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<?xml version="1.0" encoding="utf-8"?>
<refentry xmlns="http://docbook.org/ns/docbook"
xmlns:xi="http://www.w3.org/2001/XInclude">
<xi:include href="gen-refentry-extract.xml" />
<refsection>
<title>Description</title>
<para>Extract subgraphs or parts of a graph defined by query criteria.</para>
<variablelist>
<title>Options</title>
<xi:include href="input-db-argument.dbk" />
<xi:include href="output-db-argument.dbk" />
<xi:include href="threads-argument.dbk" />
<xi:include href="help-option.dbk" />
</variablelist>
<variablelist>
<title>Traverse the graph from a segment</title>
<varlistentry>
<term><option>-n <replaceable>SEGMENT</replaceable></option></term>
<term><option>--node=<replaceable>SEGMENT</replaceable></option></term>
<listitem><para>Segment name from which to begin the traversal</para></listitem>
</varlistentry>
<varlistentry>
<term><option>-c <replaceable>STEPS</replaceable></option></term>
<term><option>--context-steps=<replaceable>STEPS</replaceable></option></term>
<listitem><para>The number of segments away from the initial segments to traverse</para></listitem>
</varlistentry>
</variablelist>
<variablelist>
<title>Extract segments in path range</title>
<varlistentry>
<term><option>-r <replaceable>PATH_RANGE</replaceable></option></term>
<term><option>--path-range=<replaceable>PATH_RANGE</replaceable></option></term>
<listitem><para>Extract segments in <replaceable>PATH_RANGE</replaceable>, specified in the <replaceable>path[:pos1[-pos2]]</replaceable> format. <replaceable>pos1</replaceable> and <replaceable>pos2</replaceable> are 0-based coordinates. The extracted segments include <replaceable>pos1</replaceable> (inclusive) but not <replaceable>pos2</replaceable> (exclusive).</para></listitem>
</varlistentry>
<varlistentry>
<term><option>-d <replaceable>DISTANCE</replaceable></option></term>
<term><option>--max-distance-subpaths=<replaceable>DISTANCE</replaceable></option></term>
<listitem>
<para>Bridge subpaths that are separated by less than <replaceable>DISTANCE</replaceable>. Default <replaceable>DISTANCE</replaceable> is <literal>300000</literal>. This reduces the fragmentation of paths that are unspecified in the input path ranges. Set <replaceable>DISTANCE</replaceable> to <literal>0</literal> to disable bridging.</para>
<para>In contrast to odgi, when bridging subpaths, domagi does not use the newly extracted segments to extend the subgraph further and recursively bridge more subpaths.</para>
</listitem>
</varlistentry>
</variablelist>
</refsection>
</refentry>
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