentValidity.html#a7eede46d9951c0c2b0b4c226c6987691',1,'vg::AlignmentValidity::message()'],['../classvg_1_1NoAlignmentInBandException.html#a3cc1fd5899066709228ecea9e5a25956',1,'vg::NoAlignmentInBandException::message()']]],
- ['message_5fbuffer_12792',['message_buffer',['../structvg_1_1algorithms_1_1GFAFormatError.html#a24e4e4d2285fd970978365e2747165c8',1,'vg::algorithms::GFAFormatError']]],
- ['message_5femitter_12793',['message_emitter',['../classvg_1_1io_1_1ProtobufEmitter.html#a1bdc1e48041d69eeca45745580af19f3',1,'vg::io::ProtobufEmitter']]],
- ['message_5fhandlers_12794',['message_handlers',['../classvg_1_1io_1_1ProtobufEmitter.html#a73231a5a45811c280d1a6d346abc75eb',1,'vg::io::ProtobufEmitter']]],
- ['message_5fit_12795',['message_it',['../classvg_1_1io_1_1ProtobufIterator.html#a787d06e13a1799b7e65ee1aa19ec3bb8',1,'vg::io::ProtobufIterator']]],
- ['metadata_12796',['metadata',['../structGBWTConfig.html#a0e91b96d773182fc4e4e36314ae6bd8d',1,'GBWTConfig']]],
- ['metadata_5fmode_12797',['metadata_mode',['../structGBWTConfig.html#a102642e75fdf2b95d22a07d372ca2890',1,'GBWTConfig']]],
- ['min_12798',['min',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#ad4cda218b41dfcb1dfdb3d3c5f3924c1',1,'vg::WFAExtender::ErrorModel::Event']]],
- ['min_5fad_5flog_5flikelihood_5ffor_5ffilter_12799',['min_ad_log_likelihood_for_filter',['../classvg_1_1RatioSupportSnarlCaller.html#a16602959db7c2bc06471474b07a3c2f7',1,'vg::RatioSupportSnarlCaller']]],
- ['min_5falt_5fpath_5fsupport_12800',['min_alt_path_support',['../classvg_1_1SupportBasedSnarlCaller.html#a17f76956318b838695d8b120d553ce24',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5favg_5fqual_12801',['min_avg_qual',['../classvg_1_1Filter.html#aa2f91d1daf04d2fdd6eb75183994d834',1,'vg::Filter']]],
- ['min_5fbanded_5fmq_12802',['min_banded_mq',['../classvg_1_1Mapper.html#a4fe883a960df0bbef6d08cfbe483c179',1,'vg::Mapper']]],
- ['min_5fbase_5fquality_12803',['min_base_quality',['../classvg_1_1ReadFilter.html#a7fe13f943f153913f16aa594720d350a',1,'vg::ReadFilter']]],
- ['min_5fbase_5fquality_5ffraction_12804',['min_base_quality_fraction',['../classvg_1_1ReadFilter.html#ab8c6af52884a83d9538ea7ef42ac9eb4',1,'vg::ReadFilter']]],
- ['min_5fbp_5fedge_5foverride_12805',['min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a767e1ca73abc43065673009d115c310d',1,'vg::TraversalSupportFinder']]],
- ['min_5fchain_5fscore_5fper_5fbase_12806',['min_chain_score_per_base',['../classvg_1_1MinimizerMapper.html#a2b4cc838d0959b158c0c68b1e84e9123',1,'vg::MinimizerMapper']]],
- ['min_5fchaining_5fproblems_12807',['min_chaining_problems',['../classvg_1_1MinimizerMapper.html#a821c2a05942d63254a2485a1e0987b80',1,'vg::MinimizerMapper']]],
- ['min_5fchains_12808',['min_chains',['../classvg_1_1MinimizerMapper.html#a85797857c8e3f3bc363fa634af55889c',1,'vg::MinimizerMapper']]],
- ['min_5fcluster_5flength_12809',['min_cluster_length',['../classvg_1_1Mapper.html#a70ed23d3ba482d38f7201376e179af9f',1,'vg::Mapper']]],
- ['min_5fclustering_5fmem_5flength_12810',['min_clustering_mem_length',['../classvg_1_1MultipathMapper.html#ac656fb3b81d4cf6d06fb077551b54b7f',1,'vg::MultipathMapper']]],
- ['min_5fcount_5fto_5fkeep_12811',['min_count_to_keep',['../classvg_1_1RareVariantSimplifier.html#aa481bbf8d0d969a9f9aa350fd376500e',1,'vg::RareVariantSimplifier']]],
- ['min_5fcov_12812',['min_cov',['../classvg_1_1Filter.html#a77f731ad12fc655130808337452ba734',1,'vg::Filter']]],
- ['min_5fdepth_12813',['min_depth',['../classvg_1_1Filter.html#a941f203667435234a1e08cce0358d8c6',1,'vg::Filter']]],
- ['min_5fdiagonal_12814',['min_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#ae69b636772fc01c9bd756c2b6dd7fd05',1,'vg::WFATree::ScoreProperties']]],
- ['min_5fdistance_12815',['min_distance',['../classvg_1_1WFATree.html#a9578f5415befbcf1260abf8d4536f538',1,'vg::WFATree']]],
- ['min_5fedge_5fsupport_12816',['min_edge_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#aabc81064635f9311af46bf2b5f1417aa',1,'vg::SupportRestrictedTraversalFinder::min_edge_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a16cd92c3b27a0b6be9d9154a7d9da77a',1,'vg::RepresentativeTraversalFinder::min_edge_support()']]],
- ['min_5fend_5fmatches_12817',['min_end_matches',['../classvg_1_1ReadFilter.html#a05d07dd311e58f3fc04d510870ddf662',1,'vg::ReadFilter']]],
- ['min_5fextension_5fsets_12818',['min_extension_sets',['../classvg_1_1MinimizerMapper.html#a1df84f11e9476595bcde3584553d2830',1,'vg::MinimizerMapper']]],
- ['min_5fextensions_12819',['min_extensions',['../classvg_1_1MinimizerMapper.html#a03f18247f88d4817feef2d25a46fd5ca',1,'vg::MinimizerMapper']]],
- ['min_5ffold_5fcoverage_5ffor_5fdownsample_12820',['min_fold_coverage_for_downsample',['../classvg_1_1Surjector.html#ac21d8c91876c3522c56c4c1c2b8f8f58',1,'vg::Surjector']]],
- ['min_5ffrequency_5fto_5fkeep_12821',['min_frequency_to_keep',['../classvg_1_1RareVariantSimplifier.html#a7aca3c00c47d8a8c6261536952fd96d8',1,'vg::RareVariantSimplifier']]],
- ['min_5fhandle_12822',['min_handle',['../classvg_1_1DagifiedGraph.html#a80c29e6e7494413dd631ea741d77f8c0',1,'vg::DagifiedGraph::min_handle()'],['../classxg_1_1XGPath.html#a59c1b92f21b5d102f70808266b457e7e',1,'xg::XGPath::min_handle()']]],
- ['min_5fid_12823',['min_id',['../classvg_1_1SubHandleGraph.html#a81878c5b09f4863b125f9de74ce11315',1,'vg::SubHandleGraph::min_id()'],['../classxg_1_1XG.html#a89a7150cd2c37698fc33ce0953f6019b',1,'xg::XG::min_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af225cef56e4c7af36ea3252d86502238',1,'handlegraph::algorithms::SubHandleGraph::min_id()']]],
- ['min_5fidentity_12824',['min_identity',['../classvg_1_1Mapper.html#a9b1d4bad7b2b7e96253006b4625329ac',1,'vg::Mapper']]],
- ['min_5fmad_5ffor_5ffilter_12825',['min_mad_for_filter',['../classvg_1_1SupportBasedSnarlCaller.html#aec268641676f41d2c24128cb9e17ac03',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5fmapq_12826',['min_mapq',['../classvg_1_1ReadFilter.html#a8da615d17aba7ed66be6174253ce64ce',1,'vg::ReadFilter']]],
- ['min_5fmedian_5fmem_5fcoverage_5ffor_5fsplit_12827',['min_median_mem_coverage_for_split',['../classvg_1_1MultipathMapper.html#a4aa16d72dd27681fef0f5d99fec8f0ee',1,'vg::MultipathMapper']]],
- ['min_5fmem_5flength_12828',['min_mem_length',['../classvg_1_1BaseMapper.html#a6de91c39c73a95b014b1773495985a09',1,'vg::BaseMapper']]],
- ['min_5fmultimaps_12829',['min_multimaps',['../classvg_1_1Mapper.html#a34d17aa5222b5b97e8e96d70a39c99c9',1,'vg::Mapper']]],
- ['min_5fnode_12830',['min_node',['../classvg_1_1SubgraphOverlay.html#a6fa8fb25c1244dfc3569ac1d37699334',1,'vg::SubgraphOverlay']]],
- ['min_5fnode_5fsupport_12831',['min_node_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#ae0201f741f7e5cffed2577d47e8e1830',1,'vg::SupportRestrictedTraversalFinder::min_node_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a873d02fe79d020bb106879f5b478e38f',1,'vg::RepresentativeTraversalFinder::min_node_support()']]],
- ['min_5fnode_5fsupport_5fcache_12832',['min_node_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a3a150bfc048afe50f2e006f77159bf34',1,'vg::CachedPackedTraversalSupportFinder']]],
- ['min_5fpercent_5fidentity_12833',['min_percent_identity',['../classvg_1_1Filter.html#afd9cc5bfa5740f71e70a601f7f0b8199',1,'vg::Filter']]],
- ['min_5fprimary_12834',['min_primary',['../classvg_1_1ReadFilter.html#a64132e9f5f27ce6930554ad3c197e694',1,'vg::ReadFilter']]],
- ['min_5fqual_12835',['min_qual',['../classvg_1_1Filter.html#ab3ced01093210b1379fbcd7de7709a30',1,'vg::Filter']]],
- ['min_5fqueue_5fitem_5fbytes_12836',['MIN_QUEUE_ITEM_BYTES',['../classvg_1_1io_1_1StreamMultiplexer.html#afd60eacdf650f68a3989c91670655146',1,'vg::io::StreamMultiplexer']]],
- ['min_5fread_5fseparation_12837',['min_read_separation',['../classvg_1_1ComponentMinDistanceClusterer.html#a6c48555f1245310c614265e3d9d69c42',1,'vg::ComponentMinDistanceClusterer']]],
- ['min_5frecurrence_12838',['min_recurrence',['../classvg_1_1Genotyper.html#afffa8d75fd4155bc7d420a41d92f198c',1,'vg::Genotyper::min_recurrence()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa00f717b20773b41578e642425fbf73b',1,'vg::ReadRestrictedTraversalFinder::min_recurrence()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a3085d06249a54ac345e3bebde7c2378c',1,'vg::PathRestrictedTraversalFinder::min_recurrence()']]],
- ['min_5fscore_5ffactor_12839',['min_score_factor',['../classvg_1_1VariantAdder.html#aae129564bcf5ec9fd9d0838754d27323',1,'vg::VariantAdder']]],
- ['min_5fscore_5fper_5fbase_12840',['min_score_per_base',['../classvg_1_1Genotyper.html#a8fc1fdccfa9829bb29903ed5d7b21b28',1,'vg::Genotyper']]],
- ['min_5fsecondary_12841',['min_secondary',['../classvg_1_1ReadFilter.html#af85c211a4a06a1fb750958002cefba0f',1,'vg::ReadFilter']]],
- ['min_5fseparation_12842',['min_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a97ed3ff5a8770a314b138148319b9a3b',1,'vg::GreedyMinDistanceClusterer']]],
- ['min_5fshift_5ffor_5fprune_12843',['min_shift_for_prune',['../classvg_1_1Surjector.html#a731d00674b2d71044a8e404be059c2cf',1,'vg::Surjector']]],
- ['min_5fsite_5fdepth_12844',['min_site_depth',['../classvg_1_1SupportBasedSnarlCaller.html#adde07f3e5ca89a2a565e8859ee641159',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5fsize_12845',['min_size',['../classvg_1_1SmallSnarlSimplifier.html#a6efa9c6d0dc38da336a5723f87e20e46',1,'vg::SmallSnarlSimplifier']]],
- ['min_5fsoftclip_5flength_5ffor_5fsplice_12846',['min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#a2d6a193c1277d948f7155da585e60367',1,'vg::MultipathMapper']]],
- ['min_5fsoftclipped_5fscore_5ffor_5fsplice_12847',['min_softclipped_score_for_splice',['../classvg_1_1MultipathMapper.html#aaae9feaf584c64fe27628e29778359b4',1,'vg::MultipathMapper']]],
- ['min_5fsplice_5flength_12848',['min_splice_length',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a801ecf2defc628516d4a5165ff745acb',1,'vg::SplicedHTSAlignmentEmitter::min_splice_length()'],['../classvg_1_1MultipathAlignmentEmitter.html#a38e7b3d9a6dca8b5601add1a6d9023e4',1,'vg::MultipathAlignmentEmitter::min_splice_length()'],['../classvg_1_1Surjector.html#a9046bb2c7267f996a6636518e2747b89',1,'vg::Surjector::min_splice_length()']]],
- ['min_5fsplice_5frepair_5flength_12849',['min_splice_repair_length',['../classvg_1_1Surjector.html#ad5048905a75d047631f3552632f58cd3',1,'vg::Surjector']]],
- ['min_5fsplice_5frescue_5fmatches_12850',['min_splice_rescue_matches',['../classvg_1_1MultipathMapper.html#a194ce33d0517a8ccd67c4e87d26f1191',1,'vg::MultipathMapper']]],
- ['min_5ftail_5fanchor_5flength_12851',['min_tail_anchor_length',['../classvg_1_1MultipathMapper.html#a9616c4b8786af795cfd1f007c5e0c1dc',1,'vg::MultipathMapper']]],
- ['min_5fto_5ffragment_12852',['min_to_fragment',['../classvg_1_1MinimizerMapper.html#a8b9e086aeaf58ab94283f9398890a9ca',1,'vg::MinimizerMapper']]],
- ['min_5ftotal_5fsupport_5ffor_5fcall_12853',['min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#a559c8afa8e4f1f73768d7d90ff6a6db0',1,'vg::SupportBasedSnarlCaller']]],
- ['min_5funique_5fnode_5ffraction_12854',['min_unique_node_fraction',['../classvg_1_1MinimizerMapper.html#a0df762ac6300835ee936f77a1b3daf8d',1,'vg::MinimizerMapper']]],
- ['min_5funique_5fper_5fstrand_12855',['min_unique_per_strand',['../classvg_1_1Genotyper.html#a6b1feebb10944e684e417115e880fe39',1,'vg::Genotyper']]],
- ['min_5fversion_12856',['MIN_VERSION',['../structvg_1_1Haplotypes_1_1Header.html#a58665b0f0dbbb098f50a6b02653f624e',1,'vg::Haplotypes::Header']]],
- ['minimizer_5fcoverage_5fflank_12857',['minimizer_coverage_flank',['../classvg_1_1MinimizerMapper.html#abf19808c5cfabda803651ab3a049495e',1,'vg::MinimizerMapper']]],
- ['minimizer_5fdownsampling_5fmax_5fwindow_5flength_12858',['minimizer_downsampling_max_window_length',['../classvg_1_1MinimizerMapper.html#a3aea2ff3e3fa7c837f8005aedf16cc4e',1,'vg::MinimizerMapper']]],
- ['minimizer_5fdownsampling_5fwindow_5fcount_12859',['minimizer_downsampling_window_count',['../classvg_1_1MinimizerMapper.html#a6edefae974f20cbb3dfc0b9ac767bb98',1,'vg::MinimizerMapper']]],
- ['minimizer_5fdownweight_5fthreshold_12860',['minimizer_downweight_threshold',['../structvg_1_1IndexingParameters.html#a441e50494bc2037df74d3b77b9dea964',1,'vg::IndexingParameters']]],
- ['minimizer_5findex_12861',['minimizer_index',['../classvg_1_1MinimizerMapper.html#a30be171658ca4f82aaa05e0c42c0d61b',1,'vg::MinimizerMapper::minimizer_index()'],['../classvg_1_1HaplotypePartitioner.html#a450b3d9e8876b9679fca63dfba0962d2',1,'vg::HaplotypePartitioner::minimizer_index()']]],
- ['minimizer_5fs_12862',['minimizer_s',['../structvg_1_1IndexingParameters.html#a85e4148452f9a2b23d0cdb75afe0fd3d',1,'vg::IndexingParameters']]],
- ['minimizer_5fscore_5ffraction_12863',['minimizer_score_fraction',['../classvg_1_1MinimizerMapper.html#a5696bfb7029ca88ec04d0f849365b34f',1,'vg::MinimizerMapper']]],
- ['mismatch_12864',['mismatch',['../classvg_1_1GSSWAligner.html#abf06d9e9138bbbd23a451d1d0848c503',1,'vg::GSSWAligner::mismatch()'],['../classvg_1_1WFATree.html#a58f242d50871271336260013dfbcf4a8',1,'vg::WFATree::mismatch()'],['../classvg_1_1SSWAligner.html#a49756fbcff60e14c65b58f76c78a923f',1,'vg::SSWAligner::mismatch()'],['../structScoringOptions.html#ad4144b88190ac6bc4881e5bcb0a26b50',1,'ScoringOptions::mismatch()']]],
- ['mismatch_5fpositions_12865',['mismatch_positions',['../structvg_1_1GaplessExtension.html#a30b340b28d82e7070329e45aaa9e6486',1,'vg::GaplessExtension']]],
- ['mismatches_12866',['mismatches',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ae28dd39b01ceed21e1a78fd24b32bcf6',1,'vg::WFAExtender::ErrorModel']]],
- ['mixture_5fweights_12867',['mixture_weights',['../classvg_1_1SpliceStats.html#ab5f243b05a8a80f0bf80ea3d82960e7e',1,'vg::SpliceStats']]],
- ['mode_12868',['mode',['../structvg_1_1SummaryStatistics.html#a8aa060d244b54f34a06f0136d0572bd4',1,'vg::SummaryStatistics::mode()'],['../structHaplotypesConfig.html#ac5dd4d9940ef4d3d9f2dbfb7cde9754b',1,'HaplotypesConfig::mode()']]],
- ['mode_5flog_5flikelihood_12869',['mode_log_likelihood',['../classvg_1_1SpliceStats.html#ad10b6fd62bdc23e8bb7afbf8c545f0bd',1,'vg::SpliceStats']]],
- ['model_12870',['model',['../classvg_1_1MEMChainModel.html#a5f0fbf6a027827aa3a2ee1344588e7b7',1,'vg::MEMChainModel::model()'],['../classvg_1_1AlignmentChainModel.html#a18fbbeaa51ee69363983810e702fcf24',1,'vg::AlignmentChainModel::model()']]],
- ['motif_5fdata_12871',['motif_data',['../classvg_1_1SpliceStats.html#a6a48be87c666572f8e2893e8cf1df9a6',1,'vg::SpliceStats']]],
- ['motif_5fmatches_12872',['motif_matches',['../classvg_1_1SpliceRegion.html#a79697742be9ce68f77d75b430f23a896',1,'vg::SpliceRegion']]],
- ['mp_5faln_5femitter_12873',['mp_aln_emitter',['../classvg_1_1ReadFilter.html#a7baa666446be017dea5507fe5771de57',1,'vg::ReadFilter']]],
- ['mp_5faln_5femitters_12874',['mp_aln_emitters',['../classvg_1_1MultipathAlignmentEmitter.html#abf746b78f8aaf59332dc1852c91affdd',1,'vg::MultipathAlignmentEmitter']]],
- ['mq_5foverlap_12875',['mq_overlap',['../classvg_1_1Mapper.html#a6a23397e02e8522823d36ad4b11a698a',1,'vg::Mapper']]],
- ['msg_12876',['msg',['../classvg_1_1InsufficientInputException.html#a1e4d0ea31dffdc2f339bf11067c00d38',1,'vg::InsufficientInputException::msg()'],['../classvg_1_1RewindPlanException.html#a6dc3f46bfa00c1eb02030b4ff6e73f80',1,'vg::RewindPlanException::msg()'],['../classvg_1_1SizeLimitExceededException.html#ae776aba3017b9ff4c7e7b05002d0be99',1,'vg::SizeLimitExceededException::msg()']]],
- ['mtx_12877',['mtx',['../classvg_1_1ParallelKFFReader.html#a616866362b3f55b76ea1df8a65c01267',1,'vg::ParallelKFFReader']]],
- ['mu_12878',['mu',['../classvg_1_1FragmentLengthDistribution.html#a8c1fb2ac76ebdec084c599686ca12bfa',1,'vg::FragmentLengthDistribution']]],
- ['multi_5fposition_5fannotations_12879',['multi_position_annotations',['../classvg_1_1AbstractReadSampler.html#a679c8195e5411d7460725453298b50f2',1,'vg::AbstractReadSampler']]],
- ['multiallelic_5fsv_5fwarned_12880',['multiallelic_sv_warned',['../classvg_1_1Constructor.html#ad4a4e56154c62990a784f7e51e7368cd',1,'vg::Constructor']]],
- ['multiplexer_12881',['multiplexer',['../classvg_1_1HTSWriter.html#a6e2ff3f77a4265c8dcd1c47770a0bee5',1,'vg::HTSWriter::multiplexer()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a24cd277c06adf66414346ffeb22c0400',1,'vg::io::TSVAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a2f047c1205c512b44f29d0e8231c0cef',1,'vg::io::VGAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a286a69e0bb8071d101e27e501ce1e3ce',1,'vg::io::GafAlignmentEmitter::multiplexer()']]],
- ['mut_5fgraph_5fimpl_12882',['mut_graph_impl',['../structvg_1_1IndexingParameters.html#a9db2b318dee6f693544c8fc5a04c0a53',1,'vg::IndexingParameters']]],
- ['mut_5fsampler_12883',['mut_sampler',['../classvg_1_1NGSSimulator.html#a9501d39b8059ad161395f2b7ba89d424',1,'vg::NGSSimulator']]],
- ['mutation_5falphabets_12884',['mutation_alphabets',['../classvg_1_1NGSSimulator.html#a4a8eacfde748b35453a54ab40c195680',1,'vg::NGSSimulator']]],
- ['mutex_5fgraph_12885',['mutex_graph',['../classvg_1_1Transcriptome.html#a881ee68ca1a43b0ab10494f62e7b127f',1,'vg::Transcriptome']]],
- ['mutex_5ftranscript_5fpaths_12886',['mutex_transcript_paths',['../classvg_1_1Transcriptome.html#a3c6d64194201d695fdcb07078463161a',1,'vg::Transcriptome']]],
- ['my_5fmapper_12887',['my_mapper',['../classvg_1_1Filter.html#a13678a95a03ae4feb7e6ebc0fa00a69f',1,'vg::Filter']]],
- ['my_5fmax_5fdistance_12888',['my_max_distance',['../classvg_1_1Filter.html#ab9ec8e13d2cd4fc50aa86981a0b6475f',1,'vg::Filter']]],
- ['my_5fnames_12889',['my_names',['../classVectorizer.html#a5702f38d3e6d29866e2135d29f7496fd',1,'Vectorizer']]],
- ['my_5fpath_5fposition_5fgraph_12890',['my_path_position_graph',['../classvg_1_1Filter.html#af17db75bb83c6d2ad00b813a4812d30d',1,'vg::Filter']]],
- ['my_5fvectors_12891',['my_vectors',['../classVectorizer.html#af370e810d055623deaa0bfaac120fe8d',1,'Vectorizer']]],
- ['my_5fvg_12892',['my_vg',['../classvg_1_1Filter.html#ac849cd8534ba9b7eb7daa8485d6c9d45',1,'vg::Filter']]],
- ['my_5fxg_12893',['my_xg',['../classVectorizer.html#adebb6c75ae3b7c1199143ab2f166d284',1,'Vectorizer']]]
+ ['m_5fa_12617',['m_a',['../classvg_1_1uniform__real__distribution.html#a7504f90f6d4dea77942a9ca0c0cc3f57',1,'vg::uniform_real_distribution::m_a()'],['../classvg_1_1uniform__int__distribution.html#a2d084a9d58cbc2f4a202d7ba640207ac',1,'vg::uniform_int_distribution::m_a()']]],
+ ['m_5falpha_12618',['m_alpha',['../classvg_1_1truncated__normal__distribution.html#a103e91e1a5b135b61ef12bb1396b073d',1,'vg::truncated_normal_distribution']]],
+ ['m_5fb_12619',['m_b',['../classvg_1_1uniform__real__distribution.html#a736effb600abacbb4ad5dbd9960449b7',1,'vg::uniform_real_distribution::m_b()'],['../classvg_1_1uniform__int__distribution.html#a8fcf808d445c2826852f79c4bac7f594',1,'vg::uniform_int_distribution::m_b()']]],
+ ['m_5fbeta_12620',['m_beta',['../classvg_1_1truncated__normal__distribution.html#ab4ba11d217ace97234dbc707180a388a',1,'vg::truncated_normal_distribution']]],
+ ['m_5fdistu1_12621',['m_distU1',['../classvg_1_1normal__distribution.html#a88845be3c45acd203b683f83a658b3bd',1,'vg::normal_distribution::m_distU1()'],['../classvg_1_1truncated__normal__distribution.html#a0020a9172587312e5342375bb0730ec5',1,'vg::truncated_normal_distribution::m_distU1()']]],
+ ['m_5fmean_12622',['m_mean',['../classvg_1_1normal__distribution.html#ac215210d6799c86403804a8700f8870f',1,'vg::normal_distribution']]],
+ ['m_5fmu_12623',['m_mu',['../classvg_1_1truncated__normal__distribution.html#a16eb85a95c575485c51f3915c27fb206',1,'vg::truncated_normal_distribution']]],
+ ['m_5fsigma_12624',['m_sigma',['../classvg_1_1truncated__normal__distribution.html#acc168175a443e25b3b7a49ddbd2d0d65',1,'vg::truncated_normal_distribution']]],
+ ['m_5fstddev_12625',['m_stddev',['../classvg_1_1normal__distribution.html#a4940854c4f61e99e8c62acb754619bed',1,'vg::normal_distribution']]],
+ ['m_5fsums_12626',['m_sums',['../classvg_1_1discrete__distribution.html#a175dbe373664d84a0a354f1d2febb1b1',1,'vg::discrete_distribution']]],
+ ['m_5fweights_12627',['m_weights',['../classvg_1_1discrete__distribution.html#aae17bac88e7ee1c979e4c44287f9a2fe',1,'vg::discrete_distribution']]],
+ ['magic_5fbytes_12628',['MAGIC_BYTES',['../classvg_1_1StreamIndexBase.html#a9bbb2b0134f0e831fc2ec5db056b7397',1,'vg::StreamIndexBase']]],
+ ['magic_5fnumber_12629',['MAGIC_NUMBER',['../structvg_1_1Haplotypes_1_1Header.html#a08c60e1b376c1a451b42810f5131758b',1,'vg::Haplotypes::Header::MAGIC_NUMBER()'],['../structvg_1_1Haplotypes_1_1Header.html#ae84cdbdc1d89ebf53496eed304acafd3',1,'vg::Haplotypes::Header::magic_number()'],['../classvg_1_1ZipCodeCollection.html#a27434270b2b8b6e6a66f783efb8150c2',1,'vg::ZipCodeCollection::magic_number()']]],
+ ['main_5ffunction_12630',['main_function',['../classvg_1_1subcommand_1_1Subcommand.html#a8c500a86e1c9c51cea715508a19c75fa',1,'vg::subcommand::Subcommand']]],
+ ['manager_12631',['manager',['../classvg_1_1GenomeState.html#a6c9277391547084f77ff1dbfbe481310',1,'vg::GenomeState']]],
+ ['many_5flimit_12632',['MANY_LIMIT',['../classvg_1_1MinimizerMapper.html#aecc1f538f9a05a7f3fd29b5a425ec522',1,'vg::MinimizerMapper']]],
+ ['map_5forder_5fto_5foriginal_12633',['map_order_to_original',['../classvg_1_1WindowedVcfBuffer.html#ab62203851ffc243bd9183f9174739bbd',1,'vg::WindowedVcfBuffer']]],
+ ['mapper_5falignment_5fcutoff_12634',['mapper_alignment_cutoff',['../classvg_1_1VariantAdder.html#aa4281d59699cd880523cb47a146e5462',1,'vg::VariantAdder']]],
+ ['mapping_12635',['mapping',['../classvg_1_1PhaseUnfolder.html#ae30c8d79f4461cae38e4ec2268a22022',1,'vg::PhaseUnfolder::mapping()'],['../structvg_1_1Path.html#a5d91e68bc4c6f7a5915cb4a42cc21caf',1,'vg::Path::mapping()']]],
+ ['mapping_5fedits_12636',['mapping_edits',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a9eb8dcec1e61b69092af38a89e82917a',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['mapping_5fitr_12637',['mapping_itr',['../classvg_1_1Paths.html#ae2bd0d7232fb84776841ac7c4bfea0d2',1,'vg::Paths']]],
+ ['mapping_5fpositions_12638',['mapping_positions',['../structvg_1_1PathIndex.html#acc0b1da5ad0b4f428ceb623a4d3f806f',1,'vg::PathIndex']]],
+ ['mapping_5fquality_12639',['mapping_quality',['../structvg_1_1Alignment.html#a78851a70cc8a3e8f3e71409693130230',1,'vg::Alignment::mapping_quality()'],['../structvg_1_1MultipathAlignment.html#add653bff58eeb96872463fdc21b3dfd5',1,'vg::MultipathAlignment::mapping_quality()']]],
+ ['mapping_5fquality_5fmethod_12640',['mapping_quality_method',['../classvg_1_1BaseMapper.html#a0b1fe81d11d92332f613d8a29dcadb37',1,'vg::BaseMapper']]],
+ ['mappings_12641',['mappings',['../structvg_1_1RebuildJob.html#a82f413afdbd0c9f3c697ab84774542bf',1,'vg::RebuildJob']]],
+ ['mappings_5fby_5frank_12642',['mappings_by_rank',['../classvg_1_1Paths.html#a27d349c3f4795f1389d3824e1c1e3e8f',1,'vg::Paths']]],
+ ['mapq_12643',['mapq',['../structgafkluge_1_1GafRecord.html#a09ffb165e71177223d73e2fea5ed1399',1,'gafkluge::GafRecord']]],
+ ['mapq_5fscaling_5ffactor_12644',['mapq_scaling_factor',['../classvg_1_1MultipathMapper.html#aadbb94f74824864d7bed5c63cb85687e',1,'vg::MultipathMapper']]],
+ ['mapq_5fscore_5fscale_12645',['mapq_score_scale',['../classvg_1_1MinimizerMapper.html#a0e13799b9b7e3f64d06d10bde825924c',1,'vg::MinimizerMapper']]],
+ ['mapq_5fscore_5fwindow_12646',['mapq_score_window',['../classvg_1_1MinimizerMapper.html#ace4a8ce19de89dd8f42f807b71c66dd3',1,'vg::MinimizerMapper']]],
+ ['margin_5fafter_12647',['margin_after',['../classvg_1_1algorithms_1_1Anchor.html#ade738d4df1585fa0dc6fc935da262ee0',1,'vg::algorithms::Anchor']]],
+ ['margin_5fbefore_12648',['margin_before',['../classvg_1_1algorithms_1_1Anchor.html#a545c9c26a24e8d37459944c5632c79e2',1,'vg::algorithms::Anchor']]],
+ ['mask_12649',['mask',['../classvg_1_1ReadMasker.html#ad6d292712ead5b6f89940f020fd8fcc2',1,'vg::ReadMasker::mask()'],['../classvg_1_1GaplessExtender.html#a9824f8144fd4f3515c7333fbeb6e2afd',1,'vg::GaplessExtender::mask()'],['../classvg_1_1WFAExtender.html#a1af2acef8bd391f46798288e9322019b',1,'vg::WFAExtender::mask()']]],
+ ['match_12650',['match',['../classvg_1_1GSSWAligner.html#a7323efd4ef078ab5866b8c2b9fea87a8',1,'vg::GSSWAligner::match()'],['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a4fdc2b0adb79d04c4e928a61e891aa84',1,'vg::BandedGlobalAligner::BAMatrix::match()'],['../classvg_1_1SSWAligner.html#a8ec16a3583a2d8347ee9eaf1853b8cc8',1,'vg::SSWAligner::match()'],['../structScoringOptions.html#a3a450e63987f79011a51819efd5420a4',1,'ScoringOptions::match()']]],
+ ['match_5fcount_12651',['match_count',['../classvg_1_1MaximalExactMatch.html#ab7a9c66468635a1498efdeb394c1fad6',1,'vg::MaximalExactMatch']]],
+ ['matches_12652',['MATCHES',['../structvg_1_1WFANode.html#a0188bfd686597181c42f2384c21e9e19',1,'vg::WFANode::MATCHES()'],['../structvg_1_1SeqComplexity.html#a03e3682e2a96bbf0595d38694d3818ad',1,'vg::SeqComplexity::matches()'],['../structgafkluge_1_1GafRecord.html#a0cac64f74ee1a099fafc4148d08a630c',1,'gafkluge::GafRecord::matches()']]],
+ ['matching_12653',['matching',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a6bb2874bc8c41f0606f8f142a465e469',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['mate_5fmapped_5fto_5fdisjoint_5fsubgraph_12654',['mate_mapped_to_disjoint_subgraph',['../structvg_1_1Alignment.html#a95ed4d8c7a57e34a96871b74ff851821',1,'vg::Alignment']]],
+ ['mate_5fon_5freverse_5fstrand_12655',['mate_on_reverse_strand',['../structvg_1_1Alignment.html#aef312ed490cb8adf8b89eb36b46ee7d6',1,'vg::Alignment']]],
+ ['mate_5frescues_12656',['mate_rescues',['../classvg_1_1Mapper.html#a56cec2a0bdc2a2398bd494cf0acb80a2',1,'vg::Mapper']]],
+ ['mate_5funmapped_12657',['mate_unmapped',['../structvg_1_1Alignment.html#a061bf4ec65ccf7ff88e73e9e4ff268b7',1,'vg::Alignment']]],
+ ['mates_12658',['mates',['../structvg_1_1BREAKPOINT.html#a7469d5658b49020a71529d1704b962f9',1,'vg::BREAKPOINT']]],
+ ['matrix_5fstate_12659',['matrix_state',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a5b8b44e10a1bc42b694728459e4b4271',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['max_12660',['max',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#a45c40bccc3fd5b000987f633c8ec8df4',1,'vg::WFAExtender::ErrorModel::Event']]],
+ ['max_5falignment_5fgap_12661',['max_alignment_gap',['../classvg_1_1MultipathMapper.html#aaf8af884f81cfd5ed869f26a8b8403d4',1,'vg::MultipathMapper']]],
+ ['max_5falignments_12662',['max_alignments',['../classvg_1_1MinimizerMapper.html#a6062b78a7f795cb2a585eb6695bde675',1,'vg::MinimizerMapper']]],
+ ['max_5falt_5fmappings_12663',['max_alt_mappings',['../classvg_1_1MultipathMapper.html#a87223306ba0d983104e48d4ded4e685d',1,'vg::MultipathMapper']]],
+ ['max_5fanchors_12664',['max_anchors',['../classvg_1_1Surjector.html#a5a735901a421d305e6cbf13a016fdc9d',1,'vg::Surjector']]],
+ ['max_5fattempts_12665',['max_attempts',['../classvg_1_1Mapper.html#ac9973fcf3d75d4396f6b6bdec58156a6',1,'vg::Mapper']]],
+ ['max_5fband_5fcells_12666',['max_band_cells',['../classvg_1_1Surjector.html#a0e22a6f6da976c0b505caa6c1ad10ed8',1,'vg::Surjector']]],
+ ['max_5fband_5fjump_12667',['max_band_jump',['../classvg_1_1Mapper.html#a916fd22fce2ebf7953863590c45f5150',1,'vg::Mapper']]],
+ ['max_5fbranch_5ftrim_5flength_12668',['max_branch_trim_length',['../classvg_1_1MultipathMapper.html#a9e260c61a4b39d27286957c4f012a26a',1,'vg::MultipathMapper']]],
+ ['max_5fbubble_5fpaths_12669',['max_bubble_paths',['../classvg_1_1LegacyCaller.html#a807ba6e24d16bac14c24fdc973cb837b',1,'vg::LegacyCaller::max_bubble_paths()'],['../classvg_1_1RepresentativeTraversalFinder.html#ad2de8e0f74e29d2338d0e9f99a764e23',1,'vg::RepresentativeTraversalFinder::max_bubble_paths()']]],
+ ['max_5fbuf_5fsize_12670',['max_buf_size',['../classvg_1_1StreamSorter.html#a192491eeef2fa2c99522f2ad23f12035',1,'vg::StreamSorter']]],
+ ['max_5fchain_5fconnection_12671',['max_chain_connection',['../classvg_1_1MinimizerMapper.html#a4d54618686eb23ac6a4a2c3579f3fec9',1,'vg::MinimizerMapper']]],
+ ['max_5fchaining_5fproblems_12672',['max_chaining_problems',['../classvg_1_1MinimizerMapper.html#a034098134b882ab3e4c8dc0542763f97',1,'vg::MinimizerMapper']]],
+ ['max_5fchains_5fper_5ftree_12673',['max_chains_per_tree',['../classvg_1_1MinimizerMapper.html#ada8578ed33c349fa8f9e5ff7562ac71f',1,'vg::MinimizerMapper']]],
+ ['max_5fcluster_5fmapping_5fquality_12674',['max_cluster_mapping_quality',['../classvg_1_1Mapper.html#a92ea8476aae3d65f0b46f6c7353c21be',1,'vg::Mapper']]],
+ ['max_5fcontext_5fradius_12675',['max_context_radius',['../classvg_1_1VariantAdder.html#a943bba24f9a1a7197744e74ee5465e5d',1,'vg::VariantAdder']]],
+ ['max_5fdagify_5fduplications_12676',['max_dagify_duplications',['../classvg_1_1MultipathMapper.html#a10c136d72e6f32ff28cd608efc1f31db',1,'vg::MultipathMapper']]],
+ ['max_5fdegree_12677',['max_degree',['../structPruningParameters.html#a58d4dca5e0623280f669e386a5eadd2f',1,'PruningParameters']]],
+ ['max_5fdeletion_5fscan_5fnodes_12678',['max_deletion_scan_nodes',['../classvg_1_1VCFTraversalFinder.html#a3e61ffdb1cf6733311b444df38928137',1,'vg::VCFTraversalFinder']]],
+ ['max_5fdepth_12679',['max_depth',['../classvg_1_1RepresentativeTraversalFinder.html#a79339337af609bc33f77cf4696962492',1,'vg::RepresentativeTraversalFinder']]],
+ ['max_5fdiagonal_12680',['max_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#abde71e96e8aac83b5233fa782b514290',1,'vg::WFATree::ScoreProperties']]],
+ ['max_5fdirect_5fto_5fchain_12681',['max_direct_to_chain',['../classvg_1_1MinimizerMapper.html#adfe5996aca0f60eace262a8c06f76f30',1,'vg::MinimizerMapper']]],
+ ['max_5fdisplayed_5fsuggestions_5fper_5fcategory_12682',['MAX_DISPLAYED_SUGGESTIONS_PER_CATEGORY',['../classvg_1_1DiagramExplainer.html#abb72da5ad3b5613b80c4a39c7e4b8f18',1,'vg::DiagramExplainer']]],
+ ['max_5fdistance_12683',['max_distance',['../classvg_1_1WFATree.html#a761ae97d39a69d470cae27ef7cfb28a9',1,'vg::WFATree::max_distance()'],['../classvg_1_1IncrementalSubgraph.html#a06d0598eae084de70fa40ed859ce9704',1,'vg::IncrementalSubgraph::max_distance()']]],
+ ['max_5fdozeu_5fcells_12684',['max_dozeu_cells',['../classvg_1_1MinimizerMapper.html#aa462df061307b0b35996a6ecd33091f7',1,'vg::MinimizerMapper']]],
+ ['max_5fdp_5fcells_12685',['max_dp_cells',['../classvg_1_1MinimizerMapper.html#af673f62cfdb402e93acaf2eb81680772',1,'vg::MinimizerMapper']]],
+ ['max_5fexpected_5fdist_5fapprox_5ferror_12686',['max_expected_dist_approx_error',['../classvg_1_1OrientedDistanceClusterer.html#a74174c834516a6b4116ff6b9972ae10c',1,'vg::OrientedDistanceClusterer::max_expected_dist_approx_error()'],['../classvg_1_1MultipathMapper.html#a23d02e5f180a337a4b9eff178fc0b65d',1,'vg::MultipathMapper::max_expected_dist_approx_error()']]],
+ ['max_5fexponential_5frate_5fintercept_12687',['max_exponential_rate_intercept',['../classvg_1_1MultipathMapper.html#a3b9f8d9eb806a7dd7e05a0b1c4851bc8',1,'vg::MultipathMapper']]],
+ ['max_5fexponential_5frate_5fslope_12688',['max_exponential_rate_slope',['../classvg_1_1MultipathMapper.html#a0c2252c568582797db9b65756694eaff',1,'vg::MultipathMapper']]],
+ ['max_5fexponential_5fshape_5fintercept_12689',['max_exponential_shape_intercept',['../classvg_1_1MultipathMapper.html#a2e7f7551674fa412abd1333c0baf6672',1,'vg::MultipathMapper']]],
+ ['max_5fexponential_5fshape_5fslope_12690',['max_exponential_shape_slope',['../classvg_1_1MultipathMapper.html#a8ea8f5c8ad1906ccf0b878a6821a16e2',1,'vg::MultipathMapper']]],
+ ['max_5fextension_5fmismatches_12691',['max_extension_mismatches',['../classvg_1_1MinimizerMapper.html#a30fd35c63e316b4a1fcdeca3752ea667',1,'vg::MinimizerMapper']]],
+ ['max_5fextensions_12692',['max_extensions',['../classvg_1_1MinimizerMapper.html#a5d03747a37700e9a3f73c308709f70d1',1,'vg::MinimizerMapper']]],
+ ['max_5ffan_5fin_12693',['max_fan_in',['../classvg_1_1StreamSorter.html#a673ce446e1ba8b9917f9475b9003364d',1,'vg::StreamSorter']]],
+ ['max_5ffanout_5fbase_5fquality_12694',['max_fanout_base_quality',['../classvg_1_1MultipathMapper.html#a63f9b0403dceed8c8055ce5c423dd8fe',1,'vg::MultipathMapper']]],
+ ['max_5ffans_5fout_12695',['max_fans_out',['../classvg_1_1MultipathMapper.html#a46f2835eebe0c9ab495e697c975534b6',1,'vg::MultipathMapper']]],
+ ['max_5ffragment_5flength_12696',['max_fragment_length',['../classvg_1_1MinimizerMapper.html#a4575d140e45d04d3d36e6a99bf7b0241',1,'vg::MinimizerMapper']]],
+ ['max_5ffragments_12697',['max_fragments',['../classvg_1_1MinimizerMapper.html#a50848190e760fb1f3c45fd785f57c8a3',1,'vg::MinimizerMapper']]],
+ ['max_5fgap_12698',['max_gap',['../classvg_1_1MEMClusterer.html#a9b8459888ec7b51e739c3be04825b4fd',1,'vg::MEMClusterer']]],
+ ['max_5fgroup_5fsize_12699',['max_group_size',['../classvg_1_1io_1_1MessageEmitter.html#a4bcef07ec2af1cb44f4cd3abfe58f29c',1,'vg::io::MessageEmitter']]],
+ ['max_5fhandle_12700',['max_handle',['../classvg_1_1DozeuPinningOverlay.html#a63162330a1caec7a81abf6b5f747da32',1,'vg::DozeuPinningOverlay']]],
+ ['max_5fhandle_5fmemo_5fsize_12701',['max_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a478ef9dbdebaccadc78679868baa350d',1,'vg::MemoizingGraph']]],
+ ['max_5fhet_5fbias_12702',['max_het_bias',['../classvg_1_1Genotyper.html#a96285d96b960d50199ad3167c20ddf91',1,'vg::Genotyper::max_het_bias()'],['../classvg_1_1RatioSupportSnarlCaller.html#a78f0c7800c9c27021c66d68cbd0335b7',1,'vg::RatioSupportSnarlCaller::max_het_bias()']]],
+ ['max_5fid_12703',['max_id',['../structvg_1_1ConstructedChunk.html#aca49ac5cc43f6390443ab02496fdfd74',1,'vg::ConstructedChunk::max_id()'],['../classvg_1_1Constructor.html#a8466741ece82babe9e892a50bd06a1d9',1,'vg::Constructor::max_id()'],['../classvg_1_1DagifiedGraph.html#a154919be0eb8719eb2fa0181584a9c66',1,'vg::DagifiedGraph::max_id()'],['../classvg_1_1SubHandleGraph.html#ad0090894570f0c53d4c3011472a01d37',1,'vg::SubHandleGraph::max_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a90afa5abb895d5bb6800cd99759de14a',1,'vg::algorithms::GFAIDMapInfo::max_id()'],['../classxg_1_1XG.html#a2cf5a51e7056900fd3872792ef5fa2a5',1,'xg::XG::max_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#ade12e1983845ebfbf47782b8867c708c',1,'handlegraph::algorithms::SubHandleGraph::max_id()']]],
+ ['max_5findel_5fbases_12704',['max_indel_bases',['../classvg_1_1MinimizerMapper.html#a05b1280ff66b9ad01015c490f35fc005',1,'vg::MinimizerMapper']]],
+ ['max_5findel_5fbases_5fper_5fbase_12705',['max_indel_bases_per_base',['../classvg_1_1MinimizerMapper.html#a82da9f52e8af8e9dde669c903d441adc',1,'vg::MinimizerMapper']]],
+ ['max_5findel_5fhet_5fbias_12706',['max_indel_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a9298ec62feb5ab8f593fdf2c6cd2b620',1,'vg::RatioSupportSnarlCaller']]],
+ ['max_5finput_5fversion_12707',['MAX_INPUT_VERSION',['../classvg_1_1StreamIndexBase.html#aa497c1ad37621af86f5f40d45e0f30b2',1,'vg::StreamIndexBase']]],
+ ['max_5fintron_5flength_12708',['max_intron_length',['../classvg_1_1MultipathMapper.html#a51be0d0325abe9a3afa023477d9c2ab0',1,'vg::MultipathMapper']]],
+ ['max_5fiterations_12709',['max_iterations',['../classvg_1_1SmallSnarlSimplifier.html#a212bd3bc07ab19cb42edef936ee62f7a',1,'vg::SmallSnarlSimplifier::max_iterations()'],['../minimizer__main_8cpp.html#a932fcab549241f3cf9efead93803fabc',1,'MAX_ITERATIONS(): minimizer_main.cpp']]],
+ ['max_5fkmers_5fper_5fblock_12710',['max_kmers_per_block',['../classvg_1_1ParallelKFFReader.html#a0179377c78c5e599f903b70c954ffd12',1,'vg::ParallelKFFReader']]],
+ ['max_5flength_12711',['max_length',['../classvg_1_1ReadFilter.html#a2afae0acb031354f67f95f20dda1c4b8',1,'vg::ReadFilter']]],
+ ['max_5flocal_5fextensions_12712',['max_local_extensions',['../classvg_1_1MinimizerMapper.html#a4e6142c1ccdde28230769e5a8b629d9f',1,'vg::MinimizerMapper']]],
+ ['max_5flookback_5fbases_12713',['max_lookback_bases',['../classvg_1_1MinimizerMapper.html#ae94869146878dba80c980d4e35830abe',1,'vg::MinimizerMapper']]],
+ ['max_5flookback_5fbases_5fper_5fbase_12714',['max_lookback_bases_per_base',['../classvg_1_1MinimizerMapper.html#a48ec2ca2886d6f069546d6a424becb61',1,'vg::MinimizerMapper']]],
+ ['max_5flow_5fcomplexity_5fanchor_5fprune_12715',['max_low_complexity_anchor_prune',['../classvg_1_1Surjector.html#a0f304005022b214c309ff60a1f186b1f',1,'vg::Surjector']]],
+ ['max_5flow_5fcomplexity_5fanchor_5ftrim_12716',['max_low_complexity_anchor_trim',['../classvg_1_1Surjector.html#a9c0cf333d85aef40eda8354075dfa01e',1,'vg::Surjector']]],
+ ['max_5fma_5fbias_12717',['max_ma_bias',['../classvg_1_1RatioSupportSnarlCaller.html#ac6d48f0372786d80db440fa67523af9e',1,'vg::RatioSupportSnarlCaller']]],
+ ['max_5fmapping_5fp_5fvalue_12718',['max_mapping_p_value',['../classvg_1_1MultipathMapper.html#aa7656b2372ae8450e48a9db512ce309d',1,'vg::MultipathMapper']]],
+ ['max_5fmapping_5fquality_12719',['max_mapping_quality',['../classvg_1_1BaseMapper.html#a467884235c316072a1ed7136faa14be3',1,'vg::BaseMapper']]],
+ ['max_5fmemory_5fproportion_12720',['max_memory_proportion',['../structvg_1_1IndexingParameters.html#a28aa7110447f9ba3a74e1e3326959751',1,'vg::IndexingParameters']]],
+ ['max_5fmessage_5fsize_12721',['MAX_MESSAGE_SIZE',['../classvg_1_1io_1_1MessageEmitter.html#a67ece9e5b7c411ccb40169b650e1f5ae',1,'vg::io::MessageEmitter::MAX_MESSAGE_SIZE()'],['../classvg_1_1io_1_1MessageIterator.html#a5b2b881e4032fb2ecfa8da35ad13e602',1,'vg::io::MessageIterator::MAX_MESSAGE_SIZE()']]],
+ ['max_5fmiddle_5fdp_5flength_12722',['max_middle_dp_length',['../classvg_1_1MinimizerMapper.html#aa8bdbd3ae354863aaa50bcd0fdfb340f',1,'vg::MinimizerMapper']]],
+ ['max_5fmiddle_5fgap_12723',['max_middle_gap',['../classvg_1_1MinimizerMapper.html#a9e0bcb7de51be992126d051cf343a9c5',1,'vg::MinimizerMapper']]],
+ ['max_5fmin_5fchain_5fscore_12724',['max_min_chain_score',['../classvg_1_1MinimizerMapper.html#a5dc73dddd111a8a64b5285a2e75e3ba5',1,'vg::MinimizerMapper']]],
+ ['max_5fmismatches_12725',['MAX_MISMATCHES',['../classvg_1_1GaplessExtender.html#aaa77a2fc74630664d12527818826e28b',1,'vg::GaplessExtender']]],
+ ['max_5fmissing_5fvariant_5fwarnings_12726',['max_missing_variant_warnings',['../classvg_1_1HaplotypeIndexer.html#a512203218e3b78afa0fc5c0e594e6516',1,'vg::HaplotypeIndexer']]],
+ ['max_5fmotif_5fpairs_12727',['max_motif_pairs',['../classvg_1_1MultipathMapper.html#a7427a85cc5f4ff850524ecf929ca72c8',1,'vg::MultipathMapper']]],
+ ['max_5fmulti_5falns_12728',['max_multi_alns',['../classvg_1_1BandedGlobalAligner.html#a7191ef47a3e2a5232e5ba74283c646b6',1,'vg::BandedGlobalAligner::max_multi_alns()'],['../classvg_1_1BandedGlobalAligner_1_1AltTracebackStack.html#a9114c48d4516fb6115fe47e910624377',1,'vg::BandedGlobalAligner::AltTracebackStack::max_multi_alns()']]],
+ ['max_5fmultimaps_12729',['max_multimaps',['../classvg_1_1Mapper.html#a462268836d2c5f5f4acde6ca9060e593',1,'vg::Mapper::max_multimaps()'],['../classvg_1_1MinimizerMapper.html#aede601962425752ec75ea1d890505357',1,'vg::MinimizerMapper::max_multimaps()']]],
+ ['max_5fnode_12730',['max_node',['../classvg_1_1SubgraphOverlay.html#a6eb5155328921c3a0ec46e62c7edfdca',1,'vg::SubgraphOverlay']]],
+ ['max_5fnode_5fsize_12731',['max_node_size',['../classvg_1_1Constructor.html#a6ca9a0b7785c1c9c6e859cc75ea2a2f4',1,'vg::Constructor::max_node_size()'],['../structvg_1_1IndexingParameters.html#a6b392a212907d34c6f586cb7cefeac1f',1,'vg::IndexingParameters::max_node_size()'],['../classvg_1_1VariantAdder.html#a3e1dae34969d5779d09819de627a6bd5',1,'vg::VariantAdder::max_node_size()']]],
+ ['max_5fnum_5fnodes_12732',['max_num_nodes',['../classvg_1_1IncrementalSubgraph.html#a37038271292f8c25f63b9d3e8400d13e',1,'vg::IncrementalSubgraph']]],
+ ['max_5foverhang_12733',['max_overhang',['../classvg_1_1ReadFilter.html#a54c30818834f623c78a2cb0a0e9b4a91',1,'vg::ReadFilter']]],
+ ['max_5fp_5fvalue_5fmemo_5fsize_12734',['max_p_value_memo_size',['../classvg_1_1MultipathMapper.html#ada39acac8f403bf92632024be4e448e1',1,'vg::MultipathMapper']]],
+ ['max_5fparsed_5fvariant_5fsize_12735',['max_parsed_variant_size',['../classvg_1_1Constructor.html#a2725e8e6876deb0ca0ccf597955163c2',1,'vg::Constructor']]],
+ ['max_5fpath_5fid_12736',['max_path_id',['../classvg_1_1Paths.html#ac5e9e182ecf09166f516c6fbf9923a29',1,'vg::Paths']]],
+ ['max_5fpath_5flength_12737',['max_path_length',['../classvg_1_1Filter.html#a77225b4859a55b509396332e96c81c0e',1,'vg::Filter']]],
+ ['max_5fpath_5fsearch_5fsteps_12738',['max_path_search_steps',['../classvg_1_1Genotyper.html#a500af110546f9572fe40d5ef098552d9',1,'vg::Genotyper::max_path_search_steps()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa61be13e0e070bd8af8fe890b47dfde5',1,'vg::ReadRestrictedTraversalFinder::max_path_search_steps()'],['../classvg_1_1PathRestrictedTraversalFinder.html#af24fb970905bbb3d2e04631fd3d0918b',1,'vg::PathRestrictedTraversalFinder::max_path_search_steps()']]],
+ ['max_5fprune_5fiterations_12739',['max_prune_iterations',['../classvg_1_1VCFTraversalFinder.html#a667a1499ac092df03deaa7ec0813d6df',1,'vg::VCFTraversalFinder']]],
+ ['max_5freads_12740',['max_reads',['../classvg_1_1ReadFilter.html#a1a4d052b3060e2b8a434310ce6dc14f5',1,'vg::ReadFilter']]],
+ ['max_5freads_5fused_12741',['max_reads_used',['../classvg_1_1ReadFilter.html#a06835480f40ef09dd073cc14a469f760',1,'vg::ReadFilter']]],
+ ['max_5fref_5fhet_5fbias_12742',['max_ref_het_bias',['../classvg_1_1RatioSupportSnarlCaller.html#a6012c94aabfcffde89851c587ed34f9e',1,'vg::RatioSupportSnarlCaller']]],
+ ['max_5frescue_5fattempts_12743',['max_rescue_attempts',['../classvg_1_1MinimizerMapper.html#a0985bcf3a1ed28098bf0271b251dd6e2',1,'vg::MinimizerMapper::max_rescue_attempts()'],['../classvg_1_1MultipathMapper.html#a87f585b42e49cd2e642ab092e54a309a',1,'vg::MultipathMapper::max_rescue_attempts()']]],
+ ['max_5frescue_5fp_5fvalue_12744',['max_rescue_p_value',['../classvg_1_1MultipathMapper.html#afe5cb57d342ca46e5ee2e132d1d238d3',1,'vg::MultipathMapper']]],
+ ['max_5frgfa_5frank_12745',['max_rgfa_rank',['../classvg_1_1algorithms_1_1GFAParser.html#ae5841a4a832376b2894cbbb956c89569',1,'vg::algorithms::GFAParser']]],
+ ['max_5fsearch_5fdepth_12746',['max_search_depth',['../classvg_1_1LegacyCaller.html#a321503fbe153735736a542d4ad5d9235',1,'vg::LegacyCaller']]],
+ ['max_5fsearch_5fwidth_12747',['max_search_width',['../classvg_1_1LegacyCaller.html#a01572bf56d35cc89232fac3dce35c891',1,'vg::LegacyCaller']]],
+ ['max_5fseparation_12748',['max_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a1094dccc104bf859b2bdb8b5fac6bec6',1,'vg::GreedyMinDistanceClusterer']]],
+ ['max_5fsingle_5fend_5fmappings_5ffor_5frescue_12749',['max_single_end_mappings_for_rescue',['../classvg_1_1MultipathMapper.html#a1dc8310407eabb6cbe419d5765364df7',1,'vg::MultipathMapper']]],
+ ['max_5fskipped_5fbases_12750',['max_skipped_bases',['../classvg_1_1MinimizerMapper.html#ad72974afc9d7fadd23716fba49b7e82f',1,'vg::MinimizerMapper']]],
+ ['max_5fslide_12751',['max_slide',['../classvg_1_1Surjector.html#a0e40286284b27ccef7fbcc028fc40142',1,'vg::Surjector']]],
+ ['max_5fsnarl_5fcut_5fsize_12752',['max_snarl_cut_size',['../classvg_1_1MultipathMapper.html#a507872f1a20d6b0e34b6f9b8dac2639f',1,'vg::MultipathMapper']]],
+ ['max_5fsnarl_5fedges_12753',['max_snarl_edges',['../classvg_1_1FlowCaller.html#a07f59c5945984d13f67ec660923c0f81',1,'vg::FlowCaller']]],
+ ['max_5fsnarl_5fshallow_5fsize_12754',['max_snarl_shallow_size',['../classvg_1_1NestedFlowCaller.html#ab5e10be4ba6c1d33235e5844cfb8b8c0',1,'vg::NestedFlowCaller']]],
+ ['max_5fsoftclip_5fiterations_12755',['max_softclip_iterations',['../classvg_1_1Mapper.html#a145a97f0859865815bba2562024078e9',1,'vg::Mapper']]],
+ ['max_5fsoftclip_5foverlap_12756',['max_softclip_overlap',['../classvg_1_1MultipathMapper.html#afcacb8b30589b82487cca2a1755320f3',1,'vg::MultipathMapper']]],
+ ['max_5fsplice_5foverhang_12757',['max_splice_overhang',['../classvg_1_1MultipathMapper.html#a8c71d1bf28c8567e878c5cd004b94e8b',1,'vg::MultipathMapper']]],
+ ['max_5fsplice_5fref_5fsearch_5flength_12758',['max_splice_ref_search_length',['../classvg_1_1MultipathMapper.html#a4f4bca24b9dbe1a7a40499a30e91c4f6',1,'vg::MultipathMapper']]],
+ ['max_5fsteps_5fof_5fhandle_5fmemo_5fsize_12759',['max_steps_of_handle_memo_size',['../classvg_1_1MemoizingGraph.html#a55aadb2458a395d6fd47f9a9c5ddf415',1,'vg::MemoizingGraph']]],
+ ['max_5fsub_5fmem_5frecursion_5fdepth_12760',['max_sub_mem_recursion_depth',['../classvg_1_1BaseMapper.html#ac12496865e23fd68ba1f579dcb050037',1,'vg::BaseMapper']]],
+ ['max_5fsubgraph_5fbases_5fper_5fread_5fbase_12761',['max_subgraph_bases_per_read_base',['../classvg_1_1Surjector.html#a14e20f641f120ca8fa5206ace84be331',1,'vg::Surjector']]],
+ ['max_5fsuboptimal_5fpath_5fscore_5fratio_12762',['max_suboptimal_path_score_ratio',['../classvg_1_1MultipathMapper.html#ac117889984b58f3c0fd3d389a8ee7f26',1,'vg::MultipathMapper']]],
+ ['max_5ftag_5flength_12763',['MAX_TAG_LENGTH',['../classvg_1_1io_1_1Registry.html#a8791c3355999775f973ab74fa4111fa2',1,'vg::io::Registry']]],
+ ['max_5ftail_5fanchor_5fprune_12764',['max_tail_anchor_prune',['../classvg_1_1Surjector.html#a59034e11562bb0969c25defd215f166b',1,'vg::Surjector']]],
+ ['max_5ftail_5fdp_5flength_12765',['max_tail_dp_length',['../classvg_1_1MinimizerMapper.html#ab333ad05b05cdcd8d59bd0c6b2733e04',1,'vg::MinimizerMapper']]],
+ ['max_5ftail_5fgap_12766',['max_tail_gap',['../classvg_1_1MinimizerMapper.html#a25dccb476876cf2797743ec916c3d661',1,'vg::MinimizerMapper']]],
+ ['max_5ftail_5flength_12767',['max_tail_length',['../classvg_1_1MinimizerMapper.html#ad041c860d77e6ad2bd025bd2da337d7a',1,'vg::MinimizerMapper::max_tail_length()'],['../classvg_1_1Surjector.html#a185cc3fad9b021b08f03880ae0119db6',1,'vg::Surjector::max_tail_length()']]],
+ ['max_5ftail_5fmerge_5fsupress_5flength_12768',['max_tail_merge_supress_length',['../classvg_1_1MultipathMapper.html#a8de58bf1942c4aa16b762554268d3e3d',1,'vg::MultipathMapper']]],
+ ['max_5ftarget_5ffactor_12769',['max_target_factor',['../classvg_1_1Mapper.html#a5ecf825b76d29c8b8242d8167fae6cc4',1,'vg::Mapper']]],
+ ['max_5fto_5ffragment_12770',['max_to_fragment',['../classvg_1_1MinimizerMapper.html#ab6b8884b622acf26ceeae7ea1f2204d6',1,'vg::MinimizerMapper']]],
+ ['max_5ftrav_5fsize_12771',['max_trav_size',['../structvg_1_1PoissonSupportSnarlCaller_1_1PoissonCallInfo.html#a4842f02f38903b12e0c7de54bf0482e3',1,'vg::PoissonSupportSnarlCaller::PoissonCallInfo']]],
+ ['max_5ftraversal_5fcutoff_12772',['max_traversal_cutoff',['../classvg_1_1VCFTraversalFinder.html#a2ece2a9a96c909c7859bd88d54daa559',1,'vg::VCFTraversalFinder']]],
+ ['max_5ftraversal_5flength_12773',['max_traversal_length',['../classvg_1_1FlowTraversalFinder.html#a1dbaa147e49e103151629a210977c58b',1,'vg::FlowTraversalFinder']]],
+ ['max_5ftries_12774',['max_tries',['../classvg_1_1AbstractReadSampler.html#a68421d544f78d22ed080321929c9fd01',1,'vg::AbstractReadSampler']]],
+ ['max_5funcalled_5falleles_12775',['max_uncalled_alleles',['../classvg_1_1VCFOutputCaller.html#acf04132e0a3cf52b5ba58a88f0b2d3d4',1,'vg::VCFOutputCaller']]],
+ ['max_5funique_5fmin_12776',['max_unique_min',['../classvg_1_1MinimizerMapper.html#a8862622f6f711cc6a797b26990c9f195',1,'vg::MinimizerMapper']]],
+ ['max_5fvalue_12777',['max_value',['../structvg_1_1SummaryStatistics.html#ad86748ae17ecc7acce49364a9fa93a74',1,'vg::SummaryStatistics::max_value()'],['../structvg_1_1varint__vector__t.html#a92149196c806e2230f53f2d62e9bf8b3',1,'vg::varint_vector_t::MAX_VALUE()']]],
+ ['max_5fvcf_5fline_5flength_12778',['max_vcf_line_length',['../classvg_1_1VCFOutputCaller.html#a549336b5a84bfdef74b8ae8116b1b151',1,'vg::VCFOutputCaller']]],
+ ['max_5fwalk_12779',['max_walk',['../classvg_1_1PathOrientedDistanceMeasurer.html#a6d8dc74ae9eaaabf35ba1c89cfae8a11',1,'vg::PathOrientedDistanceMeasurer']]],
+ ['max_5fwidth_12780',['max_width',['../classvg_1_1RepresentativeTraversalFinder.html#aac2939337439d7566246889b3a4655c6',1,'vg::RepresentativeTraversalFinder']]],
+ ['max_5fxdrop_5fgap_5flength_12781',['max_xdrop_gap_length',['../classvg_1_1Mapper.html#a2754b67772ef25cb66d06b66b8caeb55',1,'vg::Mapper']]],
+ ['maximum_5fquality_12782',['maximum_quality',['../classvg_1_1Packer.html#a0de02be2009ac1d477d5cc8fefccab1c',1,'vg::Packer']]],
+ ['maximum_5fsample_5fsize_12783',['maximum_sample_size',['../classvg_1_1FragmentLengthDistribution.html#a82ad9fe36dc81ea108a530b7f9792b78',1,'vg::FragmentLengthDistribution']]],
+ ['maybe_5fmq_5fthreshold_12784',['maybe_mq_threshold',['../classvg_1_1Mapper.html#a26d2d7d3964d9210c963b325c64678b0',1,'vg::Mapper']]],
+ ['mean_12785',['mean',['../structvg_1_1SummaryStatistics.html#a275cb7138ffd1285cbdad3ae7017cbe8',1,'vg::SummaryStatistics']]],
+ ['median_12786',['median',['../structvg_1_1SummaryStatistics.html#ae98f01cfb86f82f0e9185c63fb57445f',1,'vg::SummaryStatistics']]],
+ ['mem_12787',['mem',['../classvg_1_1MEMChainModelVertex.html#acd9990963345deb38096763554ae4b3d',1,'vg::MEMChainModelVertex::mem()'],['../classvg_1_1MEMClusterer_1_1HitNode.html#a9f3480f5d231cf8d4325ae558a379f10',1,'vg::MEMClusterer::HitNode::mem()']]],
+ ['mem_5fcoverage_5fmin_5fratio_12788',['mem_coverage_min_ratio',['../classvg_1_1MultipathMapper.html#ae977e7bbf30ca7634e7422aa76c16e71',1,'vg::MultipathMapper']]],
+ ['mem_5freseed_5flength_12789',['mem_reseed_length',['../classvg_1_1BaseMapper.html#abaea877646c1be5aea6200201d28c4cf',1,'vg::BaseMapper']]],
+ ['memo_12790',['memo',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#a382739dd7136e759c6a01725ddebd301',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['memory_5fhigh_5fwater_5fkb_12791',['memory_high_water_kb',['../classvg_1_1Watchdog.html#aa759f3d73ebe15aeb95a13a8c86a0b59',1,'vg::Watchdog']]],
+ ['merge_12792',['merge',['../structGBWTConfig.html#a850f9f30af38996cc64f1fabb20a6458',1,'GBWTConfig']]],
+ ['merge_5fparameters_12793',['merge_parameters',['../structGBWTConfig.html#a77aea6d71d3a6904f01eeccf1f950318',1,'GBWTConfig']]],
+ ['merged_5fgroup_12794',['merged_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#acd6301aa5e085df9fa56ba8b102cdde6',1,'vg::IndexedVG::CacheEntry']]],
+ ['message_12795',['message',['../structvg_1_1AlignmentValidity.html#a7eede46d9951c0c2b0b4c226c6987691',1,'vg::AlignmentValidity::message()'],['../classvg_1_1NoAlignmentInBandException.html#a3cc1fd5899066709228ecea9e5a25956',1,'vg::NoAlignmentInBandException::message()']]],
+ ['message_5fbuffer_12796',['message_buffer',['../structvg_1_1algorithms_1_1GFAFormatError.html#a24e4e4d2285fd970978365e2747165c8',1,'vg::algorithms::GFAFormatError']]],
+ ['message_5femitter_12797',['message_emitter',['../classvg_1_1io_1_1ProtobufEmitter.html#a1bdc1e48041d69eeca45745580af19f3',1,'vg::io::ProtobufEmitter']]],
+ ['message_5fhandlers_12798',['message_handlers',['../classvg_1_1io_1_1ProtobufEmitter.html#a73231a5a45811c280d1a6d346abc75eb',1,'vg::io::ProtobufEmitter']]],
+ ['message_5fit_12799',['message_it',['../classvg_1_1io_1_1ProtobufIterator.html#a787d06e13a1799b7e65ee1aa19ec3bb8',1,'vg::io::ProtobufIterator']]],
+ ['metadata_12800',['metadata',['../structGBWTConfig.html#a0e91b96d773182fc4e4e36314ae6bd8d',1,'GBWTConfig']]],
+ ['metadata_5fmode_12801',['metadata_mode',['../structGBWTConfig.html#a102642e75fdf2b95d22a07d372ca2890',1,'GBWTConfig']]],
+ ['min_12802',['min',['../structvg_1_1WFAExtender_1_1ErrorModel_1_1Event.html#ad4cda218b41dfcb1dfdb3d3c5f3924c1',1,'vg::WFAExtender::ErrorModel::Event']]],
+ ['min_5fad_5flog_5flikelihood_5ffor_5ffilter_12803',['min_ad_log_likelihood_for_filter',['../classvg_1_1RatioSupportSnarlCaller.html#a16602959db7c2bc06471474b07a3c2f7',1,'vg::RatioSupportSnarlCaller']]],
+ ['min_5falt_5fpath_5fsupport_12804',['min_alt_path_support',['../classvg_1_1SupportBasedSnarlCaller.html#a17f76956318b838695d8b120d553ce24',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5favg_5fqual_12805',['min_avg_qual',['../classvg_1_1Filter.html#aa2f91d1daf04d2fdd6eb75183994d834',1,'vg::Filter']]],
+ ['min_5fbanded_5fmq_12806',['min_banded_mq',['../classvg_1_1Mapper.html#a4fe883a960df0bbef6d08cfbe483c179',1,'vg::Mapper']]],
+ ['min_5fbase_5fquality_12807',['min_base_quality',['../classvg_1_1ReadFilter.html#a7fe13f943f153913f16aa594720d350a',1,'vg::ReadFilter']]],
+ ['min_5fbase_5fquality_5ffraction_12808',['min_base_quality_fraction',['../classvg_1_1ReadFilter.html#ab8c6af52884a83d9538ea7ef42ac9eb4',1,'vg::ReadFilter']]],
+ ['min_5fbp_5fedge_5foverride_12809',['min_bp_edge_override',['../classvg_1_1TraversalSupportFinder.html#a767e1ca73abc43065673009d115c310d',1,'vg::TraversalSupportFinder']]],
+ ['min_5fchain_5fscore_5fper_5fbase_12810',['min_chain_score_per_base',['../classvg_1_1MinimizerMapper.html#a2b4cc838d0959b158c0c68b1e84e9123',1,'vg::MinimizerMapper']]],
+ ['min_5fchaining_5fproblems_12811',['min_chaining_problems',['../classvg_1_1MinimizerMapper.html#a821c2a05942d63254a2485a1e0987b80',1,'vg::MinimizerMapper']]],
+ ['min_5fchains_12812',['min_chains',['../classvg_1_1MinimizerMapper.html#a85797857c8e3f3bc363fa634af55889c',1,'vg::MinimizerMapper']]],
+ ['min_5fcluster_5flength_12813',['min_cluster_length',['../classvg_1_1Mapper.html#a70ed23d3ba482d38f7201376e179af9f',1,'vg::Mapper']]],
+ ['min_5fclustering_5fmem_5flength_12814',['min_clustering_mem_length',['../classvg_1_1MultipathMapper.html#ac656fb3b81d4cf6d06fb077551b54b7f',1,'vg::MultipathMapper']]],
+ ['min_5fcount_5fto_5fkeep_12815',['min_count_to_keep',['../classvg_1_1RareVariantSimplifier.html#aa481bbf8d0d969a9f9aa350fd376500e',1,'vg::RareVariantSimplifier']]],
+ ['min_5fcov_12816',['min_cov',['../classvg_1_1Filter.html#a77f731ad12fc655130808337452ba734',1,'vg::Filter']]],
+ ['min_5fdepth_12817',['min_depth',['../classvg_1_1Filter.html#a941f203667435234a1e08cce0358d8c6',1,'vg::Filter']]],
+ ['min_5fdiagonal_12818',['min_diagonal',['../structvg_1_1WFATree_1_1ScoreProperties.html#ae69b636772fc01c9bd756c2b6dd7fd05',1,'vg::WFATree::ScoreProperties']]],
+ ['min_5fdistance_12819',['min_distance',['../classvg_1_1WFATree.html#a9578f5415befbcf1260abf8d4536f538',1,'vg::WFATree']]],
+ ['min_5fedge_5fsupport_12820',['min_edge_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#aabc81064635f9311af46bf2b5f1417aa',1,'vg::SupportRestrictedTraversalFinder::min_edge_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a16cd92c3b27a0b6be9d9154a7d9da77a',1,'vg::RepresentativeTraversalFinder::min_edge_support()']]],
+ ['min_5fend_5fmatches_12821',['min_end_matches',['../classvg_1_1ReadFilter.html#a05d07dd311e58f3fc04d510870ddf662',1,'vg::ReadFilter']]],
+ ['min_5fextension_5fsets_12822',['min_extension_sets',['../classvg_1_1MinimizerMapper.html#a1df84f11e9476595bcde3584553d2830',1,'vg::MinimizerMapper']]],
+ ['min_5fextensions_12823',['min_extensions',['../classvg_1_1MinimizerMapper.html#a03f18247f88d4817feef2d25a46fd5ca',1,'vg::MinimizerMapper']]],
+ ['min_5ffold_5fcoverage_5ffor_5fdownsample_12824',['min_fold_coverage_for_downsample',['../classvg_1_1Surjector.html#ac21d8c91876c3522c56c4c1c2b8f8f58',1,'vg::Surjector']]],
+ ['min_5ffrequency_5fto_5fkeep_12825',['min_frequency_to_keep',['../classvg_1_1RareVariantSimplifier.html#a7aca3c00c47d8a8c6261536952fd96d8',1,'vg::RareVariantSimplifier']]],
+ ['min_5fhandle_12826',['min_handle',['../classvg_1_1DagifiedGraph.html#a80c29e6e7494413dd631ea741d77f8c0',1,'vg::DagifiedGraph::min_handle()'],['../classxg_1_1XGPath.html#a59c1b92f21b5d102f70808266b457e7e',1,'xg::XGPath::min_handle()']]],
+ ['min_5fid_12827',['min_id',['../classvg_1_1SubHandleGraph.html#a81878c5b09f4863b125f9de74ce11315',1,'vg::SubHandleGraph::min_id()'],['../classxg_1_1XG.html#a89a7150cd2c37698fc33ce0953f6019b',1,'xg::XG::min_id()'],['../classhandlegraph_1_1algorithms_1_1SubHandleGraph.html#af225cef56e4c7af36ea3252d86502238',1,'handlegraph::algorithms::SubHandleGraph::min_id()']]],
+ ['min_5fidentity_12828',['min_identity',['../classvg_1_1Mapper.html#a9b1d4bad7b2b7e96253006b4625329ac',1,'vg::Mapper']]],
+ ['min_5fmad_5ffor_5ffilter_12829',['min_mad_for_filter',['../classvg_1_1SupportBasedSnarlCaller.html#aec268641676f41d2c24128cb9e17ac03',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5fmapq_12830',['min_mapq',['../classvg_1_1ReadFilter.html#a8da615d17aba7ed66be6174253ce64ce',1,'vg::ReadFilter']]],
+ ['min_5fmedian_5fmem_5fcoverage_5ffor_5fsplit_12831',['min_median_mem_coverage_for_split',['../classvg_1_1MultipathMapper.html#a4aa16d72dd27681fef0f5d99fec8f0ee',1,'vg::MultipathMapper']]],
+ ['min_5fmem_5flength_12832',['min_mem_length',['../classvg_1_1BaseMapper.html#a6de91c39c73a95b014b1773495985a09',1,'vg::BaseMapper']]],
+ ['min_5fmultimaps_12833',['min_multimaps',['../classvg_1_1Mapper.html#a34d17aa5222b5b97e8e96d70a39c99c9',1,'vg::Mapper']]],
+ ['min_5fnode_12834',['min_node',['../classvg_1_1SubgraphOverlay.html#a6fa8fb25c1244dfc3569ac1d37699334',1,'vg::SubgraphOverlay']]],
+ ['min_5fnode_5fsupport_12835',['min_node_support',['../classvg_1_1SupportRestrictedTraversalFinder.html#ae0201f741f7e5cffed2577d47e8e1830',1,'vg::SupportRestrictedTraversalFinder::min_node_support()'],['../classvg_1_1RepresentativeTraversalFinder.html#a873d02fe79d020bb106879f5b478e38f',1,'vg::RepresentativeTraversalFinder::min_node_support()']]],
+ ['min_5fnode_5fsupport_5fcache_12836',['min_node_support_cache',['../classvg_1_1CachedPackedTraversalSupportFinder.html#a3a150bfc048afe50f2e006f77159bf34',1,'vg::CachedPackedTraversalSupportFinder']]],
+ ['min_5fpercent_5fidentity_12837',['min_percent_identity',['../classvg_1_1Filter.html#afd9cc5bfa5740f71e70a601f7f0b8199',1,'vg::Filter']]],
+ ['min_5fprimary_12838',['min_primary',['../classvg_1_1ReadFilter.html#a64132e9f5f27ce6930554ad3c197e694',1,'vg::ReadFilter']]],
+ ['min_5fqual_12839',['min_qual',['../classvg_1_1Filter.html#ab3ced01093210b1379fbcd7de7709a30',1,'vg::Filter']]],
+ ['min_5fqueue_5fitem_5fbytes_12840',['MIN_QUEUE_ITEM_BYTES',['../classvg_1_1io_1_1StreamMultiplexer.html#afd60eacdf650f68a3989c91670655146',1,'vg::io::StreamMultiplexer']]],
+ ['min_5fread_5fseparation_12841',['min_read_separation',['../classvg_1_1ComponentMinDistanceClusterer.html#a6c48555f1245310c614265e3d9d69c42',1,'vg::ComponentMinDistanceClusterer']]],
+ ['min_5frecurrence_12842',['min_recurrence',['../classvg_1_1Genotyper.html#afffa8d75fd4155bc7d420a41d92f198c',1,'vg::Genotyper::min_recurrence()'],['../classvg_1_1ReadRestrictedTraversalFinder.html#aa00f717b20773b41578e642425fbf73b',1,'vg::ReadRestrictedTraversalFinder::min_recurrence()'],['../classvg_1_1PathRestrictedTraversalFinder.html#a3085d06249a54ac345e3bebde7c2378c',1,'vg::PathRestrictedTraversalFinder::min_recurrence()']]],
+ ['min_5fscore_5ffactor_12843',['min_score_factor',['../classvg_1_1VariantAdder.html#aae129564bcf5ec9fd9d0838754d27323',1,'vg::VariantAdder']]],
+ ['min_5fscore_5fper_5fbase_12844',['min_score_per_base',['../classvg_1_1Genotyper.html#a8fc1fdccfa9829bb29903ed5d7b21b28',1,'vg::Genotyper']]],
+ ['min_5fsecondary_12845',['min_secondary',['../classvg_1_1ReadFilter.html#af85c211a4a06a1fb750958002cefba0f',1,'vg::ReadFilter']]],
+ ['min_5fseparation_12846',['min_separation',['../classvg_1_1GreedyMinDistanceClusterer.html#a97ed3ff5a8770a314b138148319b9a3b',1,'vg::GreedyMinDistanceClusterer']]],
+ ['min_5fshift_5ffor_5fprune_12847',['min_shift_for_prune',['../classvg_1_1Surjector.html#a731d00674b2d71044a8e404be059c2cf',1,'vg::Surjector']]],
+ ['min_5fsite_5fdepth_12848',['min_site_depth',['../classvg_1_1SupportBasedSnarlCaller.html#adde07f3e5ca89a2a565e8859ee641159',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5fsize_12849',['min_size',['../classvg_1_1SmallSnarlSimplifier.html#a6efa9c6d0dc38da336a5723f87e20e46',1,'vg::SmallSnarlSimplifier']]],
+ ['min_5fsoftclip_5flength_5ffor_5fsplice_12850',['min_softclip_length_for_splice',['../classvg_1_1MultipathMapper.html#a2d6a193c1277d948f7155da585e60367',1,'vg::MultipathMapper']]],
+ ['min_5fsoftclipped_5fscore_5ffor_5fsplice_12851',['min_softclipped_score_for_splice',['../classvg_1_1MultipathMapper.html#aaae9feaf584c64fe27628e29778359b4',1,'vg::MultipathMapper']]],
+ ['min_5fsplice_5flength_12852',['min_splice_length',['../classvg_1_1SplicedHTSAlignmentEmitter.html#a801ecf2defc628516d4a5165ff745acb',1,'vg::SplicedHTSAlignmentEmitter::min_splice_length()'],['../classvg_1_1MultipathAlignmentEmitter.html#a38e7b3d9a6dca8b5601add1a6d9023e4',1,'vg::MultipathAlignmentEmitter::min_splice_length()'],['../classvg_1_1Surjector.html#a9046bb2c7267f996a6636518e2747b89',1,'vg::Surjector::min_splice_length()']]],
+ ['min_5fsplice_5frepair_5flength_12853',['min_splice_repair_length',['../classvg_1_1Surjector.html#ad5048905a75d047631f3552632f58cd3',1,'vg::Surjector']]],
+ ['min_5fsplice_5frescue_5fmatches_12854',['min_splice_rescue_matches',['../classvg_1_1MultipathMapper.html#a194ce33d0517a8ccd67c4e87d26f1191',1,'vg::MultipathMapper']]],
+ ['min_5ftail_5fanchor_5flength_12855',['min_tail_anchor_length',['../classvg_1_1MultipathMapper.html#a9616c4b8786af795cfd1f007c5e0c1dc',1,'vg::MultipathMapper']]],
+ ['min_5fto_5ffragment_12856',['min_to_fragment',['../classvg_1_1MinimizerMapper.html#a8b9e086aeaf58ab94283f9398890a9ca',1,'vg::MinimizerMapper']]],
+ ['min_5ftotal_5fsupport_5ffor_5fcall_12857',['min_total_support_for_call',['../classvg_1_1SupportBasedSnarlCaller.html#a559c8afa8e4f1f73768d7d90ff6a6db0',1,'vg::SupportBasedSnarlCaller']]],
+ ['min_5funique_5fnode_5ffraction_12858',['min_unique_node_fraction',['../classvg_1_1MinimizerMapper.html#a0df762ac6300835ee936f77a1b3daf8d',1,'vg::MinimizerMapper']]],
+ ['min_5funique_5fper_5fstrand_12859',['min_unique_per_strand',['../classvg_1_1Genotyper.html#a6b1feebb10944e684e417115e880fe39',1,'vg::Genotyper']]],
+ ['min_5fversion_12860',['MIN_VERSION',['../structvg_1_1Haplotypes_1_1Header.html#a58665b0f0dbbb098f50a6b02653f624e',1,'vg::Haplotypes::Header']]],
+ ['minimizer_5fcoverage_5fflank_12861',['minimizer_coverage_flank',['../classvg_1_1MinimizerMapper.html#abf19808c5cfabda803651ab3a049495e',1,'vg::MinimizerMapper']]],
+ ['minimizer_5fdownsampling_5fmax_5fwindow_5flength_12862',['minimizer_downsampling_max_window_length',['../classvg_1_1MinimizerMapper.html#a3aea2ff3e3fa7c837f8005aedf16cc4e',1,'vg::MinimizerMapper']]],
+ ['minimizer_5fdownsampling_5fwindow_5fcount_12863',['minimizer_downsampling_window_count',['../classvg_1_1MinimizerMapper.html#a6edefae974f20cbb3dfc0b9ac767bb98',1,'vg::MinimizerMapper']]],
+ ['minimizer_5fdownweight_5fthreshold_12864',['minimizer_downweight_threshold',['../structvg_1_1IndexingParameters.html#a441e50494bc2037df74d3b77b9dea964',1,'vg::IndexingParameters']]],
+ ['minimizer_5findex_12865',['minimizer_index',['../classvg_1_1MinimizerMapper.html#a30be171658ca4f82aaa05e0c42c0d61b',1,'vg::MinimizerMapper::minimizer_index()'],['../classvg_1_1HaplotypePartitioner.html#a450b3d9e8876b9679fca63dfba0962d2',1,'vg::HaplotypePartitioner::minimizer_index()']]],
+ ['minimizer_5fs_12866',['minimizer_s',['../structvg_1_1IndexingParameters.html#a85e4148452f9a2b23d0cdb75afe0fd3d',1,'vg::IndexingParameters']]],
+ ['minimizer_5fscore_5ffraction_12867',['minimizer_score_fraction',['../classvg_1_1MinimizerMapper.html#a5696bfb7029ca88ec04d0f849365b34f',1,'vg::MinimizerMapper']]],
+ ['mismatch_12868',['mismatch',['../classvg_1_1GSSWAligner.html#abf06d9e9138bbbd23a451d1d0848c503',1,'vg::GSSWAligner::mismatch()'],['../classvg_1_1WFATree.html#a58f242d50871271336260013dfbcf4a8',1,'vg::WFATree::mismatch()'],['../classvg_1_1SSWAligner.html#a49756fbcff60e14c65b58f76c78a923f',1,'vg::SSWAligner::mismatch()'],['../structScoringOptions.html#ad4144b88190ac6bc4881e5bcb0a26b50',1,'ScoringOptions::mismatch()']]],
+ ['mismatch_5fpositions_12869',['mismatch_positions',['../structvg_1_1GaplessExtension.html#a30b340b28d82e7070329e45aaa9e6486',1,'vg::GaplessExtension']]],
+ ['mismatches_12870',['mismatches',['../structvg_1_1WFAExtender_1_1ErrorModel.html#ae28dd39b01ceed21e1a78fd24b32bcf6',1,'vg::WFAExtender::ErrorModel']]],
+ ['mixture_5fweights_12871',['mixture_weights',['../classvg_1_1SpliceStats.html#ab5f243b05a8a80f0bf80ea3d82960e7e',1,'vg::SpliceStats']]],
+ ['mode_12872',['mode',['../structvg_1_1SummaryStatistics.html#a8aa060d244b54f34a06f0136d0572bd4',1,'vg::SummaryStatistics::mode()'],['../structHaplotypesConfig.html#ac5dd4d9940ef4d3d9f2dbfb7cde9754b',1,'HaplotypesConfig::mode()']]],
+ ['mode_5flog_5flikelihood_12873',['mode_log_likelihood',['../classvg_1_1SpliceStats.html#ad10b6fd62bdc23e8bb7afbf8c545f0bd',1,'vg::SpliceStats']]],
+ ['model_12874',['model',['../classvg_1_1MEMChainModel.html#a5f0fbf6a027827aa3a2ee1344588e7b7',1,'vg::MEMChainModel::model()'],['../classvg_1_1AlignmentChainModel.html#a18fbbeaa51ee69363983810e702fcf24',1,'vg::AlignmentChainModel::model()']]],
+ ['motif_5fdata_12875',['motif_data',['../classvg_1_1SpliceStats.html#a6a48be87c666572f8e2893e8cf1df9a6',1,'vg::SpliceStats']]],
+ ['motif_5fmatches_12876',['motif_matches',['../classvg_1_1SpliceRegion.html#a79697742be9ce68f77d75b430f23a896',1,'vg::SpliceRegion']]],
+ ['mp_5faln_5femitter_12877',['mp_aln_emitter',['../classvg_1_1ReadFilter.html#a7baa666446be017dea5507fe5771de57',1,'vg::ReadFilter']]],
+ ['mp_5faln_5femitters_12878',['mp_aln_emitters',['../classvg_1_1MultipathAlignmentEmitter.html#abf746b78f8aaf59332dc1852c91affdd',1,'vg::MultipathAlignmentEmitter']]],
+ ['mq_5foverlap_12879',['mq_overlap',['../classvg_1_1Mapper.html#a6a23397e02e8522823d36ad4b11a698a',1,'vg::Mapper']]],
+ ['msg_12880',['msg',['../classvg_1_1InsufficientInputException.html#a1e4d0ea31dffdc2f339bf11067c00d38',1,'vg::InsufficientInputException::msg()'],['../classvg_1_1RewindPlanException.html#a6dc3f46bfa00c1eb02030b4ff6e73f80',1,'vg::RewindPlanException::msg()'],['../classvg_1_1SizeLimitExceededException.html#ae776aba3017b9ff4c7e7b05002d0be99',1,'vg::SizeLimitExceededException::msg()']]],
+ ['mtx_12881',['mtx',['../classvg_1_1ParallelKFFReader.html#a616866362b3f55b76ea1df8a65c01267',1,'vg::ParallelKFFReader']]],
+ ['mu_12882',['mu',['../classvg_1_1FragmentLengthDistribution.html#a8c1fb2ac76ebdec084c599686ca12bfa',1,'vg::FragmentLengthDistribution']]],
+ ['multi_5fposition_5fannotations_12883',['multi_position_annotations',['../classvg_1_1AbstractReadSampler.html#a679c8195e5411d7460725453298b50f2',1,'vg::AbstractReadSampler']]],
+ ['multiallelic_5fsv_5fwarned_12884',['multiallelic_sv_warned',['../classvg_1_1Constructor.html#ad4a4e56154c62990a784f7e51e7368cd',1,'vg::Constructor']]],
+ ['multiplexer_12885',['multiplexer',['../classvg_1_1HTSWriter.html#a6e2ff3f77a4265c8dcd1c47770a0bee5',1,'vg::HTSWriter::multiplexer()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a24cd277c06adf66414346ffeb22c0400',1,'vg::io::TSVAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a2f047c1205c512b44f29d0e8231c0cef',1,'vg::io::VGAlignmentEmitter::multiplexer()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a286a69e0bb8071d101e27e501ce1e3ce',1,'vg::io::GafAlignmentEmitter::multiplexer()']]],
+ ['mut_5fgraph_5fimpl_12886',['mut_graph_impl',['../structvg_1_1IndexingParameters.html#a9db2b318dee6f693544c8fc5a04c0a53',1,'vg::IndexingParameters']]],
+ ['mut_5fsampler_12887',['mut_sampler',['../classvg_1_1NGSSimulator.html#a9501d39b8059ad161395f2b7ba89d424',1,'vg::NGSSimulator']]],
+ ['mutation_5falphabets_12888',['mutation_alphabets',['../classvg_1_1NGSSimulator.html#a4a8eacfde748b35453a54ab40c195680',1,'vg::NGSSimulator']]],
+ ['mutex_5fgraph_12889',['mutex_graph',['../classvg_1_1Transcriptome.html#a881ee68ca1a43b0ab10494f62e7b127f',1,'vg::Transcriptome']]],
+ ['mutex_5ftranscript_5fpaths_12890',['mutex_transcript_paths',['../classvg_1_1Transcriptome.html#a3c6d64194201d695fdcb07078463161a',1,'vg::Transcriptome']]],
+ ['my_5fmapper_12891',['my_mapper',['../classvg_1_1Filter.html#a13678a95a03ae4feb7e6ebc0fa00a69f',1,'vg::Filter']]],
+ ['my_5fmax_5fdistance_12892',['my_max_distance',['../classvg_1_1Filter.html#ab9ec8e13d2cd4fc50aa86981a0b6475f',1,'vg::Filter']]],
+ ['my_5fnames_12893',['my_names',['../classVectorizer.html#a5702f38d3e6d29866e2135d29f7496fd',1,'Vectorizer']]],
+ ['my_5fpath_5fposition_5fgraph_12894',['my_path_position_graph',['../classvg_1_1Filter.html#af17db75bb83c6d2ad00b813a4812d30d',1,'vg::Filter']]],
+ ['my_5fvectors_12895',['my_vectors',['../classVectorizer.html#af370e810d055623deaa0bfaac120fe8d',1,'Vectorizer']]],
+ ['my_5fvg_12896',['my_vg',['../classvg_1_1Filter.html#ac849cd8534ba9b7eb7daa8485d6c9d45',1,'vg::Filter']]],
+ ['my_5fxg_12897',['my_xg',['../classVectorizer.html#adebb6c75ae3b7c1199143ab2f166d284',1,'Vectorizer']]]
];
diff --git a/search/variables_e.js b/search/variables_e.js
index fb09014ef7..f39e7827be 100644
--- a/search/variables_e.js
+++ b/search/variables_e.js
@@ -1,109 +1,109 @@
var searchData=
[
- ['n_5fbins_12894',['n_bins',['../classvg_1_1Packer.html#a3e753cd974d4411036081d252b6eb7bf',1,'vg::Packer']]],
- ['n_5fiterations_12895',['n_iterations',['../classvg_1_1MCMCGenotyper.html#a1d5684e63858e5362578bc85d638a870',1,'vg::MCMCGenotyper']]],
- ['name_12896',['name',['../structvg_1_1BenchmarkResult.html#a406a53ba511e3f0f28d20a542b41355a',1,'vg::BenchmarkResult::name()'],['../structvg_1_1BREAKPOINT.html#a098f871767e6bbb25ec840acfabae12b',1,'vg::BREAKPOINT::name()'],['../structvg_1_1Funnel_1_1Stage.html#a709200eef7b97eb16aaaeaad95aab6fe',1,'vg::Funnel::Stage::name()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ac72259c3b34d4ec70dcb14225a546c0a',1,'vg::Recombinator::LocalHaplotype::name()'],['../structvg_1_1Transcript.html#a91a919300bda880406cf56a4f78cffda',1,'vg::Transcript::name()'],['../classvg_1_1VG.html#a1f6fcd5a907e9bee524cf37a62ad5be2',1,'vg::VG::name()'],['../structvg_1_1VG_1_1Plan.html#aba1bea59a4b1db998936d5d99eff9c4e',1,'vg::VG::Plan::name()'],['../classvg_1_1subcommand_1_1Subcommand.html#a1873ba1dfd0eec7c8db3303f18971e08',1,'vg::subcommand::Subcommand::name()'],['../structgafkluge_1_1GafStep.html#a9cf80aad32be2824f3a2196e669851ca',1,'gafkluge::GafStep::name()'],['../structvg_1_1Node.html#a3a4827f5d3eb097a4ef9e542e56c1e2c',1,'vg::Node::name()'],['../structvg_1_1Position.html#ae2e1a55adad827628c58ec06489c54ed',1,'vg::Position::name()'],['../structvg_1_1Path.html#a24e6f7ffbbe8fcbd7444937b7fcd1601',1,'vg::Path::name()'],['../structvg_1_1Alignment.html#ad20cac38e0bd25d2b32862fe1f5409ab',1,'vg::Alignment::name()'],['../structvg_1_1MultipathAlignment.html#a9427bb485b73bc6d3e2f077ee5df303d',1,'vg::MultipathAlignment::name()'],['../structvg_1_1Snarl.html#ac6e2f21c606af930c7f77f8f4027f833',1,'vg::Snarl::name()'],['../structvg_1_1Visit.html#ac0dae7bcea098cf39bbba443e7b45cbf',1,'vg::Visit::name()'],['../structvg_1_1SnarlTraversal.html#a1c8921481ba23cd8fe8725212f376b21',1,'vg::SnarlTraversal::name()'],['../structvg_1_1Locus.html#a39e5699f029942f81777d7e0ab203189',1,'vg::Locus::name()']]],
- ['name_5fprefixes_12897',['name_prefixes',['../classvg_1_1ReadFilter.html#a59dd97c0eadf3aebd852ae3b0aabe31d',1,'vg::ReadFilter']]],
- ['name_5fto_5fid_12898',['name_to_id',['../classvg_1_1Paths.html#a032139e6fadea366f224508c8f8385df',1,'vg::Paths::name_to_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a349cfce46078beef8d6169874b5b29b9',1,'vg::algorithms::GFAIDMapInfo::name_to_id()']]],
- ['need_5fcomma_12899',['need_comma',['../classvg_1_1ProblemDumpExplainer.html#af1f3a4b525a0c5b4daeee2a3ae9a3a18',1,'vg::ProblemDumpExplainer']]],
- ['need_5fline_12900',['need_line',['../classvg_1_1TSVExplainer.html#a810b272c339e543614686bce35a82f76',1,'vg::TSVExplainer']]],
- ['need_5ftab_12901',['need_tab',['../classvg_1_1TSVExplainer.html#ad9f986f075d4dbe3033a2102376e12e5',1,'vg::TSVExplainer']]],
- ['nested_5fdecomposition_12902',['nested_decomposition',['../classvg_1_1Deconstructor.html#aa6cf4f15fa2a53976ee40443e63df36f',1,'vg::Deconstructor']]],
- ['nested_5fsupport_5ffinder_12903',['nested_support_finder',['../classvg_1_1NestedFlowCaller.html#a2c0bda955a72c10f4040ea42203b8f39',1,'vg::NestedFlowCaller']]],
- ['net_5fgraphs_12904',['net_graphs',['../classvg_1_1GenomeState.html#a7745fd8de0051a478dbf5b4e47ebce8c',1,'vg::GenomeState']]],
- ['net_5fhandle_12905',['net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#a9288aae0c2945e8b6213368b9bf99eec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
- ['net_5fhandle_5fto_5fnode_5fproblem_5findex_12906',['net_handle_to_node_problem_index',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#ada18575df8f9870a5063c99ac6167612',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
- ['net_5fnode_5flanes_12907',['net_node_lanes',['../classvg_1_1SnarlState.html#a01d595bd630d0d550176cade6897b491',1,'vg::SnarlState']]],
- ['new_5fnode_12908',['new_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ab98205bb3934c92fec2a63a0360339b4',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['next_12909',['next',['../structvg_1_1PathBranch.html#acf21b2d9bb36f687d4727c56a4b2e940',1,'vg::PathBranch::next()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#ae6ca62f71e4ab5a266170af025ec97dd',1,'vg::PhasedGenome::HaplotypeNode::next()'],['../structvg_1_1Subpath.html#ae8d4a9f246eae61420b666aa0665930d',1,'vg::Subpath::next()'],['../structvg_1_1Connection.html#a151e393bbacd7904d71afd4939950509',1,'vg::Connection::next()']]],
- ['next_5fchar_12910',['next_char',['../structvg_1_1kmer__t.html#a844852956a93c48eadc3557a0da7ab66',1,'vg::kmer_t']]],
- ['next_5fchars_12911',['next_chars',['../structvg_1_1KmerPosition.html#ae56be5485cffba06cdab7c949487ea3f',1,'vg::KmerPosition']]],
- ['next_5fcost_12912',['next_cost',['../classvg_1_1MEMChainModelVertex.html#af972fee5a48a5eb92466395cdffe38c4',1,'vg::MEMChainModelVertex::next_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#ab4300ed3dcbce1f434b6db7d28aa6a0f',1,'vg::AlignmentChainModelVertex::next_cost()']]],
- ['next_5fexplanation_5fnumber_12913',['next_explanation_number',['../classvg_1_1Explainer.html#ad6f34855ed8bf99838f158ed027b3a6a',1,'vg::Explainer']]],
- ['next_5fgroup_12914',['next_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a5dee6816359ccf56409120cff36a759b',1,'vg::IndexedVG::CacheEntry']]],
- ['next_5fpos_12915',['next_pos',['../structvg_1_1kmer__t.html#a4af3ee75920ba66867f991ec823b2bf4',1,'vg::kmer_t']]],
- ['next_5fpositions_12916',['next_positions',['../structvg_1_1KmerPosition.html#ad6a841261ad5205e4dc10503f5ec8ba7',1,'vg::KmerPosition']]],
- ['no_5fclustering_12917',['no_clustering',['../classvg_1_1MultipathMapper.html#ad4a0793bd06a62ca2e267e5a1ceb4643',1,'vg::MultipathMapper']]],
- ['no_5fcode_12918',['NO_CODE',['../structvg_1_1MIPayload.html#aad1e599cc16dec3115ea845eada83bb3',1,'vg::MIPayload']]],
- ['no_5fend_5fposition_12919',['NO_END_POSITION',['../classhandlegraph_1_1PathMetadata.html#a2b966a3af9aac1a11236de902cae6f8b',1,'handlegraph::PathMetadata']]],
- ['no_5fhaplotype_12920',['NO_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#a22d67bfb9356f42b46aaa6cefc1ee24b',1,'handlegraph::PathMetadata']]],
- ['no_5findex_12921',['NO_INDEX',['../namespacevg.html#a0fc209aaa8c7c17499d70452d2816f44',1,'vg']]],
- ['no_5flocus_5fname_12922',['NO_LOCUS_NAME',['../classhandlegraph_1_1PathMetadata.html#ae7ee0795aa13f7ad34189f2982d64c42',1,'handlegraph::PathMetadata']]],
- ['no_5fns_12923',['no_Ns',['../classvg_1_1Sampler.html#aa71ef9078ed81b2406357f0dd4fdda3a',1,'vg::Sampler']]],
- ['no_5fphase_5fblock_12924',['NO_PHASE_BLOCK',['../classhandlegraph_1_1PathMetadata.html#a03fdf276dc586f22039aa3e70dd9bf77',1,'handlegraph::PathMetadata']]],
- ['no_5fprogress_12925',['NO_PROGRESS',['../namespacevg_1_1io.html#a33939950704e2d4439b93cde15139172',1,'vg::io']]],
- ['no_5fread_5findex_12926',['NO_READ_INDEX',['../namespacevg.html#aa32104605c22b25e9ec17d69fbc61a4b',1,'vg']]],
- ['no_5fsample_5fname_12927',['NO_SAMPLE_NAME',['../classhandlegraph_1_1PathMetadata.html#a9770508967dec07997d8ad31dbbe5a95',1,'handlegraph::PathMetadata']]],
- ['no_5fsplice_5flog_5fodds_12928',['no_splice_log_odds',['../classvg_1_1MultipathMapper.html#a3130f372f82437af2f7733901a47c142',1,'vg::MultipathMapper']]],
- ['no_5fsplice_5fnatural_5flog_5fodds_12929',['no_splice_natural_log_odds',['../classvg_1_1MultipathMapper.html#a3903979b6a7b5e297335f823864cd511',1,'vg::MultipathMapper']]],
- ['no_5fsubrange_12930',['NO_SUBRANGE',['../classhandlegraph_1_1PathMetadata.html#a8524bdffc330d58553459074c57fc889',1,'handlegraph::PathMetadata']]],
- ['no_5fvalue_12931',['NO_VALUE',['../structvg_1_1MIPayload.html#a90c2f3f622099c6920b28356d49d9a4e',1,'vg::MIPayload']]],
- ['no_5fwait_12932',['NO_WAIT',['../namespacevg_1_1io.html#a21ec64ee292cf76a61bff68a727471e9',1,'vg::io']]],
- ['node_12933',['node',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a15ee21b9bf2ed37f9892ca0291964d28',1,'vg::BandedGlobalAligner::BAMatrix::node()'],['../structvg_1_1CactusSide.html#a1e590f9e0956cdd491c9758a89bc4e1e',1,'vg::CactusSide::node()'],['../classvg_1_1NodeSide.html#a11a48024eddd85edf22b6e0748049fa0',1,'vg::NodeSide::node()'],['../classvg_1_1NodeTraversal.html#a73ca27b85d0f387740425dea434763ed',1,'vg::NodeTraversal::node()'],['../structvg_1_1Graph.html#ac16f6921068e2ae84b0d2166b2eb3b4e',1,'vg::Graph::node()']]],
- ['node_5fby_5fid_12934',['node_by_id',['../classvg_1_1VG.html#ad84c5c18cddf1ef2c469e0db0fd7b9dc',1,'vg::VG']]],
- ['node_5fcache_12935',['node_cache',['../classvg_1_1Sampler.html#a7fe30513fb778b219886100865cb33e8',1,'vg::Sampler']]],
- ['node_5fchain_5fcomponent_5foffset_12936',['NODE_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#aa4fb1284d9b1da36db4e87fb5f8a1510',1,'vg::ZipCode']]],
- ['node_5fcount_12937',['node_count',['../classvg_1_1DagifiedGraph.html#add99aae0a2ea95cbb54a1eeebc29087a',1,'vg::DagifiedGraph::node_count()'],['../classxg_1_1XG.html#a8324b23c3162c729f8336df7355b13a1',1,'xg::XG::node_count()']]],
- ['node_5fhandle_12938',['node_handle',['../structvg_1_1MIPayload.html#a360ac8861d30614205e7637d6ac443b4',1,'vg::MIPayload']]],
- ['node_5fid_12939',['node_id',['../structvg_1_1Position.html#aef891b22e577fdcce6062cf78edd2474',1,'vg::Position::node_id()'],['../structvg_1_1KmerMatch.html#a6d59f7a7bc30d06c055d768324410853',1,'vg::KmerMatch::node_id()'],['../structvg_1_1NodePileup.html#a3ed5e4d46aadb0402badb75e3138dac2',1,'vg::NodePileup::node_id()'],['../structvg_1_1Visit.html#a0dc6e6745e330afc09f338fd50f7fa6c',1,'vg::Visit::node_id()'],['../structvg_1_1LocationSupport.html#a5729cf43650d3357ae350f91291823d3',1,'vg::LocationSupport::node_id()']]],
- ['node_5fid_5fto_5fidx_12940',['node_id_to_idx',['../classvg_1_1BandedGlobalAligner.html#ad892d2f28a60a26de8f9afb4461765d0',1,'vg::BandedGlobalAligner']]],
- ['node_5fids_12941',['node_ids',['../classvg_1_1ContractingGraph.html#a639c5892160dd053bc66066b53493253',1,'vg::ContractingGraph::node_ids()'],['../classvg_1_1SparseUnionFind.html#a650957ef3de935c615ef8e28e35d4721',1,'vg::SparseUnionFind::node_ids()']]],
- ['node_5findex_12942',['node_index',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a24f308c69c1dfc5da67e3bb5eda3e017',1,'vg::DozeuInterface::graph_pos_s::node_index()'],['../classvg_1_1VG.html#a2ce9aecf57e0684821ee277d983eb248',1,'vg::VG::node_index()']]],
- ['node_5fis_5freversed_5foffset_12943',['NODE_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a26bad855c31c5f57abbadbc681c08803',1,'vg::ZipCode']]],
- ['node_5flength_12944',['node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af4071b87357c2a091b98ddb1032d5bdf',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::node_length()'],['../classvg_1_1SourceSinkOverlay.html#aeba2436177cd49e0ec49c1447ba55180',1,'vg::SourceSinkOverlay::node_length()'],['../structvg_1_1MIPayload.html#a787342925dee2293cd58ecc2346f0c4e',1,'vg::MIPayload::node_length()']]],
- ['node_5flength_5foffset_12945',['NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a94d890670c72b9e6639b55200cac921c',1,'vg::ZipCode']]],
- ['node_5flengths_12946',['node_lengths',['../structhaplo_1_1gbwt__thread__t.html#afb9949e8024637afcf7f254f91fd0c97',1,'haplo::gbwt_thread_t']]],
- ['node_5flisteners_12947',['node_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#af8e9a128ae89863a958de09962a50dae',1,'vg::algorithms::GFAParser']]],
- ['node_5flocations_12948',['node_locations',['../classvg_1_1PhasedGenome.html#a00b61ff3ca8566865774b0661d5f47c6',1,'vg::PhasedGenome']]],
- ['node_5fmapping_12949',['node_mapping',['../classvg_1_1Paths.html#a724b545027d19a3fd4658494d676f61a',1,'vg::Paths']]],
- ['node_5fmappings_12950',['node_mappings',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a1704e01ce31452b48d51de4258295b09',1,'vg::BandedGlobalAligner::BABuilder']]],
- ['node_5foccurrences_12951',['node_occurrences',['../structvg_1_1PathIndex.html#a057c79ab3b7c3d4a2827af2e7698b1f1',1,'vg::PathIndex']]],
- ['node_5foffset_12952',['node_offset',['../structvg_1_1MatchPos.html#aee7d8f1091e860ccd367ea9042a451bc',1,'vg::MatchPos::node_offset()'],['../structvg_1_1WFAPoint.html#a70ee87f31f5aa70364a43e7416af677e',1,'vg::WFAPoint::node_offset()'],['../structvg_1_1WFAAlignment.html#a7c7ab8f31a4259c0ddd4d188c7596a7f',1,'vg::WFAAlignment::node_offset()']]],
- ['node_5foffset_5foffset_12953',['NODE_OFFSET_OFFSET',['../classvg_1_1ZipCode.html#a23f1322b4bb418f265261d790a5477ae',1,'vg::ZipCode']]],
- ['node_5fpileups_12954',['node_pileups',['../structvg_1_1Pileup.html#aa70628ddc77e14378831220ea88480c6',1,'vg::Pileup']]],
- ['node_5fqual_5fbin_5fsize_12955',['node_qual_bin_size',['../classvg_1_1Packer.html#ab74d4e3fe0a2a0942e82cdcae0d1bad6',1,'vg::Packer']]],
- ['node_5fquality_5fciv_12956',['node_quality_civ',['../classvg_1_1Packer.html#a8491169478e16d232cdb9b1100acdade',1,'vg::Packer']]],
- ['node_5fquality_5fdynamic_12957',['node_quality_dynamic',['../classvg_1_1Packer.html#a7ff3c9e1c9147389485b0da01d5eb2db',1,'vg::Packer']]],
- ['node_5fquality_5flocks_12958',['node_quality_locks',['../classvg_1_1Packer.html#ac06fff3568beec54bb343011fc8f6786',1,'vg::Packer']]],
- ['node_5fsequence_12959',['node_sequence',['../structvg_1_1WFANode.html#a1a923918d714be1ab7c32f27a5ed31e9',1,'vg::WFANode']]],
- ['node_5fsize_12960',['NODE_SIZE',['../classvg_1_1ZipCode.html#a0237b30c6e57eb94d71e67af989cbf03',1,'vg::ZipCode']]],
- ['node_5fsubset_12961',['node_subset',['../classvg_1_1SubgraphOverlay.html#a68a505e96443fd85b5498cf785fc372d',1,'vg::SubgraphOverlay']]],
- ['node_5fsupports_12962',['node_supports',['../structvg_1_1SupportAugmentedGraph.html#ad904715950e1e9ffcb6ed6676868debe',1,'vg::SupportAugmentedGraph']]],
- ['node_5fto_5fposition_12963',['node_to_position',['../classvg_1_1Filter.html#aa3a0cf6a83085d33f0983e681c078625',1,'vg::Filter']]],
- ['node_5fto_5fsegment_5fand_5foffsets_12964',['node_to_segment_and_offsets',['../classvg_1_1FlatFileBackTranslation.html#a019b9f65e0fbd404da5fe42f8a338e22',1,'vg::FlatFileBackTranslation']]],
- ['node_5fto_5fvariant_12965',['node_to_variant',['../classvg_1_1VCFTraversalFinder.html#a133068b1a172eb5f5490ff7c47fd567f',1,'vg::VCFTraversalFinder']]],
- ['node_5ftraversal_12966',['node_traversal',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a6347ba68d0d1a79fa623928b2d2eadcc',1,'vg::PhasedGenome::HaplotypeNode']]],
- ['node_5fweight_5fcallback_12967',['node_weight_callback',['../classvg_1_1FlowTraversalFinder.html#a345a65197b9a0cd215d616dfcfcd5519',1,'vg::FlowTraversalFinder']]],
- ['nodes_12968',['nodes',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aa1c634ccdab6c61d7fc0b9971014b276',1,'vg::MEMClusterer::HitGraph::nodes()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a348fbee890bd78dc50c7c84368c5b2f6',1,'vg::MEMClusterer::DPScoreComparator::nodes()'],['../classvg_1_1DiagramExplainer.html#ac48c36394b081ec619056ce38cde5d13',1,'vg::DiagramExplainer::nodes()'],['../structvg_1_1FlowSort_1_1Growth.html#ace41b35679169dfbe0a6dda4c4837681',1,'vg::FlowSort::Growth::nodes()'],['../classvg_1_1WFATree.html#a786ffc1f75cffa39bb4fe43cf22b0926',1,'vg::WFATree::nodes()'],['../structhaplo_1_1gbwt__thread__t.html#a88bae446203703780f81cbcee5ff75cd',1,'haplo::gbwt_thread_t::nodes()'],['../classvg_1_1MaximalExactMatch.html#a1c34a3529b17b7ca55a3d29c0777f5e8',1,'vg::MaximalExactMatch::nodes()'],['../structvg_1_1algorithms_1_1Graph.html#a838a14a80429547309f3e9a1c75e491e',1,'vg::algorithms::Graph::nodes()']]],
- ['nonce_12969',['nonce',['../classvg_1_1Sampler.html#a36388c416226dd9c343b2da154aada5c',1,'vg::Sampler']]],
- ['normal_5faligners_12970',['normal_aligners',['../classvg_1_1Genotyper.html#a91d6174a20ca4f121f68766fbf7fb4b0',1,'vg::Genotyper']]],
- ['normal_5fsupports_12971',['normal_supports',['../structvg_1_1BREAKPOINT.html#a08a0810aad3ba05efd04908b4911d57d',1,'vg::BREAKPOINT']]],
- ['np_5fbv_12972',['np_bv',['../classxg_1_1XG.html#a7c8fe296641f19779727ab5857b834ea',1,'xg::XG']]],
- ['np_5fbv_5fselect_12973',['np_bv_select',['../classxg_1_1XG.html#a077bdb48fbea43751a6cf5c5d731cfbe',1,'xg::XG']]],
- ['np_5fiv_12974',['np_iv',['../classxg_1_1XG.html#a1bb51062742302890454d1d5552c011d',1,'xg::XG']]],
- ['nr_5fiv_12975',['nr_iv',['../classxg_1_1XG.html#a8516a2b79e6326c6b2e7c2a3033ef9d4',1,'xg::XG']]],
- ['nt_5ftable_12976',['nt_table',['../classvg_1_1GSSWAligner.html#a73b117b8b0b894ce486bdb2c4eeeeb10',1,'vg::GSSWAligner::nt_table()'],['../classvg_1_1DinucleotideMachine.html#a42eb3d5ffd684edcd69e43c3bc28eb95',1,'vg::DinucleotideMachine::nt_table()']]],
- ['num_5falt_5falns_12977',['num_alt_alns',['../classvg_1_1MultipathMapper.html#ad29e0a45fcb921023bd6479a15cfef78',1,'vg::MultipathMapper']]],
- ['num_5fbases_12978',['num_bases',['../structvg_1_1BasePileup.html#aca3e40a479d777aaaa687ca8ab7ce49a',1,'vg::BasePileup']]],
- ['num_5fbases_5fdynamic_12979',['num_bases_dynamic',['../classvg_1_1Packer.html#a34e4dcd2100f889a0f3e673f1a794d29',1,'vg::Packer']]],
- ['num_5fbp_5fper_5fmin_12980',['num_bp_per_min',['../classvg_1_1MinimizerMapper.html#af96dfe389dbee27c52f253bb473d94de',1,'vg::MinimizerMapper']]],
- ['num_5fcandidates_12981',['NUM_CANDIDATES',['../classvg_1_1Recombinator.html#a5768e471a3447a31b14f1d8d94a11588',1,'vg::Recombinator']]],
- ['num_5fedges_5fdynamic_12982',['num_edges_dynamic',['../classvg_1_1Packer.html#ae05325e714e72b76815740f03dc10a3b',1,'vg::Packer']]],
- ['num_5fforward_5freads_12983',['num_forward_reads',['../structvg_1_1EdgePileup.html#a5a61f1d9489561ede0ca1afcbcd7c1d9',1,'vg::EdgePileup']]],
- ['num_5fhaplotypes_12984',['NUM_HAPLOTYPES',['../classvg_1_1Recombinator.html#a06515509b2d56e644d5a89d1bab3b239',1,'vg::Recombinator::NUM_HAPLOTYPES()'],['../structvg_1_1Recombinator_1_1Parameters.html#a253f1e11aa0a36a9f1cf0251de316066',1,'vg::Recombinator::Parameters::num_haplotypes()']]],
- ['num_5finline_12985',['NUM_INLINE',['../structvg_1_1MatchPos_1_1PathList.html#ac2b88a61013598a9ed786f65137c888f',1,'vg::MatchPos::PathList']]],
- ['num_5fitems_12986',['num_items',['../classvg_1_1ShuffledPairs.html#af7af129e1f60b59e78ed6d92d693d599',1,'vg::ShuffledPairs']]],
- ['num_5fjobs_12987',['num_jobs',['../structvg_1_1RebuildParameters.html#a25c12cba31a60be2c6bdfd5ece960ad7',1,'vg::RebuildParameters']]],
- ['num_5fleft_5fhandles_12988',['num_left_handles',['../classvg_1_1JoinedSpliceGraph.html#acb848555db862533ceda5be3136b7040',1,'vg::JoinedSpliceGraph']]],
- ['num_5fmapping_5fattempts_12989',['num_mapping_attempts',['../classvg_1_1MultipathMapper.html#acd259da737785206d02cc2807ab831fa',1,'vg::MultipathMapper']]],
- ['num_5fnodes_5fdynamic_12990',['num_nodes_dynamic',['../classvg_1_1Packer.html#a9f406ddaf008b85d23ea1262ab95ad68',1,'vg::Packer']]],
- ['num_5fnull_5fnodes_12991',['num_null_nodes',['../classvg_1_1DozeuPinningOverlay.html#aad4a7969c5c7263cfd5072169b60f6fa',1,'vg::DozeuPinningOverlay::num_null_nodes()'],['../classvg_1_1NullMaskingGraph.html#a789adb0e97e25f480f18c7158aec51ac',1,'vg::NullMaskingGraph::num_null_nodes()']]],
- ['num_5fpairs_12992',['num_pairs',['../classvg_1_1ShuffledPairs.html#abf8913c70ff6595d8b288bdab3c88981',1,'vg::ShuffledPairs']]],
- ['num_5fpaths_12993',['num_paths',['../structGBWTConfig.html#ad3dc88b3f829f932b976fc182257b987',1,'GBWTConfig']]],
- ['num_5fpaths_5fset_12994',['num_paths_set',['../structGBWTConfig.html#aefbd9bdd79f88ab07ee18a12df56e513',1,'GBWTConfig']]],
- ['num_5freads_12995',['num_reads',['../structvg_1_1EdgePileup.html#aa95aa0337a5bc6229762abaa56dcdbff',1,'vg::EdgePileup']]],
- ['num_5fthreads_12996',['num_threads',['../classvg_1_1Transcriptome.html#ac2261cd2e4236c02dbfded216253c923',1,'vg::Transcriptome']]],
- ['number_5fof_5fvalues_12997',['number_of_values',['../structvg_1_1SummaryStatistics.html#a0960315b33bca238ec069a1c23eefba5',1,'vg::SummaryStatistics']]],
- ['numeric_5fmode_12998',['numeric_mode',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#af2a10466f1ac4f49fb670ffd43d48a19',1,'vg::algorithms::GFAIDMapInfo']]],
- ['nx_5fiv_12999',['nx_iv',['../classxg_1_1XG.html#a48563ff2d8a9e68e67ec75ad93b6272e',1,'xg::XG']]]
+ ['n_5fbins_12898',['n_bins',['../classvg_1_1Packer.html#a3e753cd974d4411036081d252b6eb7bf',1,'vg::Packer']]],
+ ['n_5fiterations_12899',['n_iterations',['../classvg_1_1MCMCGenotyper.html#a1d5684e63858e5362578bc85d638a870',1,'vg::MCMCGenotyper']]],
+ ['name_12900',['name',['../structvg_1_1BenchmarkResult.html#a406a53ba511e3f0f28d20a542b41355a',1,'vg::BenchmarkResult::name()'],['../structvg_1_1BREAKPOINT.html#a098f871767e6bbb25ec840acfabae12b',1,'vg::BREAKPOINT::name()'],['../structvg_1_1Funnel_1_1Stage.html#a709200eef7b97eb16aaaeaad95aab6fe',1,'vg::Funnel::Stage::name()'],['../structvg_1_1Recombinator_1_1LocalHaplotype.html#ac72259c3b34d4ec70dcb14225a546c0a',1,'vg::Recombinator::LocalHaplotype::name()'],['../structvg_1_1Transcript.html#a91a919300bda880406cf56a4f78cffda',1,'vg::Transcript::name()'],['../classvg_1_1VG.html#a1f6fcd5a907e9bee524cf37a62ad5be2',1,'vg::VG::name()'],['../structvg_1_1VG_1_1Plan.html#aba1bea59a4b1db998936d5d99eff9c4e',1,'vg::VG::Plan::name()'],['../classvg_1_1subcommand_1_1Subcommand.html#a1873ba1dfd0eec7c8db3303f18971e08',1,'vg::subcommand::Subcommand::name()'],['../structgafkluge_1_1GafStep.html#a9cf80aad32be2824f3a2196e669851ca',1,'gafkluge::GafStep::name()'],['../structvg_1_1Node.html#a3a4827f5d3eb097a4ef9e542e56c1e2c',1,'vg::Node::name()'],['../structvg_1_1Position.html#ae2e1a55adad827628c58ec06489c54ed',1,'vg::Position::name()'],['../structvg_1_1Path.html#a24e6f7ffbbe8fcbd7444937b7fcd1601',1,'vg::Path::name()'],['../structvg_1_1Alignment.html#ad20cac38e0bd25d2b32862fe1f5409ab',1,'vg::Alignment::name()'],['../structvg_1_1MultipathAlignment.html#a9427bb485b73bc6d3e2f077ee5df303d',1,'vg::MultipathAlignment::name()'],['../structvg_1_1Snarl.html#ac6e2f21c606af930c7f77f8f4027f833',1,'vg::Snarl::name()'],['../structvg_1_1Visit.html#ac0dae7bcea098cf39bbba443e7b45cbf',1,'vg::Visit::name()'],['../structvg_1_1SnarlTraversal.html#a1c8921481ba23cd8fe8725212f376b21',1,'vg::SnarlTraversal::name()'],['../structvg_1_1Locus.html#a39e5699f029942f81777d7e0ab203189',1,'vg::Locus::name()']]],
+ ['name_5fprefixes_12901',['name_prefixes',['../classvg_1_1ReadFilter.html#a59dd97c0eadf3aebd852ae3b0aabe31d',1,'vg::ReadFilter']]],
+ ['name_5fto_5fid_12902',['name_to_id',['../classvg_1_1Paths.html#a032139e6fadea366f224508c8f8385df',1,'vg::Paths::name_to_id()'],['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#a349cfce46078beef8d6169874b5b29b9',1,'vg::algorithms::GFAIDMapInfo::name_to_id()']]],
+ ['need_5fcomma_12903',['need_comma',['../classvg_1_1ProblemDumpExplainer.html#af1f3a4b525a0c5b4daeee2a3ae9a3a18',1,'vg::ProblemDumpExplainer']]],
+ ['need_5fline_12904',['need_line',['../classvg_1_1TSVExplainer.html#a810b272c339e543614686bce35a82f76',1,'vg::TSVExplainer']]],
+ ['need_5ftab_12905',['need_tab',['../classvg_1_1TSVExplainer.html#ad9f986f075d4dbe3033a2102376e12e5',1,'vg::TSVExplainer']]],
+ ['nested_5fdecomposition_12906',['nested_decomposition',['../classvg_1_1Deconstructor.html#aa6cf4f15fa2a53976ee40443e63df36f',1,'vg::Deconstructor']]],
+ ['nested_5fsupport_5ffinder_12907',['nested_support_finder',['../classvg_1_1NestedFlowCaller.html#a2c0bda955a72c10f4040ea42203b8f39',1,'vg::NestedFlowCaller']]],
+ ['net_5fgraphs_12908',['net_graphs',['../classvg_1_1GenomeState.html#a7745fd8de0051a478dbf5b4e47ebce8c',1,'vg::GenomeState']]],
+ ['net_5fhandle_12909',['net_handle',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem_1_1SnarlTreeChild.html#a9288aae0c2945e8b6213368b9bf99eec',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeChild']]],
+ ['net_5fhandle_5fto_5fnode_5fproblem_5findex_12910',['net_handle_to_node_problem_index',['../structvg_1_1SnarlDistanceIndexClusterer_1_1ClusteringProblem.html#ada18575df8f9870a5063c99ac6167612',1,'vg::SnarlDistanceIndexClusterer::ClusteringProblem']]],
+ ['net_5fnode_5flanes_12911',['net_node_lanes',['../classvg_1_1SnarlState.html#a01d595bd630d0d550176cade6897b491',1,'vg::SnarlState']]],
+ ['new_5fnode_12912',['new_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ab98205bb3934c92fec2a63a0360339b4',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['next_12913',['next',['../structvg_1_1PathBranch.html#acf21b2d9bb36f687d4727c56a4b2e940',1,'vg::PathBranch::next()'],['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#ae6ca62f71e4ab5a266170af025ec97dd',1,'vg::PhasedGenome::HaplotypeNode::next()'],['../structvg_1_1Subpath.html#ae8d4a9f246eae61420b666aa0665930d',1,'vg::Subpath::next()'],['../structvg_1_1Connection.html#a151e393bbacd7904d71afd4939950509',1,'vg::Connection::next()']]],
+ ['next_5fchar_12914',['next_char',['../structvg_1_1kmer__t.html#a844852956a93c48eadc3557a0da7ab66',1,'vg::kmer_t']]],
+ ['next_5fchars_12915',['next_chars',['../structvg_1_1KmerPosition.html#ae56be5485cffba06cdab7c949487ea3f',1,'vg::KmerPosition']]],
+ ['next_5fcost_12916',['next_cost',['../classvg_1_1MEMChainModelVertex.html#af972fee5a48a5eb92466395cdffe38c4',1,'vg::MEMChainModelVertex::next_cost()'],['../classvg_1_1AlignmentChainModelVertex.html#ab4300ed3dcbce1f434b6db7d28aa6a0f',1,'vg::AlignmentChainModelVertex::next_cost()']]],
+ ['next_5fexplanation_5fnumber_12917',['next_explanation_number',['../classvg_1_1Explainer.html#ad6f34855ed8bf99838f158ed027b3a6a',1,'vg::Explainer']]],
+ ['next_5fgroup_12918',['next_group',['../structvg_1_1IndexedVG_1_1CacheEntry.html#a5dee6816359ccf56409120cff36a759b',1,'vg::IndexedVG::CacheEntry']]],
+ ['next_5fpos_12919',['next_pos',['../structvg_1_1kmer__t.html#a4af3ee75920ba66867f991ec823b2bf4',1,'vg::kmer_t']]],
+ ['next_5fpositions_12920',['next_positions',['../structvg_1_1KmerPosition.html#ad6a841261ad5205e4dc10503f5ec8ba7',1,'vg::KmerPosition']]],
+ ['no_5fclustering_12921',['no_clustering',['../classvg_1_1MultipathMapper.html#ad4a0793bd06a62ca2e267e5a1ceb4643',1,'vg::MultipathMapper']]],
+ ['no_5fcode_12922',['NO_CODE',['../structvg_1_1MIPayload.html#aad1e599cc16dec3115ea845eada83bb3',1,'vg::MIPayload']]],
+ ['no_5fend_5fposition_12923',['NO_END_POSITION',['../classhandlegraph_1_1PathMetadata.html#a2b966a3af9aac1a11236de902cae6f8b',1,'handlegraph::PathMetadata']]],
+ ['no_5fhaplotype_12924',['NO_HAPLOTYPE',['../classhandlegraph_1_1PathMetadata.html#a22d67bfb9356f42b46aaa6cefc1ee24b',1,'handlegraph::PathMetadata']]],
+ ['no_5findex_12925',['NO_INDEX',['../namespacevg.html#a0fc209aaa8c7c17499d70452d2816f44',1,'vg']]],
+ ['no_5flocus_5fname_12926',['NO_LOCUS_NAME',['../classhandlegraph_1_1PathMetadata.html#ae7ee0795aa13f7ad34189f2982d64c42',1,'handlegraph::PathMetadata']]],
+ ['no_5fns_12927',['no_Ns',['../classvg_1_1Sampler.html#aa71ef9078ed81b2406357f0dd4fdda3a',1,'vg::Sampler']]],
+ ['no_5fphase_5fblock_12928',['NO_PHASE_BLOCK',['../classhandlegraph_1_1PathMetadata.html#a03fdf276dc586f22039aa3e70dd9bf77',1,'handlegraph::PathMetadata']]],
+ ['no_5fprogress_12929',['NO_PROGRESS',['../namespacevg_1_1io.html#a33939950704e2d4439b93cde15139172',1,'vg::io']]],
+ ['no_5fread_5findex_12930',['NO_READ_INDEX',['../namespacevg.html#aa32104605c22b25e9ec17d69fbc61a4b',1,'vg']]],
+ ['no_5fsample_5fname_12931',['NO_SAMPLE_NAME',['../classhandlegraph_1_1PathMetadata.html#a9770508967dec07997d8ad31dbbe5a95',1,'handlegraph::PathMetadata']]],
+ ['no_5fsplice_5flog_5fodds_12932',['no_splice_log_odds',['../classvg_1_1MultipathMapper.html#a3130f372f82437af2f7733901a47c142',1,'vg::MultipathMapper']]],
+ ['no_5fsplice_5fnatural_5flog_5fodds_12933',['no_splice_natural_log_odds',['../classvg_1_1MultipathMapper.html#a3903979b6a7b5e297335f823864cd511',1,'vg::MultipathMapper']]],
+ ['no_5fsubrange_12934',['NO_SUBRANGE',['../classhandlegraph_1_1PathMetadata.html#a8524bdffc330d58553459074c57fc889',1,'handlegraph::PathMetadata']]],
+ ['no_5fvalue_12935',['NO_VALUE',['../structvg_1_1MIPayload.html#a90c2f3f622099c6920b28356d49d9a4e',1,'vg::MIPayload']]],
+ ['no_5fwait_12936',['NO_WAIT',['../namespacevg_1_1io.html#a21ec64ee292cf76a61bff68a727471e9',1,'vg::io']]],
+ ['node_12937',['node',['../classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#a15ee21b9bf2ed37f9892ca0291964d28',1,'vg::BandedGlobalAligner::BAMatrix::node()'],['../structvg_1_1CactusSide.html#a1e590f9e0956cdd491c9758a89bc4e1e',1,'vg::CactusSide::node()'],['../classvg_1_1NodeSide.html#a11a48024eddd85edf22b6e0748049fa0',1,'vg::NodeSide::node()'],['../classvg_1_1NodeTraversal.html#a73ca27b85d0f387740425dea434763ed',1,'vg::NodeTraversal::node()'],['../structvg_1_1Graph.html#ac16f6921068e2ae84b0d2166b2eb3b4e',1,'vg::Graph::node()']]],
+ ['node_5fby_5fid_12938',['node_by_id',['../classvg_1_1VG.html#ad84c5c18cddf1ef2c469e0db0fd7b9dc',1,'vg::VG']]],
+ ['node_5fcache_12939',['node_cache',['../classvg_1_1Sampler.html#a7fe30513fb778b219886100865cb33e8',1,'vg::Sampler']]],
+ ['node_5fchain_5fcomponent_5foffset_12940',['NODE_CHAIN_COMPONENT_OFFSET',['../classvg_1_1ZipCode.html#aa4fb1284d9b1da36db4e87fb5f8a1510',1,'vg::ZipCode']]],
+ ['node_5fcount_12941',['node_count',['../classvg_1_1DagifiedGraph.html#add99aae0a2ea95cbb54a1eeebc29087a',1,'vg::DagifiedGraph::node_count()'],['../classxg_1_1XG.html#a8324b23c3162c729f8336df7355b13a1',1,'xg::XG::node_count()']]],
+ ['node_5fhandle_12942',['node_handle',['../structvg_1_1MIPayload.html#a360ac8861d30614205e7637d6ac443b4',1,'vg::MIPayload']]],
+ ['node_5fid_12943',['node_id',['../structvg_1_1Position.html#aef891b22e577fdcce6062cf78edd2474',1,'vg::Position::node_id()'],['../structvg_1_1KmerMatch.html#a6d59f7a7bc30d06c055d768324410853',1,'vg::KmerMatch::node_id()'],['../structvg_1_1NodePileup.html#a3ed5e4d46aadb0402badb75e3138dac2',1,'vg::NodePileup::node_id()'],['../structvg_1_1Visit.html#a0dc6e6745e330afc09f338fd50f7fa6c',1,'vg::Visit::node_id()'],['../structvg_1_1LocationSupport.html#a5729cf43650d3357ae350f91291823d3',1,'vg::LocationSupport::node_id()']]],
+ ['node_5fid_5fto_5fidx_12944',['node_id_to_idx',['../classvg_1_1BandedGlobalAligner.html#ad892d2f28a60a26de8f9afb4461765d0',1,'vg::BandedGlobalAligner']]],
+ ['node_5fids_12945',['node_ids',['../classvg_1_1ContractingGraph.html#a639c5892160dd053bc66066b53493253',1,'vg::ContractingGraph::node_ids()'],['../classvg_1_1SparseUnionFind.html#a650957ef3de935c615ef8e28e35d4721',1,'vg::SparseUnionFind::node_ids()']]],
+ ['node_5findex_12946',['node_index',['../structvg_1_1DozeuInterface_1_1graph__pos__s.html#a24f308c69c1dfc5da67e3bb5eda3e017',1,'vg::DozeuInterface::graph_pos_s::node_index()'],['../classvg_1_1VG.html#a2ce9aecf57e0684821ee277d983eb248',1,'vg::VG::node_index()']]],
+ ['node_5fis_5freversed_5foffset_12947',['NODE_IS_REVERSED_OFFSET',['../classvg_1_1ZipCode.html#a26bad855c31c5f57abbadbc681c08803',1,'vg::ZipCode']]],
+ ['node_5flength_12948',['node_length',['../structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#af4071b87357c2a091b98ddb1032d5bdf',1,'vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::node_length()'],['../classvg_1_1SourceSinkOverlay.html#aeba2436177cd49e0ec49c1447ba55180',1,'vg::SourceSinkOverlay::node_length()'],['../structvg_1_1MIPayload.html#a787342925dee2293cd58ecc2346f0c4e',1,'vg::MIPayload::node_length()']]],
+ ['node_5flength_5foffset_12949',['NODE_LENGTH_OFFSET',['../classvg_1_1ZipCode.html#a94d890670c72b9e6639b55200cac921c',1,'vg::ZipCode']]],
+ ['node_5flengths_12950',['node_lengths',['../structhaplo_1_1gbwt__thread__t.html#afb9949e8024637afcf7f254f91fd0c97',1,'haplo::gbwt_thread_t']]],
+ ['node_5flisteners_12951',['node_listeners',['../classvg_1_1algorithms_1_1GFAParser.html#af8e9a128ae89863a958de09962a50dae',1,'vg::algorithms::GFAParser']]],
+ ['node_5flocations_12952',['node_locations',['../classvg_1_1PhasedGenome.html#a00b61ff3ca8566865774b0661d5f47c6',1,'vg::PhasedGenome']]],
+ ['node_5fmapping_12953',['node_mapping',['../classvg_1_1Paths.html#a724b545027d19a3fd4658494d676f61a',1,'vg::Paths']]],
+ ['node_5fmappings_12954',['node_mappings',['../classvg_1_1BandedGlobalAligner_1_1BABuilder.html#a1704e01ce31452b48d51de4258295b09',1,'vg::BandedGlobalAligner::BABuilder']]],
+ ['node_5foccurrences_12955',['node_occurrences',['../structvg_1_1PathIndex.html#a057c79ab3b7c3d4a2827af2e7698b1f1',1,'vg::PathIndex']]],
+ ['node_5foffset_12956',['node_offset',['../structvg_1_1MatchPos.html#aee7d8f1091e860ccd367ea9042a451bc',1,'vg::MatchPos::node_offset()'],['../structvg_1_1WFAPoint.html#a70ee87f31f5aa70364a43e7416af677e',1,'vg::WFAPoint::node_offset()'],['../structvg_1_1WFAAlignment.html#a7c7ab8f31a4259c0ddd4d188c7596a7f',1,'vg::WFAAlignment::node_offset()']]],
+ ['node_5foffset_5foffset_12957',['NODE_OFFSET_OFFSET',['../classvg_1_1ZipCode.html#a23f1322b4bb418f265261d790a5477ae',1,'vg::ZipCode']]],
+ ['node_5fpileups_12958',['node_pileups',['../structvg_1_1Pileup.html#aa70628ddc77e14378831220ea88480c6',1,'vg::Pileup']]],
+ ['node_5fqual_5fbin_5fsize_12959',['node_qual_bin_size',['../classvg_1_1Packer.html#ab74d4e3fe0a2a0942e82cdcae0d1bad6',1,'vg::Packer']]],
+ ['node_5fquality_5fciv_12960',['node_quality_civ',['../classvg_1_1Packer.html#a8491169478e16d232cdb9b1100acdade',1,'vg::Packer']]],
+ ['node_5fquality_5fdynamic_12961',['node_quality_dynamic',['../classvg_1_1Packer.html#a7ff3c9e1c9147389485b0da01d5eb2db',1,'vg::Packer']]],
+ ['node_5fquality_5flocks_12962',['node_quality_locks',['../classvg_1_1Packer.html#ac06fff3568beec54bb343011fc8f6786',1,'vg::Packer']]],
+ ['node_5fsequence_12963',['node_sequence',['../structvg_1_1WFANode.html#a1a923918d714be1ab7c32f27a5ed31e9',1,'vg::WFANode']]],
+ ['node_5fsize_12964',['NODE_SIZE',['../classvg_1_1ZipCode.html#a0237b30c6e57eb94d71e67af989cbf03',1,'vg::ZipCode']]],
+ ['node_5fsubset_12965',['node_subset',['../classvg_1_1SubgraphOverlay.html#a68a505e96443fd85b5498cf785fc372d',1,'vg::SubgraphOverlay']]],
+ ['node_5fsupports_12966',['node_supports',['../structvg_1_1SupportAugmentedGraph.html#ad904715950e1e9ffcb6ed6676868debe',1,'vg::SupportAugmentedGraph']]],
+ ['node_5fto_5fposition_12967',['node_to_position',['../classvg_1_1Filter.html#aa3a0cf6a83085d33f0983e681c078625',1,'vg::Filter']]],
+ ['node_5fto_5fsegment_5fand_5foffsets_12968',['node_to_segment_and_offsets',['../classvg_1_1FlatFileBackTranslation.html#a019b9f65e0fbd404da5fe42f8a338e22',1,'vg::FlatFileBackTranslation']]],
+ ['node_5fto_5fvariant_12969',['node_to_variant',['../classvg_1_1VCFTraversalFinder.html#a133068b1a172eb5f5490ff7c47fd567f',1,'vg::VCFTraversalFinder']]],
+ ['node_5ftraversal_12970',['node_traversal',['../structvg_1_1PhasedGenome_1_1HaplotypeNode.html#a6347ba68d0d1a79fa623928b2d2eadcc',1,'vg::PhasedGenome::HaplotypeNode']]],
+ ['node_5fweight_5fcallback_12971',['node_weight_callback',['../classvg_1_1FlowTraversalFinder.html#a345a65197b9a0cd215d616dfcfcd5519',1,'vg::FlowTraversalFinder']]],
+ ['nodes_12972',['nodes',['../classvg_1_1MEMClusterer_1_1HitGraph.html#aa1c634ccdab6c61d7fc0b9971014b276',1,'vg::MEMClusterer::HitGraph::nodes()'],['../structvg_1_1MEMClusterer_1_1DPScoreComparator.html#a348fbee890bd78dc50c7c84368c5b2f6',1,'vg::MEMClusterer::DPScoreComparator::nodes()'],['../classvg_1_1DiagramExplainer.html#ac48c36394b081ec619056ce38cde5d13',1,'vg::DiagramExplainer::nodes()'],['../structvg_1_1FlowSort_1_1Growth.html#ace41b35679169dfbe0a6dda4c4837681',1,'vg::FlowSort::Growth::nodes()'],['../classvg_1_1WFATree.html#a786ffc1f75cffa39bb4fe43cf22b0926',1,'vg::WFATree::nodes()'],['../structhaplo_1_1gbwt__thread__t.html#a88bae446203703780f81cbcee5ff75cd',1,'haplo::gbwt_thread_t::nodes()'],['../classvg_1_1MaximalExactMatch.html#a1c34a3529b17b7ca55a3d29c0777f5e8',1,'vg::MaximalExactMatch::nodes()'],['../structvg_1_1algorithms_1_1Graph.html#a838a14a80429547309f3e9a1c75e491e',1,'vg::algorithms::Graph::nodes()']]],
+ ['nonce_12973',['nonce',['../classvg_1_1Sampler.html#a36388c416226dd9c343b2da154aada5c',1,'vg::Sampler']]],
+ ['normal_5faligners_12974',['normal_aligners',['../classvg_1_1Genotyper.html#a91d6174a20ca4f121f68766fbf7fb4b0',1,'vg::Genotyper']]],
+ ['normal_5fsupports_12975',['normal_supports',['../structvg_1_1BREAKPOINT.html#a08a0810aad3ba05efd04908b4911d57d',1,'vg::BREAKPOINT']]],
+ ['np_5fbv_12976',['np_bv',['../classxg_1_1XG.html#a7c8fe296641f19779727ab5857b834ea',1,'xg::XG']]],
+ ['np_5fbv_5fselect_12977',['np_bv_select',['../classxg_1_1XG.html#a077bdb48fbea43751a6cf5c5d731cfbe',1,'xg::XG']]],
+ ['np_5fiv_12978',['np_iv',['../classxg_1_1XG.html#a1bb51062742302890454d1d5552c011d',1,'xg::XG']]],
+ ['nr_5fiv_12979',['nr_iv',['../classxg_1_1XG.html#a8516a2b79e6326c6b2e7c2a3033ef9d4',1,'xg::XG']]],
+ ['nt_5ftable_12980',['nt_table',['../classvg_1_1GSSWAligner.html#a73b117b8b0b894ce486bdb2c4eeeeb10',1,'vg::GSSWAligner::nt_table()'],['../classvg_1_1DinucleotideMachine.html#a42eb3d5ffd684edcd69e43c3bc28eb95',1,'vg::DinucleotideMachine::nt_table()']]],
+ ['num_5falt_5falns_12981',['num_alt_alns',['../classvg_1_1MultipathMapper.html#ad29e0a45fcb921023bd6479a15cfef78',1,'vg::MultipathMapper']]],
+ ['num_5fbases_12982',['num_bases',['../structvg_1_1BasePileup.html#aca3e40a479d777aaaa687ca8ab7ce49a',1,'vg::BasePileup']]],
+ ['num_5fbases_5fdynamic_12983',['num_bases_dynamic',['../classvg_1_1Packer.html#a34e4dcd2100f889a0f3e673f1a794d29',1,'vg::Packer']]],
+ ['num_5fbp_5fper_5fmin_12984',['num_bp_per_min',['../classvg_1_1MinimizerMapper.html#af96dfe389dbee27c52f253bb473d94de',1,'vg::MinimizerMapper']]],
+ ['num_5fcandidates_12985',['NUM_CANDIDATES',['../classvg_1_1Recombinator.html#a5768e471a3447a31b14f1d8d94a11588',1,'vg::Recombinator']]],
+ ['num_5fedges_5fdynamic_12986',['num_edges_dynamic',['../classvg_1_1Packer.html#ae05325e714e72b76815740f03dc10a3b',1,'vg::Packer']]],
+ ['num_5fforward_5freads_12987',['num_forward_reads',['../structvg_1_1EdgePileup.html#a5a61f1d9489561ede0ca1afcbcd7c1d9',1,'vg::EdgePileup']]],
+ ['num_5fhaplotypes_12988',['NUM_HAPLOTYPES',['../classvg_1_1Recombinator.html#a06515509b2d56e644d5a89d1bab3b239',1,'vg::Recombinator::NUM_HAPLOTYPES()'],['../structvg_1_1Recombinator_1_1Parameters.html#a253f1e11aa0a36a9f1cf0251de316066',1,'vg::Recombinator::Parameters::num_haplotypes()']]],
+ ['num_5finline_12989',['NUM_INLINE',['../structvg_1_1MatchPos_1_1PathList.html#ac2b88a61013598a9ed786f65137c888f',1,'vg::MatchPos::PathList']]],
+ ['num_5fitems_12990',['num_items',['../classvg_1_1ShuffledPairs.html#af7af129e1f60b59e78ed6d92d693d599',1,'vg::ShuffledPairs']]],
+ ['num_5fjobs_12991',['num_jobs',['../structvg_1_1RebuildParameters.html#a25c12cba31a60be2c6bdfd5ece960ad7',1,'vg::RebuildParameters']]],
+ ['num_5fleft_5fhandles_12992',['num_left_handles',['../classvg_1_1JoinedSpliceGraph.html#acb848555db862533ceda5be3136b7040',1,'vg::JoinedSpliceGraph']]],
+ ['num_5fmapping_5fattempts_12993',['num_mapping_attempts',['../classvg_1_1MultipathMapper.html#acd259da737785206d02cc2807ab831fa',1,'vg::MultipathMapper']]],
+ ['num_5fnodes_5fdynamic_12994',['num_nodes_dynamic',['../classvg_1_1Packer.html#a9f406ddaf008b85d23ea1262ab95ad68',1,'vg::Packer']]],
+ ['num_5fnull_5fnodes_12995',['num_null_nodes',['../classvg_1_1DozeuPinningOverlay.html#aad4a7969c5c7263cfd5072169b60f6fa',1,'vg::DozeuPinningOverlay::num_null_nodes()'],['../classvg_1_1NullMaskingGraph.html#a789adb0e97e25f480f18c7158aec51ac',1,'vg::NullMaskingGraph::num_null_nodes()']]],
+ ['num_5fpairs_12996',['num_pairs',['../classvg_1_1ShuffledPairs.html#abf8913c70ff6595d8b288bdab3c88981',1,'vg::ShuffledPairs']]],
+ ['num_5fpaths_12997',['num_paths',['../structGBWTConfig.html#ad3dc88b3f829f932b976fc182257b987',1,'GBWTConfig']]],
+ ['num_5fpaths_5fset_12998',['num_paths_set',['../structGBWTConfig.html#aefbd9bdd79f88ab07ee18a12df56e513',1,'GBWTConfig']]],
+ ['num_5freads_12999',['num_reads',['../structvg_1_1EdgePileup.html#aa95aa0337a5bc6229762abaa56dcdbff',1,'vg::EdgePileup']]],
+ ['num_5fthreads_13000',['num_threads',['../classvg_1_1Transcriptome.html#ac2261cd2e4236c02dbfded216253c923',1,'vg::Transcriptome']]],
+ ['number_5fof_5fvalues_13001',['number_of_values',['../structvg_1_1SummaryStatistics.html#a0960315b33bca238ec069a1c23eefba5',1,'vg::SummaryStatistics']]],
+ ['numeric_5fmode_13002',['numeric_mode',['../structvg_1_1algorithms_1_1GFAIDMapInfo.html#af2a10466f1ac4f49fb670ffd43d48a19',1,'vg::algorithms::GFAIDMapInfo']]],
+ ['nx_5fiv_13003',['nx_iv',['../classxg_1_1XG.html#a48563ff2d8a9e68e67ec75ad93b6272e',1,'xg::XG']]]
];
diff --git a/search/variables_f.js b/search/variables_f.js
index 95aeee29a7..7146601289 100644
--- a/search/variables_f.js
+++ b/search/variables_f.js
@@ -1,66 +1,66 @@
var searchData=
[
- ['occs_13000',['occs',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ad0254616466743533fd8b6fd59c70e0c',1,'vg::MinimizerMapper::Minimizer']]],
- ['off_5fref_5fpaths_13001',['off_ref_paths',['../classvg_1_1Deconstructor.html#adb3fbf24c904974bf655ef76145dac5a',1,'vg::Deconstructor']]],
- ['offset_13002',['offset',['../structvg_1_1GaplessExtension.html#a713e8ef2aad7aa94ae4ef91fbe83e159',1,'vg::GaplessExtension::offset()'],['../structvg_1_1PathBranch.html#ad07bed1fbba0e7c94c218f285c2e51cd',1,'vg::PathBranch::offset()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a5a3aa6577a357cc3067c7a8fbaae1349',1,'vg::Haplotypes::TopLevelChain::offset()'],['../structvg_1_1VectorView_1_1const__iterator.html#a658783ba6132302706230422eae39ce2',1,'vg::VectorView::const_iterator::offset()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a67955816b4446c3b57660e18d9626450',1,'vg::ZipCode::decoder_t::offset()'],['../structvg_1_1Position.html#a1244220d4c8ae90633fd7a7e361d309a',1,'vg::Position::offset()']]],
- ['offsets_13003',['offsets',['../classxg_1_1XGPath.html#a062c1a4ce4f13b67a90f8b57ec57e91e',1,'xg::XGPath']]],
- ['offsets_5frank_13004',['offsets_rank',['../classxg_1_1XGPath.html#aa6f1e3a71e8ceb8242a4b1f5157a789b',1,'xg::XGPath']]],
- ['offsets_5fselect_13005',['offsets_select',['../classxg_1_1XGPath.html#a22511bf04c45ce0c8620069781e3cdee',1,'xg::XGPath']]],
- ['ok_13006',['ok',['../structvg_1_1WFAAlignment.html#a64f88d651eb19e3045ab6f9b5552e6c6',1,'vg::WFAAlignment']]],
- ['old_5fedge_5ftype_5fend_5fend_13007',['OLD_EDGE_TYPE_END_END',['../classxg_1_1XG.html#a42c04fbecadef083a270c715b250e0cd',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fend_5fstart_13008',['OLD_EDGE_TYPE_END_START',['../classxg_1_1XG.html#a00a6fd4ed46f08eff821566c078b744c',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fmax_13009',['OLD_EDGE_TYPE_MAX',['../classxg_1_1XG.html#a720a6ad7d985ff3f67b3cc1f49328992',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fmin_13010',['OLD_EDGE_TYPE_MIN',['../classxg_1_1XG.html#a5ea5ab4b3c152cff2dd9568c99b14f36',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fstart_5fend_13011',['OLD_EDGE_TYPE_START_END',['../classxg_1_1XG.html#a204c73be3278d6e2edb0302f467acf8f',1,'xg::XG']]],
- ['old_5fedge_5ftype_5fstart_5fstart_13012',['OLD_EDGE_TYPE_START_START',['../classxg_1_1XG.html#a2201290a423753452c4a2943735d0c6e',1,'xg::XG']]],
- ['old_5fg_5fedge_5flength_13013',['OLD_G_EDGE_LENGTH',['../classxg_1_1XG.html#a2996e32eb2afb8b783956fb997b0a1f9',1,'xg::XG']]],
- ['old_5fg_5fedge_5foffset_5foffset_13014',['OLD_G_EDGE_OFFSET_OFFSET',['../classxg_1_1XG.html#a44e391542f4cd27cbbbb493319e37d3a',1,'xg::XG']]],
- ['old_5fg_5fedge_5ftype_5foffset_13015',['OLD_G_EDGE_TYPE_OFFSET',['../classxg_1_1XG.html#a41a462402155eb20a1549048ef12f4da',1,'xg::XG']]],
- ['old_5fg_5fnode_5ffrom_5fcount_5foffset_13016',['OLD_G_NODE_FROM_COUNT_OFFSET',['../classxg_1_1XG.html#a4885ba0ab6f74adc04b97504d6fd4f38',1,'xg::XG']]],
- ['old_5fg_5fnode_5fto_5fcount_5foffset_13017',['OLD_G_NODE_TO_COUNT_OFFSET',['../classxg_1_1XG.html#af3b654ed719981eecf06b7b5d9ddd0a8',1,'xg::XG']]],
- ['old_5fnode_13018',['old_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac101c3ba66f96fa569c1de71bf6c51fe',1,'haplo::hDP_gbwt_graph_accessor']]],
- ['old_5fscore_13019',['old_score',['../structvg_1_1GaplessExtension.html#a868af12d5411848f3b8e0e682d053337',1,'vg::GaplessExtension']]],
- ['old_5fversion_5fpath_5fname_5fend_13020',['old_version_path_name_end',['../classxg_1_1XG.html#ac0112b557633896a5c03e7e806b76f73',1,'xg::XG']]],
- ['old_5fversion_5fpath_5fname_5fstart_13021',['old_version_path_name_start',['../classxg_1_1XG.html#aa5ca99b933d49ff2b036650008b68cbd',1,'xg::XG']]],
- ['oneof_5flocation_13022',['oneof_location',['../structvg_1_1LocationSupport.html#a9a000a5b773e07f7cc30614d77c927a0',1,'vg::LocationSupport']]],
- ['only_5fcorrectly_5fmapped_13023',['only_correctly_mapped',['../classvg_1_1ReadFilter.html#ab0f19128ff55e1e2c1cad90adcfc0d6e',1,'vg::ReadFilter']]],
- ['only_5ffirst_5falignment_13024',['only_first_alignment',['../classvg_1_1ReadFilter.html#a5747bfc6146fa25db9fd96f1f760f6f0',1,'vg::ReadFilter']]],
- ['only_5fmapped_13025',['only_mapped',['../classvg_1_1ReadFilter.html#ab19be8fc638af431bb1a629aeff77f4f',1,'vg::ReadFilter']]],
- ['only_5fproper_5fpairs_13026',['only_proper_pairs',['../classvg_1_1ReadFilter.html#ac41003be9ee710a1003288e2a6ba9c7d',1,'vg::ReadFilter']]],
- ['open_5fchains_13027',['open_chains',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a43af493f53945324b203009c974ab0d2',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['open_5fintervals_13028',['open_intervals',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a75768315ee176ee34dc33da021696810',1,'vg::ZipCodeForest::forest_growing_state_t']]],
- ['opt_5ffields_13029',['opt_fields',['../structgafkluge_1_1GafRecord.html#a999647c3cab6cb89fdaaae902c867b8b',1,'gafkluge::GafRecord']]],
- ['option_13030',['option',['../structvg_1_1subcommand_1_1BaseValuation.html#abe97905c1fa0321a619e15146a1ede7f',1,'vg::subcommand::BaseValuation::option()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ab8b3cbd45bd3048d233359cd451347a1',1,'vg::subcommand::BaseArgSpec::option()']]],
- ['option_5fid_13031',['option_id',['../structvg_1_1subcommand_1_1BaseArgSpec.html#aef2794c913cd5f8c07f79a0e88a6eba7',1,'vg::subcommand::BaseArgSpec']]],
- ['option_5foffsets_13032',['option_offsets',['../classvg_1_1Configurable.html#a6c5fb72d68761ab4b157c817259164a5',1,'vg::Configurable']]],
- ['option_5fto_5findex_13033',['option_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a06f1cbc473d47bb7579f75a22dd99811',1,'vg::subcommand::OptionGroup']]],
- ['options_5fby_5fcode_13034',['options_by_code',['../classvg_1_1ConfigurableParser.html#a8bdfad847167513663ef67839a574e92',1,'vg::ConfigurableParser']]],
- ['order_13035',['order',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#ae776df11d1881a7ac95ca8775b6f53d6',1,'vg::DozeuInterface::OrderedGraph::order()'],['../classvg_1_1StreamSorter.html#a03c4547e213a4be6f8f9164cf599b3c3',1,'vg::StreamSorter::order()']]],
- ['order_5flength_5frepeat_5fhit_5fmax_13036',['order_length_repeat_hit_max',['../classvg_1_1MultipathMapper.html#ae87f55f358023f5c881494ccc4ed884f',1,'vg::MultipathMapper']]],
- ['os_13037',['OS',['../classvg_1_1Version.html#a60cb5fa1efa9969bcdfa529484ea4280',1,'vg::Version']]],
- ['other_13038',['other',['../structvg_1_1algorithms_1_1Edge.html#a3a831a365cea8d70a5c9817c9a7243ee',1,'vg::algorithms::Edge::other()'],['../classvg_1_1io_1_1streaminbuf.html#a91cfbc8581e4aa70e52268897747d764',1,'vg::io::streaminbuf::other()']]],
- ['other_5forientation_5ftimeout_13039',['other_orientation_timeout',['../classvg_1_1RepresentativeTraversalFinder.html#a5d5136f771fe4566506ff486fb17df49',1,'vg::RepresentativeTraversalFinder']]],
- ['other_5fsupports_13040',['other_supports',['../structvg_1_1BREAKPOINT.html#a2f08ace3f57cff47b7f703fef1ae9792',1,'vg::BREAKPOINT']]],
- ['out_13041',['out',['../classvg_1_1TSVExplainer.html#a2ee20849b7d26e1ce2915996dd0b9912',1,'vg::TSVExplainer::out()'],['../classvg_1_1ProblemDumpExplainer.html#aae8b802f7d2db844b8a576420d0a37bd',1,'vg::ProblemDumpExplainer::out()']]],
- ['out_5ffile_13042',['out_file',['../classvg_1_1HTSWriter.html#aff12605f14901844666bf6775b7c0971',1,'vg::HTSWriter::out_file()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a7b3a7d580d6a585a4d8205caf452ce63',1,'vg::io::TSVAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a1408267254d15464a52b44317e6c780d',1,'vg::io::VGAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a1cdca9c9f2e7f42feb6160a42e072027',1,'vg::io::GafAlignmentEmitter::out_file()']]],
- ['out_5fmutex_13043',['out_mutex',['../classvg_1_1io_1_1ProtobufEmitter.html#acb50db8c0f33135ae2e246ae26efb9d0',1,'vg::io::ProtobufEmitter']]],
- ['out_5fstream_13044',['out_stream',['../classvg_1_1MCMCCaller.html#a240022048423d2922858aaf9cfae0fc0',1,'vg::MCMCCaller']]],
- ['out_5fto_13045',['out_to',['../classvg_1_1ExtraNodeGraph.html#a0f31e37f1e4398d6f8e057c1c8c92495',1,'vg::ExtraNodeGraph']]],
- ['outfile_13046',['outfile',['../classvg_1_1Viz.html#a78a53d3a62a503ff6c29e93cb9a12a88',1,'vg::Viz']]],
- ['output_13047',['output',['../structvg_1_1io_1_1hFILE__cppstream.html#a1b13eb012084d4b68b0f30a1cddebb41',1,'vg::io::hFILE_cppstream']]],
- ['output_5ffields_13048',['output_fields',['../classvg_1_1ReadFilter.html#ade1a4a40379d72d2811fe0e32bece8f7',1,'vg::ReadFilter']]],
- ['output_5fin_5fprogress_13049',['output_in_progress',['../classvg_1_1Funnel.html#ae946f8189275c0f4b77f29433406a24b',1,'vg::Funnel']]],
- ['output_5fis_5fbgzf_13050',['output_is_bgzf',['../classvg_1_1HTSWriter.html#a440cfc6e79f5790976ebac5e648a3696',1,'vg::HTSWriter']]],
- ['output_5fnames_13051',['output_names',['../classVectorizer.html#aadb47085d4b369b1c9ea341b06311341',1,'Vectorizer']]],
- ['output_5fpng_13052',['output_png',['../classvg_1_1Viz.html#a8b50b34356875c1c0aa3917c7c67e445',1,'vg::Viz']]],
- ['output_5fprefix_13053',['output_prefix',['../classvg_1_1IndexRegistry.html#a24555b7ccd83df8e2ccb28b900a6b5b1',1,'vg::IndexRegistry']]],
- ['output_5fsvg_13054',['output_svg',['../classvg_1_1Viz.html#a82a23ca5a5a6ababff6176743247be04',1,'vg::Viz']]],
- ['output_5ftabbed_13055',['output_tabbed',['../classVectorizer.html#a7be5208d3a51438a989dd406fb808fd9',1,'Vectorizer']]],
- ['output_5fvariants_13056',['output_variants',['../classvg_1_1VCFOutputCaller.html#aa9a532dbc58fe6031595ed819d31b02a',1,'vg::VCFOutputCaller']]],
- ['output_5fvcf_13057',['output_vcf',['../classvg_1_1VCFOutputCaller.html#a1556bdec270d47b22e5c91b6956a23c0',1,'vg::VCFOutputCaller']]],
- ['output_5fversion_13058',['OUTPUT_VERSION',['../classvg_1_1StreamIndexBase.html#ad5ce82f31552d36c073e65ced2af529e',1,'vg::StreamIndexBase']]],
- ['overall_5fsupport_13059',['overall_support',['../structvg_1_1Locus.html#a04ac3427a7318a28984c8114cd216675',1,'vg::Locus']]],
- ['overlap_13060',['overlap',['../structvg_1_1Edge.html#aafdc39a954fd8de9dc3850ad9ecb9ade',1,'vg::Edge']]],
- ['overlap_5fthreshold_13061',['OVERLAP_THRESHOLD',['../classvg_1_1GaplessExtender.html#a3d436577897604304729afc521928ee8',1,'vg::GaplessExtender']]],
- ['own_5fsnarl_5fmanager_13062',['own_snarl_manager',['../classvg_1_1Masker.html#aa58433090d15c4a8235aec717dcef987',1,'vg::Masker']]]
+ ['occs_13004',['occs',['../structvg_1_1MinimizerMapper_1_1Minimizer.html#ad0254616466743533fd8b6fd59c70e0c',1,'vg::MinimizerMapper::Minimizer']]],
+ ['off_5fref_5fpaths_13005',['off_ref_paths',['../classvg_1_1Deconstructor.html#adb3fbf24c904974bf655ef76145dac5a',1,'vg::Deconstructor']]],
+ ['offset_13006',['offset',['../structvg_1_1GaplessExtension.html#a713e8ef2aad7aa94ae4ef91fbe83e159',1,'vg::GaplessExtension::offset()'],['../structvg_1_1PathBranch.html#ad07bed1fbba0e7c94c218f285c2e51cd',1,'vg::PathBranch::offset()'],['../structvg_1_1Haplotypes_1_1TopLevelChain.html#a5a3aa6577a357cc3067c7a8fbaae1349',1,'vg::Haplotypes::TopLevelChain::offset()'],['../structvg_1_1VectorView_1_1const__iterator.html#a658783ba6132302706230422eae39ce2',1,'vg::VectorView::const_iterator::offset()'],['../structvg_1_1ZipCode_1_1decoder__t.html#a67955816b4446c3b57660e18d9626450',1,'vg::ZipCode::decoder_t::offset()'],['../structvg_1_1Position.html#a1244220d4c8ae90633fd7a7e361d309a',1,'vg::Position::offset()']]],
+ ['offsets_13007',['offsets',['../classxg_1_1XGPath.html#a062c1a4ce4f13b67a90f8b57ec57e91e',1,'xg::XGPath']]],
+ ['offsets_5frank_13008',['offsets_rank',['../classxg_1_1XGPath.html#aa6f1e3a71e8ceb8242a4b1f5157a789b',1,'xg::XGPath']]],
+ ['offsets_5fselect_13009',['offsets_select',['../classxg_1_1XGPath.html#a22511bf04c45ce0c8620069781e3cdee',1,'xg::XGPath']]],
+ ['ok_13010',['ok',['../structvg_1_1WFAAlignment.html#a64f88d651eb19e3045ab6f9b5552e6c6',1,'vg::WFAAlignment']]],
+ ['old_5fedge_5ftype_5fend_5fend_13011',['OLD_EDGE_TYPE_END_END',['../classxg_1_1XG.html#a42c04fbecadef083a270c715b250e0cd',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fend_5fstart_13012',['OLD_EDGE_TYPE_END_START',['../classxg_1_1XG.html#a00a6fd4ed46f08eff821566c078b744c',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fmax_13013',['OLD_EDGE_TYPE_MAX',['../classxg_1_1XG.html#a720a6ad7d985ff3f67b3cc1f49328992',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fmin_13014',['OLD_EDGE_TYPE_MIN',['../classxg_1_1XG.html#a5ea5ab4b3c152cff2dd9568c99b14f36',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fstart_5fend_13015',['OLD_EDGE_TYPE_START_END',['../classxg_1_1XG.html#a204c73be3278d6e2edb0302f467acf8f',1,'xg::XG']]],
+ ['old_5fedge_5ftype_5fstart_5fstart_13016',['OLD_EDGE_TYPE_START_START',['../classxg_1_1XG.html#a2201290a423753452c4a2943735d0c6e',1,'xg::XG']]],
+ ['old_5fg_5fedge_5flength_13017',['OLD_G_EDGE_LENGTH',['../classxg_1_1XG.html#a2996e32eb2afb8b783956fb997b0a1f9',1,'xg::XG']]],
+ ['old_5fg_5fedge_5foffset_5foffset_13018',['OLD_G_EDGE_OFFSET_OFFSET',['../classxg_1_1XG.html#a44e391542f4cd27cbbbb493319e37d3a',1,'xg::XG']]],
+ ['old_5fg_5fedge_5ftype_5foffset_13019',['OLD_G_EDGE_TYPE_OFFSET',['../classxg_1_1XG.html#a41a462402155eb20a1549048ef12f4da',1,'xg::XG']]],
+ ['old_5fg_5fnode_5ffrom_5fcount_5foffset_13020',['OLD_G_NODE_FROM_COUNT_OFFSET',['../classxg_1_1XG.html#a4885ba0ab6f74adc04b97504d6fd4f38',1,'xg::XG']]],
+ ['old_5fg_5fnode_5fto_5fcount_5foffset_13021',['OLD_G_NODE_TO_COUNT_OFFSET',['../classxg_1_1XG.html#af3b654ed719981eecf06b7b5d9ddd0a8',1,'xg::XG']]],
+ ['old_5fnode_13022',['old_node',['../classhaplo_1_1hDP__gbwt__graph__accessor.html#ac101c3ba66f96fa569c1de71bf6c51fe',1,'haplo::hDP_gbwt_graph_accessor']]],
+ ['old_5fscore_13023',['old_score',['../structvg_1_1GaplessExtension.html#a868af12d5411848f3b8e0e682d053337',1,'vg::GaplessExtension']]],
+ ['old_5fversion_5fpath_5fname_5fend_13024',['old_version_path_name_end',['../classxg_1_1XG.html#ac0112b557633896a5c03e7e806b76f73',1,'xg::XG']]],
+ ['old_5fversion_5fpath_5fname_5fstart_13025',['old_version_path_name_start',['../classxg_1_1XG.html#aa5ca99b933d49ff2b036650008b68cbd',1,'xg::XG']]],
+ ['oneof_5flocation_13026',['oneof_location',['../structvg_1_1LocationSupport.html#a9a000a5b773e07f7cc30614d77c927a0',1,'vg::LocationSupport']]],
+ ['only_5fcorrectly_5fmapped_13027',['only_correctly_mapped',['../classvg_1_1ReadFilter.html#ab0f19128ff55e1e2c1cad90adcfc0d6e',1,'vg::ReadFilter']]],
+ ['only_5ffirst_5falignment_13028',['only_first_alignment',['../classvg_1_1ReadFilter.html#a5747bfc6146fa25db9fd96f1f760f6f0',1,'vg::ReadFilter']]],
+ ['only_5fmapped_13029',['only_mapped',['../classvg_1_1ReadFilter.html#ab19be8fc638af431bb1a629aeff77f4f',1,'vg::ReadFilter']]],
+ ['only_5fproper_5fpairs_13030',['only_proper_pairs',['../classvg_1_1ReadFilter.html#ac41003be9ee710a1003288e2a6ba9c7d',1,'vg::ReadFilter']]],
+ ['open_5fchains_13031',['open_chains',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a43af493f53945324b203009c974ab0d2',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['open_5fintervals_13032',['open_intervals',['../structvg_1_1ZipCodeForest_1_1forest__growing__state__t.html#a75768315ee176ee34dc33da021696810',1,'vg::ZipCodeForest::forest_growing_state_t']]],
+ ['opt_5ffields_13033',['opt_fields',['../structgafkluge_1_1GafRecord.html#a999647c3cab6cb89fdaaae902c867b8b',1,'gafkluge::GafRecord']]],
+ ['option_13034',['option',['../structvg_1_1subcommand_1_1BaseValuation.html#abe97905c1fa0321a619e15146a1ede7f',1,'vg::subcommand::BaseValuation::option()'],['../structvg_1_1subcommand_1_1BaseArgSpec.html#ab8b3cbd45bd3048d233359cd451347a1',1,'vg::subcommand::BaseArgSpec::option()']]],
+ ['option_5fid_13035',['option_id',['../structvg_1_1subcommand_1_1BaseArgSpec.html#aef2794c913cd5f8c07f79a0e88a6eba7',1,'vg::subcommand::BaseArgSpec']]],
+ ['option_5foffsets_13036',['option_offsets',['../classvg_1_1Configurable.html#a6c5fb72d68761ab4b157c817259164a5',1,'vg::Configurable']]],
+ ['option_5fto_5findex_13037',['option_to_index',['../structvg_1_1subcommand_1_1OptionGroup.html#a06f1cbc473d47bb7579f75a22dd99811',1,'vg::subcommand::OptionGroup']]],
+ ['options_5fby_5fcode_13038',['options_by_code',['../classvg_1_1ConfigurableParser.html#a8bdfad847167513663ef67839a574e92',1,'vg::ConfigurableParser']]],
+ ['order_13039',['order',['../structvg_1_1DozeuInterface_1_1OrderedGraph.html#ae776df11d1881a7ac95ca8775b6f53d6',1,'vg::DozeuInterface::OrderedGraph::order()'],['../classvg_1_1StreamSorter.html#a03c4547e213a4be6f8f9164cf599b3c3',1,'vg::StreamSorter::order()']]],
+ ['order_5flength_5frepeat_5fhit_5fmax_13040',['order_length_repeat_hit_max',['../classvg_1_1MultipathMapper.html#ae87f55f358023f5c881494ccc4ed884f',1,'vg::MultipathMapper']]],
+ ['os_13041',['OS',['../classvg_1_1Version.html#a60cb5fa1efa9969bcdfa529484ea4280',1,'vg::Version']]],
+ ['other_13042',['other',['../structvg_1_1algorithms_1_1Edge.html#a3a831a365cea8d70a5c9817c9a7243ee',1,'vg::algorithms::Edge::other()'],['../classvg_1_1io_1_1streaminbuf.html#a91cfbc8581e4aa70e52268897747d764',1,'vg::io::streaminbuf::other()']]],
+ ['other_5forientation_5ftimeout_13043',['other_orientation_timeout',['../classvg_1_1RepresentativeTraversalFinder.html#a5d5136f771fe4566506ff486fb17df49',1,'vg::RepresentativeTraversalFinder']]],
+ ['other_5fsupports_13044',['other_supports',['../structvg_1_1BREAKPOINT.html#a2f08ace3f57cff47b7f703fef1ae9792',1,'vg::BREAKPOINT']]],
+ ['out_13045',['out',['../classvg_1_1TSVExplainer.html#a2ee20849b7d26e1ce2915996dd0b9912',1,'vg::TSVExplainer::out()'],['../classvg_1_1ProblemDumpExplainer.html#aae8b802f7d2db844b8a576420d0a37bd',1,'vg::ProblemDumpExplainer::out()']]],
+ ['out_5ffile_13046',['out_file',['../classvg_1_1HTSWriter.html#aff12605f14901844666bf6775b7c0971',1,'vg::HTSWriter::out_file()'],['../classvg_1_1io_1_1TSVAlignmentEmitter.html#a7b3a7d580d6a585a4d8205caf452ce63',1,'vg::io::TSVAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1VGAlignmentEmitter.html#a1408267254d15464a52b44317e6c780d',1,'vg::io::VGAlignmentEmitter::out_file()'],['../classvg_1_1io_1_1GafAlignmentEmitter.html#a1cdca9c9f2e7f42feb6160a42e072027',1,'vg::io::GafAlignmentEmitter::out_file()']]],
+ ['out_5fmutex_13047',['out_mutex',['../classvg_1_1io_1_1ProtobufEmitter.html#acb50db8c0f33135ae2e246ae26efb9d0',1,'vg::io::ProtobufEmitter']]],
+ ['out_5fstream_13048',['out_stream',['../classvg_1_1MCMCCaller.html#a240022048423d2922858aaf9cfae0fc0',1,'vg::MCMCCaller']]],
+ ['out_5fto_13049',['out_to',['../classvg_1_1ExtraNodeGraph.html#a0f31e37f1e4398d6f8e057c1c8c92495',1,'vg::ExtraNodeGraph']]],
+ ['outfile_13050',['outfile',['../classvg_1_1Viz.html#a78a53d3a62a503ff6c29e93cb9a12a88',1,'vg::Viz']]],
+ ['output_13051',['output',['../structvg_1_1io_1_1hFILE__cppstream.html#a1b13eb012084d4b68b0f30a1cddebb41',1,'vg::io::hFILE_cppstream']]],
+ ['output_5ffields_13052',['output_fields',['../classvg_1_1ReadFilter.html#ade1a4a40379d72d2811fe0e32bece8f7',1,'vg::ReadFilter']]],
+ ['output_5fin_5fprogress_13053',['output_in_progress',['../classvg_1_1Funnel.html#ae946f8189275c0f4b77f29433406a24b',1,'vg::Funnel']]],
+ ['output_5fis_5fbgzf_13054',['output_is_bgzf',['../classvg_1_1HTSWriter.html#a440cfc6e79f5790976ebac5e648a3696',1,'vg::HTSWriter']]],
+ ['output_5fnames_13055',['output_names',['../classVectorizer.html#aadb47085d4b369b1c9ea341b06311341',1,'Vectorizer']]],
+ ['output_5fpng_13056',['output_png',['../classvg_1_1Viz.html#a8b50b34356875c1c0aa3917c7c67e445',1,'vg::Viz']]],
+ ['output_5fprefix_13057',['output_prefix',['../classvg_1_1IndexRegistry.html#a24555b7ccd83df8e2ccb28b900a6b5b1',1,'vg::IndexRegistry']]],
+ ['output_5fsvg_13058',['output_svg',['../classvg_1_1Viz.html#a82a23ca5a5a6ababff6176743247be04',1,'vg::Viz']]],
+ ['output_5ftabbed_13059',['output_tabbed',['../classVectorizer.html#a7be5208d3a51438a989dd406fb808fd9',1,'Vectorizer']]],
+ ['output_5fvariants_13060',['output_variants',['../classvg_1_1VCFOutputCaller.html#aa9a532dbc58fe6031595ed819d31b02a',1,'vg::VCFOutputCaller']]],
+ ['output_5fvcf_13061',['output_vcf',['../classvg_1_1VCFOutputCaller.html#a1556bdec270d47b22e5c91b6956a23c0',1,'vg::VCFOutputCaller']]],
+ ['output_5fversion_13062',['OUTPUT_VERSION',['../classvg_1_1StreamIndexBase.html#ad5ce82f31552d36c073e65ced2af529e',1,'vg::StreamIndexBase']]],
+ ['overall_5fsupport_13063',['overall_support',['../structvg_1_1Locus.html#a04ac3427a7318a28984c8114cd216675',1,'vg::Locus']]],
+ ['overlap_13064',['overlap',['../structvg_1_1Edge.html#aafdc39a954fd8de9dc3850ad9ecb9ade',1,'vg::Edge']]],
+ ['overlap_5fthreshold_13065',['OVERLAP_THRESHOLD',['../classvg_1_1GaplessExtender.html#a3d436577897604304729afc521928ee8',1,'vg::GaplessExtender']]],
+ ['own_5fsnarl_5fmanager_13066',['own_snarl_manager',['../classvg_1_1Masker.html#aa58433090d15c4a8235aec717dcef987',1,'vg::Masker']]]
];
diff --git a/vg__git__version_8hpp.html b/vg__git__version_8hpp.html
index 7d9ed2a0bf..e442d598f8 100644
--- a/vg__git__version_8hpp.html
+++ b/vg__git__version_8hpp.html
@@ -75,7 +75,7 @@
@@ -86,7 +86,7 @@
- #define VG_GIT_VERSION "v1.62.0-196-gdb3cfbb5" |
+ #define VG_GIT_VERSION "v1.62.0-197-g834a1f69" |