Commit new auto-generated docs

vgteam · Jan 21, 2025 · f2b2538 · f2b2538
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diff --git a/classvg_1_1Paths.html b/classvg_1_1Paths.html
@@ -2179,7 +2179,6 @@ <h2 class="memtitle"><span class="permalink"><a href="#a3e8fd05a0a584cbae2f2919b
 <div class="line">    </div>
 <div class="line">    </div>
 <div class="line">    <span class="keywordtype">string</span> prefix(<span class="stringliteral">&quot;_alt_&quot;</span>);</div>
-<div class="line">    </div>
 <div class="line">    <span class="keywordflow">if</span> (path_name.length() &lt; prefix.length() || !std::equal(prefix.begin(), prefix.end(), path_name.begin())) {</div>
 <div class="line">        </div>
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diff --git a/namespacemembers_f.html b/namespacemembers_f.html
@@ -183,7 +183,7 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 : <a class="el" href="namespacevg.html#a1f4eaa1a100e433af698e794afa8857b">vg</a>
 </li>
 <li>for_each()
-: <a class="el" href="namespacevg_1_1io.html#a08997ecc2a7d17c35a27418b5f21ab3d">vg::io</a>
+: <a class="el" href="namespacevg_1_1io.html#a6e19f6d7cb7f7c3d6a396268dcbd8007">vg::io</a>
 </li>
 <li>for_each_basic_annotation()
 : <a class="el" href="namespacevg.html#a8f0eee097c87cbab2bc44f096b463d8b">vg</a>
@@ -216,6 +216,9 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 <li>for_each_parallel_impl()
 : <a class="el" href="namespacevg_1_1io.html#a1347d6f25fb95f2e4fd6cf5d2ff7f92d">vg::io</a>
 </li>
+<li>for_each_subpath_of()
+: <a class="el" href="namespacevg.html#a9534c53c98412f2d43982fc0b809e7bd">vg</a>
+</li>
 <li>for_each_walk()
 : <a class="el" href="namespacevg_1_1algorithms.html#ace1ad4f4eccc7041eb1e700463492540">vg::algorithms</a>
 </li>

diff --git a/namespacemembers_func_f.html b/namespacemembers_func_f.html
@@ -216,6 +216,9 @@ <h3><a id="index_f"></a>- f -</h3><ul>
 <li>for_each_parallel_impl()
 : <a class="el" href="namespacevg_1_1io.html#a1347d6f25fb95f2e4fd6cf5d2ff7f92d">vg::io</a>
 </li>
+<li>for_each_subpath_of()
+: <a class="el" href="namespacevg.html#a9534c53c98412f2d43982fc0b809e7bd">vg</a>
+</li>
 <li>for_each_walk()
 : <a class="el" href="namespacevg_1_1algorithms.html#ace1ad4f4eccc7041eb1e700463492540">vg::algorithms</a>
 </li>

diff --git a/namespacemembers_func_g.html b/namespacemembers_func_g.html
@@ -228,6 +228,9 @@ <h3><a id="index_g"></a>- g -</h3><ul>
 <li>get_path()
 : <a class="el" href="namespacevg.html#a3d972910bf64084a1ee50ca4350c5b59">vg</a>
 </li>
+<li>get_path_base_name()
+: <a class="el" href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">vg</a>
+</li>
 <li>get_proc_status_value()
 : <a class="el" href="namespacevg.html#a9fb67697fd1e49bcb389a735ba9fa8f2">vg</a>
 </li>
@@ -263,10 +266,10 @@ <h3><a id="index_g"></a>- g -</h3><ul>
 : <a class="el" href="namespacevg.html#a2dc613a63afb3f23851c96494006630d">vg</a>
 </li>
 <li>gfa_to_handle_graph()
-: <a class="el" href="namespacevg_1_1algorithms.html#adca14b7dcba0bb21f3fdb0c98d867c72">vg::algorithms</a>
+: <a class="el" href="namespacevg_1_1algorithms.html#aedfca626dc003dc3fee77c6bbfcde297">vg::algorithms</a>
 </li>
 <li>gfa_to_path_handle_graph()
-: <a class="el" href="namespacevg_1_1algorithms.html#a8baa82611439357dc02996ba17ce6aa9">vg::algorithms</a>
+: <a class="el" href="namespacevg_1_1algorithms.html#a9f5c41c06269c778d2c97f39cbc79de8">vg::algorithms</a>
 </li>
 <li>golden_section_search()
 : <a class="el" href="namespacevg.html#a314ff925fad534d112e4531617e408fa">vg</a>

diff --git a/namespacemembers_g.html b/namespacemembers_g.html
@@ -232,7 +232,10 @@ <h3><a id="index_g"></a>- g -</h3><ul>
 : <a class="el" href="namespacevg.html#ae2a0425675c4a85289b230eef2c985b8">vg</a>
 </li>
 <li>get_path()
-: <a class="el" href="namespacevg.html#aa5fc35eee866d216357a5818cd1fb927">vg</a>
+: <a class="el" href="namespacevg.html#a3d972910bf64084a1ee50ca4350c5b59">vg</a>
+</li>
+<li>get_path_base_name()
+: <a class="el" href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">vg</a>
 </li>
 <li>get_proc_status_value()
 : <a class="el" href="namespacevg.html#a9fb67697fd1e49bcb389a735ba9fa8f2">vg</a>
@@ -269,10 +272,10 @@ <h3><a id="index_g"></a>- g -</h3><ul>
 : <a class="el" href="namespacevg.html#a2dc613a63afb3f23851c96494006630d">vg</a>
 </li>
 <li>gfa_to_handle_graph()
-: <a class="el" href="namespacevg_1_1algorithms.html#aedfca626dc003dc3fee77c6bbfcde297">vg::algorithms</a>
+: <a class="el" href="namespacevg_1_1algorithms.html#adca14b7dcba0bb21f3fdb0c98d867c72">vg::algorithms</a>
 </li>
 <li>gfa_to_path_handle_graph()
-: <a class="el" href="namespacevg_1_1algorithms.html#a8baa82611439357dc02996ba17ce6aa9">vg::algorithms</a>
+: <a class="el" href="namespacevg_1_1algorithms.html#a61f2c7006c531ad5dd319ea30ec0087f">vg::algorithms</a>
 </li>
 <li>golden_section_search()
 : <a class="el" href="namespacevg.html#a314ff925fad534d112e4531617e408fa">vg</a>

diff --git a/namespacevg.html b/namespacevg.html
@@ -2023,6 +2023,11 @@
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 <tr class="separator:abcf3c5c3332d721a86740ef23fb9e6e2"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a9534c53c98412f2d43982fc0b809e7bd"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a9534c53c98412f2d43982fc0b809e7bd">for_each_subpath_of</a> (const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;graph, const string &amp;path_name, const std::function&lt; bool(const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;path)&gt; &amp;iteratee)</td></tr>
+<tr class="separator:a9534c53c98412f2d43982fc0b809e7bd"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">get_path_base_name</a> (const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;graph, const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;path)</td></tr>
+<tr class="memdesc:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the base path name for this path (i.e. the path's name without any subrange).  <a href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">More...</a><br /></td></tr>
+<tr class="separator:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a4b8b4c6f298818989d39189d631980a8"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a4b8b4c6f298818989d39189d631980a8">from_proto_edit</a> (const <a class="el" href="structvg_1_1Edit.html">Edit</a> &amp;proto_edit, <a class="el" href="classvg_1_1edit__t.html">edit_t</a> &amp;edit)</td></tr>
 <tr class="separator:a4b8b4c6f298818989d39189d631980a8"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a84c5dd6c830450f9100b5e9c11522050"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a84c5dd6c830450f9100b5e9c11522050">to_proto_edit</a> (const <a class="el" href="classvg_1_1edit__t.html">edit_t</a> &amp;edit, <a class="el" href="structvg_1_1Edit.html">Edit</a> &amp;proto_edit)</td></tr>
@@ -10426,6 +10431,45 @@ <h2 class="memtitle"><span class="permalink"><a href="#ab3d4de4fa2fda6bfcd6eaa77
 </div><div class="memdoc">
 <p>Iterate over all the kmers in the graph, running lambda on each If the stop flag is included, stop execution if it ever evaluates to true </p>
 
+</div>
+</div>
+<a id="a9534c53c98412f2d43982fc0b809e7bd"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a9534c53c98412f2d43982fc0b809e7bd">&#9670;&nbsp;</a></span>for_each_subpath_of()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">bool vg::for_each_subpath_of </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;&#160;</td>
+          <td class="paramname"><em>graph</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const string &amp;&#160;</td>
+          <td class="paramname"><em>path_name</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const std::function&lt; bool(const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;path)&gt; &amp;&#160;</td>
+          <td class="paramname"><em>iteratee</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<p>Run the given iteratee for each path that is either the path with the given name (if present), or a subrange of a path with the given name as the base name (otherwise).</p>
+<p>If a path and subpaths both exist, only look at the full path.</p>
+<p>If the name describes a subpath, look only at that subpath.</p>
+<p>Iteratee returns false to stop.</p>
+<p>Returns true if we reached the end, and false if asked to stop. </p>
+
 </div>
 </div>
 <a id="a3ae70effc22331b3e4667ed48808602c"></a>
@@ -11996,6 +12040,36 @@ <h2 class="memtitle"><span class="permalink"><a href="#aa5fc35eee866d216357a5818
       </table>
 </div><div class="memdoc">
 
+</div>
+</div>
+<a id="a94b1b2969f088d4fa3fdf8c73bac7f65"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a94b1b2969f088d4fa3fdf8c73bac7f65">&#9670;&nbsp;</a></span>get_path_base_name()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">std::string vg::get_path_base_name </td>
+          <td>(</td>
+          <td class="paramtype">const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;&#160;</td>
+          <td class="paramname"><em>graph</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;&#160;</td>
+          <td class="paramname"><em>path</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+
+<p>Returns the base path name for this path (i.e. the path's name without any subrange). </p>
+
 </div>
 </div>
 <a id="a9fb67697fd1e49bcb389a735ba9fa8f2"></a>

diff --git a/path_8cpp.html b/path_8cpp.html
@@ -224,6 +224,11 @@
 <tr class="separator:a864fe6e3e163b18e84db0783f9a2e17d"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:abcf3c5c3332d721a86740ef23fb9e6e2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structvg_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#abcf3c5c3332d721a86740ef23fb9e6e2">vg::alignment_from_path</a> (const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;graph, const <a class="el" href="structvg_1_1Path.html">Path</a> &amp;path)</td></tr>
 <tr class="separator:abcf3c5c3332d721a86740ef23fb9e6e2"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a9534c53c98412f2d43982fc0b809e7bd"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a9534c53c98412f2d43982fc0b809e7bd">vg::for_each_subpath_of</a> (const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;graph, const string &amp;path_name, const std::function&lt; bool(const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;path)&gt; &amp;iteratee)</td></tr>
+<tr class="separator:a9534c53c98412f2d43982fc0b809e7bd"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">vg::get_path_base_name</a> (const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;graph, const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;path)</td></tr>
+<tr class="memdesc:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the base path name for this path (i.e. the path's name without any subrange).  <a href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">More...</a><br /></td></tr>
+<tr class="separator:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a4b8b4c6f298818989d39189d631980a8"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a4b8b4c6f298818989d39189d631980a8">vg::from_proto_edit</a> (const <a class="el" href="structvg_1_1Edit.html">Edit</a> &amp;proto_edit, <a class="el" href="classvg_1_1edit__t.html">edit_t</a> &amp;edit)</td></tr>
 <tr class="separator:a4b8b4c6f298818989d39189d631980a8"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a84c5dd6c830450f9100b5e9c11522050"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a84c5dd6c830450f9100b5e9c11522050">vg::to_proto_edit</a> (const <a class="el" href="classvg_1_1edit__t.html">edit_t</a> &amp;edit, <a class="el" href="structvg_1_1Edit.html">Edit</a> &amp;proto_edit)</td></tr>

diff --git a/path_8hpp.html b/path_8hpp.html
@@ -245,6 +245,11 @@
 <tr class="separator:a864fe6e3e163b18e84db0783f9a2e17d"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:abcf3c5c3332d721a86740ef23fb9e6e2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structvg_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#abcf3c5c3332d721a86740ef23fb9e6e2">vg::alignment_from_path</a> (const <a class="el" href="classhandlegraph_1_1HandleGraph.html">HandleGraph</a> &amp;graph, const <a class="el" href="structvg_1_1Path.html">Path</a> &amp;path)</td></tr>
 <tr class="separator:abcf3c5c3332d721a86740ef23fb9e6e2"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a9534c53c98412f2d43982fc0b809e7bd"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a9534c53c98412f2d43982fc0b809e7bd">vg::for_each_subpath_of</a> (const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;graph, const string &amp;path_name, const std::function&lt; bool(const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;path)&gt; &amp;iteratee)</td></tr>
+<tr class="separator:a9534c53c98412f2d43982fc0b809e7bd"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">vg::get_path_base_name</a> (const <a class="el" href="classhandlegraph_1_1PathPositionHandleGraph.html">PathPositionHandleGraph</a> &amp;graph, const <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &amp;path)</td></tr>
+<tr class="memdesc:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the base path name for this path (i.e. the path's name without any subrange).  <a href="namespacevg.html#a94b1b2969f088d4fa3fdf8c73bac7f65">More...</a><br /></td></tr>
+<tr class="separator:a94b1b2969f088d4fa3fdf8c73bac7f65"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a4b8b4c6f298818989d39189d631980a8"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a4b8b4c6f298818989d39189d631980a8">vg::from_proto_edit</a> (const <a class="el" href="structvg_1_1Edit.html">Edit</a> &amp;proto_edit, <a class="el" href="classvg_1_1edit__t.html">edit_t</a> &amp;edit)</td></tr>
 <tr class="separator:a4b8b4c6f298818989d39189d631980a8"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a84c5dd6c830450f9100b5e9c11522050"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a84c5dd6c830450f9100b5e9c11522050">vg::to_proto_edit</a> (const <a class="el" href="classvg_1_1edit__t.html">edit_t</a> &amp;edit, <a class="el" href="structvg_1_1Edit.html">Edit</a> &amp;proto_edit)</td></tr>