Commit new auto-generated docs

namespacemembers_func_m.html

@@ -204,6 +204,9 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 <li>merge_edits_in_place()
 : <a class="el" href="namespacevg.html#a20ebf02d59df03f906550e695a1aa00d">vg</a>
 </li>
+<li>merge_equivalent_traversals_in_graph()
+: <a class="el" href="namespacevg.html#a7548e624cfa580a585f79d9027cf2e96">vg</a>
+</li>
 <li>merge_non_branching_subpaths()
 : <a class="el" href="namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43">vg</a>
 </li>
@@ -214,7 +217,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="namespacevg.html#aa539af4f481d4e955ede26ee85c320c5">vg</a>
 </li>
 <li>middle_signature()
-: <a class="el" href="namespacevg.html#a7848d492a243a93f37b1ac52a541a96a">vg</a>
+: <a class="el" href="namespacevg.html#af64c67658563ff567bc0b103ef1d8af4">vg</a>
 </li>
 <li>min_approx_path_distance()
 : <a class="el" href="namespacevg_1_1algorithms.html#ae18b50d29d9accb763b44d6e065dac58">vg::algorithms</a>

namespacemembers_m.html

@@ -199,14 +199,17 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="namespacevg_1_1algorithms.html#a91a6bbd822f6380421a973f75036c3d3">vg::algorithms</a>
 </li>
 <li>merge_adjacent_edits()
-: <a class="el" href="namespacevg.html#a2c9985bf70965bd36bb54f910ab74e3b">vg</a>
+: <a class="el" href="namespacevg.html#a30a83a9e127a0c7d75118dc14a8985f6">vg</a>
 </li>
 <li>merge_alignments()
-: <a class="el" href="namespacevg.html#afa2d2a5d955cff1e7a99369055ebe75d">vg</a>
+: <a class="el" href="namespacevg.html#a9d71527a132d7e6bf364d2108b269e09">vg</a>
 </li>
 <li>merge_edits_in_place()
 : <a class="el" href="namespacevg.html#a20ebf02d59df03f906550e695a1aa00d">vg</a>
 </li>
+<li>merge_equivalent_traversals_in_graph()
+: <a class="el" href="namespacevg.html#a7548e624cfa580a585f79d9027cf2e96">vg</a>
+</li>
 <li>merge_non_branching_subpaths()
 : <a class="el" href="namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43">vg</a>
 </li>
@@ -223,7 +226,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <a class="el" href="namespacevg_1_1io.html#a26ea41d1ec4cf44b436a345f1eefccf1">vg::io</a>
 </li>
 <li>middle_signature()
-: <a class="el" href="namespacevg.html#af64c67658563ff567bc0b103ef1d8af4">vg</a>
+: <a class="el" href="namespacevg.html#a7848d492a243a93f37b1ac52a541a96a">vg</a>
 </li>
 <li>min_approx_path_distance()
 : <a class="el" href="namespacevg_1_1algorithms.html#ae18b50d29d9accb763b44d6e065dac58">vg::algorithms</a>

namespacevg.html

@@ -2427,6 +2427,8 @@
 <tr class="separator:a392e3bc708a380e7a3d9b3a669aaf2a9"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a1ac7d2a0833215a0628a25c8195a70ab"><td class="memItemLeft" align="right" valign="top">vector&lt; vector&lt; int &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a1ac7d2a0833215a0628a25c8195a70ab">assign_child_snarls_to_traversals</a> (const <a class="el" href="classhandlegraph_1_1PathHandleGraph.html">PathHandleGraph</a> *graph, const vector&lt; <a class="el" href="namespacevg.html#a4ea210eff71c5a1039378130f98de166">Traversal</a> &gt; &amp;traversals, const vector&lt; pair&lt; <a class="el" href="structhandlegraph_1_1handle__t.html">handle_t</a>, <a class="el" href="structhandlegraph_1_1handle__t.html">handle_t</a> &gt;&gt; &amp;child_snarls)</td></tr>
 <tr class="separator:a1ac7d2a0833215a0628a25c8195a70ab"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a7548e624cfa580a585f79d9027cf2e96"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#a7548e624cfa580a585f79d9027cf2e96">merge_equivalent_traversals_in_graph</a> (<a class="el" href="classhandlegraph_1_1MutablePathHandleGraph.html">MutablePathHandleGraph</a> *graph, const unordered_set&lt; <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &gt; &amp;selected_paths)</td></tr>
+<tr class="separator:a7548e624cfa580a585f79d9027cf2e96"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:aff10785a6df2466c851785b406172e89"><td class="memTemplParams" colspan="2">template&lt;typename T , typename U &gt; </td></tr>
 <tr class="memitem:aff10785a6df2466c851785b406172e89"><td class="memTemplItemLeft" align="right" valign="top">double&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="namespacevg.html#aff10785a6df2466c851785b406172e89">jaccard_coefficient</a> (const T &amp;target, const U &amp;query)</td></tr>
 <tr class="separator:aff10785a6df2466c851785b406172e89"><td class="memSeparator" colspan="2">&#160;</td></tr>
@@ -16185,6 +16187,36 @@ <h2 class="memtitle"><span class="permalink"><a href="#a20ebf02d59df03f906550e69
 
 <p>Glom the second edit into the first, assuming adjacency. </p>
 
+</div>
+</div>
+<a id="a7548e624cfa580a585f79d9027cf2e96"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a7548e624cfa580a585f79d9027cf2e96">&#9670;&nbsp;</a></span>merge_equivalent_traversals_in_graph()</h2>
+
+<div class="memitem">
+<div class="memproto">
+      <table class="memname">
+        <tr>
+          <td class="memname">void vg::merge_equivalent_traversals_in_graph </td>
+          <td>(</td>
+          <td class="paramtype"><a class="el" href="classhandlegraph_1_1MutablePathHandleGraph.html">MutablePathHandleGraph</a> *&#160;</td>
+          <td class="paramname"><em>graph</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">const unordered_set&lt; <a class="el" href="structhandlegraph_1_1path__handle__t.html">path_handle_t</a> &gt; &amp;&#160;</td>
+          <td class="paramname"><em>selected_paths</em>&#160;</td>
+        </tr>
+        <tr>
+          <td></td>
+          <td>)</td>
+          <td></td><td></td>
+        </tr>
+      </table>
+</div><div class="memdoc">
+<p>For every top-level snarl in the graph, compute the traversal strings of every embedded path that spans it If two or more traversals share an allele string, then a "canoncial" path is chosen and all remaining paths are edited so that they share the exact same interval through the snarl as the canonical path's traversal. A path is considered "canoncial" if it's in the "selected_paths" and the other paths are not (otherwise the lowest name is used as a fallback)</p>
+<p>Note: this doesn't modify the graph toplogy, so uncovered nodes and edges as a result of path editing would usually need removale with vg clip afterwards </p>
+
 </div>
 </div>
 <a id="a86fd22ae591c4923588d20b9b5c52e43"></a>

paths__main_8cpp.html

@@ -82,6 +82,8 @@
 <code>#include &quot;<a class="el" href="vg_8hpp.html">../vg.hpp</a>&quot;</code><br />
 <code>#include &quot;../xg.hpp&quot;</code><br />
 <code>#include &quot;<a class="el" href="gbwt__helper_8hpp.html">../gbwt_helper.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="traversal__clusters_8hpp.html">../traversal_clusters.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="save__handle__graph_8hpp.html">../io/save_handle_graph.hpp</a>&quot;</code><br />
 <code>#include &lt;<a class="el" href="vpkg_8hpp.html">vg/io/vpkg.hpp</a>&gt;</code><br />
 <code>#include &lt;<a class="el" href="stream_8hpp.html">vg/io/stream.hpp</a>&gt;</code><br />
 <code>#include &lt;<a class="el" href="alignment__emitter_8hpp.html">vg/io/alignment_emitter.hpp</a>&gt;</code><br />