Commit new auto-generated docs

vgteam · Feb 26, 2024 · 292c99a · 292c99a
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diff --git a/classvg_1_1Aligner-members.html b/classvg_1_1Aligner-members.html
@@ -75,8 +75,8 @@
 <table class="directory">
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a0e2376f882d3164e798f2bb0d7da4359">align</a>(Alignment &amp;alignment, const HandleGraph &amp;g, bool traceback_aln) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a735b995cc89b1d526a21293b187d44d8">align</a>(Alignment &amp;alignment, const HandleGraph &amp;g, const std::vector&lt; handle_t &gt; &amp;topological_order) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a7d0af54853dfa98e238e1457faa00f4f">align_global_banded</a>(Alignment &amp;alignment, const HandleGraph &amp;g, int32_t band_padding=0, bool permissive_banding=true) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a86579ab7dbf7799ae998bcac6ac4c9d0">align_global_banded_multi</a>(Alignment &amp;alignment, vector&lt; Alignment &gt; &amp;alt_alignments, const HandleGraph &amp;g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a23391205007eb9ed1c14c023dc744924">align_global_banded</a>(Alignment &amp;alignment, const HandleGraph &amp;g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a7cf5d0a98af2eceeced2aeb0d21bf1a1">align_global_banded_multi</a>(Alignment &amp;alignment, vector&lt; Alignment &gt; &amp;alt_alignments, const HandleGraph &amp;g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true, const unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a9e1056e34d9b67a80b4268d6408a7e7c">align_internal</a>(Alignment &amp;alignment, vector&lt; Alignment &gt; *multi_alignments, const HandleGraph &amp;g, bool pinned, bool pin_left, int32_t max_alt_alns, bool traceback_aln) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a90a7be445aa931365b940fa2f26570ff">align_pinned</a>(Alignment &amp;alignment, const HandleGraph &amp;g, bool pin_left, bool xdrop=false, uint16_t xdrop_max_gap_length=default_xdrop_max_gap_length) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1Aligner.html#a6c2efe87216772df9cb3d3d7d0e61a26">align_pinned_multi</a>(Alignment &amp;alignment, vector&lt; Alignment &gt; &amp;alt_alignments, const HandleGraph &amp;g, bool pin_left, int32_t max_alt_alns) const</td><td class="entry"><a class="el" href="classvg_1_1Aligner.html">vg::Aligner</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>

diff --git a/classvg_1_1Aligner.html b/classvg_1_1Aligner.html
@@ -102,10 +102,10 @@
 <tr class="separator:a90a7be445aa931365b940fa2f26570ff"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a6c2efe87216772df9cb3d3d7d0e61a26"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Aligner.html#a6c2efe87216772df9cb3d3d7d0e61a26">align_pinned_multi</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;alignment, vector&lt; <a class="el" href="structvg_1_1Alignment.html">Alignment</a> &gt; &amp;alt_alignments, const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;g, bool pin_left, int32_t max_alt_alns) const</td></tr>
 <tr class="separator:a6c2efe87216772df9cb3d3d7d0e61a26"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:a7d0af54853dfa98e238e1457faa00f4f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Aligner.html#a7d0af54853dfa98e238e1457faa00f4f">align_global_banded</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;alignment, const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;g, int32_t band_padding=0, bool permissive_banding=true) const</td></tr>
-<tr class="separator:a7d0af54853dfa98e238e1457faa00f4f"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:a86579ab7dbf7799ae998bcac6ac4c9d0"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Aligner.html#a86579ab7dbf7799ae998bcac6ac4c9d0">align_global_banded_multi</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;alignment, vector&lt; <a class="el" href="structvg_1_1Alignment.html">Alignment</a> &gt; &amp;alt_alignments, const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true) const</td></tr>
-<tr class="separator:a86579ab7dbf7799ae998bcac6ac4c9d0"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a23391205007eb9ed1c14c023dc744924"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Aligner.html#a23391205007eb9ed1c14c023dc744924">align_global_banded</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;alignment, const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map&lt; <a class="el" href="structhandlegraph_1_1handle__t.html">handle_t</a>, bool &gt; *left_align_strand=nullptr) const</td></tr>
+<tr class="separator:a23391205007eb9ed1c14c023dc744924"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a7cf5d0a98af2eceeced2aeb0d21bf1a1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Aligner.html#a7cf5d0a98af2eceeced2aeb0d21bf1a1">align_global_banded_multi</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;alignment, vector&lt; <a class="el" href="structvg_1_1Alignment.html">Alignment</a> &gt; &amp;alt_alignments, const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true, const unordered_map&lt; <a class="el" href="structhandlegraph_1_1handle__t.html">handle_t</a>, bool &gt; *left_align_strand=nullptr) const</td></tr>
+<tr class="separator:a7cf5d0a98af2eceeced2aeb0d21bf1a1"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a186815e37fef05cb774d257ceca32b36"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Aligner.html#a186815e37fef05cb774d257ceca32b36">align_xdrop</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;alignment, const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;g, const vector&lt; <a class="el" href="classvg_1_1MaximalExactMatch.html">MaximalExactMatch</a> &gt; &amp;mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const</td></tr>
 <tr class="memdesc:a186815e37fef05cb774d257ceca32b36"><td class="mdescLeft">&#160;</td><td class="mdescRight">xdrop aligner  <a href="classvg_1_1Aligner.html#a186815e37fef05cb774d257ceca32b36">More...</a><br /></td></tr>
 <tr class="separator:a186815e37fef05cb774d257ceca32b36"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -404,8 +404,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#a735b995cc89b1d526a21293b
 
 </div>
 </div>
-<a id="a7d0af54853dfa98e238e1457faa00f4f"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a7d0af54853dfa98e238e1457faa00f4f">&#9670;&nbsp;</a></span>align_global_banded()</h2>
+<a id="a23391205007eb9ed1c14c023dc744924"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a23391205007eb9ed1c14c023dc744924">&#9670;&nbsp;</a></span>align_global_banded()</h2>
 
 <div class="memitem">
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@@ -435,7 +435,13 @@ <h2 class="memtitle"><span class="permalink"><a href="#a7d0af54853dfa98e238e1457
           <td class="paramkey"></td>
           <td></td>
           <td class="paramtype">bool&#160;</td>
-          <td class="paramname"><em>permissive_banding</em> = <code>true</code>&#160;</td>
+          <td class="paramname"><em>permissive_banding</em> = <code>true</code>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const unordered_map&lt; <a class="el" href="structhandlegraph_1_1handle__t.html">handle_t</a>, bool &gt; *&#160;</td>
+          <td class="paramname"><em>left_align_strand</em> = <code>nullptr</code>&#160;</td>
         </tr>
         <tr>
           <td></td>
@@ -451,12 +457,12 @@ <h2 class="memtitle"><span class="permalink"><a href="#a7d0af54853dfa98e238e1457
 </div><div class="memdoc">
 <p>store optimal global alignment against a graph within a specified band in the <a class="el" href="structvg_1_1Alignment.html">Alignment</a> object permissive banding auto detects the width of band needed so that paths can travel through every node in the graph </p>
 
-<p>Implements <a class="el" href="classvg_1_1GSSWAligner.html#a350908e38cee67ddbe77395624a1cb50">vg::GSSWAligner</a>.</p>
+<p>Implements <a class="el" href="classvg_1_1GSSWAligner.html#a75d946105738eca7793da2a5c77bf57e">vg::GSSWAligner</a>.</p>
 
 </div>
 </div>
-<a id="a86579ab7dbf7799ae998bcac6ac4c9d0"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a86579ab7dbf7799ae998bcac6ac4c9d0">&#9670;&nbsp;</a></span>align_global_banded_multi()</h2>
+<a id="a7cf5d0a98af2eceeced2aeb0d21bf1a1"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7cf5d0a98af2eceeced2aeb0d21bf1a1">&#9670;&nbsp;</a></span>align_global_banded_multi()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -498,7 +504,13 @@ <h2 class="memtitle"><span class="permalink"><a href="#a86579ab7dbf7799ae998bcac
           <td class="paramkey"></td>
           <td></td>
           <td class="paramtype">bool&#160;</td>
-          <td class="paramname"><em>permissive_banding</em> = <code>true</code>&#160;</td>
+          <td class="paramname"><em>permissive_banding</em> = <code>true</code>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const unordered_map&lt; <a class="el" href="structhandlegraph_1_1handle__t.html">handle_t</a>, bool &gt; *&#160;</td>
+          <td class="paramname"><em>left_align_strand</em> = <code>nullptr</code>&#160;</td>
         </tr>
         <tr>
           <td></td>
@@ -514,7 +526,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a86579ab7dbf7799ae998bcac
 </div><div class="memdoc">
 <p>store top scoring global alignments in the vector in descending score order up to a maximum number of alternate alignments (including the optimal alignment). if there are fewer than the maximum number of alignments in the return value, then the vector contains all possible alignments. the optimal alignment will be stored in both the vector and the original alignment object </p>
 
-<p>Implements <a class="el" href="classvg_1_1GSSWAligner.html#ab3b92372eb75a5b54311b74aa6fe9190">vg::GSSWAligner</a>.</p>
+<p>Implements <a class="el" href="classvg_1_1GSSWAligner.html#ab942a7b77fbe5169e35a09bd8fee3198">vg::GSSWAligner</a>.</p>
 
 </div>
 </div>

diff --git a/classvg_1_1BandedGlobalAligner-members.html b/classvg_1_1BandedGlobalAligner-members.html
@@ -78,9 +78,9 @@
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#ab0cb70d08f759c4f661206b318a96bd7">alignment</a></td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#a72ad87c059fc959b0258feb87c8dd4bd">alt_alignments</a></td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#ab61c92f8ff975ce22553b7118267b9c7">banded_matrices</a></td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#a0369cef48d72ad20c99ae1d890873c3b">BandedGlobalAligner</a>(Alignment &amp;alignment, const HandleGraph &amp;g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#a1103b21b80c4c0404b5d51970d32e760">BandedGlobalAligner</a>(Alignment &amp;alignment, const HandleGraph &amp;g, vector&lt; Alignment &gt; &amp;alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"></td></tr>
-  <tr><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#a99da8a313043f84ce2bb83a4d83b782f">BandedGlobalAligner</a>(Alignment &amp;alignment, const HandleGraph &amp;g, vector&lt; Alignment &gt; *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#ad208d9c58549c45af8e6ac9a3adaa87c">BandedGlobalAligner</a>(Alignment &amp;alignment, const HandleGraph &amp;g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#aa7c22fd30bb72a2ba8cc6e1134f9dc9b">BandedGlobalAligner</a>(Alignment &amp;alignment, const HandleGraph &amp;g, vector&lt; Alignment &gt; &amp;alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"></td></tr>
+  <tr><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#a89646664f5742c1dc8fb513319c4fdaa">BandedGlobalAligner</a>(Alignment &amp;alignment, const HandleGraph &amp;g, vector&lt; Alignment &gt; *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map&lt; handle_t, bool &gt; *left_align_strand=nullptr)</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#adfad0975f34dcf90211d239ee6c126a8">find_banded_paths</a>(bool permissive_banding, int64_t band_padding, vector&lt; bool &gt; &amp;node_masked, vector&lt; pair&lt; int64_t, int64_t &gt;&gt; &amp;band_ends)</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#af5168385acfc1ca71f0757269452e5a7">graph</a></td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html#a5f62e09b67082ec3c7ed538b930d8e2faa0a1ece7d481572fa684460331afbfa4">InsertCol</a> enum value</td><td class="entry"><a class="el" href="classvg_1_1BandedGlobalAligner.html">vg::BandedGlobalAligner&lt; IntType &gt;</a></td><td class="entry"><span class="mlabel">private</span></td></tr>