Commit new auto-generated docs

alignment_8cpp.html

@@ -76,7 +76,9 @@
 <div class="textblock"><code>#include &quot;<a class="el" href="alignment_8hpp.html">alignment.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="gafkluge_8hpp.html">vg/io/gafkluge.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="annotation_8hpp.html">annotation.hpp</a>&quot;</code><br />
+<code>#include &lt;<a class="el" href="stream_8hpp.html">vg/io/stream.hpp</a>&gt;</code><br />
 <code>#include &lt;sstream&gt;</code><br />
+<code>#include &lt;chrono&gt;</code><br />
 </div><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
 Namespaces</h2></td></tr>

annotated.html

@@ -574,19 +574,22 @@
 <tr id="row_6_1_" style="display:none;"><td class="entry"><span style="width:32px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classxg_1_1XG.html" target="_self">XG</a></td><td class="desc"></td></tr>
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-<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structGBWTConfig.html" target="_self">GBWTConfig</a></td><td class="desc"></td></tr>
-<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structGiraffeMainOptions.html" target="_self">GiraffeMainOptions</a></td><td class="desc">Options struct for options for the Giraffe driver (i.e. this file) </td></tr>
-<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structGraphHandler.html" target="_self">GraphHandler</a></td><td class="desc"></td></tr>
-<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structHaplotypesConfig.html" target="_self">HaplotypesConfig</a></td><td class="desc"></td></tr>
-<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structhFILE__backend.html" target="_self">hFILE_backend</a></td><td class="desc"></td></tr>
-<tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classj2pb__error.html" target="_self">j2pb_error</a></td><td class="desc"></td></tr>
-<tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structjob__type.html" target="_self">job_type</a></td><td class="desc"></td></tr>
-<tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structjson__autoptr.html" target="_self">json_autoptr</a></td><td class="desc"></td></tr>
-<tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structMappingRun.html" target="_self">MappingRun</a></td><td class="desc"></td></tr>
-<tr id="row_16_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structPruningParameters.html" target="_self">PruningParameters</a></td><td class="desc"></td></tr>
-<tr id="row_17_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structReferenceInterval.html" target="_self">ReferenceInterval</a></td><td class="desc"></td></tr>
-<tr id="row_18_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structScoringOptions.html" target="_self">ScoringOptions</a></td><td class="desc">Options struct for scoring-related parameters. Defaults are in <a class="el" href="aligner_8hpp.html">aligner.hpp</a> </td></tr>
-<tr id="row_19_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classVectorizer.html" target="_self">Vectorizer</a></td><td class="desc"></td></tr>
+<tr id="row_7_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structcompare__gaf.html" target="_self">compare_gaf</a></td><td class="desc"></td></tr>
+<tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structGafFile.html" target="_self">GafFile</a></td><td class="desc"></td></tr>
+<tr id="row_9_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structGBWTConfig.html" target="_self">GBWTConfig</a></td><td class="desc"></td></tr>
+<tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structGiraffeMainOptions.html" target="_self">GiraffeMainOptions</a></td><td class="desc">Options struct for options for the Giraffe driver (i.e. this file) </td></tr>
+<tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structGraphHandler.html" target="_self">GraphHandler</a></td><td class="desc"></td></tr>
+<tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structgreater__gaffile.html" target="_self">greater_gaffile</a></td><td class="desc"></td></tr>
+<tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structHaplotypesConfig.html" target="_self">HaplotypesConfig</a></td><td class="desc"></td></tr>
+<tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structhFILE__backend.html" target="_self">hFILE_backend</a></td><td class="desc"></td></tr>
+<tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classj2pb__error.html" target="_self">j2pb_error</a></td><td class="desc"></td></tr>
+<tr id="row_16_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structjob__type.html" target="_self">job_type</a></td><td class="desc"></td></tr>
+<tr id="row_17_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structjson__autoptr.html" target="_self">json_autoptr</a></td><td class="desc"></td></tr>
+<tr id="row_18_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structMappingRun.html" target="_self">MappingRun</a></td><td class="desc"></td></tr>
+<tr id="row_19_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structPruningParameters.html" target="_self">PruningParameters</a></td><td class="desc"></td></tr>
+<tr id="row_20_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structReferenceInterval.html" target="_self">ReferenceInterval</a></td><td class="desc"></td></tr>
+<tr id="row_21_"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="structScoringOptions.html" target="_self">ScoringOptions</a></td><td class="desc">Options struct for scoring-related parameters. Defaults are in <a class="el" href="aligner_8hpp.html">aligner.hpp</a> </td></tr>
+<tr id="row_22_" class="even"><td class="entry"><span style="width:16px;display:inline-block;">&#160;</span><span class="icona"><span class="icon">C</span></span><a class="el" href="classVectorizer.html" target="_self">Vectorizer</a></td><td class="desc"></td></tr>
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