diff --git a/algorithms_2subgraph_8cpp.html b/algorithms_2subgraph_8cpp.html index e9ddbf0705..a10672c586 100644 --- a/algorithms_2subgraph_8cpp.html +++ b/algorithms_2subgraph_8cpp.html @@ -75,6 +75,7 @@
#include "subgraph.hpp"
#include "../path.hpp"
+#include "../crash.hpp"
@@ -105,8 +106,8 @@ - - + +

Namespaces

 
void vg::algorithms::extract_path_range (const PathPositionHandleGraph &source, path_handle_t path_handle, int64_t start, int64_t end, MutableHandleGraph &subgraph)
 
void vg::algorithms::add_subpaths_to_subgraph (const PathPositionHandleGraph &source, MutablePathHandleGraph &subgraph, bool subpath_naming)
 
void vg::algorithms::add_subpaths_to_subgraph (const PathPositionHandleGraph &source, MutablePathHandleGraph &subgraph)
 
void vg::algorithms::add_connecting_edges_to_subgraph (const HandleGraph &source, MutableHandleGraph &subgraph)
 
diff --git a/algorithms_2subgraph_8hpp.html b/algorithms_2subgraph_8hpp.html index f7075f3238..52cbcdd9f4 100644 --- a/algorithms_2subgraph_8hpp.html +++ b/algorithms_2subgraph_8hpp.html @@ -107,8 +107,8 @@   void vg::algorithms::extract_path_range (const PathPositionHandleGraph &source, path_handle_t path_handle, int64_t start, int64_t end, MutableHandleGraph &subgraph)   -void vg::algorithms::add_subpaths_to_subgraph (const PathPositionHandleGraph &source, MutablePathHandleGraph &subgraph, bool subpath_naming) -  +void vg::algorithms::add_subpaths_to_subgraph (const PathPositionHandleGraph &source, MutablePathHandleGraph &subgraph) +  void vg::algorithms::add_connecting_edges_to_subgraph (const HandleGraph &source, MutableHandleGraph &subgraph)   diff --git a/chunker_8cpp.html b/chunker_8cpp.html index 2c52a2997c..b1d1b5296e 100644 --- a/chunker_8cpp.html +++ b/chunker_8cpp.html @@ -79,6 +79,7 @@ #include "algorithms/subgraph.hpp"
#include "vg.hpp"
#include "clip.hpp"
+#include "crash.hpp"
diff --git a/classvg_1_1PathChunker-members.html b/classvg_1_1PathChunker-members.html index 1a497f73c8..3716c95051 100644 --- a/classvg_1_1PathChunker-members.html +++ b/classvg_1_1PathChunker-members.html @@ -73,7 +73,7 @@

This is the complete list of members for vg::PathChunker, including all inherited members.

Namespaces

- + diff --git a/classvg_1_1PathChunker.html b/classvg_1_1PathChunker.html index 42f7a25822..ddfe0589b0 100644 --- a/classvg_1_1PathChunker.html +++ b/classvg_1_1PathChunker.html @@ -89,8 +89,8 @@ - - + + @@ -140,8 +140,8 @@

Member Function Documentation

- -

◆ extract_component()

+ +

◆ extract_component()

@@ -156,13 +156,7 @@

- - - - - - - + @@ -171,7 +165,7 @@

-

Extract a connected component starting from an id set

+

Extract a connected component starting from an id set. Processes path metadata and creates subpaths.

@@ -265,7 +259,7 @@

-

Extract a connected component containing a given path

+

Extract a connected component containing a given path. Processes path metadata and creates subpaths.

@@ -353,7 +347,8 @@

-

Extract subgraph corresponding to given path region into its own vg graph, and send it to out_stream. The boundaries of the extracted graph (which can be different because we expand context and don't cut nodes) are written to out_region. If forward_only set, context is only expanded in the forward direction

+

Extract subgraph corresponding to given path region into its own vg graph, and send it to out_stream. The boundaries of the extracted region of the target path (which can be different because we expand context and don't cut nodes) are written to out_region. If the target path goes through the extracted region multiple times, only the extended bounds of the visit containing the target region are produced.

+

If forward_only set, context is only expanded in the forward direction

NOTE: we follow convention of Region coordinates being 0-based inclusive.

diff --git a/find__main_8cpp.html b/find__main_8cpp.html index 8f4488df4c..6ae2602f49 100644 --- a/find__main_8cpp.html +++ b/find__main_8cpp.html @@ -73,6 +73,7 @@
#include "subcommand.hpp"
+#include "../crash.hpp"
#include "../utility.hpp"
#include "../mapper.hpp"
#include <vg/io/stream.hpp>
diff --git a/functions_e.html b/functions_e.html index a2071c9ee1..0791e9d55e 100644 --- a/functions_e.html +++ b/functions_e.html @@ -698,7 +698,7 @@

- e -

    : vg::MultipathMapper
  • extract_component() -: vg::PathChunker +: vg::PathChunker
  • extract_id_range() : vg::PathChunker diff --git a/functions_func_e.html b/functions_func_e.html index 1f4df8d462..e253189310 100644 --- a/functions_func_e.html +++ b/functions_func_e.html @@ -461,7 +461,7 @@

    - e -

      : vg::MultipathMapper
    • extract_component() -: vg::PathChunker +: vg::PathChunker
    • extract_id_range() : vg::PathChunker diff --git a/namespacemembers.html b/namespacemembers.html index 7d7bc4c258..04d1f5317c 100644 --- a/namespacemembers.html +++ b/namespacemembers.html @@ -99,7 +99,7 @@

      - a -

        : vg
      • add_subpaths_to_subgraph() -: vg::algorithms +: vg::algorithms
      • add_thread_edges_to_set() : vg diff --git a/namespacemembers_func.html b/namespacemembers_func.html index 2c87cbb7c3..4067bbabb8 100644 --- a/namespacemembers_func.html +++ b/namespacemembers_func.html @@ -96,7 +96,7 @@

        - a -

          : vg
        • add_subpaths_to_subgraph() -: vg::algorithms +: vg::algorithms
        • add_thread_edges_to_set() : vg diff --git a/namespacevg_1_1algorithms.html b/namespacevg_1_1algorithms.html index 09e8e581b2..8dde7380ff 100644 --- a/namespacevg_1_1algorithms.html +++ b/namespacevg_1_1algorithms.html @@ -371,8 +371,8 @@

- - + + @@ -532,8 +532,8 @@

-

◆ add_subpaths_to_subgraph()

+ +

◆ add_subpaths_to_subgraph()

@@ -548,13 +548,7 @@

- - - - - - - + @@ -563,7 +557,8 @@

-

add subpaths to the subgraph, providing a concatenation of subpaths that are discontiguous over the subgraph based on their order in the path position index provided by the source graph will clear any path found in both graphs before writing the new steps into it if subpath_naming is true, a suffix will be added to each path in the subgraph denoting its offset in the source graph (unless the subpath was not cut up at all)

+

Add subpaths to the subgraph for all paths visiting its nodes in the source graph.

+

Always generates correct path metadata, and a path for each contiguous fragment of any base path. Assumes the source graph does not contain any overlapping path fragments on a given base path, and that the subgraph does not already contain any paths on a base path also present in the source graph.

diff --git a/search/all_1.js b/search/all_1.js index efb6f02d6f..1365d8e014 100644 --- a/search/all_1.js +++ b/search/all_1.js @@ -65,7 +65,7 @@ var searchData= ['add_5fstart_97',['add_start',['../classvg_1_1multipath__alignment__t.html#a793ba830eaa6fd21ec7af7c7fc12cfed',1,'vg::multipath_alignment_t']]], ['add_5fstart_5fend_5fmarkers_98',['add_start_end_markers',['../classvg_1_1VG.html#a91eaa395f197ca65f38c6139bc57d161',1,'vg::VG']]], ['add_5fsubpath_99',['add_subpath',['../classvg_1_1multipath__alignment__t.html#ad313d9942fcd375b7b073fa2d5276fe7',1,'vg::multipath_alignment_t']]], - ['add_5fsubpaths_5fto_5fsubgraph_100',['add_subpaths_to_subgraph',['../namespacevg_1_1algorithms.html#ad37fc704de99f02f0bf767d6ab41fe4e',1,'vg::algorithms']]], + ['add_5fsubpaths_5fto_5fsubgraph_100',['add_subpaths_to_subgraph',['../namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c',1,'vg::algorithms']]], ['add_5fthread_5fedges_5fto_5fset_101',['add_thread_edges_to_set',['../namespacevg.html#afe2d6096dfe672a486e44df018c713c2',1,'vg']]], ['add_5fthread_5fnodes_5fto_5fset_102',['add_thread_nodes_to_set',['../namespacevg.html#a2adfa9e81b2553fefdd5e1d6b24c7a77',1,'vg']]], ['add_5ftranscripts_5fto_5fgbwt_103',['add_transcripts_to_gbwt',['../classvg_1_1Transcriptome.html#ab7fbe9d1f6688cc06381ff863a345dc4',1,'vg::Transcriptome']]], diff --git a/search/all_5.js b/search/all_5.js index 7831abd1d1..f88ffdffb2 100644 --- a/search/all_5.js +++ b/search/all_5.js @@ -227,7 +227,7 @@ var searchData= ['extract_1462',['extract',['../classvg_1_1algorithms_1_1GFAParser.html#af845e3a9176f98ccbb7c04b31f4f6dc0',1,'vg::algorithms::GFAParser']]], ['extract_5fas_5fgbwt_5fpath_1463',['extract_as_gbwt_path',['../namespacevg.html#a0d1c00a44e9aeb5c4294edd60fcbaa61',1,'vg']]], ['extract_5fcluster_5fgraph_1464',['extract_cluster_graph',['../classvg_1_1MultipathMapper.html#a411882d1f1f4908582333944ac346443',1,'vg::MultipathMapper']]], - ['extract_5fcomponent_1465',['extract_component',['../classvg_1_1PathChunker.html#ae971765e047d0f1747b7f481003c73c7',1,'vg::PathChunker']]], + ['extract_5fcomponent_1465',['extract_component',['../classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54',1,'vg::PathChunker']]], ['extract_5fconnecting_5fgraph_1466',['extract_connecting_graph',['../namespacevg_1_1algorithms.html#ac0d0446bde00e10bd77816c968ae97b0',1,'vg::algorithms']]], ['extract_5fconnecting_5fgraph_2ecpp_1467',['extract_connecting_graph.cpp',['../extract__connecting__graph_8cpp.html',1,'']]], ['extract_5fconnecting_5fgraph_2ehpp_1468',['extract_connecting_graph.hpp',['../extract__connecting__graph_8hpp.html',1,'']]], diff --git a/search/functions_1.js b/search/functions_1.js index 26e5624e0e..9f32721535 100644 --- a/search/functions_1.js +++ b/search/functions_1.js @@ -55,7 +55,7 @@ var searchData= ['add_5fstart_7529',['add_start',['../classvg_1_1multipath__alignment__t.html#a793ba830eaa6fd21ec7af7c7fc12cfed',1,'vg::multipath_alignment_t']]], ['add_5fstart_5fend_5fmarkers_7530',['add_start_end_markers',['../classvg_1_1VG.html#a91eaa395f197ca65f38c6139bc57d161',1,'vg::VG']]], ['add_5fsubpath_7531',['add_subpath',['../classvg_1_1multipath__alignment__t.html#ad313d9942fcd375b7b073fa2d5276fe7',1,'vg::multipath_alignment_t']]], - ['add_5fsubpaths_5fto_5fsubgraph_7532',['add_subpaths_to_subgraph',['../namespacevg_1_1algorithms.html#ad37fc704de99f02f0bf767d6ab41fe4e',1,'vg::algorithms']]], + ['add_5fsubpaths_5fto_5fsubgraph_7532',['add_subpaths_to_subgraph',['../namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c',1,'vg::algorithms']]], ['add_5fthread_5fedges_5fto_5fset_7533',['add_thread_edges_to_set',['../namespacevg.html#afe2d6096dfe672a486e44df018c713c2',1,'vg']]], ['add_5fthread_5fnodes_5fto_5fset_7534',['add_thread_nodes_to_set',['../namespacevg.html#a2adfa9e81b2553fefdd5e1d6b24c7a77',1,'vg']]], ['add_5ftranscripts_5fto_5fgbwt_7535',['add_transcripts_to_gbwt',['../classvg_1_1Transcriptome.html#ab7fbe9d1f6688cc06381ff863a345dc4',1,'vg::Transcriptome']]], diff --git a/search/functions_5.js b/search/functions_5.js index ea2068311c..5e08dba34b 100644 --- a/search/functions_5.js +++ b/search/functions_5.js @@ -136,7 +136,7 @@ var searchData= ['extract_8272',['extract',['../classvg_1_1algorithms_1_1GFAParser.html#af845e3a9176f98ccbb7c04b31f4f6dc0',1,'vg::algorithms::GFAParser']]], ['extract_5fas_5fgbwt_5fpath_8273',['extract_as_gbwt_path',['../namespacevg.html#a0d1c00a44e9aeb5c4294edd60fcbaa61',1,'vg']]], ['extract_5fcluster_5fgraph_8274',['extract_cluster_graph',['../classvg_1_1MultipathMapper.html#a411882d1f1f4908582333944ac346443',1,'vg::MultipathMapper']]], - ['extract_5fcomponent_8275',['extract_component',['../classvg_1_1PathChunker.html#ae971765e047d0f1747b7f481003c73c7',1,'vg::PathChunker']]], + ['extract_5fcomponent_8275',['extract_component',['../classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54',1,'vg::PathChunker']]], ['extract_5fconnecting_5fgraph_8276',['extract_connecting_graph',['../namespacevg_1_1algorithms.html#ac0d0446bde00e10bd77816c968ae97b0',1,'vg::algorithms']]], ['extract_5fcontaining_5fgraph_8277',['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_8278',['extract_context',['../namespacevg_1_1algorithms.html#a38ea20ebc7800702ec0cdb96920c6184',1,'vg::algorithms']]], diff --git a/vg__git__version_8hpp.html b/vg__git__version_8hpp.html index 6f6945ba78..d0d3f804c7 100644 --- a/vg__git__version_8hpp.html +++ b/vg__git__version_8hpp.html @@ -75,7 +75,7 @@

extract_component(const unordered_set< nid_t > &node_ids, MutablePathMutableHandleGraph &subgraph, bool subpath_naming)vg::PathChunker
extract_component(const unordered_set< nid_t > &node_ids, MutablePathMutableHandleGraph &subgraph)vg::PathChunker
extract_id_range(vg::id_t start, vg::id_t end, int64_t context, int64_t length, bool forward_only, MutablePathMutableHandleGraph &subgraph, Region &out_region)vg::PathChunker
extract_path_component(const string &path_name, MutablePathMutableHandleGraph &subgraph, Region &out_region)vg::PathChunker
extract_snarls(const Region &region, SnarlManager &snarl_manager, MutablePathMutableHandleGraph &subgraph)vg::PathChunker
 
void extract_path_component (const string &path_name, MutablePathMutableHandleGraph &subgraph, Region &out_region)
 
void extract_component (const unordered_set< nid_t > &node_ids, MutablePathMutableHandleGraph &subgraph, bool subpath_naming)
 
void extract_component (const unordered_set< nid_t > &node_ids, MutablePathMutableHandleGraph &subgraph)
 
void extract_id_range (vg::id_t start, vg::id_t end, int64_t context, int64_t length, bool forward_only, MutablePathMutableHandleGraph &subgraph, Region &out_region)
 
set< pair< pair< id_t, bool >, pair< id_t, bool > > > get_path_edge_index (step_handle_t start_step, step_handle_t end_step, int64_t context) const
MutablePathMutableHandleGraph & subgraph,
bool subpath_naming subgraph 
 
void extract_path_range (const PathPositionHandleGraph &source, path_handle_t path_handle, int64_t start, int64_t end, MutableHandleGraph &subgraph)
 
void add_subpaths_to_subgraph (const PathPositionHandleGraph &source, MutablePathHandleGraph &subgraph, bool subpath_naming)
 
void add_subpaths_to_subgraph (const PathPositionHandleGraph &source, MutablePathHandleGraph &subgraph)
 
void add_connecting_edges_to_subgraph (const HandleGraph &source, MutableHandleGraph &subgraph)
 
void three_edge_connected_component_merges_dense (size_t node_count, size_t first_root, const function< void(size_t, const function< void(size_t)> &)> &for_each_connected_node, const function< void(size_t, size_t)> &same_component)
MutablePathHandleGraph & subgraph,
bool subpath_naming subgraph 
- +

Macros

#define VG_GIT_VERSION   "v1.61.0-16-g519656f2"
#define VG_GIT_VERSION   "v1.61.0-26-g62ccb557"
 

Macro Definition Documentation

@@ -86,7 +86,7 @@

- +
#define VG_GIT_VERSION   "v1.61.0-16-g519656f2"#define VG_GIT_VERSION   "v1.61.0-26-g62ccb557"