Commit new auto-generated docs

classvg_1_1MinimizerMapper.html

@@ -473,6 +473,8 @@
 <tr class="separator:a98117858da937a277f445898bcc2d125"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:ab6a0d266ef94fbda125ebdde64617c84"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1MinimizerMapper.html#ab6a0d266ef94fbda125ebdde64617c84">fix_dozeu_score</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;rescued_alignment, const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;rescue_graph, const std::vector&lt; <a class="el" href="structhandlegraph_1_1handle__t.html">handle_t</a> &gt; &amp;topological_order) const</td></tr>
 <tr class="separator:ab6a0d266ef94fbda125ebdde64617c84"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a4ec441e3df74303c16a60529f08cb70a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1MinimizerMapper.html#a4ec441e3df74303c16a60529f08cb70a">fix_dozeu_end_deletions</a> (<a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;rescued_alignment) const</td></tr>
+<tr class="separator:a4ec441e3df74303c16a60529f08cb70a"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:af68c4bd9915413525c9c66b668779331"><td class="memItemLeft" align="right" valign="top">int64_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1MinimizerMapper.html#af68c4bd9915413525c9c66b668779331">distance_between</a> (const <a class="el" href="namespacevg.html#a8232142f432c4dd8e7cfe96e1f50e039">pos_t</a> &amp;pos1, const <a class="el" href="namespacevg.html#a8232142f432c4dd8e7cfe96e1f50e039">pos_t</a> &amp;pos2)</td></tr>
 <tr class="separator:af68c4bd9915413525c9c66b668779331"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:ae68add551501e3b58c9329d9297d620d"><td class="memItemLeft" align="right" valign="top">int64_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1MinimizerMapper.html#ae68add551501e3b58c9329d9297d620d">distance_between</a> (const <a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;aln1, const <a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;aln2)</td></tr>
@@ -2006,6 +2008,33 @@ <h2 class="memtitle"><span class="permalink"><a href="#a6b2b57632c13416d6626d3cf
 </div><div class="memdoc">
 <p>Find seeds for all minimizers passing the filters. </p>
 
+</div>
+</div>
+<a id="a4ec441e3df74303c16a60529f08cb70a"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a4ec441e3df74303c16a60529f08cb70a">&#9670;&nbsp;</a></span>fix_dozeu_end_deletions()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">void vg::MinimizerMapper::fix_dozeu_end_deletions </td>
+          <td>(</td>
+          <td class="paramtype"><a class="el" href="structvg_1_1Alignment.html">Alignment</a> &amp;&#160;</td>
+          <td class="paramname"><em>rescued_alignment</em></td><td>)</td>
+          <td> const</td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">protected</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+<p>When dozeu doesn't have any seeds, it's scan heuristic can lead to inaccurate anchoring with the end result that one end of the alignment has a deletion that doesn't connect to an aligned base. This function removes those deletions </p>
+
 </div>
 </div>
 <a id="ab6a0d266ef94fbda125ebdde64617c84"></a>

functions_f.html

@@ -376,6 +376,9 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 <li>first_mapping_quality_exact()
 : <a class="el" href="classvg_1_1GSSWAligner.html#a25cb693e3eb45f8c7d1e0ae7c6dcf0af">vg::GSSWAligner</a>
 </li>
+<li>fix_dozeu_end_deletions()
+: <a class="el" href="classvg_1_1MinimizerMapper.html#a4ec441e3df74303c16a60529f08cb70a">vg::MinimizerMapper</a>
+</li>
 <li>fix_dozeu_score()
 : <a class="el" href="classvg_1_1MinimizerMapper.html#ab6a0d266ef94fbda125ebdde64617c84">vg::MinimizerMapper</a>
 </li>
@@ -528,7 +531,7 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 <li>for_each_edge()
 : <a class="el" href="classhandlegraph_1_1HandleGraph.html#a61570ded026f825d62ea7608a1e92349">handlegraph::HandleGraph</a>
 , <a class="el" href="classvg_1_1DiagramExplainer.html#a9509e0d2a9b1cd5dce5bf058ba9f0511">vg::DiagramExplainer</a>
-, <a class="el" href="classvg_1_1VG.html#a3d7fdd8c951cbf8b25e116435b5e1e0e">vg::VG</a>
+, <a class="el" href="classvg_1_1VG.html#aed86f57c2e9766da9757e18ef543d35d">vg::VG</a>
 </li>
 <li>for_each_edge_parallel()
 : <a class="el" href="classvg_1_1VG.html#a46a20aa427767a27fd15d181ccca8c42">vg::VG</a>

functions_func_f.html

@@ -304,6 +304,9 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 <li>first_mapping_quality_exact()
 : <a class="el" href="classvg_1_1GSSWAligner.html#a25cb693e3eb45f8c7d1e0ae7c6dcf0af">vg::GSSWAligner</a>
 </li>
+<li>fix_dozeu_end_deletions()
+: <a class="el" href="classvg_1_1MinimizerMapper.html#a4ec441e3df74303c16a60529f08cb70a">vg::MinimizerMapper</a>
+</li>
 <li>fix_dozeu_score()
 : <a class="el" href="classvg_1_1MinimizerMapper.html#ab6a0d266ef94fbda125ebdde64617c84">vg::MinimizerMapper</a>
 </li>
@@ -443,7 +446,7 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 <li>for_each_edge()
 : <a class="el" href="classhandlegraph_1_1HandleGraph.html#a61570ded026f825d62ea7608a1e92349">handlegraph::HandleGraph</a>
 , <a class="el" href="classvg_1_1DiagramExplainer.html#a9509e0d2a9b1cd5dce5bf058ba9f0511">vg::DiagramExplainer</a>
-, <a class="el" href="classvg_1_1VG.html#a3d7fdd8c951cbf8b25e116435b5e1e0e">vg::VG</a>
+, <a class="el" href="classvg_1_1VG.html#aed86f57c2e9766da9757e18ef543d35d">vg::VG</a>
 </li>
 <li>for_each_edge_parallel()
 : <a class="el" href="classvg_1_1VG.html#a46a20aa427767a27fd15d181ccca8c42">vg::VG</a>
@@ -509,7 +512,7 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 : <a class="el" href="structvg_1_1DozeuInterface_1_1OrderedGraph.html#a1e63b71aba9a614f17b497908c638797">vg::DozeuInterface::OrderedGraph</a>
 </li>
 <li>for_each_node()
-: <a class="el" href="classvg_1_1VG.html#a23b34b164590c0537bf704dd1b816760">vg::VG</a>
+: <a class="el" href="classvg_1_1VG.html#af585f2161de09403d197e05fbcfb9a07">vg::VG</a>
 </li>
 <li>for_each_node_parallel()
 : <a class="el" href="classvg_1_1VG.html#a39790d52fe4c09804086d58164258fcf">vg::VG</a>
@@ -529,7 +532,7 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 , <a class="el" href="classxg_1_1XG.html#aff636eab67405c3c27ba4f2be4f0a6f5">xg::XG</a>
 </li>
 <li>for_each_path_matching()
-: <a class="el" href="classhandlegraph_1_1PathMetadata.html#a01967c3713408b24ed6c3c20ff2ddd23">handlegraph::PathMetadata</a>
+: <a class="el" href="classhandlegraph_1_1PathMetadata.html#aef274133ea4ac6c96fd5e5330e2c620c">handlegraph::PathMetadata</a>
 </li>
 <li>for_each_path_matching_impl()
 : <a class="el" href="classhandlegraph_1_1PathMetadata.html#af040579085f8d49fcb6733e1f9cc8c27">handlegraph::PathMetadata</a>

functions_p.html

@@ -1037,12 +1037,12 @@ <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>

functions_r.html

@@ -763,7 +763,7 @@ <h3><a id="index_r"></a>- r -</h3><ul>
 : <a class="el" href="classvg_1_1FlowSort.html#a095e96bd8ef6f016a600bdbc6af730ee">vg::FlowSort</a>
 </li>
 <li>ReverseGraph()
-: <a class="el" href="classvg_1_1ReverseGraph.html#a9122b516caa1f30b202ef7ef4cd83d60">vg::ReverseGraph</a>
+: <a class="el" href="classvg_1_1ReverseGraph.html#a4715727accf496a2b7f908688638d873">vg::ReverseGraph</a>
 </li>
 <li>reversing_filter()
 : <a class="el" href="classvg_1_1Filter.html#a5ac9ddf9392d973aa726ad6ee4d53b9f">vg::Filter</a>

functions_s.html

@@ -1167,7 +1167,7 @@ <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>
@@ -1410,7 +1410,7 @@ <h3><a id="index_s"></a>- s -</h3><ul>
 : <a class="el" href="classvg_1_1multipath__alignment__t.html#a3b6820ac77fa5438c55300ba1eb7a97d">vg::multipath_alignment_t</a>
 </li>
 <li>subpath_t()
-: <a class="el" href="classvg_1_1subpath__t.html#a17ac16fd98564bfa3ab34e9b9b20517e">vg::subpath_t</a>
+: <a class="el" href="classvg_1_1subpath__t.html#a096b12ec158dd2cf139dbe38f55ca2f3">vg::subpath_t</a>
 </li>
 <li>subpath_to_length
 : <a class="el" href="classvg_1_1HTSWriter.html#a24dca4e57dcfb498da8f18946194f600">vg::HTSWriter</a>
@@ -1541,7 +1541,7 @@ <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#afee31880eaf65a1a6d1a250663271b54">vg::VG</a>
+: <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>

functions_t.html

@@ -504,7 +504,7 @@ <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#ac23acdcea38566f2e68005eca4afff73">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>
@@ -648,7 +648,7 @@ <h3><a id="index_t"></a>- t -</h3><ul>
 : <a class="el" href="classvg_1_1io_1_1VPKG.html#a12f9922d4b17194d248dc3f19a449f60">vg::io::VPKG</a>
 </li>
 <li>try_load_one()
-: <a class="el" href="classvg_1_1io_1_1VPKG.html#a0d7f96d4dd7fe5b1fe47b330ca617623">vg::io::VPKG</a>
+: <a class="el" href="classvg_1_1io_1_1VPKG.html#ab3a2026ac79ee1539271ba1791108c66">vg::io::VPKG</a>
 </li>
 <li>TSVAlignmentEmitter()
 : <a class="el" href="classvg_1_1io_1_1TSVAlignmentEmitter.html#aa8778347f51972fcb03f74565c5e3117">vg::io::TSVAlignmentEmitter</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#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>
@@ -198,24 +198,26 @@ <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="structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579">vg::IndexingParameters</a>
+: <a class="el" href="classvg_1_1HaplotypePartitioner.html#ac5d1210d753c0fe6ed936f18f02e2cd2">vg::HaplotypePartitioner</a>
 </li>
 <li>Verbosity
-: <a class="el" href="structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3">vg::IndexingParameters</a>
+: <a class="el" href="classvg_1_1Haplotypes.html#a2e2fbea03cc9fb69389a653d3d8fc28a">vg::Haplotypes</a>
+, <a class="el" href="structvg_1_1IndexingParameters.html#aa4d63cb22547d603bece7ba32e41c9f3">vg::IndexingParameters</a>
 </li>
 <li>verbosity
-: <a class="el" href="classvg_1_1Recombinator.html#a634aa461ea8f2e934d54eac098fd3a12">vg::Recombinator</a>
+: <a class="el" href="structvg_1_1IndexingParameters.html#a049ee4a66bf7bb31d99ac77df0984579">vg::IndexingParameters</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>
@@ -234,12 +236,12 @@ <h3><a id="index_v"></a>- v -</h3><ul>
 <li>verify_valid_log_odds_score_matrix()
 : <a class="el" href="classvg_1_1GSSWAligner.html#acc5d3a8c0c22cbd966e96a42eb095cd8">vg::GSSWAligner</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>
+</li>
 <li>Version()
 : <a class="el" href="classvg_1_1Version.html#a05bb9f14c7597bf90a2981db7e59b058">vg::Version</a>
 </li>
@@ -251,7 +253,7 @@ <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#af4d321b31b873153431c261090d052af">vg::VG</a>
 </li>
 <li>vg_filename
 : <a class="el" href="classvg_1_1IndexedVG.html#a0399d7902920da48ad515ef358aa65e0">vg::IndexedVG</a>