Commit new auto-generated docs

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>

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>
 <tr class="separator:ae92d109c2e7baf0b7ddded8df80a6f70"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<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>

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>

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>

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>

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>
 : <a class="el" href="classvg_1_1multipath__alignment__t.html#a43e30d76e7ac0596fc15c868fbbd603c">vg::multipath_alignment_t</a>
 </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>