diff --git a/classvg_1_1HaplotypeIndexer-members.html b/classvg_1_1HaplotypeIndexer-members.html
index a3ca67f343..bb4413517f 100644
--- a/classvg_1_1HaplotypeIndexer-members.html
+++ b/classvg_1_1HaplotypeIndexer-members.html
@@ -76,7 +76,7 @@
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html#aa818eebd7cffc81773e8bea65bd398cb">batch_file_prefix</a></td><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html">vg::HaplotypeIndexer</a></td><td class="entry"></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html#a0389ee96c5ce8a6d9c158fda39aca9d9">build_gbwt</a>(const std::vector&lt; std::string &gt; &amp;vcf_parse_files, const std::string &amp;job_name=&quot;GBWT&quot;, const PathHandleGraph *graph=nullptr, const std::unordered_set&lt; path_handle_t &gt; *paths=nullptr, bool skip_unvisited_paths=false) const</td><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html">vg::HaplotypeIndexer</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html#ae92d109c2e7baf0b7ddded8df80a6f70">build_gbwt</a>(const PathHandleGraph &amp;graph) const</td><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html">vg::HaplotypeIndexer</a></td><td class="entry"></td></tr>
-  <tr><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html#a1ea59157f7b2a4b8f720841e0ec35db8">build_gbwt</a>(const PathHandleGraph &amp;graph, const std::vector&lt; std::string &gt; &amp;aln_filenames, const std::string &amp;aln_format) const</td><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html">vg::HaplotypeIndexer</a></td><td class="entry"></td></tr>
+  <tr><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html#a34fc36c5ba77f4cedd32073dda118b84">build_gbwt</a>(const HandleGraph &amp;graph, const std::vector&lt; std::string &gt; &amp;aln_filenames, const std::string &amp;aln_format, size_t parallel_jobs=1) const</td><td class="entry"><a class="el" href="classvg_1_1HaplotypeIndexer.html">vg::HaplotypeIndexer</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1Progressive.html#a1cce3f715516ed2bbb4ce3a312b01e02">create_progress</a>(const string &amp;message, long count)</td><td class="entry"><a class="el" href="classvg_1_1Progressive.html">vg::Progressive</a></td><td class="entry"></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1Progressive.html#a75d4e92a36a277be5bc0cee5d01f5ca1">create_progress</a>(long count)</td><td class="entry"><a class="el" href="classvg_1_1Progressive.html">vg::Progressive</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1Progressive.html#aaab8c6ae92870077bb59f86a15c8d18f">destroy_progress</a>(void)</td><td class="entry"><a class="el" href="classvg_1_1Progressive.html">vg::Progressive</a></td><td class="entry"></td></tr>
diff --git a/classvg_1_1HaplotypeIndexer.html b/classvg_1_1HaplotypeIndexer.html
index b37bbdd094..07af46187d 100644
--- a/classvg_1_1HaplotypeIndexer.html
+++ b/classvg_1_1HaplotypeIndexer.html
@@ -99,8 +99,8 @@
 <tr class="separator:a0389ee96c5ce8a6d9c158fda39aca9d9"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:ae92d109c2e7baf0b7ddded8df80a6f70"><td class="memItemLeft" align="right" valign="top">std::unique_ptr&lt; gbwt::DynamicGBWT &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1HaplotypeIndexer.html#ae92d109c2e7baf0b7ddded8df80a6f70">build_gbwt</a> (const <a class="el" href="classhandlegraph_1_1PathHandleGraph.html">PathHandleGraph</a> &amp;graph) const</td></tr>
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-<tr class="memitem:a1ea59157f7b2a4b8f720841e0ec35db8"><td class="memItemLeft" align="right" valign="top">std::unique_ptr&lt; gbwt::DynamicGBWT &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1HaplotypeIndexer.html#a1ea59157f7b2a4b8f720841e0ec35db8">build_gbwt</a> (const <a class="el" href="classhandlegraph_1_1PathHandleGraph.html">PathHandleGraph</a> &amp;graph, const std::vector&lt; std::string &gt; &amp;aln_filenames, const std::string &amp;aln_format) const</td></tr>
-<tr class="separator:a1ea59157f7b2a4b8f720841e0ec35db8"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a34fc36c5ba77f4cedd32073dda118b84"><td class="memItemLeft" align="right" valign="top">std::unique_ptr&lt; gbwt::GBWT &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1HaplotypeIndexer.html#a34fc36c5ba77f4cedd32073dda118b84">build_gbwt</a> (const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;graph, const std::vector&lt; std::string &gt; &amp;aln_filenames, const std::string &amp;aln_format, size_t parallel_jobs=1) const</td></tr>
+<tr class="separator:a34fc36c5ba77f4cedd32073dda118b84"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="inherit_header pub_methods_classvg_1_1Progressive"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classvg_1_1Progressive')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classvg_1_1Progressive.html">vg::Progressive</a></td></tr>
 <tr class="memitem:a4eb5050eb36ed519cbfa398748ef183b inherit pub_methods_classvg_1_1Progressive"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Progressive.html#a4eb5050eb36ed519cbfa398748ef183b">preload_progress</a> (const string &amp;message)</td></tr>
 <tr class="separator:a4eb5050eb36ed519cbfa398748ef183b inherit pub_methods_classvg_1_1Progressive"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -181,35 +181,16 @@ <h2 class="memtitle"><span class="permalink"><a href="#ae0b8cbfe64f32152ceefa57d
 </div>
 </div>
 <h2 class="groupheader">Member Function Documentation</h2>
-<a id="ae92d109c2e7baf0b7ddded8df80a6f70"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#ae92d109c2e7baf0b7ddded8df80a6f70">&#9670;&nbsp;</a></span>build_gbwt() <span class="overload">[1/3]</span></h2>
+<a id="a34fc36c5ba77f4cedd32073dda118b84"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a34fc36c5ba77f4cedd32073dda118b84">&#9670;&nbsp;</a></span>build_gbwt() <span class="overload">[1/3]</span></h2>
 
 <div class="memitem">
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">std::unique_ptr&lt; gbwt::DynamicGBWT &gt; vg::HaplotypeIndexer::build_gbwt </td>
+          <td class="memname">std::unique_ptr&lt; gbwt::GBWT &gt; vg::HaplotypeIndexer::build_gbwt </td>
           <td>(</td>
-          <td class="paramtype">const <a class="el" href="classhandlegraph_1_1PathHandleGraph.html">PathHandleGraph</a> &amp;&#160;</td>
-          <td class="paramname"><em>graph</em></td><td>)</td>
-          <td> const</td>
-        </tr>
-      </table>
-</div><div class="memdoc">
-<p>Build a GBWT from the embedded non-alt paths in the graph. </p>
-
-</div>
-</div>
-<a id="a1ea59157f7b2a4b8f720841e0ec35db8"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a1ea59157f7b2a4b8f720841e0ec35db8">&#9670;&nbsp;</a></span>build_gbwt() <span class="overload">[2/3]</span></h2>
-
-<div class="memitem">
-<div class="memproto">
-      <table class="memname">
-        <tr>
-          <td class="memname">std::unique_ptr&lt; gbwt::DynamicGBWT &gt; vg::HaplotypeIndexer::build_gbwt </td>
-          <td>(</td>
-          <td class="paramtype">const <a class="el" href="classhandlegraph_1_1PathHandleGraph.html">PathHandleGraph</a> &amp;&#160;</td>
+          <td class="paramtype">const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;&#160;</td>
           <td class="paramname"><em>graph</em>, </td>
         </tr>
         <tr>
@@ -222,7 +203,13 @@ <h2 class="memtitle"><span class="permalink"><a href="#a1ea59157f7b2a4b8f720841e
           <td class="paramkey"></td>
           <td></td>
           <td class="paramtype">const std::string &amp;&#160;</td>
-          <td class="paramname"><em>aln_format</em>&#160;</td>
+          <td class="paramname"><em>aln_format</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">size_t&#160;</td>
+          <td class="paramname"><em>parallel_jobs</em> = <code>1</code>&#160;</td>
         </tr>
         <tr>
           <td></td>
@@ -232,7 +219,27 @@ <h2 class="memtitle"><span class="permalink"><a href="#a1ea59157f7b2a4b8f720841e
       </table>
 </div><div class="memdoc">
 <p>Build a GBWT from the alignments. Each distinct alignment name becomes a sample in the GBWT metadata. If there are multiple alignments with the same name, the corresponding GBWT path names will have the same sample identifier but different values in the count field.</p>
-<p>aln_format can be "GAM" or "GAF" </p>
+<p>aln_format can be "GAM" or "GAF".</p>
+<p>Runs approximately the given number of jobs in parallel. The exact number depends on the sizes of weakly connected components in the graph. Each job uses at most 2 threads. </p>
+
+</div>
+</div>
+<a id="ae92d109c2e7baf0b7ddded8df80a6f70"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ae92d109c2e7baf0b7ddded8df80a6f70">&#9670;&nbsp;</a></span>build_gbwt() <span class="overload">[2/3]</span></h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::unique_ptr&lt; gbwt::DynamicGBWT &gt; vg::HaplotypeIndexer::build_gbwt </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="classhandlegraph_1_1PathHandleGraph.html">PathHandleGraph</a> &amp;&#160;</td>
+          <td class="paramname"><em>graph</em></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<p>Build a GBWT from the embedded non-alt paths in the graph. </p>
 
 </div>
 </div>
diff --git a/functions_b.html b/functions_b.html
index abbc4f3c38..1fe9866805 100644
--- a/functions_b.html
+++ b/functions_b.html
@@ -347,7 +347,7 @@ <h3><a id="index_b"></a>- b -</h3><ul>
 : <a class="el" href="classvg_1_1VG.html#af63d4a22a3baa5b21623128b81a14872">vg::VG</a>
 </li>
 <li>build_gbwt()
-: <a class="el" href="classvg_1_1HaplotypeIndexer.html#a1ea59157f7b2a4b8f720841e0ec35db8">vg::HaplotypeIndexer</a>
+: <a class="el" href="classvg_1_1HaplotypeIndexer.html#a34fc36c5ba77f4cedd32073dda118b84">vg::HaplotypeIndexer</a>
 </li>
 <li>build_gbwtgraph
 : <a class="el" href="structGBWTConfig.html#ab9b3a2e3dd7bdbd76f43dc418f4bc685a53ad04440251531f5f139c800eea46b8">GBWTConfig</a>
diff --git a/functions_c.html b/functions_c.html
index 215c716e0f..c24c2c04fe 100644
--- a/functions_c.html
+++ b/functions_c.html
@@ -817,12 +817,12 @@ <h3><a id="index_c"></a>- c -</h3><ul>
 <li>count_of_max
 : <a class="el" href="structvg_1_1SummaryStatistics.html#a3245d457bac967cb81a89a1351016b9b">vg::SummaryStatistics</a>
 </li>
+<li>count_paths
+: <a class="el" href="structGBWTConfig.html#a9a0bd4ea251be07cbe2336a93981b614">GBWTConfig</a>
+</li>
 <li>count_reachability_edges()
 : <a class="el" href="classvg_1_1MultipathAlignmentGraph.html#ae053f01b2505d284a43a5d0c2046c82b">vg::MultipathAlignmentGraph</a>
 </li>
-<li>count_threads
-: <a class="el" href="structGBWTConfig.html#a31e7a91a5698d2561b555bcdc1cf59d7">GBWTConfig</a>
-</li>
 <li>Counts()
 : <a class="el" href="structvg_1_1Counts.html#a87773870a3b04302bec59e41e5bdbc2e">vg::Counts</a>
 </li>
diff --git a/functions_func_n.html b/functions_func_n.html
index dc922d7dc8..c4180f5664 100644
--- a/functions_func_n.html
+++ b/functions_func_n.html
@@ -219,7 +219,7 @@ <h3><a id="index_n"></a>- n -</h3><ul>
 : <a class="el" href="classvg_1_1VG.html#a0b084d958fd8069839884dc3a01ed745">vg::VG</a>
 </li>
 <li>nodes_prev()
-: <a class="el" href="classvg_1_1VG.html#ac08e778396904ad3b3f20f605f54628d">vg::VG</a>
+: <a class="el" href="classvg_1_1VG.html#a0f3e69ced0c3135f3f363c14bf752aad">vg::VG</a>
 </li>
 <li>NodeSide()
 : <a class="el" href="classvg_1_1NodeSide.html#ac4bde3f59ff17ea8c7415fcd9fdd4a0b">vg::NodeSide</a>
@@ -249,7 +249,7 @@ <h3><a id="index_n"></a>- n -</h3><ul>
 : <a class="el" href="classvg_1_1NullClusterer.html#a63ae2e8bfe748f6557df52cddf4b41e8">vg::NullClusterer</a>
 </li>
 <li>NullMaskingGraph()
-: <a class="el" href="classvg_1_1NullMaskingGraph.html#addeb1ab4002f516c686a5af59018597f">vg::NullMaskingGraph</a>
+: <a class="el" href="classvg_1_1NullMaskingGraph.html#a2d348fa5aa3bd9216fc4133d320575ef">vg::NullMaskingGraph</a>
 </li>
 <li>num_haplotypes()
 : <a class="el" href="classvg_1_1PhasedGenome.html#af17e5f99a07028d41f94885480cdddf7">vg::PhasedGenome</a>
diff --git a/functions_m.html b/functions_m.html
index 4c010e6bb8..664579a6a6 100644
--- a/functions_m.html
+++ b/functions_m.html
@@ -1316,7 +1316,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="classvg_1_1MultipathMapper.html#a7af0cb7af3f7a3e3ab60627f3793aa0a">vg::MultipathMapper</a>
 </li>
 <li>multipath_alignment_t()
-: <a class="el" href="classvg_1_1multipath__alignment__t.html#ae7f715f63023d3043c01ed29193ea6a1">vg::multipath_alignment_t</a>
+: <a class="el" href="classvg_1_1multipath__alignment__t.html#a55b4c1fee893c4b596f0a654a624bccc">vg::multipath_alignment_t</a>
 </li>
 <li>multipath_map()
 : <a class="el" href="classvg_1_1MultipathMapper.html#a9ea318c04336aa79020b7c012e468ef8">vg::MultipathMapper</a>
@@ -1352,7 +1352,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="classvg_1_1subpath__t.html#a271236a46bdb6105f216a630c0c67a74">vg::subpath_t</a>
 </li>
 <li>mutable_edit()
-: <a class="el" href="classvg_1_1path__mapping__t.html#a56c059138a051e7889f4083a74c5401f">vg::path_mapping_t</a>
+: <a class="el" href="classvg_1_1path__mapping__t.html#aeb9d50accda37c8829c49cd8567f72bc">vg::path_mapping_t</a>
 </li>
 <li>mutable_mapping()
 : <a class="el" href="classvg_1_1path__t.html#aac0ad10ace8970358d471d779061b22d">vg::path_t</a>
@@ -1377,7 +1377,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
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 </li>
 <li>mutable_subpath()
-: <a class="el" href="classvg_1_1multipath__alignment__t.html#a65ee05140e26b51a60f7d33a7b9b9c54">vg::multipath_alignment_t</a>
+: <a class="el" href="classvg_1_1multipath__alignment__t.html#a727e5e6bc04955e46efe83bc5d668bdf">vg::multipath_alignment_t</a>
 </li>
 <li>MutableGraphImplementation
 : <a class="el" href="structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10">vg::IndexingParameters</a>
diff --git a/functions_p.html b/functions_p.html
index 2c6e739e63..ef53c60cfd 100644
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@@ -503,6 +503,9 @@ <h3><a id="index_p"></a>- p -</h3><ul>
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 : <a class="el" href="classvg_1_1path__mapping__t.html#af53a6e6f24b6bc9fbd611bcf826845bd">vg::path_mapping_t</a>
 </li>
+<li>path_mode
+: <a class="el" href="structGBWTConfig.html#a218c5f96dd7101b89bdf8e64de3b9949">GBWTConfig</a>
+</li>
 <li>path_name
 : <a class="el" href="structvg_1_1FeatureSet_1_1Feature.html#a645900ed3044cc3359c18e109f7460a7">vg::FeatureSet::Feature</a>
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 <li>path_names
-: <a class="el" href="classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138">vg::VariantAdder</a>
+: <a class="el" href="structGBWTConfig.html#a96ccf4e2605d4dad1a32511169f51969">GBWTConfig</a>
+, <a class="el" href="classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138">vg::VariantAdder</a>
 </li>
 <li>path_names_by_prefix()
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@@ -526,6 +530,9 @@ <h3><a id="index_p"></a>- p -</h3><ul>
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 : <a class="el" href="classvg_1_1HTSWriter.html#a2b0a5d9268a4b4901a699f82d857d6e2">vg::HTSWriter</a>
 </li>
+<li>path_output
+: <a class="el" href="structGBWTConfig.html#a91e5194d120c0dbae060bdfe5c60667a">GBWTConfig</a>
+</li>
 <li>path_position_handle_graph
 : <a class="el" href="classvg_1_1MCMCCaller.html#a240741cadefa13b2b4d472f0b6e3b8d3">vg::MCMCCaller</a>
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-, <a class="el" href="classvg_1_1PhasedGenome.html#a0e96410c065eb722e527be06b710c5d7">vg::PhasedGenome</a>
+, <a class="el" href="classvg_1_1PhasedGenome.html#aa7a7cce5f88f52d20c659e64966ece28">vg::PhasedGenome</a>
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 <li>PhaseUnfolder()
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 </li>
 <li>position_t()
-: <a class="el" href="classvg_1_1position__t.html#a34def1328db6dda2482ccb6c64951704">vg::position_t</a>
+: <a class="el" href="classvg_1_1position__t.html#a1ad8e0a1fe655c7ebb31ff094e43f466">vg::position_t</a>
 </li>
 <li>positions
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 <li>prepend_mapping()
-: <a class="el" href="classvg_1_1Paths.html#acd1f02b9d6d41036a24a9aee1a261dc3">vg::Paths</a>
+: <a class="el" href="classvg_1_1Paths.html#ab5679411e308c578583066e020dc4d4f">vg::Paths</a>
 </li>
 <li>prepend_step()
 : <a class="el" href="classhandlegraph_1_1MutablePathHandleGraph.html#aed17038a0104017d37ff74e15f7f436a">handlegraph::MutablePathHandleGraph</a>
@@ -993,7 +1000,7 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 , <a class="el" href="structvg_1_1Recombinator_1_1Statistics.html#a8cc215e629110af71f6d35da557eb0e8">vg::Recombinator::Statistics</a>
 , <a class="el" href="structvg_1_1subcommand_1_1BaseArgSpec.html#a54a62acb9b731fa86d34fff03df2cd68">vg::subcommand::BaseArgSpec&lt; Receiver &gt;</a>
 , <a class="el" href="structvg_1_1subcommand_1_1FlagArgSpec.html#a1b8d3bb745714e7c9f9bd0ce5592e3a2">vg::subcommand::FlagArgSpec&lt; Receiver &gt;</a>
-, <a class="el" href="structvg_1_1WFAAlignment.html#a37156be6786114a37da73499f8fe49da">vg::WFAAlignment</a>
+, <a class="el" href="structvg_1_1WFAAlignment.html#a455ada9f59d934bd167217583b2fbd92">vg::WFAAlignment</a>
 </li>
 <li>print_band()
 : <a class="el" href="classvg_1_1BandedGlobalAligner_1_1BAMatrix.html#ac248371cbaae3b95340035f88de09e0a">vg::BandedGlobalAligner&lt; IntType &gt;::BAMatrix</a>
@@ -1038,7 +1045,7 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 : <a class="el" href="classvg_1_1IndexedVG.html#a08b7d5f9e8ad7c9b42d58ce8d2629000">vg::IndexedVG</a>
 </li>
 <li>print_snarl()
-: <a class="el" href="classvg_1_1VCFOutputCaller.html#a3b9cfe228287ac605825ed4b0c8ea990">vg::VCFOutputCaller</a>
+: <a class="el" href="classvg_1_1VCFOutputCaller.html#acd9942cb6cd9427e38c868efb23d8bda">vg::VCFOutputCaller</a>
 </li>
 <li>print_statistics()
 : <a class="el" href="classvg_1_1Genotyper.html#aadb967b3ab9daa067f8451c29fda0a5e">vg::Genotyper</a>
@@ -1067,12 +1074,12 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 <li>prob_sampler
 : <a class="el" href="classvg_1_1NGSSimulator.html#a36ca291ed15a9a3942809d21d0574bc1">vg::NGSSimulator</a>
 </li>
-<li>problem
-: <a class="el" href="structvg_1_1AlignmentValidity.html#a1ca7f243aa52fe313bdfac808f4eba92">vg::AlignmentValidity</a>
-</li>
 <li>Problem
 : <a class="el" href="structvg_1_1AlignmentValidity.html#acbf722cab695a00b651bab515806a7e9">vg::AlignmentValidity</a>
 </li>
+<li>problem
+: <a class="el" href="structvg_1_1AlignmentValidity.html#a1ca7f243aa52fe313bdfac808f4eba92">vg::AlignmentValidity</a>
+</li>
 <li>ProblemDumpExplainer()
 : <a class="el" href="classvg_1_1ProblemDumpExplainer.html#a51e4e904203bd8817e6a93a454ee1e10">vg::ProblemDumpExplainer</a>
 </li>
@@ -1155,10 +1162,10 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 : <a class="el" href="structvg_1_1io_1_1Registry_1_1Tables.html#a9959a1192210db895c2d127dc6a197fc">vg::io::Registry::Tables</a>
 </li>
 <li>ProtobufEmitter()
-: <a class="el" href="classvg_1_1io_1_1ProtobufEmitter.html#ab9d133fa3604ba677c12337ccf609ba7">vg::io::ProtobufEmitter&lt; T &gt;</a>
+: <a class="el" href="classvg_1_1io_1_1ProtobufEmitter.html#a1adf66f9c9242369dcdd38746f925855">vg::io::ProtobufEmitter&lt; T &gt;</a>
 </li>
 <li>ProtobufIterator()
-: <a class="el" href="classvg_1_1io_1_1ProtobufIterator.html#a0f2996a9653a98470e7c944879a69d70">vg::io::ProtobufIterator&lt; T &gt;</a>
+: <a class="el" href="classvg_1_1io_1_1ProtobufIterator.html#a50ad0e8d7ee212617dbf9e456ea43e07">vg::io::ProtobufIterator&lt; T &gt;</a>
 </li>
 <li>provide()
 : <a class="el" href="classvg_1_1IndexFile.html#a116a29bacf28f3889ea318ac25a11dc7">vg::IndexFile</a>
@@ -1213,7 +1220,7 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 : <a class="el" href="structjson__autoptr.html#a8eeb7c64d99d1378d9524ede91d6faa4">json_autoptr</a>
 </li>
 <li>purge_unmapped_alignments()
-: <a class="el" href="classvg_1_1MultipathMapper.html#a009000ee2da67a965a4f627be468d976">vg::MultipathMapper</a>
+: <a class="el" href="classvg_1_1MultipathMapper.html#ab1c9f02cbadcd8df05b691e4ff5294f2">vg::MultipathMapper</a>
 </li>
 <li>push()
 : <a class="el" href="structvg_1_1MatchPos_1_1PathList.html#a2979222c63cb87e2f530fceda30e56a5">vg::MatchPos::PathList</a>
diff --git a/functions_s.html b/functions_s.html
index 65193d80f5..cdfcf09666 100644
--- a/functions_s.html
+++ b/functions_s.html
@@ -1324,7 +1324,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classvg_1_1io_1_1streamistream.html#a0b87c404670f610d20f49f1e2c166648">vg::io::streamistream</a>
 </li>
 <li>StreamMultiplexer()
-: <a class="el" href="classvg_1_1io_1_1StreamMultiplexer.html#af8352f0fcbb63f162734d48d2ec573ce">vg::io::StreamMultiplexer</a>
+: <a class="el" href="classvg_1_1io_1_1StreamMultiplexer.html#ae72f4179a6cb14beb1b6460603d88233">vg::io::StreamMultiplexer</a>
 </li>
 <li>StreamSorter()
 : <a class="el" href="classvg_1_1StreamSorter.html#a0abd72f6a1ec534bb2071b3389231d97">vg::StreamSorter&lt; Message &gt;</a>
@@ -1405,7 +1405,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 , <a class="el" href="classvg_1_1SubHandleGraph.html#a1426a494a5d412485f5c4959f3b853c8">vg::SubHandleGraph</a>
 </li>
 <li>subpath()
-: <a class="el" href="classvg_1_1multipath__alignment__t.html#a5544e1c157233fda1b528bdd3e426f90">vg::multipath_alignment_t</a>
+: <a class="el" href="classvg_1_1multipath__alignment__t.html#a87bb864c7cd6e424fe9487cc662cade6">vg::multipath_alignment_t</a>
 , <a class="el" href="structvg_1_1MultipathAlignment.html#aa92c4cbfee9b5e076c41ca466b44617c">vg::MultipathAlignment</a>
 </li>
 <li>subpath_handles
@@ -1552,7 +1552,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classvg_1_1VG.html#a63f2ffa39d84f80e5ab8068a25a03ee9">vg::VG</a>
 </li>
 <li>swap_node_ids()
-: <a class="el" href="classvg_1_1Paths.html#a3190f22ab39a9039ec9288e1c065ca9c">vg::Paths</a>
+: <a class="el" href="classvg_1_1Paths.html#aba01c4d1b1d415622634db97f62b1188">vg::Paths</a>
 </li>
 <li>swap_nodes()
 : <a class="el" href="classvg_1_1VG.html#aa402d1cf817f83ca44f72f6112b6a2e3">vg::VG</a>
diff --git a/functions_t.html b/functions_t.html
index 8a0570897e..b4b21bfe0b 100644
--- a/functions_t.html
+++ b/functions_t.html
@@ -185,15 +185,6 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 <li>thread_extension
 : <a class="el" href="classvg_1_1Mapper.html#ad2f2408aba30a38eda90a10c28cbf410">vg::Mapper</a>
 </li>
-<li>thread_mode
-: <a class="el" href="structGBWTConfig.html#a29d22bd446de745309cc7e268e4e82ed">GBWTConfig</a>
-</li>
-<li>thread_names
-: <a class="el" href="structGBWTConfig.html#a37dae4a23dc8dda4fef850773a15e89b">GBWTConfig</a>
-</li>
-<li>thread_output
-: <a class="el" href="structGBWTConfig.html#af4ae9d4211462e129482d136d35b0734">GBWTConfig</a>
-</li>
 <li>thread_queue_byte_counts
 : <a class="el" href="classvg_1_1io_1_1StreamMultiplexer.html#a9ec3374dee16f6ee0ce853b04a4d6967">vg::io::StreamMultiplexer</a>
 </li>
@@ -459,7 +450,7 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 : <a class="el" href="classvg_1_1Transcriptome.html#a041373349b45b5d190316229a5b8c562">vg::Transcriptome</a>
 </li>
 <li>TranscriptPath()
-: <a class="el" href="structvg_1_1TranscriptPath.html#ad87c876af2acb7bcbbbb52b33ad25e8d">vg::TranscriptPath</a>
+: <a class="el" href="structvg_1_1TranscriptPath.html#aef6b201d9d87a24f2c9e7ed6e9e9e1e7">vg::TranscriptPath</a>
 </li>
 <li>transform()
 : <a class="el" href="classvg_1_1VGset.html#aaa5f1b0e3e71bb00a5ad82f210065e81">vg::VGset</a>
@@ -477,7 +468,7 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 : <a class="el" href="classvg_1_1Surjector.html#a2149d1e5e6aba2e07b92030e6afc617d">vg::Surjector</a>
 </li>
 <li>translate()
-: <a class="el" href="classvg_1_1Translator.html#a3407f68503febdc2bd4366947e96d003">vg::Translator</a>
+: <a class="el" href="classvg_1_1Translator.html#a6e27eb192e227afe777de2dc6488eb26">vg::Translator</a>
 </li>
 <li>translate_back()
 : <a class="el" href="classhandlegraph_1_1NamedNodeBackTranslation.html#a4005088073dfdd8d3da33803198ee737">handlegraph::NamedNodeBackTranslation</a>
@@ -509,7 +500,7 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 , <a class="el" href="classvg_1_1Genotyper.html#ad14928554aace83524e80d8c109e17b2">vg::Genotyper</a>
 </li>
 <li>Translator()
-: <a class="el" href="classvg_1_1Translator.html#aeab811097e483365bbd273efc4c4445e">vg::Translator</a>
+: <a class="el" href="classvg_1_1Translator.html#a99602b3868ae6f8f1efc6bf7adcde6f6">vg::Translator</a>
 </li>
 <li>trav
 : <a class="el" href="classvg_1_1MCMCCaller.html#a44187bff29621c4b3ff13560ea748223">vg::MCMCCaller</a>
@@ -602,7 +593,7 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 : <a class="el" href="classvg_1_1ReadFilter.html#ac5d77581ac1d34661c62f446692217ab">vg::ReadFilter&lt; Read &gt;</a>
 </li>
 <li>trim_ambiguous_ends()
-: <a class="el" href="classvg_1_1ReadFilter.html#a266b5aeeb2081d2bd5f29ae43fdc00f8">vg::ReadFilter&lt; Read &gt;</a>
+: <a class="el" href="classvg_1_1ReadFilter.html#ac49bf695fadbdaf8b41c972587493630">vg::ReadFilter&lt; Read &gt;</a>
 </li>
 <li>trim_and_check_for_empty()
 : <a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a114d073d4422c085a2c5768b6f165001">vg::MultipathAlignmentGraph</a>
diff --git a/functions_v.html b/functions_v.html
index 7bf0edf79a..0016f1edd3 100644
--- a/functions_v.html
+++ b/functions_v.html
@@ -90,7 +90,7 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 : <a class="el" href="classvg_1_1Option_3_01vector_3_01Item_01_4_00_01Parser_01_4.html#a74a157bf3bce2696b04754f1c6dd72b9">vg::Option&lt; vector&lt; Item &gt;, Parser &gt;</a>
 </li>
 <li>value()
-: <a class="el" href="classvg_1_1ProblemDumpExplainer.html#a97c2e3c2f810e01cf79d3e4c0cf4ae47">vg::ProblemDumpExplainer</a>
+: <a class="el" href="classvg_1_1ProblemDumpExplainer.html#a9847ed10905a3633101e1c71f36abc7a">vg::ProblemDumpExplainer</a>
 , <a class="el" href="classvg_1_1SmallBitset.html#a486a8a8a5a30fab268ae96a9cf464fdd">vg::SmallBitset</a>
 , <a class="el" href="structvg_1_1subcommand_1_1Valuation.html#a88e369b92873968c8d7b68cc78ce1b1d">vg::subcommand::Valuation&lt; T &gt;</a>
 , <a class="el" href="structvg_1_1subcommand_1_1ValueArgSpec.html#a518e378dc3759f070912c8cf42ae83cd">vg::subcommand::ValueArgSpec&lt; T, Receiver, Holder &gt;</a>
@@ -198,26 +198,24 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 </li>
 <li>verbosity
 : <a class="el" href="structHaplotypesConfig.html#ad04e07b242265b989bc2b93479676b84">HaplotypesConfig</a>
+, <a class="el" href="classvg_1_1HaplotypePartitioner.html#ac5d1210d753c0fe6ed936f18f02e2cd2">vg::HaplotypePartitioner</a>
 </li>
 <li>Verbosity
 : <a class="el" href="classvg_1_1HaplotypePartitioner.html#a7b5fa99a041f7c61f73644541dd926b1">vg::HaplotypePartitioner</a>
+, <a class="el" href="classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28a">vg::Haplotypes</a>
 </li>
 <li>verbosity
-: <a class="el" href="classvg_1_1HaplotypePartitioner.html#ac5d1210d753c0fe6ed936f18f02e2cd2">vg::HaplotypePartitioner</a>
+: <a class="el" href="structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579">vg::IndexingParameters</a>
 </li>
 <li>Verbosity
-: <a class="el" href="classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28a">vg::Haplotypes</a>
-, <a class="el" href="structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3">vg::IndexingParameters</a>
+: <a class="el" href="structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3">vg::IndexingParameters</a>
 </li>
 <li>verbosity
-: <a class="el" href="structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579">vg::IndexingParameters</a>
+: <a class="el" href="classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12">vg::Recombinator</a>
 </li>
 <li>Verbosity
 : <a class="el" href="classvg_1_1Recombinator.html#a097faaea0512d01e5e7732dd1991f129">vg::Recombinator</a>
 </li>
-<li>verbosity
-: <a class="el" href="classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12">vg::Recombinator</a>
-</li>
 <li>verbosity_basic
 : <a class="el" href="classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28aa718364c23222ec5e7444240be0799449">vg::Haplotypes</a>
 </li>
@@ -251,7 +249,7 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 </li>
 <li>VG
 : <a class="el" href="structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a5e978449ccc729202c33e2dc543b8327">vg::IndexingParameters</a>
-, <a class="el" href="classvg_1_1VG.html#a3148455330df9ac055c6bd1eb7da3167">vg::VG</a>
+, <a class="el" href="classvg_1_1VG.html#abeafee2d3bc6e0039e99fccdea10f4f9">vg::VG</a>
 </li>
 <li>vg_filename
 : <a class="el" href="classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0">vg::IndexedVG</a>
@@ -260,7 +258,7 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 : <a class="el" href="classvg_1_1io_1_1VGAlignmentEmitter.html#af278878b244808a182eae17640f23a45">vg::io::VGAlignmentEmitter</a>
 </li>
 <li>VGset()
-: <a class="el" href="classvg_1_1VGset.html#a6adbb25be82de20911fd901da4e9fe41">vg::VGset</a>
+: <a class="el" href="classvg_1_1VGset.html#a5ff9a6c4fa0223bcee7072f86a657751">vg::VGset</a>
 </li>
 <li>visit
 : <a class="el" href="structvg_1_1SnarlTraversal.html#aff14559c1e4fb55bdf87320f3a4ee636">vg::SnarlTraversal</a>
diff --git a/functions_vars_c.html b/functions_vars_c.html
index 74e9d6d1ba..3e34e095e0 100644
--- a/functions_vars_c.html
+++ b/functions_vars_c.html
@@ -326,8 +326,8 @@ <h3><a id="index_c"></a>- c -</h3><ul>
 <li>count_of_max
 : <a class="el" href="structvg_1_1SummaryStatistics.html#a3245d457bac967cb81a89a1351016b9b">vg::SummaryStatistics</a>
 </li>
-<li>count_threads
-: <a class="el" href="structGBWTConfig.html#a31e7a91a5698d2561b555bcdc1cf59d7">GBWTConfig</a>
+<li>count_paths
+: <a class="el" href="structGBWTConfig.html#a9a0bd4ea251be07cbe2336a93981b614">GBWTConfig</a>
 </li>
 <li>counts
 : <a class="el" href="structvg_1_1Counts.html#ada1e3e24df7c078970806cb6da1fce51">vg::Counts</a>
diff --git a/functions_vars_p.html b/functions_vars_p.html
index 01561d4732..28e45a8f8e 100644
--- a/functions_vars_p.html
+++ b/functions_vars_p.html
@@ -245,6 +245,9 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 <li>path_listeners
 : <a class="el" href="classvg_1_1algorithms_1_1GFAParser.html#aa856090842dafbe0dbaf22bed66fd411">vg::algorithms::GFAParser</a>
 </li>
+<li>path_mode
+: <a class="el" href="structGBWTConfig.html#a218c5f96dd7101b89bdf8e64de3b9949">GBWTConfig</a>
+</li>
 <li>path_name
 : <a class="el" href="structvg_1_1FeatureSet_1_1Feature.html#a645900ed3044cc3359c18e109f7460a7">vg::FeatureSet::Feature</a>
 , <a class="el" href="classvg_1_1GraphSynchronizer_1_1Lock.html#ad19c5f9cbb68abb1bcfe6e3a9fd65382">vg::GraphSynchronizer::Lock</a>
@@ -253,7 +256,8 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 : <a class="el" href="classxg_1_1XG.html#a5b2791b586efb23a131c2d5c00d85593">xg::XG</a>
 </li>
 <li>path_names
-: <a class="el" href="classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138">vg::VariantAdder</a>
+: <a class="el" href="structGBWTConfig.html#a96ccf4e2605d4dad1a32511169f51969">GBWTConfig</a>
+, <a class="el" href="classvg_1_1VariantAdder.html#a3f40d9f81c27adf5afffe04d551ac138">vg::VariantAdder</a>
 </li>
 <li>path_nodes
 : <a class="el" href="classvg_1_1MultipathAlignmentGraph.html#a76f9356cd0afea7dea3003caea2526eb">vg::MultipathAlignmentGraph</a>
@@ -264,6 +268,9 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 <li>path_order_and_length
 : <a class="el" href="classvg_1_1HTSWriter.html#a2b0a5d9268a4b4901a699f82d857d6e2">vg::HTSWriter</a>
 </li>
+<li>path_output
+: <a class="el" href="structGBWTConfig.html#a91e5194d120c0dbae060bdfe5c60667a">GBWTConfig</a>
+</li>
 <li>path_position_handle_graph
 : <a class="el" href="classvg_1_1MCMCCaller.html#a240741cadefa13b2b4d472f0b6e3b8d3">vg::MCMCCaller</a>
 </li>
diff --git a/functions_vars_t.html b/functions_vars_t.html
index d3f8f79643..53bdaf9aae 100644
--- a/functions_vars_t.html
+++ b/functions_vars_t.html
@@ -136,15 +136,6 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 <li>thread_extension
 : <a class="el" href="classvg_1_1Mapper.html#ad2f2408aba30a38eda90a10c28cbf410">vg::Mapper</a>
 </li>
-<li>thread_mode
-: <a class="el" href="structGBWTConfig.html#a29d22bd446de745309cc7e268e4e82ed">GBWTConfig</a>
-</li>
-<li>thread_names
-: <a class="el" href="structGBWTConfig.html#a37dae4a23dc8dda4fef850773a15e89b">GBWTConfig</a>
-</li>
-<li>thread_output
-: <a class="el" href="structGBWTConfig.html#af4ae9d4211462e129482d136d35b0734">GBWTConfig</a>
-</li>
 <li>thread_queue_byte_counts
 : <a class="el" href="classvg_1_1io_1_1StreamMultiplexer.html#a9ec3374dee16f6ee0ce853b04a4d6967">vg::io::StreamMultiplexer</a>
 </li>
diff --git a/functions_vars_v.html b/functions_vars_v.html
index 7cf8b1fdab..7b242c0ec3 100644
--- a/functions_vars_v.html
+++ b/functions_vars_v.html
@@ -137,12 +137,14 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 , <a class="el" href="structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579">vg::IndexingParameters</a>
 , <a class="el" href="classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12">vg::Recombinator</a>
 </li>
+<li>VERSION
+: <a class="el" href="structvg_1_1Haplotypes_1_1Header.html#a68bfc0fe68e8fc1b42ad078eaa234777">vg::Haplotypes::Header</a>
+</li>
 <li>version
 : <a class="el" href="structvg_1_1Haplotypes_1_1Header.html#ac2e1810f289c24ac4c2f74d8df9df5ec">vg::Haplotypes::Header</a>
 </li>
 <li>VERSION
-: <a class="el" href="structvg_1_1Haplotypes_1_1Header.html#a68bfc0fe68e8fc1b42ad078eaa234777">vg::Haplotypes::Header</a>
-, <a class="el" href="classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222">vg::Version</a>
+: <a class="el" href="classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222">vg::Version</a>
 </li>
 <li>vg
 : <a class="el" href="classvg_1_1FlowSort.html#abd481c5b9e6c9c5aeaf846652dd3c76f">vg::FlowSort</a>
diff --git a/gbwt__helper_8cpp.html b/gbwt__helper_8cpp.html
index 4a5978ba41..1d83389272 100644
--- a/gbwt__helper_8cpp.html
+++ b/gbwt__helper_8cpp.html
@@ -98,9 +98,6 @@
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 <tr class="memdesc:ada6300e45d21f1171c5ff2b71f4d173b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Determine the node width in bits for the GBWT nodes based on the given graph.  <a href="namespacevg.html#ada6300e45d21f1171c5ff2b71f4d173b">More...</a><br /></td></tr>
 <tr class="separator:ada6300e45d21f1171c5ff2b71f4d173b"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ac2fee40d55dfda86b1e0cc2f2500b280"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#ac2fee40d55dfda86b1e0cc2f2500b280">vg::finish_gbwt_constuction</a> (gbwt::GBWTBuilder &amp;builder, const std::vector&lt; std::string &gt; &amp;sample_names, const std::vector&lt; std::string &gt; &amp;contig_names, size_t haplotype_count, bool <a class="el" href="gbwt__main_8cpp.html#af705c69cda26007b3ea9bb76849e21b1">print_metadata</a>, const std::string &amp;header=&quot;GBWT&quot;)</td></tr>
-<tr class="memdesc:ac2fee40d55dfda86b1e0cc2f2500b280"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finish GBWT construction and optionally print the metadata.  <a href="namespacevg.html#ac2fee40d55dfda86b1e0cc2f2500b280">More...</a><br /></td></tr>
-<tr class="separator:ac2fee40d55dfda86b1e0cc2f2500b280"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:af077c13bde9c0e8f5ee88d7000a0803e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e">vg::load_gbwt</a> (gbwt::GBWT &amp;index, const std::string &amp;filename, bool show_progress=false)</td></tr>
 <tr class="memdesc:af077c13bde9c0e8f5ee88d7000a0803e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Load a compressed GBWT from the file.  <a href="namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e">More...</a><br /></td></tr>
 <tr class="separator:af077c13bde9c0e8f5ee88d7000a0803e"><td class="memSeparator" colspan="2">&#160;</td></tr>
diff --git a/gbwt__helper_8hpp.html b/gbwt__helper_8hpp.html
index c1f5ef3253..9ccf99c19c 100644
--- a/gbwt__helper_8hpp.html
+++ b/gbwt__helper_8hpp.html
@@ -125,9 +125,6 @@
 <tr class="memitem:ada6300e45d21f1171c5ff2b71f4d173b"><td class="memItemLeft" align="right" valign="top">gbwt::size_type&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#ada6300e45d21f1171c5ff2b71f4d173b">vg::gbwt_node_width</a> (const HandleGraph &amp;graph)</td></tr>
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 <tr class="separator:ada6300e45d21f1171c5ff2b71f4d173b"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ac2fee40d55dfda86b1e0cc2f2500b280"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#ac2fee40d55dfda86b1e0cc2f2500b280">vg::finish_gbwt_constuction</a> (gbwt::GBWTBuilder &amp;builder, const std::vector&lt; std::string &gt; &amp;sample_names, const std::vector&lt; std::string &gt; &amp;contig_names, size_t haplotype_count, bool <a class="el" href="gbwt__main_8cpp.html#af705c69cda26007b3ea9bb76849e21b1">print_metadata</a>, const std::string &amp;header=&quot;GBWT&quot;)</td></tr>
-<tr class="memdesc:ac2fee40d55dfda86b1e0cc2f2500b280"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finish GBWT construction and optionally print the metadata.  <a href="namespacevg.html#ac2fee40d55dfda86b1e0cc2f2500b280">More...</a><br /></td></tr>
-<tr class="separator:ac2fee40d55dfda86b1e0cc2f2500b280"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:af077c13bde9c0e8f5ee88d7000a0803e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e">vg::load_gbwt</a> (gbwt::GBWT &amp;index, const std::string &amp;filename, bool show_progress=false)</td></tr>
 <tr class="memdesc:af077c13bde9c0e8f5ee88d7000a0803e"><td class="mdescLeft">&#160;</td><td class="mdescRight">Load a compressed GBWT from the file.  <a href="namespacevg.html#af077c13bde9c0e8f5ee88d7000a0803e">More...</a><br /></td></tr>
 <tr class="separator:af077c13bde9c0e8f5ee88d7000a0803e"><td class="memSeparator" colspan="2">&#160;</td></tr>
diff --git a/gbwt__main_8cpp.html b/gbwt__main_8cpp.html
index 7c2b8d7bc9..87f120cc96 100644
--- a/gbwt__main_8cpp.html
+++ b/gbwt__main_8cpp.html
@@ -118,8 +118,8 @@
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-<tr class="memitem:a3e40453d9e28e3e88bd4058a10e43d77"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="gbwt__main_8cpp.html#a3e40453d9e28e3e88bd4058a10e43d77">step_8_threads</a> (<a class="el" href="structvg_1_1GBWTHandler.html">GBWTHandler</a> &amp;gbwts, <a class="el" href="structGBWTConfig.html">GBWTConfig</a> &amp;config)</td></tr>
-<tr class="separator:a3e40453d9e28e3e88bd4058a10e43d77"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a859c16083955e4f1ab36c130fe6cce27"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="gbwt__main_8cpp.html#a859c16083955e4f1ab36c130fe6cce27">step_8_paths</a> (<a class="el" href="structvg_1_1GBWTHandler.html">GBWTHandler</a> &amp;gbwts, <a class="el" href="structGBWTConfig.html">GBWTConfig</a> &amp;config)</td></tr>
+<tr class="separator:a859c16083955e4f1ab36c130fe6cce27"><td class="memSeparator" colspan="2">&#160;</td></tr>
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@@ -658,14 +658,14 @@ <h2 class="memtitle"><span class="permalink"><a href="#a7d810cefdbee01df4d4fe504
 
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-<a id="a3e40453d9e28e3e88bd4058a10e43d77"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a3e40453d9e28e3e88bd4058a10e43d77">&#9670;&nbsp;</a></span>step_8_threads()</h2>
+<a id="a859c16083955e4f1ab36c130fe6cce27"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a859c16083955e4f1ab36c130fe6cce27">&#9670;&nbsp;</a></span>step_8_paths()</h2>
 
 <div class="memitem">
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">void step_8_threads </td>
+          <td class="memname">void step_8_paths </td>
           <td>(</td>
           <td class="paramtype"><a class="el" href="structvg_1_1GBWTHandler.html">GBWTHandler</a> &amp;&#160;</td>
           <td class="paramname"><em>gbwts</em>, </td>
diff --git a/globals_func_m.html b/globals_func_m.html
index 0543f8bb03..f553d4d38d 100644
--- a/globals_func_m.html
+++ b/globals_func_m.html
@@ -257,9 +257,6 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 <li>mode_name()
 : <a class="el" href="prune__main_8cpp.html#a9b89c7a3b7a8efd51b246bc312140bb8">prune_main.cpp</a>
 </li>
-<li>multiple_thread_sources()
-: <a class="el" href="index__main_8cpp.html#a062cdaf3861860d3cc8b5e937f92a93e">index_main.cpp</a>
-</li>
 </ul>
 </div><!-- contents -->
 <!-- HTML footer for doxygen 1.8.9.1-->
diff --git a/globals_func_s.html b/globals_func_s.html
index 3ab8b3b824..2e5901b145 100644
--- a/globals_func_s.html
+++ b/globals_func_s.html
@@ -99,8 +99,8 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 <li>step_7_metadata()
 : <a class="el" href="gbwt__main_8cpp.html#a7d810cefdbee01df4d4fe50406806e30">gbwt_main.cpp</a>
 </li>
-<li>step_8_threads()
-: <a class="el" href="gbwt__main_8cpp.html#a3e40453d9e28e3e88bd4058a10e43d77">gbwt_main.cpp</a>
+<li>step_8_paths()
+: <a class="el" href="gbwt__main_8cpp.html#a859c16083955e4f1ab36c130fe6cce27">gbwt_main.cpp</a>
 </li>
 <li>strip_suffixes()
 : <a class="el" href="giraffe__main_8cpp.html#ada042c5c5040b9b72848655d3dc5fcf8">giraffe_main.cpp</a>
diff --git a/globals_m.html b/globals_m.html
index 067e264a74..2f41ef9fd0 100644
--- a/globals_m.html
+++ b/globals_m.html
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 : <a class="el" href="autoindex__main_8cpp.html#a95ea1f250ba974749a30b213bede7969">autoindex_main.cpp</a>
 </li>
 <li>MISMATCH
-: <a class="el" href="xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a9f6e5ca49fdffa107270afa3f5e16cda">xdrop_aligner.cpp</a>
+: <a class="el" href="dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba9f6e5ca49fdffa107270afa3f5e16cda">dozeu_interface.cpp</a>
+, <a class="el" href="xdrop__aligner_8cpp.html#abc6126af1d45847bc59afa0aa3216b04a9f6e5ca49fdffa107270afa3f5e16cda">xdrop_aligner.cpp</a>
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-, <a class="el" href="dozeu__interface_8cpp.html#a06fc87d81c62e9abb8790b6e5713c55ba9f6e5ca49fdffa107270afa3f5e16cda">dozeu_interface.cpp</a>
 </li>
 <li>mode_name()
 : <a class="el" href="prune__main_8cpp.html#a9b89c7a3b7a8efd51b246bc312140bb8">prune_main.cpp</a>
@@ -279,9 +279,6 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 <li>mode_unfold
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 </li>
-<li>multiple_thread_sources()
-: <a class="el" href="index__main_8cpp.html#a062cdaf3861860d3cc8b5e937f92a93e">index_main.cpp</a>
-</li>
 </ul>
 </div><!-- contents -->
 <!-- HTML footer for doxygen 1.8.9.1-->
diff --git a/globals_s.html b/globals_s.html
index a985aec8c7..7cd5d137a1 100644
--- a/globals_s.html
+++ b/globals_s.html
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-<li>step_8_threads()
-: <a class="el" href="gbwt__main_8cpp.html#a3e40453d9e28e3e88bd4058a10e43d77">gbwt_main.cpp</a>
+<li>step_8_paths()
+: <a class="el" href="gbwt__main_8cpp.html#a859c16083955e4f1ab36c130fe6cce27">gbwt_main.cpp</a>
 </li>
 <li>STR
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diff --git a/haplotype__indexer_8cpp.html b/haplotype__indexer_8cpp.html
index bfe72bedcf..79f34c1a88 100644
--- a/haplotype__indexer_8cpp.html
+++ b/haplotype__indexer_8cpp.html
@@ -72,16 +72,18 @@
 <div class="title">haplotype_indexer.cpp File Reference</div>  </div>
 </div><!--header-->
 <div class="contents">
-<div class="textblock"><code>#include &lt;iostream&gt;</code><br />
-<code>#include &lt;map&gt;</code><br />
+<div class="textblock"><code>#include &quot;<a class="el" href="haplotype__indexer_8hpp.html">haplotype_indexer.hpp</a>&quot;</code><br />
+<code>#include &lt;iostream&gt;</code><br />
+<code>#include &lt;mutex&gt;</code><br />
 <code>#include &lt;vector&gt;</code><br />
 <code>#include &lt;string&gt;</code><br />
 <code>#include &lt;<a class="el" href="stream_8hpp.html">vg/io/stream.hpp</a>&gt;</code><br />
+<code>#include &lt;gbwtgraph/algorithms.h&gt;</code><br />
 <code>#include &lt;gbwtgraph/path_cover.h&gt;</code><br />
 <code>#include &quot;<a class="el" href="gbwt__helper_8hpp.html">gbwt_helper.hpp</a>&quot;</code><br />
-<code>#include &quot;<a class="el" href="haplotype__indexer_8hpp.html">haplotype_indexer.hpp</a>&quot;</code><br />
-<code>#include &quot;<a class="el" href="path_8hpp.html">path.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="alignment_8hpp.html">alignment.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="hash__map_8hpp.html">hash_map.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="path_8hpp.html">path.hpp</a>&quot;</code><br />
 </div><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
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diff --git a/index__main_8cpp.html b/index__main_8cpp.html
index a1fae7a48d..863b3c8ef7 100644
--- a/index__main_8cpp.html
+++ b/index__main_8cpp.html
@@ -81,7 +81,6 @@
 <code>#include &lt;vector&gt;</code><br />
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 <code>#include &lt;<a class="el" href="stream_8hpp.html">vg/io/stream.hpp</a>&gt;</code><br />
 <code>#include &lt;<a class="el" href="vpkg_8hpp.html">vg/io/vpkg.hpp</a>&gt;</code><br />
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 <code>#include &quot;<a class="el" href="snarl__distance__index_8hpp.html">../snarl_distance_index.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="source__sink__overlay_8hpp.html">../source_sink_overlay.hpp</a>&quot;</code><br />
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 <code>#include &quot;<a class="el" href="gbwtgraph__helper_8hpp.html">../gbwtgraph_helper.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="gcsa__helper_8hpp.html">../gcsa_helper.hpp</a>&quot;</code><br />
 <code>#include &lt;gcsa/algorithms.h&gt;</code><br />
-<code>#include &lt;gbwt/variants.h&gt;</code><br />
 <code>#include &lt;bdsg/overlays/packed_subgraph_overlay.hpp&gt;</code><br />
 <code>#include &lt;handlegraph/algorithms/weakly_connected_components.hpp&gt;</code><br />
 </div><table class="memberdecls">
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 Functions</h2></td></tr>
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-<div class="memproto">
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diff --git a/namespacemembers_f.html b/namespacemembers_f.html
index 7718af5ff6..ccbfeb4ce4 100644
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diff --git a/namespacevg.html b/namespacevg.html
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