Commit new auto-generated docs

vgteam · Nov 7, 2024 · 61ea08c · 61ea08c
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diff --git a/algorithms_2subgraph_8cpp.html b/algorithms_2subgraph_8cpp.html
@@ -75,6 +75,7 @@
 <div class="contents">
 <div class="textblock"><code>#include &quot;<a class="el" href="algorithms_2subgraph_8hpp.html">subgraph.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="path_8hpp.html">../path.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="crash_8hpp.html">../crash.hpp</a>&quot;</code><br />
 </div><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
 Namespaces</h2></td></tr>
@@ -105,8 +106,8 @@
 <tr class="separator:ac53dd7f2ff1b53bec309f368a79db951"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a6da60961fae57a5568354ef5b541bcf7"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#a6da60961fae57a5568354ef5b541bcf7">vg::algorithms::extract_path_range</a> (const PathPositionHandleGraph &amp;source, path_handle_t path_handle, int64_t start, int64_t end, MutableHandleGraph &amp;subgraph)</td></tr>
 <tr class="separator:a6da60961fae57a5568354ef5b541bcf7"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ad37fc704de99f02f0bf767d6ab41fe4e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#ad37fc704de99f02f0bf767d6ab41fe4e">vg::algorithms::add_subpaths_to_subgraph</a> (const PathPositionHandleGraph &amp;source, MutablePathHandleGraph &amp;subgraph, bool subpath_naming)</td></tr>
-<tr class="separator:ad37fc704de99f02f0bf767d6ab41fe4e"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a90946d442f4b518bb61154cde44d109c"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c">vg::algorithms::add_subpaths_to_subgraph</a> (const PathPositionHandleGraph &amp;source, MutablePathHandleGraph &amp;subgraph)</td></tr>
+<tr class="separator:a90946d442f4b518bb61154cde44d109c"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a6347e00229560b4adb7cc7cb6332b21a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#a6347e00229560b4adb7cc7cb6332b21a">vg::algorithms::add_connecting_edges_to_subgraph</a> (const HandleGraph &amp;source, MutableHandleGraph &amp;subgraph)</td></tr>
 <tr class="separator:a6347e00229560b4adb7cc7cb6332b21a"><td class="memSeparator" colspan="2">&#160;</td></tr>
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diff --git a/algorithms_2subgraph_8hpp.html b/algorithms_2subgraph_8hpp.html
@@ -107,8 +107,8 @@
 <tr class="separator:ac53dd7f2ff1b53bec309f368a79db951"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a6da60961fae57a5568354ef5b541bcf7"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#a6da60961fae57a5568354ef5b541bcf7">vg::algorithms::extract_path_range</a> (const PathPositionHandleGraph &amp;source, path_handle_t path_handle, int64_t start, int64_t end, MutableHandleGraph &amp;subgraph)</td></tr>
 <tr class="separator:a6da60961fae57a5568354ef5b541bcf7"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ad37fc704de99f02f0bf767d6ab41fe4e"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#ad37fc704de99f02f0bf767d6ab41fe4e">vg::algorithms::add_subpaths_to_subgraph</a> (const PathPositionHandleGraph &amp;source, MutablePathHandleGraph &amp;subgraph, bool subpath_naming)</td></tr>
-<tr class="separator:ad37fc704de99f02f0bf767d6ab41fe4e"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a90946d442f4b518bb61154cde44d109c"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c">vg::algorithms::add_subpaths_to_subgraph</a> (const PathPositionHandleGraph &amp;source, MutablePathHandleGraph &amp;subgraph)</td></tr>
+<tr class="separator:a90946d442f4b518bb61154cde44d109c"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a6347e00229560b4adb7cc7cb6332b21a"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacevg_1_1algorithms.html#a6347e00229560b4adb7cc7cb6332b21a">vg::algorithms::add_connecting_edges_to_subgraph</a> (const HandleGraph &amp;source, MutableHandleGraph &amp;subgraph)</td></tr>
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diff --git a/chunker_8cpp.html b/chunker_8cpp.html
@@ -79,6 +79,7 @@
 <code>#include &quot;<a class="el" href="algorithms_2subgraph_8hpp.html">algorithms/subgraph.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="vg_8hpp.html">vg.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="clip_8hpp.html">clip.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="crash_8hpp.html">crash.hpp</a>&quot;</code><br />
 </div><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="namespaces"></a>
 Namespaces</h2></td></tr>

diff --git a/classvg_1_1PathChunker-members.html b/classvg_1_1PathChunker-members.html
@@ -73,7 +73,7 @@
 
 <p>This is the complete list of members for <a class="el" href="classvg_1_1PathChunker.html">vg::PathChunker</a>, including all inherited members.</p>
 <table class="directory">
-  <tr class="even"><td class="entry"><a class="el" href="classvg_1_1PathChunker.html#ae971765e047d0f1747b7f481003c73c7">extract_component</a>(const unordered_set&lt; nid_t &gt; &amp;node_ids, MutablePathMutableHandleGraph &amp;subgraph, bool subpath_naming)</td><td class="entry"><a class="el" href="classvg_1_1PathChunker.html">vg::PathChunker</a></td><td class="entry"></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54">extract_component</a>(const unordered_set&lt; nid_t &gt; &amp;node_ids, MutablePathMutableHandleGraph &amp;subgraph)</td><td class="entry"><a class="el" href="classvg_1_1PathChunker.html">vg::PathChunker</a></td><td class="entry"></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1PathChunker.html#a140b4a86b4f8ea18d29a39c7b1aab66f">extract_id_range</a>(vg::id_t start, vg::id_t end, int64_t context, int64_t length, bool forward_only, MutablePathMutableHandleGraph &amp;subgraph, Region &amp;out_region)</td><td class="entry"><a class="el" href="classvg_1_1PathChunker.html">vg::PathChunker</a></td><td class="entry"></td></tr>
   <tr class="even"><td class="entry"><a class="el" href="classvg_1_1PathChunker.html#aca0d2bec2834fdc534d42238a0a53b46">extract_path_component</a>(const string &amp;path_name, MutablePathMutableHandleGraph &amp;subgraph, Region &amp;out_region)</td><td class="entry"><a class="el" href="classvg_1_1PathChunker.html">vg::PathChunker</a></td><td class="entry"></td></tr>
   <tr><td class="entry"><a class="el" href="classvg_1_1PathChunker.html#a20d6a2e56df993a7420e5b1c62df5154">extract_snarls</a>(const Region &amp;region, SnarlManager &amp;snarl_manager, MutablePathMutableHandleGraph &amp;subgraph)</td><td class="entry"><a class="el" href="classvg_1_1PathChunker.html">vg::PathChunker</a></td><td class="entry"></td></tr>

diff --git a/classvg_1_1PathChunker.html b/classvg_1_1PathChunker.html
@@ -89,8 +89,8 @@
 <tr class="separator:a20d6a2e56df993a7420e5b1c62df5154"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:aca0d2bec2834fdc534d42238a0a53b46"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1PathChunker.html#aca0d2bec2834fdc534d42238a0a53b46">extract_path_component</a> (const string &amp;path_name, <a class="el" href="classhandlegraph_1_1MutablePathMutableHandleGraph.html">MutablePathMutableHandleGraph</a> &amp;subgraph, <a class="el" href="structvg_1_1Region.html">Region</a> &amp;out_region)</td></tr>
 <tr class="separator:aca0d2bec2834fdc534d42238a0a53b46"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ae971765e047d0f1747b7f481003c73c7"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1PathChunker.html#ae971765e047d0f1747b7f481003c73c7">extract_component</a> (const unordered_set&lt; <a class="el" href="namespacevg.html#a26f660292f00451f15d1c95d9b8c6ffb">nid_t</a> &gt; &amp;node_ids, <a class="el" href="classhandlegraph_1_1MutablePathMutableHandleGraph.html">MutablePathMutableHandleGraph</a> &amp;subgraph, bool subpath_naming)</td></tr>
-<tr class="separator:ae971765e047d0f1747b7f481003c73c7"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a99497d311a2a2adfc4d7a78f8b6d7f54"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54">extract_component</a> (const unordered_set&lt; <a class="el" href="namespacevg.html#a26f660292f00451f15d1c95d9b8c6ffb">nid_t</a> &gt; &amp;node_ids, <a class="el" href="classhandlegraph_1_1MutablePathMutableHandleGraph.html">MutablePathMutableHandleGraph</a> &amp;subgraph)</td></tr>
+<tr class="separator:a99497d311a2a2adfc4d7a78f8b6d7f54"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a140b4a86b4f8ea18d29a39c7b1aab66f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1PathChunker.html#a140b4a86b4f8ea18d29a39c7b1aab66f">extract_id_range</a> (<a class="el" href="namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821">vg::id_t</a> start, <a class="el" href="namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821">vg::id_t</a> end, int64_t context, int64_t length, bool forward_only, <a class="el" href="classhandlegraph_1_1MutablePathMutableHandleGraph.html">MutablePathMutableHandleGraph</a> &amp;subgraph, <a class="el" href="structvg_1_1Region.html">Region</a> &amp;out_region)</td></tr>
 <tr class="separator:a140b4a86b4f8ea18d29a39c7b1aab66f"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:aef30dd2569597b64d36b19824ebee37f"><td class="memItemLeft" align="right" valign="top">set&lt; pair&lt; pair&lt; <a class="el" href="namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821">id_t</a>, bool &gt;, pair&lt; <a class="el" href="namespacevg.html#afaa15fd8bdfd688d48561e1b12aee821">id_t</a>, bool &gt; &gt; &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classvg_1_1PathChunker.html#aef30dd2569597b64d36b19824ebee37f">get_path_edge_index</a> (<a class="el" href="structhandlegraph_1_1step__handle__t.html">step_handle_t</a> start_step, <a class="el" href="structhandlegraph_1_1step__handle__t.html">step_handle_t</a> end_step, int64_t context) const</td></tr>
@@ -140,8 +140,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#a49b9500998c8e6faace1206d
 </div>
 </div>
 <h2 class="groupheader">Member Function Documentation</h2>
-<a id="ae971765e047d0f1747b7f481003c73c7"></a>
-<h2 class="memtitle"><span class="permalink"><a href="#ae971765e047d0f1747b7f481003c73c7">&#9670;&nbsp;</a></span>extract_component()</h2>
+<a id="a99497d311a2a2adfc4d7a78f8b6d7f54"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#a99497d311a2a2adfc4d7a78f8b6d7f54">&#9670;&nbsp;</a></span>extract_component()</h2>
 
 <div class="memitem">
 <div class="memproto">
@@ -156,13 +156,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#ae971765e047d0f1747b7f481
           <td class="paramkey"></td>
           <td></td>
           <td class="paramtype"><a class="el" href="classhandlegraph_1_1MutablePathMutableHandleGraph.html">MutablePathMutableHandleGraph</a> &amp;&#160;</td>
-          <td class="paramname"><em>subgraph</em>, </td>
-        </tr>
-        <tr>
-          <td class="paramkey"></td>
-          <td></td>
-          <td class="paramtype">bool&#160;</td>
-          <td class="paramname"><em>subpath_naming</em>&#160;</td>
+          <td class="paramname"><em>subgraph</em>&#160;</td>
         </tr>
         <tr>
           <td></td>
@@ -171,7 +165,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#ae971765e047d0f1747b7f481
         </tr>
       </table>
 </div><div class="memdoc">
-<p>Extract a connected component starting from an id set </p>
+<p>Extract a connected component starting from an id set. Processes path metadata and creates subpaths. </p>
 
 </div>
 </div>
@@ -265,7 +259,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#aca0d2bec2834fdc534d42238
         </tr>
       </table>
 </div><div class="memdoc">
-<p>Extract a connected component containing a given path </p>
+<p>Extract a connected component containing a given path. Processes path metadata and creates subpaths. </p>
 
 </div>
 </div>
@@ -353,7 +347,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#a90aac076d1669b467ca5ca58
         </tr>
       </table>
 </div><div class="memdoc">
-<p>Extract subgraph corresponding to given path region into its own vg graph, and send it to out_stream. The boundaries of the extracted graph (which can be different because we expand context and don't cut nodes) are written to out_region. If forward_only set, context is only expanded in the forward direction</p>
+<p>Extract subgraph corresponding to given path region into its own vg graph, and send it to out_stream. The boundaries of the extracted region of the target path (which can be different because we expand context and don't cut nodes) are written to out_region. If the target path goes through the extracted region multiple times, only the extended bounds of the visit containing the target region are produced.</p>
+<p>If forward_only set, context is only expanded in the forward direction</p>
 <p>NOTE: we follow convention of <a class="el" href="structvg_1_1Region.html">Region</a> coordinates being 0-based inclusive. </p>
 
 </div>

diff --git a/find__main_8cpp.html b/find__main_8cpp.html
@@ -73,6 +73,7 @@
 </div><!--header-->
 <div class="contents">
 <div class="textblock"><code>#include &quot;<a class="el" href="subcommand_8hpp.html">subcommand.hpp</a>&quot;</code><br />
+<code>#include &quot;<a class="el" href="crash_8hpp.html">../crash.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="utility_8hpp.html">../utility.hpp</a>&quot;</code><br />
 <code>#include &quot;<a class="el" href="mapper_8hpp.html">../mapper.hpp</a>&quot;</code><br />
 <code>#include &lt;<a class="el" href="stream_8hpp.html">vg/io/stream.hpp</a>&gt;</code><br />

diff --git a/functions_e.html b/functions_e.html
@@ -698,7 +698,7 @@ <h3><a id="index_e"></a>- e -</h3><ul>
 : <a class="el" href="classvg_1_1MultipathMapper.html#a411882d1f1f4908582333944ac346443">vg::MultipathMapper</a>
 </li>
 <li>extract_component()
-: <a class="el" href="classvg_1_1PathChunker.html#ae971765e047d0f1747b7f481003c73c7">vg::PathChunker</a>
+: <a class="el" href="classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54">vg::PathChunker</a>
 </li>
 <li>extract_id_range()
 : <a class="el" href="classvg_1_1PathChunker.html#a140b4a86b4f8ea18d29a39c7b1aab66f">vg::PathChunker</a>

diff --git a/functions_func_e.html b/functions_func_e.html
@@ -461,7 +461,7 @@ <h3><a id="index_e"></a>- e -</h3><ul>
 : <a class="el" href="classvg_1_1MultipathMapper.html#a411882d1f1f4908582333944ac346443">vg::MultipathMapper</a>
 </li>
 <li>extract_component()
-: <a class="el" href="classvg_1_1PathChunker.html#ae971765e047d0f1747b7f481003c73c7">vg::PathChunker</a>
+: <a class="el" href="classvg_1_1PathChunker.html#a99497d311a2a2adfc4d7a78f8b6d7f54">vg::PathChunker</a>
 </li>
 <li>extract_id_range()
 : <a class="el" href="classvg_1_1PathChunker.html#a140b4a86b4f8ea18d29a39c7b1aab66f">vg::PathChunker</a>

diff --git a/namespacemembers.html b/namespacemembers.html
@@ -99,7 +99,7 @@ <h3><a id="index_a"></a>- a -</h3><ul>
 : <a class="el" href="namespacevg.html#a7ac200a1dbeaf55eb41bebbfd2ce4bdf">vg</a>
 </li>
 <li>add_subpaths_to_subgraph()
-: <a class="el" href="namespacevg_1_1algorithms.html#ad37fc704de99f02f0bf767d6ab41fe4e">vg::algorithms</a>
+: <a class="el" href="namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c">vg::algorithms</a>
 </li>
 <li>add_thread_edges_to_set()
 : <a class="el" href="namespacevg.html#afe2d6096dfe672a486e44df018c713c2">vg</a>

diff --git a/namespacemembers_func.html b/namespacemembers_func.html
@@ -96,7 +96,7 @@ <h3><a id="index_a"></a>- a -</h3><ul>
 : <a class="el" href="namespacevg.html#a7ac200a1dbeaf55eb41bebbfd2ce4bdf">vg</a>
 </li>
 <li>add_subpaths_to_subgraph()
-: <a class="el" href="namespacevg_1_1algorithms.html#ad37fc704de99f02f0bf767d6ab41fe4e">vg::algorithms</a>
+: <a class="el" href="namespacevg_1_1algorithms.html#a90946d442f4b518bb61154cde44d109c">vg::algorithms</a>
 </li>
 <li>add_thread_edges_to_set()
 : <a class="el" href="namespacevg.html#afe2d6096dfe672a486e44df018c713c2">vg</a>