Commit new auto-generated docs

classvg_1_1Transcriptome.html

@@ -164,8 +164,10 @@
 <tr class="separator:af764ab28d6d866807d09a4482dd96523"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:ae6f600db9b276fe332d4f14919bba983"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Transcriptome.html#ae6f600db9b276fe332d4f14919bba983">reorder_exons</a> (<a class="el" href="structvg_1_1Transcript.html">Transcript</a> *transcript) const</td></tr>
 <tr class="separator:ae6f600db9b276fe332d4f14919bba983"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a4cba921dae9fe3eae2361b0b7391b7b3"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Transcriptome.html#a4cba921dae9fe3eae2361b0b7391b7b3">has_incorrect_order_exons</a> (const vector&lt; <a class="el" href="structvg_1_1Exon.html">Exon</a> &gt; &amp;exons) const</td></tr>
+<tr class="separator:a4cba921dae9fe3eae2361b0b7391b7b3"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a405f6a2b87ab7d919d0cb8780b1362a5"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Transcriptome.html#a405f6a2b87ab7d919d0cb8780b1362a5">has_overlapping_exons</a> (const vector&lt; <a class="el" href="structvg_1_1Exon.html">Exon</a> &gt; &amp;exons) const</td></tr>
-<tr class="memdesc:a405f6a2b87ab7d919d0cb8780b1362a5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Checks whether any adjacent exons overlap.  <a href="classvg_1_1Transcriptome.html#a405f6a2b87ab7d919d0cb8780b1362a5">More...</a><br /></td></tr>
+<tr class="memdesc:a405f6a2b87ab7d919d0cb8780b1362a5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Assumes exons are in increasing order.  <a href="classvg_1_1Transcriptome.html#a405f6a2b87ab7d919d0cb8780b1362a5">More...</a><br /></td></tr>
 <tr class="separator:a405f6a2b87ab7d919d0cb8780b1362a5"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:aab8e9e4cf0cf855de888086388577d56"><td class="memItemLeft" align="right" valign="top">list&lt; <a class="el" href="structvg_1_1EditedTranscriptPath.html">EditedTranscriptPath</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1Transcriptome.html#aab8e9e4cf0cf855de888086388577d56">construct_reference_transcript_paths_embedded</a> (const vector&lt; <a class="el" href="structvg_1_1Transcript.html">Transcript</a> &gt; &amp;transcripts, const bdsg::PositionOverlay &amp;graph_path_pos_overlay) const</td></tr>
 <tr class="separator:aab8e9e4cf0cf855de888086388577d56"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -1103,6 +1105,33 @@ <h2 class="memtitle"><span class="permalink"><a href="#a8103dfe99f0bb36e806cab44
 
 <p>Returns the haplotype transcript paths. </p>
 
+</div>
+</div>
+<a id="a4cba921dae9fe3eae2361b0b7391b7b3"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4cba921dae9fe3eae2361b0b7391b7b3">&#9670;&nbsp;</a></span>has_incorrect_order_exons()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool vg::Transcriptome::has_incorrect_order_exons </td>
+          <td>(</td>
+          <td class="paramtype">const vector&lt; <a class="el" href="structvg_1_1Exon.html">Exon</a> &gt; &amp;&#160;</td>
+          <td class="paramname"><em>exons</em></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">private</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+<p>Checks whether any adjacent exons are out of order Assumes exons are in increasing order (to be correct) </p>
+
 </div>
 </div>
 <a id="aaf34b6da5110fa44f787994be4ea2791"></a>
@@ -1167,6 +1196,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#a405f6a2b87ab7d919d0cb878
 </table>
 </div><div class="memdoc">
 
+<p>Assumes exons are in increasing order. </p>
 <p>Checks whether any adjacent exons overlap. </p>
 
 </div>

functions_func_h.html

@@ -164,6 +164,9 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 <li>has_fixed_fragment_length_distr()
 : <a class="el" href="classvg_1_1PairedEndMapper.html#ad0a2d836cfcaddae8569bf1a024aa56b">vg::PairedEndMapper</a>
 </li>
+<li>has_incorrect_order_exons()
+: <a class="el" href="classvg_1_1Transcriptome.html#a4cba921dae9fe3eae2361b0b7391b7b3">vg::Transcriptome</a>
+</li>
 <li>has_incremental_search()
 : <a class="el" href="classhaplo_1_1GBWTScoreProvider.html#abe35e78c1d11af952b27dc8c36c1909f">haplo::GBWTScoreProvider&lt; GBWTType &gt;</a>
 , <a class="el" href="classhaplo_1_1ScoreProvider.html#a1455c3ccb6a9d03e5d79636e79be301a">haplo::ScoreProvider</a>
@@ -216,11 +219,11 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 , <a class="el" href="classvg_1_1SubHandleGraph.html#a66e144a38ed8437cbf71a186a6e8afa0">vg::SubHandleGraph</a>
 , <a class="el" href="classvg_1_1SubpathOverlay.html#a7c9a83697a1f3041e3dfbcb10f3a831b">vg::SubpathOverlay</a>
 , <a class="el" href="classvg_1_1TreeSubgraph.html#a84c11ffd899e018587d6ccb25dd1211b">vg::TreeSubgraph</a>
-, <a class="el" href="classvg_1_1VG.html#a049bd863e2ac7e93aec79404d56b4a34">vg::VG</a>
+, <a class="el" href="classvg_1_1VG.html#ac9339913ecff654569a9c81ae091ebfe">vg::VG</a>
 , <a class="el" href="classxg_1_1XG.html#a60dd1cf3ec755863aabc99e6948011e0">xg::XG</a>
 </li>
 <li>has_node_mapping()
-: <a class="el" href="classvg_1_1Paths.html#a4f744ed09e266781a366dd11a73993b8">vg::Paths</a>
+: <a class="el" href="classvg_1_1Paths.html#a48f74571d94bdd9845ff761d51701034">vg::Paths</a>
 </li>
 <li>has_novel_exon_boundaries()
 : <a class="el" href="classvg_1_1Transcriptome.html#aaf34b6da5110fa44f787994be4ea2791">vg::Transcriptome</a>
@@ -280,10 +283,10 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 : <a class="el" href="classvg_1_1Pictographs.html#a91309563adbfaaf7eab19a51623d66c2">vg::Pictographs</a>
 </li>
 <li>hDP_gbwt_graph_accessor()
-: <a class="el" href="classhaplo_1_1hDP__gbwt__graph__accessor.html#a7a8d1f9ad8428fe0ff0b6071dc6f47ef">haplo::hDP_gbwt_graph_accessor&lt; GBWTType &gt;</a>
+: <a class="el" href="classhaplo_1_1hDP__gbwt__graph__accessor.html#a63ed5e1c48904968ae61ff21f411c0db">haplo::hDP_gbwt_graph_accessor&lt; GBWTType &gt;</a>
 </li>
 <li>head_nodes()
-: <a class="el" href="classvg_1_1VG.html#a7eecc0bd555c31d1c541c3ce44b421c3">vg::VG</a>
+: <a class="el" href="classvg_1_1VG.html#a3a44c415fb5882c184e2f35bb3999700">vg::VG</a>
 </li>
 <li>HitEdge()
 : <a class="el" href="classvg_1_1MEMClusterer_1_1HitEdge.html#adfc12ed7c93d550e05882555d0004235">vg::MEMClusterer::HitEdge</a>
@@ -298,7 +301,7 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 : <a class="el" href="classvg_1_1HTSAlignmentEmitter.html#a780156f43d54cf16906948ad8286c20f">vg::HTSAlignmentEmitter</a>
 </li>
 <li>HTSWriter()
-: <a class="el" href="classvg_1_1HTSWriter.html#ae2fc6b2a60e3bc9441956faf87ff6a07">vg::HTSWriter</a>
+: <a class="el" href="classvg_1_1HTSWriter.html#a8257b1e35ac5abf92b43b8a823c66aa5">vg::HTSWriter</a>
 </li>
 </ul>
 </div><!-- contents -->

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#a0f3e69ced0c3135f3f363c14bf752aad">vg::VG</a>
+: <a class="el" href="classvg_1_1VG.html#ac08e778396904ad3b3f20f605f54628d">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#a2d348fa5aa3bd9216fc4133d320575ef">vg::NullMaskingGraph</a>
+: <a class="el" href="classvg_1_1NullMaskingGraph.html#addeb1ab4002f516c686a5af59018597f">vg::NullMaskingGraph</a>
 </li>
 <li>num_haplotypes()
 : <a class="el" href="classvg_1_1PhasedGenome.html#af17e5f99a07028d41f94885480cdddf7">vg::PhasedGenome</a>

functions_h.html

@@ -249,6 +249,9 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 <li>has_grandparent_handle
 : <a class="el" href="structvg_1_1SnarlDistanceIndexClusterer_1_1SnarlTreeNodeProblem.html#a4d823f95b1440029399ae07f5d5ce0ec">vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem</a>
 </li>
+<li>has_incorrect_order_exons()
+: <a class="el" href="classvg_1_1Transcriptome.html#a4cba921dae9fe3eae2361b0b7391b7b3">vg::Transcriptome</a>
+</li>
 <li>has_incremental_search()
 : <a class="el" href="classhaplo_1_1GBWTScoreProvider.html#abe35e78c1d11af952b27dc8c36c1909f">haplo::GBWTScoreProvider&lt; GBWTType &gt;</a>
 , <a class="el" href="classhaplo_1_1ScoreProvider.html#a1455c3ccb6a9d03e5d79636e79be301a">haplo::ScoreProvider</a>
@@ -301,7 +304,7 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 , <a class="el" href="classvg_1_1SubHandleGraph.html#a66e144a38ed8437cbf71a186a6e8afa0">vg::SubHandleGraph</a>
 , <a class="el" href="classvg_1_1SubpathOverlay.html#a7c9a83697a1f3041e3dfbcb10f3a831b">vg::SubpathOverlay</a>
 , <a class="el" href="classvg_1_1TreeSubgraph.html#a84c11ffd899e018587d6ccb25dd1211b">vg::TreeSubgraph</a>
-, <a class="el" href="classvg_1_1VG.html#a049bd863e2ac7e93aec79404d56b4a34">vg::VG</a>
+, <a class="el" href="classvg_1_1VG.html#ac9339913ecff654569a9c81ae091ebfe">vg::VG</a>
 , <a class="el" href="classxg_1_1XG.html#a60dd1cf3ec755863aabc99e6948011e0">xg::XG</a>
 </li>
 <li>has_node_mapping()
@@ -381,10 +384,10 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 : <a class="el" href="structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a88fe737c0668785017687666e0aa74a8">vg::IndexingParameters</a>
 </li>
 <li>hDP_gbwt_graph_accessor()
-: <a class="el" href="classhaplo_1_1hDP__gbwt__graph__accessor.html#a7a8d1f9ad8428fe0ff0b6071dc6f47ef">haplo::hDP_gbwt_graph_accessor&lt; GBWTType &gt;</a>
+: <a class="el" href="classhaplo_1_1hDP__gbwt__graph__accessor.html#a63ed5e1c48904968ae61ff21f411c0db">haplo::hDP_gbwt_graph_accessor&lt; GBWTType &gt;</a>
 </li>
 <li>head_nodes()
-: <a class="el" href="classvg_1_1VG.html#a3a44c415fb5882c184e2f35bb3999700">vg::VG</a>
+: <a class="el" href="classvg_1_1VG.html#a7eecc0bd555c31d1c541c3ce44b421c3">vg::VG</a>
 </li>
 <li>head_tail_nodes
 : <a class="el" href="classvg_1_1Paths.html#a3fd42adbd3d58aee08370f043dc1643d">vg::Paths</a>
@@ -441,7 +444,7 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 : <a class="el" href="classvg_1_1MEMClusterer_1_1HitGraph.html#a9895e95cdaa1b95876c79c07d29fe852">vg::MEMClusterer::HitGraph</a>
 </li>
 <li>HitNode()
-: <a class="el" href="classvg_1_1MEMClusterer_1_1HitNode.html#a3156b62ac2208fdac8d0b12475011472">vg::MEMClusterer::HitNode</a>
+: <a class="el" href="classvg_1_1MEMClusterer_1_1HitNode.html#aaeb6e6e2bb1c2ce2cda76adce19a40d6">vg::MEMClusterer::HitNode</a>
 </li>
 <li>hits
 : <a class="el" href="structvg_1_1MinimizerMapper_1_1Minimizer.html#aa60067efaa8910104760c8d910471a29">vg::MinimizerMapper::Minimizer</a>
@@ -457,10 +460,10 @@ <h3><a id="index_h"></a>- h -</h3><ul>
 : <a class="el" href="classvg_1_1HTSWriter.html#ab2151e3837dd1503111bf7d1daa1fa56">vg::HTSWriter</a>
 </li>
 <li>HTSAlignmentEmitter()
-: <a class="el" href="classvg_1_1HTSAlignmentEmitter.html#acc9b5714c55e4b644216066eda386dbd">vg::HTSAlignmentEmitter</a>
+: <a class="el" href="classvg_1_1HTSAlignmentEmitter.html#a0c76946bf064ecac88e21a2467ea2410">vg::HTSAlignmentEmitter</a>
 </li>
 <li>HTSWriter()
-: <a class="el" href="classvg_1_1HTSWriter.html#a8257b1e35ac5abf92b43b8a823c66aa5">vg::HTSWriter</a>
+: <a class="el" href="classvg_1_1HTSWriter.html#a0a23221d8449a4b4e0b1278995ad0207">vg::HTSWriter</a>
 </li>
 </ul>
 </div><!-- contents -->

functions_n.html

@@ -398,12 +398,14 @@ <h3><a id="index_n"></a>- n -</h3><ul>
 <li>NODE_RECORD_MASK
 : <a class="el" href="structvg_1_1MIPayload.html#a10e8da4bbb1bbb2444c06e339bc46f6d">vg::MIPayload</a>
 </li>
+<li>node_record_offset()
+: <a class="el" href="structvg_1_1MIPayload.html#add455aacb3257a7f7a4046e0c98c855b">vg::MIPayload</a>
+</li>
 <li>NODE_RECORD_OFFSET
 : <a class="el" href="structvg_1_1MIPayload.html#a467c44f8e2b91fd1ab029d7f963291c4">vg::MIPayload</a>
 </li>
-<li>node_record_offset()
-: <a class="el" href="structvg_1_1MIPayload.html#add455aacb3257a7f7a4046e0c98c855b">vg::MIPayload</a>
-, <a class="el" href="structvg_1_1MIPayloadValues.html#ae6ab44e011b6e3c022b7069fb4d068b7">vg::MIPayloadValues</a>
+<li>node_record_offset
+: <a class="el" href="structvg_1_1MIPayloadValues.html#ae6ab44e011b6e3c022b7069fb4d068b7">vg::MIPayloadValues</a>
 </li>
 <li>NODE_RECORD_OFFSET_MASK
 : <a class="el" href="structvg_1_1MIPayload.html#a1b561b7fbbb6654e64ecd69a078cbf18">vg::MIPayload</a>

functions_p.html

@@ -1074,12 +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#acbf722cab695a00b651bab515806a7e9">vg::AlignmentValidity</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>ProblemDumpExplainer()
 : <a class="el" href="classvg_1_1ProblemDumpExplainer.html#a51e4e904203bd8817e6a93a454ee1e10">vg::ProblemDumpExplainer</a>
 </li>
@@ -1169,7 +1169,7 @@ <h3><a id="index_p"></a>- p -</h3><ul>
 </li>
 <li>provide()
 : <a class="el" href="classvg_1_1IndexFile.html#a116a29bacf28f3889ea318ac25a11dc7">vg::IndexFile</a>
-, <a class="el" href="classvg_1_1IndexRegistry.html#a72c4f8ea143cd9a982366234a8eed71e">vg::IndexRegistry</a>
+, <a class="el" href="classvg_1_1IndexRegistry.html#a430536c995544af29060b78d04e3f5c1">vg::IndexRegistry</a>
 </li>
 <li>provided_directly
 : <a class="el" href="classvg_1_1IndexFile.html#a32bf1b5189843cdcc3ba7eb6068dd46f">vg::IndexFile</a>
@@ -1220,7 +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#ab1c9f02cbadcd8df05b691e4ff5294f2">vg::MultipathMapper</a>
+: <a class="el" href="classvg_1_1MultipathMapper.html#a009000ee2da67a965a4f627be468d976">vg::MultipathMapper</a>
 </li>
 <li>push()
 : <a class="el" href="structvg_1_1MatchPos_1_1PathList.html#a2979222c63cb87e2f530fceda30e56a5">vg::MatchPos::PathList</a>

functions_s.html

@@ -1178,7 +1178,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 , <a class="el" href="classvg_1_1GraphSynchronizer_1_1Lock.html#af564269e9eaf8eb68f4c4c3ce1ba3932">vg::GraphSynchronizer::Lock</a>
 , <a class="el" href="structvg_1_1HaplotypePartitioner_1_1Subchain.html#a16932e227f0ac0972fb63bc300a5374d">vg::HaplotypePartitioner::Subchain</a>
 , <a class="el" href="structvg_1_1Haplotypes_1_1Subchain.html#af3baaf52c08ac684ac2571a9f4f56ec0">vg::Haplotypes::Subchain</a>
-, <a class="el" href="classvg_1_1multipath__alignment__t.html#ae79344b60aed1577a39391b4b42574f3">vg::multipath_alignment_t</a>
+, <a class="el" href="classvg_1_1multipath__alignment__t.html#a4cd9b91704e89c799019d9c8962b16bb">vg::multipath_alignment_t</a>
 , <a class="el" href="structvg_1_1MultipathAlignment.html#a8003b8991108e99465d8fd80fc74cc03">vg::MultipathAlignment</a>
 , <a class="el" href="classvg_1_1NetGraph.html#a2d7b0b659aae1f47312bb76aae43dda0">vg::NetGraph</a>
 , <a class="el" href="structvg_1_1Range.html#a372fbc9ba00e9eb4785fcd049b2451cf">vg::Range&lt; Number &gt;</a>
@@ -1507,7 +1507,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classvg_1_1Viz.html#ad93aa239a30c3b7a017348e22f184b85">vg::Viz</a>
 </li>
 <li>surject()
-: <a class="el" href="classvg_1_1Surjector.html#a80afa331fde9e8bcff66c4e87400217a">vg::Surjector</a>
+: <a class="el" href="classvg_1_1Surjector.html#a4e4e4c28b1313850e647f4d258a0ea82">vg::Surjector</a>
 </li>
 <li>surject_alignments_in_place()
 : <a class="el" href="classvg_1_1SurjectingAlignmentEmitter.html#a5ba8aab649ae5f31c64be2c5461c743c">vg::SurjectingAlignmentEmitter</a>
@@ -1549,7 +1549,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classvg_1_1PhasedGenome.html#a181b4e71f8debc78ceccf476ce36abcd">vg::PhasedGenome</a>
 </li>
 <li>swap_node_id()
-: <a class="el" href="classvg_1_1VG.html#a63f2ffa39d84f80e5ab8068a25a03ee9">vg::VG</a>
+: <a class="el" href="classvg_1_1VG.html#afee31880eaf65a1a6d1a250663271b54">vg::VG</a>
 </li>
 <li>swap_node_ids()
 : <a class="el" href="classvg_1_1Paths.html#aba01c4d1b1d415622634db97f62b1188">vg::Paths</a>

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#a9847ed10905a3633101e1c71f36abc7a">vg::ProblemDumpExplainer</a>
+: <a class="el" href="classvg_1_1ProblemDumpExplainer.html#a97c2e3c2f810e01cf79d3e4c0cf4ae47">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>
@@ -239,17 +239,19 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 </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>
 </li>
 <li>Version()
 : <a class="el" href="classvg_1_1Version.html#a05bb9f14c7597bf90a2981db7e59b058">vg::Version</a>
 </li>
+<li>VERSION
+: <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>
 </li>
 <li>VG
 : <a class="el" href="structvg_1_1IndexingParameters.html#af607873fad40d1de55b8f4f6e04fdf10a5e978449ccc729202c33e2dc543b8327">vg::IndexingParameters</a>
-, <a class="el" href="classvg_1_1VG.html#abeafee2d3bc6e0039e99fccdea10f4f9">vg::VG</a>
+, <a class="el" href="classvg_1_1VG.html#a0fbb777fd8ab6050124a6eaf9eca9133">vg::VG</a>
 </li>
 <li>vg_filename
 : <a class="el" href="classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0">vg::IndexedVG</a>
@@ -277,7 +279,7 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 : <a class="el" href="classvg_1_1SnarlManager.html#a567554948e5dc03604a46972eb42d295">vg::SnarlManager</a>
 </li>
 <li>Viz()
-: <a class="el" href="classvg_1_1Viz.html#a8e9440d6c67fde7f10fe9c0366759041">vg::Viz</a>
+: <a class="el" href="classvg_1_1Viz.html#a5d343eb2d20b2db1eb66def4b8d3081c">vg::Viz</a>
 </li>
 </ul>
 </div><!-- contents -->

functions_vars_v.html

@@ -137,14 +137,12 @@ <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="classvg_1_1Version.html#a06ae288f165de69ddbfdec65c217d222">vg::Version</a>
+: <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>
 </li>
 <li>vg
 : <a class="el" href="classvg_1_1FlowSort.html#abd481c5b9e6c9c5aeaf846652dd3c76f">vg::FlowSort</a>