Commit new auto-generated docs

vgteam · Nov 3, 2024 · 7473eb0 · 7473eb0
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diff --git a/namespacemembers_func_m.html b/namespacemembers_func_m.html
@@ -205,7 +205,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <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>
+: <a class="el" href="namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1">vg</a>
 </li>
 <li>merge_non_branching_subpaths()
 : <a class="el" href="namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43">vg</a>

diff --git a/namespacemembers_m.html b/namespacemembers_m.html
@@ -208,7 +208,7 @@ <h3><a id="index_m"></a>- m -</h3><ul>
 : <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>
+: <a class="el" href="namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1">vg</a>
 </li>
 <li>merge_non_branching_subpaths()
 : <a class="el" href="namespacevg.html#a86fd22ae591c4923588d20b9b5c52e43">vg</a>

diff --git a/namespacevg.html b/namespacevg.html
@@ -2427,8 +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>
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-<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:adcc7a98e5291c4354fc575289cc50fe1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1">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, bool use_snarl_manager)</td></tr>
+<tr class="separator:adcc7a98e5291c4354fc575289cc50fe1"><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>
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@@ -16195,8 +16195,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#a20ebf02d59df03f906550e69
 
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-<a id="a7548e624cfa580a585f79d9027cf2e96"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#a7548e624cfa580a585f79d9027cf2e96">&#9670;&nbsp;</a></span>merge_equivalent_traversals_in_graph()</h2>
+<a id="adcc7a98e5291c4354fc575289cc50fe1"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#adcc7a98e5291c4354fc575289cc50fe1">&#9670;&nbsp;</a></span>merge_equivalent_traversals_in_graph()</h2>
 
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           <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>
+          <td class="paramname"><em>selected_paths</em>, </td>
+        </tr>
+        <tr>
+          <td class="paramkey"></td>
+          <td></td>
+          <td class="paramtype">bool&#160;</td>
+          <td class="paramname"><em>use_snarl_manager</em> = <code>false</code>&#160;</td>
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 <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>
+<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>
+<p>the use_snarl_manager toggles between distnace index and snarl manager for computing snarls (adding this option to (hopefully) temporarily revert to the snarl manager for performance reasons) </p>
 
 </div>
 </div>

diff --git a/search/all_d.js b/search/all_d.js
diff --git a/search/functions_d.js b/search/functions_d.js
diff --git a/traversal__clusters_8cpp.html b/traversal__clusters_8cpp.html
@@ -77,6 +77,7 @@
 <code>#include &quot;<a class="el" href="traversal__finder_8hpp.html">traversal_finder.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="integrated__snarl__finder_8hpp.html">integrated_snarl_finder.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="snarl__distance__index_8hpp.html">snarl_distance_index.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="snarls_8hpp.html">snarls.hpp</a>&quot;</code><br />
 </div><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
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@@ -93,8 +94,8 @@
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 <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">vg::assign_child_snarls_to_traversals</a> (const PathHandleGraph *graph, const vector&lt; Traversal &gt; &amp;traversals, const vector&lt; pair&lt; handle_t, handle_t &gt;&gt; &amp;child_snarls)</td></tr>
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-<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">vg::merge_equivalent_traversals_in_graph</a> (MutablePathHandleGraph *graph, const unordered_set&lt; path_handle_t &gt; &amp;selected_paths)</td></tr>
-<tr class="separator:a7548e624cfa580a585f79d9027cf2e96"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:adcc7a98e5291c4354fc575289cc50fe1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1">vg::merge_equivalent_traversals_in_graph</a> (MutablePathHandleGraph *graph, const unordered_set&lt; path_handle_t &gt; &amp;selected_paths, bool use_snarl_manager)</td></tr>
+<tr class="separator:adcc7a98e5291c4354fc575289cc50fe1"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 </div><!-- contents -->
 <!-- HTML footer for doxygen 1.8.9.1-->

diff --git a/traversal__clusters_8hpp.html b/traversal__clusters_8hpp.html
@@ -102,8 +102,8 @@
 <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">vg::assign_child_snarls_to_traversals</a> (const PathHandleGraph *graph, const vector&lt; Traversal &gt; &amp;traversals, const vector&lt; pair&lt; handle_t, handle_t &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">vg::merge_equivalent_traversals_in_graph</a> (MutablePathHandleGraph *graph, const unordered_set&lt; path_handle_t &gt; &amp;selected_paths)</td></tr>
-<tr class="separator:a7548e624cfa580a585f79d9027cf2e96"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:adcc7a98e5291c4354fc575289cc50fe1"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg.html#adcc7a98e5291c4354fc575289cc50fe1">vg::merge_equivalent_traversals_in_graph</a> (MutablePathHandleGraph *graph, const unordered_set&lt; path_handle_t &gt; &amp;selected_paths, bool use_snarl_manager)</td></tr>
+<tr class="separator:adcc7a98e5291c4354fc575289cc50fe1"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
 <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
 <div class="textblock"><p>Utilities for finding and clustering similar snarl traversals </p>

diff --git a/vg__environment__version_8hpp.html b/vg__environment__version_8hpp.html
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-          <td class="memname">#define VG_BUILD_HOST&#160;&#160;&#160;&quot;runner-jqc6opwmy-project-4-concurrent-0&quot;</td>
+          <td class="memname">#define VG_BUILD_HOST&#160;&#160;&#160;&quot;runner-8apr64d7j-project-4-concurrent-0&quot;</td>
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diff --git a/vg__git__version_8hpp.html b/vg__git__version_8hpp.html
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-<tr class="memitem:a5df50394a80dec8f6151eb57db04a38a"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="vg__git__version_8hpp.html#a5df50394a80dec8f6151eb57db04a38a">VG_GIT_VERSION</a>&#160;&#160;&#160;&quot;v1.60.0-261-gee562cca&quot;</td></tr>
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+          <td class="memname">#define VG_GIT_VERSION&#160;&#160;&#160;&quot;v1.60.0-273-g0097fb15&quot;</td>
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